Identification of sensory and signal-transducing domains in two-component signaling systems

Abstract

The availability of complete genome sequences of diverse bacteria and archaea makes comparative sequence analysis a powerful tool for analyzing signal transduction systems encoded in these genomes. However, most signal transduction proteins consist of two or more individual protein domains, which significantly complicates their functional annotation and makes automated annotation of these proteins in the course of large-scale genome sequencing projects particularly unreliable. This chapter describes certain common-sense protocols for sequence analysis of two-component histidine kinases and response regulators, as well as other components of the prokaryotic signal transduction machinery: Ser/Thr/Tyr protein kinases and protein phosphatases, adenylate and diguanylate cyclases, and c-di-GMP phosphodiesterases. These protocols rely on publicly available computational tools and databases and can be utilized by anyone with Internet access.

Figure 1

Sequence logo of the MASE3 domain, generated using the WebLogo (http://weblogo.berkeley.edu) tool from a multiple alignment of 35 different sequences of the MASE3 domain aligned to the Methanosarcina acetivorans histidine kinase MA_3481. Residue numbering starts from Gly-4 of the MA_3481 sequence.