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Volume 3

Special Issue
BGRS 2002

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In Silico Biology 3, 0002 (2003); ©2002, Bioinformation Systems e.V.  

Bioinformatics classification and functional analysis of PhoH homologs

Alexei E. Kazakov1, Olga Vassieva2, *, Mikhail S. Gelfand1, Andrei Osterman3, Ross Overbeek3

1 Integrated Genomics Inc., Postbox 348, 117333, Moscow, Russia
2 CXR Biosciences, James Lindsay Place, DD15JJ , Dundee UK
3 Integrated Genomics Inc.,2201 W.Campbell Park Dr., Chicago, IL 60612

* corresponding author

Edited by D. Landsman; received September 30, 2002; revised and accepted December 10, 2002; published December 30, 2002


PhoH protein is a putative ATPase belonging to the phosphate regulon in Escherichia coli. EC-PhoH homologs are present in different organisms, but it is not clear if they are functionally related, besides nothing is known about their regulation. To distinguish true functional orthologs of EC-PhoH in different classes of bacteria and to identify their functional role in bacterial metabolic network we performed phylogenetic analysis of these proteins and comparative study of position and regulation of the related genes. Three groups of proteins were identified. Proteins of the first group (BS-PhoH orthologs) are present in most of bacteria and are proposed to be functionally linked to phospholipid metabolism and RNA modification. Proteins of the second group (BS-YlaK orthologs) are present in most of aerobes and Actinobacterial YlaK orthologs are shown to be members of a fatty acid beta-oxidation regulons. EC-PhoH orthologs are classified in a third group, specific for Enterobacteria. Functional role of PhoH homologs in the lipid and RNA metabolism and proposed interrelation of PhoH paralogs in one organism are discussed.

Key words: PhoH, regulon, Mycobacterium, phylogenetic analysis, gene clusters, phospholipid