Bioinformatics, Vol 14, 391-400, Copyright © 1998 by Oxford University Press
D Thieffry, H Salgado, AM Huerta and J Collado-Vides
MOTIVATION: As one of the best-characterized free-living organisms,
Escherichia coli and its recently completed genomic sequence offer a
special opportunity to exploit systematically the variety of regulatory
data available in the literature in order to make a comprehensive set of
regulatory predictions in the whole genome. RESULTS: The complete genome
sequence of E.coli was analyzed for the binding of transcriptional
regulators upstream of coding sequences.The biological information
contained in RegulonDB (Huerta, A.M. et al., Nucleic Acids Res.,26,55-60,
1998) for 56 different transcriptional proteins was the support to
implement a stringent strategy combining string search and weight matrices.
We estimate that our search included representatives of 15-25% of the total
number of regulatory binding proteins in E.coli. This search was performed
on the set of 4288 putative regulatory regions, each 450 bp long. Within
the regions with predicted sites, 89% are regulated by one protein and 81%
involve only one site. These numbers are reasonably consistent with the
distribution of experimental regulatory sites. Regulatory sites are found
in 603 regions corresponding to 16% of operon regions and 10% of
intra-operonic regions. Additional evidence gives stronger support to some
of these predictions, including the position of the site, biological
consistency with the function of the downstream gene, as well as genetic
evidence for the regulatory interaction. The predictions described here
were incorporated into the map presented in the paper describing the
complete E.coli genome (Blattner,F.R. et al., Science, 277, 1453-1461,
1997). AVAILABILITY: The complete set of predictions in GenBank format is
available at the url: http://www.
cifn.unam.mx/Computational_Biology/E.coli-predictions CONTACT: ecoli-
reg@cifn.unam.mx, collado@cifn.unam.mx
ARTICLES
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
Centro de Investigacion sobre Fijacion de Nitrogeno, Universidad Nacional Autonoma de Mexico, AP 565-A, Cuernavaca, Morelos 62100, Mexico.
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