The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Abstract

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host-pathogen interaction. Here we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type Three Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the LEE pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity.

Intracellular d -Serine Accumulation Promotes Genetic Diversity via Modulated Induction of RecA in Enterohemorrhagic Escherichia coli

“…Previous work by our group identified D-serine as an important niche-specific signal that is involved in the regulation of the infection process by repressing the EHEC T3SS essential for colonization of the host (31). Transcriptomic analysis showed that exposure to millimolar concentrations of D-serine (similar to those found in the urinary tract) also resulted in upregulation of the SOS response regulon, and this was dependent on D-serine accumulation independently of T3SS repression.…”

“…As a control, whole-cell lysates were also probed with anti-DnaK antibody to demonstrate normalized total protein levels and equal loading of the lanes. This indicates that this SOS response is unique to D-serine, as was the repression of the EHEC T3SS (31). D-Serine-induced RecA production does not activate lysogenic stx phages.…”

“…Cleavage of the SOS repressor LexA was not detectable after D-serine induction, suggesting a very controlled response and maintenance of normal LexA levels. Indeed, transcriptomic analysis of the response to D-serine has previously shown that the members of the SOS regulon upregulated include the cell division inhibitor sulA and the RecA destabilizers recX and dinI, as well as lexA itself (31,45). This suggests that the response may be modulated in some way to maintain normal and controlled cellular replication.…”

“…Three DNA polymerases are induced as part of the SOS response in E. coli, high-fidelity PolB, error-prone DinB, and Pol V (UmuDC) (1). We previously demonstrated by transcriptome sequencing that multiple members of the SOS regulon were induced by D-serine accumulation in EHEC, including dinB, umuDC, and polB (31). The enzymes encoded by these genes are key members of the DNA repair process, but it is known that error-prone polymerase activity can lead to mutations in the population and that this can occur spontaneously in stationary phase or in response to antibiotic treatment, even at subinhibitory concentrations (38)(39)(40).…”

“…For this reason, antibiotic treatment of EHEC infections is not recommended, as induction of stx-carrying phages would result in lysis of the host cell and release of the Stx toxin (27). We recently reported that D-serine, a host metabolite found in abundance at extraintestinal sites such as the urinary tract, was capable of independently repressing the T3SS and triggering transcription of the SOS regulon in EHEC O157:H7 (31). This D-serine-mediated "SOS response" is dependent on the intracellular accumulation of this amino acid by E. coli isolates that cannot catabolize it, such as EHEC, because of a lack of functional D-serine catabolic genes.…”