Microbial computational genomics of gene regulation*
Julio Collado-Vides, Gabriel Moreno-Hagelsieb, and Arturo Medrano-Soto**
Program of Computational Genomics, CIFN-UNAM, Av. Universidad
s/n, Cuernavaca, 62100 Morelos, Mexico
Abstract: Escherichia coli is a free-living bacterium
that condensates a large legacy of knowledge as a result of years of
experimental work in molecular biology. It represents a point of departure
for analyses and comparisons with the ever-increasing number of finished
microbial genomes. For years, we have been gathering knowledge from
the literature on transcriptional regulation and operon organization
in E. coli K-12, and organizing it in a relational database, RegulonDB.
RegulonDB contains information of 2025 % of the expected total
sets of regulatory interactions at the level of transcription initiation.
We have used this knowledge to generate computational methods to predict
the missing sets in the genome of E. coli, focusing on prediction of
promoters, regulatory sites, regulatory proteins, operons, and transcription
units. These predictions constitute separate pieces of a single puzzle.
By putting them all together, we shall be able to predict the complete
set of regulatory interactions and transcription unit organization of
E. coli. Orthologous genes in other genomes of known co-regulated sets
of genes in E. coli, along with their corresponding predicted operons,
and their predicted transcriptional regulators, shall permit the extension
of the previous goal to many more microbial genomes.
* Plenary lecture presented at the International Conference
on Bioinformatics 2002: North-South Networking, Bangkok, Thailand, 6-8
February 2002. Other presentations are presented in this issue, pp.
881-914.
** Corresponding author.
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