1
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Jones JD, Franco MK, Giles RN, Eyler DE, Tardu M, Smith TJ, Snyder LR, Polikanov YS, Kennedy RT, Niederer RO, Koutmou KS. Conserved 5-methyluridine tRNA modification modulates ribosome translocation. Proc Natl Acad Sci U S A 2024; 121:e2401743121. [PMID: 39159370 PMCID: PMC11363252 DOI: 10.1073/pnas.2401743121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/05/2024] [Indexed: 08/21/2024] Open
Abstract
While the centrality of posttranscriptional modifications to RNA biology has long been acknowledged, the function of the vast majority of modified sites remains to be discovered. Illustrative of this, there is not yet a discrete biological role assigned for one of the most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m5U54). Here, we uncover contributions of m5U54 to both tRNA maturation and protein synthesis. Our mass spectrometry analyses demonstrate that cells lacking the enzyme that installs m5U in the T-loop (TrmA in Escherichia coli, Trm2 in Saccharomyces cerevisiae) exhibit altered tRNA modification patterns. Furthermore, m5U54-deficient tRNAs are desensitized to small molecules that prevent translocation in vitro. This finding is consistent with our observations that relative to wild-type cells, trm2Δ cell growth and transcriptome-wide gene expression are less perturbed by translocation inhibitors. Together our data suggest a model in which m5U54 acts as an important modulator of tRNA maturation and translocation of the ribosome during protein synthesis.
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Affiliation(s)
- Joshua D. Jones
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Monika K. Franco
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
| | - Rachel N. Giles
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Daniel E. Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Mehmet Tardu
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Tyler J. Smith
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Laura R. Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois, Chicago, IL60607
| | | | - Rachel O. Niederer
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI48109
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2
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Villa S, Dwivedi P, Stahl A, Hinkle T, Rose CM, Kirkpatrick DS, Tomchik SM, Dixit VM, Wolf FW. OTUD6 deubiquitination of RPS7/eS7 on the free 40 S ribosome regulates global protein translation and stress. Nat Commun 2024; 15:6873. [PMID: 39127721 PMCID: PMC11316749 DOI: 10.1038/s41467-024-51284-y] [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: 12/15/2022] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
Ribosomes are regulated by evolutionarily conserved ubiquitination/deubiquitination events. We uncover the role of the deubiquitinase OTUD6 in regulating global protein translation through deubiquitination of the RPS7/eS7 subunit on the free 40 S ribosome in vivo in Drosophila. Coimmunoprecipitation and enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies reveal RPS7 as the ribosomal substrate. The 40 S protein RACK1 and E3 ligases CNOT4 and RNF10 function upstream of OTUD6 to regulate alkylation stress. OTUD6 interacts with RPS7 specifically on the free 40 S, and not on 43 S/48 S initiation complexes or the translating ribosome. Global protein translation levels are bidirectionally regulated by OTUD6 protein abundance. OTUD6 protein abundance is physiologically regulated in aging and in response to translational and alkylation stress. Thus, OTUD6 may promote translation initiation, the rate limiting step in protein translation, by titering the amount of 40 S ribosome that recycles.
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Affiliation(s)
- Sammy Villa
- Quantitative and Systems Biology, University of California, Merced, CA, 95343, USA
- Calico Life Sciences, 1170 Veterans Boulevard, South San Francisco, CA, 94080, USA
| | - Pankaj Dwivedi
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
- Merck, West Point, PA, 19486, USA
| | - Aaron Stahl
- Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, 52242, USA
- Department of Neuroscience, Scripps Research, Jupiter, FL, 33458, USA
| | - Trent Hinkle
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
- Xaira Therapeutics, Brisbane, CA, 94005, USA
| | - Seth M Tomchik
- Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, 52242, USA
- Department of Neuroscience, Scripps Research, Jupiter, FL, 33458, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, 52242, USA
- Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Fred W Wolf
- Quantitative and Systems Biology, University of California, Merced, CA, 95343, USA.
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
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3
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Sinha NK, McKenney C, Yeow ZY, Li JJ, Nam KH, Yaron-Barir TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Regot S, Green R. The ribotoxic stress response drives UV-mediated cell death. Cell 2024; 187:3652-3670.e40. [PMID: 38843833 PMCID: PMC11246228 DOI: 10.1016/j.cell.2024.05.018] [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: 08/03/2023] [Revised: 03/03/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.
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Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhong Y Yeow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey J Li
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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4
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Ye X, Li Z, Ye S, Liang X, Bao C, He M, Wang H, Xia L, Cao X. Accurate identification of 8-oxoguanine in RNA with single-nucleotide resolution using ligase-dependent qPCR. Org Biomol Chem 2024; 22:5629-5635. [PMID: 38912549 DOI: 10.1039/d4ob00786g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
8-oxoguanine (o8G), a prevalent oxidative modification in RNA induced by reactive oxygen species (ROS), plays a pivotal role in regulating RNA functions. Accurate detection and quantification of o8G modifications is critical to understanding their biological significance and potential as disease biomarkers, but effective detection methods remain limited. Here, we have developed a highly specific T3 DNA ligase-dependent qPCR assay that exploits the enzyme's ability to discriminate o8G from guanine (G) with single-nucleotide resolution. This method can detect o8G in RNA at levels as low as 500 fM, with an up to 18-fold higher selectivity for discriminating o8G from G. By simulating oxidative stress conditions in SH-SY5Y and HS683 cell lines treated with rotenone, we successfully identified site-specific o8G modifications in key miRNAs associated with neuroprotective responses, including miR-124, let-7a and miR-29a. The developed assay holds significant promise for the practical identification of o8G, facilitating its potential for detailed studies of o8G dynamics in various biological contexts and diseases.
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Affiliation(s)
- Xidong Ye
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Zengguang Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Shangde Ye
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Xinqi Liang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Chenyu Bao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Mingyang He
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Hailan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Laixin Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Xin Cao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
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5
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McGirr T, Onar O, Jafarnejad SM. Dysregulated ribosome quality control in human diseases. FEBS J 2024. [PMID: 38949989 DOI: 10.1111/febs.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.
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Affiliation(s)
- Tom McGirr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Okan Onar
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
- Department of Biology, Faculty of Science, Ankara University, Turkey
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6
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Gao Y, Zhu Y, Sun Q, Chen D. Ribosome-associated protein quality control: Implications for neurodegenerative diseases and therapeutic potential. Sci Bull (Beijing) 2024; 69:1165-1169. [PMID: 38278708 DOI: 10.1016/j.scib.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China.
