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Bioinformatics Advance Access originally published online on October 25, 2005
Bioinformatics 2006 22(1):3-6; doi:10.1093/bioinformatics/bti739
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Published by Oxford University Press 2005
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PilZ domain is part of the bacterial c-di-GMP binding protein

Dorit Amikam 1,2 and Michael Y. Galperin 3,*

1Department of Biotechnology and Environmental Sciences, Tel-Hai Academic College Tel-Hai, Israel
2Sharett Institute of Oncology, Hadassah University Medical Center Ein-Kerem, Jerusalem, Israel
3National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, MD 20894, USA

*To whom correspondence should be addressed.

Recent studies identified c-di-GMP as a universal bacterial secondary messenger regulating biofilm formation, motility, production of extracellular polysaccharide and multicellular behavior in diverse bacteria. However, except for cellulose synthase, no protein has been shown to bind c-di-GMP and the targets for c-di-GMP action remain unknown. Here we report identification of the PilZ (‘pills’) domain (Pfam domain PF07238) in the sequences of bacterial cellulose synthases, alginate biosynthesis protein Alg44, proteins of enterobacterial YcgR and firmicute YpfA families, and other proteins encoded in bacterial genomes and present evidence indicating that this domain is (part of) the long-sought c-di-GMP-binding protein. Association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development.

Contact: galperin{at}ncbi.nlm.nih.gov

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

Received on October 17, 2005; revised on October 20, 2005; accepted on October 21, 2005

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