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Sequence Features of E. coli mRNAs Affect Their Degradation

Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect it...

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Autores principales: Lenz, Gal, Doron-Faigenboim, Adi, Ron, Eliora Z., Tuller, Tamir, Gophna, Uri
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233582/
https://www.ncbi.nlm.nih.gov/pubmed/22163312
http://dx.doi.org/10.1371/journal.pone.0028544
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author Lenz, Gal
Doron-Faigenboim, Adi
Ron, Eliora Z.
Tuller, Tamir
Gophna, Uri
author_facet Lenz, Gal
Doron-Faigenboim, Adi
Ron, Eliora Z.
Tuller, Tamir
Gophna, Uri
author_sort Lenz, Gal
collection PubMed
description Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5′ termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes.
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spelling pubmed-32335822011-12-12 Sequence Features of E. coli mRNAs Affect Their Degradation Lenz, Gal Doron-Faigenboim, Adi Ron, Eliora Z. Tuller, Tamir Gophna, Uri PLoS One Research Article Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5′ termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes. Public Library of Science 2011-12-07 /pmc/articles/PMC3233582/ /pubmed/22163312 http://dx.doi.org/10.1371/journal.pone.0028544 Text en Lenz et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Lenz, Gal
Doron-Faigenboim, Adi
Ron, Eliora Z.
Tuller, Tamir
Gophna, Uri
Sequence Features of E. coli mRNAs Affect Their Degradation
title Sequence Features of E. coli mRNAs Affect Their Degradation
title_full Sequence Features of E. coli mRNAs Affect Their Degradation
title_fullStr Sequence Features of E. coli mRNAs Affect Their Degradation
title_full_unstemmed Sequence Features of E. coli mRNAs Affect Their Degradation
title_short Sequence Features of E. coli mRNAs Affect Their Degradation
title_sort sequence features of e. coli mrnas affect their degradation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233582/
https://www.ncbi.nlm.nih.gov/pubmed/22163312
http://dx.doi.org/10.1371/journal.pone.0028544
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