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7
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Nanjaraj Urs AN, Lasehinde V, Kim L, McDonald E, Yan LL, Zaher HS. Inability to rescue stalled ribosomes results in overactivation of the integrated stress response. J Biol Chem 2024; 300:107290. [PMID: 38636664 PMCID: PMC11106528 DOI: 10.1016/j.jbc.2024.107290] [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: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Endogenous and exogenous chemical agents are known to compromise the integrity of RNA and cause ribosome stalling and collisions. Recent studies have shown that collided ribosomes serve as sensors for multiple processes, including ribosome quality control (RQC) and the integrated stress response (ISR). Since RQC and the ISR have distinct downstream consequences, it is of great importance that organisms activate the appropriate process. We previously showed that RQC is robustly activated in response to collisions and suppresses the ISR activation. However, the molecular mechanics behind this apparent competition were not immediately clear. Here we show that Hel2 does not physically compete with factors of the ISR, but instead its ribosomal-protein ubiquitination activity, and downstream resolution of collided ribosomes, is responsible for suppressing the ISR. Introducing a mutation in the RING domain of Hel2-which inhibits its ubiquitination activity and downstream RQC but imparts higher affinity of the factor for collided ribosomes-resulted in increased activation of the ISR upon MMS-induced alkylation stress. Similarly, mutating Hel2's lysine targets in uS10, which is responsible for RQC activation, resulted in increased Gcn4 target induction. Remarkably, the entire process of RQC appears to be limited by the action of Hel2, as the overexpression of this one factor dramatically suppressed the activation of the ISR. Collectively, our data suggest that cells evolved Hel2 to bind collided ribosomes with a relatively high affinity but kept its concentration relatively low, ensuring that it gets exhausted under stress conditions that cannot be resolved by quality control processes.
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Affiliation(s)
| | - Victor Lasehinde
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Lucas Kim
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Elesa McDonald
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Liewei L Yan
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA.
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8
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Kumar A, Mathew V, Stirling PC. Dynamics of DNA damage-induced nuclear inclusions are regulated by SUMOylation of Btn2. Nat Commun 2024; 15:3215. [PMID: 38615096 PMCID: PMC11016081 DOI: 10.1038/s41467-024-47615-8] [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: 08/16/2023] [Accepted: 04/05/2024] [Indexed: 04/15/2024] Open
Abstract
Spatial compartmentalization is a key facet of protein quality control that serves to store disassembled or non-native proteins until triage to the refolding or degradation machinery can occur in a regulated manner. Yeast cells sequester nuclear proteins at intranuclear quality control bodies (INQ) in response to various stresses, although the regulation of this process remains poorly understood. Here we reveal the SUMO modification of the small heat shock protein Btn2 under DNA damage and place Btn2 SUMOylation in a pathway promoting protein clearance from INQ structures. Along with other chaperones, and degradation machinery, Btn2-SUMO promotes INQ clearance from cells recovering from genotoxic stress. These data link small heat shock protein post-translational modification to the regulation of protein sequestration in the yeast nucleus.
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Affiliation(s)
- Arun Kumar
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Veena Mathew
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
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9
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Parker MD, Brunk ES, Getzler AJ, Karbstein K. The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage. PLoS Biol 2024; 22:e3001767. [PMID: 39038273 PMCID: PMC11045238 DOI: 10.1371/journal.pbio.3001767] [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: 07/20/2022] [Accepted: 03/05/2024] [Indexed: 07/24/2024] Open
Abstract
The 18S rRNA sequence is highly conserved, particularly at its 3'-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3'-end is degenerate with similar sites nearby. Here, we used yeast genetics, biochemistry, and next-generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3'-end. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control (QC) step, but not in healthy cells with intact QC mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weaker than its binding to accurately processed 18S rRNA. Accordingly, excess Rio1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA can translate, albeit more slowly, thereby inviting collisions with trailing ribosomes. These collisions result in degradation of the defective ribosomes utilizing parts of the machinery for mRNA QC. Altogether, the data support a model in which Rio1 inspects the 3'-end of the nascent 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions purify cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Elise S. Brunk
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Adam J. Getzler
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
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10
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Zhou Y, Panhale A, Shvedunova M, Balan M, Gomez-Auli A, Holz H, Seyfferth J, Helmstädter M, Kayser S, Zhao Y, Erdogdu NU, Grzadzielewska I, Mittler G, Manke T, Akhtar A. RNA damage compartmentalization by DHX9 stress granules. Cell 2024; 187:1701-1718.e28. [PMID: 38503283 DOI: 10.1016/j.cell.2024.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Biomolecules incur damage during stress conditions, and damage partitioning represents a vital survival strategy for cells. Here, we identified a distinct stress granule (SG), marked by dsRNA helicase DHX9, which compartmentalizes ultraviolet (UV)-induced RNA, but not DNA, damage. Our FANCI technology revealed that DHX9 SGs are enriched in damaged intron RNA, in contrast to classical SGs that are composed of mature mRNA. UV exposure causes RNA crosslinking damage, impedes intron splicing and decay, and triggers DHX9 SGs within daughter cells. DHX9 SGs promote cell survival and induce dsRNA-related immune response and translation shutdown, differentiating them from classical SGs that assemble downstream of translation arrest. DHX9 modulates dsRNA abundance in the DHX9 SGs and promotes cell viability. Autophagy receptor p62 is activated and important for DHX9 SG disassembly. Our findings establish non-canonical DHX9 SGs as a dedicated non-membrane-bound cytoplasmic compartment that safeguards daughter cells from parental RNA damage.
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Affiliation(s)
- Yilong Zhou
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Amol Panhale
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Mirela Balan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Martin Helmstädter
- EMcore, Renal Division, Department of Medicine, University Freiburg, Hospital Freiburg, University Faculty of Medicine, Freiburg, Germany
| | - Séverine Kayser
- EMcore, Renal Division, Department of Medicine, University Freiburg, Hospital Freiburg, University Faculty of Medicine, Freiburg, Germany
| | - Yuling Zhao
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Iga Grzadzielewska
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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11
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Taylor KE, Miller LG, Contreras LM. RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding. Biochem Soc Trans 2024; 52:111-122. [PMID: 38174726 DOI: 10.1042/bst20230254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Cells encounter a variety of stresses throughout their lifetimes. Oxidative stress can occur via a myriad of factors, including exposure to chemical toxins or UV light. Importantly, these stressors induce chemical changes (e.g. chemical modifications) to biomolecules, such as RNA. Commonly, guanine is oxidized to form 8-oxo-7,8-hydroxyguanine (8-oxoG) and this modification can disrupt a plethora of cellular processes including messenger RNA translation and stability. Polynucleotide phosphorylase (PNPase), heterogeneous nuclear ribonucleoprotein D (HNRPD/Auf1), poly(C)-binding protein (PCBP1/HNRNP E1), and Y-box binding protein 1 (YB-1) have been identified as four RNA-binding proteins that preferentially bind 8-oxoG-modified RNA over unmodified RNA. All four proteins are native to humans and PNPase is additionally found in bacteria. Additionally, under oxidative stress, cell survival declines in mutants that lack PNPase, Auf1, or PCBP1, suggesting they are critical to the oxidative stress response. This mini-review captures the current understanding of the PNPase, HNRPD/Auf1, PCBP1, and YB-1 proteins and the mechanism that has been outlined so far by which they recognize and interact with 8-oxoG-modified RNAs.
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Affiliation(s)
- Kathleen E Taylor
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Lucas G Miller
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
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12
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Monem PC, Arribere JA. A ubiquitin language communicates ribosomal distress. Semin Cell Dev Biol 2024; 154:131-137. [PMID: 36963992 PMCID: PMC10878831 DOI: 10.1016/j.semcdb.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023]
Abstract
Cells entrust ribosomes with the critical task of identifying problematic mRNAs and facilitating their degradation. Ribosomes must communicate when they encounter and stall on an aberrant mRNA, lest they expose the cell to toxic and disease-causing proteins, or they jeopardize ribosome homeostasis and cellular translation. In recent years, ribosomal ubiquitination has emerged as a central signaling step in this process, and proteomic studies across labs and experimental systems show a myriad of ubiquitination sites throughout the ribosome. Work from many labs zeroed in on ubiquitination in one region of the small ribosomal subunit as being functionally significant, with the balance and exact ubiquitination sites determined by stall type, E3 ubiquitin ligases, and deubiquitinases. This review discusses the current literature surrounding ribosomal ubiquitination during translational stress and considers its role in committing translational complexes to decay.
