Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors

Bhatia, Rama P, Kirit, Hande A, Predeus, Alexander V ORCID: 0000-0002-2750-1599 and Bollback, Jonathan P ORCID: 0000-0002-4624-4612 (2022) Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors. SCIENTIFIC REPORTS, 12 (1). 8788-.

Text
Bhatia_et_al-2022-Scientific_Reports.pdf - Published version
Download (5MB) | Preview

Official URL: http://dx.doi.org/10.1038/s41598-022-12463-3

Abstract

Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.

Item Type:	Article
Uncontrolled Keywords:	Escherichia coli, Escherichia coli K12, Transcription Factors, Gene Expression Profiling, Gene Regulatory Networks, Transcriptome
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User:	Symplectic Admin
Date Deposited:	21 Jun 2022 08:23
Last Modified:	18 Oct 2023 08:44
DOI:	10.1038/s41598-022-12463-3
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3156846