1
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Schult P, Kümmerer BM, Hafner M, Paeschke K. Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control. Cell Host Microbe 2024; 32:1579-1593.e8. [PMID: 39094585 DOI: 10.1016/j.chom.2024.07.006] [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: 04/17/2023] [Revised: 04/02/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024]
Abstract
Viral genomes are enriched with G-quadruplexes (G4s), non-canonical structures formed in DNA or RNA upon assembly of four guanine stretches into stacked quartets. Because of their critical roles, G4s are potential antiviral targets, yet their function remains largely unknown. Here, we characterize the formation and functions of a conserved G4 within the polymerase coding region of orthoflaviviruses of the Flaviviridae family. Using yellow fever virus, we determine that this G4 promotes viral replication and suppresses host stress responses via interactions with hnRNPH1, a host nuclear protein involved in RNA processing. G4 binding to hnRNPH1 causes its cytoplasmic retention with subsequent impacts on G4-containing tRNA fragments (tiRNAs) involved in stress-mediated reductions in translation. As a result, these host stress responses and associated antiviral effects are impaired. These data reveal that the interplay between hnRNPH1 and both host and viral G4 targets controls the integrated stress response and viral replication.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany; Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Beate Mareike Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, 53127 Bonn, Germany
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany; Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany.
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2
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Tilliole P, Fix S, Godin JD. hnRNPs: roles in neurodevelopment and implication for brain disorders. Front Mol Neurosci 2024; 17:1411639. [PMID: 39086926 PMCID: PMC11288931 DOI: 10.3389/fnmol.2024.1411639] [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: 04/03/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a family of multifunctional RNA-binding proteins able to process nuclear pre-mRNAs into mature mRNAs and regulate gene expression in multiple ways. They comprise at least 20 different members in mammals, named from A (HNRNP A1) to U (HNRNP U). Many of these proteins are components of the spliceosome complex and can modulate alternative splicing in a tissue-specific manner. Notably, while genes encoding hnRNPs exhibit ubiquitous expression, increasing evidence associate these proteins to various neurodevelopmental and neurodegenerative disorders, such as intellectual disability, epilepsy, microcephaly, amyotrophic lateral sclerosis, or dementias, highlighting their crucial role in the central nervous system. This review explores the evolution of the hnRNPs family, highlighting the emergence of numerous new members within this family, and sheds light on their implications for brain development.
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Affiliation(s)
- Pierre Tilliole
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Simon Fix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Juliette D. Godin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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3
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Levengood JD, Potoyan D, Penumutchu S, Kumar A, Zhou Q, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions. SCIENCE ADVANCES 2024; 10:eadk6580. [PMID: 38985864 PMCID: PMC11235170 DOI: 10.1126/sciadv.adk6580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The functional properties of RNA binding proteins (RBPs) require allosteric regulation through interdomain communication. Despite the importance of allostery to biological regulation, only a few studies have been conducted to describe the biophysical nature by which interdomain communication manifests in RBPs. Here, we show for hnRNP A1 that interdomain communication is vital for the unique stability of its amino-terminal domain, which consists of two RNA recognition motifs (RRMs). These RRMs exhibit drastically different stability under pressure. RRM2 unfolds as an individual domain but remains stable when appended to RRM1. Variants that disrupt interdomain communication between the tandem RRMs show a significant decrease in stability. Carrying these mutations over to the full-length protein for in vivo experiments revealed that the mutations affected the ability of the disordered carboxyl-terminal domain to engage in protein-protein interactions and influenced the protein's RNA binding capacity. Collectively, this work reveals that thermodynamic coupling between the tandem RRMs of hnRNP A1 accounts for its allosteric regulatory functions.
