1
|
Glauninger H, Bard JA, Wong Hickernell CJ, Airoldi EM, Li W, Singer RH, Paul S, Fei J, Sosnick TR, Wallace EWJ, Drummond DA. Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589678. [PMID: 38659805 PMCID: PMC11042329 DOI: 10.1101/2024.04.15.589678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.
Collapse
Affiliation(s)
- Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Jared A.M. Bard
- Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Edo M. Airoldi
- Fox School of Business and Management, Temple University, Philadelphia, PA, USA
| | - Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sneha Paul
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jingyi Fei
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - D. Allan Drummond
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
2
|
Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
Collapse
Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
| |
Collapse
|
3
|
Grove DJ, Russell PJ, Kearse MG. To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1833. [PMID: 38433101 DOI: 10.1002/wrna.1833] [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: 10/31/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.
Collapse
Affiliation(s)
- Daisy J Grove
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Paul J Russell
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G Kearse
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
4
|
Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [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: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
Collapse
Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
| |
Collapse
|
5
|
Gentry RC, Ide NA, Comunale VM, Hartwick EW, Kinz-Thompson CD, Gonzalez RL. The mechanism of mRNA activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567265. [PMID: 38014128 PMCID: PMC10680758 DOI: 10.1101/2023.11.15.567265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During translation initiation, messenger RNA molecules must be identified and activated for loading into a ribosome. In this rate-limiting step, the heterotrimeric protein eukaryotic initiation factor eIF4F must recognize and productively interact with the 7-methylguanosine cap at the 5' end of the messenger RNA and subsequently activate the message. Despite its fundamental, regulatory role in gene expression, the molecular events underlying cap recognition and messenger RNA activation remain mysterious. Here, we generate a unique, single-molecule fluorescence imaging system to interrogate the dynamics with which eIF4F discriminates productive and non-productive locations on full-length, native messenger RNA molecules. At the single-molecule level, we observe stochastic sampling of eIF4F along the length of the messenger RNA and identify allosteric communication between the eIF4F subunits which ultimately drive cap-recognition and subsequent activation of the message. Our experiments uncover novel functions for each subunit of eIF4F and we conclude by presenting a model for messenger RNA activation which precisely defines the composition of the activated message. This model provides a general framework for understanding how messenger RNA molecules may be discriminated from one another, and how other RNA-binding proteins may control the efficiency of translation initiation.
Collapse
Affiliation(s)
- Riley C Gentry
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nicholas A Ide
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: BioChemistry Krios Electron Microscopy Facility, Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Colin D Kinz-Thompson
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: Department of Chemistry, Rutgers University-Newark, Newark, NJ 07102
| | | |
Collapse
|
6
|
Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. Nat Struct Mol Biol 2023; 30:1816-1825. [PMID: 37957305 DOI: 10.1038/s41594-023-01119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. Start codon-associated ribosomal frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra that are unannotated in the human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational 'noise' in nutrient stress adaptation.
Collapse
Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Longfei Jia
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
7
|
Livingston NM, Kwon J, Valera O, Saba JA, Sinha NK, Reddy P, Nelson B, Wolfe C, Ha T, Green R, Liu J, Wu B. Bursting translation on single mRNAs in live cells. Mol Cell 2023; 83:2276-2289.e11. [PMID: 37329884 PMCID: PMC10330622 DOI: 10.1016/j.molcel.2023.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/27/2023] [Accepted: 05/14/2023] [Indexed: 06/19/2023]
Abstract
Stochasticity has emerged as a mechanism of gene regulation. Much of this so-called "noise" has been attributed to bursting transcription. Although bursting transcription has been studied extensively, the role of stochasticity in translation has not been fully investigated due to the lack of enabling imaging technology. In this study, we developed techniques to track single mRNAs and their translation in live cells for hours, allowing the measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics and found that, like transcription, translation is not a constitutive process but instead cycles between inactive and active states, or "bursts." However, unlike transcription, which is largely frequency-modulated, complex structures in the 5'-untranslated region alter burst amplitudes. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single-molecule imaging with stochastic modeling to quantitatively determine the kinetic parameters of translational bursting.