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Affiliation(s)
- Parissa C Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Joshua A Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.
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13
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Dar SA, Malla S, Martinek V, Payea MJ, Lee CT, Martin J, Khandeshi AJ, Martindale JL, Belair C, Maragkakis M. Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.31.555629. [PMID: 37693505 PMCID: PMC10491209 DOI: 10.1101/2023.08.31.555629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on removal of the poly(A) tail. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome. Inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 fully rescues RNA length and suppresses stress-induced decay. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.
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Affiliation(s)
- Showkat A. Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sulochan Malla
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vlastimil Martinek
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Matthew J. Payea
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | | | - Jessica Martin
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aditya J. Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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14
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Di Fraia D, Marino A, Lee JH, Kelmer Sacramento E, Baumgart M, Bagnoli S, Tomaz da Silva P, Kumar Sahu A, Siano G, Tiessen M, Terzibasi-Tozzini E, Gagneur J, Frydman J, Cellerino A, Ori A. Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.20.549210. [PMID: 38260253 PMCID: PMC10802395 DOI: 10.1101/2023.07.20.549210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Aging and neurodegeneration entail diverse cellular and molecular hallmarks. Here, we studied the effects of aging on the transcriptome, translatome, and multiple layers of the proteome in the brain of a short-lived killifish. We reveal that aging causes widespread reduction of proteins enriched in basic amino acids that is independent of mRNA regulation, and it is not due to impaired proteasome activity. Instead, we identify a cascade of events where aberrant translation pausing leads to reduced ribosome availability resulting in proteome remodeling independently of transcriptional regulation. Our research uncovers a vulnerable point in the aging brain's biology - the biogenesis of basic DNA/RNA binding proteins. This vulnerability may represent a unifying principle that connects various aging hallmarks, encompassing genome integrity and the biosynthesis of macromolecules.
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Affiliation(s)
- Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Antonio Marino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jae Ho Lee
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Pedro Tomaz da Silva
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Amit Kumar Sahu
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Max Tiessen
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alessandro Cellerino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- BIO@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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15
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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16
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Meydan S, Barros GC, Simões V, Harley L, Cizubu BK, Guydosh NR, Silva GM. The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress. Cell Rep 2023; 42:113359. [PMID: 37917585 PMCID: PMC10755677 DOI: 10.1016/j.celrep.2023.113359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore perform Ribo-seq and Disome-seq in Saccharomyces cerevisiae and show that oxidative stress causes ribosome pausing at specific amino acid motifs, which also leads to ribosome collisions. However, these redox-pausing signatures are lost in the absence of Rad6 and do not depend on the ribosome-associated quality control (RQC) pathway. We also show that Rad6 is needed to inhibit overall translation in response to oxidative stress and that its deletion leads to increased expression of antioxidant genes. Finally, we observe that the lack of Rad6 leads to changes during translation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Fellowship, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20982, USA
| | | | - Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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17
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Jones JD, Franco MK, Tardu M, Smith TJ, Snyder LR, Eyler DE, Polikanov Y, Kennedy RT, Niederer RO, Koutmou KS. Conserved 5-methyluridine tRNA modification modulates ribosome translocation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.12.566704. [PMID: 37986750 PMCID: PMC10659410 DOI: 10.1101/2023.11.12.566704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
While the centrality of post-transcriptional modifications to RNA biology has long been acknowledged, the function of the vast majority of modified sites remains to be discovered. Illustrative of this, there is not yet a discrete biological role assigned for one the most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m 5 U54). Here, we uncover contributions of m 5 U54 to both tRNA maturation and protein synthesis. Our mass spectrometry analyses demonstrate that cells lacking the enzyme that installs m 5 U in the T-loop (TrmA in E. coli , Trm2 in S. cerevisiae ) exhibit altered tRNA modifications patterns. Furthermore, m 5 U54 deficient tRNAs are desensitized to small molecules that prevent translocation in vitro. This finding is consistent with our observations that, relative to wild-type cells, trm2 Δ cell growth and transcriptome-wide gene expression are less perturbed by translocation inhibitors. Together our data suggest a model in which m 5 U54 acts as an important modulator of tRNA maturation and translocation of the ribosome during protein synthesis.
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18
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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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19
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Meydan S, Guydosh NR. Is there a localized role for translational quality control? RNA (NEW YORK, N.Y.) 2023; 29:1623-1643. [PMID: 37582617 PMCID: PMC10578494 DOI: 10.1261/rna.079683.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
It is known that mRNAs and the machinery that translates them are not uniformly distributed throughout the cytoplasm. As a result, the expression of some genes is localized to particular parts of the cell and this makes it possible to carry out important activities, such as growth and signaling, in three-dimensional space. However, the functions of localized gene expression are not fully understood, and the underlying mechanisms that enable localized expression have not been determined in many cases. One consideration that could help in addressing these challenges is the role of quality control (QC) mechanisms that monitor translating ribosomes. On a global level, QC pathways are critical for detecting aberrant translation events, such as a ribosome that stalls while translating, and responding by activating stress pathways and resolving problematic ribosomes and mRNAs at the molecular level. However, it is unclear how these pathways, even when uniformly active throughout the cell, affect local translation. Importantly, some QC pathways have themselves been reported to be enriched in the proximity of particular organelles, but the extent of such localized activity remains largely unknown. Here, we describe the major QC pathways and review studies that have begun to explore their roles in localized translation. Given the limited data in this area, we also pose broad questions about the possibilities and limitations for how QC pathways could facilitate localized gene expression in the cell with the goal of offering ideas for future experimentation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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20
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McGuffey JC, Jackson-Litteken CD, Di Venanzio G, Zimmer AA, Lewis JM, Distel JS, Kim KQ, Zaher HS, Alfonzo J, Scott NE, Feldman MF. The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection. mBio 2023; 14:e0141623. [PMID: 37589464 PMCID: PMC10653896 DOI: 10.1128/mbio.01416-23] [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: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
IMPORTANCE As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.
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Affiliation(s)
- Jenna C. McGuffey
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Clay D. Jackson-Litteken
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Aubree A. Zimmer
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jessica M. Lewis
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Juan Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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21
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Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem 2023; 24:e202300264. [PMID: 37382189 DOI: 10.1002/cbic.202300264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
During translation, messenger RNAs (mRNAs) are decoded by ribosomes which can stall for various reasons. These include chemical damage, codon composition, starvation, or translation inhibition. Trailing ribosomes can collide with stalled ribosomes, potentially leading to dysfunctional or toxic proteins. Such aberrant proteins can form aggregates and favor diseases, especially neurodegeneration. To prevent this, both eukaryotes and bacteria have evolved different pathways to remove faulty nascent peptides, mRNAs and defective ribosomes from the collided complex. In eukaryotes, ubiquitin ligases play central roles in triggering downstream responses and several complexes have been characterized that split affected ribosomes and facilitate degradation of the various components. As collided ribosomes signal translation stress to affected cells, in eukaryotes additional stress response pathways are triggered when collisions are sensed. These pathways inhibit translation and modulate cell survival and immune responses. Here, we summarize the current state of knowledge about rescue and stress response pathways triggered by ribosome collisions.