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Affiliation(s)
- Jeffrey D. Levengood
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abhishek Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Qianzi Zhou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yiqing Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alexandar L. Hansen
- CCIC and Gateway NMR Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Sebla Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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4
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Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024; 16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Type I interferons (IFN-Is) are pivotal in innate immunity against human immunodeficiency virus I (HIV-1) by eliciting the expression of IFN-stimulated genes (ISGs), which encompass potent host restriction factors. While ISGs restrict the viral replication within the host cell by targeting various stages of the viral life cycle, the lesser-known IFN-repressed genes (IRepGs), including RNA-binding proteins (RBPs), affect the viral replication by altering the expression of the host dependency factors that are essential for efficient HIV-1 gene expression. Both the host restriction and dependency factors determine the viral replication efficiency; however, the understanding of the IRepGs implicated in HIV-1 infection remains greatly limited at present. This review provides a comprehensive overview of the current understanding regarding the impact of the RNA-binding protein families, specifically the two families of splicing-associated proteins SRSF and hnRNP, on HIV-1 gene expression and viral replication. Since the recent findings show specifically that SRSF1 and hnRNP A0 are regulated by IFN-I in various cell lines and primary cells, including intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs), we particularly discuss their role in the context of the innate immunity affecting HIV-1 replication.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katleen Klaassen
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Stefanie Heß
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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5
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Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JPWE, Denomy C, Hutchinson C, Abidullah HM, Austin Hammond S, Pastushok L, Vizeacoumar FS, Levin MC. hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nat Commun 2024; 15:356. [PMID: 38191621 PMCID: PMC10774274 DOI: 10.1038/s41467-023-44658-1] [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: 06/23/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.
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Affiliation(s)
- Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Yulian Ding
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
- Division of Biomedical Engineering, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Joseph-Patrick W E Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Connor Denomy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Hashim M Abidullah
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Landon Pastushok
- Advanced Diagnostics Research Laboratory, Department of Pathology and Lab Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada.
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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6
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Tang KS, Tsai CM, Cheng MC, Huang YH, Chang CH, Yu HR. Salivary Biomarkers to Differentiate between Streptococcus pneumoniae and Influenza A Virus-Related Pneumonia in Children. Diagnostics (Basel) 2023; 13:diagnostics13081468. [PMID: 37189569 DOI: 10.3390/diagnostics13081468] [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: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Community-acquired pneumonia (CAP) is common among children and can be fatal in certain conditions. In children, CAP can be caused by viral or bacterial infections. Identification of pathogens can help select appropriate therapeutic strategies. Salivary analysis may be a potential diagnostic tool because it is noninvasive, patient-friendly, and easy to perform in children. A prospective study was conducted in children with pneumonia admitted to a hospital. Salivary samples from patients with definite Streptococcus pneumoniae and influenza A strains were used for gel-free (isobaric tag for relative and absolute quantitation (iTRAQ)) proteomics. No statistically significant difference was detected in salivary CRP levels between Streptococcus pneumoniae and influenza A pneumonia in children. Several potential salivary biomarkers were identified using gel-free iTRAQ proteomics to differentiate pneumonia from Streptococcus pneumoniae or influenza A virus infections in pediatric patients. ELISA validated that Streptococcus pneumoniae group has a higher abundance of salivary alpha 1-antichymotrypsin than those in the influenza A group. Whether these salivary biomarkers can be used to distinguish other bacteria from viral pneumonia requires further verification.
