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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
ABSTRACT
Khan F, Singh SP, Mishra BN Conservation
of the regulatory pho-box in acetoacetyl-CoAreductase promoters across bacterial PHB biosynthetic
metabolic pathway Online J Bioinformatics 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.