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ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response

The alternative sigma factor σ(E) functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σ(E) in Salmonella and E. coli has been examin...

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Autores principales: Li, Jie, Overall, Christopher C., Johnson, Rudd C., Jones, Marcus B., McDermott, Jason E., Heffron, Fred, Adkins, Joshua N., Cambronne, Eric D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577112/
https://www.ncbi.nlm.nih.gov/pubmed/26389830
http://dx.doi.org/10.1371/journal.pone.0138466
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author Li, Jie
Overall, Christopher C.
Johnson, Rudd C.
Jones, Marcus B.
McDermott, Jason E.
Heffron, Fred
Adkins, Joshua N.
Cambronne, Eric D.
author_facet Li, Jie
Overall, Christopher C.
Johnson, Rudd C.
Jones, Marcus B.
McDermott, Jason E.
Heffron, Fred
Adkins, Joshua N.
Cambronne, Eric D.
author_sort Li, Jie
collection PubMed
description The alternative sigma factor σ(E) functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σ(E) in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σ(E)–binding sites in Salmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σ(E)–binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cell division factor, and a signal transduction modulator. The consensus sequence identified for σ(E) in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σ(E)–binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σ(E) modulates transcription. By dissecting direct and indirect modes of σ(E)-mediated regulation, we found that σ(E) activates gene expression through recognition of both canonical and reversed consensus sequence. New σ(E) regulated genes (greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.
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spelling pubmed-45771122015-09-25 ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response Li, Jie Overall, Christopher C. Johnson, Rudd C. Jones, Marcus B. McDermott, Jason E. Heffron, Fred Adkins, Joshua N. Cambronne, Eric D. PLoS One Research Article The alternative sigma factor σ(E) functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σ(E) in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σ(E)–binding sites in Salmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σ(E)–binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cell division factor, and a signal transduction modulator. The consensus sequence identified for σ(E) in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σ(E)–binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σ(E) modulates transcription. By dissecting direct and indirect modes of σ(E)-mediated regulation, we found that σ(E) activates gene expression through recognition of both canonical and reversed consensus sequence. New σ(E) regulated genes (greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses. Public Library of Science 2015-09-21 /pmc/articles/PMC4577112/ /pubmed/26389830 http://dx.doi.org/10.1371/journal.pone.0138466 Text en 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
Li, Jie
Overall, Christopher C.
Johnson, Rudd C.
Jones, Marcus B.
McDermott, Jason E.
Heffron, Fred
Adkins, Joshua N.
Cambronne, Eric D.
ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title_full ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title_fullStr ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title_full_unstemmed ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title_short ChIP-Seq Analysis of the σ(E) Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response
title_sort chip-seq analysis of the σ(e) regulon of salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577112/
https://www.ncbi.nlm.nih.gov/pubmed/26389830
http://dx.doi.org/10.1371/journal.pone.0138466
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