Characterization of the SOS meta-regulon in the human gut microbiome

Bioinformatics. 2014 May 1;30(9):1193-7. doi: 10.1093/bioinformatics/btt753. Epub 2014 Jan 8.


Motivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome.

Results: We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacteriophages / genetics
  • Base Sequence
  • Binding Sites
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Metagenome
  • Metagenomics / methods*
  • Microbiota*
  • Regulon*
  • SOS Response, Genetics*
  • Serine Endopeptidases / genetics
  • Serine Endopeptidases / metabolism


  • Bacterial Proteins
  • LexA protein, Bacteria
  • Serine Endopeptidases