Collapse
Affiliation(s)
- Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiwoong Kwon
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oliver Valera
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pranav Reddy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clara Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, 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
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
8
|
Prabhakar A, Pavlov MY, Zhang J, Indrisiunaite G, Wang J, Lawson M, Ehrenberg M, Puglisi JD. Dynamics of release factor recycling during translation termination in bacteria. Nucleic Acids Res 2023; 51:5774-5790. [PMID: 37102635 PMCID: PMC10287982 DOI: 10.1093/nar/gkad286] [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: 07/02/2022] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
In bacteria, release of newly synthesized proteins from ribosomes during translation termination is catalyzed by class-I release factors (RFs) RF1 or RF2, reading UAA and UAG or UAA and UGA codons, respectively. Class-I RFs are recycled from the post-termination ribosome by a class-II RF, the GTPase RF3, which accelerates ribosome intersubunit rotation and class-I RF dissociation. How conformational states of the ribosome are coupled to the binding and dissociation of the RFs remains unclear and the importance of ribosome-catalyzed guanine nucleotide exchange on RF3 for RF3 recycling in vivo has been disputed. Here, we profile these molecular events using a single-molecule fluorescence assay to clarify the timings of RF3 binding and ribosome intersubunit rotation that trigger class-I RF dissociation, GTP hydrolysis, and RF3 dissociation. These findings in conjunction with quantitative modeling of intracellular termination flows reveal rapid ribosome-dependent guanine nucleotide exchange to be crucial for RF3 action in vivo.
Collapse
Affiliation(s)
- Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Program in Biophysics, Stanford University, Stanford, CA 94305-5126, USA
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Gabriele Indrisiunaite
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Michael R Lawson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| |
Collapse
|
9
|
Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
Collapse
Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
10
|
Hang R, Xu Y, Wang X, Hu H, Flynn N, You C, Chen X. Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation. Proc Natl Acad Sci U S A 2023; 120:e2301081120. [PMID: 37011204 PMCID: PMC10104536 DOI: 10.1073/pnas.2301081120] [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: 01/24/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023] Open
Abstract
Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S ribosomal RNA (rRNA) 3' end maturation during late-stage 40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the genome-wide effects of eIF5B have not been studied at the single-nucleotide resolution in any organism, and 18S rRNA 3' end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3' end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3' end maturation or metabolism. We quantitatively defined processing hotspots and identified adenylation as the prevalent nontemplated RNA addition at the 3' ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNA interference to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3' portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions and were not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late 40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, messenger RNA (mRNA) translation initiation, and siRNA biogenesis in plants.
Collapse
Affiliation(s)
- Runlai Hang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Xufeng Wang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Hao Hu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Nora Flynn
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Chenjiang You
- College of Life Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong510642, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing100871, China
| |
Collapse
|
11
|
Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528768. [PMID: 36824937 PMCID: PMC9949036 DOI: 10.1101/2023.02.15.528768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. The start codon-associated ribosome frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra unannotated from human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational "noise" in nutrient stress adaptation.
Collapse
|
12
|
Single-molecule visualization of mRNA circularization during translation. Exp Mol Med 2023; 55:283-289. [PMID: 36720916 PMCID: PMC9981743 DOI: 10.1038/s12276-023-00933-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E-eIF4G-PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional "functional circularization" theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
Collapse
|
13
|
Wang J, Shin BS, Alvarado C, Kim JR, Bohlen J, Dever TE, Puglisi JD. Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell 2022; 185:4474-4487.e17. [PMID: 36334590 PMCID: PMC9691599 DOI: 10.1016/j.cell.2022.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 08/22/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
How the eukaryotic 43S preinitiation complex scans along the 5' untranslated region (5' UTR) of a capped mRNA to locate the correct start codon remains elusive. Here, we directly track yeast 43S-mRNA binding, scanning, and 60S subunit joining by real-time single-molecule fluorescence spectroscopy. 43S engagement with mRNA occurs through a slow, ATP-dependent process driven by multiple initiation factors including the helicase eIF4A. Once engaged, 43S scanning occurs rapidly and directionally at ∼100 nucleotides per second, independent of multiple cycles of ATP hydrolysis by RNA helicases post ribosomal loading. Scanning ribosomes can proceed through RNA secondary structures, but 5' UTR hairpin sequences near start codons drive scanning ribosomes at start codons backward in the 5' direction, requiring rescanning to arrive once more at a start codon. Direct observation of scanning ribosomes provides a mechanistic framework for translational regulation by 5' UTR structures and upstream near-cognate start codons.
