title: Transcription factors in Escherichia coli prefer the holo conformation.
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.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México. balderas@ccg.unam.mx
authors.forename: Yalbi Itzel
authors.initials: YI
authors.lastname: Balderas-Martínez
authors.forename: Michael
authors.initials: M
authors.lastname: Savageau
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Ernesto
authors.initials: E
authors.lastname: Pérez-Rueda
authors.forename: Enrique
authors.initials: E
authors.lastname: Morett
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D011487:Protein Conformation; D018085:Regulon / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry* / Q000145:classification
chemical_list: D014157:Transcription Factors