Open AccessGlobal Analysis of Salmonella Alternative Sigma Factor E on Protein Translation
Author(s) -
Jie Li,
Ernesto Nakayasu,
Chris Overall,
Rudd C. Johnson,
Afshan S. Kidwai,
Jason McDermott,
Charles Ansong,
Fred Heffron,
Eric D. Cambronne,
Joshua N. Adkins
Publication year - 2015
Publication title -
journal of proteome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.644
H-Index - 161
eISSN - 1535-3907
pISSN - 1535-3893
DOI - 10.1021/pr5010423
Subject(s) - sigma factor , proteome , transcriptome , biology , salmonella , mutant , translation (biology) , transcriptional regulation , gene , gene expression , regulon , regulation of gene expression , translational regulation , proteomics , post transcriptional regulation , microbiology and biotechnology , genetics , messenger rna , promoter , bacteria
The alternative sigma factor E (σ(E)) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σ(E)-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σ(E) may indirectly participate in post-transcriptional regulation. In this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by σ(E) in Salmonella. Samples were analyzed from wild-type and isogenic rpoE mutant Salmonella cultivated in three different conditions: nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of the observed proteome was regulated by σ(E) combining all three conditions. In different growth conditions, σ(E) affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by σ(E) and found that post-transcriptional regulation was responsible for a majority of changes observed in the σ(E)-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that σ(E)-mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.