title: Regulation by transcription factors in bacteria: beyond description.
abstract: Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. In this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts. We review recent concepts and developments: cis elements and trans regulatory factors, chromosome organization and structure, transcriptional regulatory networks (TRNs) and transcriptomics. We also summarize new important discoveries that will probably affect the direction of research in gene regulation: epigenetics and stochasticity in transcriptional regulation, synthetic circuits and plasticity and evolution of TRNs. Many of the new discoveries in gene regulation are not extensively tested with wetlab approaches. Consequently, we review this broad area in Inference of TRNs and Dynamical Models of TRNs. Finally, we have stepped backwards to trace the origins of these modern concepts, synthesizing their history in a timeline schema.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Enrique
authors.initials: E
authors.lastname: Balleza
authors.forename: Lucia N
authors.initials: LN
authors.lastname: López-Bojorquez
authors.forename: Agustino
authors.initials: A
authors.lastname: Martínez-Antonio
authors.forename: Osbaldo
authors.initials: O
authors.lastname: Resendis-Antonio
authors.forename: Irma
authors.initials: I
authors.lastname: Lozada-Chávez
authors.forename: Yalbi I
authors.initials: YI
authors.lastname: Balderas-Martínez
authors.forename: Sergio
authors.initials: S
authors.lastname: Encarnación
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors