1
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Dutcher HA, Gasch AP. Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604323. [PMID: 39091809 PMCID: PMC11291059 DOI: 10.1101/2024.07.19.604323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1 Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global over-expression screen that identified genes whose duplication complements ssd1 Δ aneuploid sensitivity. The resulting network points to a sub-group of proteins with shared roles in translational repression and p-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.
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2
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [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] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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3
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Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024; 300:107488. [PMID: 38908752 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
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4
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Mir DA, Ma Z, Horrocks J, Rogers AN. Stress-induced Eukaryotic Translational Regulatory Mechanisms. ARXIV 2024:arXiv:2405.01664v1. [PMID: 38745702 PMCID: PMC11092689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The eukaryotic protein synthesis process entails intricate stages governed by diverse mechanisms to tightly regulate translation. Translational regulation during stress is pivotal for maintaining cellular homeostasis, ensuring the accurate expression of essential proteins crucial for survival. This selective translational control mechanism is integral to cellular adaptation and resilience under adverse conditions. This review manuscript explores various mechanisms involved in selective translational regulation, focusing on mRNA-specific and global regulatory processes. Key aspects of translational control include translation initiation, which is often a rate-limiting step, and involves the formation of the eIF4F complex and recruitment of mRNA to ribosomes. Regulation of translation initiation factors, such as eIF4E, eIF4E2, and eIF2, through phosphorylation and interactions with binding proteins, modulates translation efficiency under stress conditions. This review also highlights the control of translation initiation through factors like the eIF4F complex and the ternary complex and also underscores the importance of eIF2α phosphorylation in stress granule formation and cellular stress responses. Additionally, the impact of amino acid deprivation, mTOR signaling, and ribosome biogenesis on translation regulation and cellular adaptation to stress is also discussed. Understanding the intricate mechanisms of translational regulation during stress provides insights into cellular adaptation mechanisms and potential therapeutic targets for various diseases, offering valuable avenues for addressing conditions associated with dysregulated protein synthesis.
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Affiliation(s)
- Dilawar Ahmad Mir
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Zhengxin Ma
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Jordan Horrocks
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Aric N Rogers
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
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5
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Jun SE, Cho KH, Schaffrath R, Kim GT. Evolutionary Conservation in Protein-Protein Interactions and Structures of the Elongator Sub-Complex ELP456 from Arabidopsis and Yeast. Int J Mol Sci 2024; 25:4370. [PMID: 38673955 PMCID: PMC11050213 DOI: 10.3390/ijms25084370] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the precise details of the evolutionary conservation of the holo-Elongator complex and its individual sub-complexes (i.e., ELP123; ELP456) in plants remain limited. In this study, we conducted an in vivo analysis of protein-protein interactions among Arabidopsis ELP4, ELP5, and ELP6 proteins. Additionally, we predicted their structural configurations and performed a comparative analysis with the structure of the yeast Elp456 sub-complex. Protein-protein interaction analysis revealed that AtELP4 interacts with AtELP6 but not directly with AtELP5. Furthermore, we found that the Arabidopsis Elongator-associated protein, Deformed Roots and Leaves 1 (DRL1), did not directly bind to AtELP proteins. The structural comparison of the ELP456 sub-complex between Arabidopsis and yeast demonstrated high similarity, encompassing the RecA-ATPase fold and the positions of hydrogen bonds, despite their relatively low sequence homology. Our findings suggest that Arabidopsis ELP4, ELP5, and ELP6 proteins form a heterotrimer, with ELP6 serving as a bridge, indicating high structural conservation between the ELP456 sub-complexes from Arabidopsis and yeast.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Gyeongbuk Institute for Bioindustry, Andong 36618, Republic of Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany;
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Graduate School of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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6
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Añazco-Guenkova AM, Miguel-López B, Monteagudo-García Ó, García-Vílchez R, Blanco S. The impact of tRNA modifications on translation in cancer: identifying novel therapeutic avenues. NAR Cancer 2024; 6:zcae012. [PMID: 38476632 PMCID: PMC10928989 DOI: 10.1093/narcan/zcae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Recent advancements have illuminated the critical role of RNA modifications in post-transcriptional regulation, shaping the landscape of gene expression. This review explores how tRNA modifications emerge as critical players, fine-tuning functionalities that not only maintain the fidelity of protein synthesis but also dictate gene expression and translation profiles. Highlighting their dysregulation as a common denominator in various cancers, we systematically investigate the intersection of both cytosolic and mitochondrial tRNA modifications with cancer biology. These modifications impact key processes such as cell proliferation, tumorigenesis, migration, metastasis, bioenergetics and the modulation of the tumor immune microenvironment. The recurrence of altered tRNA modification patterns across different cancer types underscores their significance in cancer development, proposing them as potential biomarkers and as actionable targets to disrupt tumorigenic processes, offering new avenues for precision medicine in the battle against cancer.
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Affiliation(s)
- Ana M Añazco-Guenkova
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Óscar Monteagudo-García
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
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7
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del Dedo JE, Segundo RLS, Vázquez-Bolado A, Sun J, García-Blanco N, Suárez MB, García P, Tricquet P, Chen JS, Dedon PC, Gould KL, Hidalgo E, Hermand D, Moreno S. The Greatwall-Endosulfine-PP2A/B55 pathway controls entry into quiescence by promoting translation of Elongator-tuneable transcripts. RESEARCH SQUARE 2023:rs.3.rs-3616701. [PMID: 38105947 PMCID: PMC10723533 DOI: 10.21203/rs.3.rs-3616701/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Quiescent cells require a continuous supply of proteins to maintain protein homeostasis. In fission yeast, entry into quiescence is triggered by nitrogen stress, leading to the inactivation of TORC1 and the activation of TORC2. Here, we report that the Greatwall-Endosulfine-PPA/B55 pathway connects the downregulation of TORC1 with the upregulation of TORC2, resulting in the activation of Elongator-dependent tRNA modifications essential for sustaining the translation programme during entry into quiescence. This process promotes U34 and A37 tRNA modifications at the anticodon stem loop, enhancing translation efficiency and fidelity of mRNAs enriched for AAA versus AAG lysine codons. Notably, some of these mRNAs encode inhibitors of TORC1, activators of TORC2, tRNA modifiers, and proteins necessary for telomeric and subtelomeric functions. Therefore, we propose a novel mechanism by which cells respond to nitrogen stress at the level of translation, involving a coordinated interplay between the tRNA epitranscriptome and biased codon usage.
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Affiliation(s)
- Javier Encinar del Dedo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Rafael López-San Segundo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Alicia Vázquez-Bolado
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Jingjing Sun
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Natalia García-Blanco
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - M. Belén Suárez
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Patricia García
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Pauline Tricquet
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Peter C. Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Damien Hermand
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
- Lead contact
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8
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DeAngelo SL, Győrffy B, Koutmos M, Shah YM. Selenoproteins and tRNA-Sec: regulators of cancer redox homeostasis. Trends Cancer 2023; 9:1006-1018. [PMID: 37716885 PMCID: PMC10843386 DOI: 10.1016/j.trecan.2023.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/18/2023]
Abstract
In the past two decades significant progress has been made in uncovering the biological function of selenium. Selenium, an essential trace element, is required for the biogenesis of selenocysteine which is then incorporated into selenoproteins. These selenoproteins have emerged as central regulators of cellular antioxidant capacity and maintenance of redox homeostasis. This review provides a comprehensive examination of the multifaceted functions of selenoproteins with a particular emphasis on their contributions to cellular antioxidant capacity. Additionally, we highlight the promising potential of targeting selenoproteins and the biogenesis of selenocysteine as avenues for therapeutic intervention in cancer. By understanding the intricate relationship between selenium, selenoproteins, and reactive oxygen species (ROS), insights can be gained to develop therapies that exploit the inherent vulnerabilities of cancer cells.
