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Decoding stoichiometric protein synthesis in E. coli through translation rate parameters
E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E. coli. One of the prominent examples in this conte...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542608/ https://www.ncbi.nlm.nih.gov/pubmed/37789867 http://dx.doi.org/10.1016/j.bpr.2023.100131 |
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author | Irshad, Inayat Ullah Sharma, Ajeet K. |
author_facet | Irshad, Inayat Ullah Sharma, Ajeet K. |
author_sort | Irshad, Inayat Ullah |
collection | PubMed |
description | E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E. coli. One of the prominent examples in this context is the proportional synthesis in multiprotein complexes where all of their obligate subunits are produced in proportion to their stoichiometry. In this work, by combining the next-generation sequencing data with the stochastic simulations of protein synthesis, we explain the origin of proportional protein synthesis in multicomponent complexes. We find that the estimated initiation rates for the translation of all subunits in those complexes are proportional to their stoichiometry. This constraint on protein synthesis kinetics enforces proportional protein synthesis without requiring any feedback mechanism. We also find that the translation initiation rates in E. coli are influenced by the coding sequence length and the enrichment of A and C nucleotides near the start codon. Thus, this study rationalizes the role of conserved and nonrandom features of genes in regulating the translation kinetics and unravels a key principle of the regulation of protein synthesis. |
format | Online Article Text |
id | pubmed-10542608 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-105426082023-10-03 Decoding stoichiometric protein synthesis in E. coli through translation rate parameters Irshad, Inayat Ullah Sharma, Ajeet K. Biophys Rep (N Y) Article E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E. coli. One of the prominent examples in this context is the proportional synthesis in multiprotein complexes where all of their obligate subunits are produced in proportion to their stoichiometry. In this work, by combining the next-generation sequencing data with the stochastic simulations of protein synthesis, we explain the origin of proportional protein synthesis in multicomponent complexes. We find that the estimated initiation rates for the translation of all subunits in those complexes are proportional to their stoichiometry. This constraint on protein synthesis kinetics enforces proportional protein synthesis without requiring any feedback mechanism. We also find that the translation initiation rates in E. coli are influenced by the coding sequence length and the enrichment of A and C nucleotides near the start codon. Thus, this study rationalizes the role of conserved and nonrandom features of genes in regulating the translation kinetics and unravels a key principle of the regulation of protein synthesis. Elsevier 2023-09-14 /pmc/articles/PMC10542608/ /pubmed/37789867 http://dx.doi.org/10.1016/j.bpr.2023.100131 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Irshad, Inayat Ullah Sharma, Ajeet K. Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title | Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title_full | Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title_fullStr | Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title_full_unstemmed | Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title_short | Decoding stoichiometric protein synthesis in E. coli through translation rate parameters |
title_sort | decoding stoichiometric protein synthesis in e. coli through translation rate parameters |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542608/ https://www.ncbi.nlm.nih.gov/pubmed/37789867 http://dx.doi.org/10.1016/j.bpr.2023.100131 |
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