P2CS: updates of the prokaryotic two-component systems database

Philippe Ortet (1, 2) , David E. Whitworth (3) , Catherine Santaella (2, 1) , Wafa Achouak (2, 1) , ​mohamed Barakat (2, 1)

1 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
2 BVME - Biologie végétale et microbiologie environnementale - UMR7265
3 IBERS - Institute of Biological, Environmental and Rural Sciences

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 ho-mologous 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.

Mots clés: SIGNAL-TRANSDUCTION SYSTEMS; MULTIPLE SEQUENCE ALIGNMENT; RESOURCE; INFORMATION; EVOLUTION; PROTEINS

Domaines: Biologie végétale

Philippe Ortet, David E. Whitworth, Catherine Santaella, Wafa Achouak, ​mohamed Barakat. P2CS: updates of the prokaryotic two-component systems database. Nucleic Acids Research, 2015, 43, pp.D536-D541. ⟨10.1093/nar/gku968⟩. ⟨hal-01229516⟩