Genome-wide study of the transcription rate of constitutive genes in Escherichia coli for different RNA polymerase concentrations.

In Escherichia coli, the activity of constitutive genes is regulated by changes in RNAp core enzyme and sigma factor concentrations. Importantly, in the exponential growth phase, these cells are able to maintain their sigma-70 population almost constant, making constitutive gene expression almost exclusively affected by changes in RNAp numbers. The degree by which the transcription of sigma-70 constitutive genes change, due to only varying RNAp molecules, is unknown. Here, we use RNA sequencing to measure transcription rates of sigma-70 genes constitutively expressed, at different RNAp concentrations. For that, we first obtain the whole-transcriptome of E. coli MG1655 grown in varying media richness conditions, differing such that cells have different intracellular concentration of RNAp core enzymes but the same growth rates. From this data, we estimate for each gene’s transcription rate. We find that the expression levels and fold changes of sigma-70 constitutive promoters are, in general up-regulated when RNAp concentration increases, but differ widely in response levels to these changes in RNAp concentrations. The results indicate that their response to these changes is affected by parameters other than the RNAp levels.