TY - JOUR
T1 - Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella
T2 - Implications for virulence and global protein translation
AU - Ansong, Charles
AU - Yoon, Hyunjin
AU - Porwollik, Steffen
AU - Mottaz-Brewer, Heather
AU - Petritis, Brianne O.
AU - Jaitly, Navdeep
AU - Adkins, Joshua N.
AU - McClelland, Michael
AU - Heffron, Fred
AU - Smith, Richard D.
PY - 2009/3/11
Y1 - 2009/3/11
N2 - Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact, of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to Inhibit translation. However, the proteins regulated by Hfq and Smpg are not clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by-Hfq or SmpB by comparing protein: abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptioanally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central Metabolis, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella.
AB - Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact, of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to Inhibit translation. However, the proteins regulated by Hfq and Smpg are not clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by-Hfq or SmpB by comparing protein: abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptioanally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central Metabolis, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella.
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U2 - 10.1371/journal.pone.0004809
DO - 10.1371/journal.pone.0004809
M3 - Article
C2 - 19277208
AN - SCOPUS:62849101179
SN - 1932-6203
VL - 4
JO - PloS one
JF - PloS one
IS - 3
M1 - e4809
ER -