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Affiliation(s)
- Stephen L DeAngelo
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Markos Koutmos
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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9
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Tomasi FG, Kimura S, Rubin EJ, Waldor MK. A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth. eLife 2023; 12:RP87146. [PMID: 37755167 PMCID: PMC10531406 DOI: 10.7554/elife.87146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Diverse chemical modifications fine-tune the function and metabolism of tRNA. Although tRNA modification is universal in all kingdoms of life, profiles of modifications, their functions, and physiological roles have not been elucidated in most organisms including the human pathogen, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To identify physiologically important modifications, we surveyed the tRNA of Mtb, using tRNA sequencing (tRNA-seq) and genome-mining. Homology searches identified 23 candidate tRNA modifying enzymes that are predicted to create 16 tRNA modifications across all tRNA species. Reverse transcription-derived error signatures in tRNA-seq predicted the sites and presence of nine modifications. Several chemical treatments prior to tRNA-seq expanded the number of predictable modifications. Deletion of Mtb genes encoding two modifying enzymes, TruB and MnmA, eliminated their respective tRNA modifications, validating the presence of modified sites in tRNA species. Furthermore, the absence of mnmA attenuated Mtb growth in macrophages, suggesting that MnmA-dependent tRNA uridine sulfation contributes to Mtb intracellular growth. Our results lay the foundation for unveiling the roles of tRNA modifications in Mtb pathogenesis and developing new therapeutics against tuberculosis.
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Affiliation(s)
- Francesca G Tomasi
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public HealthBostonUnited States
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's HospitalBostonUnited States
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public HealthBostonUnited States
| | - Matthew K Waldor
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public HealthBostonUnited States
- Division of Infectious Diseases, Brigham and Women's HospitalBostonUnited States
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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10
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Park J, Lee HH, Moon H, Lee N, Kim S, Kim JE, Lee Y, Min K, Kim H, Choi GJ, Lee YW, Seo YS, Son H. A combined transcriptomic and physiological approach to understanding the adaptive mechanisms to cope with oxidative stress in Fusarium graminearum. Microbiol Spectr 2023; 11:e0148523. [PMID: 37671872 PMCID: PMC10581207 DOI: 10.1128/spectrum.01485-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/04/2023] [Indexed: 09/07/2023] Open
Abstract
In plant-pathogen interactions, oxidative bursts are crucial for plants to defend themselves against pathogen infections. Rapid production and accumulation of reactive oxygen species kill pathogens directly and cause local cell death, preventing pathogens from spreading to adjacent cells. Meanwhile, the pathogens have developed several mechanisms to tolerate oxidative stress and successfully colonize plant tissues. In this study, we investigated the mechanisms responsible for resistance to oxidative stress by analyzing the transcriptomes of six oxidative stress-sensitive strains of the plant pathogenic fungus Fusarium graminearum. Weighted gene co-expression network analysis identified several pathways related to oxidative stress responses, including the DNA repair system, autophagy, and ubiquitin-mediated proteolysis. We also identified hub genes with high intramodular connectivity in key modules and generated deletion or conditional suppression mutants. Phenotypic characterization of those mutants showed that the deletion of FgHGG4, FgHGG10, and FgHGG13 caused sensitivity to oxidative stress, and further investigation on those genes revealed that transcriptional elongation and DNA damage responses play roles in oxidative stress response and pathogenicity. The suppression of FgHGL7 also led to hypersensitivity to oxidative stress, and we demonstrated that FgHGL7 plays a crucial role in heme biosynthesis and is essential for peroxidase activity. This study increases the understanding of the adaptive mechanisms to cope with oxidative stress in plant pathogenic fungi. IMPORTANCE Fungal pathogens have evolved various mechanisms to overcome host-derived stresses for successful infection. Oxidative stress is a representative defense system induced by the host plant, and fungi have complex response systems to cope with it. Fusarium graminearum is one of the devastating plant pathogenic fungi, and understanding its pathosystem is crucial for disease control. In this study, we investigated adaptive mechanisms for coping with oxidative stress at the transcriptome level using oxidative stress-sensitive strains. In addition, by introducing genetic modification technique such as CRISPR-Cas9 and the conditional gene expression system, we identified pathways/genes required for resistance to oxidative stress and also for virulence. Overall, this study advances the understanding of the oxidative stress response and related mechanisms in plant pathogenic fungi.
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Affiliation(s)
- Jiyeun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Heeji Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Nahyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sieun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jung-Eun Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Jeju, Republic of Korea
| | - Yoonji Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hun Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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11
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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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12
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Tomasi FG, Kimura S, Rubin EJ, Waldor MK. A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529267. [PMID: 36865327 PMCID: PMC9979996 DOI: 10.1101/2023.02.20.529267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Diverse chemical modifications fine-tune the function and metabolism of tRNA. Although tRNA modification is universal in all kingdoms of life, profiles of modifications, their functions, and physiological roles have not been elucidated in most organisms including the human pathogen, Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis. To identify physiologically important modifications, we surveyed the tRNA of Mtb , using tRNA sequencing (tRNA-seq) and genome-mining. Homology searches identified 23 candidate tRNA modifying enzymes that are predicted to create 16 tRNA modifications across all tRNA species. Reverse transcription-derived error signatures in tRNA-seq predicted the sites and presence of 9 modifications. Several chemical treatments prior to tRNA-seq expanded the number of predictable modifications. Deletion of Mtb genes encoding two modifying enzymes, TruB and MnmA, eliminated their respective tRNA modifications, validating the presence of modified sites in tRNA species. Furthermore, the absence of mnmA attenuated Mtb growth in macrophages, suggesting that MnmA-dependent tRNA uridine sulfation contributes to Mtb intracellular growth. Our results lay the foundation for unveiling the roles of tRNA modifications in Mtb pathogenesis and developing new therapeutics against tuberculosis.
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Affiliation(s)
- Francesca G. Tomasi
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public Health, Boston, MA USA
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public Health, Boston, MA USA
| | - Matthew K. Waldor
- Department of Immunology and Infectious Diseases Harvard T. H. Chan School of Public Health, Boston, MA USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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13
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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14
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Cheney AM, Costello SM, Pinkham NV, Waldum A, Broadaway SC, Cotrina-Vidal M, Mergy M, Tripet B, Kominsky DJ, Grifka-Walk HM, Kaufmann H, Norcliffe-Kaufmann L, Peach JT, Bothner B, Lefcort F, Copié V, Walk ST. Gut microbiome dysbiosis drives metabolic dysfunction in Familial dysautonomia. Nat Commun 2023; 14:218. [PMID: 36639365 PMCID: PMC9839693 DOI: 10.1038/s41467-023-35787-8] [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: 06/13/2022] [Accepted: 12/18/2022] [Indexed: 01/15/2023] Open
Abstract
Familial dysautonomia (FD) is a rare genetic neurologic disorder caused by impaired neuronal development and progressive degeneration of both the peripheral and central nervous systems. FD is monogenic, with >99.4% of patients sharing an identical point mutation in the elongator acetyltransferase complex subunit 1 (ELP1) gene, providing a relatively simple genetic background in which to identify modifiable factors that influence pathology. Gastrointestinal symptoms and metabolic deficits are common among FD patients, which supports the hypothesis that the gut microbiome and metabolome are altered and dysfunctional compared to healthy individuals. Here we show significant differences in gut microbiome composition (16 S rRNA gene sequencing of stool samples) and NMR-based stool and serum metabolomes between a cohort of FD patients (~14% of patients worldwide) and their cohabitating, healthy relatives. We show that key observations in human subjects are recapitulated in a neuron-specific Elp1-deficient mouse model, and that cohousing mutant and littermate control mice ameliorates gut microbiome dysbiosis, improves deficits in gut transit, and reduces disease severity. Our results provide evidence that neurologic deficits in FD alter the structure and function of the gut microbiome, which shifts overall host metabolism to perpetuate further neurodegeneration.
