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

Abstract

We recently discovered that exposure of enterohemorrhagic Escherichia coli (EHEC) to D-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon, and downregulation of the type III secretion system that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx toxin-carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response. We found that RecA elevation in response to D-serine, while being significant, was heterogeneous and not capable of activating stx expression or stx phage transduction to a nonlysogenic recipient. This "SOS-like response" was, however, capable of increasing the mutation frequency associated with low-level RecA activity, thus promoting genetic diversity. Furthermore, this response was entirely dependent on RecA and enhanced in the presence of a DNA-damaging agent, indicating a functional SOS response, but did not result in observable cleavage of the LexA repressor alone, indicating a controlled mechanism of induction. This work demonstrates that environmental factors not usually associated with DNA damage are capable of promoting an SOS-like response. We propose that this modulated induction of RecA allows EHEC to adapt to environmental insults such as D-serine while avoiding unwanted phage-induced lysis. IMPORTANCEThe SOS response is a global stress network that is triggered by the presence of DNA damage due to breakage or stalled replication forks. Activation of the SOS response can trigger the replication of lytic bacteriophages and promote genetic diversification through error-prone polymerases. We have demonstrated that the host-associated metabolite D-serine contributes to Escherichia coli niche specification and accumulates inside cells that cannot catabolize it. This results in a modulated activation of the SOS antirepressor RecA that is insufficient to trigger lytic bacteriophage but capable of increasing the SOS-associated mutation frequency. These findings describe how relevant signals not normally associated with DNA damage can hijack the SOS response, promoting diversity as E. coli strains adapt while avoiding unwanted phage lysis. The bacterial SOS response is a global network of DNA repair proteins that is triggered in the presence of DNA replication inhibition, DNA strand breaks, or DNA-damaging agents such as antibiotics, UV light, reactive oxygen species, and pressure (1, 2). The SOS regulon is under the control of the LexA repressor and consists of Ͼ40 genes in Escherichia coli (1, 3-5). Upon DNA damage, the LexA antirepressor RecA is activated by forming a filament structure with single-stranded DNA and promotes autocatalytic cleavage of LexA, thus relieving the repression of SOSregulated genes (6-9). A second mechanism of SOS induction has also been described that involves the two-component sensor DpiAB, which activates the SOS network in response to ␤-lactam an...

Genomic plasticity of pathogenic Escherichia coli mediates d -serine tolerance via multiple adaptive mechanisms

“…Before characterizing the molecular basis of d -Ser tolerance, it was crucial to establish whether this tolerance phenotype had any implications for the distinct transcriptional responses that we have previously associated with exposure of EHEC to d -Ser, namely repression of type 3 secretion-mediated colonization ( 10 ) and activation of an SOS-like response via RecA induction ( 10 , 22 ). We used transcriptional reporters of the LEE master regulator ( Fig.…”

“…This allows for restriction of EHEC to a more favorable niche within the gut where d -Ser concentrations are low ( 10 ), compared with environments such as the bladder, where d -Ser levels are higher ( 11 ). In addition to virulence repression by d -Ser, an SOS-like response is activated, leading to a higher rate of genomic variability ( 22 ), likely reflecting the bacterium attempting to overcome the stress induced by d -Ser exposure. Together with the observation that LEE-positive enteric E. coli have evolved to lose the ability to catabolize d -Ser ( 10 ), these findings corroborate the role of d -Ser in niche restriction of LEE-positive E. coli .…”

D-serine induces distinct transcriptomes in diverse Escherichia coli pathotypes

“…This is believed to be important in pathogenesis in the bladder and brain where D-ser concentrations are higher than that of the gut. We previously described how exposure of EHEC to D-ser results in a global transcriptional shift affecting virulence and inducing stress (1, 9). We therefore hypothesised that D-ser could promote distinct transcriptomes in pathotypes not susceptible to D-ser toxicity.…”

Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria

“…Conversely, uropathogenic E. coli that cause infections in the bladder, where D-serine concentrations are up to one thousand-fold higher, are predominantly capable of metabolising D-serine (Anfora et al 2007;Connolly et al 2015). Importantly, while D-serine supports the growth of UPEC, it inhibits growth, induces an SOS-like response and causes transcriptional repression of the LEE in EHEC (Connolly et al 2015;Connolly and Roe 2016). This indicates that E. coli occupying distinct niches have evolved contrasting responses to this metabolite.…”