Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach.
Bacteria develop a number of devices for sensing, responding, and adapting to different environmental conditions. Understanding within a genomic perspective how the transcriptional machinery of bacteria is modulated, as a response for changing conditions, is a major challenge for biologists. Knowledge of which genes are turned on or turned off under specific conditions is essential for our understanding of cell behavior. In this study we describe how the information pertaining to gene expression and associated growth conditions (even with very little knowledge of the associated regulatory mechanisms) is gathered from the literature and incorporated into RegulonDB, a database on transcriptional regulation and operon organization in E. coli. The link between growth conditions, signal transduction, and transcriptional regulation is modeled in the database in a simple format that highlights biological relevant information. As far as we know, there is no other database that explicitly clarifies the effect of environmental conditions on gene transcription. We discuss how this knowledge constitutes a benchmark that will impact future research aimed at integration of regulatory responses in the cell; for instance, analysis of microarrays, predicting culture behavior in biotechnological processes, and comprehension of dynamics of regulatory networks. This integrated knowledge will contribute to the future goal of modeling the behavior of E. coli as an entire cell. The RegulonDB database can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/.
Martínez-Antonio
Agustino
A
Program of Computational Genomics, CIFN, UNAM AP 565-A Cuernavaca, Morelos 62100, Mexico. ecoli-t1@cifn.unam.mx
Salgado
Heladia
H
Gama-Castro
Socorro
S
Gutiérrez-Ríos
Rosa María
RM
Jiménez-Jacinto
Verónica
V
Collado-Vides
Julio
J
D000222:Adaptation, Physiological / Q000502:physiology; D003628:Database Management Systems; D030541:Databases, Genetic; D004777:Environment; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D016247:Information Storage and Retrieval / Q000379:methods; D009876:Operon / Q000502:physiology; D018085:Regulon / Q000235:genetics; D018511:Systems Integration; D014158:Transcription, Genetic / Q000502:physiology*; D015533:Transcriptional Activation / Q000502:physiology