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Affiliation(s)
- Alexandra M Cheney
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Stephanann M Costello
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Nicholas V Pinkham
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Annie Waldum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Susan C Broadaway
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Maria Cotrina-Vidal
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Marc Mergy
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Douglas J Kominsky
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Heather M Grifka-Walk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | | | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
| | - Seth T Walk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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15
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Lee MY, Ojeda-Britez S, Ehrbar D, Samwer A, Begley TJ, Melendez JA. Selenoproteins and the senescence-associated epitranscriptome. Exp Biol Med (Maywood) 2022; 247:2090-2102. [PMID: 36036467 PMCID: PMC9837304 DOI: 10.1177/15353702221116592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Selenium is a naturally found trace element, which provides multiple benefits including antioxidant, anticancer, and antiaging, as well as boosting immunity. One unique feature of selenium is its incorporation as selenocysteine, a rare 21st amino acid, into selenoproteins. Twenty-five human selenoproteins have been discovered, and a majority of these serve as crucial antioxidant enzymes for redox homeostasis. Unlike other amino acids, incorporation of selenocysteine requires a distinctive UGA stop codon recoding mechanism. Although many studies correlating selenium, selenoproteins, aging, and senescence have been performed, it has not yet been explored if the upstream events regulating selenoprotein synthesis play a role in senescence-associated pathologies. The epitranscriptomic writer alkylation repair homolog 8 (ALKBH8) is critical for selenoprotein production, and its deficiency can significantly decrease levels of selenoproteins that are essential for reactive oxygen species (ROS) detoxification, and increase oxidative stress, one of the major drivers of cellular senescence. Here, we review the potential role of epitranscriptomic marks that govern selenocysteine utilization in regulating the senescence program.
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Affiliation(s)
- May Y Lee
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Stephen Ojeda-Britez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Dylan Ehrbar
- The RNA Institute, University at Albany, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | | | - Thomas J Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - J Andres Melendez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
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16
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Boutoual R, Jo H, Heckenbach I, Tiwari R, Kasler H, Lerner CA, Shah S, Schilling B, Calvanese V, Rardin MJ, Scheibye-Knudsen M, Verdin E. A novel splice variant of Elp3/Kat9 regulates mitochondrial tRNA modification and function. Sci Rep 2022; 12:14804. [PMID: 36045139 PMCID: PMC9433433 DOI: 10.1038/s41598-022-18114-x] [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: 04/08/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
Post-translational modifications, such as lysine acetylation, regulate the activity of diverse proteins across many cellular compartments. Protein deacetylation in mitochondria is catalyzed by the enzymatic activity of the NAD+-dependent deacetylase sirtuin 3 (SIRT3), however it remains unclear whether corresponding mitochondrial acetyltransferases exist. We used a bioinformatics approach to search for mitochondrial proteins with an acetyltransferase catalytic domain, and identified a novel splice variant of ELP3 (mt-ELP3) of the elongator complex, which localizes to the mitochondrial matrix in mammalian cells. Unexpectedly, mt-ELP3 does not mediate mitochondrial protein acetylation but instead induces a post-transcriptional modification of mitochondrial-transfer RNAs (mt-tRNAs). Overexpression of mt-ELP3 leads to the protection of mt-tRNAs against the tRNA-specific RNase angiogenin, increases mitochondrial translation, and furthermore increases expression of OXPHOS complexes. This study thus identifies mt-ELP3 as a non-canonical mt-tRNA modifying enzyme.
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Affiliation(s)
- Rachid Boutoual
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
| | - Hyunsun Jo
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Indra Heckenbach
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ritesh Tiwari
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Herbert Kasler
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Chad A Lerner
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Samah Shah
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | | | - Vincenzo Calvanese
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA. .,Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA.
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17
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Tolman Z, Chaverra M, George L, Lefcort F. Elp1 is required for development of visceral sensory peripheral and central circuitry. Dis Model Mech 2022; 15:275184. [PMID: 35481599 PMCID: PMC9187870 DOI: 10.1242/dmm.049274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Cardiovascular instability and a blunted respiratory drive in hypoxic conditions are hallmark features of the genetic sensory and autonomic neuropathy, familial dysautonomia (FD). FD results from a mutation in the gene ELP1, the encoded protein of which is a scaffolding subunit of the six-subunit Elongator complex. In mice, we and others have shown that Elp1 is essential for the normal development of neural crest-derived dorsal root ganglia sensory neurons. Whether Elp1 is also required for development of ectodermal placode-derived visceral sensory receptors, which are required for normal baroreception and chemosensory responses, has not been investigated. Using mouse models for FD, we here show that the entire circuitry underlying baroreception and chemoreception is impaired due to a requirement for Elp1 in the visceral sensory neuron ganglia, as well as for normal peripheral target innervation, and in their central nervous system synaptic partners in the medulla. Thus, Elp1 is required in both placode- and neural crest-derived sensory neurons, and its reduction aborts the normal development of neuronal circuitry essential for autonomic homeostasis and interoception. This article has an associated First Person interview with the first author of the paper. Summary: Our data indicate that Elp1 is required in both placode- and neural crest-derived sensory neurons, and that it exerts comparable effects, including survival, axonal morphology and target innervation in both lineages.
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Affiliation(s)
- Zariah Tolman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Marta Chaverra
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Lynn George
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.,Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
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18
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Leonard CE, Quiros J, Lefcort F, Taneyhill LA. Loss of Elp1 disrupts trigeminal ganglion neurodevelopment in a model of familial dysautonomia. eLife 2022; 11:71455. [PMID: 35713404 PMCID: PMC9273214 DOI: 10.7554/elife.71455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 06/17/2022] [Indexed: 01/28/2023] Open
Abstract
Familial dysautonomia (FD) is a sensory and autonomic neuropathy caused by mutations in elongator complex protein 1 (ELP1). FD patients have small trigeminal nerves and impaired facial pain and temperature perception. These signals are relayed by nociceptive neurons in the trigeminal ganglion, a structure that is composed of both neural crest- and placode-derived cells. Mice lacking Elp1 in neural crest derivatives ('Elp1 CKO') are born with small trigeminal ganglia, suggesting Elp1 is important for trigeminal ganglion development, yet the function of Elp1 in this context is unknown. We demonstrate that Elp1, expressed in both neural crest- and placode-derived neurons, is not required for initial trigeminal ganglion formation. However, Elp1 CKO trigeminal neurons exhibit abnormal axon outgrowth and deficient target innervation. Developing nociceptors expressing the receptor TrkA undergo early apoptosis in Elp1 CKO, while TrkB- and TrkC-expressing neurons are spared, indicating Elp1 supports the target innervation and survival of trigeminal nociceptors. Furthermore, we demonstrate that specific TrkA deficits in the Elp1 CKO trigeminal ganglion reflect the neural crest lineage of most TrkA neurons versus the placodal lineage of most TrkB and TrkC neurons. Altogether, these findings explain defects in cranial gangliogenesis that may lead to loss of facial pain and temperature sensation in FD.
