1
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Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024; 52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [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: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024] Open
Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
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Affiliation(s)
- Attila Horvath
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Yoshika Janapala
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Alice Cleynen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier, France
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The National Platelet Research and Referral Centre, The Australian National University, Canberra, ACT 2601, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia 4067, Australia
| | - Eduardo Eyras
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Centre for Computational Biomedical Sciences, The Australian National University, Canberra, ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
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Calabrese L, Ciandrini L, Cosentino Lagomarsino M. How total mRNA influences cell growth. Proc Natl Acad Sci U S A 2024; 121:e2400679121. [PMID: 38753514 PMCID: PMC11126920 DOI: 10.1073/pnas.2400679121] [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: 01/23/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
Experimental observations tracing back to the 1960s imply that ribosome quantities play a prominent role in determining a cell's growth. Nevertheless, in biologically relevant scenarios, growth can also be influenced by the levels of mRNA and RNA polymerase. Here, we construct a quantitative model of biosynthesis providing testable scenarios for these situations. The model explores a theoretically motivated regime where RNA polymerases compete for genes and ribosomes for transcripts and gives general expressions relating growth rate, mRNA concentrations, ribosome, and RNA polymerase levels. On general grounds, the model predicts how the fraction of ribosomes in the proteome depends on total mRNA concentration and inspects an underexplored regime in which the trade-off between transcript levels and ribosome abundances sets the cellular growth rate. In particular, we show that the model predicts and clarifies three important experimental observations, in budding yeast and Escherichia coli bacteria: i) that the growth-rate cost of unneeded protein expression can be affected by mRNA levels, ii) that resource optimization leads to decreasing trends in mRNA levels at slow growth, and iii) that ribosome allocation may increase, stay constant, or decrease, in response to transcription-inhibiting antibiotics. Since the data indicate that a regime of joint limitation may apply in physiological conditions and not only to perturbations, we speculate that this regime is likely self-imposed.
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Affiliation(s)
- Ludovico Calabrese
- IFOM-ETS–The AIRC Institute of Molecular Oncology, The Associazione Italiana di Ricerca sul Cancro (AIRC) Institute of Molecular Oncology, Milan20139, Italy
| | - Luca Ciandrini
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM, Montpellier, France
- Institut Universitaire de France
| | - Marco Cosentino Lagomarsino
- IFOM-ETS–The AIRC Institute of Molecular Oncology, The Associazione Italiana di Ricerca sul Cancro (AIRC) Institute of Molecular Oncology, Milan20139, Italy
- Dipartimento di Fisica, Universitá degli Studi di Milano, Milano20133, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Milano, Milano20133, Italy
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3
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Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
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Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
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Weber M, Sogues A, Yus E, Burgos R, Gallo C, Martínez S, Lluch‐Senar M, Serrano L. Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium. Mol Syst Biol 2023; 19:e11301. [PMID: 37642167 PMCID: PMC10568206 DOI: 10.15252/msb.202211301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Adrià Sogues
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martínez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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5
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Chevalier C, Dorignac J, Ibrahim Y, Choquet A, David A, Ripoll J, Rivals E, Geniet F, Walliser NO, Palmeri J, Parmeggiani A, Walter JC. Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model. PLoS Comput Biol 2023; 19:e1011522. [PMID: 37862386 PMCID: PMC10659217 DOI: 10.1371/journal.pcbi.1011522] [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: 03/31/2023] [Revised: 11/20/2023] [Accepted: 09/17/2023] [Indexed: 10/22/2023] Open
Abstract
Gene expression is the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique in order to obtain the kinetic rates. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.
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Affiliation(s)
- Carole Chevalier
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Jérôme Dorignac
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Yahaya Ibrahim
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- Department of Physics, Faculty of Natural and Applied Sciences, Umaru Musa Yar’adua University, Katsina, Nigeria
| | - Armelle Choquet
- Institut de Génétique Fonctionelle (IGF), Montpellier University, CNRS, Montpellier, France
| | - Alexandre David
- Institut de Génétique Fonctionelle (IGF), Montpellier University, CNRS, Montpellier, France
| | - Julie Ripoll
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Montpellier University, CNRS, Montpellier, France
| | - Eric Rivals
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Montpellier University, CNRS, Montpellier, France
| | - Frédéric Geniet
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Nils-Ole Walliser
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
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Yu P, Zhou S, Gao Y, Liang Y, Guo W, Wang DO, Ding S, Lin S, Wang J, Cun Y. Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:834-849. [PMID: 35952936 PMCID: PMC10787195 DOI: 10.1016/j.gpb.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Although the function of tRNAs in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.
