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OJB®
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 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.
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