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Online Journal of Bioinformatics ©
Volume 12(1):167-174, 2011
Detection and classification of two-component osmoregulatory systems
Srividhya K V and S Krishnaswamy.
Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai-625021, Tamilnadu, India
Srividhya KV, Krishnaswamy S., Detection and classification of two-component osmoregulatory systems, Onl J Bioinform., 12(1):167-174, 2011. Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as in some plants, fungi, protozoa and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, thereby causing a change in cellular behavior. Osmoregulation is one of the well studied two-component system operative in bacteria and plays a crucial role in regulating the cellular response to varied solute environments. In E coli EnvZ, a transmembrane protein acts as sensor and its cognate response regulator OmpR coordinates the osmoregulatory switch by controlling the expression of porins, OmpC and OmpF. In this report, genome-wide identification of osmoregulatory two-component protein orthologs has been carried out. 29 genomes are associated with EnvZ-OmpR system, which clustered into 6 subgroups based on genus with both EnvZ and OmpR from all sources clustering together. 17 E coli encoded two-component systems are homologous to EnvZ-OmpR. With EnvZ and OmpR all domain loci are conserved. The sensor and regulator partners show same clustering trends. Hidden Markov models (HMMs) built for EnvZ sensor kinase and OmpR response regulators families were used to search for homologs in other species. 39 two component systems were identified using PSI BLAST and HMM based approach. All tend to be conserved only in the domain locus. Most of them are systems associated with stress mediated responses. Most of sensors and their regulators fetched from different search methods using EnvZ -OmpR systems as template are also seen to be co-evolved. In conclusion, analysis revealed the homology of osmoregulatory family with most of the stress related or adaptive response related two-component systems.
Keywords: Osmoregulation, EnvZ, OmpR, Porins, profile searches, two-component system