Collapse
Affiliation(s)
- Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Alvarado
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France; University of Paris, Imagine Institute, Paris, France
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
14
|
Çetin B, O’Leary SE. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res 2022; 50:8240-8261. [PMID: 35871304 PMCID: PMC9371892 DOI: 10.1093/nar/gkac631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
mRNA 5′ cap recognition by eIF4F is a key element of eukaryotic translational control. Kinetic differences in eIF4F–mRNA interactions have long been proposed to mediate translation-efficiency differences between mRNAs, and recent transcriptome-wide studies have revealed significant heterogeneity in eIF4F engagement with differentially-translated mRNAs. However, detailed kinetic information exists only for eIF4F interactions with short model RNAs. We developed and applied single-molecule fluorescence approaches to directly observe real-time Saccharomyces cerevisiae eIF4F subunit interactions with full-length polyadenylated mRNAs. We found that eIF4E–mRNA association rates linearly anticorrelate with mRNA length. eIF4G–mRNA interaction accelerates eIF4E–mRNA association in proportion to mRNA length, as does an eIF4F-independent activity of eIF4A, though cap-proximal secondary structure still plays an important role in defining the final association rates. eIF4F–mRNA interactions remained dominated by effects of eIF4G, but were modulated to different extents for different mRNAs by the presence of eIF4A and ATP. We also found that eIF4A-catalyzed ATP hydrolysis ejects eIF4E, and likely eIF4E•eIF4G from the mRNA after initial eIF4F•mRNA complex formation, suggesting a mechanism to prepare the mRNA 5′ end for ribosome recruitment. Our results support a role for mRNA-specific, factor-driven eIF4F association rates in kinetically controlling translation.
Collapse
Affiliation(s)
- Burak Çetin
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
| | - Seán E O’Leary
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
- Department of Biochemistry, University of California Riverside , Riverside, CA 92521, USA
| |
Collapse
|
15
|
Lapointe CP, Grosely R, Sokabe M, Alvarado C, Wang J, Montabana E, Villa N, Shin BS, Dever TE, Fraser CS, Fernández IS, Puglisi JD. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Nature 2022; 607:185-190. [PMID: 35732735 PMCID: PMC9728550 DOI: 10.1038/s41586-022-04858-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
Collapse
Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Carlos Alvarado
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth Montabana
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nancy Villa
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Byung-Sik Shin
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Thomas E Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Israel S Fernández
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
16
|
Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E. Role of aIF5B in archaeal translation initiation. Nucleic Acids Res 2022; 50:6532-6548. [PMID: 35694843 PMCID: PMC9226500 DOI: 10.1093/nar/gkac490] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/22/2023] Open
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
Collapse
Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, PMC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| |
Collapse
|
17
|
Zheng T, Zhang Q, Peng Z, Li D, Wu X, Liu Y, Li P, Zhang J, Du G. Metabolite-based cell sorting workflow for identifying microbes producing carbonyls in tobacco leaves. Appl Microbiol Biotechnol 2022; 106:4199-4209. [PMID: 35599257 DOI: 10.1007/s00253-022-11982-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
Carbonyl compounds represented by aldehydes and ketones make an important contribution to the flavor of tobacco. Since most carbonyl compounds are produced by microbes during tobacco fermentation, identifying their producers is important to improve the quality of tobacco. Here, we created an efficient workflow that combines metabolite labeling with fluorescence-activated cell sorting (ML-FACS), 16S rRNA gene sequencing, and microbial culture to identify the microbes that produce aldehydes or ketones in fermented cigar tobacco leaves (FCTL). Microbes were labeled with a specific fluorescent dye (cyanine5 hydrazide) and separated by flow cytometry. Subsequently, the sorted microbes were identified and cultured under laboratory conditions. Four genera, Acinetobacter, Sphingomonas, Solibacillus, and Lysinibacillus, were identified as the main carbonyl compound-producing microbes in FCTL. In addition, these microorganisms could produce flavor-related aldehydes and ketones in a simple synthetic medium, such as benzaldehyde, phenylacetaldehyde, 4-hydroxy-3-ethoxy-benzaldehyde, and 3,5,5-trimethyl-2-cyclohexene-1-one. On the whole, this research has developed a new method to quickly isolate and identify microorganisms that produce aldehydes or ketones from complex microbial communities. ML-FACS would also be used to identify other compound-producing microorganisms in other systems. KEY POINTS: • An approach was developed to identify target microbes in complex communities. • Microbes that produce aldehyde/ketone flavor compounds in fermented cigar tobacco leaves were identified. • Functional microbes that produce aldehyde/ketone flavor compounds from the native environment were captured in pure cultures.
