In this project we present our own analysis of publicly deposited transcriptomic data from 3 pathogenic strains of E.coli in the presence of D-serine, which was originally published by Connolly et al. (2021). The authors describe highly distinct transcriptional responses to this common metabolite in the three strains, suggesting a role for pleiotrophy in niche adaptation.

Here, we have taken the raw RNASeq transcriptomic data and processed it using our standard bioinformatics pipeline for uploading to MORF. We also used the tool OrthoFinder to identifiy orthologous genes between the three strains in the study. Using LIMMA to compare the transcriptional responses to D-serine for each strain we confirm the authors' conclusion that these strains respond very differently to D-serine, with very few significantly changing orthologs responding in the same way betwen strains.

The ability to matabolise D-serine is mediated by the transcriptional regulator dsdC. Two copies of dsdC are present in NMEC, while UPEC has one copy and EHEC has no copies; thus leading to differences in susceptibility to D-serine toxicity. Transcriptome analysis of single and double ΔdsdC knockout mutants for UPEC and NMEC are also included in this dataset.

Citation: James P R Connolly, Natasha C A Turner, Jennifer C Hallam, Patricia T Rimbi, Tom Flett, Mhairi J McCormack, Andrew J Roe, Nicky O'Boyle. D-Serine induces distinct transcriptomes in diverse Escherichia coli pathotypes. Microbiology. 2021;167(10). doi: 10.1099/mic.0.001093

Gene Details: cutA