Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli

Abstract

The carbon storage regulator A (CsrA) is a conserved global regulatory system known to control central carbon pathways, biofilm formation, motility, and pathogenicity. The aim of this study was to characterize changes in major metabolic pathways induced by CsrA in human enteropathogenic Escherichia coli (EPEC) grown under virulence factor-inducing conditions. For this purpose, the metabolomes and transcriptomes of EPEC and an isogenic ∆csrA mutant derivative were analyzed by untargeted mass spectrometry and RNA sequencing, respectively. Of the 159 metabolites identified from untargeted GC/MS and LC/MS data, 97 were significantly (fold change ≥ 1.5; corrected p-value ≤ 0.05) regulated between the knockout and the wildtype strain. A lack of csrA led to an accumulation of fructose-6-phosphate (F6P) and glycogen synthesis pathway products, whereas metabolites in lower glycolysis and the citric acid cycle were downregulated. Associated pathways from the citric acid cycle like aromatic amino acid and siderophore biosynthesis were also negatively influenced. The nucleoside salvage pathways were featured by an accumulation of nucleosides and nucleobases, and a downregulation of nucleotides. In addition, a pronounced downregulation of lyso-lipid metabolites was observed. A drastic change in the morphology in the form of vesicle-like structures of the ∆csrA knockout strain was visible by electron microscopy. Colanic acid synthesis genes were strongly (up to 50 fold) upregulated, and the abundance of colanic acid was 3 fold increased according to a colorimetric assay. The findings expand the scope of pathways affected by the csrA regulon and emphasize its importance as a global regulator.

Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA

“…A study conducted in EPEC showed that deletion of csrA resulted in a significant change in over half of the metabolites observed (Berndt et al, 2019). In line with previous work conducted in CsrA transposon insertion mutants, the deletion led to an accumulation of glycogen and fructose-6-phosphate (Berndt et al, 2019).…”

“…Studies in E. coli Nissle 1917 revealed that the influence of CsrA on metabolite levels and metabolic flux were conditional, differing dependent upon the metabolic fate of the carbon source that was used for growth (Revelles et al, 2013). A study conducted in EPEC showed that deletion of csrA resulted in a significant change in over half of the metabolites observed (Berndt et al, 2019). In line with previous work conducted in CsrA transposon insertion mutants, the deletion led to an accumulation of glycogen and fructose-6-phosphate (Berndt et al, 2019).…”

Effect of restricted dissolved oxygen on expression of Clostridium difficile toxin A subunit from E. coli

“…−1.25 at late-log phase) which is involved in making exopolysaccharide colanic acid (M-antigen) which increases E. coli's ability to survive in environmental stresses 52 . Recently, this ability was shown to be regulated through the master regulator csrA 53 , which was up-regulated at unrestricted DO in this study. A schematic representing the state of the major metabolic processes and regulators in E. coli at restricted and unrestricted DO during rARU expression are presented in Fig.…”

The Peptide Chain Release Factor Methyltransferase PrmC Influences the Pseudomonas aeruginosa PA14 Endo- and Exometabolome

“…The organic phase was discarded, and 1 mL of the aqueous phase was evaporated to dryness. Sample preparation, GC–MS analysis, data pre-processing and metabolite identification were performed as described by Berndt et al [ 12 ]: Metabolite extracts were derivatised by methoxyamine/pyridine and silylated using MSTFA to volatilise the analytes. The samples were separated on a 30 m column with a stationary phase of 5% phenyl arylen and 95% dimethylpolysiloxane material (ZB-5MS ® , Phenomenex, Torrance, CA, USA) using a temperature gradient from 70 C to 330 C over 32.5 min.…”