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Affiliation(s)
- Kaushik Viswanathan Iyer
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Max Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lena Sophie Tittel
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marie-Luise Winz
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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22
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Jones JD, Franco MK, Smith TJ, Snyder LR, Anders AG, Ruotolo BT, Kennedy RT, Koutmou KS. Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation. RSC Chem Biol 2023; 4:363-378. [PMID: 37181630 PMCID: PMC10170649 DOI: 10.1039/d2cb00229a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/15/2023] [Indexed: 02/22/2023] Open
Abstract
Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Laura R Snyder
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Anna G Anders
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
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23
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Yang YM, Jung Y, Abegg D, Adibekian A, Carroll KS, Karbstein K. Chaperone-directed ribosome repair after oxidative damage. Mol Cell 2023; 83:1527-1537.e5. [PMID: 37086725 PMCID: PMC10164075 DOI: 10.1016/j.molcel.2023.03.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/07/2023] [Accepted: 03/30/2023] [Indexed: 04/24/2023]
Abstract
Because of the central role ribosomes play for protein translation and ribosome-mediated mRNA and protein quality control (RQC), the ribosome pool is surveyed and dysfunctional ribosomes degraded both during assembly, as well as the functional cycle. Oxidative stress downregulates translation and damages mRNAs and ribosomal proteins (RPs). Although damaged mRNAs are detected and degraded via RQC, how cells mitigate damage to RPs is not known. Here, we show that cysteines in Rps26 and Rpl10 are readily oxidized, rendering the proteins non-functional. Oxidized Rps26 and Rpl10 are released from ribosomes by their chaperones, Tsr2 and Sqt1, and the damaged ribosomes are subsequently repaired with newly made proteins. Ablation of this pathway impairs growth, which is exacerbated under oxidative stress. These findings reveal an unanticipated mechanism for chaperone-mediated ribosome repair, augment our understanding of ribosome quality control, and explain previous observations of protein exchange in ribosomes from dendrites, with broad implications for aging and health.
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Affiliation(s)
- Yoon-Mo Yang
- Department of Integrative Structural and Computational Biology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Youngeun Jung
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Daniel Abegg
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Alexander Adibekian
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Kate S Carroll
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA; HHMI Faculty Scholar, Chevy Chase, MD 20815, USA.
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24
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Knowles CM, Goich D, Bloom ALM, Kalem MC, Panepinto JC. Contributions of Ccr4 and Gcn2 to the Translational Response of C. neoformans to Host-Relevant Stressors and Integrated Stress Response Induction. mBio 2023; 14:e0019623. [PMID: 37017529 PMCID: PMC10127693 DOI: 10.1128/mbio.00196-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
In response to the host environment, the human pathogen Cryptococcus neoformans must rapidly reprogram its translatome from one which promotes growth to one which is responsive to host stress. In this study, we investigate the two events which comprise translatome reprogramming: the removal of abundant, pro-growth mRNAs from the translating pool, and the regulated entry of stress-responsive mRNAs into the translating pool. Removal of pro-growth mRNAs from the translating pool is controlled primarily by two regulatory mechanisms, repression of translation initiation via Gcn2, and decay mediated by Ccr4. We determined that translatome reprogramming in response to oxidative stress requires both Gcn2 and Ccr4, whereas the response to temperature requires only Ccr4. Additionally, we assessed ribosome collision in response to host-relevant stress and found that collided ribosomes accumulated during temperature stress but not during oxidative stress. The phosphorylation of eIF2α that occurred as a result of translational stress led us to investigate the induction of the integrated stress response (ISR). We found that eIF2α phosphorylation varied in response to the type and magnitude of stress, yet all tested conditions induced translation of the ISR transcription factor Gcn4. However, Gcn4 translation did not necessarily result in canonical Gcn4-dependent transcription. Finally, we define the ISR regulon in response to oxidative stress. In conclusion, this study begins to reveal the translational regulation in response to host-relevant stressors in an environmental fungus which is capable of adapting to the environment inside the human host. IMPORTANCE Cryptococcus neoformans is a human pathogen capable of causing devastating infections. It must rapidly adapt to changing environments as it leaves its niche in the soil and enters the human lung. Previous work has demonstrated a need to reprogram gene expression at the level of translation to promote stress adaptation. In this work, we investigate the contributions and interplay of the major mechanisms that regulate entry of new mRNAs into the pool (translation initiation) and the clearance of unneeded mRNAs from the pool (mRNA decay). One result of this reprogramming is the induction of the integrated stress response (ISR) regulon. Surprisingly, all stresses tested led to the production of the ISR transcription factor Gcn4, but not necessarily to transcription of ISR target genes. Furthermore, stresses result in differential levels of ribosome collisions, but these are not necessarily predictive of initiation repression as has been suggested in the model yeast.
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Affiliation(s)
- Corey M. Knowles
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - David Goich
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Amanda L. M. Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Murat C. Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - John C. Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
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25
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Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO. J Fungi (Basel) 2023; 9:jof9030351. [PMID: 36983519 PMCID: PMC10057556 DOI: 10.3390/jof9030351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023] Open
Abstract
Various external and internal factors damaging DNA constantly disrupt the stability of the genome. Cells use numerous dedicated DNA repair systems to detect damage and restore genomic integrity in a timely manner. Ribonucleotide reductase (RNR) is a key enzyme providing dNTPs for DNA repair. Molecular mechanisms of indirect regulation of yeast RNR activity are well understood, whereas little is known about its direct regulation. The study was aimed at elucidation of the proteasome-dependent mechanism of direct regulation of RNR subunits in Saccharomyces cerevisiae. Proteome analysis followed by Western blot, RT-PCR, and yeast plating analysis showed that upregulation of RNR by proteasome deregulation is associated with yeast hyper resistance to 4-nitroquinoline-1-oxide (4-NQO), a UV-mimetic DNA-damaging drug used in animal models to study oncogenesis. Inhibition of RNR or deletion of RNR regulatory proteins reverses the phenotype of yeast hyper resistance to 4-NQO. We have shown for the first time that the yeast Rnr1 subunit is a substrate of the proteasome, which suggests a common mechanism of RNR regulation in yeast and mammals.
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26
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Wu X, Yang ZH, Wu J, Han J. Ribosome-rescuer PELO catalyzes the oligomeric assembly of NOD-like receptor family proteins via activating their ATPase enzymatic activity. Immunity 2023; 56:926-943.e7. [PMID: 36948192 DOI: 10.1016/j.immuni.2023.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/17/2022] [Accepted: 02/22/2023] [Indexed: 03/24/2023]
Abstract
NOD-like receptors (NLRs) are pattern recognition receptors for diverse innate immune responses. Self-oligomerization after engagement with a ligand is a generally accepted model for the activation of each NLR. We report here that a catalyzer was required for NLR self-oligomerization. PELO, a well-known surveillance factor in translational quality control and/or ribosome rescue, interacted with all cytosolic NLRs and activated their ATPase activity. In the case of flagellin-initiated NLRC4 inflammasome activation, flagellin-bound NAIP5 recruited the first NLRC4 and then PELO was required for correctly assembling the rest of NLRC4s into the NLRC4 complex, one by one, by activating the NLRC4 ATPase activity. Stoichiometric and functional data revealed that PELO was not a structural constituent of the NLRC4 inflammasome but a powerful catalyzer for its assembly. The catalytic role of PELO in the activation of cytosolic NLRs provides insight into NLR activation and provides a direction for future studies of NLR family members.