Collapse
Affiliation(s)
- Tianfei Zheng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Qianying Zhang
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Zheng Peng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Dongliang Li
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Xinying Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Yi Liu
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Pinhe Li
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Juan Zhang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
18
|
Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N. Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. Nucleic Acids Res 2022; 50:5282-5298. [PMID: 35489072 PMCID: PMC9122606 DOI: 10.1093/nar/gkac283] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 01/10/2023] Open
Abstract
Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2–GTP–Met-tRNAiMet and eIF3. The ‘open’ 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The ‘closed’ form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.
Collapse
Affiliation(s)
- Sung-Hui Yi
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Valentyn Petrychenko
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Jan Erik Schliep
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Ashwin Chari
- Research Group Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Sarah Adio
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August University of Göttingen, Göttingen 37077, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| |
Collapse
|
19
|
Abstract
Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;
| |
Collapse
|
20
|
Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| |
Collapse
|
21
|
Jobava R, Mao Y, Guan BJ, Hu D, Krokowski D, Chen CW, Shu XE, Chukwurah E, Wu J, Gao Z, Zagore LL, Merrick WC, Trifunovic A, Hsieh AC, Valadkhan S, Zhang Y, Qi X, Jankowsky E, Topisirovic I, Licatalosi DD, Qian SB, Hatzoglou M. Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. Mol Cell 2021; 81:4191-4208.e8. [PMID: 34686314 PMCID: PMC8559772 DOI: 10.1016/j.molcel.2021.09.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022]
Abstract
To survive, mammalian cells must adapt to environmental challenges. While the cellular response to mild stress has been widely studied, how cells respond to severe stress remains unclear. We show here that under severe hyperosmotic stress, cells enter a transient hibernation-like state in anticipation of recovery. We demonstrate this adaptive pausing response (APR) is a coordinated cellular response that limits ATP supply and consumption through mitochondrial fragmentation and widespread pausing of mRNA translation. This pausing is accomplished by ribosome stalling at translation initiation codons, which keeps mRNAs poised to resume translation upon recovery. We further show that recovery from severe stress involves ISR (integrated stress response) signaling that permits cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. Our findings indicate that cells can respond to severe stress via a hibernation-like mechanism that preserves vital elements of cellular function under harsh environmental conditions.
Collapse
Affiliation(s)
- Raul Jobava
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Dawid Krokowski
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA; Department of Molecular Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin 20-033, Poland
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Evelyn Chukwurah
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | | | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, CWRU, Cleveland, OH 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, CWRU, Cleveland, OH 44106, USA
| | - Xin Qi
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Donny D Licatalosi
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA.
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA.
| |
Collapse
|
22
|
Chukka PAR, Wetmore SD, Thakor N. Established and Emerging Regulatory Roles of Eukaryotic Translation Initiation Factor 5B (eIF5B). Front Genet 2021; 12:737433. [PMID: 34512736 PMCID: PMC8430213 DOI: 10.3389/fgene.2021.737433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022] Open
Abstract
Translational control (TC) is one the crucial steps that dictate gene expression and alter the outcome of physiological process like programmed cell death, metabolism, and proliferation in a eukaryotic cell. TC occurs mainly at the translation initiation stage. The initiation factor eIF5B tightly regulates global translation initiation and facilitates the expression of a subset of proteins involved in proliferation, inhibition of apoptosis, and immunosuppression under stress conditions. eIF5B enhances the expression of these survival proteins to allow cancer cells to metastasize and resist chemotherapy. Using eIF5B as a biomarker or drug target could help with diagnosis and improved prognosis, respectively. To achieve these goals, it is crucial to understand the role of eIF5B in translational regulation. This review recapitulates eIF5B's regulatory roles in the translation initiation of viral mRNA as well as the cellular mRNAs in cancer and stressed eukaryotic cells.