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Affiliation(s)
- Carrie E Leonard
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
| | - Jolie Quiros
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
| | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State UniversityBozemanUnited States
| | - Lisa A Taneyhill
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
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19
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Zhou JB, Wang ED, Zhou XL. Modifications of the human tRNA anticodon loop and their associations with genetic diseases. Cell Mol Life Sci 2021; 78:7087-7105. [PMID: 34605973 PMCID: PMC11071707 DOI: 10.1007/s00018-021-03948-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Transfer RNAs (tRNAs) harbor the most diverse posttranscriptional modifications. Among such modifications, those in the anticodon loop, either on nucleosides or base groups, compose over half of the identified posttranscriptional modifications. The derivatives of modified nucleotides and the crosstalk of different chemical modifications further add to the structural and functional complexity of tRNAs. These modifications play critical roles in maintaining anticodon loop conformation, wobble base pairing, efficient aminoacylation, and translation speed and fidelity as well as mediating various responses to different stress conditions. Posttranscriptional modifications of tRNA are catalyzed mainly by enzymes and/or cofactors encoded by nuclear genes, whose mutations are firmly connected with diverse human diseases involving genetic nervous system disorders and/or the onset of multisystem failure. In this review, we summarize recent studies about the mechanisms of tRNA modifications occurring at tRNA anticodon loops. In addition, the pathogenesis of related disease-causing mutations at these genes is briefly described.
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Affiliation(s)
- Jing-Bo Zhou
- 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, 320 Yue Yang Road, 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, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 93 Middle Huaxia Road, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- 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, 320 Yue Yang Road, Shanghai, 200031, China.
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20
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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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21
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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22
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Valadon C, Namy O. The Importance of the Epi-Transcriptome in Translation Fidelity. Noncoding RNA 2021; 7:51. [PMID: 34564313 PMCID: PMC8482273 DOI: 10.3390/ncrna7030051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases.
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Affiliation(s)
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France;
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23
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Zhang Y, Su D, Dzikovski B, Majer SH, Coleman R, Chandrasekaran S, Fenwick MK, Crane BR, Lancaster KM, Freed JH, Lin H. Dph3 Enables Aerobic Diphthamide Biosynthesis by Donating One Iron Atom to Transform a [3Fe-4S] to a [4Fe-4S] Cluster in Dph1-Dph2. J Am Chem Soc 2021; 143:9314-9319. [PMID: 34154323 PMCID: PMC8251694 DOI: 10.1021/jacs.1c03956] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All radical S-adenosylmethionine (radical-SAM) enzymes, including the noncanonical radical-SAM enzyme diphthamide biosynthetic enzyme Dph1-Dph2, require at least one [4Fe-4S](Cys)3 cluster for activity. It is well-known in the radical-SAM enzyme community that the [4Fe-4S](Cys)3 cluster is extremely air-sensitive and requires strict anaerobic conditions to reconstitute activity in vitro. Thus, how such enzymes function in vivo in the presence of oxygen in aerobic organisms is an interesting question. Working on yeast Dph1-Dph2, we found that consistent with the known oxygen sensitivity, the [4Fe-4S] cluster is easily degraded into a [3Fe-4S] cluster. Remarkably, the small iron-containing protein Dph3 donates one Fe atom to convert the [3Fe-4S] cluster in Dph1-Dph2 to a functional [4Fe-4S] cluster during the radical-SAM enzyme catalytic cycle. This mechanism to maintain radical-SAM enzyme activity in aerobic environments is likely general, and Dph3-like proteins may exist to keep other radical-SAM enzymes functional in aerobic environments.
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Affiliation(s)
- Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Dan Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rachael Coleman
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, United States
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24
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Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
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Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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25
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Rosu A, El Hachem N, Rapino F, Rouault-Pierre K, Jorssen J, Somja J, Ramery E, Thiry M, Nguyen L, Jacquemyn M, Daelemans D, Adams CM, Bonnet D, Chariot A, Close P, Bureau F, Desmet CJ. Loss of tRNA-modifying enzyme Elp3 activates a p53-dependent antitumor checkpoint in hematopoiesis. J Exp Med 2021; 218:e20200662. [PMID: 33507234 PMCID: PMC7849823 DOI: 10.1084/jem.20200662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
The hematopoietic system is highly sensitive to perturbations in the translational machinery, of which an emerging level of regulation lies in the epitranscriptomic modification of transfer RNAs (tRNAs). Here, we interrogate the role of tRNA anticodon modifications in hematopoiesis by using mouse models of conditional inactivation of Elp3, the catalytic subunit of Elongator that modifies wobble uridine in specific tRNAs. Loss of Elp3 causes bone marrow failure by inducing death in committing progenitors and compromises the grafting activity of hematopoietic stem cells. Mechanistically, Elp3 deficiency activates a p53-dependent checkpoint in what resembles a misguided amino acid deprivation response that is accompanied by Atf4 overactivation and increased protein synthesis. While deletion of p53 rescues hematopoiesis, loss of Elp3 prompts the development of p53-mutated leukemia/lymphoma, and inactivation of p53 and Elongator cooperatively promotes tumorigenesis. Specific tRNA-modifying enzymes thus condition differentiation and antitumor fate decisions in hematopoietic stem cells and progenitors.
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Affiliation(s)
- Adeline Rosu
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Francesca Rapino
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Kevin Rouault-Pierre
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, Queen Mary University of London, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Joseph Jorssen
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Joan Somja
- Laboratory of Pathological Anatomy and Cytology, Centre Hospitalier Universitaire, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Eve Ramery
- Department of Functional Sciences, Faculty of Veterinary Medicine, Liege University, Liège, Belgium
| | - Marc Thiry
- Laboratory of Cellular and Tissular Biology, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Laurent Nguyen
- Laboratory of MolecularRegulation of Neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Christopher M. Adams
- Departments of Internal Medicine and Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, Queen Mary University of London, London, UK
| | - Alain Chariot
- Laboratory of Medical Chemistry, GIGA-Stem Cells, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Fabrice Bureau
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Christophe J. Desmet
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
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26
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Li L, Gruner K, Tourtellotte WG. Retrograde nerve growth factor signaling abnormalities in familial dysautonomia. J Clin Invest 2021; 130:2478-2487. [PMID: 32281946 DOI: 10.1172/jci130401] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
Familial dysautonomia (FD) is the most prevalent form of hereditary sensory and autonomic neuropathy (HSAN). In FD, a germline mutation in the Elp1 gene leads to Elp1 protein decrease that causes sympathetic neuron death and sympathetic nervous system dysfunction (dysautonomia). Elp1 is best known as a scaffolding protein within the nuclear hetero-hexameric transcriptional Elongator protein complex, but how it functions in sympathetic neuron survival is very poorly understood. Here, we identified a cytoplasmic function for Elp1 in sympathetic neurons that was essential for retrograde nerve growth factor (NGF) signaling and neuron target tissue innervation and survival. Elp1 was found to bind to internalized TrkA receptors in an NGF-dependent manner, where it was essential for maintaining TrkA receptor phosphorylation (activation) by regulating PTPN6 (Shp1) phosphatase activity within the signaling complex. In the absence of Elp1, Shp1 was hyperactivated, leading to premature TrkA receptor dephosphorylation, which resulted in retrograde signaling failure and neuron death. Inhibiting Shp1 phosphatase activity in the absence of Elp1 rescued NGF-dependent retrograde signaling, and in an animal model of FD it rescued abnormal sympathetic target tissue innervation. These results suggest that regulation of retrograde NGF signaling in sympathetic neurons by Elp1 may explain sympathetic neuron loss and physiologic dysautonomia in patients with FD.