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Affiliation(s)
- Xiurong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
| | - Zhang-Hua Yang
- Research Unit of Cellular Stress of CAMS, Xiang'an Hospital of Xiamen University, Cancer Research Center of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Laboratory Animal Center, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Research Unit of Cellular Stress of CAMS, Xiang'an Hospital of Xiamen University, Cancer Research Center of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Laboratory Animal Center, Xiamen University, Xiamen, Fujian 361102, China.
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27
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Crosstalk between Oxidative Stress and Aging in Neurodegeneration Disorders. Cells 2023; 12:cells12050753. [PMID: 36899889 PMCID: PMC10001353 DOI: 10.3390/cells12050753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
The world population is aging rapidly, and increasing lifespan exacerbates the burden of age-related health issues. On the other hand, premature aging has begun to be a problem, with increasing numbers of younger people suffering aging-related symptoms. Advanced aging is caused by a combination of factors: lifestyle, diet, external and internal factors, as well as oxidative stress (OS). Although OS is the most researched aging factor, it is also the least understood. OS is important not only in relation to aging but also due to its strong impact on neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Parkinson's disease (PD). In this review, we will discuss the aging process in relation to OS, the function of OS in neurodegenerative disorders, and prospective therapeutics capable of relieving neurodegenerative symptoms associated with the pro-oxidative condition.
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28
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Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex. Nat Commun 2023; 14:79. [PMID: 36627279 PMCID: PMC9831982 DOI: 10.1038/s41467-022-35608-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The collision sensor Hel2 specifically recognizes colliding ribosomes and ubiquitinates the ribosomal protein uS10, leading to noncanonical subunit dissociation by the ribosome-associated quality control trigger (RQT) complex. Although uS10 ubiquitination is essential for rescuing stalled ribosomes, its function and recognition steps are not fully understood. Here, we show that the RQT complex components Cue3 and Rqt4 interact with the K63-linked ubiquitin chain and accelerate the recruitment of the RQT complex to the ubiquitinated colliding ribosome. The CUE domain of Cue3 and the N-terminal domain of Rqt4 bind independently to the K63-linked ubiquitin chain. Their deletion abolishes ribosomal dissociation mediated by the RQT complex. High-speed atomic force microscopy (HS-AFM) reveals that the intrinsically disordered regions of Rqt4 enable the expansion of the searchable area for interaction with the ubiquitin chain. These findings provide mechanistic insight into the decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex.
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29
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Eisenack TJ, Trentini DB. Ending a bad start: Triggers and mechanisms of co-translational protein degradation. Front Mol Biosci 2023; 9:1089825. [PMID: 36660423 PMCID: PMC9846516 DOI: 10.3389/fmolb.2022.1089825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
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Affiliation(s)
- Tom Joshua Eisenack
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Débora Broch Trentini
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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30
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Helton NS, Moon SL. Is bRaQCing bad? New roles for ribosome associated quality control factors in stress granule regulation. Biochem Soc Trans 2022; 50:1715-1724. [PMID: 36484689 PMCID: PMC11368206 DOI: 10.1042/bst20220549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 09/04/2024]
Abstract
Maintenance of proteostasis is of utmost importance to cellular viability and relies on the coordination of many post-transcriptional processes to respond to stressful stimuli. Stress granules (SGs) are RNA-protein condensates that form after translation initiation is inhibited, such as during the integrated stress response (ISR), and may facilitate cellular adaptation to stress. The ribosome-associated quality control (RQC) pathway is a critical translation monitoring system that recognizes aberrant mRNAs encoding potentially toxic nascent peptides to target them for degradation. Both SG regulation and the RQC pathway are directly associated with translation regulation, thus it is of no surprise recent developments have demonstrated a connection between them. VCP's function in the stress activated RQC pathway, ribosome collisions activating the ISR, and the regulation of the 40S ribosomal subunit by canonical SG proteins during the RQC all connect SGs to the RQC pathway. Because mutations in genes that are involved in both SG and RQC regulation are associated with degenerative and neurological diseases, understanding the coordination and interregulation of SGs and RQC may shed light on disease mechanisms. This minireview will highlight recent advances in understanding how SGs and the RQC pathway interact in health and disease contexts.
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Affiliation(s)
- Noah S Helton
- The Center for RNA Biomedicine and the Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Stephanie L Moon
- The Center for RNA Biomedicine and the Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, U.S.A
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31
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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32
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Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation. Nat Commun 2022; 13:4492. [PMID: 35918345 PMCID: PMC9345940 DOI: 10.1038/s41467-022-32220-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
The small intestine is a rapidly proliferating organ that is maintained by a small population of Lgr5-expressing intestinal stem cells (ISCs). However, several Lgr5-negative ISC populations have been identified, and this remarkable plasticity allows the intestine to rapidly respond to both the local environment and to damage. However, the mediators of such plasticity are still largely unknown. Using intestinal organoids and mouse models, we show that upon ribosome impairment (driven by Rptor deletion, amino acid starvation, or low dose cyclohexamide treatment) ISCs gain an Lgr5-negative, fetal-like identity. This is accompanied by a rewiring of metabolism. Our findings suggest that the ribosome can act as a sensor of nutrient availability, allowing ISCs to respond to the local nutrient environment. Mechanistically, we show that this phenotype requires the activation of ZAKɑ, which in turn activates YAP, via SRC. Together, our data reveals a central role for ribosome dynamics in intestinal stem cells, and identify the activation of ZAKɑ as a critical mediator of stem cell identity. Intestinal stem cells are responsible for replenishing cells within the high-turnover intestinal epithelium. Here they show that ribosome dynamics affect intestinal stem cell identity through a mechanism that is triggered by changes in nutrient availability.
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33
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Veltri AJ, D'Orazio KN, Lessen LN, Loll-Krippleber R, Brown GW, Green R. Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation. eLife 2022; 11:e76038. [PMID: 35894211 PMCID: PMC9352352 DOI: 10.7554/elife.76038] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully designed reporter mRNAs to perform genetic screens and functional assays in Saccharomyces cerevisiae. We characterize the roles of Hel2, Syh1, and Smy2 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 and, to a lesser extent its paralog Smy2, act in a distinct pathway from Hel2. This Syh1/Smy2-mediated pathway acts as a redundant, compensatory pathway to elicit NGD when Hel2-dependent NGD is impaired. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new insight into the role of Syh1 and Smy2 in NGD and into the ribosomal states that correlate with the activation of distinct pathways targeting mRNAs for degradation in yeast.
