First published online May 24, 2002; 10.1104/pp.004002
Plant Physiol, June 2002, Vol. 129, pp. 908-925
The Complement of Protein Phosphatase Catalytic Subunits Encoded
in the Genome of Arabidopsis1
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.)
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 (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.
1
This work was supported by the National Science
Foundation (grant nos. NSF ROA DBI-9975808/PTLOMA and NSF DBI: 9975808).
*
Corresponding author; e-mail dkerk{at}ptloma.edu; fax
619-849-2598.
© 2002 American Society of Plant Physiologists
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