First published online July 24, 2003; 10.1104/pp.103.021485
Plant Physiology 132:2152-2165 (2003)
© 2003 American Society of Plant Biologists
GENETICS, GENOMICS, AND MOLECULAR EVOLUTION
Systematic Trans-Genomic Comparison of Protein Kinases between Arabidopsis and Saccharomyces cerevisiae1
Degeng Wang*,
Jeffrey F. Harper and
Michael Gribskov
San Diego Supercomputer Center and Department of Biology, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California
92093–0537 (D.W., M.G.); and Department of Cell Biology, The Scripps
Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
(J.F.H.)
The genome of the budding yeast (Saccharomyces cerevisiae)
provides an important paradigm for transgenomic comparisons with other
eukaryotic species. Here, we report a systematic comparison of the protein
kinases of yeast (119 kinases) and a reference plant Arabidopsis (1,019
kinases). Using a whole-protein-based, hierarchical clustering approach, the
complete set of protein kinases from both species were clustered. We validated
our clustering by three observations: (a) clustering pattern of functional
orthologs proven in genetic complementation experiments, (b) consistency with
reported classifications of yeast kinases, and (c) consistency with the
biochemical properties of those Arabidopsis kinases already experimentally
characterized. The clustering pattern identified no overlap between yeast
kinases and the receptor-like kinases (RLKs) of Arabidopsis. Ten more kinase
families were found to be specific for one of the two species. Among them, the
calcium-dependent protein kinase and phosphoenolpyruvate carboxylase
kinase families are specific for plants, whereas the
Ca2+/calmodulin-dependent protein kinase and provirus insertion in
mouse-like kinase families were found only in yeast and animals. Three yeast
kinase families, nitrogen permease reactivator/halotolerance-5), polyamine
transport kinase, and negative regulator of sexual conjugation and meiosis,
are absent in both plants and animals. The majority of yeast kinase families
(21 of 26) display Arabidopsis counterparts, and all are mapped into
Arabidopsis families of intracellular kinases that are not related to RLKs.
Representatives from 11 of the common families (54 kinases from Arabidopsis
and 17 from yeast) share an extremely high degree of similarity (blast E value
< 10-80), suggesting the likelihood of orthologous functions.
Selective expansion of yeast kinase families was observed in Arabidopsis. This
is most evident for yeast genes CBK1, HRR25, and SNF1 and the kinase family
S6K. Reduction of kinase families was also observed, as in the case of the
NEK-like family. The distinguishing features between the two sets of kinases
are the selective expansion of yeast families and the generation of a limited
number of new kinase families for new functionality in Arabidopsis, most
notably, the Arabidopsis RLKs that constitute important components of plant
intercellular communication apparatus.
1 This work was supported by the National Science Foundation (grant no.
DBI–9975808) and was assisted by the facilities of the National
Biomedical Computation Resource (through grant no. P41–RR08605 from the
National Institutes of Health National Center for Research Resources).
*
Corresponding author; e-mail
dwang{at}sdsc.edu;
fax 858–822–0873.
Received February 3, 2003;
returned for revision March 26, 2003;
accepted May 7, 2003.
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