Two-component system (TCS) signal transduction pathways, are found across all three domains of life allowing adaptive responses to changes in environmental conditions. However, they are mainly found in bacteria where they control multiple aspects of bacterial metabolism, such as cell differentiation and morphogenesis, central metabolism, motility, biofilm formation and virulence. These systems were classically described as the association of two proteins that communicate through a His-Asp phosphorelay. Typical TCSs comprise a histidine kinase sensor protein which is capable of autophosphorylation on a conserved His residue, before transferring the phosphoryl group to a conserved Asp residue within the receiver domain (REC) of a response regulator.
The large number of TCS protein sequences available demands user-friendly databases to facilitate inter-genomic and intra-genomic analyses. We have therefore developed a novel resource, the P2CS (Prokaryotic 2-Component Systems) database, that contains the TCSs of all available bacterial and archaeal genomes, and 39 metagenomes. Our objective was to provide an easy to use environment for validation by experts, according to their fields/organisms of interest, with the data being completely available and consultable by all of the scientific community.
From the P2CS website the user can:
Browse genome and metagenome TCS predictions and manually curated proteins
Search for a sequence id or domain family
The P2CS homepage contains a navigation bar that allows database browsing. Among the menus, users will also find P2CS Browse, which links directly to sortable lists of analysed genomes, plasmids and metagenomes.
The P2CS database contains the TCSs of all available bacterial and archaeal genomes, and 39 metagenomes.
The selection of a microbe or microbiome displays the result of the P2CS analysis process.
The genome page contains clickable links to RR and HK trees, heatmaps and double dendrograms displaying TCS proteins associations (replicons with more than 10 RRs and 10 HKs). These pages include several options such as zooming in or out.
The genome page shows also global counts of the different categories of TCSs and detailed class counts of each category. Each class result provides a clickable link to a detailed gene list.
It shows also a search module, based on :
á gene name
á gi number
Selecting an object from the list identifiers displays a detailed gene description page with an image representing the gene in the appropriate frame. Red vertical lines represent stop codons and green lines represent potential start codons.
Blast searches can be performed for the sequence, using external links to numerous databases.
The gene description page contains a link to a cartographic gene context (Chromosome Region View), with several options such as zooming in or out, moving along the chromosome, displaying genes in upstream or downstream regions and drawing genes.
P2CS was designed to allow download of TCS data in tab-delimited format and generates a file compatible with spreadsheet programs such as Excel. Users can also download for each genome and metagenome a multi-Fasta file (nucleotide or protein sequences).
An example of a Excel file output.