Conservation of Gene Co-Regulation between Two Prokaryotes: Bacillus subtilis and Escherichia coli

Shujiro Okuda[1] (okuda@kuicr.kyoto-u.ac.jp)
Shuichi Kawashima[2] (shuichi@hgc.jp)
Susumu Goto[1] (goto@kuicr.kyoto-u.ac.jp)
Minoru Kanehisa[1] (kanehisa@kuicr.kyoto-u.ac.jp)

[1]Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan


Abstract

We measured conservation of gene co-regulation between two distantly related prokaryotes, B. subtilis and E. coli. The co-regulation between genes was extracted from knowledge of regulation of genes stored in databases. For B. subtilis operons, we obtained the data set from ODB which we have developed and, for the regulons, we used DBTBS. For E. coli data set, we used known regulons derived from RegulonDB. We obtained a reliable data set of co-regulated genes in B. subtilis and E. coli. About 60-80 % of gene pairs conserved co-regulation relationships, so co-regulation between genes are highly conserved even between distantly related species. To measure the functional relationship between these conserved genes, we used KEGG PATHWAY and COG. When two co-regulated genes are in the same biological pathway in KEGG or share the same functional category in COG, we assume that they have the same function. As a result, we also found that many conserved co-regulated gene pairs share the same functions. These observations would help to predict gene co-regulation and protein functions.

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Japanese Society for Bioinformatics