Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation

Abstract

Summary Despite decades of studies meant to analyse the bacterial response to carbon limitation, we still miss a high‐resolution overview of the situation. All gene expression changes observed in such conditions cannot solely be accounted for by the global regulator Crp either free or bound to its effector, cyclic AMP . Here, for the first time, we evaluated the response of both CDS (protein‐coding sequence) and nc RNA (non‐coding RNA ) genes to carbon limitation, revealed cellular functions of differentially expressed genes systematically, quantified the contribution of Crp‐ cAMP and other factors to regulation and deciphered regulation strategies at a genomewide scale. Approximately one‐third of the differentially expressed genes we identified responded to Crp‐ cAMP via its direct or indirect control, while the remaining genes were subject to growth rate‐dependent control or were controlled by other regulators, especially RpoS. Importantly, gene regulation mechanisms can be established by expression pattern studies. Here, we propose a comprehensive picture of how cells respond to carbon scarcity. The global regulation strategies thus exposed illustrate that the response of cell to carbon scarcity is not limited to maintaining sufficient carbon metabolism via cAMP signalling while the main response is to adjust metabolism to cope with a slow growth rate.

One‐carbon metabolism, folate, zinc and translation

“…1 are expressed in E. coli – certainly a highly evolved organism – in parallel. They collectively displayed lower expression when the growth rate was reduced during carbon limitation, as does the bulk of the translation machinery (Li et al , 2019). However, as displayed in the table, this differs from the behaviour of other genes involved in translation but not related to 1‐C metabolism, which either does not vary or displays an increased expression.…”

Escherichia coli segments its controls on carbon‐dependent gene expression into global and specific regulations

“…On one hand, as the GR dependence of Crp-regulated genes was well established by the response of genes to carbon limitation as exampled by several catabolic genes and by a hundred of proteins identified by the proteomics study which studied~1000 proteins (You, et al, 2013;Hui, et al, 2015), Crp could be one of the actors. On the other hand, the GR-related effect was recently identified to be another key factor controlling the regulation of many others genes in addition to the well-known ribosomal genes which responded to GR during carbon limitation (Li, et al, 2019), and the GR-related effect could govern the expression of some of the genes identified here that responding to GR. However, the relative contribution of Crp-and the GR-related effect to the regulation of genes responding to GR remained obscure.…”

“…This made it necessary to explore the contribution of Crp-and the GR-related effect to the whole genome at the individual gene level. We therefore identified genes regulated by Crp or sensitive to GR by comparing their expression in the wild type to that in a crp deletion strain, using a method reported previously (Li, et al, 2019) (Data S2). The key feature of this approach was to integrate the knowledge of the change trends of gene expression that paralleled GR together with the principles now described and summarized in Fig.…”

“…The shaded region indicates where A/B < 1; see equation (II) in Note S1. F. Expression levels of the GR-negative and GR-positive genes in G6P, Lac, Glc and NL4 [a nitrogen rich condition with GR at 0.9 h -1 (Li, et al, 2019)]. '***' indicates P-value < 0.001 by Student's t-test.…”

“…Obviously, this must have important consequences on gene expression (Shahrezaei and Marguerat, 2015;Thomas, et al, 2018). The relative contribution of these processes to regulation remained obscure until our recent work (Li, et al, 2019) that gave a systematic overview of how genes were controlled globally when glucose was limiting. We discovered that, to cope with glucose scarcity, E. coli superimposed adaptative responses, including Crp-mediated control of gene expression and GR reduction.…”