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Bioinformatics Advance Access published online on March 16, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl096
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Published by Oxford University Press 2006
Received February 18, 2006
Revised March 9, 2006
Accepted March 10, 2006

Article

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

Kira S. Makarova 1, Eugene V. Koonin 1, Robert Haselkorn 2, and Michael Y. Galperin 1 *

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
2 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA

* To whom correspondence should be addressed.
Michael Y. Galperin, E-mail: galperin{at}ncbi.nlm.nih.gov


  Abstract

The cyanobacterium Anabaena (Nostoc) PCC 7120 responds to starvation for nitrogen compounds by differentiating approximately every tenth cell in the filament into nitrogen-fixing cells called hetero-cysts. Heterocyst formation is subject to complex regulation, which involves an unusual response regulator PatA that contains a CheY-like phosphoacceptor (receiver, REC) domain at its C-terminus. PatA-like response regulators are widespread in cyanobacteria; one of them regulates phototaxis in Synechocystis PCC 6803. Sequence analysis of PatA revealed, in addition to the REC domain, a previously undetected, conserved domain, which we named PATAN (after PatA N-terminus), and a potential helix-turn-helix (HTH) domain. PATAN domains are encoded in a variety of environmental bacteria and archaea, often in several copies per genome, and are typically associated with REC, Roadblock, and other signal transduction domains, or with DNA-binding HTH domains. Many PATAN domains contain insertions of a small additional domain, termed {alpha}-clip, which is predicted to form a four-helix bundle. PATAN domains appear to participate in protein-protein interactions that regulate gliding motility and processes of cell development and differentiation in cyanobacteria and some proteobacteria, such as Myxococcus xanthus and Geobacter sulfurreducens.

Supplementary information: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PATAN.html.

Associate Editor: Alex Bateman
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