Affiliations: National Bioinformatics Center, Industria y San
José, Capitolio Nacional, CP. 10200, Habana Vieja, Habana, Cuba | National Laboratory for Scientific Computing, Av.
Getulio Vargas 333, Quitandinha, CEP 25651-075, Petropolis, Rio de Janeiro,
Brazil | Center of Genomics, UNAM, Cuernavaca, Mexico. AP 565-A
Cuernavaca, CP 62100, Morelos, Mexico
Abstract: Prokaryotic genomes annotation has focused on genes location and
function. The lack of regulatory information has limited the knowledge on
cellular transcriptional regulatory networks. However, as more phylogenetically
close genomes are sequenced and annotated, the implementation of phylogenetic
footprinting strategies for the recognition of regulators and their regulons
becomes more important. In this paper we describe a comparative genomics
approach to the prediction of new gamma-proteobacterial regulon members. We
take advantage of the phylogenetic proximity of Escherichia coli and
other 16 organisms of this subdivision and the intensive search of the space
sequence provided by a pattern-matching strategy. Using this approach we
complement predictions of regulatory sites made using statistical models
currently stored in Tractor_DB, and increase the number of transcriptional
regulators with predicted binding sites up to 86. All these computational
predictions may be reached at Tractor_DB (www.bioinfo.cu/Tractor_DB,
www.tractor.lncc.br, www.ccg.unam.mx/Computational_Genomics/tractorDB/). We
also take a first step in this paper towards the assessment of the conservation
of the architecture of the regulatory network in the gamma-proteobacteria
through evaluating the conservation of the overall connectivity of the
network.