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Affiliation(s)
- Kuo-Shu Tang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Chih-Min Tsai
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Ming-Chou Cheng
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Ying-Hsien Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan City 33302, Taiwan
| | - Chih-Hao Chang
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Hong-Ren Yu
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan City 33302, Taiwan
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
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7
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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8
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Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS. Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors. J Mol Biol 2022; 434:167728. [PMID: 35870649 PMCID: PMC9945881 DOI: 10.1016/j.jmb.2022.167728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/19/2023]
Abstract
Alternative splicing of the HIV transcriptome is controlled through cis regulatory elements functioning as enhancers or silencers depending on their context and the type of host RNA binding proteins they recruit. Splice site acceptor A3 (ssA3) is one of the least used acceptor sites in the HIV transcriptome and its activity determines the levels of tat mRNA. Splice acceptor 3 is regulated by a combination of cis regulatory sequences, auxiliary splicing factors, and presumably RNA structure. The mechanisms by which these multiple regulatory components coordinate to determine the frequency in which ssA3 is utilized is poorly understood. By NMR spectroscopy and phylogenetic analysis, we show that the ssA3 regulatory locus is conformationally heterogeneous and that the sequences that encompass the locus are conserved across most HIV isolates. Despite the conformational heterogeneity, the major stem loop (A3SL1) observed in vitro folds to base pair the Polypyrimdine Tract (PPyT) to the Exon Splicing Silencer 2p (ESS2p) element and to a conserved downstream linker. The 3D structure as determined by NMR spectroscopy further reveals that the A3 consensus cleavage site is embedded within a unique stereochemical environment within the apical loop, where it is surrounded by alternating base-base interactions. Despite being described as a receptor for hnRNP H, the ESS2p element is sequestered by base pairing to the 3' end of the PPyT and within this context it cannot form a stable complex with hnRNP H. By comparison, hnRNP A1 directly binds to the A3 consensus cleavage site located within the apical loop, suggesting that it can directly modulate U2AF assembly. Sequence mutations designed to destabilize the PPyT:ESS2p helix results in an increase usage of ssA3 within HIV-infected cells, consistent with the PPyT becoming more accessible for U2AF recognition. Additional mutations introduced into the downstream ESS2 element synergize with ESS2p to cause further increases in ssA3 usage. When taken together, our work provides a unifying picture by which cis regulatory sequences, splicing auxiliary factors and RNA structure cooperate to provide stringent control over ssA3. We describe this as the pair-and-lock mechanism to restrict access of the PPyT, and posit that it operates to regulate a subset of the heterogenous structures encompassing the ssA3 regulatory locus.
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Affiliation(s)
- Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States. https://twitter.com/LiangYuanChiu1
| | - Ann Emery
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Niyati Jain
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States. https://twitter.com/sugarman_andrew
| | - Nashea Kendrick
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Le Luo
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - William Ford
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Ronald Swanstrom
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, United States; Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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9
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Wang J, Sun D, Wang M, Cheng A, Zhu Y, Mao S, Ou X, Zhao X, Huang J, Gao Q, Zhang S, Yang Q, Wu Y, Zhu D, Jia R, Chen S, Liu M. Multiple functions of heterogeneous nuclear ribonucleoproteins in the positive single-stranded RNA virus life cycle. Front Immunol 2022; 13:989298. [PMID: 36119073 PMCID: PMC9478383 DOI: 10.3389/fimmu.2022.989298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that are implicated in RNA metabolism, such as alternative splicing, mRNA stabilization and translational regulation. According to their different cellular localization, hnRNPs display multiple functions. Most hnRNPs were predominantly located in the nucleus, but some of them could redistribute to the cytoplasm during virus infection. HnRNPs consist of different domains and motifs that enable these proteins to recognize predetermined nucleotide sequences. In the virus-host interactions, hnRNPs specifically bind to viral RNA or proteins. And some of the viral protein-hnRNP interactions require the viral RNA or other host factors as the intermediate. Through various mechanisms, hnRNPs could regulate viral translation, viral genome replication, the switch of translation to replication and virion release. This review highlights the common features and the distinguish roles of hnRNPs in the life cycle of positive single-stranded RNA viruses.
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Affiliation(s)
- Jingming Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- *Correspondence: Anchun Cheng,
| | - Yukun Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xuming Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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10
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Dahal S, Clayton K, Been T, Fernet-Brochu R, Ocando AV, Balachandran A, Poirier M, Maldonado RK, Shkreta L, Boligan KF, Guvenc F, Rahman F, Branch D, Bell B, Chabot B, Gray-Owen SD, Parent LJ, Cochrane A. Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency. Retrovirology 2022; 19:18. [PMID: 35986377 PMCID: PMC9389714 DOI: 10.1186/s12977-022-00605-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs). METHODS Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence. RESULTS The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC50 ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells. CONCLUSIONS These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for "Kick-and-Kill" strategies, or to silence HIV protein expression for "Block-and-Lock" strategies.
