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DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
Published on: July 21, 2014
P2CS: a two-component system resource for prokaryotic signal transduction research
Mohamed Barakat1, Philippe Ortet, Cécile Jourlin-Castelli
1CEA, DSV, IBEB, LEMiRE, CNRS, Université Aix-Marseille II, CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France. mohamed.barakat@cea.fr
BMC Genomics
|July 17, 2009
Summary
A new database, Prokaryotic 2-Component Systems (P2CS), catalogs two-component system (TCS) signal transduction proteins from prokaryotic genomes and metagenomes. P2CS aids in the computational analysis of these crucial microbial regulatory systems.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- High-throughput prokaryotic genome sequencing necessitates comprehensive databases for gene and genome characterization.
- Two-component system (TCS) signal transduction pathways are vital for microbial environmental sensing and response.
- TCSs regulate diverse physiological adjustments, including gene expression and enzymatic activity.
Purpose of the Study:
- To develop an integrated and comprehensive database for prokaryotic two-component system (TCS) signal transduction proteins.
- To facilitate the cataloging and characterization of TCS genes across prokaryotic genomes and metagenomes.
- To improve the recovery of TCS proteins by addressing gene underestimation in genome annotation.
Main Methods:
- Compilation of TCS genes from 755 completely sequenced prokaryotic genomes and 39 metagenomes.
- Detailed annotation of TCS genes, including family classification, sequence features, and functional domains.
- Utilized an ORFeome search strategy to enhance TCS protein recovery compared to proteome searches.
Main Results:
- The Prokaryotic 2-Component Systems (P2CS) database integrates TCS data from a large collection of prokaryotic genomes and metagenomes.
- P2CS offers detailed gene annotation and genomic context visualization for identified TCS proteins.
- The ORFeome approach improved the detection of TCS proteins.
Conclusions:
- P2CS provides a valuable resource for the computational analysis of prokaryotic TCSs.
- The database offers a comprehensive overview of TCS information, including predicted and probable candidate proteins requiring validation.
- P2CS is accessible via a user-friendly web interface for querying and browsing.
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