Testing the impact of Type I Restriction Modification Systems on Gene Expression in Uropathogenic Escherichia coli

ABSTRACT: Background: DNA methylation influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. The regulatory role of DNA methylation and other epigenetic marks also extends to virulence; both orphan methyltransferases and those from restriction modification systems (RMSs) have been co-opted to regulate virulence in many bacteria. However, functional characterisation of DNA methylation mediated by archetypal Type I RMSs remains limited. Results: We elucidated the methylation specificity of the Type I RMS in UTI89, a prototypical cystitis strain of E. coli. Deletion of this RMS led to loss of methylation of >750 sites across the genome but no detectable effect on gene expression, virulence, or growth in a screen of 1190 conditions. Similarly, deletion of the endogenous Type I RMS in two other E. coli strains with different methylation specificities also had no effect on gene expression or any growth phenotype. Finally, introduction of these two different RMSs into UTI89 also resulted in no detectable change in gene expression or growth phenotypes. These results stand in sharp contrast with many reports of RMSs regulating gene expression in other bacteria, leading us to propose the concept of “regulation avoidance” for these E. coli Type I RMSs. We hypothesize that regulation avoidance is a consequence of evolutionary adaptation of both the RMSs and the E. coli genome. Conclusions: Our results provide a clear and currently rare example of regulation avoidance for Type I RMSs in multiple strains of E. coli, further study of which may provide deeper insights into the evolution of gene regulation and horizontal gene transfer.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 Escherichia coli CFT073 Escherichia coli UTI89

PROVIDER: GSE165421 | GEO | 2021/07/01

REPOSITORIES: GEO