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Affiliation(s)
- Lin Li
- Department of Pathology and Laboratory Medicine
| | | | - Warren G Tourtellotte
- Department of Pathology and Laboratory Medicine.,Department of Neurology.,Department of Neurosurgery, and.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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27
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Lemaitre P, Bai Q, Legrand C, Chariot A, Close P, Bureau F, Desmet CJ. Loss of the Transfer RNA Wobble Uridine-Modifying Enzyme Elp3 Delays T Cell Cycle Entry and Impairs T Follicular Helper Cell Responses through Deregulation of Atf4. THE JOURNAL OF IMMUNOLOGY 2021; 206:1077-1087. [PMID: 33483347 DOI: 10.4049/jimmunol.2000521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The activation of T cells is accompanied by intensive posttranscriptional remodeling of their proteome. We observed that protein expression of enzymes that modify wobble uridine in specific tRNAs, namely elongator subunit 3 (Elp3) and cytosolic thiouridylase (Ctu)2, increased in the course of T cell activation. To investigate the role of these tRNA epitranscriptomic modifiers in T cell biology, we generated mice deficient for Elp3 in T cells. We show that deletion of Elp3 has discrete effects on T cells. In vitro, Elp3-deficient naive CD4+ T cells polarize normally but are delayed in entering the first cell cycle following activation. In vivo, different models of immunization revealed that Elp3-deficient T cells display reduced expansion, resulting in functional impairment of T follicular helper (TFH) responses, but not of other CD4+ effector T cell responses. Transcriptomic analyses identified a progressive overactivation of the stress-responsive transcription factor Atf4 in Elp3-deficient T cells. Overexpression of Atf4 in wild-type T cells phenocopies the effect of Elp3 loss on T cell cycle entry and TFH cell responses. Reciprocally, partial silencing of Atf4 or deletion of its downstream effector transcription factor Chop rescues TFH responses of Elp3-deficient T cells. Together, our results reveal that specific epitranscriptomic tRNA modifications contribute to T cell cycle entry and promote optimal TFH responses.
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Affiliation(s)
- Pierre Lemaitre
- Laboratory of Cellular and Molecular Immunology, Interdisciplinary Group for Applied Genoproteomics, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Qiang Bai
- Laboratory of Cellular and Molecular Immunology, Interdisciplinary Group for Applied Genoproteomics, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Céline Legrand
- Laboratory of Cellular and Molecular Immunology, Interdisciplinary Group for Applied Genoproteomics, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Alain Chariot
- Laboratory of Medical Chemistry, Interdisciplinary Group for Applied Genoproteomics, Faculty of Medicine, University of Liege, 4000 Liege, Belgium.,Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavres, Belgium; and
| | - Pierre Close
- Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavres, Belgium; and.,Laboratory of Cancer Signaling, Interdisciplinary Group for Applied Genoproteomics, Faculty of Medicine, University of Liege, 4000 Liege, Belgium
| | - Fabrice Bureau
- Laboratory of Cellular and Molecular Immunology, Interdisciplinary Group for Applied Genoproteomics, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium.,Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavres, Belgium; and
| | - Christophe J Desmet
- Laboratory of Cellular and Molecular Immunology, Interdisciplinary Group for Applied Genoproteomics, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium; .,Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavres, Belgium; and
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28
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Lentini JM, Fu D. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease. Methods Mol Biol 2021; 2298:197-216. [PMID: 34085247 DOI: 10.1007/978-1-0716-1374-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The post-transcriptional modification of tRNAs at the wobble position plays a critical role in proper mRNA decoding and efficient protein synthesis. In particular, certain wobble uridines in eukaryotes are converted to 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The mcm5s2U modification modulates decoding during translation by increasing the stringency of the wobble uridine to base pair with its canonical nucleotide partner, thereby restricting decoding to its cognate codon. Here, we outline a technique to monitor wobble uridine status in mcm5s2U-containing tRNAs using the gamma-toxin endonuclease from the yeast Kluyveromyces lactis that naturally cleaves tRNAs containing the mcm5s2U modification. This technique is coupled to Northern blotting or reverse transcription-PCR to enable rapid and sensitive detection of changes in mcm5s2U modification state.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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29
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Gregorova P, Sipari NH, Sarin LP. Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS. RNA Biol 2020; 18:1382-1389. [PMID: 33356826 PMCID: PMC8494288 DOI: 10.1080/15476286.2020.1853385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Post-transcriptional RNA modifications play an important role in cellular metabolism with homoeostatic disturbances manifesting as a wide repertoire of phenotypes, reduced stress tolerance and translational perturbation, developmental defects, and diseases, such as type II diabetes, leukaemia, and carcinomas. Hence, there has been an intense effort to develop various methods for investigating RNA modifications and their roles in various organisms, including sequencing-based approaches and, more frequently, liquid chromatography–mass spectrometry (LC-MS)-based methods. Although LC-MS offers numerous advantages, such as being highly sensitive and quantitative over a broad detection range, some stationary phase chemistries struggle to resolve positional isomers. Furthermore, the demand for detailed analyses of complex biological samples often necessitates long separation times, hampering sample-to-sample turnover and making multisample analyses time consuming. To overcome this limitation, we have developed an ultra-performance LC-MS (UPLC-MS) method that uses an octadecyl carbon chain (C18)-bonded silica matrix for the efficient separation of 50 modified ribonucleosides, including positional isomers, in a single 9-min sample-to-sample run. To validate the performance and versatility of our method, we analysed tRNA modification patterns of representative microorganisms from each domain of life, namely Archaea (Methanosarcina acetivorans), Bacteria (Pseudomonas syringae), and Eukarya (Saccharomyces cerevisiae). Additionally, our method is flexible and readily applicable for detection and relative quantification using stable isotope labelling and targeted approaches like multiple reaction monitoring (MRM). In conclusion, this method represents a fast and robust tool for broad-range exploration and quantification of ribonucleosides, facilitating future homoeostasis studies of RNA modification in complex biological samples.
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Affiliation(s)
- Pavlina Gregorova
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Nina H Sipari
- Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki Finland
| | - L Peter Sarin
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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30
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Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA (NEW YORK, N.Y.) 2020; 26:1957-1975. [PMID: 32994183 PMCID: PMC7668247 DOI: 10.1261/rna.077537.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 05/22/2023]
Abstract
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Laura Antoine
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Henri Grosjean
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
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31
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Wang C, van Tran N, Jactel V, Guérineau V, Graille M. Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator. Nucleic Acids Res 2020; 48:11068-11082. [PMID: 33035335 PMCID: PMC7641767 DOI: 10.1093/nar/gkaa830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 01/20/2023] Open
Abstract
tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Nhan van Tran
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, Ecole polytechnique, ENSTA, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
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32
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Cruz-Gordillo P, Honeywell ME, Harper NW, Leete T, Lee MJ. ELP-dependent expression of MCL1 promotes resistance to EGFR inhibition in triple-negative breast cancer cells. Sci Signal 2020; 13:13/658/eabb9820. [PMID: 33203722 DOI: 10.1126/scisignal.abb9820] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeted therapeutics for cancer generally exploit "oncogene addiction," a phenomenon in which the growth and survival of tumor cells depend on the activity of a particular protein. However, the efficacy of oncogene-targeted therapies varies substantially. For instance, targeting epidermal growth factor receptor (EGFR) signaling is effective in some non-small cell lung cancer (NSCLC) but not in triple-negative breast cancer (TNBC), although these cancers show a similar degree of increase in EGFR activity. Using a genome-wide CRISPR-Cas9 genetic knockout screen, we found that the Elongator (ELP) complex mediates insensitivity to the EGFR inhibitor erlotinib in TNBC cells by promoting the synthesis of the antiapoptotic protein Mcl-1. Depleting ELP proteins promoted apoptotic cell death in an EGFR inhibition-dependent manner. Pharmacological inhibition of Mcl-1 synergized with EGFR inhibition in a panel of genetically diverse TNBC cells. The findings indicate that TNBC "addiction" to EGFR signaling is masked by the ELP complex and that resistance to EGFR inhibitors in TNBC might be overcome by cotargeting Mcl-1.
