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Vol. 17, Issue 4, 1734-1743, April 2006

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A "Holistic" Kinesin Phylogeny Reveals New Kinesin Families and Predicts Protein Functions

Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom

Submitted November 30, 2005; Revised February 2, 2006; Accepted February 3, 2006
Monitoring Editor: Tim Stearns

Kinesin superfamily proteins are ubiquitous to all eukaryotes and essential for several key cellular processes. With the establishment of genome sequence data for a substantial number of eukaryotes, it is now possible for the first time to analyze the complete kinesin repertoires of a diversity of organisms from most eukaryotic kingdoms. Such a "holistic" approach using 486 kinesin-like sequences from 19 eukaryotes and analyzed by Bayesian techniques, identifies three new kinesin families, two new phylum-specific groups, and unites two previously identified families. The paralogue distribution suggests that the eukaryotic cenancestor possessed nearly all kinesin families. However, multiple losses in individual lineages mean that no family is ubiquitous to all organisms and that the present day distribution reflects common biology more than it does common ancestry. In particular, the distribution of four families—Kinesin-2, -9, and the proposed new families Kinesin-16 and -17—correlates with the possession of cilia/flagella, and this can be used to predict a flagellar function for two new kinesin families. Finally, we present a set of hidden Markov models that can reliably place most new kinesin sequences into families, even when from an organism at a great evolutionary distance from those in the analysis.

The online version of this article contains supplemental material at MBC Online (http://www.molbiolcell.org).

Address correspondence to: Bill Wickstead (bill.wickstead{at}path.ox.ac.uk).

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