Single-target regulators form a minor group of transcription factors in Escherichia coli K-12

Nucleic Acids Res. 2018 May 4;46(8):3921-3936. doi: 10.1093/nar/gky138.


The identification of regulatory targets of all TFs is critical for understanding the entire network of the genome regulation. The lac regulon of Escherichia coli K-12 W3110 is composed of the lacZYA operon and its repressor lacI gene, and has long been recognized as the seminal model of transcription regulation in bacteria with only one highly preferred target. After the Genomic SELEX screening in vitro of more than 200 transcription factors (TFs) from E. coli K-12, however, we found that most TFs regulate multiple target genes. With respect to the number of regulatory targets, a total of these 200 E. coli TFs form a hierarchy ranging from a single target to as many as 1000 targets. Here we focus a total of 13 single-target TFs, 9 known TFs (BetI, KdpE, LacI, MarR, NanR, RpiR, TorR, UlaR and UxuR) and 4 uncharacterized TFs (YagI, YbaO, YbiH and YeaM), altogether forming only a minor group of TFs in E. coli. These single-target TFs were classified into three groups based on their functional regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli K12 / genetics*
  • Escherichia coli K12 / metabolism*
  • Escherichia coli Proteins / classification*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial
  • Gene Regulatory Networks
  • Genome, Bacterial
  • Lac Operon
  • Lac Repressors / classification
  • Lac Repressors / genetics
  • Lac Repressors / metabolism
  • Models, Biological
  • Regulon
  • SELEX Aptamer Technique
  • Transcription Factors / classification*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Escherichia coli Proteins
  • Lac Repressors
  • LacI protein, E coli
  • Transcription Factors