Collapse
Affiliation(s)
- Prakash Amruth Raj Chukka
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada.,Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre of Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, Lethbridge, AB, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada.,Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre of Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, Lethbridge, AB, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.,Department of Neuroscience, Canadian Centre for Behavioral Neuroscience (CCBN), University of Lethbridge, Lethbridge, AB, Canada.,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
23
|
Lawson MR, Lessen LN, Wang J, Prabhakar A, Corsepius NC, Green R, Puglisi JD. Mechanisms that ensure speed and fidelity in eukaryotic translation termination. Science 2021; 373:876-882. [PMID: 34413231 PMCID: PMC9017434 DOI: 10.1126/science.abi7801] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/07/2021] [Indexed: 11/02/2022]
Abstract
Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bound together to recognize stop codons rapidly and elicit termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.
Collapse
Affiliation(s)
- Michael R Lawson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura N Lessen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Prabhakar
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas C Corsepius
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
24
|
Zheng X, Su H, Wang L, Yao R, Ma Y, Bai L, Wang Y, Guo X, Wang Z. Phosphoproteomics Analysis Reveals a Pivotal Mechanism Related to Amino Acid Signals in Goat Fetal Fibroblast. Front Vet Sci 2021; 8:685548. [PMID: 34414225 PMCID: PMC8370256 DOI: 10.3389/fvets.2021.685548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/05/2021] [Indexed: 11/25/2022] Open
Abstract
In addition to serving as the building blocks for protein synthesis, amino acids serve as critical signaling molecules in cells. However, the mechanism through which amino acid signals are sensed in cells is not yet fully understood. This study examined differences in the phosphorylation levels of proteins in response to amino acid signals in Cashmere goat fetal fibroblasts (GFb). Amino acid deficiency was found to induce autophagy and attenuate mammalian/mechanistic target of rapamycin complex (mTORC1)/Unc-51-like autophagy activating kinase 1 (ULK1) signaling in GFb cells. A total of 144 phosphosites on 102 proteins positively associated with amino acid signaling were screened using phosphorylation-based proteomics analysis. The mitogen-activated protein kinase (MAPK) signaling pathway was found to play a potentially important role in the interaction network involved in the response to amino acid signals, according to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and MAPK1/3 may serve as a central hub for the entire network. Motif analysis identified three master motifs, xxx_S_Pxx, xxx_S_xxE, and xxx_S_xDx, which were centered on those phosphosites at which phosphorylation was positively regulated by amino acid signaling. Additionally, the phosphorylation levels of three membrane proteins, the zinc transporter SLC39A7, the sodium-dependent neutral amino acid transporters SLC1A5 and SLC38A7, and three translation initiation factors, eukaryotic initiation factor (eIF)5B, eIF4G, and eIF3C, were positively regulated by amino acid signals. These pivotal proteins were added to currently known signaling pathways to generate a novel model of the network pathways associated with amino acid signals. Finally, the phosphorylation levels of threonine 203 and tyrosine 205 on MAPK3 in response to amino acid signals were examined by western blot analysis, and the results were consistent with the data from the phosphoproteomics analysis. The findings of this study provide new evidence and insights into the precise mechanism through which amino acid signals are sensed and conducted in Cashmere goat fetal fibroblasts.
Collapse
Affiliation(s)
- Xu Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Clinical Laboratory, The Hulunbuir People's Hospital, Hailar, China
| | - Huimin Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Liping Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ruiyuan Yao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuze Ma
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Linfeng Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xudong Guo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Zhigang Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| |
Collapse
|
25
|
Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN. DDX3 depletion represses translation of mRNAs with complex 5' UTRs. Nucleic Acids Res 2021; 49:5336-5350. [PMID: 33905506 PMCID: PMC8136831 DOI: 10.1093/nar/gkab287] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
DDX3 is an RNA chaperone of the DEAD-box family that regulates translation. Ded1, the yeast ortholog of DDX3, is a global regulator of translation, whereas DDX3 is thought to preferentially affect a subset of mRNAs. However, the set of mRNAs that are regulated by DDX3 are unknown, along with the relationship between DDX3 binding and activity. Here, we use ribosome profiling, RNA-seq, and PAR-CLIP to define the set of mRNAs that are regulated by DDX3 in human cells. We find that while DDX3 binds highly expressed mRNAs, depletion of DDX3 particularly affects the translation of a small subset of the transcriptome. We further find that DDX3 binds a site on helix 16 of the human ribosomal rRNA, placing it immediately adjacent to the mRNA entry channel. Translation changes caused by depleting DDX3 levels or expressing an inactive point mutation are different, consistent with different association of these genetic variant types with disease. Taken together, this work defines the subset of the transcriptome that is responsive to DDX3 inhibition, with relevance for basic biology and disease states where DDX3 is altered.
