Published online 31 May 2006
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Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
Division of Gene Regulation and Expression, University of Dundee Dundee DD1 5EH, Scotland, UK 1 Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of Dundee Dundee DD1 5EH, Scotland, UK
*To whom correspondence should be addressed. Tel: +44 0 1382 385796; Fax: +44 0 1382 388702; Email: t.a.owenhughes{at}dundee.ac.uk
Received February 3, 2006. Revised March 18, 2006. Accepted April 5, 2006.
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
Present address: Andrew Flaus, Department of Biochemistry, National University of Ireland Galway, Ireland
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