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Published on May 24, 2002; 10.1104/pp.004002

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Received February 7, 2002
Returned for revision March 5, 2002
Accepted May 4, 2002

The Complement of Protein Phosphatase Catalytic Subunits Encoded in the Genome of Arabidopsis

David Kerk *, Joshua Bulgrien , Douglas W. Smith , Brooke Barsam , Stella Veretnik , and Michael Gribskov

Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106 (D.K., J.B., B.B.); Division of Biology, 0116, University of California San Diego, La Jolla, California 92093--0116 (D.W.S.); and San Diego Supercomputer Center, 0505, University of California San Diego, La Jolla, California 92093--0505 (S.V., M.G.)

* Corresponding author; email: dkerk{at}ptloma.edu.

Reversible protein phosphorylation is critically important in the modulation of a wide variety of cellular functions. Several families of protein phosphatases remove phosphate groups placed on key cellular proteins by protein kinases. The complete genomic sequence of the model plant Arabidopsis permits a comprehensive survey of the phosphatases encoded by this organism. Several errors in the sequencing project gene models were found via analysis of predicted phosphatase coding sequences. Structural sequence probes from aligned and unaligned sequence models, and all-against-all BLAST searches, were used to identify 112 phosphatase catalytic subunit sequences, distributed among the serine (Ser)/threonine (Thr) phosphatases (STs) of the protein phosphatase P family (PPP) family, STs of the protein phosphatase M (PPM) family (protein phosphatases 2C [PP2Cs] subfamily, protein tyrosine (Tyr) phosphatases (PTPs), low-Mr protein Tyr phosphatases, and dual-specificity (Tyr and Ser/Thr) phosphatases (DSPs). The Arabidopsis genome contains an abundance of PP2Cs (69) and a dearth of PTPs (one). Eight sequences were identified as new protein phosphatase candidates: five dual-specificity phosphatases and three PP2Cs. We used phylogenetic analyses to infer clustering patterns reflecting sequence similarity and evolutionary ancestry. These clusters, particularly for the largely unexplored PP2C set, will be a rich source of material for plant biologists, allowing the systematic sampling of protein function by genetic and biochemical means.




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