Collapse
Affiliation(s)
- Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karol J Rogowski
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Kevin Wilkins
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Malvika Tejura
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bao Thai
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jacek Krol
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.,IRI Life Sciences, Institut für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
26
|
Alghoul F, Laure S, Eriani G, Martin F. Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition. eLife 2021; 10:e66369. [PMID: 34076576 PMCID: PMC8172242 DOI: 10.7554/elife.66369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
Collapse
Affiliation(s)
- Fatima Alghoul
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Schaeffer Laure
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| |
Collapse
|
27
|
Feng XA, Poyton MF, Ha T. Multicolor single-molecule FRET for DNA and RNA processes. Curr Opin Struct Biol 2021; 70:26-33. [PMID: 33894656 DOI: 10.1016/j.sbi.2021.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 12/31/2022]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a useful tool for observing the dynamics of protein-nucleic acid interactions. Although most smFRET measurements have used two fluorophores, multicolor smFRET measurements using more than two fluorophores offer more information about how protein-nucleic acid complexes dynamically move, assemble, and disassemble. Multicolor smFRET experiments include three or more fluorophores and at least one donor-acceptor pair. This review highlights how multicolor smFRET is being used to probe the dynamics of three different classes of biochemical processes-protein-DNA interactions, chromatin remodeling, and protein translation.
Collapse
Affiliation(s)
- Xinyu A Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew F Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
| |
Collapse
|
28
|
Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021; 118:e2017715118. [PMID: 33479166 PMCID: PMC8017934 DOI: 10.1073/pnas.2017715118] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
Collapse
Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
| |
Collapse
|
29
|
Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021. [PMID: 33479166 DOI: 10.1101/2020.08.20.259770] [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] [Indexed: 05/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
Collapse
Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
| |
Collapse
|
30
|
Dong L, Mao Y, Zhou A, Liu XM, Zhou J, Wan J, Qian SB. Relaxed initiation pausing of ribosomes drives oncogenic translation. SCIENCE ADVANCES 2021; 7:7/8/eabd6927. [PMID: 33597240 PMCID: PMC7888950 DOI: 10.1126/sciadv.abd6927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/30/2020] [Indexed: 05/13/2023]
Abstract
Translation is a crucial process in cancer development and progression. Many oncogenic signaling pathways target the translation initiation stage to satisfy the increased anabolic demands of cancer cells. Using quantitative profiling of initiating ribosomes, we found that ribosomal pausing at the start codon serves as a "brake" to restrain the translational output. In response to oncogenic RAS signaling, the initiation pausing relaxes and contributes to the increased translational flux. Intriguingly, messenger RNA (mRNA) m6A modification in the vicinity of start codons influences the behavior of initiating ribosomes. Under oncogenic RAS signaling, the reduced mRNA methylation leads to relaxed initiation pausing, thereby promoting malignant transformation and tumor growth. Restored initiation pausing by inhibiting m6A demethylases suppresses RAS-mediated oncogenic translation and subsequent tumorigenesis. Our findings unveil a paradigm of translational control that is co-opted by RAS mutant cancer cells to drive malignant phenotypes.
Collapse
Affiliation(s)
- Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Aidong Zhou
- Department of Cell Biology, Southern Medical University, Guangzhou 510515, China
| | - Xiao-Min Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jun Zhou
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
31
|
Minnee E, Faller WJ. Translation initiation and its relevance in colorectal cancer. FEBS J 2021; 288:6635-6651. [PMID: 33382175 PMCID: PMC9291299 DOI: 10.1111/febs.15690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 01/08/2023]
Abstract
Protein synthesis is one of the most essential processes in every kingdom of life, and its dysregulation is a known driving force in cancer development. Multiple signaling pathways converge on the translation initiation machinery, and this plays a crucial role in regulating differential gene expression. In colorectal cancer, dysregulation of initiation results in translational reprogramming, which promotes the selective translation of mRNAs required for many oncogenic processes. The majority of upstream mutations found in colorectal cancer, including alterations in the WNT, MAPK, and PI3K\AKT pathways, have been demonstrated to play a significant role in translational reprogramming. Many translation initiation factors are also known to be dysregulated, resulting in translational reprogramming during tumor initiation and/or maintenance. In this review, we outline the role of translational reprogramming that occurs during colorectal cancer development and progression and highlight some of the most critical factors affecting the etiology of this disease.
