Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium

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• dc.contributor.author Weber, Marc
• dc.contributor.author Sogues, Adrià
• dc.contributor.author Yus, Eva
• dc.contributor.author Burgos, Raul
• dc.contributor.author Gallo López, Carolina, 1984-
• dc.contributor.author Martínez, Sira
• dc.contributor.author Lluch-Senar, Maria 1982-
• dc.contributor.author Serrano Pubull, Luis, 1982-
• dc.date.accessioned 2023-12-19T07:04:24Z
• dc.date.available 2023-12-19T07:04:24Z
• dc.date.issued 2023
• dc.description.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.
• dc.description.sponsorship We acknowledge the support of the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation to the EMBL partnership, and the Centro de Excelencia Severo Ochoa. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement no. 101020135 (LUNG‐BIOREPAIR) and 670216 (MYCOCHASSIS). ML‐S acknowledges the support from FEDER project from Instituto Carlos III (ISCIII, Acción Estratégica en Salud 2016) (reference CP16/00094). The proteomics analyses were performed in the CRG/UPF Proteomics Unit which is part of the Proteored, PRB3 and is supported by grant PT17/0019, of the PE I+D+i 2013‐2016, funded by ISCIII and ERDF. The authors would like to thank the CRG Genomics Unit for assistance with the design and sequencing of the RNA‐seq and ribosome profiling. We thank the Bukau lab (Heidelberg University) and in particular Carla Galmozzi for their help and assistance with the ribosome profiling technique. MW thanks Flomics Biotech S.L. for support during part of the research study.
• dc.format.mimetype application/pdf
• dc.identifier.citation 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 Oct 12;19(10):e11301. DOI: 10.15252/msb.202211301
• dc.identifier.doi http://dx.doi.org/10.15252/msb.202211301
• dc.identifier.issn 1744-4292
• dc.identifier.uri http://hdl.handle.net/10230/58589
• dc.language.iso eng
• dc.publisher EMBO Press
• dc.relation.ispartof Mol Syst Biol. 2023 Oct 12;19(10):e11301
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/670216
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/101020135
• dc.rights © 2023 The Authors. Published under the terms of the CC BY 4.0 license. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Mycoplasma pneumoniae
• dc.subject.keyword Data integration
• dc.subject.keyword Protein synthesis
• dc.subject.keyword Ribosome profiling
• dc.subject.keyword Translation efficiency
• dc.title Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion