1
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Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. eLife 2024; 12:RP90316. [PMID: 38814682 PMCID: PMC11139479 DOI: 10.7554/elife.90316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wild-type human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
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Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jessica H Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
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2
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Aouabdi S, Nedjadi T, Alsiary R, Mouffouk F, Ansari HR. Transcriptomics Demonstrates Significant Biological Effect of Growing Stem Cells on RGD-Cotton Scaffold. Tissue Eng Part A 2024. [PMID: 38666698 DOI: 10.1089/ten.tea.2023.0333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
Stem cell therapy provides a viable alternative treatment for degenerated or damaged tissue. Stem cells have been used either alone or in conjunction with an artificial scaffold. The latter provides a structural advantage by enabling the cells to thrive in three-dimensional (3D) settings, closely resembling the natural in vivo environments. Previously, we disclosed the development of a 3D scaffold made from cotton, which was conjugated with arginyl-glycyl-aspartic acid (RGD), to facilitate the growth and proliferation of mesenchymal stem cells (MSCs). This scaffold allowed the MSCs to adhere and proliferate without compromising their viability or their stem cell markers. A comprehensive analysis investigation of the molecular changes occurring in MSCs adhering to the cotton fibers will contribute to the advancement of therapy. The objective of this study is to analyze the molecular processes occurring in the growth of MSCs on a cotton-RGD conjugated-based scaffold by examining their gene expression profiles. To achieve this, we conducted an experiment where MSCs were seeded with and without the scaffold for a duration of 48 h. Subsequently, cells were collected for RNA extraction, cDNA synthesis, and whole-transcriptomic analysis performed on both populations. Our analysis revealed several upregulated and downregulated differently expressed genes in the MSCs adhering to the scaffold compared with the control cells. Through gene ontology analysis, we were able to identify enriched biological processes, molecular functions, pathways, and protein-protein interactions in these differentially expressed genes. Our data suggest that the scaffold may have the potential to enhance osteogenesis in the MSCs. Furthermore, our results indicate that the scaffold does not induce oxidative stress, inflammation, or aging in the MSCs. These findings provide valuable insights for the application of MSCs in tissue engineering and regenerative medicine.
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Affiliation(s)
- Sihem Aouabdi
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Taoufik Nedjadi
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Rawiah Alsiary
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Fouzi Mouffouk
- Department of Chemistry, Kuwait University, Kuwait, Kuwait
| | - Hifzur Rahman Ansari
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
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3
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Krueger J, Preusse M, Oswaldo Gomez N, Frommeyer YN, Doberenz S, Lorenz A, Kordes A, Grobe S, Müsken M, Depledge DP, Svensson SL, Weiss S, Kaever V, Pich A, Sharma CM, Ignatova Z, Häussler S. tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2312874121. [PMID: 38451943 PMCID: PMC10945773 DOI: 10.1073/pnas.2312874121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/29/2023] [Indexed: 03/09/2024] Open
Abstract
The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche.
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Affiliation(s)
- Jonas Krueger
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Yannick Noah Frommeyer
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Sebastian Doberenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Anne Lorenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Adrian Kordes
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
| | - Svenja Grobe
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig38124, Germany
| | - Daniel P. Depledge
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Institute of Virology, Hannover Medical School, Hannover30625, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover30625, Germany
| | - Sarah L. Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover, Hannover30625, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Andreas Pich
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Cynthia M. Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University Hamburg, 20146, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital—Rigshospitalet, Copenhagen2100, Denmark
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4
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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5
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Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.10.527147. [PMID: 37502865 PMCID: PMC10370084 DOI: 10.1101/2023.02.10.527147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wildtype human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
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Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jessica H. Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
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6
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Porat J, Vakiloroayaei A, Remnant BM, Talebi M, Cargill T, Bayfield MA. Crosstalk between the tRNA methyltransferase Trm1 and RNA chaperone La influences eukaryotic tRNA maturation. J Biol Chem 2023; 299:105326. [PMID: 37805140 PMCID: PMC10652106 DOI: 10.1016/j.jbc.2023.105326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
tRNAs undergo an extensive maturation process involving posttranscriptional modifications often associated with tRNA structural stability and promoting the native fold. Impaired posttranscriptional modification has been linked to human disease, likely through defects in translation, mitochondrial function, and increased susceptibility to degradation by various tRNA decay pathways. More recently, evidence has emerged that bacterial tRNA modification enzymes can act as tRNA chaperones to guide tRNA folding in a manner independent from catalytic activity. Here, we provide evidence that the fission yeast tRNA methyltransferase Trm1, which dimethylates nuclear- and mitochondrial-encoded tRNAs at G26, can also promote tRNA functionality in the absence of catalysis. We show that WT and catalytic-dead Trm1 are active in an in vivo tRNA-mediated suppression assay and possess RNA strand annealing and dissociation activity in vitro, similar to previously characterized RNA chaperones. Trm1 and the RNA chaperone La have previously been proposed to function synergistically in promoting tRNA maturation, yet we surprisingly demonstrate that La binding to nascent pre-tRNAs decreases Trm1 tRNA dimethylation in vivo and in vitro. Collectively, these results support the hypothesis for tRNA modification enzymes that combine catalytic and noncatalytic activities to promote tRNA maturation, as well as expand our understanding of how La function can influence tRNA modification.
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7
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Hogan CA, Gratz SJ, Dumouchel JL, Thakur RS, Delgado A, Lentini JM, Madhwani KR, Fu D, O'Connor‐Giles KM. Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function. EMBO Rep 2023; 24:e56808. [PMID: 37642556 PMCID: PMC10561368 DOI: 10.15252/embr.202356808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Nervous system function rests on the formation of functional synapses between neurons. We have identified TRMT9B as a new regulator of synapse formation and function in Drosophila. TRMT9B has been studied for its role as a tumor suppressor and is one of two metazoan homologs of yeast tRNA methyltransferase 9 (Trm9), which methylates tRNA wobble uridines. Whereas Trm9 homolog ALKBH8 is ubiquitously expressed, TRMT9B is enriched in the nervous system. However, in the absence of animal models, TRMT9B's role in the nervous system has remained unstudied. Here, we generate null alleles of TRMT9B and find it acts postsynaptically to regulate synaptogenesis and promote neurotransmission. Through liquid chromatography-mass spectrometry, we find that ALKBH8 catalyzes canonical tRNA wobble uridine methylation, raising the question of whether TRMT9B is a methyltransferase. Structural modeling studies suggest TRMT9B retains methyltransferase function and, in vivo, disruption of key methyltransferase residues blocks TRMT9B's ability to rescue synaptic overgrowth, but not neurotransmitter release. These findings reveal distinct roles for TRMT9B in the nervous system and highlight the significance of tRNA methyltransferase family diversification in metazoans.
