A Novel Nucleoid Protein of Escherichia Coli Induced Under Anaerobiotic Growth Conditions

Nucleic Acids Res. 2010 Jun;38(11):3605-18. doi: 10.1093/nar/gkq077. Epub 2010 Feb 15.


A systematic search was performed for DNA-binding sequences of YgiP, an uncharacterized transcription factor of Escherichia coli, by using the Genomic SELEX. A total of 688 YgiP-binding loci were identified after genome-wide profiling of SELEX fragments with a high-density microarray (SELEX-chip). Gel shift and DNase-I footprinting assays indicated that YgiP binds to multiple sites along DNA probes with a consensus GTTNATT sequence. Atomic force microscope observation indicated that at low concentrations, YgiP associates at various sites on DNA probes, but at high concentrations, YgiP covers the entire DNA surface supposedly through protein-protein contact. The intracellular concentration of YgiP is very low in growing E. coli cells under aerobic conditions, but increases more than 100-fold to the level as high as the major nucleoid proteins under anaerobic conditions. An E. coli mutant lacking ygiP showed retarded growth under anaerobic conditions. High abundance and large number of binding sites together indicate that YgiP is a nucleoid-associated protein with both architectural and regulatory roles as the nucleoid proteins Fis and IHF. We then propose that YgiP is a novel nucleoid protein of E. coli under anaerobiosis and propose to rename it Dan (DNA-binding protein under anaerobic conditions).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anaerobiosis
  • Base Sequence
  • Binding Sites
  • DNA Footprinting
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA, Bacterial / ultrastructure
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • DNA-Binding Proteins / ultrastructure
  • Electrophoretic Mobility Shift Assay
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / ultrastructure
  • Genomics
  • Microscopy, Atomic Force
  • Molecular Sequence Data
  • SELEX Aptamer Technique
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Factors / ultrastructure


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Transcription Factors
  • TtdR protein, E coli