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Affiliation(s)
- Subha Dahal
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Kiera Clayton
- grid.168645.80000 0001 0742 0364Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Terek Been
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Raphaële Fernet-Brochu
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Alonso Villasmil Ocando
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
| | - Ahalya Balachandran
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Mikaël Poirier
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Rebecca Kaddis Maldonado
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Lulzim Shkreta
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Kayluz Frias Boligan
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Furkan Guvenc
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Fariha Rahman
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Donald Branch
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Brendan Bell
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Benoit Chabot
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Scott D. Gray-Owen
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Leslie J. Parent
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Alan Cochrane
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
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11
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Gallardo CM, Nguyen AVT, Routh AL, Torbett BE. Selective ablation of 3' RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts. Nucleic Acids Res 2022; 50:e98. [PMID: 35736235 PMCID: PMC9508845 DOI: 10.1093/nar/gkac516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/25/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is necessary for viral proliferation in host cells and a critical regulatory component of viral gene expression. Conventional RNA-seq approaches provide incomplete coverage of AS due to their short read lengths and are susceptible to biases and artifacts introduced in prevailing library preparation methodologies. Moreover, viral splicing studies are often conducted separately from host cell transcriptome analysis, precluding an assessment of the viral manipulation of host splicing machinery. To address current limitations, we developed a quantitative full-length direct cDNA sequencing strategy to simultaneously profile viral and host cell transcripts. This nanopore-based approach couples processive reverse transcriptases with a novel one-step chemical ablation of 3' RNA ends (termed CASPR), which decreases ribosomal RNA reads and enriches polyadenylated coding sequences. We extensively validate our approach using synthetic reference transcripts and show that CASPR doubles the breadth of coverage per transcript and increases detection of long transcripts (>4 kb), while being functionally equivalent to PolyA+ selection for transcript quantification. We used our approach to interrogate host cell and HIV-1 transcript dynamics during viral reactivation and identified novel putative HIV-1 host factors containing exon skipping or novel intron retentions and delineated the HIV-1 transcriptional state associated with these differentially regulated host factors.
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Affiliation(s)
- Christian M Gallardo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Anh-Viet T Nguyen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bruce E Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98101, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
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12
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Hu Q, Chen Y, Zhao Y, Gu J, Ma M, Li H, Li C, Wang ZY. Overexpression of SCL30A from cassava (Manihot esculenta) negatively regulates salt tolerance in Arabidopsis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1213-1224. [PMID: 34782061 DOI: 10.1071/fp21165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 05/24/2023]
Abstract
Soil salinity is a significant threat to sustainable agricultural production. Plants must adjust their developmental and physiological processes to deal with environmental salt conditions. We previously identified 18 serine-arginine-rich (SR) proteins from cassava (Manihot esculenta Crantz) that play pivotal roles in alternative splicing when encountering the external stress condition. However, functional characterisation of SR proteins is less reported in cassava, which is an important staple crop in the world. In the current study, we found that the expression of cassava spliceosomal component 35-like 30A (MeSCL30A) was significantly induced in response to drought and salt stress. The MeSCL30A overexpressing lines were also obtained in Arabidopsis thaliana L., which flowered earlier when compared with Col-0. Moreover, the MeSCL30A overexpressing lines were hypersensitive to salt and drought stress with lower germination and greening rate in comparison to Col-0. Importantly, soil-grown overexpression lines exhibited salt sensitivity through modulating the reactive oxygen species homeostasis and negatively regulating the gene expression that involved in ionic stress pathway. Therefore, these findings refined the SR protein-coding genes and provided novel insights for enhancing the resistance to environmental stress in plant.