Collapse
Affiliation(s)
- Emma Minnee
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - William James Faller
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
32
|
Wang J, Wang J, Shin BS, Kim JR, Dever TE, Puglisi JD, Fernández IS. Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Nat Commun 2020; 11:5003. [PMID: 33024099 PMCID: PMC7538418 DOI: 10.1038/s41467-020-18829-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/16/2020] [Indexed: 11/09/2022] Open
Abstract
Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.
Collapse
Affiliation(s)
- Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA.
| |
Collapse
|
33
|
Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
Collapse
Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
| |
Collapse
|
34
|
Schmitt E, Coureux PD, Kazan R, Bourgeois G, Lazennec-Schurdevin C, Mechulam Y. Recent Advances in Archaeal Translation Initiation. Front Microbiol 2020; 11:584152. [PMID: 33072057 PMCID: PMC7531240 DOI: 10.3389/fmicb.2020.584152] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed. However, even if the general principles are the same in the three domains of life, the molecular mechanisms are different in bacteria, eukaryotes, and archaea and may also vary depending on the mRNA. Because TI mechanisms have evolved lately, their studies bring important information about the evolutionary relationships between extant organisms. In this context, recent structural data on ribosomal complexes and genome-wide studies are particularly valuable. This review focuses on archaeal translation initiation highlighting its relationships with either the eukaryotic or the bacterial world. Eukaryotic features of the archaeal small ribosomal subunit are presented. Ribosome evolution and TI mechanisms diversity in archaeal branches are discussed. Next, the use of leaderless mRNAs and that of leadered mRNAs having Shine-Dalgarno sequences is analyzed. Finally, the current knowledge on TI mechanisms of SD-leadered and leaderless mRNAs is detailed.
Collapse
Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| |
Collapse
|
35
|
Bacic L, Sabantsev A, Deindl S. Recent advances in single-molecule fluorescence microscopy render structural biology dynamic. Curr Opin Struct Biol 2020; 65:61-68. [PMID: 32634693 DOI: 10.1016/j.sbi.2020.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 01/30/2023]
Abstract
Single-molecule fluorescence microscopy has long been appreciated as a powerful tool to study the structural dynamics that enable biological function of macromolecules. Recent years have witnessed the development of more complex single-molecule fluorescence techniques as well as powerful combinations with structural approaches to obtain mechanistic insights into the workings of various molecular machines and protein complexes. In this review, we highlight these developments that together bring us one step closer to a dynamic understanding of biological processes in atomic details.
Collapse
Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
36
|
Ghosh A, Shcherbik N. Effects of Oxidative Stress on Protein Translation: Implications for Cardiovascular Diseases. Int J Mol Sci 2020; 21:E2661. [PMID: 32290431 PMCID: PMC7215667 DOI: 10.3390/ijms21082661] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are a group of disorders that affect the heart and blood vessels. Due to their multifactorial nature and wide variation, CVDs are the leading cause of death worldwide. Understanding the molecular alterations leading to the development of heart and vessel pathologies is crucial for successfully treating and preventing CVDs. One of the causative factors of CVD etiology and progression is acute oxidative stress, a toxic condition characterized by elevated intracellular levels of reactive oxygen species (ROS). Left unabated, ROS can damage virtually any cellular component and affect essential biological processes, including protein synthesis. Defective or insufficient protein translation results in production of faulty protein products and disturbances of protein homeostasis, thus promoting pathologies. The relationships between translational dysregulation, ROS, and cardiovascular disorders will be examined in this review.
