The post‐transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli

Abstract

Metabolic control in Escherichia coli is a complex process involving multilevel regulatory systems but the involvement of post-transcriptional regulation is uncertain. The post-transcriptional factor CsrA is stated as being the only regulator essential for the use of glycolytic substrates. A dozen enzymes in the central carbon metabolism (CCM) have been reported as potentially controlled by CsrA, but its impact on the CCM functioning has not been demonstrated. Here, a multiscale analysis was performed in a wild-type strain and its isogenic mutant attenuated for CsrA (including growth parameters, gene expression levels, metabolite pools, abundance of enzymes and fluxes). Data integration and regulation analysis showed a coordinated control of the expression of glycolytic enzymes. This also revealed the imbalance of metabolite pools in the csrA mutant upper glycolysis, before the phosphofructokinase PfkA step. This imbalance is associated with a glucose-phosphate stress. Restoring PfkA activity in the csrA mutant strain suppressed this stress and increased the mutant growth rate on glucose. Thus, the carbon storage regulator system is essential for the effective functioning of the upper glycolysis mainly through its control of PfkA. This work demonstrates the pivotal role of post-transcriptional regulation to shape the carbon metabolism.

Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli

“…The biochemical mechanisms involved in these sensory processes remain to be determined. In E. coli, CsrA positively regulates several enzymes of glycolysis, in particular, the enzyme phosphofructokinase A, which drives metabolic flux beyond the upper trunk of the glycolysis pathway (7,13). By inference, products of carbon metabolism downregulate CsrA activity and glycolytic flux through the Embeden-Meyerhof-Parnas pathway, while they activate gluconeogenesis, glycogen synthesis, synthesis of the biofilm exopolysaccharide dPNAG, and pathways and processes favoring stress resistance and survival, which are repressed by CsrA (Fig.…”

“…In support of this hypothesis, results of modeling studies with genes of the Csr system suggest that the CsrD-dependent decay pathway for CsrB/C sRNAs enhances rates of Csr response to signals, although the involvement of glucose or carbon metabolites in this process has not been demonstrated (71). In view of the hundreds of genes and numerous pathways and processes that are controlled by CsrA (13,25,33), the proposed operation of a futile cycle of CsrB/C synthesis and turnover when a preferred carbon source is available may be a small price to pay to poise the Csr system for rapid response.…”

“…CsrA regulates the expression of genes involved in lifestyle transitions. In Escherichia coli, CsrA activates glycolysis and central carbon pathways (7)(8)(9)(10)(11)(12)(13) and motility (14,15). Conversely, it represses gluconeogenesis (7), glycogen biosynthesis (16)(17)(18)(19)(20), biofilm formation (21)(22)(23)(24), the stringent response (25), and expression of genes involved in other stress resistance and stationary-phase processes, e.g., cstA, hfq, cel, sdiA, and nhaR (24,(26)(27)(28)(29)(30).…”

Glycolysis and Its Metabolic Engineering Applications

“…60,61 In E. coli, carbon storage regulator protein CsrA is global regulator that negatively impacts PEP synthesis by repressing pckA and ppsA while activating pykF, which channels flux away from PEP. 14,62,63 Repression or disruption of csrA will result in increased levels of PEP and increased production of aromatic amino acids. 15,61 Deletion of CsrA, additional overexpression of feedbackinhibitionresistant aromatic path way enzymes like AroG fbr (DAHP synthase) and TyrA fbr (chorismate mutase/prephenate dehydrogenase), and/or deletion of transcriptional repressor gene tyrR or trpR, will further enhance the production of aro matic compounds.…”

Mathematical modelling of microbes: metabolism, gene expression and growth

“…If these measurements are sufficiently precise, then a subset of solutions may be obtained in which the possible values for intracellular, nonmeasured fluxes remain within tight bounds. This approach, called (stoichiometric) metabolic flux analysis (MFA) [91], underlies, for example, the analysis of the influence of a post-transcriptional regulator, CsrA, on the flux distribution in central carbon metabolism in E. coli [92]. From measurements of the uptake and excretion fluxes of wild-type and mutant strains growing on glucose, estimates of glycolytic fluxes were obtained that, combined with measurements of metabolite pools and gene expression, allowed one to rsif.royalsocietypublishing.org J. R. Soc.…”