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Affiliation(s)
- Anthony J Veltri
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Karole N D'Orazio
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Laura N Lessen
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | | | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Canada
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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34
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Stoneley M, Harvey RF, Mulroney TE, Mordue R, Jukes-Jones R, Cain K, Lilley KS, Sawarkar R, Willis AE. Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress. Mol Cell 2022; 82:1557-1572.e7. [PMID: 35180429 PMCID: PMC9098122 DOI: 10.1016/j.molcel.2022.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 01/01/2023]
Abstract
During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by translation elongation inhibitors or methylated mRNA are short lived in human cells because they are split by the ASCC. In contrast, although ultraviolet light and 4-nitroquinoline 1-oxide induce ribosome stalling by damaging mRNA, and the ASCC is recruited to these stalled ribosomes, we found that they are refractory to the ASCC. Consequently, unresolved UV- and 4NQO-stalled ribosomes persist in human cells. We show that ribosome stalling activates cell-cycle arrest, partly through ZAK-p38MAPK signaling, and that this cell-cycle delay is prolonged when the ASCC cannot resolve stalled ribosomes. Thus, we propose that the sensitivity of stalled ribosomes to the ASCC influences the kinetics of stall resolution, which in turn controls the adaptive stress response.
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Affiliation(s)
- Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Thomas E Mulroney
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ryan Mordue
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Rebekah Jukes-Jones
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kelvin Cain
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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35
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Kim KQ, Zaher HS. Canary in a coal mine: collided ribosomes as sensors of cellular conditions. Trends Biochem Sci 2022; 47:82-97. [PMID: 34607755 PMCID: PMC8688274 DOI: 10.1016/j.tibs.2021.09.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023]
Abstract
The recent discovery that collision of ribosomes triggers quality control and stress responses in eukaryotes has shifted the perspective of the field. Collided eukaryotic ribosomes adopt a unique structure, acting as a ubiquitin signaling platform for various response factors. While several of the signals that determine which downstream pathways are activated have been uncovered, we are only beginning to learn how the specificity for the activation of each process is achieved during collisions. This review will summarize those findings and how ribosome-associated factors act as molecular sentinels, linking aberrations in translation to the overall cellular state. Insights into how cells respond to ribosome collision events will provide greater understanding of the role of the ribosome in the maintenance of cellular homeostasis.
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Affiliation(s)
| | - Hani S. Zaher
- Correspondence to: , Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO, USA 63130, Phone: (314) 935-7832, Fax: (314) 935-4432
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36
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Phillips CN, Schowe S, Langeberg CJ, Siddique N, Chapman EG, Resendiz MJE. Processing of RNA Containing 8-Oxo-7,8-Dihydroguanosine (8-oxoG) by the Exoribonuclease Xrn-1. Front Mol Biosci 2021; 8:780315. [PMID: 34869601 PMCID: PMC8634602 DOI: 10.3389/fmolb.2021.780315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding how oxidatively damaged RNA is handled intracellularly is of relevance due to the link between oxidized RNA and the progression/development of some diseases as well as aging. Among the ribonucleases responsible for the decay of modified (chemically or naturally) RNA is the exonuclease Xrn-1, a processive enzyme that catalyzes the hydrolysis of 5′-phosphorylated RNA in a 5′→3′ direction. We set out to explore the reactivity of this exonuclease towards oligonucleotides (ONs, 20-nt to 30-nt long) of RNA containing 8-oxo-7,8-dihydroguanosine (8-oxoG), obtained via solid-phase synthesis. The results show that Xrn-1 stalled at sites containing 8-oxoG, evidenced by the presence of a slower moving band (via electrophoretic analyses) than that observed for the canonical analogue. The observed fragment(s) were characterized via PAGE and MALDI-TOF to confirm that the oligonucleotide fragment(s) contained a 5′-phosphorylated 8-oxoG. Furthermore, the yields for this stalling varied from app. 5–30% with 8-oxoG located at different positions and in different sequences. To gain a better understanding of the decreased nuclease efficiency, we probed: 1) H-bonding and spatial constraints; 2) anti-syn conformational changes; 3) concentration of divalent cation; and 4) secondary structure. This was carried out by introducing methylated or brominated purines (m1G, m6,6A, or 8-BrG), probing varying [Mg2+], and using circular dichroism (CD) to explore the formation of structured RNA. It was determined that spatial constraints imposed by conformational changes around the glycosidic bond may be partially responsible for stalling, however, the results do not fully explain some of the observed higher stalling yields. We hypothesize that altered π-π stacking along with induced H-bonding interactions between 8-oxoG and residues within the binding site may also play a role in the decreased Xrn-1 efficiency. Overall, these observations suggest that other factors, yet to be discovered/established, are likely to contribute to the decay of oxidized RNA. In addition, Xrn-1 degraded RNA containing m1G, and stalled mildly at sites where it encountered m6,6A, or 8-BrG, which is of particular interest given that the former two are naturally occurring modifications.
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Affiliation(s)
- Cheyenne N Phillips
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Shawn Schowe
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Conner J Langeberg
- Department of Chemistry, University of Denver, Denver, CO, United States
| | - Namoos Siddique
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Erich G Chapman
- Department of Chemistry, University of Denver, Denver, CO, United States
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
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37
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Trainor BM, Pestov DG, Shcherbik N. Development, validation, and application of the ribosome separation and reconstitution system for protein translation in vitro. RNA (NEW YORK, N.Y.) 2021; 27:1602-1616. [PMID: 34452990 PMCID: PMC8594471 DOI: 10.1261/rna.078852.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Stress-induced molecular damage to ribosomes can impact protein synthesis in cells, but cell-based assays do not provide a clear way to distinguish the effects of ribosome damage from stress responses and damage to other parts of the translation machinery. Here we describe a detailed protocol for the separation of yeast ribosomes from other translational machinery constituents, followed by reconstitution of the translation mixture in vitro. This technique, which we refer to as ribosome separation and reconstitution (RSR), allows chemical modifications of yeast ribosomes without compromising other key translational components. In addition to the characterization of stress-induced ribosome damage, RSR can be applied to a broad range of experimental problems in studies of yeast translation.
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Affiliation(s)
- Brandon M Trainor
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
- Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey 08084, USA
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
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38
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Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H. Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Rep 2021; 37:109877. [PMID: 34706231 DOI: 10.1016/j.celrep.2021.109877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/21/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Xin Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Melissa Pires-Alves
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Christopher W Hawk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
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39
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Tsao N, Brickner JR, Rodell R, Ganguly A, Wood M, Oyeniran C, Ahmad T, Sun H, Bacolla A, Zhang L, Lukinović V, Soll JM, Townley BA, Casanova AG, Tainer JA, He C, Vindigni A, Reynoird N, Mosammaparast N. Aberrant RNA methylation triggers recruitment of an alkylation repair complex. Mol Cell 2021; 81:4228-4242.e8. [PMID: 34686315 DOI: 10.1016/j.molcel.2021.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the mechanistic basis for the selectivity of this pathway was not immediately obvious. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. In turn, recruitment of ASCC during alkylation damage, which is mediated by the E3 ubiquitin ligase RNF113A, suppresses transcription and R-loop formation. We further show that alkylated pre-mRNA is sufficient to activate RNF113A E3 ligase in vitro in a manner dependent on its RNA binding Zn-finger domain. Together, our work identifies an unexpected role for RNA damage in eliciting a specific response to genotoxins.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Rodell
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Adit Ganguly
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Clement Oyeniran
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Tanveer Ahmad
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Hua Sun
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisheng Zhang
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA
| | - Valentina Lukinović
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Jennifer M Soll
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Brittany A Townley
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Alexandre G Casanova
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chuan He
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago IL 60637, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.
