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

Minli Xu,Zhengchang Su

doi:10.1186/1471-2164-10-23

Abstract

BackgroundCyclic 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.ResultsWe 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 transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution.ConclusionThe CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The loss of CRPs in these species leads to the rapid loss of their binding sites in the genomes.

Highlights

Cyclic AMP receptor protein (CRP), known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria
Conservation of the DNA binding domain (DBD) of the CRP proteins in cyanobacterial genomes Using the bidirectional best hit (BDBH) algorithm and the criterion described in Methods, we identified orthologues of SyCRP1 of PCC 6803 (PCC6803) in 12 of the 29 sequenced cyanobacterial genomes
The residues of the DBD that are in direct interaction with the DNA counterpart as revealed by the crystal structure of E. coli CRP/DNA complex [39], are highly conserved in all these cyanobacterial CRP sequences, suggesting that they might bind to similar DNA sequences (Figure 1b)

Summary

Introduction

Cyclic AMP receptor protein (CRP), known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. Cyclic AMP receptor protein (CRP), known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in a variety of bacterial groups [1,2]. The CRP dimer is activated by the binding of two cAMP molecules to the effector binding domain of each subunit, which causes a conformational change in the DBDs, allowing each to bind to half of a specific pseudo-palindromic DNA sequence in the promoters of the genes that are under CRP regulation [13]. CRP interacts with the C-terminal domain of the alpha subunit of the RNA polymerase, affecting the RNA polymerase binding to the promoter, and leads to the change of the transcription initiation rate of the target gene [14,15,16,17,18]

Methods

Results

Discussion

Conclusion