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The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-ter...

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Autores principales: Favate, John S, Liang, Shun, Cope, Alexander L, Yadavalli, Srujana S, Shah, Premal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645810/
https://www.ncbi.nlm.nih.gov/pubmed/36214449
http://dx.doi.org/10.7554/eLife.81979
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author Favate, John S
Liang, Shun
Cope, Alexander L
Yadavalli, Srujana S
Shah, Premal
author_facet Favate, John S
Liang, Shun
Cope, Alexander L
Yadavalli, Srujana S
Shah, Premal
author_sort Favate, John S
collection PubMed
description Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.
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spelling pubmed-96458102022-11-15 The landscape of transcriptional and translational changes over 22 years of bacterial adaptation Favate, John S Liang, Shun Cope, Alexander L Yadavalli, Srujana S Shah, Premal eLife Evolutionary Biology Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution. eLife Sciences Publications, Ltd 2022-10-10 /pmc/articles/PMC9645810/ /pubmed/36214449 http://dx.doi.org/10.7554/eLife.81979 Text en © 2022, Favate et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Favate, John S
Liang, Shun
Cope, Alexander L
Yadavalli, Srujana S
Shah, Premal
The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title_full The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title_fullStr The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title_full_unstemmed The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title_short The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
title_sort landscape of transcriptional and translational changes over 22 years of bacterial adaptation
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645810/
https://www.ncbi.nlm.nih.gov/pubmed/36214449
http://dx.doi.org/10.7554/eLife.81979
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