d-Serine induces distinct transcriptomes in diverse Escherichia coli pathotypes

Abstract

Appropriate interpretation of environmental signals facilitates niche specificity in pathogenic bacteria. However, the responses of niche-specific pathogens to common host signals are poorly understood. d-Serine (d-ser) is a toxic metabolite present in highly variable concentrations at different colonization sites within the human host that we previously found is capable of inducing changes in gene expression. In this study, we made the striking observation that the global transcriptional response of three Escherichia coli pathotypes – enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis-associated E. coli (NMEC) – to d-ser was highly distinct. In fact, we identified no single differentially expressed gene common to all three strains. We observed the induction of ribosome-associated genes in extraintestinal pathogens UPEC and NMEC only, and the induction of purine metabolism genes in gut-restricted EHEC, and UPEC indicating distinct transcriptional responses to a common signal. UPEC and NMEC encode dsdCXA – a genetic locus required for detoxification and hence normal growth in the presence of d-ser. Specific transcriptional responses were induced in strains accumulating d-ser (WT EHEC and UPEC/NMEC mutants lacking the d-ser-responsive transcriptional activator DsdC), corroborating the notion that d-ser is an unfavourable metabolite if not metabolized. Importantly, many of the UPEC-associated transcriptome alterations correlate with published data on the urinary transcriptome, supporting the hypothesis that d-ser sensing forms a key part of urinary niche adaptation in this pathotype. Collectively, our results demonstrate distinct pleiotropic responses to a common metabolite in diverse E. coli pathotypes, with important implications for niche selectivity.

The therapeutic potential of D-Serine in reducing expression of the cytopathic genotoxin colibactin

“…Relative expression and P -values for all amino acids tested can be found in Table S4 for CFT073, and S5 for Nissle 1917. Our RT-qPCR results corroborated the findings of our previous RNA-Seq study [21] and confirmed that D-Serine repressed expression of the colibactin synthesis genes in CFT073. In addition, D-Serine was shown to suppress clbB expression in Nissle 1917.…”

“…Relative expression and P-values for all amino acids tested can be found in Table S4 for CFT073, and S5 for Nissle 1917. Our RT-qPCR results corroborated the findings of our previous RNA-Seq study [21]…”

“…Therefore, this prompted an investigation into how exposure to D-Serine implicated gene expression in E. coli that encoded the complete dsdCXA locus. Previous work examining the transcriptome of CFT073 exposed to D-Serine revealed many significant differentially expressed genes throughout the genome, but of particular interest was the downregulation of several genes encoding proteins involved in the synthesis of the genotoxin colibactin [21]. Comparison of read data from D-Serine treated (red) and untreated control respectively.…”

“…Indeed, the role of dsdCXA is to prevent UPEC strains from succumbing to inhibitory concentrations of D-Serine in the urinary tract, by converting the substrate to ammonia and pyruvate [9,16,19]. While there have been conflicting reports surrounding the role of D-Serine in regulating virulence in UPEC [9,18,20], recent transcriptome analysis has demonstrated that D-Serine exhibits the ability to modulate the expression of genes beyond the dsdCXA locus in both dsd - and dsd + strains [21].…”

“…Indeed, the role of dsdCXA is to prevent UPEC strains from succumbing to inhibitory concentrations of D-Serine in the urinary tract, by converting the substrate to ammonia and pyruvate [9,16,19]. While there have been conflicting reports surrounding the role of D-Serine in regulating virulence in UPEC [9,18,20], recent transcriptome analysis has demonstrated that D-Serine exhibits the ability to modulate the expression of genes beyond the dsdCXA locus in both dsd-and dsd+ strains [21].Recently, we described the transcriptional response to D-Serine in strains from three distinct E. coli pathotypes; enterohaemorrhagic E. coli (EHEC), neonatal meningitis associated E. coli (NMEC) and UPEC [21]. Strikingly, the results revealed a unique transcription profile for each pathotype with not a single differentially expressed gene shared between the strains.…”