Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes

Luis Romero, Sebastian Contreras-Riquelme, Manuel Lira, Alberto J.M. Martin*, Ernesto Perez-Rueda*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Gene regulation is a key process for all microorganisms, as it allows them to adapt to different environmental stimuli. However, despite the relevance of gene expression control, for only a handful of organisms is there related information about genome regulation. In this work, we inferred the gene regulatory networks (GRNs) of bacterial and archaeal genomes by comparisons with six organisms with well-known regulatory interactions. The references we used are: Escherichia coli K-12 MG1655, Bacillus subtilis 168, Mycobacterium tuberculosis, Pseudomonas aeruginosa PAO1, Salmonella enterica subsp. enterica serovar typhimurium LT2, and Staphylococcus aureus N315. To this end, the inferences were achieved in two steps. First, the six model organisms were contrasted in an all-vs-all comparison of known interactions based on Transcription Factor (TF)-Target Gene (TG) orthology relationships and Transcription Unit (TU) assignments. In the second step, we used a guilt-by-association approach to infer the GRNs for 12,230 bacterial and 649 archaeal genomes based on TF-TG orthology relationships of the six bacterial models determined in the first step. Finally, we discuss examples to show the most relevant results obtained from these inferences. A web server with all the predicted GRNs is available at https://regulatorynetworks.unam.mx/ or http://132.247.46.6/.

Original languageEnglish
Article number923105
JournalFrontiers in Microbiology
Volume13
DOIs
StatePublished - 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright © 2022 Romero, Contreras-Riquelme, Lira, Martin and Perez-Rueda.

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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