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40
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English AM, Green KM, Moon SL. A (dis)integrated stress response: Genetic diseases of eIF2α regulators. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1689. [PMID: 34463036 DOI: 10.1002/wrna.1689] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/28/2023]
Abstract
The integrated stress response (ISR) is a conserved mechanism by which eukaryotic cells remodel gene expression to adapt to intrinsic and extrinsic stressors rapidly and reversibly. The ISR is initiated when stress-activated protein kinases phosphorylate the major translation initiation factor eukaryotic translation initiation factor 2ɑ (eIF2ɑ), which globally suppresses translation initiation activity and permits the selective translation of stress-induced genes including important transcription factors such as activating transcription factor 4 (ATF4). Translationally repressed messenger RNAs (mRNAs) and noncoding RNAs assemble into cytoplasmic RNA-protein granules and polyadenylated RNAs are concomitantly stabilized. Thus, regulated changes in mRNA translation, stability, and localization to RNA-protein granules contribute to the reprogramming of gene expression that defines the ISR. We discuss fundamental mechanisms of RNA regulation during the ISR and provide an overview of a growing class of genetic disorders associated with mutant alleles of key translation factors in the ISR pathway. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease Translation > Translation Regulation RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Alyssa M English
- Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katelyn M Green
- Department of Chemistry, Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie L Moon
- Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
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41
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Wollen KL, Hagen L, Vågbø CB, Rabe R, Iveland TS, Aas PA, Sharma A, Sporsheim B, Erlandsen HO, Palibrk V, Bjørås M, Fonseca DM, Mosammaparast N, Slupphaug G. ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA. J Transl Med 2021; 19:287. [PMID: 34217309 PMCID: PMC8254245 DOI: 10.1186/s12967-021-02948-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. Methods Here we use quantitative mass spectrometry to determine the fate of chemically induced methylbases in the mRNA of human cells. Concomitant alteration in the mRNA binding proteome was analyzed by SILAC mass spectrometry. Results MMS induced prominent direct mRNA methylations that were chemically identical to endogenous methylbases. Transient loss of 40S ribosomal proteins from isolated mRNA suggests that aberrant methylbases mediate arrested translational initiation and potentially also no-go decay of the affected mRNA. Four proteins (ASCC3, YTHDC2, TRIM25 and GEMIN5) displayed increased mRNA binding after MMS treatment. ASCC3 is a binding partner of the DNA/RNA demethylase ALKBH3 and was recently shown to promote disassembly of collided ribosomes as part of the ribosome quality control (RQC) trigger complex. We find that ASCC3-deficient cells display delayed removal of MMS-induced 1-methyladenosine (m1A) and 3-methylcytosine (m3C) from mRNA and impaired formation of MMS-induced P-bodies. Conclusions Our findings conform to a model in which ASCC3-mediated disassembly of collided ribosomes allows demethylation of aberrant m1A and m3C by ALKBH3. Our findings constitute first evidence of selective sanitation of aberrant mRNA methylbases over their endogenous counterparts and warrant further studies on RNA-mediated effects of chemical alkylators commonly used in the clinic. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02948-6.
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Affiliation(s)
- Kristian Lied Wollen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Renana Rabe
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Bjørnar Sporsheim
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,CMIC Cellular & Molecular Imaging Core Facility, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Hilde O Erlandsen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Vuk Palibrk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Davi M Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway. .,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway. .,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway.
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42
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Tanaka M, Chock PB. Oxidative Modifications of RNA and Its Potential Roles in Biosystem. Front Mol Biosci 2021; 8:685331. [PMID: 34055897 PMCID: PMC8149912 DOI: 10.3389/fmolb.2021.685331] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Elevated level of oxidized RNA was detected in vulnerable neurons in Alzheimer patients. Subsequently, several diseases and pathological conditions were reported to be associated with RNA oxidation. In addition to several oxidized derivatives, cross-linking and unique strand breaks are generated by RNA oxidation. With a premise that dysfunctional RNA mediated by oxidation is the pathogenetic molecular mechanism, intensive investigations have revealed the mechanism for translation errors, including premature termination, which gives rise to aberrant polypeptides. To this end, we and others revealed that mRNA oxidation could compromise its translational activity and fidelity. Under certain conditions, oxidized RNA can also induce several signaling pathways, to mediate inflammatory response and induce apoptosis. In this review, we focus on the oxidative modification of RNA and its resulting effect on protein synthesis as well as cell signaling. In addition, we will also discuss the potential roles of enzymatic oxidative modification of RNA in mediating cellular effects.
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Affiliation(s)
- Mikiei Tanaka
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - P Boon Chock
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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43
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Yip MCJ, Shao S. Detecting and Rescuing Stalled Ribosomes. Trends Biochem Sci 2021; 46:731-743. [PMID: 33966939 DOI: 10.1016/j.tibs.2021.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
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Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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44
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Kim J, Lee S, Kim H, Lee H, Seong KM, Youn H, Youn B. Autophagic Organelles in DNA Damage Response. Front Cell Dev Biol 2021; 9:668735. [PMID: 33912571 PMCID: PMC8072393 DOI: 10.3389/fcell.2021.668735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Autophagy is an important subcellular event engaged in the maintenance of cellular homeostasis via the degradation of cargo proteins and malfunctioning organelles. In response to cellular stresses, like nutrient deprivation, infection, and DNA damaging agents, autophagy is activated to reduce the damage and restore cellular homeostasis. One of the responses to cellular stresses is the DNA damage response (DDR), the intracellular pathway that senses and repairs damaged DNA. Proper regulation of these pathways is crucial for preventing diseases. The involvement of autophagy in the repair and elimination of DNA aberrations is essential for cell survival and recovery to normal conditions, highlighting the importance of autophagy in the resolution of cell fate. In this review, we summarized the latest information about autophagic recycling of mitochondria, endoplasmic reticulum (ER), and ribosomes (called mitophagy, ER-phagy, and ribophagy, respectively) in response to DNA damage. In addition, we have described the key events necessary for a comprehensive understanding of autophagy signaling networks. Finally, we have highlighted the importance of the autophagy activated by DDR and appropriate regulation of autophagic organelles, suggesting insights for future studies. Especially, DDR from DNA damaging agents including ionizing radiation (IR) or anti-cancer drugs, induces damage to subcellular organelles and autophagy is the key mechanism for removing impaired organelles.
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Affiliation(s)
- Jeongha Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Hyunwoo Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Haksoo Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Ki Moon Seong
- Laboratory of Low Dose Risk Assessment, National Radiation Emergency Medical Center, Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea.,Department of Biological Sciences, Pusan National University, Busan, South Korea
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45
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D'Orazio KN, Green R. Ribosome states signal RNA quality control. Mol Cell 2021; 81:1372-1383. [PMID: 33713598 PMCID: PMC8041214 DOI: 10.1016/j.molcel.2021.02.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Eukaryotic cells integrate multiple quality control (QC) responses during protein synthesis in the cytoplasm. These QC responses are signaled by slow or stalled elongating ribosomes. Depending on the nature of the delay, the signal may lead to translational repression, messenger RNA decay, ribosome rescue, and/or nascent protein degradation. Here, we discuss how the structure and composition of an elongating ribosome in a troubled state determine the downstream quality control pathway(s) that ensue. We highlight the intersecting pathways involved in RNA decay and the crosstalk that occurs between RNA decay and ribosome rescue.