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Affiliation(s)
- Qing Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; and Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Yunfeng Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Muqing Ma
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Hua Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China; and Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong 524300, China
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13
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Pal LR, Cheng K, Nair NU, Martin-Sancho L, Sinha S, Pu Y, Riva L, Yin X, Schischlik F, Lee JS, Chanda SK, Ruppin E. Synthetic lethality-based prediction of anti-SARS-CoV-2 targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.09.14.460408. [PMID: 34545363 PMCID: PMC8452092 DOI: 10.1101/2021.09.14.460408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Novel strategies are needed to identify drug targets and treatments for the COVID-19 pandemic. The altered gene expression of virus-infected host cells provides an opportunity to specifically inhibit viral propagation via targeting the synthetic lethal (SL) partners of such altered host genes. Pursuing this antiviral strategy, here we comprehensively analyzed multiple in vitro and in vivo bulk and single-cell RNA-sequencing datasets of SARS-CoV-2 infection to predict clinically relevant candidate antiviral targets that are SL with altered host genes. The predicted SL-based targets are highly enriched for infected cell inhibiting genes reported in four SARS-CoV-2 CRISPR-Cas9 genome-wide genetic screens. Integrating our predictions with the results of these screens, we further selected a focused subset of 26 genes that we experimentally tested in a targeted siRNA screen using human Caco-2 cells. Notably, as predicted, knocking down these targets reduced viral replication and cell viability only under the infected condition without harming non-infected cells. Our results are made publicly available, to facilitate their in vivo testing and further validation.
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Affiliation(s)
- Lipika R. Pal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanju Sinha
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Fiorella Schischlik
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joo Sang Lee
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
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14
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Tanu T, Taniue K, Imamura K, Onoguchi-Mizutani R, Han H, Jensen TH, Akimitsu N. hnRNPH1-MTR4 complex-mediated regulation of NEAT1v2 stability is critical for IL8 expression. RNA Biol 2021; 18:537-547. [PMID: 34470577 DOI: 10.1080/15476286.2021.1971439] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many long noncoding RNAs (lncRNAs) are localized in the nucleus and play important roles in various biological processes, including cell proliferation, differentiation and antiviral response. Yet, it remains unclear how some nuclear lncRNAs are turned over. Here we show that the heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) controls expression levels of NEAT1v2, a lncRNA involved in the formation of nuclear paraspeckles. hnRNPH1 associates, in an RNA-independent manner, with the RNA helicase MTR4/MTREX, an essential co-factor of the nuclear ribonucleolytic RNA exosome. hnRNPH1 localizes in nuclear speckles and depletion of hnRNPH1 enhances NEAT1v2-mediated expression of the IL8 mRNA, encoding a cytokine involved in the innate immune response. Taken together, our results indicate that the hnRNPH1-MTR4 linkage regulates IL8 expression through the degradation of NEAT1v2 RNA.
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Affiliation(s)
- Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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15
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Alternative splicing events implicated in carcinogenesis and prognosis of thyroid gland cancer. Sci Rep 2021; 11:4841. [PMID: 33649373 PMCID: PMC7921437 DOI: 10.1038/s41598-021-84403-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative splicing (AS), a critical post-transcriptional regulatory mechanism, expands gene expression patterns, thereby leading to increased protein diversity. Indeed, more than 95% of human genes undergo alternative splicing events (ASEs). In this study, we drew an all-around AS profile of thyroid cancer cells based on RNA-seq data. In total, there were 45,150 AS in 10,446 thyroid cancer cell genes derived from 506 patients, suggesting that ASEs is a common process in TC. Moreover, 1819 AS signatures were found to be significantly associated with the overall survival (OS) of TC patients. Kaplan–Meier survival analyses suggested that seven types of ASEs were associated with poor prognosis of TC (P < 0.05). Among them, exon skipping (ES) was the most common, with alternate promoter (AP) and alternate terminator (AT) coming second and third, respectively. Our results indicated that acceptor sites (AA) (AUC: 0.937), alternate donor sites (AD) (AUC: 0.965), AT (AUC: 0.964), ES (AUC: 0.999), mutually exclusive exons (ME) (AUC: 0.999), and retained intron (RI) (AUC: 0.837) exhibited an AUC greater than 0.6. In addition, age and risk score (All) were risk factors for TC patients. We also evaluated whether TC-ASEs are regulated by various splicing factors (SFs). We found that the expression of 90 SFs was associated with 469 ASEs and OS of TC patients. Our findings provide an insight into the role of spliceosomes in TC, which may offer novel perspectives in tumor research.