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Affiliation(s)
- Caley A Hogan
- Genetics Training ProgramUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Scott J Gratz
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | | | - Rajan S Thakur
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Ambar Delgado
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Jenna M Lentini
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | | | - Dragony Fu
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | - Kate M O'Connor‐Giles
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
- Carney Institute for Brain ScienceProvidenceRIUSA
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8
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Xiong QP, Li J, Li H, Huang ZX, Dong H, Wang ED, Liu RJ. Human TRMT1 catalyzes m 2G or m 22G formation on tRNAs in a substrate-dependent manner. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2295-2309. [PMID: 37204604 DOI: 10.1007/s11427-022-2295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 05/20/2023]
Abstract
TRMT1 is an N2-methylguanosine (m2G) and N2,N2-methylguanosine (m22G) methyltransferase that targets G26 of both cytoplasmic and mitochondrial tRNAs. In higher eukaryotes, most cytoplasmic tRNAs with G26 carry m22G26, although the majority of mitochondrial G26-containing tRNAs carry m2G26 or G26, suggesting differences in the mechanisms by which TRMT1 catalyzes modification of these tRNAs. Loss-of-function mutations of human TRMT1 result in neurological disorders and completely abrogate tRNA:m22G26 formation. However, the mechanism underlying the independent catalytic activity of human TRMT1 and identity of its specific substrate remain elusive, hindering a comprehensive understanding of the pathogenesis of neurological disorders caused by TRMT1 mutations. Here, we showed that human TRMT1 independently catalyzes formation of the tRNA:m2G26 or m22G26 modification in a substrate-dependent manner, which explains the distinct distribution of m2G26 and m22G26 on cytoplasmic and mitochondrial tRNAs. For human TRMT1-mediated tRNA:m22G26 formation, the semi-conserved C11:G24 serves as the determinant, and the U10:A25 or G10:C25 base pair is also required, while the size of the variable loop has no effect. We defined the requirements of this recognition mechanism as the "m22G26 criteria". We found that the m22G26 modification occurred in almost all the higher eukaryotic tRNAs conforming to these criteria, suggesting the "m22G26 criteria" are applicable to other higher eukaryotic tRNAs.
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Affiliation(s)
- Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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9
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Juiputta J, Chankitisakul V, Boonkum W. Appropriate Genetic Approaches for Heat Tolerance and Maintaining Good Productivity in Tropical Poultry Production: A Review. Vet Sci 2023; 10:591. [PMID: 37888543 PMCID: PMC10611393 DOI: 10.3390/vetsci10100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Heat stress is a major environmental threat to poultry production systems, especially in tropical areas. The effects of heat stress have been discovered in several areas, including reduced growth rate, reduced egg production, low feed efficiency, impaired immunological responses, changes in intestinal microflora, metabolic changes, and deterioration of meat quality. Although several methods have been used to address the heat stress problem, it persists. The answer to this problem can be remedied sustainably if genetic improvement approaches are available. Therefore, the purpose of this review article was to present the application of different approaches to genetic improvement in poultry in the hope that users will find suitable solutions for their poultry population and be able to plan future poultry breeding programs.
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Affiliation(s)
- Jiraporn Juiputta
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
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10
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D′Oliviera A, Dai X, Mottaghinia S, Geissler EP, Etienne L, Zhang Y, Mugridge JS. Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529306. [PMID: 36865253 PMCID: PMC9980103 DOI: 10.1101/2023.02.20.529306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.
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Affiliation(s)
- Angel D′Oliviera
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Xuhang Dai
- Department of Chemistry, New York University, New York, NY 10003
| | - Saba Mottaghinia
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Evan P. Geissler
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Lucie Etienne
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
| | - Jeffrey S. Mugridge
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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11
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Lu JL, Zhou XL. SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1. J Mol Cell Biol 2023; 15:mjad024. [PMID: 37073102 PMCID: PMC10399916 DOI: 10.1093/jmcb/mjad024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/20/2023] Open
Affiliation(s)
- Jia-Li Lu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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12
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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13
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Wu H, Eckhardt CM, Baccarelli AA. Molecular mechanisms of environmental exposures and human disease. Nat Rev Genet 2023; 24:332-344. [PMID: 36717624 PMCID: PMC10562207 DOI: 10.1038/s41576-022-00569-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/01/2023]
Abstract
A substantial proportion of disease risk for common complex disorders is attributable to environmental exposures and pollutants. An appreciation of how environmental pollutants act on our cells to produce deleterious health effects has led to advances in our understanding of the molecular mechanisms underlying the pathogenesis of chronic diseases, including cancer and cardiovascular, neurodegenerative and respiratory diseases. Here, we discuss emerging research on the interplay of environmental pollutants with the human genome and epigenome. We review evidence showing the environmental impact on gene expression through epigenetic modifications, including DNA methylation, histone modification and non-coding RNAs. We also highlight recent studies that evaluate recently discovered molecular processes through which the environment can exert its effects, including extracellular vesicles, the epitranscriptome and the mitochondrial genome. Finally, we discuss current challenges when studying the exposome - the cumulative measure of environmental influences over the lifespan - and its integration into future environmental health research.
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Affiliation(s)
- Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Christina M Eckhardt
- Department of Pulmonary, Allergy and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
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14
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Singh A, Pandey KK, Agrawal SK, Srivastava RK, Bhattacharyya S, Verma B. The SARS-CoV-2 UTR’s Intrudes Host RBP’s and Modulates Cellular Splicing. Adv Virol 2023; 2023:2995443. [PMID: 37065904 PMCID: PMC10098413 DOI: 10.1155/2023/2995443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5′ and 3′UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5′ and 3’UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5′ and 3′UTRs, using in-silico approaches. Our results suggest that 5′ and 3′UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.
