Transcription Factors in Escherichia coli Prefer the Holo Conformation

Yalbi Itzel Balderas-Martínez, Michael Savageau, Heladia Salgado, Ernesto Pérez-Rueda, Enrique Morett, Julio Collado-Vides

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

The transcriptional regulatory network of Escherichia coli K-12 is among the best studied gene networks of any living cell. Transcription factors bind to DNA either with their effector bound (holo conformation), or as a free protein (apo conformation) regulating transcription initiation. By using RegulonDB, the functional conformations (holo or apo) of transcription factors, and their mode of regulation (activator, repressor, or dual) were exhaustively analyzed. We report a striking discovery in the architecture of the regulatory network, finding a strong under-representation of the apo conformation (without allosteric metabolite) of transcription factors when binding to their DNA sites to activate transcription. This observation is supported at the level of individual regulatory interactions on promoters, even if we exclude the promoters regulated by global transcription factors, where three-quarters of the known promoters are regulated by a transcription factor in holo conformation. This genome-scale analysis enables us to ask what are the implications of these observations for the physiology and for our understanding of the ecology of E. coli. We discuss these ideas within the framework of the demand theory of gene regulation.

Original languageEnglish (US)
Article numbere65723
JournalPLoS One
Volume8
Issue number6
DOIs
StatePublished - Jun 12 2013

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Escherichia coli
Conformations
Transcription Factors
transcription factors
Gene Regulatory Networks
promoter regions
Transcription
transcription (genetics)
Genes
Escherichia coli K12
Protein Conformation
DNA
Physiology
Ecology
Metabolites
Gene expression
physiology
Cells
Genome
metabolites

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Balderas-Martínez, Y. I., Savageau, M., Salgado, H., Pérez-Rueda, E., Morett, E., & Collado-Vides, J. (2013). Transcription Factors in Escherichia coli Prefer the Holo Conformation. PLoS One, 8(6), [e65723]. https://doi.org/10.1371/journal.pone.0065723

Transcription Factors in Escherichia coli Prefer the Holo Conformation. / Balderas-Martínez, Yalbi Itzel; Savageau, Michael; Salgado, Heladia; Pérez-Rueda, Ernesto; Morett, Enrique; Collado-Vides, Julio.

In: PLoS One, Vol. 8, No. 6, e65723, 12.06.2013.

Research output: Contribution to journalArticle

Balderas-Martínez, YI, Savageau, M, Salgado, H, Pérez-Rueda, E, Morett, E & Collado-Vides, J 2013, 'Transcription Factors in Escherichia coli Prefer the Holo Conformation', PLoS One, vol. 8, no. 6, e65723. https://doi.org/10.1371/journal.pone.0065723
Balderas-Martínez YI, Savageau M, Salgado H, Pérez-Rueda E, Morett E, Collado-Vides J. Transcription Factors in Escherichia coli Prefer the Holo Conformation. PLoS One. 2013 Jun 12;8(6). e65723. https://doi.org/10.1371/journal.pone.0065723
Balderas-Martínez, Yalbi Itzel ; Savageau, Michael ; Salgado, Heladia ; Pérez-Rueda, Ernesto ; Morett, Enrique ; Collado-Vides, Julio. / Transcription Factors in Escherichia coli Prefer the Holo Conformation. In: PLoS One. 2013 ; Vol. 8, No. 6.
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