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Jérôme Izard - Growth control and gene regulation in Escherichia coli

PhD thesis defense at INRIA Grenoble Rhône-Alpes, Montbonnot, December 6, 2012


Abstract

Bacteria can adapt to many different environmental conditions. This capacity of adaptation is conferred to the organism by a complex regulatory network, composed of specific regulators and the global gene expression machinery. We have studied the expression dynamics of Crl, a global regulator of Escherichia coli, and observed a peak of transcription during the exponential phase of growth. In order to identify potential regulators of crl expression, we have measured the expression profile of crl in about one hundred different mutant strains. This screen has revealed that CRP-cAMP represses indirectly the transcription of crl and the nucleoprotein Fis activates transcription of the crl promoter by binding to the crl promoter region. We noted that the expression of most global regulators of E. coli have an expression profile similar to the one of Crl. We have therefore studied the relationship between global gene expression machinery and cellular growth. We constructed a bacterium where the transcription of the two large subunits of RNA polymerase, et ’, is under external control. A small concentration of RNA polymerase leads to a small growth rate of this engineered bacterium and the cells start to filament, whereas a high concentration of RNA polymerase produces phenotypically wild-type cells. We have characterized the control of growth rate by our system at the population level and in single cells. An analysis of the global transcription pattern of this strain by RNA-seq shows that the transcription of genes in all functional classes, with the possible exception of genes coding for ribosomal proteins, are almost equally affected by the modifications of the intracellular concentration of RNA polymerase.