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Affiliation(s)
- Anjali Singh
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- Nebraska Center for Virology and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln 68583, NE, USA
| | - Shubham Kumar Agrawal
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rupesh K. Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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15
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. ARCHIVES OF IRANIAN MEDICINE 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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16
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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17
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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18
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Some natural compounds and their analogues having potent anti- SARS-CoV-2 and anti-proteases activities as lead molecules in drug discovery for COVID-19. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY REPORTS 2022; 6:100079. [PMID: 36060987 PMCID: PMC9420082 DOI: 10.1016/j.ejmcr.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022]
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19
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Generalov EA, Simonenko EY, Kulchenko NG, Yakovenko LV. [Molecular basis of biological activity of polysaccharides in COVID-19 associated conditions]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:403-418. [PMID: 36573407 DOI: 10.18097/pbmc20226806403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The review considers the main molecular biological features of the COVID-19 causative agent, the SARS-CoV-2 virus: life cycle, viral cell penetration strategies, interactions of viral proteins with human proteins, cytopathic effects. We also analyze pathological conditions that occur both during the course of the COVID-19 disease and after virus elimination. A brief review of the biological activities of polysaccharides isolated from various sources is given, and possible molecular biological mechanisms of these activities are considered. Data analysis shows that polysaccharides are a class of biological molecules with wide potential for use in the treatment of both acute conditions in COVID-19 and post-COVID syndrome.
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Affiliation(s)
- E A Generalov
- Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russia; Faculty of Medicine, Moscow University for Industry and Finance "Synergy", Moscow, Russia
| | - E Yu Simonenko
- Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - N G Kulchenko
- Medical Institute of the Peoples' Friendship University of Russia, Moscow, Russia
| | - L V Yakovenko
- Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russia
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20
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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21
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Perez M, Nance KD, Bak DW, Gamage ST, Najera SS, Conte AN, Linehan WM, Weerapana E, Meier JL. Conditional Covalent Lethality Driven by Oncometabolite Accumulation. ACS Chem Biol 2022; 17:2789-2800. [PMID: 36190452 PMCID: PMC10612128 DOI: 10.1021/acschembio.2c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a cancer predisposition syndrome driven by mutation of the tumor suppressor fumarate hydratase (FH). Inactivation of FH causes accumulation of the electrophilic oncometabolite fumarate. In the absence of methods for reactivation, tumor suppressors can be targeted via identification of synthetic lethal interactions using genetic screens. Inspired by recent advances in chemoproteomic target identification, here, we test the hypothesis that the electrophilicity of the HLRCC metabolome may produce unique susceptibilities to covalent small molecules, a phenomenon we term conditional covalent lethality. Screening a panel of chemically diverse electrophiles, we identified a covalent ligand, MP-1, that exhibits FH-dependent cytotoxicity. Synthesis and structure-activity profiling identified key molecular determinants underlying the molecule's effects. Chemoproteomic profiling of cysteine reactivity together with clickable probes validated the ability of MP-1 to engage an array of functional cysteines, including one lying in the Zn-finger domain of the tRNA methyltransferase enzyme TRMT1. TRMT1 overexpression rescues tRNA methylation from inhibition by MP-1 and partially attenuates the covalent ligand's cytotoxicity. Our studies highlight the potential for covalent metabolites and small molecules to synergistically produce novel synthetic lethal interactions and raise the possibility of applying phenotypic screening with chemoproteomic target identification to identify new functional oncometabolite targets.
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Affiliation(s)
- Minervo Perez
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland, 21072, USA
| | - Kellie D. Nance
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland, 21072, USA
| | - Daniel W. Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, 02467, USA
| | | | - Susana S. Najera
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland, 21072, USA
- Urologic Oncology Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Amy N. Conte
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland, 21072, USA
| | - W. Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, 02467, USA
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland, 21072, USA
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22
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Stakišaitis D, Kapočius L, Valančiūtė A, Balnytė I, Tamošuitis T, Vaitkevičius A, Sužiedėlis K, Urbonienė D, Tatarūnas V, Kilimaitė E, Gečys D, Lesauskaitė V. SARS-CoV-2 Infection, Sex-Related Differences, and a Possible Personalized Treatment Approach with Valproic Acid: A Review. Biomedicines 2022; 10:biomedicines10050962. [PMID: 35625699 PMCID: PMC9138665 DOI: 10.3390/biomedicines10050962] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
Sex differences identified in the COVID-19 pandemic are necessary to study. It is essential to investigate the efficacy of the drugs in clinical trials for the treatment of COVID-19, and to analyse the sex-related beneficial and adverse effects. The histone deacetylase inhibitor valproic acid (VPA) is a potential drug that could be adapted to prevent the progression and complications of SARS-CoV-2 infection. VPA has a history of research in the treatment of various viral infections. This article reviews the preclinical data, showing that the pharmacological impact of VPA may apply to COVID-19 pathogenetic mechanisms. VPA inhibits SARS-CoV-2 virus entry, suppresses the pro-inflammatory immune cell and cytokine response to infection, and reduces inflammatory tissue and organ damage by mechanisms that may appear to be sex-related. The antithrombotic, antiplatelet, anti-inflammatory, immunomodulatory, glucose- and testosterone-lowering in blood serum effects of VPA suggest that the drug could be promising for therapy of COVID-19. Sex-related differences in the efficacy of VPA treatment may be significant in developing a personalised treatment strategy for COVID-19.
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Affiliation(s)
- Donatas Stakišaitis
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania;
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (A.V.); (I.B.); (E.K.)
- Correspondence: (D.S.); (V.L.)
| | - Linas Kapočius
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (A.V.); (I.B.); (E.K.)
| | - Angelija Valančiūtė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (A.V.); (I.B.); (E.K.)
| | - Ingrida Balnytė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (A.V.); (I.B.); (E.K.)
| | - Tomas Tamošuitis
- Department of Intensive Care Medicine, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania;
| | - Arūnas Vaitkevičius
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University Hospital Santaros Klinikos, Vilnius University, 08661 Vilnius, Lithuania;
| | - Kęstutis Sužiedėlis
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania;
| | - Daiva Urbonienė
- Department of Laboratory Medicine, Medical Academy, Lithuanian University of Health Sciences, Eiveniu 2, 50161 Kaunas, Lithuania;
| | - Vacis Tatarūnas
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, Sukileliu Ave., 50161 Kaunas, Lithuania; (V.T.); (D.G.)
| | - Evelina Kilimaitė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (A.V.); (I.B.); (E.K.)
| | - Dovydas Gečys
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, Sukileliu Ave., 50161 Kaunas, Lithuania; (V.T.); (D.G.)
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, Sukileliu Ave., 50161 Kaunas, Lithuania; (V.T.); (D.G.)
- Correspondence: (D.S.); (V.L.)