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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46
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Moon SL, Morisaki T, Stasevich TJ, Parker R. Coupling of translation quality control and mRNA targeting to stress granules. J Cell Biol 2021; 219:151851. [PMID: 32520986 PMCID: PMC7401812 DOI: 10.1083/jcb.202004120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Stress granules are dynamic assemblies of proteins and nontranslating RNAs that form when translation is inhibited in response to diverse stresses. Defects in ubiquitin–proteasome system factors including valosin-containing protein (VCP) and the proteasome impact the kinetics of stress granule induction and dissolution as well as being implicated in neuropathogenesis. However, the impacts of dysregulated proteostasis on mRNA regulation and stress granules are not well understood. Using single mRNA imaging, we discovered ribosomes stall on some mRNAs during arsenite stress, and the release of transcripts from stalled ribosomes for their partitioning into stress granules requires the activities of VCP, components of the ribosome-associated quality control (RQC) complex, and the proteasome. This is an unexpected contribution of the RQC system in releasing mRNAs from translation under stress, thus identifying a new type of stress-activated RQC (saRQC) distinct from canonical RQC pathways in mRNA substrates, cellular context, and mRNA fate.
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Affiliation(s)
- Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI
| | - Tatsuya Morisaki
- Department of Biochemistry, Colorado State University, Fort Collins, CO
| | - Timothy J Stasevich
- Department of Biochemistry, Colorado State University, Fort Collins, CO.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO.,Howard Hughes Medical Institute, Chevy Chase, MD
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47
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Kumar S, Mohapatra T. Deciphering Epitranscriptome: Modification of mRNA Bases Provides a New Perspective for Post-transcriptional Regulation of Gene Expression. Front Cell Dev Biol 2021; 9:628415. [PMID: 33816473 PMCID: PMC8010680 DOI: 10.3389/fcell.2021.628415] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022] Open
Abstract
Gene regulation depends on dynamic and reversibly modifiable biological and chemical information in the epigenome/epitranscriptome. Accumulating evidence suggests that messenger RNAs (mRNAs) are generated in flashing bursts in the cells in a precisely regulated manner. However, the different aspects of the underlying mechanisms are not fully understood. Cellular RNAs are post-transcriptionally modified at the base level, which alters the metabolism of mRNA. The current understanding of epitranscriptome in the animal system is far ahead of that in plants. The accumulating evidence indicates that the epitranscriptomic changes play vital roles in developmental processes and stress responses. Besides being non-genetically encoded, they can be of reversible nature and involved in fine-tuning the expression of gene. However, different aspects of base modifications in mRNAs are far from adequate to assign the molecular basis/functions to the epitranscriptomic changes. Advances in the chemogenetic RNA-labeling and high-throughput next-generation sequencing techniques are enabling functional analysis of the epitranscriptomic modifications to reveal their roles in mRNA biology. Mapping of the common mRNA modifications, including N 6-methyladenosine (m6A), and 5-methylcytidine (m5C), have enabled the identification of other types of modifications, such as N 1-methyladenosine. Methylation of bases in a transcript dynamically regulates the processing, cellular export, translation, and stability of the mRNA; thereby influence the important biological and physiological processes. Here, we summarize the findings in the field of mRNA base modifications with special emphasis on m6A, m5C, and their roles in growth, development, and stress tolerance, which provide a new perspective for the regulation of gene expression through post-transcriptional modification. This review also addresses some of the scientific and technical issues in epitranscriptomic study, put forward the viewpoints to resolve the issues, and discusses the future perspectives of the research in this area.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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48
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Yan LL, Zaher HS. Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes. Mol Cell 2020; 81:614-628.e4. [PMID: 33338396 DOI: 10.1016/j.molcel.2020.11.033] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022]
Abstract
Stalling during translation triggers ribosome quality control (RQC) to maintain proteostasis. Recently, stalling has also been linked to the activation of integrated stress response (ISR) by Gcn2. How the two processes are coordinated is unclear. Here, we show that activation of RQC by Hel2 suppresses that of Gcn2. We further show that Hel2 and Gcn2 are activated by a similar set of agents that cause ribosome stalling, with maximal activation of Hel2 observed at a lower frequency of stalling. Interestingly, inactivation of one pathway was found to result in the overactivation of the other, suggesting that both are activated by the same signal of ribosome collisions. Notably, the processes do not appear to be in direct competition with each other; ISR prefers a vacant A site, whereas RQC displays no preference. Collectively, our findings provide important details about how multiple pathways that recognize stalled ribosomes coordinate to mount the appropriate response.
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Affiliation(s)
- Liewei L Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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49
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Skinner A, Yang C, Hincks K, Wang H, Resendiz MJE. Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo-7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA. Biopolymers 2020; 111:e23410. [PMID: 33216981 PMCID: PMC7780609 DOI: 10.1002/bip.23410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm ) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.
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Affiliation(s)
- Austin Skinner
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Chou‐Hsun Yang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Kazuki Hincks
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Haobin Wang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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50
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Martínez-Calvo M, Guerrini L, Rodríguez J, Álvarez-Puebla RA, Mascareñas JL. Surface-Enhanced Raman Scattering Detection of Nucleic Acids Exhibiting Sterically Accessible Guanines Using Ruthenium-Polypyridyl Reagents. J Phys Chem Lett 2020; 11:7218-7223. [PMID: 32787310 DOI: 10.1021/acs.jpclett.0c02148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, we report the application of surface-enhanced Raman scattering (SERS) spectroscopy as a rapid and practical tool for assessing the formation of coordinative adducts between nucleic acid guanines and ruthenium polypyridyl reagents. The technology provides a practical approach for the wash-free and quick identification of nucleic acid structures exhibiting sterically accessible guanines. This is demonstrated for the detection of a quadruplex-forming sequence present in the promoter region of the c-myc oncogene, which exhibits a nonpaired, reactive guanine at a flanking position of the G-quartets.
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Affiliation(s)
- Miguel Martínez-Calvo
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, Rúa Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
- Centro de Investigaciones Avanzadas (CICA), AE CICA-INIBIC, Departamento de Quı́mica, Facultade de Ciencias, Universidade da Coruña, Rúa As Carballeiras s/n, 15071 A Coruña, Galicia, Spain
| | - Luca Guerrini
- Universitat Rovira i Virgili, Departament de Quı́mica Fı́sica i Inorgànica, EmaS. Carrer de Marcel-lí Domingo s/n, 43007 Tarragona, Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, Rúa Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ramón A Álvarez-Puebla
- Universitat Rovira i Virgili, Departament de Quı́mica Fı́sica i Inorgànica, EmaS. Carrer de Marcel-lí Domingo s/n, 43007 Tarragona, Spain
- ICREA, Passeig Lluı́s Companys 23, 08010 Barcelona, Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, Rúa Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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