D-Serine reduces the expression of the cytopathic genotoxin colibactin

Abstract

Some Escherichia coli strains harbour the pks island, a 54 kb genomic island en-coding the biosynthesis genes for a genotoxic compound named colibactin. In eukaryotic cells, colibactin can induce DNA damage, cell cycle arrest and chro-mosomal instability. Production of colibactin has been implicated in the devel-opment of colorectal cancer (CRC). In this study, we demonstrate the inhibito-ry effect of D-Serine on the expression of the pks island in both prototypic and clinically-associated colibactin-producing strains and determine the implications for cytopathic effects on host cells. We also tested a comprehensive panel of proteinogenic L-amino acids and corresponding D-enantiomers for their ability to modulate clbB transcription. Whilst several D-amino acids exhibited the abil-ity to inhibit expression of clbB, D-Serine exerted the strongest repressing ac-tivity (>3.8-fold) and thus, we focussed additional experiments on D-Serine. To investigate the cellular effect, we investigated if repression of colibactin by D-Serine could reduce the cytopathic responses normally observed during infec-tion of HeLa cells with pks+ strains. Levels of γ-H2AX (a marker of DNA double strand breaks) were reduced 2.75-fold in cells infected with D-Serine treat-ment. Moreover, exposure of pks+ E. coli to D-Serine during infection caused a reduction in cellular senescence that was observable at 72 h post infection. The recent finding of an association between pks-carrying commensal E. coli and CRC, highlights the necessity for the development of colibactin targeting thera-peutics. Here we show that D-Serine can reduce expression of colibactin, and inhibit downstream cellular cytopathy, illuminating its potential to prevent colibactin-associated disease.

Current understandings of colibactin regulation

“…d-Serine can be obtained through dietary sources, such as fermented and fortified foods, or by conversion from l-Serine. Recent work by Hallam et al, (2023) has shown that d-Serine downregulates colibactin synthesis and reduces subsequent genotoxicity [96]. Repression of clb genes by d-Serine was found to be independent of the serine tolerance locus dsdCXA and the exact mechanism of d-Serine-induced clb gene repression still remains to be elucidated.…”

“…Repression of clb genes by d -Serine was found to be independent of the serine tolerance locus dsdCXA and the exact mechanism of d -Serine-induced clb gene repression still remains to be elucidated. It is possible that d -Serine, or a subsequent metabolic product of its catabolism, may act as a cofactor to a transcriptional regulator of the pks island [ 96 ].…”

“…Diet is known to have profound consequences on the microbiota and environment of the intestinal tract, and many dietary modulators of colibactin gene expression have been identified, including oligosaccharides such as inulin and short chain fatty acids produced by dietary fibres [98,99]. d-Serine has also been shown to downregulate transcription of clb genes and repress colibactin synthesis [96].…”