P2CS: updates of the prokaryotic two-component systems database

Abstract

The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164,651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and homologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes. HK and RR trees are annotated with gene organization and domain architecture, providing insights into the evolutionary origin of the contemporary gene set. The majority of TCSs are encoded by adjacent HK and RR genes, however, 'orphan' unpaired TCS genes are also abundant and identifying their partner proteins is challenging. P2CS now provides paired HK and RR trees with proteins from the same genetic locus indicated. This allows the appraisal of evolutionary relationships across entire TCSs and in some cases the identification of candidate partners for orphan TCS proteins.

Figure 1.

Circular dendrogram from Hyphomicrobium sp. MC1. Each locus tag on the dendrogram provides a clickable link to a detailed gene description page.

Figure 2.

A section of the P2CS receiver domain dendrogram output for Hyphomicrobium sp. MC1. Bars beside each locus tag show gene organization, as defined previously (10) and colored according to the figure legend. Locus tags are colored according to similarity as defined in the text and the domain architecture and family membership is also indicated alongside the dendrogram.

Figure 3.

Paired dendrogram from Acetobacter pasteurianus IFO 3283–01. The tree of HK sequences (right) is presented opposite that of the receiver domains. Proteins that are encoded by paired genes are joined by purple/blue lines. Red lines connect domains within single hybrid or unorthodox HKs. Red squares next to locus tags indicate that the gene belongs to a locus containing four TCS genes (tetrad organization), blue squares indicate the domain belongs to one of a pair of TCS genes, while a yellow square denotes the gene is orphan.