AUTHOR=Ledezma-Tejeida Daniela , Ishida Cecilia , Collado-Vides Julio 

TITLE=Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 8 - 2017

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.01466

DOI=10.3389/fmicb.2017.01466

ISSN=1664-302X

ABSTRACT=In the face of changes in their environment, bacteria adjust gene expression and produce an appropriate response. The individual layers of this process have been widely studied: the Transcriptional Regulatory Network describes the regulatory interactions that produce changes in the Metabolic Network, both coordinated by the Signaling Network; but the interplay between them has never been described in a systematic fashion. Here, we formalize the process of detection and processing of environmental information mediated by individual transcription factors in a concept termed Genetic Sensory Response Unit (GENSOR Unit), composed of four components: 1) signal, 2) signal transduction, 3) genetic switch, and 4) response. We used experimentally validated datasets from two databases to assemble a GENSOR Unit for each of the 189 local Transcription factors of Escherichia coli K-12 present in RegulonDB. Further analysis suggested that feedback is a common occurrence in signal processing and showed a gradient of functional complexity in the response mediated by each Transcription factor, as opposed to a one regulator-one pathway rule. Finally, we provide examples of other GENSOR Unit applications such as hypothesis generation, detailed description of cellular decision-making and elucidation of indirect regulatory mechanisms.