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23
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Zhang W, Foo M, Eren AM, Pan T. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell 2022; 82:891-906. [PMID: 35032425 PMCID: PMC8897278 DOI: 10.1016/j.molcel.2021.12.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022]
Abstract
tRNA is the most extensively modified RNA in cells. On average, a bacterial tRNA contains 8 modifications per molecule and a eukaryotic tRNA contains 13 modifications per molecule. Recent studies reveal that tRNA modifications are highly dynamic and respond extensively to environmental conditions. Functions of tRNA modification dynamics include enhanced, on-demand decoding of specific codons in response genes and regulation of tRNA fragment biogenesis. This review summarizes recent advances in the studies of tRNA modification dynamics in biological processes, tRNA modification erasers, and human-associated bacteria. Furthermore, we use the term "metaepitranscriptomics" to describe the potential and approach of tRNA modification studies in natural biological communities such as microbiomes. tRNA is highly modified in cells, and tRNA modifications respond extensively to environmental conditions to enhance translation of specific genes and produce tRNA fragments on demand. We review recent advances in tRNA sequencing methods, tRNA modification dynamics in biological processes, and tRNA modification studies in natural communities such as the microbiomes.
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Affiliation(s)
- Wen Zhang
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Marcus Foo
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - A. Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA;,Department of Medicine, University of Chicago, Chicago, IL 60637, USA;,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
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24
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Lentini JM, Bargabos R, Chen C, Fu D. Methyltransferase METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs. J Biol Chem 2022; 298:101788. [PMID: 35247384 PMCID: PMC8980813 DOI: 10.1016/j.jbc.2022.101788] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/03/2023] Open
Abstract
A subset of eukaryotic tRNAs is methylated in the anticodon loop, forming 3-methylcytosine (m3C) modifications. In mammals, the number of tRNAs containing m3C modifications has been expanded to include mitochondrial (mt) tRNA-Ser-UGA and mt-tRNA-Thr-UGU. However, whereas the enzymes catalyzing m3C formation in nuclear-encoded tRNAs have been identified, the proteins responsible for m3C modification in mt-tRNAs are unknown. Here, we show that m3C formation in human mt-tRNAs is dependent upon the Methyltransferase-Like 8 (METTL8) enzyme. We find that METTL8 is a mitochondria-associated protein that interacts with mitochondrial seryl-tRNA synthetase, as well as with mt-tRNAs containing m3C. We demonstrate that human cells deficient in METTL8 exhibit loss of m3C modification in mt-tRNAs, but not nuclear-encoded tRNAs. Consistent with the mitochondrial import of METTL8, the formation of m3C in METTL8-deficient cells could be rescued by re-expression of wildtype METTL8, but not by a METTL8 variant lacking the N-terminal mitochondrial localization signal. Notably, we found METTL8-deficiency in human cells causes alterations in the native migration pattern of mt-tRNA-Ser-UGA, suggesting a role for m3C in tRNA folding. Altogether, these findings demonstrate that METTL8 is required for m3C formation in mitochondrial tRNAs and uncover a potential function for m3C modification in mitochondrial tRNA structure.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Rachel Bargabos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Chen Chen
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.
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25
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Khalique A, Mattijssen S, Maraia RJ. A versatile tRNA modification-sensitive northern blot method with enhanced performance. RNA (NEW YORK, N.Y.) 2022; 28:418-432. [PMID: 34930808 PMCID: PMC8848930 DOI: 10.1261/rna.078929.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
The 22 mitochondrial and ∼45 cytosolic tRNAs in human cells contain several dozen different post-transcriptional modified nucleotides such that each carries a unique constellation that complements its function. Many tRNA modifications are linked to altered gene expression, and deficiencies due to mutations in tRNA modification enzymes (TMEs) are responsible for numerous diseases. Easily accessible methods to detect tRNA hypomodifications can facilitate progress in advancing such molecular studies. Our laboratory developed a northern blot method that can quantify relative levels of base modifications on multiple specific tRNAs ∼10 yr ago, which has been used to characterize four different TME deficiencies and is likely further extendable. The assay method depends on differential annealing efficiency of a DNA-oligo probe to the modified versus unmodified tRNA. The signal of this probe is then normalized by a second probe elsewhere on the same tRNA. This positive hybridization in the absence of modification (PHAM) assay has proven useful for i6A37, t6A37, m3C32, and m2,2G26 in multiple laboratories. Yet, over the years we have observed idiosyncratic inconsistency and variability in the assay. Here we document these for some tRNAs and probes and illustrate principles and practices for improved reliability and uniformity in performance. We provide an overview of the method and illustrate benefits of the improved conditions. This is followed by data that demonstrate quantitative validation of PHAM using a TME deletion control, and that nearby modifications can falsely alter the calculated apparent modification efficiency. Finally, we include a calculator tool for matching probe and hybridization conditions.
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Affiliation(s)
- Abdul Khalique
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard J Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Huang Y, Chen S, Xiao L, Qin W, Li L, Wang Y, Ma L, Yuan X. A Novel Prognostic Signature for Survival Prediction and Immune Implication Based on SARS-CoV-2–Related Genes in Kidney Renal Clear Cell Carcinoma. Front Bioeng Biotechnol 2022; 9:744659. [PMID: 35141213 PMCID: PMC8819071 DOI: 10.3389/fbioe.2021.744659] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is a common aggressive malignancy of the urinary system. COVID-19, a highly infectious and severe disease caused by SARS-CoV-2, has become a significant challenge for global public health. Cancer patients have been reported to be more vulnerable to SARS-CoV-2 infection and have a higher risk for serious complications than the general population. However, the correlation between KIRC and COVID-19 remains incompletely elucidated. In this study, we comprehensively investigated the expression and prognostic significance of 333 SARS-CoV-2 infection–related genes in KIRC using the TCGA dataset and identified 31 SARS-CoV-2–related differently expressed genes between KIRC and normal renal tissues. Based on these genes, we constructed and validated a 5-gene prognostic signature (including ACADM, CENPF, KDELC1, PLOD2, and TRMT1) to distinguish low- and high-risk KIRC patients of poor survival in TCGA and E-MTAB-1980 cohorts. Gene set enrichment analysis (GSEA) showed that some inflammatory/immune-related pathways were significantly enriched in the high-risk group. The ESTIMATE analysis indicated that patients in the high-risk group had higher stromal and immune cell scores, therefore lower tumor purity. Moreover, they presented higher proportions of macrophages M0, regulatory T cells (Tregs), and T follicular helper cells and higher expression of immune checkpoints CTLA-4, LAG-3, TIGIT, and PDCD1 than low-risk patients. Besides, we also developed a nomogram to expand clinical applicability, which exhibits excellent predictive accuracy for survival. In conclusion, we identified a novel prognostic signature and nomogram based on SARS-CoV-2–related genes as reliable prognostic predictors for KIRC patients and provided potential therapeutic targets for KIRC and COVID-19.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Lingyan Xiao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Ma
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Xianglin Yuan,
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27
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tRNA modifications and their potential roles in pancreatic cancer. Arch Biochem Biophys 2021; 714:109083. [PMID: 34785212 DOI: 10.1016/j.abb.2021.109083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022]
Abstract
Since the breakthrough discovery of N6-methyladenosine (m6A), the field of RNA epitranscriptomics has attracted increasing interest in the biological sciences. Transfer RNAs (tRNAs) are extensively modified, and various modifications play a crucial role in the formation and stability of tRNA, which is universally required for accurate and efficient functioning of tRNA. Abnormal tRNA modification can lead to tRNA degradation or specific cleavage of tRNA into fragmented derivatives, thus affecting the translation process and frequently accompanying a variety of human diseases. Increasing evidence suggests that tRNA modification pathways are also misregulated in human cancers. In this review, we summarize tRNA modifications and their biological functions, describe the type and frequency of tRNA modification alterations in cancer, and highlight variations in tRNA-modifying enzymes and the multiple functions that they regulate in different types of cancers. Furthermore, the current implications and the potential role of tRNA modifications in the progression of pancreatic cancer are discussed. Collectively, this review describes recent advances in tRNA modification in cancers and its potential significance in pancreatic cancer. Further study of the mechanism of tRNA modifications in pancreatic cancer may provide possibilities for therapies targeting enzymes responsible for regulating tRNA modifications in pancreatic cancer.
