Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes.

BMC Genomics
Minli Xu, Zhengchang Su

Abstract

Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal tr...Continue Reading

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Citations

Jun 10, 2011·Molecular Biology and Evolution·Alexis Criscuolo, Simonetta Gribaldo
Oct 6, 2010·BMC Genomics·Shan LiZhengchang Su
Mar 31, 2009·Future Microbiology·Kristina JonasUte Römling
Apr 21, 2016·Biotechnology for Biofuels·Nadin PadeMartin Hagemann
Oct 2, 2015·Visual Neuroscience·Bruce C HansenEdward A Essock

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Datasets Mentioned

BETA
MBIC11017

Methods Mentioned

BETA
footprinting
phylogenetic footprinting
electrophoresis

Software Mentioned

ClustalW
CUBIC
MEGA
OFS
Operon Finder Software ( OFS )
BLASTP
BioProspector

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