The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli.
Bacterial adaptation requires large-scale regulation of gene expression. We have performed a genome-wide analysis of the Csr system, which regulates many important cellular functions. The Csr system is involved in post-transcriptional regulation, but a role in transcriptional regulation has also been suggested. Two proteins, an RNA-binding protein CsrA and an atypical signaling protein CsrD, participate in the Csr system. Genome-wide transcript stabilities and levels were compared in wildtype E. coli (MG1655) and isogenic mutant strains deficient in CsrA or CsrD activity demonstrating for the first time that CsrA and CsrD are global negative and positive regulators of transcription, respectively. The role of CsrA in transcription regulation may be indirect due to the 4.6-fold increase in csrD mRNA concentration in the CsrA deficient strain. Transcriptional action of CsrA and CsrD on a few genes was validated by transcriptional fusions. In addition to an effect on transcription, CsrA stabilizes thousands of mRNAs. This is the first demonstration that CsrA is a global positive regulator of mRNA stability. For one hundred genes, we predict that direct control of mRNA stability by CsrA might contribute to metabolic adaptation by regulating expression of genes involved in carbon metabolism and transport independently of transcriptional regulation.
Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France.|CNRS, UMR5504, 31400 Toulouse, France.|Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
Thomas
T
Esquerré
Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
Marie
M
Bouvier
Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
Catherine
C
Turlan
Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
Agamemnon J
AJ
Carpousis
Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France.|CNRS, UMR5504, 31400 Toulouse, France.
Laurence
L
Girbal
Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France.|CNRS, UMR5504, 31400 Toulouse, France.
Muriel
M
Cocaign-Bousquet
D002244:Carbon / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
C093587:CsrA protein, E coli; C516590:CsrD protein, E coli; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; D002244:Carbon