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16
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Zhu HE, Li T, Shi S, Chen DX, Chen W, Chen H. ESCO2 promotes lung adenocarcinoma progression by regulating hnRNPA1 acetylation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:64. [PMID: 33573689 PMCID: PMC7876794 DOI: 10.1186/s13046-021-01858-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Emerging evidence indicates that metabolism reprogramming and abnormal acetylation modification play an important role in lung adenocarcinoma (LUAD) progression, although the mechanism is largely unknown. METHODS Here, we used three public databases (Oncomine, Gene Expression Omnibus [GEO], The Cancer Genome Atlas [TCGA]) to analyze ESCO2 (establishment of cohesion 1 homolog 2) expression in LUAD. The biological function of ESCO2 was studiedusing cell proliferation, colony formation, cell migration, and invasion assays in vitro, and mouse xenograft models in vivo. ESCO2 interacting proteins were searched using gene set enrichment analysis (GSEA) and mass spectrometry. Pyruvate kinase M1/2 (PKM) mRNA splicing assay was performed using RT-PCR together with restriction digestion. LUAD cell metabolism was studied using glucose uptake assays and lactate production. ESCO2 expression was significantly upregulated in LUAD tissues, and higher ESCO2 expression indicated worse prognosis for patients with LUAD. RESULTS We found that ESCO2 promoted LUAD cell proliferation and metastasis metabolic reprogramming in vitro and in vivo. Mechanistically, ESCO2 increased hnRNPA1 (heterogeneous nuclear ribonucleoprotein A1) binding to the intronic sequences flanking exon 9 (EI9) of PKM mRNA by inhibiting hnRNPA1 nuclear translocation, eventually inhibiting PKM1 isoform formation and inducing PKM2 isoform formation. CONCLUSIONS Our findings confirm that ESCO2 is a key factor in promoting LUAD malignant progression and suggest that it is a new target for treating LUAD.
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Affiliation(s)
- Hui-Er Zhu
- Department of General Practice, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Tao Li
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Shengnan Shi
- State Key Laboratory of Animal Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, South China Key Laboratory of Animal Nutrition and Feed, Ministry of Agriculture, Guangzhou, 510640, P. R. China
| | - De-Xiong Chen
- Department of General Practice, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Weiping Chen
- Department of Respiratory, The People's Hospital of Qingyuan, Sixth Affiliate Hospital of Guangzhou Medical University, Qingyuan, 511518, P. R. China.
| | - Hui Chen
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China.