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28
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Li H, Dong H, Xu B, Xiong QP, Li CT, Yang WQ, Li J, Huang ZX, Zeng QY, Wang ED, Liu RJ. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. EMBO J 2021; 41:e108544. [PMID: 34850409 PMCID: PMC8922252 DOI: 10.15252/embj.2021108544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
Since numerous RNAs and RBPs prevalently localize to active chromatin regions, many RNA-binding proteins (RBPs) may be potential transcriptional regulators. RBPs are generally thought to regulate transcription via noncoding RNAs. Here, we describe a distinct, dual mechanism of transcriptional regulation by the previously uncharacterized tRNA-modifying enzyme, hTrmt13. On one hand, hTrmt13 acts in the cytoplasm to catalyze 2'-O-methylation of tRNAs, thus regulating translation in a manner depending on its tRNA-modification activity. On the other hand, nucleus-localized hTrmt13 directly binds DNA as a transcriptional co-activator of key epithelial-mesenchymal transition factors, thereby promoting cell migration independent of tRNA-modification activity. These dual functions of hTrmt13 are mutually exclusive, as it can bind either DNA or tRNA through its CHHC zinc finger domain. Finally, we find that hTrmt13 expression is tightly associated with poor prognosis and survival in diverse cancer patients. Our discovery of the noncatalytic roles of an RNA-modifying enzyme provides a new perspective for understanding epitranscriptomic regulation.
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Affiliation(s)
- Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhi-Xuan Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Qi-Yu Zeng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - En-Duo Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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29
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Das AS, Alfonzo JD, Accornero F. The importance of RNA modifications: From cells to muscle physiology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1700. [PMID: 34664402 DOI: 10.1002/wrna.1700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022]
Abstract
Naturally occurring post-transcriptional chemical modifications serve critical roles in impacting RNA structure and function. More directly, modifications may affect RNA stability, intracellular transport, translational efficiency, and fidelity. The combination of effects caused by modifications are ultimately linked to gene expression regulation at a genome-wide scale. The latter is especially true in systems that undergo rapid metabolic and or translational remodeling in response to external stimuli, such as the presence of stressors, but beyond that, modifications may also affect cell homeostasis. Although examples of the importance of RNA modifications in translation are accumulating rapidly, still what these contribute to the function of complex physiological systems such as muscle is only recently emerging. In the present review, we will introduce key information on various modifications and highlight connections between those and cellular malfunctions. In passing, we will describe well-documented roles for modifications in the nervous system and use this information as a stepping stone to emphasize a glaring paucity of knowledge on the role of RNA modifications in heart and skeletal muscle, with particular emphasis on mitochondrial function in those systems. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA.,The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA.,The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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30
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Zhang LS, Xiong QP, Perez SP, Liu C, Wei J, Le C, Zhang L, Harada BT, Dai Q, Feng X, Hao Z, Wang Y, Dong X, Hu L, Wang ED, Pan T, Klungland A, Liu RJ, He C. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol 2021; 23:684-691. [PMID: 34253897 PMCID: PMC8716185 DOI: 10.1038/s41556-021-00709-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Members of the mammalian AlkB family are known to mediate nucleic acid demethylation1,2. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria and affects metabolism3, but its function and mechanism of action are unknown. Here we report an approach to site-specifically detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates m22G and m1A within mitochondrial Ile and Leu1 pre-tRNA regions, respectively, in nascent polycistronic mitochondrial RNA4-6. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mitochondrial RNAs. Depletion of ALKBH7 leads to increased polycistronic mitochondrial RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, and notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China
| | - Sonia Peña Perez
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Chang Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cassy Le
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Linda Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Bryan T. Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Xueyang Dong
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ru-Juan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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31
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Li C, Yao Y, Long D, Lin X. KDELC1 and TRMT1 Serve as Prognosis-Related SARS-CoV-2 Proteins Binding Human mRNAs and Promising Biomarkers in Clear Cell Renal Cell Carcinoma. Int J Gen Med 2021; 14:2475-2490. [PMID: 34163216 PMCID: PMC8214210 DOI: 10.2147/ijgm.s312416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background SARS-CoV-2 proteins binding human mRNAs (SPBRs) have been proven to regulate a variety of tumor-related functions in different types of cancer. However, their biological roles and potential mechanisms in clear cell renal cell carcinoma (ccRCC) are still elusive. Herein, we investigate the expression and prognostic value of SPBRs in ccRCC through bioinformatics methods. Methods Data downloaded from the Cancer Genome Atlas (TCGA) database was used to screen differentially expressed SPBRs (DE-SPBRs) between ccRCC samples and noncancerous samples. Metascape was utilized to perform function and pathway enrichment analyses of these DE-SPBRs. Kaplan–Meier method of overall survival (OS) was used to assess the prognostic value of DE-SPBRs in ccRCC patients. Univariate and multivariate Cox regression analyses were applied to identify candidate SPBRs, which were independently associated with overall survival of ccRCC patients. Subsequently, several internationally renowned databases were employed to conduct a comprehensive analysis of candidate SPBRs to further investigate their roles and mechanisms in ccRCC. Results A total of 33 DE-SPBRs, including 18 upregulated SPBRs and 17 downregulated SPBRs, were screened between ccRCC samples and noncancerous samples. Among them, two candidate SPBRs, KDELC1 and TRMT1, were identified. Additionally, we observed that upregulated KDELC1/TRMT1 expression in ccRCC at both gene and protein levels was significantly associated with clinicopathological features. Furthermore, we found that KDELC1/TRMT1 genetic mutation has an unfavorable influence on prognosis of patients with ccRCC. Functional enrichment analysis revealed that KDELC1/TRMT1 was closely enriched in several vital biological processes and pathways. Finally, we noticed that KDELC1/TRMT1 was remarkably associated with immune infiltrates. Conclusion In summary, we screened DE-SPBRs of ccRCC, which were enriched mainly in various biological and signaling pathways with tumor progression. Furthermore, we identified two candidate DE-SPBRs (KDELC1 and TRMT1), which could serve as promising biomarkers and therapeutic targets of patients with ccRCC.
