It has been demonstrated that about 10% of the Escherichia coli genes are under direct or indirect control of RpoS. Therefore, Weber et al. [2005] proposed that this sigma subunit should be considered a second vegetative sigma factor under non-optimal growth conditions. In this report we demonstrate that in the phosphoenolpyruvate:carbohydrate phosphotransferase system-deficient (PTS(-)) derivatives, PB11 and PB12 of strain JM101 that permanently grow slowly on glucose, the inactivation of rpoS resulted in decreased growth rates of 50 and 10%, respectively. Real-time PCR (RT-PCR) analysis confirmed the important role of this sigma factor in the PTS- strains and allowed the identification of 19 genes including almost all the glycolytic genes, not previously reported, to be at least partially dependent on RpoS. The transcription level of gpp, spoT, ppa and ndk whose products are involved in ppGpp metabolism was upregulated in strain PB12 as compared to the parental strains PB11 and JM101. In the PTS- strains, at least three of these genes (gpp, spoT and ppa) were mainly or partially regulated by RpoS which is known to require ppGpp for activation, while only gpp was highly RpoS-dependent in the parental PTS+ strain JM101. The role of RpoS in the transcription of these genes was analyzed and evidence that the expression of this group of genes could be regulated by a common factor in addition to RpoS was discussed.
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