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17
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Yeh YHJ, Jenike KM, Calvi RM, Chiarella J, Hoh R, Deeks SG, Ho YC. Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation. J Clin Invest 2021; 130:4969-4984. [PMID: 32573496 DOI: 10.1172/jci137371] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Despite effective antiretroviral therapy, HIV-1-infected cells continue to produce viral antigens and induce chronic immune exhaustion. We propose to identify HIV-1-suppressing agents that can inhibit HIV-1 reactivation and reduce HIV-1-induced immune activation. Using a newly developed dual-reporter system and a high-throughput drug screen, we identified FDA-approved drugs that can suppress HIV-1 reactivation in both cell line models and CD4+ T cells from virally suppressed HIV-1-infected individuals. We identified 11 cellular pathways required for HIV-1 reactivation as druggable targets. Using differential expression analysis, gene set enrichment analysis, and exon-intron landscape analysis, we examined the impact of drug treatment on the cellular environment at a genome-wide level. We identified what we believe to be a new function of a JAK inhibitor, filgotinib, that suppresses HIV-1 splicing. First, filgotinib preferentially suppresses spliced HIV-1 RNA transcription. Second, filgotinib suppresses HIV-1-driven aberrant cancer-related gene expression at the integration site. Third, we found that filgotinib suppresses HIV-1 transcription by inhibiting T cell activation and by modulating RNA splicing. Finally, we found that filgotinib treatment reduces the proliferation of HIV-1-infected cells. Overall, the combination of a drug screen and transcriptome analysis provides systematic understanding of cellular targets required for HIV-1 reactivation and drug candidates that may reduce HIV-1-related immune activation.
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Affiliation(s)
- Yang-Hui Jimmy Yeh
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katharine M Jenike
- Human Genetics PhD Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rachela M Calvi
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebecca Hoh
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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18
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Emery A, Swanstrom R. HIV-1: To Splice or Not to Splice, That Is the Question. Viruses 2021; 13:181. [PMID: 33530363 PMCID: PMC7912102 DOI: 10.3390/v13020181] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023] Open
Abstract
The transcription of the HIV-1 provirus results in only one type of transcript-full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.
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MESH Headings
- Alternative Splicing
- Exons
- Gene Expression Regulation, Viral
- HIV-1/genetics
- Nucleic Acid Conformation
- RNA Splicing
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Nucleic Acid
- Virus Latency/genetics
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Ann Emery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
- Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599, USA
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Haddad C, Davila-Calderon J, Tolbert BS. Integrated approaches to reveal mechanisms by which RNA viruses reprogram the cellular environment. Methods 2020; 183:50-56. [PMID: 32622045 PMCID: PMC7329689 DOI: 10.1016/j.ymeth.2020.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets.
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Clip for studying protein-RNA interactions that regulate virus replication. Methods 2020; 183:84-92. [PMID: 31765715 DOI: 10.1016/j.ymeth.2019.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/24/2023] Open
Abstract
Viral and cellular RNA-binding proteins regulate numerous key steps in the replication of diverse virus genera. Viruses efficiently co-opt the host cell machinery for purposes such as transcription, splicing and subcellular localization of viral genomes. Though viral RNAs often need to resemble cellular RNAs to effectively utilize the cellular machinery, they still retain unique sequence and structural features for recognition by viral proteins for processes such as RNA polymerization, RNA export and selective packaging into virus particles. While beneficial for virus replication, distinct features of viral nucleic acids can also be recognized as foreign by several host defense proteins. Development of the crosslinking immunoprecipitation coupled with sequencing (CLIP) approach has allowed the study of viral and cellular RNA binding proteins that regulate critical aspects of viral replication in unprecedented detail. By combining immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, CLIP provides a global account of RNA sequences bound by RNA-binding proteins of interest in physiological settings and at near-nucleotide resolution. Here, we describe the step-by-step application of the CLIP methodology within the context of two cellular splicing regulatory proteins, hnRNP A1 and hnRNP H1 that regulate HIV-1 splicing. In principle, this versatile protocol can be applied to many other viral and cellular RNA-binding proteins.
