Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: transcriptomic data

Authors: Carter, Michelle; HU, BIN - LOS ALAMOS NATIONAL RESEARCH LABORATORY; CHAIN, PATRICK - LOS ALAMOS NATIONAL RESEARCH LABORATORY

Submitted to: Data in Brief
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2021
Publication Date: 4/20/2021
Citation: Carter, M.Q., Hu, B., Chain, P.S. 2021. Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: transcriptomic data. Data in Brief. 36:107065. https://doi.org/10.1016/j.dib.2021.107065.
DOI: https://doi.org/10.1016/j.dib.2021.107065

Interpretive Summary: Methylation-mediated epigenetic regulation plays important roles in bacteria including regulation of gene expression. In this study, we examined the contribution of a prophage encoded type II restriction-modification system (PstI R-M) and of a core-genome encoded DNA adenine methylase (Dam) in Shiga toxin-producing Escherichia coli (STEC). Strain RM13514 is a clinical isolate linked to the 2010 romaine lettuce-associated outbreak in the U.S. We first deleted the genes encoding a PstI R-M system and the gene encoding Dam in strain RM13514, generating two mutant strains MQC599 and MQC602, respectively. We then compared the global gene expression profile in wild-type (WT) strain RM13514 with each mutant strain by the RNA-Seq based functional genomic approach. A total of 21 libraries were generated using message RNA extracted from cells grown in Luria-Bertani broth at exponential and stationary phase. The combined library was run on an Illumina HighSeq 2000 instrument with the Paired End 100 bp read format, resulting in a total of 45.83 Gbp sequence read. This set of data is now available in the SRA database at NCBI under the BioProject accession number PRJNA684587. This set of transcriptomic data provides information on methylation-mediated epigenetic regulation in STEC, an important foodborne pathogen frequently associated with large epidemic outbreaks and capable of causing life-threatening disease in humans. This set of data will be useful for researchers who are interested in physiology and pathogenicity of foodborne pathogens as well as epigenetic regulation in general. Furthermore, this set of data will contribute to our understanding of Dam, a well conserved DNA methylase in bacteria, and the type II Restriction-Modification systems as well as their roles in bacterial physiology and pathogenicity.

Technical Abstract: Shiga toxin-producing Escherichia coli (STEC) strain RM13514 is a clinical isolate linked to the 2010 romaine lettuce-associated outbreak in the U.S. The genes encoding a type II restriction and modification system, PstI R-M, are located in a prophage genome that is also encoding Shiga toxin. In-frame deletion of the PstI R-M genes or dam, encoding a DNA adenine methylase, in strain RM13514 were generated, resulting in two mutant strains MQC599 and MQC602, respectively. The mutant strain MQC599 exhibited a similar growth rate as the wild-type (WT) strain RM13514 when grown in Luria-Bertani (LB) broth at 37'C. In contrast, the growth of mutant strain MQC602 was significantly slower than either RM13514 or MQC599. Genes transcriptionally regulated by the PstI R-M system or by Dam were examined by the RNA-Seq based comparative transcriptomics. The total RNA was extracted from cells of each strain grown in LB broth at exponential and stationary phases. Three biological replicates were collected for each strain. After removal of ribosomal RNA, the mRNAs were converted to cDNAs followed by Illumina sequence library construction. For strains RM13514 and MQC599, six libraires were generated for each, three from the cells in the exponential growth phase and three from the cells in the stationary phase. For strain MQC602, three additional libraries were constructed from the cells in the early exponential growth phase. The resulting 21 libraries were combined in equal amounts and sequenced on an Illumina HighSeq 2000 instrument with the Paired End 100 bp (PE100) read format, generating a total of 45.83 Gbp sequence reads. This set of sequence data is available in the NCBI SRA database under the BioProject accession number PRJNA684587. This set of transcriptomic data provides information on methylation-mediated epigenetic regulation in STEC, an important foodborne pathogen that is frequently associated with large epidemic outbreaks and can cause life-threatening disease in humans. This set of data will be useful for researchers who are interested in physiology and pathogenicity of foodborne pathogens or in the fundamental mechanisms of epigenetic regulation in bacteria.