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Affiliation(s)
- Peter Cruz-Gordillo
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Megan E Honeywell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Nicholas W Harper
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Thomas Leete
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Michael J Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA. .,Program in Molecular Medicine, Department of Molecular, Cell, and Cancer Biology (MCCB), University of Massachusetts Medical School, Worcester MA 01605, USA
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33
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Fernandes De Abreu DA, Salinas-Giegé T, Drouard L, Remy JJ. Alanine tRNAs Translate Environment Into Behavior in Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:571359. [PMID: 33195203 PMCID: PMC7662486 DOI: 10.3389/fcell.2020.571359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Caenorhabditis elegans nematodes produce and maintain imprints of attractive chemosensory cues to which they are exposed early in life. Early odor-exposure increases adult chemo-attraction to the same cues. Imprinting is transiently or stably inherited, depending on the number of exposed generations. We show here that the Alanine tRNA (UGC) plays a central role in regulating C. elegans chemo-attraction. Naive worms fed on tRNAAla (UGC) purified from odor-experienced worms, acquire odor-specific imprints. Chemo-attractive responses require the tRNA-modifying Elongator complex sub-units 1 (elpc-1) and 3 (elpc-3) genes. elpc-3 deletions impair chemo-attraction, which is fully restored by wild-type tRNAAla (UGC) feeding. A stably inherited decrease of odor-specific responses ensues from early odor-exposition of elpc-1 deletion mutants. tRNAAla (UGC) may adopt various chemical forms to mediate the cross-talk between innately-programmed and environment-directed chemo-attractive behavior.
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Affiliation(s)
- Diana Andrea Fernandes De Abreu
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Jacques Remy
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
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Xu Y, Zhang L, Ou S, Wang R, Wang Y, Chu C, Yao S. Natural variations of SLG1 confer high-temperature tolerance in indica rice. Nat Commun 2020; 11:5441. [PMID: 33116138 PMCID: PMC7595236 DOI: 10.1038/s41467-020-19320-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/06/2020] [Indexed: 01/28/2023] Open
Abstract
With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe. Understanding the mechanism of high-temperature tolerance will help to breed crops adaptive to warming climate. Here, the authors show SLG1, a cytosolic tRNA 2-thiolation protein 2 encoding gene, is differentiated between the two Asian cultivated rice subspecies and confers high temperature tolerance of indica rice.
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Affiliation(s)
- Yufang Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Li Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ruci Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yueming Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Shanguo Yao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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35
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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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36
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Krutyhołowa R, Reinhardt-Tews A, Chramiec-Głąbik A, Breunig KD, Glatt S. Fungal Kti12 proteins display unusual linker regions and unique ATPase p-loops. Curr Genet 2020; 66:823-833. [PMID: 32236652 PMCID: PMC7363723 DOI: 10.1007/s00294-020-01070-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Kti12 (Kluyveromyces lactis toxin insensitive 12) is an evolutionary highly conserved ATPase, crucial for the tRNA-modification activity of the eukaryotic Elongator complex. The protein consists of an N-terminal ATPase and a C-terminal tRNA-binding domain, which are connected by a flexible linker. The precise role of the linker region and its involvement in the communication between the two domains and their activities remain elusive. Here, we analyzed all available Kti12 protein sequences and report the discovery of a subset of Kti12 proteins with abnormally long linker regions. These Kti12 proteins are characterized by a co-occurring lysine to leucine substitution in their Walker A motif, previously thought to be invariable. We show that the K14L substitution lowers the affinity to ATP, but does not affect the catalytic activity of Kti12 at high ATP concentrations. We compare the activity of mutated variants of Kti12 in vitro with complementation assays in vivo in yeast. Ultimately, we compared Kti12 to other known p-loop ATPase family members known to carry a similar deviant Walker A motif. Our data establish Kti12 of Eurotiomycetes as an example of eukaryotic ATPase harboring a significantly deviating but still functional Walker A motif.
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Affiliation(s)
- Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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37
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2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae. PLoS One 2020; 15:e0229103. [PMID: 32053677 PMCID: PMC7018073 DOI: 10.1371/journal.pone.0229103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
Chemical modifications that regulate protein expression at the translational level are emerging as vital components of the cellular stress response. Transfer RNAs (tRNAs) are significant targets for methyl-based modifications, which are catalyzed by tRNA methyltransferases (Trms). Here, Saccharomyces cerevisiae served as a model eukaryote system to investigate the role of 2'-O-ribose tRNA methylation in the cell's response to oxidative stress. Using 2'-O-ribose deletion mutants for trms 3, 7, 13, and 44, in acute and chronic exposure settings, we demonstrate a broad cell sensitivity to oxidative stress-inducing toxicants (i.e., hydrogen peroxide, rotenone, and acetic acid). A global analysis of hydrogen peroxide-induced tRNA modifications shows a complex profile of decreased, or undetectable, 2'-O-ribose modification events in 2’-O-ribose trm mutant strains, providing a critical link between this type of modification event and Trm status post-exposure. Based on the pronounced oxidative stress sensitivity observed for trm7 mutants, we used a bioinformatic tool to identify transcripts as candidates for regulation by Trm7-catalyzed modifications (i.e., enriched in UUC codons decoded by tRNAPheGmAA). This screen identified transcripts linked to diverse biological processes that promote cellular recovery after oxidative stress exposure, including DNA repair, chromatin remodeling, and nutrient acquisition (i.e., CRT10, HIR3, HXT2, and GNP1); moreover, these mutants were also oxidative stress-sensitive. Together, these results solidify a role for TRM3, 7, 13, and 44, in the cellular response to oxidative stress, and implicate 2'-O-ribose tRNA modification as an epitranscriptomic strategy for oxidative stress recovery.
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38
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SSD1 modifies phenotypes of Elongator mutants. Curr Genet 2019; 66:481-485. [PMID: 31776648 PMCID: PMC7198479 DOI: 10.1007/s00294-019-01048-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/15/2022]
Abstract
The translational decoding properties of tRNAs are influenced by post-transcriptional modification of nucleosides in their anticodon region. The Elongator complex promotes the first step in the formation of 5-methoxycarbonylmethyl (mcm5), 5-methoxycarbonylhydroxymethyl (mchm5), and 5-carbamoylmethyl (ncm5) groups on wobble uridine residues in eukaryotic cytosolic tRNAs. Elongator mutants in yeast, worms, plants, mice, and humans not only show a tRNA modification defect, but also a diverse range of additional phenotypes. Even though the phenotypes are almost certainly caused by the reduced functionality of the hypomodified tRNAs in translation, the basis for specific phenotypes is not well understood. Here, we discuss the recent finding that the phenotypes of Saccharomyces cerevisiae Elongator mutants are modulated by the genetic background. This background-effect is largely due to the allelic variation at the SSD1 locus, which encodes an mRNA-binding protein involved in post-transcriptional regulation of gene expression. A nonsense ssd1 allele is found in several wild-type laboratory strains and the presence of this allele aggravates the stress-induced phenotypes of Elongator mutants. Moreover, other phenotypes, such as the histone acetylation and telomeric gene silencing defects, are dependent on the mutant ssd1 allele. Thus, SSD1 is a genetic modifier of the phenotypes of Elongator-deficient yeast cells.
