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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

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 inSalmonella 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. Lastly, new σ E regulated genes ( greA, luxS, ompA andmore » ompX) are shown to be involved in heat shock and oxidative stress responses.« less
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [2] ;  [1] ;  [2] ;  [1] ;  [4]
  1. Oregon Health & Science Univ., Portland, OR (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  3. Human Longevity, Inc., San Diego, CA (United States); J. Craig Venter Institute, Rockville, MD (United States)
  4. Univ. of Osnabrueck (Germany)
Publication Date:
Report Number(s):
PNNL-SA-115504
Journal ID: ISSN 1932-6203; 400412000
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Salmonella Typhimurium; ChIP-seq; sequence motif analysis; gene expression; gene regulation; post-transcriptional gene regulation; oxidative stress; Salmonella; DNA transcription
OSTI Identifier:
1337292

Li, Jie, Overall, Christopher C., Johnson, Rudd C., Jones, Marcus B., McDermott, Jason E., Heffron, Fred, Adkins, Joshua N., Cambronne, Eric D., and Hensel, Michael. ChIP-seq analysis of the σE regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response. United States: N. p., Web. doi:10.1371/journal.pone.0138466.
Li, Jie, Overall, Christopher C., Johnson, Rudd C., Jones, Marcus B., McDermott, Jason E., Heffron, Fred, Adkins, Joshua N., Cambronne, Eric D., & Hensel, Michael. ChIP-seq analysis of the σE regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response. United States. doi:10.1371/journal.pone.0138466.
Li, Jie, Overall, Christopher C., Johnson, Rudd C., Jones, Marcus B., McDermott, Jason E., Heffron, Fred, Adkins, Joshua N., Cambronne, Eric D., and Hensel, Michael. 2015. "ChIP-seq analysis of the σE regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response". United States. doi:10.1371/journal.pone.0138466. https://www.osti.gov/servlets/purl/1337292.
@article{osti_1337292,
title = {ChIP-seq analysis of the σE regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response},
author = {Li, Jie and Overall, Christopher C. and Johnson, Rudd C. and Jones, Marcus B. and McDermott, Jason E. and Heffron, Fred and Adkins, Joshua N. and Cambronne, Eric D. and Hensel, Michael},
abstractNote = {The alternative sigma factor σE 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 σE in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σE–binding sites inSalmonella 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 σE–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 σE 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 σE–binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σE modulates transcription. By dissecting direct and indirect modes of σE-mediated regulation, we found that σE activates gene expression through recognition of both canonical and reversed consensus sequence. Lastly, new σE regulated genes (greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.},
doi = {10.1371/journal.pone.0138466},
journal = {PLoS ONE},
number = 9,
volume = 10,
place = {United States},
year = {2015},
month = {9}
}