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Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes
The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that coul...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2006
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635534/ https://www.ncbi.nlm.nih.gov/pubmed/17096598 http://dx.doi.org/10.1371/journal.pgen.0020185 |
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author | Huerta, Araceli M Francino, M. Pilar Morett, Enrique Collado-Vides, Julio |
author_facet | Huerta, Araceli M Francino, M. Pilar Morett, Enrique Collado-Vides, Julio |
author_sort | Huerta, Araceli M |
collection | PubMed |
description | The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes. |
format | Text |
id | pubmed-1635534 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-16355342006-11-29 Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes Huerta, Araceli M Francino, M. Pilar Morett, Enrique Collado-Vides, Julio PLoS Genet Research Article The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes. Public Library of Science 2006-11 2006-11-10 /pmc/articles/PMC1635534/ /pubmed/17096598 http://dx.doi.org/10.1371/journal.pgen.0020185 Text en This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
spellingShingle | Research Article Huerta, Araceli M Francino, M. Pilar Morett, Enrique Collado-Vides, Julio Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title | Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title_full | Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title_fullStr | Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title_full_unstemmed | Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title_short | Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes |
title_sort | selection for unequal densities of σ(70) promoter-like signals in different regions of large bacterial genomes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635534/ https://www.ncbi.nlm.nih.gov/pubmed/17096598 http://dx.doi.org/10.1371/journal.pgen.0020185 |
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