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Affiliation(s)
- Canxuan Li
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People's Republic of China
| | - Yuzhi Yao
- Department of Breast Surgery and General Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China.,Guangzhou Women and Children's Medical Center, Department of Paediatric Surgery Clinic, Guangzhou, Guangdong, People's Republic of China
| | - Dan Long
- Respiratory medicine, Shenshan Central Hospital, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Shanwei, Guangdong, People's Republic of China
| | - Xiaobin Lin
- Department of Breast Surgery and General Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China.,Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Guangdong, People's Republic of China
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32
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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33
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Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021; 27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
Abstract
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding of misfolded substrates into functional conformations. The best characterized tRNA chaperone is the La protein, which interacts with nascent RNA polymerase III transcripts to promote folding and offers protection from exonucleases. More recently, certain tRNA modification enzymes have also been demonstrated to possess tRNA folding activity distinct from their catalytic activity, suggesting that they may act as tRNA chaperones. In this review, we will discuss pioneering studies relating post-transcriptional modification to tRNA stability and decay pathways, present recent advances into the mechanism by which the RNA chaperone La assists pre-tRNA maturation, and summarize emerging research directions aimed at characterizing modification enzymes as tRNA chaperones. Together, these findings shed light on the importance of tRNA folding and how tRNA chaperones, in particular, increase the fraction of nascent pre-tRNAs that adopt a folded, functional conformation.
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34
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Jonkhout N, Cruciani S, Santos Vieira HG, Tran J, Liu H, Liu G, Pickford R, Kaczorowski D, Franco GR, Vauti F, Camacho N, Abedini SS, Najmabadi H, Ribas de Pouplana L, Christ D, Schonrock N, Mattick JS, Novoa EM. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol 2021; 18:1905-1919. [PMID: 33499731 DOI: 10.1080/15476286.2021.1881291] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ganqiang Liu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Current Address: School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | | | - Gloria R Franco
- Departamento De Bioquímica E Imunologia, Universidade Federal De Minas Gerais,Belo Horizonte,Minas Gerais, Brazil
| | - Franz Vauti
- Division of Cellular & Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Noelia Camacho
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain
| | - Seyedeh Sedigheh Abedini
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
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35
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Chujo T, Tomizawa K. Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications. FEBS J 2021; 288:7096-7122. [PMID: 33513290 PMCID: PMC9255597 DOI: 10.1111/febs.15736] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as 'tRNA modopathies'. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
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Affiliation(s)
- Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
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36
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Chang R, Mamun A, Dominic A, Le NT. SARS-CoV-2 Mediated Endothelial Dysfunction: The Potential Role of Chronic Oxidative Stress. Front Physiol 2021; 11:605908. [PMID: 33519510 PMCID: PMC7844210 DOI: 10.3389/fphys.2020.605908] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
Endothelial cells have emerged as key players in SARS-CoV-2 infection and COVID-19 inflammatory pathologies. Dysfunctional endothelial cells can promote chronic inflammation and disease processes like thrombosis, atherosclerosis, and lung injury. In endothelial cells, mitochondria regulate these inflammatory pathways via redox signaling, which is primarily achieved through mitochondrial reactive oxygen species (mtROS). Excess mtROS causes oxidative stress that can initiate and exacerbate senescence, a state that promotes inflammation and chronic endothelial dysfunction. Oxidative stress can also activate feedback loops that perpetuate mitochondrial dysfunction, mtROS overproduction, and inflammation. In this review, we provide an overview of phenotypes mediated by mtROS in endothelial cells - such as mitochondrial dysfunction, inflammation, and senescence - as well as how these chronic states may be initiated by SARS-CoV-2 infection of endothelial cells. We also propose that SARS-CoV-2 activates mtROS-mediated feedback loops that cause long-term changes in host redox status and endothelial function, promoting cardiovascular disease and lung injury after recovery from COVID-19. Finally, we discuss the implications of these proposed pathways on long-term vascular health and potential treatments to address these chronic conditions.
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Affiliation(s)
- Ryan Chang
- College of Arts & Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Abrar Mamun
- Wiess School of Natural Sciences, Rice University, Houston, TX, United States
| | - Abishai Dominic
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX, United States
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States
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37
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Mukhopadhyay S, Deogharia M, Gupta R. Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA. RNA (NEW YORK, N.Y.) 2021; 27:66-79. [PMID: 33023933 PMCID: PMC7749629 DOI: 10.1261/rna.076810.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 05/10/2023]
Abstract
Most mammalian cytoplasmic tRNAs contain ribothymidine (T) and pseudouridine (Ψ) at positions 54 and 55, respectively. However, some tRNAs contain Ψ at both positions. Several Ψ54-containing tRNAs function as primers in retroviral DNA synthesis. The Ψ54 of these tRNAs is produced by PUS10, which can also synthesize Ψ55. Two other enzymes, TRUB1 and TRUB2, can also produce Ψ55. By nearest-neighbor analyses of tRNAs treated with recombinant proteins and subcellular extracts of wild-type and specific Ψ55 synthase knockdown cells, we determined that while TRUB1, PUS10, and TRUB2 all have tRNA Ψ55 synthase activities, they have different tRNA structural requirements. Moreover, these activities are primarily present in the nucleus, cytoplasm, and mitochondria, respectively, suggesting a compartmentalization of Ψ55 synthase activity. TRUB1 produces the Ψ55 of most elongator tRNAs, but cytoplasmic PUS10 produces both Ψs of the tRNAs with Ψ54Ψ55. The nuclear isoform of PUS10 is catalytically inactive and specifically binds the unmodified U54U55 versions of Ψ54Ψ55-containing tRNAs, as well as the A54U55-containing tRNAiMet This binding inhibits TRUB1-mediated U55 to Ψ55 conversion in the nucleus. Consequently, the U54U55 of Ψ54Ψ55-containing tRNAs are modified by the cytoplasmic PUS10. Nuclear PUS10 does not bind the U55 versions of T54Ψ55- and A54Ψ55-containing elongator tRNAs. Therefore, TRUB1 is able to produce Ψ55 in these tRNAs. In summary, the tRNA Ψ55 synthase activities of TRUB1 and PUS10 are not redundant but rather are compartmentalized and act on different sets of tRNAs. The significance of this compartmentalization needs further study.