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39
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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40
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Pérez-Martínez ME, Benet M, Alepuz P, Tordera V. Nut1/Hos1 and Sas2/Rpd3 control the H3 acetylation of two different sets of osmotic stress-induced genes. Epigenetics 2019; 15:251-271. [PMID: 31512982 DOI: 10.1080/15592294.2019.1664229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Epigenetic information is able to interact with the cellular environment and could be especially useful for reprograming gene expression in response to a physiological perturbation. In fact the genes induced or repressed by osmotic stress undergo significant changes in terms of the levels of various histone modifications, especially in the acetylation levels of histone H3. Exposing yeast to high osmolarity results in the activation of stress-activated protein kinase Hog1, which plays a central role in gene expression control. We evaluated the connection between the presence of Hog1 and changes in histone H3 acetylation in stress-regulated genes. We found a parallel increase in the acetylation of lysines 9 and 14 of H3 in induced genes during stress, which was largely dependent on Hog1 at the genome-wide level. Conversely, we observed that acetylation decreased in repressed genes and was not dependent on Hog1. However, lack of Hog1 sometimes produced different, and even opposite, effects on the induction and acetylation of H3 of each gene. We also found that the acetylation state of lysine 9 of H3 was altered in the strains deficient in Nut1 HAT and Hos1 HDAC in the genes up-regulated during osmotic stress in an Msn2/Msn4-independent manner, while lysine 9 acetylation of H3 varied in the strains deficient in Sas2 HAT and Rpd3 HDAC for the Msn2/Msn4-dependent induced genes. The results presented here show new, unexpected participants in gene regulation processes in response to environmental perturbations.
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Affiliation(s)
- María E Pérez-Martínez
- Departament de Bioquímica i Biologia Molecular and ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Marta Benet
- Departament de Bioquímica i Biologia Molecular and ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Paula Alepuz
- Departament de Bioquímica i Biologia Molecular and ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Vicente Tordera
- Departament de Bioquímica i Biologia Molecular and ERI Biotecmed, Universitat de València, Burjassot, Spain
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41
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ELP3 Acetyltransferase is phosphorylated and regulated by the oncogenic anaplastic lymphoma kinase (ALK). Biochem J 2019; 476:2239-2254. [DOI: 10.1042/bcj20190106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
AbstractProtein lysine acetylation is one of the major posttranslational modifications (PTMs) with several thousands of proteins identified to be acetylated in mammalian tissues. Mechanistic studies have revealed important functions of acetylation in the regulation of protein function. Much less is known on how the acetyltransferases themselves are regulated. In the current study, we discover that the Elongator protein 3 (ELP3) acetyltransferase is modified by tyrosine phosphorylation. We demonstrate that the anaplastic lymphoma kinase (ALK) is the major tyrosine kinase responsible for ELP3 tyrosine phosphorylation. ELP3 is phosphorylated in tumor cells expressing oncogenic NPM–ALK fusion protein. We further identify Tyr202 as the major ALK phosphorylation site in ELP3. Importantly, the introduction of Y202 phosphorylation mutant ELP3 into ALK-positive tumor cells reduced cell growth and impaired gene expression. Collectively, our study reveals a novel regulatory mechanism for ELP3, provides an example that acetyltransferase itself can be regulated by PTM, and suggests a potential target for ALK-positive cancer therapies.
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42
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Xu F, Byström AS, Johansson MJO. SSD1 suppresses phenotypes induced by the lack of Elongator-dependent tRNA modifications. PLoS Genet 2019; 15:e1008117. [PMID: 31465447 PMCID: PMC6738719 DOI: 10.1371/journal.pgen.1008117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/11/2019] [Accepted: 08/16/2019] [Indexed: 11/19/2022] Open
Abstract
The Elongator complex promotes formation of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) side-chains on uridines at the wobble position of cytosolic eukaryotic tRNAs. In all eukaryotic organisms tested to date, the inactivation of Elongator not only leads to the lack of mcm5/ncm5 groups in tRNAs, but also a wide variety of additional phenotypes. Although the phenotypes are most likely caused by a translational defect induced by reduced functionality of the hypomodified tRNAs, the mechanism(s) underlying individual phenotypes are poorly understood. In this study, we show that the genetic background modulates the phenotypes induced by the lack of mcm5/ncm5 groups in Saccharomyces cerevisiae. We show that the stress-induced growth defects of Elongator mutants are stronger in the W303 than in the closely related S288C genetic background and that the phenotypic differences are caused by the known polymorphism at the locus for the mRNA binding protein Ssd1. Moreover, the mutant ssd1 allele found in W303 cells is required for the reported histone H3 acetylation and telomeric gene silencing defects of Elongator mutants. The difference at the SSD1 locus also partially explains why the simultaneous lack of mcm5 and 2-thio groups at wobble uridines is lethal in the W303 but not in the S288C background. Collectively, our results demonstrate that the SSD1 locus modulates phenotypes induced by the lack of Elongator-dependent tRNA modifications.
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Affiliation(s)
- Fu Xu
- Department of Molecular Biology, Umeå University, Umeå, Sweden
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43
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Sheikh BN, Akhtar A. The many lives of KATs - detectors, integrators and modulators of the cellular environment. Nat Rev Genet 2019; 20:7-23. [PMID: 30390049 DOI: 10.1038/s41576-018-0072-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response. Concurrently, researchers are continuously uncovering how deregulation of KAT activity drives disease, including cancer and developmental syndromes characterized by severe intellectual disability. These novel findings are reshaping our view of KATs away from mere modulators of chromatin to detectors of the cellular environment and integrators of diverse signalling pathways with the ability to modify cellular phenotype.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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44
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Advani VM, Ivanov P. Translational Control under Stress: Reshaping the Translatome. Bioessays 2019; 41:e1900009. [PMID: 31026340 PMCID: PMC6541386 DOI: 10.1002/bies.201900009] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/06/2019] [Indexed: 01/01/2023]
Abstract
Adequate reprogramming of cellular metabolism in response to stresses or suboptimal growth conditions involves a myriad of coordinated changes that serve to promote cell survival. As protein synthesis is an energetically expensive process, its regulation under stress is of critical importance. Reprogramming of messenger RNA (mRNA) translation involves well-understood stress-activated kinases that target components of translation initiation machinery, resulting in the robust inhibition of general translation and promotion of the translation of stress-responsive proteins. Translational arrest of mRNAs also results in the accumulation of transcripts in cytoplasmic foci called stress granules. Recent studies focus on the key roles of transfer RNA (tRNA) in stress-induced translational reprogramming. These include stress-specific regulation of tRNA pools, codon-biased translation influenced by tRNA modifications, tRNA miscoding, and tRNA cleavage. In combination, signal transduction pathways and tRNA metabolism changes regulate translation during stress, resulting in adaptation and cell survival. This review examines molecular mechanisms that regulate protein synthesis in response to stress.
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Affiliation(s)
- Vivek M. Advani
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts, United States of America
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45
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Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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46
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Tuorto F, Parlato R. rRNA and tRNA Bridges to Neuronal Homeostasis in Health and Disease. J Mol Biol 2019; 431:1763-1779. [PMID: 30876917 DOI: 10.1016/j.jmb.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Dysregulation of protein translation is emerging as a unifying mechanism in the pathogenesis of many neuronal disorders. Ribosomal RNA (rRNA) and transfer RNA (tRNA) are structural molecules that have complementary and coordinated functions in protein synthesis. Defects in both rRNAs and tRNAs have been described in mammalian brain development, neurological syndromes, and neurodegeneration. In this review, we present the molecular mechanisms that link aberrant rRNA and tRNA transcription, processing and modifications to translation deficits, and neuropathogenesis. We also discuss the interdependence of rRNA and tRNA biosynthesis and how their metabolism brings together proteotoxic stress and impaired neuronal homeostasis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Albert Einstein Allee 11, 89081 Ulm, Germany; Institute of Anatomy and Cell Biology, Medical Cell Biology, University of Heidelberg, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany.