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Affiliation(s)
- Peng Yu
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510080, China
| | - Siting Zhou
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Gao
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yu Liang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Dan Ohtan Wang
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuaiwen Ding
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China; RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China.
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7
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Höllerer S, Jeschek M. Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript. Nucleic Acids Res 2023; 51:2377-2396. [PMID: 36727459 PMCID: PMC10018350 DOI: 10.1093/nar/gkad040] [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: 06/17/2022] [Revised: 12/05/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023] Open
Abstract
Translation is a key determinant of gene expression and an important biotechnological engineering target. In bacteria, 5'-untranslated region (5'-UTR) and coding sequence (CDS) are well-known mRNA parts controlling translation and thus cellular protein levels. However, the complex interaction of 5'-UTR and CDS has so far only been studied for few sequences leading to non-generalisable and partly contradictory conclusions. Herein, we systematically assess the dynamic translation from over 1.2 million 5'-UTR-CDS pairs in Escherichia coli to investigate their collective effect using a new method for ultradeep sequence-function mapping. This allows us to disentangle and precisely quantify effects of various sequence determinants of translation. We find that 5'-UTR and CDS individually account for 53% and 20% of variance in translation, respectively, and show conclusively that, contrary to a common hypothesis, tRNA abundance does not explain expression changes between CDSs with different synonymous codons. Moreover, the obtained large-scale data provide clear experimental evidence for a base-pairing interaction between initiator tRNA and mRNA beyond the anticodon-codon interaction, an effect that is often masked for individual sequences and therefore inaccessible to low-throughput approaches. Our study highlights the indispensability of ultradeep sequence-function mapping to accurately determine the contribution of parts and phenomena involved in gene regulation.
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Affiliation(s)
- Simon Höllerer
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology – ETH Zurich, Basel CH-4058, Switzerland
| | - Markus Jeschek
- To whom correspondence should be addressed. Tel: +49 941 943 3161; Fax: +49 941 943 2403;
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8
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Fedorova AD, Tierney JA, Michel AM, Baranov PV. RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.168043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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9
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Mok A, Tunney R, Benegas G, Wallace EWJ, Lareau LF. choros: correction of sequence-based biases for accurate quantification of ribosome profiling data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529452. [PMID: 36865295 PMCID: PMC9980091 DOI: 10.1101/2023.02.21.529452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation lead to pervasive sequence artifacts that obscure translation dynamics. Widespread over- and under-representation of ribosome footprints can dominate local footprint densities and skew estimates of elongation rates by up to five fold. To address these biases and uncover true patterns of translation, we present choros, a computational method that models ribosome footprint distributions to provide bias-corrected footprint counts. choros uses negative binomial regression to accurately estimate two sets of parameters: (i) biological contributions from codon-specific translation elongation rates; and (ii) technical contributions from nuclease digestion and ligation efficiencies. We use these parameter estimates to generate bias correction factors that eliminate sequence artifacts. Applying choros to multiple ribosome profiling datasets, we are able to accurately quantify and attenuate ligation biases to provide more faithful measurements of ribosome distribution. We show that a pattern interpreted as pervasive ribosome pausing near the beginning of coding regions is likely to arise from technical biases. Incorporating choros into standard analysis pipelines will improve biological discovery from measurements of translation.