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MESH Headings
- Animals
- Binding Sites
- Cell Compartmentation
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cytoplasm/genetics
- Cytoplasm/metabolism
- Gene Expression
- HEK293 Cells
- Humans
- Hydro-Lyases/genetics
- Hydro-Lyases/metabolism
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- PC-3 Cells
- Protein Binding
- Pseudouridine/metabolism
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Trp/genetics
- RNA, Transfer, Trp/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sf9 Cells
- Spodoptera
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Affiliation(s)
- Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Manisha Deogharia
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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38
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Suryawanshi RK, Koganti R, Agelidis A, Patil CD, Shukla D. Dysregulation of Cell Signaling by SARS-CoV-2. Trends Microbiol 2020; 29:224-237. [PMID: 33451855 PMCID: PMC7836829 DOI: 10.1016/j.tim.2020.12.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022]
Abstract
Pathogens usurp host pathways to generate a permissive environment for their propagation. The current spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection presents the urgent need to understand the complex pathogen–host interplay for effective control of the virus. SARS-CoV-2 reorganizes the host cytoskeleton for efficient cell entry and controls host transcriptional processes to support viral protein translation. The virus also dysregulates innate cellular defenses using various structural and nonstructural proteins. This results in substantial but delayed hyperinflammation alongside a weakened interferon (IFN) response. We provide an overview of SARS-CoV-2 and its uniquely aggressive life cycle and discuss the interactions of various viral proteins with host signaling pathways. We also address the functional changes in SARS-CoV-2 proteins, relative to SARS-CoV. Our comprehensive assessment of host signaling in SARS-CoV-2 pathogenesis provides some complex yet important strategic clues for the development of novel therapeutics against this rapidly emerging worldwide crisis.
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Affiliation(s)
- Rahul K Suryawanshi
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Raghuram Koganti
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alex Agelidis
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Chandrashekhar D Patil
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA.
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39
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Funk HM, Zhao R, Thomas M, Spigelmyer SM, Sebree NJ, Bales RO, Burchett JB, Mamaril JB, Limbach PA, Guy MP. Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants. PLoS One 2020; 15:e0242737. [PMID: 33253256 PMCID: PMC7704012 DOI: 10.1371/journal.pone.0242737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Posttranscriptional modification of tRNA is critical for efficient protein translation and proper cell growth, and defects in tRNA modifications are often associated with human disease. Although most of the enzymes required for eukaryotic tRNA modifications are known, many of these enzymes have not been identified and characterized in several model multicellular eukaryotes. Here, we present two related approaches to identify the genes required for tRNA modifications in multicellular organisms using primer extension assays with fluorescent oligonucleotides. To demonstrate the utility of these approaches we first use expression of exogenous genes in yeast to experimentally identify two TRM1 orthologs capable of forming N2,N2-dimethylguanosine (m2,2G) on residue 26 of cytosolic tRNA in the model plant Arabidopsis thaliana. We also show that a predicted catalytic aspartate residue is required for function in each of the proteins. We next use RNA interference in cultured Drosophila melanogaster cells to identify the gene required for m2,2G26 formation on cytosolic tRNA. Additionally, using these approaches we experimentally identify D. melanogaster gene CG10050 as the corresponding ortholog of human DTWD2, which encodes the protein required for formation of 3-amino-3-propylcarboxyuridine (acp3U) on residue 20a of cytosolic tRNA. We further show that A. thaliana gene AT2G41750 can form acp3U20b on an A. thaliana tRNA expressed in yeast cells, and that the aspartate and tryptophan residues in the DXTW motif of this protein are required for modification activity. These results demonstrate that these approaches can be used to study tRNA modification enzymes.
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Affiliation(s)
- Holly M. Funk
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Maggie Thomas
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Sarah M. Spigelmyer
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Nichlas J. Sebree
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Regan O. Bales
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Jamison B. Burchett
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Justen B. Mamaril
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Michael P. Guy
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
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40
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Ramos J, Proven M, Halvardson J, Hagelskamp F, Kuchinskaya E, Phelan B, Bell R, Kellner SM, Feuk L, Thuresson AC, Fu D. Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder. RNA (NEW YORK, N.Y.) 2020; 26:1654-1666. [PMID: 32763916 PMCID: PMC7566568 DOI: 10.1261/rna.076380.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.
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Affiliation(s)
- Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Melissa Proven
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | | | - Ekaterina Kuchinskaya
- Department of Clinical Genetics, and Department of Clinical Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Benjamin Phelan
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Ryan Bell
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | | | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
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41
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Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:e202006159. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
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Affiliation(s)
- Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Arti T. Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Biochemistry, University of Washington, Seattle, WA
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42
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De Zoysa T, Phizicky EM. Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences. PLoS Genet 2020; 16:e1008893. [PMID: 32841241 PMCID: PMC7473580 DOI: 10.1371/journal.pgen.1008893] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/04/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
All tRNAs are extensively modified, and modification deficiency often results in growth defects in the budding yeast Saccharomyces cerevisiae and neurological or other disorders in humans. In S. cerevisiae, lack of any of several tRNA body modifications results in rapid tRNA decay (RTD) of certain mature tRNAs by the 5'-3' exonucleases Rat1 and Xrn1. As tRNA quality control decay mechanisms are not extensively studied in other eukaryotes, we studied trm8Δ mutants in the evolutionarily distant fission yeast Schizosaccharomyces pombe, which lack 7-methylguanosine at G46 (m7G46) of their tRNAs. We report here that S. pombe trm8Δ mutants are temperature sensitive primarily due to decay of tRNATyr(GUA) and that spontaneous mutations in the RAT1 ortholog dhp1+ restored temperature resistance and prevented tRNA decay, demonstrating conservation of the RTD pathway. We also report for the first time evidence linking the RTD and the general amino acid control (GAAC) pathways, which we show in both S. pombe and S. cerevisiae. In S. pombe trm8Δ mutants, spontaneous GAAC mutations restored temperature resistance and tRNA levels, and the trm8Δ temperature sensitivity was precisely linked to GAAC activation due to tRNATyr(GUA) decay. Similarly, in the well-studied S. cerevisiae trm8Δ trm4Δ RTD mutant, temperature sensitivity was closely linked to GAAC activation due to tRNAVal(AAC) decay; however, in S. cerevisiae, GAAC mutations increased tRNA loss and exacerbated temperature sensitivity. A similar exacerbated growth defect occurred upon GAAC mutation in S. cerevisiae trm8Δ and other single modification mutants that triggered RTD. Thus, these results demonstrate a conserved GAAC activation coincident with RTD in S. pombe and S. cerevisiae, but an opposite impact of the GAAC response in the two organisms. We speculate that the RTD pathway and its regulation of the GAAC pathway is widely conserved in eukaryotes, extending to other mutants affecting tRNA body modifications.