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47
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Xu CP, Sun HT, Yang YJ, Cui Z, Wang J, Yu B, Wang FZ, Yang QP, Qi Y. ELP2 negatively regulates osteoblastic differentiation impaired by tumor necrosis factor α in MC3T3-E1 cells through STAT3 activation. J Cell Physiol 2019; 234:18075-18085. [PMID: 30847950 PMCID: PMC6618314 DOI: 10.1002/jcp.28440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 02/06/2023]
Abstract
Tumor necrosis factor‐α (TNF‐α) is a pluripotent signaling molecule. The biological effect of TNF‐α includes slowing down osteogenic differentiation, which can lead to bone dysplasia in long‐term inflammatory microenvironments. Signal transducer and activator of transcription 3 (STAT3)‐interacting protein 1 (StIP1, also known as elongator complex protein 2, ELP2) play a role in inhibiting TNF‐α‐induced osteoblast differentiation. In the present study, we investigated whether and how ELP2 activation mediates the effects of TNF‐α on osteoblastic differentiation. Using in vitro cell cultures of preosteoblastic MC3T3‐E1 cells, we found that TNF‐α inhibited osteoblastic differentiation accompanied by an increase in ELP2 expression and STAT3 activation. Forced ELP2 expression inhibited osteogenic differentiation of MC3T3‐E1 cells, with a decrease in the expression of osteoblast marker genes, alkaline phosphatase activity, and matrix mineralization capacity. In contrast, ELP2 silencing ameliorated osteogenic differentiation in MC3T3‐E1 cells, even after TNF‐α stimulation. The TNF‐α‐induced inhibitory effect on osteoblastic differentiation was therefore mediated by ELP2, which was associated with Janus kinase 2 (JAK2)/STAT3 activation. These results suggest that ELP2 is upregulated at the differentiation of MC3T3‐E1 cells into osteoblasts and inhibits osteogenic differentiation in response to TNF‐α through STAT3 activation.
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Affiliation(s)
- Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Hong-Tao Sun
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Ya-Jun Yang
- Department of Pharmacology, Guangdong Medical University, Zhanjiang, Guangdong, People's Republic of China
| | - Zhuang Cui
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jian Wang
- Department of Orthopaedics, The Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, People's Republic of China
| | - Bin Yu
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Fa-Zheng Wang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, People's Republic of China
| | - Qing-Po Yang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, People's Republic of China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People's Republic of China
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48
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tRNA modification and cancer: potential for therapeutic prevention and intervention. Future Med Chem 2019; 11:885-900. [PMID: 30744422 DOI: 10.4155/fmc-2018-0404] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transfer RNAs (tRNAs) undergo extensive chemical modification within cells through the activity of tRNA methyltransferase enzymes (TRMs). Although tRNA modifications are dynamic, how they impact cell behavior after stress and during tumorigenesis is not well understood. This review discusses how tRNA modifications influence the translation of codon-biased transcripts involved in responses to oxidative stress. We further discuss emerging mechanistic details about how aberrant TRM activity in cancer cells can direct programs of codon-biased translation that drive cancer cell phenotypes. The studies reviewed here predict future preventative therapies aimed at augmenting TRM activity in individuals at risk for cancer due to exposure. They further predict that attenuating TRM-dependent translation in cancer cells may limit disease progression while leaving noncancerous cells unharmed.
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49
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Sehin Y, Koshla O, Dacyuk Y, Zhao R, Ross R, Myronovskyi M, Limbach PA, Luzhetskyy A, Walker S, Fedorenko V, Ostash B. Gene ssfg_01967 (miaB) for tRNA modification influences morphogenesis and moenomycin biosynthesis in Streptomyces ghanaensis ATCC14672. MICROBIOLOGY (READING, ENGLAND) 2019; 165:233-245. [PMID: 30543507 PMCID: PMC7003650 DOI: 10.1099/mic.0.000747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/31/2018] [Indexed: 12/26/2022]
Abstract
Streptomyces ghanaensis ATCC14672 is remarkable for its production of phosphoglycolipid compounds, moenomycins, which serve as a blueprint for the development of a novel class of antibiotics based on inhibition of peptidoglycan glycosyltransferases. Here we employed mariner transposon (Tn) mutagenesis to find new regulatory genes essential for moenomycin production. We generated a library of 3000 mutants which were screened for altered antibiotic activity. Our focus centred on a single mutant, HIM5, which accumulated lower amounts of moenomycin and was impaired in morphogenesis as compared to the parental strain. HIM5 carried the Tn insertion within gene ssfg_01967 for putative tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase, or MiaB, and led to a reduced level of thiomethylation at position 37 in the anticodon of S. ghanaensis transfer ribonucleic acid (tRNA). It is likely that the mutant phenotype of HIM5 stems from the way in which ssfg_01967::Tn influences translation of the rare leucine codon UUA in several genes for moenomycin production and life cycle progression in S. ghanaensis. This is the first report showing that quantitative changes in tRNA modification status in Streptomyces have physiological consequences.
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Affiliation(s)
- Yuliia Sehin
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Yuriy Dacyuk
- Department of Physics of the Earth, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Robert Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Maksym Myronovskyi
- Helmholtz Institute for Pharmaceutical Research Saarland Campus, Building C2.3, 66123 Saarbrucken, Germany
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland Campus, Building C2.3, 66123 Saarbrucken, Germany
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
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50
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Bento-Abreu A, Jager G, Swinnen B, Rué L, Hendrickx S, Jones A, Staats KA, Taes I, Eykens C, Nonneman A, Nuyts R, Timmers M, Silva L, Chariot A, Nguyen L, Ravits J, Lemmens R, Cabooter D, Van Den Bosch L, Van Damme P, Al-Chalabi A, Bystrom A, Robberecht W. Elongator subunit 3 (ELP3) modifies ALS through tRNA modification. Hum Mol Genet 2019; 27:1276-1289. [PMID: 29415125 PMCID: PMC6159532 DOI: 10.1093/hmg/ddy043] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal degenerative motor neuron disorder of which the progression is influenced by several disease-modifying factors. Here, we investigated ELP3, a subunit of the elongator complex that modifies tRNA wobble uridines, as one of such ALS disease modifiers. ELP3 attenuated the axonopathy of a mutant SOD1, as well as of a mutant C9orf72 ALS zebrafish model. Furthermore, the expression of ELP3 in the SOD1G93A mouse extended the survival and attenuated the denervation in this model. Depletion of ELP3 in vitro reduced the modified tRNA wobble uridine mcm5s2U and increased abundance of insoluble mutant SOD1, which was reverted by exogenous ELP3 expression. Interestingly, the expression of ELP3 in the motor cortex of ALS patients was reduced and correlated with mcm5s2U levels. Our results demonstrate that ELP3 is a modifier of ALS and suggest a link between tRNA modification and neurodegeneration.
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Affiliation(s)
- Andre Bento-Abreu
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Gunilla Jager
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Laura Rué
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Stijn Hendrickx
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ashley Jones
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Kim A Staats
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Ines Taes
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Caroline Eykens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Annelies Nonneman
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Rik Nuyts
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Mieke Timmers
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Lara Silva
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Alain Chariot
- GIGA-Molecular Biology of Diseases and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - Laurent Nguyen
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - John Ravits
- Department of Neurosciences, ALS Translational Research, University of California, San Diego, La Jolla, CA, USA
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Deirdre Cabooter
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ammar Al-Chalabi
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Anders Bystrom
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
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