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Online Journal of Bioinformatics

Volume 7 (2) : 57-68, 2006 .

Conservation of the regulatory pho-box in acetoacetyl-CoA reductase promoters
across bacterial PHB biosynthetic metabolic pathway

Khan F1, Singh SP2, Mishra BN3*

1,2,3 Department of Biotechnology, Institute of Engineering & Technology, U. P. Technical University, Sitapur Road, Lucknow-226021 (U.P.) INDIA



Khan F, Singh SP, Mishra BN Conservation of the regulatory pho-box in acetoacetyl-CoAreductase promoters across bacterial PHB biosynthetic metabolic pathway Onl J Bioinform., 7 (1) : 57-68, 2006. PhoB, a protein transcription factor common in many bacteria, activates expression of different pho genes participating in phosphate metabolism and regulates the phbB gene of polyhydroxyalkanoic acids (PHAs) in the biopolymer biosynthetic pathway. The DNA binding motifs or pho-box sequence for PhoB transcription factor has been characterized in the upstream sequences of regulated genes of both E. coli and Acinetobacter sp. This pattern information has been used for construction of new motif profile or matrix through existing different algorithms based tools for motif discovery viz. CONSENSUS & GIBBS SAMPLER tools at RSAT webserver and EM-algorithm based MEME tool. For evaluation of PFM performance, predicted results were first compared with the existing known PhoB matrix of RegulonDB; an E. coli regulatory network database. Orthologs of PhoB transcription factors were identified in the complete genomes of all studied bacteria. Candidate PhoB activator binding sites (or pho-box) were identified in the upstream sequences of putative regulated phbB gene orthologs of poly-β-hydroxybutyrate (PHB) metabolic pathway. The methodology involved new positional frequency matrix (PFM) construction through different algorithms based web tools and further statistical evaluation of prediction accuracy for each matrix. Finally PhoB consensus matrix was found appropriate in terms of prediction sensitivity and specificity and showed potential PhoB binding sites with 18 bp in length highly conserved pho-box like conserved DNA motifs (i.e. max. 81.28% sequence similarity with known pho-box motif). It was found that the PhoB recognition binding site is conserved in those completely sequenced bacterial genomes which have PHB biosynthetic metabolic pathway genes and contain genes encoding orthologous PhoB transcription factor. All studied genomes contain pho-box like consensus sequence, revealing the existence of an alternative phbB gene regulation in the PHB metabolic pathway or phbBAC operons. It was concluded that for efficient PHB biosynthesis, the acetoacetyl-CoA reductase is a limiting enzyme and only under condition of phosphate limitation, the PHB biosynthesis pathway would be optimally induced. 

Key-words:- PHA biopolymer, phbBCA operon, alternative regulation in PHA biosynthesis metabolic pathways, phbB gene orthologs, pho-box in PHB biosynthetic pathway, PhoB transcription factor, E. coli & Acinetobacter sp. as reference model bacteria for pho-box study.