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Affiliation(s)
- Thareendra De Zoysa
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- * E-mail:
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43
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Management of epigenomic networks entailed in coronavirus infections and COVID-19. Clin Epigenetics 2020; 12:118. [PMID: 32758273 PMCID: PMC7404079 DOI: 10.1186/s13148-020-00912-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) are highly diverse single-stranded RNA viruses owing to their susceptibility to numerous genomic mutations and recombination. Such viruses involve human and animal pathogens including the etiologic agents of acute respiratory tract illnesses: severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the highly morbific SARS-CoV-2. Coronavirus disease 2019 (COVID-19), an emerging disease with a quick rise in infected cases and deaths, was recently identified causing a worldwide pandemic. COVID-19 disease outcomes were found to increase in elderly and patients with a compromised immune system. Evidences indicated that the main culprit behind COVID-19 deaths is the cytokine storm, which is illustrated by an uncontrolled over-production of soluble markers of inflammation. The regulation process of coronavirus pathogenesis through molecular mechanism comprise virus-host interactions linked to viral entry, replication and transcription, escape, and immune system control. Recognizing coronavirus infections and COVID-19 through epigenetics lens will lead to potential alteration in gene expression thus limiting coronavirus infections. Focusing on epigenetic therapies reaching clinical trials, clinically approved epigenetic-targeted agents, and combination therapy of antivirals and epigenetic drugs is currently considered an effective and valuable approach for viral replication and inflammatory overdrive control.
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44
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Hagelskamp F, Borland K, Ramos J, Hendrick AG, Fu D, Kellner S. Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Res 2020; 48:e41. [PMID: 32083657 PMCID: PMC7144906 DOI: 10.1093/nar/gkaa091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/23/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA.
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Affiliation(s)
- Felix Hagelskamp
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alan G Hendrick
- STORM Therapeutics, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT UK
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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45
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020; 583:459-468. [PMID: 32353859 PMCID: PMC7431030 DOI: 10.1038/s41586-020-2286-9] [Citation(s) in RCA: 2958] [Impact Index Per Article: 739.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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46
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Lentini JM, Alsaif HS, Faqeih E, Alkuraya FS, Fu D. DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Nat Commun 2020; 11:2510. [PMID: 32427860 PMCID: PMC7237682 DOI: 10.1038/s41467-020-16321-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific tRNA arginine species for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein to recognize particular arginine tRNAs destined for m3C modification. DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in tRNA-Arg species. Notably, we identify a homozygous nonsense mutation in the DALRD3 gene that impairs m3C formation in human patients exhibiting developmental delay and early-onset epileptic encephalopathy. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification and suggest a crucial biological role for DALRD3-dependent tRNA modification in proper neurological development.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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47
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He Q, Yang L, Gao K, Ding P, Chen Q, Xiong J, Yang W, Song Y, Wang L, Wang Y, Ling L, Wu W, Yan J, Zou P, Chen Y, Zhai R. FTSJ1 regulates tRNA 2'-O-methyladenosine modification and suppresses the malignancy of NSCLC via inhibiting DRAM1 expression. Cell Death Dis 2020; 11:348. [PMID: 32393790 PMCID: PMC7214438 DOI: 10.1038/s41419-020-2525-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/28/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide. The mechanisms underlying NSCLC tumorigenesis are incompletely understood. Transfer RNA (tRNA) modification is emerging as a novel regulatory mechanism for carcinogenesis. However, the role of tRNA modification in NSCLC remains obscure. In this study, HPLC/MS assay was used to quantify tRNA modification levels in NSCLC tissues and cells. tRNA-modifying enzyme genes were identified by comparative genomics and validated by qRT-PCR analysis. The biological functions of tRNA-modifying gene in NSCLC were investigated in vitro and in vivo. The mechanisms of tRNA-modifying gene in NSCLC were explored by RNA-seq, qRT-PCR, and rescue assays. The results showed that a total of 18 types of tRNA modifications and up to seven tRNA-modifying genes were significantly downregulated in NSCLC tumor tissues compared with that in normal tissues, with the 2'-O-methyladenosine (Am) modification displaying the lowest level in tumor tissues. Loss- and gain-of-function assays revealed that the amount of Am in tRNAs was significantly associated with expression levels of FTSJ1, which was also downregulated in NSCLC tissues and cells. Upregulation of FTSJ1 inhibited proliferation, migration, and promoted apoptosis of NSCLC cells in vitro. Silencing of FTSJ1 resulted in the opposite effects. In vivo assay confirmed that overexpression of FTSJ1 significantly suppressed the growth of NSCLC cells. Mechanistically, overexpression of FTSJ1 led to a decreased expression of DRAM1. Whereas knockdown of FTSJ1 resulted in an increased expression of DRAM1. Furthermore, silencing of DRAM1 substantially augmented the antitumor effect of FTSJ1 on NSCLC cells. Our findings suggested an important mechanism of tRNA modifications in NSCLC and demonstrated novel roles of FTSJ1 as both tRNA Am modifier and tumor suppressor in NSCLC.
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Affiliation(s)
- Qihan He
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Lin Yang
- Department of Thoracic Surgery, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Kaiping Gao
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Peikun Ding
- Department of Thoracic Surgery, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Qianqian Chen
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Juan Xiong
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Wenhan Yang
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Yi Song
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Liang Wang
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Yejun Wang
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Lijuan Ling
- Department of Thoracic Surgery, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Weiming Wu
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Jisong Yan
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Peng Zou
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Yuchen Chen
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Rihong Zhai
- School of Public Health, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China.
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48
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020. [PMID: 32353859 DOI: 10.1038/s41586‐020‐2286‐9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,J. David Gladstone Institutes, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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49
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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50
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 67 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Huettenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Jose Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Phillip P Sharp
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin A Cavero
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Oren S Rosenberg
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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