Genomic analysis of the histidine kinase family in bacteria and archaea

Two-component signal transduction systems, consisting of histidine kinase ( HK) sensors and DNA-binding response regulators, allow bacteria and archaea to respond to diverse environmental stimuli. HKs possess a conserved domai n (H-box region) which contains the site of phosphorylation and an ATP-bind ing kinase domain. In this study, a genomic approach was taken to analyse t he HK family in bacteria and archaea. Based on phylogenetic analysis, diffe rences in the sequence and organization of the H-box and kinase domains, an d the predicted secondary structure of the H-box region, five major HK type s were identified. Of the 336 HKs analysed, 92% could be assigned to one of the five major HK types. The Type I HKs were found predominantly in bacter ia while Type II HKs were not prevalent in bacteria but constituted the maj or type (13 of 15 HKs) in the archaeon Archaeoglobus fulgidus. Type III HKs were generally more prevalent in Gram-positive bacteria and were the major HK type (14 of 15 HKs) in the archaeon Methanobacterium thermoautotrophicu m. Type IV HKs represented a minor type found in bacteria. The fifth HK typ e was composed of the chemosensor HKs, CheA. Several bacterial genomes cont ained all five HK types. In contrast, archaeal genomes either contained a s pecific HK type or lacked HKs altogether. These findings suggest that the d ifferent HK types originated in bacteria and that specific HK types were ac quired in archaea by horizontal gene transfer.