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HIV-1 Lethality and Loss of Env Protein Expression Induced by Single Synonymous Substitutions in the Virus Genome Intronic-Splicing Silencer. J Virol 2020; 94:JVI.01108-20. [PMID: 32817222 DOI: 10.1128/jvi.01108-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/06/2020] [Indexed: 01/13/2023] Open
Abstract
Synonymous genome recoding has been widely used to study different aspects of virus biology. Codon usage affects the temporal regulation of viral gene expression. In this study, we performed synonymous codon mutagenesis to investigate whether codon usage affected HIV-1 Env protein expression and virus viability. We replaced the codons AGG, GAG, CCU, ACU, CUC, and GGG of the HIV-1 env gene with the synonymous codons CGU, GAA, CCG, ACG, UUA, and GGA, respectively. We found that recoding the Env protein gp120 coding region (excluding the Rev response element [RRE]) did not significantly affect virus replication capacity, even though we introduced 15 new CpG dinucleotides. In contrast, changing a single codon (AGG to CGU) located in the gp41 coding region (HXB2 env position 2125 to 2127), which was included in the intronic splicing silencer (ISS), completely abolished virus replication and Env expression. Computational analyses of this mutant revealed a severe disruption in the ISS RNA secondary structure. A variant that restored ISS secondary RNA structure also reestablished Env production and virus viability. Interestingly, this codon variant prevented both virus replication and Env translation in a eukaryotic expression system. These findings suggested that disrupting mRNA splicing was not the only means of inhibiting translation. Our findings indicated that synonymous gp120 recoding was not always deleterious to HIV-1 replication. Importantly¸ we found that disrupting an external ISS loop strongly affected HIV-1 replication and Env translation.IMPORTANCE Synonymous substitutions can influence virus phenotype, replication capacity, and virulence. In this study, we explored how synonymous codon mutations impacted HIV-1 Env protein expression and virus replication capacity. We changed a single codon, AGG to CGU, which was located in the gp41 coding region (env nucleotide residues 2125 to 2127) and was included in the HIV-1 intronic splicing silencer. This change completely abolished virus replication and Env expression. We also found that changing codon usage in the gp120 region by including an increased number of CpG dinucleotides did not significantly affect Env expression or virus viability. Our findings showed that synonymous recoding was useful for altering viral phenotype and exploring virus biology.
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Barrera A, Ramos H, Vera-Otarola J, Fernández-García L, Angulo J, Olguín V, Pino K, Mouland AJ, López-Lastra M. Post-translational modifications of hnRNP A1 differentially modulate retroviral IRES-mediated translation initiation. Nucleic Acids Res 2020; 48:10479-10499. [PMID: 32960212 PMCID: PMC7544202 DOI: 10.1093/nar/gkaa765] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 08/09/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
The full-length mRNAs of the human immunodeficiency virus type-1 (HIV-1), the human T-cell lymphotropic virus type-1 (HTLV-1), and the mouse mammary tumor virus (MMTV) harbor IRESs. The activity of the retroviral-IRESs requires IRES-transacting factors (ITAFs), being hnRNP A1, a known ITAF for the HIV-1 IRES. In this study, we show that hnRNP A1 is also an ITAF for the HTLV-1 and MMTV IRESs. The MMTV IRES proved to be more responsive to hnRNP A1 than either the HTLV-1 or the HIV-1 IRESs. The impact of post-translational modifications of hnRNP A1 on HIV-1, HTLV-1 and MMTV IRES activity was also assessed. Results show that the HIV-1 and HTLV-1 IRESs were equally responsive to hnRNP A1 and its phosphorylation mutants S4A/S6A, S4D/S6D and S199A/D. However, the S4D/S6D mutant stimulated the activity from the MMTV-IRES to levels significantly higher than the wild type hnRNP A1. PRMT5-induced symmetrical di-methylation of arginine residues of hnRNP A1 enabled the ITAF to stimulate the HIV-1 and HTLV-1 IRESs while reducing the stimulatory ability of the ITAF over the MMTV IRES. We conclude that retroviral IRES activity is not only dependent on the recruited ITAFs but also relies on how these proteins are modified at the post-translational level.
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Affiliation(s)
- Aldo Barrera
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Hade Ramos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Leandro Fernández-García
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jenniffer Angulo
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Karla Pino
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
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