In silico identification of a putative two-component system in Pectobacterium brasiliense

Abstract

Two component systems (TCSs) are one of the predominant methods for bacteria to detect and respond to environmental change. A typical TCS consists of a histidine kinase (HK), responsible for sensing inter- and intracellular changes, and a response regulator (RR) which as the name suggests responds to the detected stimuli, mostly by regulating DNA expression. In this project two predicted domains (Response_reg-like and HEF_like) were detected in 628 bacteria strains which share a high similarity to typical HKs and RRs with a 91.6% linkage observed across 644 genomic regions. The adjacent co-localisation between these genes carrying the novel predicted domains in addition to the conserved structural features of typical HKs and RRs, indicate that the Response_reg-like and HEF_HK-like domains could incorporate a new TCS in bacteria. With these HEF_HK-like and Response_reg-like domains, an overrepresented presence of restriction modification (RM) systems, especially type II RM was observed. The established presence of RM systems in the GHKL family domain HATPase_c_3 across most of the HEF_HK-containing genes could indicate an evolutionary relationship with the paraMORC family of ATPases. The aim of this project was to functionally characterize the putative HK and ultimately the entire novel TCS in Pectobacterium carotovorum subsp. brasiliense 1692 and optimise mutation analysis protocols for effective use in this enterobacteria species.