Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates.

Thomas Esquerré,Agamemnon J Carpousis,Sandrine Laguerre,Catherine Turlan,Muriel Cocaign-Bousquet,Laurence Girbal

doi:10.1093/nar/gkt1150

Abstract

Microorganisms extensively reorganize gene expression to adjust growth rate to changes in growth conditions. At the genomic scale, we measured the contribution of both transcription and transcript stability to regulating messenger RNA (mRNA) concentration in Escherichia coli. Transcriptional control was the dominant regulatory process. Between growth rates of 0.10 and 0.63 h−1, there was a generic increase in the bulk mRNA transcription. However, many transcripts became less stable and the median mRNA half-life decreased from 4.2 to 2.8 min. This is the first evidence that mRNA turnover is slower at extremely low-growth rates. The destabilization of many, but not all, transcripts at high-growth rate correlated with transcriptional upregulation of genes encoding the mRNA degradation machinery. We identified five classes of growth-rate regulation ranging from mainly transcriptional to mainly degradational. In general, differential stability within polycistronic messages encoded by operons does not appear to be affected by growth rate. We show here that the substantial reorganization of gene expression involving downregulation of tricarboxylic acid cycle genes and acetyl-CoA synthetase at high-growth rates is controlled mainly by transcript stability. Overall, our results demonstrate that the control of transcript stability has an important role in fine-tuning mRNA concentration during changes in growth rate.

Highlights

IntroductionThe doubling time (or growth rate) of bacterial cells is determined by their metabolic activity, which is in turn dependent on genetic content and environmental conditions (including growth medium composition and temperature) [1]
The doubling time of bacterial cells is determined by their metabolic activity, which is in turn dependent on genetic content and environmental conditions [1]
To investigate the effects of growth rate on messenger RNA (mRNA) stability, we cultured E. coli MG1655 in synthetic medium in glucose-limited chemostat cultures maintained at steady state at four different growth rates (m): 0.10, 0.20, 0.30 and 0.40 hÀ1

Summary

Introduction

The doubling time (or growth rate) of bacterial cells is determined by their metabolic activity, which is in turn dependent on genetic content and environmental conditions (including growth medium composition and temperature) [1]. Studies with bacterial cells growing at imposed doubling times in continuous cultures report overall adaptation of the gene expression network in response to changing growth rate [2,3,4,5]. The rate of transcription of all genes is affected by the growth-rate dependent activity of (free) RNA polymerase and its partitioning into the synthesis of stable RNA species (rRNA and tRNA) and of messenger RNA (mRNA) [7]. Global regulators [transcriptional regulators such as the Crp, Fis and FNR [8] or sigma factors such as RpoS [9]] activate or inhibit transcription of target genes to enable Escherichia coli to adapt rapidly to changing environment.

Methods

Results

Conclusion