Affiliation:
1. Department of Bioengineering, University of California, San Diego, San Diego, California, USA
2. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
Abstract
E. coli
is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis.
E. coli
’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in
E. coli
and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.
Publisher
American Society for Microbiology
Subject
Computer Science Applications,Genetics,Molecular Biology,Modelling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology
Cited by
25 articles.
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