Collapse
Affiliation(s)
- Arnab Ghosh
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| |
Collapse
|
37
|
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep 2020; 31:107497. [PMID: 32268096 PMCID: PMC7166083 DOI: 10.1016/j.celrep.2020.03.061] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/17/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022] Open
Abstract
In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
Collapse
MESH Headings
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Animals
- Codon, Initiator/genetics
- Codon, Initiator/ultrastructure
- Cryoelectron Microscopy/methods
- Enhancer Elements, Genetic/genetics
- Eukaryotic Initiation Factor-1/genetics
- Eukaryotic Initiation Factor-1/metabolism
- Eukaryotic Initiation Factor-2/genetics
- Eukaryotic Initiation Factor-2/metabolism
- Eukaryotic Initiation Factor-3/genetics
- Eukaryotic Initiation Factor-3/metabolism
- Eukaryotic Initiation Factors/metabolism
- Eukaryotic Initiation Factors/ultrastructure
- Humans
- Mice
- Peptide Chain Initiation, Translational
- Protein Biosynthesis
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Transfer/metabolism
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Transcription Initiation, Genetic/physiology
- beta-Globins/genetics
- beta-Globins/ultrastructure
Collapse
Affiliation(s)
- Angelita Simonetti
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France
| | - Ewelina Guca
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Anthony Bochler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France; INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Lauriane Kuhn
- Proteomic Platform Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Yaser Hashem
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.
| |
Collapse
|
38
|
Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet 2020; 21:25. [PMID: 32138667 PMCID: PMC7059407 DOI: 10.1186/s12863-020-0828-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/19/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.
Collapse
Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Andrew E Firth
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| |
Collapse
|
39
|
Long-range interdomain communications in eIF5B regulate GTP hydrolysis and translation initiation. Proc Natl Acad Sci U S A 2020; 117:1429-1437. [PMID: 31900355 PMCID: PMC6983393 DOI: 10.1073/pnas.1916436117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Translation is a key regulatory step in the control of gene expression. The first stage of translation, initiation, establishes the foundation for the sequential synthesis of a protein. In eukaryotes, 2 GTP-regulated checkpoints ensure the efficiency and fidelity of translation initiation. The GTPase eIF5B is responsible for the correct functioning of the second checkpoint. Molecular interactions of eIF5B with other correctly assembled components on the ribosome lead to GTP hydrolysis that allows the machinery of protein production to transition from initiation into elongation. Here, we show how a highly conserved stretch of residues in eIF5B, identified using electron cryomicroscopy, coordinates the gating into elongation, underscoring the importance of modular architecture in translation factors to sense and communicate ribosomal states. Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of protein factors and 2 GTP-regulated steps. The GTPase eIF5B gates progression to elongation during the second GTP-regulated step. Using electron cryomicroscopy (cryo-EM), we imaged an in vitro initiation reaction which is set up with purified yeast components and designed to stall with eIF5B and a nonhydrolyzable GTP analog. A high-resolution reconstruction of a “dead-end” intermediate at 3.6 Å allowed us to visualize eIF5B in its ribosome-bound conformation. We identified a stretch of residues in eIF5B, located close to the γ-phosphate of GTP and centered around the universally conserved tyrosine 837 (Saccharomyces cerevisiae numbering), that contacts the catalytic histidine of eIF5B (H480). Site-directed mutagenesis confirmed the essential role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initiation both in vitro and in vivo. Our results illustrate how eIF5B transmits the presence of a properly delivered initiator aminoacyl-tRNA at the P site to the distant GTPase center through interdomain communications and underscore the importance of the multidomain architecture in translation factors to sense and communicate ribosomal states.
Collapse
|
40
|
Neupane R, Pisareva VP, Rodriguez CF, Pisarev AV, Fernández IS. A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate. eLife 2020; 9:54575. [PMID: 32286223 PMCID: PMC7190351 DOI: 10.7554/elife.54575] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/13/2020] [Indexed: 01/21/2023] Open
Abstract
Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called Internal Ribosomal Entry Sites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs.
Collapse
Affiliation(s)
- Ritam Neupane
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States,Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| | - Vera P Pisareva
- Department of Cell Biology, SUNY Downstate Medical CenterBrooklynUnited States
| | - Carlos F Rodriguez
- Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO)MadridSpain
| | - Andrey V Pisarev
- Department of Cell Biology, SUNY Downstate Medical CenterBrooklynUnited States
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| |
Collapse
|