ChIP-seq analysis of the σ^E regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response

Journal Article · Mon Sep 21 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0138466· OSTI ID:1337292

Li, Jie ^[1]; Overall, Christopher C. ^[2]; Johnson, Rudd C. ^[1]; Jones, Marcus B. ^[3]; McDermott, Jason E. ^[2]; Heffron, Fred ^[1]; Adkins, Joshua N. ^[2]; Cambronne, Eric D. ^[1]; Hensel, Michael ^[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)

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 and ompX) are shown to be involved in heat shock and oxidative stress responses.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• Grant/Contract Number: AC05-76RL01830
• OSTI ID: 1337292
• Report Number(s): PNNL-SA-115504; 400412000
• Journal Information: PLoS ONE, Vol. 10, Issue 9; ISSN 1932-6203
• Publisher: Public Library of Science
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Salmonella Typhimurium
ChIP-seq
sequence motif analysis
gene expression
gene regulation
post-transcriptional gene regulation
oxidative stress
Salmonella
DNA transcription