The MiST2 database: a comprehensive genomics resource on microbial signal transduction

By Luke E. Ulrich, Igor B. Zhulin. 2009

277 citations recorded by the source corpus.

The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%).

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Direct-coupling analysis of residue coevolution captures native contacts across many protein families (2011, background): “To test this hypothesis, the bacterial two-component signaling (TCS) proteins (12) have been used due to the large number of TCS protein sequences, which numbered in the thousands already 5 years ago (13). Simple co-variance based analysis was first applied to characterize interactions between resid”
Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks (2011, neutral): “responses to environmental and cellular conditions [2].”
The Evolution of Two-Component Signal Transduction Systems (2012, background): “Extreme cases include Myxococcus xanthus, with 136 histidine kinases and 127 response regulators and Nostoc punctiforme, with 160 kinases and 98 regulators (81) (Figure 2).”
Microbial Surface Colonization and Biofilm Development in Marine Environments (2015, background): “2 Microbial Signal Transduction Database (last accessed 10 October 2014) predicted 421,394 gene sequences that encode TCS proteins (not including chemotactic proteins) from a total of 7,937 (complete and draft) bacterial and archaeal genomes (380).”