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Affiliation(s)
- Amanda Mok
- Center for Computational Biology, University of California, Berkeley
| | - Robert Tunney
- Center for Computational Biology, University of California, Berkeley
| | - Gonzalo Benegas
- Center for Computational Biology, University of California, Berkeley
| | | | - Liana F. Lareau
- Center for Computational Biology, University of California, Berkeley
- Department of Bioengineering, University of California, Berkeley
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10
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Flanagan K, Baradaran-Heravi A, Yin Q, Dao Duc K, Spradling AC, Greenblatt EJ. FMRP-dependent production of large dosage-sensitive proteins is highly conserved. Genetics 2022; 221:6613139. [PMID: 35731217 PMCID: PMC9339308 DOI: 10.1093/genetics/iyac094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
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Affiliation(s)
- Keegan Flanagan
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Qi Yin
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Ethan J Greenblatt
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
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11
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 PMCID: PMC9048916 DOI: 10.1093/plcell/koac056] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/04/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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12
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 DOI: 10.1093/plcell/koac056%jtheplantcell] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/28/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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13
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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14
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Yadav V, Ullah Irshad I, Kumar H, Sharma AK. Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data. Front Mol Biosci 2021; 8:688700. [PMID: 34262940 PMCID: PMC8274658 DOI: 10.3389/fmolb.2021.688700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to extract these rate parameters. Various methods have been developed in the past few years to measure translation-initiation and codon translation rates from ribosome profiling data. In the review, we provide a detailed analysis of the key methods employed to extract the translation rate parameters from ribosome profiling data. We further discuss how these approaches were used to decipher the role of various structural and sequence-based features of mRNA molecules in the regulation of gene expression. The utilization of these accurate rate parameters in computational modeling of protein synthesis may provide new insights into the kinetic control of the process of gene expression.
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Affiliation(s)
- Vandana Yadav
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | | | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology Jammu, Jammu, India
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15
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Relevance of 2'-O-Methylation and Pseudouridylation for the Malignant Melanoma. Cancers (Basel) 2021; 13:cancers13051167. [PMID: 33803145 PMCID: PMC7963185 DOI: 10.3390/cancers13051167] [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: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 01/23/2023] Open
Abstract
Simple Summary This study investigates the expression, the histological localization, and the influence of the factors involved in 2′-O-methylation and pseudouridylation on prognostic relevant markers, proliferation markers, overall survival, molecular immune surveillance and evasion mechanisms within the malignant melanoma. Statistically significant positive correlations to the expression of markers involved in cell proliferation were observed. The upregulation of the RNA modifying factors was of prognostic relevance in this tumor disease with a negative impact on the overall survival of melanoma patients. Furthermore, the factors involved in 2′-O-methylation and pseudouridylation were statistically significant negative correlated to the expression of human leukocyte antigen class I genes as well as of components of the antigen processing machinery. Abstract The two RNA modifications 2′-O-methylation and pseudouridylation occur on several RNA species including ribosomal RNAs leading to an increased translation as well as cell proliferation associated with distinct functions. Using malignant melanoma (MM) as a model system the proteins mediating these RNA modifications were for the first time analyzed by different bioinformatics tools and public available databases regarding their expression and histological localization. Next to this, the impact of these RNA-modifying factors on prognostic relevant processes and marker genes of malignant melanoma was investigated and correlated to immune surveillance and evasion strategies. The RNA modifying factors exerted statistically significant positive correlations to the expression of genes involved in cell proliferation and were statistically significant negative correlated to the expression of human leukocyte antigen class I genes as well as of components of the antigen processing machinery in malignant melanoma. Upregulation of the RNA modifying proteins was of prognostic relevance in this tumor disease with a negative impact on the overall survival of melanoma patients. Furthermore, the expression of known oncogenic miRs, which are induced in malignant melanoma, directly correlated to the expression of factors involved in these two RNA modifications.
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16
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do Couto Bordignon P, Pechmann S. Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling. FEBS J 2021; 288:4541-4559. [PMID: 33539640 DOI: 10.1111/febs.15748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo-seq) has revolutionized the study of translation by revealing many of its underlying mechanisms. However, equally many aspects of translation remain mysterious, in part also due to persisting challenges in the interpretation of data obtained from Ribo-seq experiments. Here, we show that some of the variability observed in Ribo-seq data has biological origins and reflects programmed heterogeneity of translation. Through a comparative analysis of Ribo-seq data from Saccharomyces cerevisiae, we systematically identify short 3-codon sequences that are differentially translated (DT) across mRNAs, that is, identical sequences that are translated sometimes fast and sometimes slowly beyond what can be attributed to variability between experiments. Remarkably, the thus identified DT sequences link to mechanisms known to regulate translation elongation and are enriched in genes important for protein and organelle biosynthesis. Our results thus highlight examples of translational heterogeneity that are encoded in the genomic sequences and tuned to optimizing cellular homeostasis. More generally, our work highlights the power of Ribo-seq to understand the complexities of translation regulation.
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