title: The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis.
abstract: 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-M(r) 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.
authors.affiliation: Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, CA 92106, USA. dkerk@ptloma.edu
authors.forename: David
authors.initials: D
authors.lastname: Kerk
authors.forename: Joshua
authors.initials: J
authors.lastname: Bulgrien
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Smith
authors.forename: Brooke
authors.initials: B
authors.lastname: Barsam
authors.forename: Stella
authors.initials: S
authors.lastname: Veretnik
authors.forename: Michael
authors.initials: M
authors.lastname: Gribskov
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics; D020134:Catalytic Domain / Q000235:genetics; D030561:Databases, Nucleic Acid; D054637:Dual-Specificity Phosphatases; D019143:Evolution, Molecular; D018745:Genome, Plant; D006801:Humans; D054639:Mitogen-Activated Protein Kinase Phosphatases; D010749:Phosphoprotein Phosphatases / Q000235:genetics*; D010802:Phylogeny; D054648:Protein Phosphatase 2; D000071636:Protein Phosphatase 2C; D017027:Protein Tyrosine Phosphatases / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D054639:Mitogen-Activated Protein Kinase Phosphatases; C087358:PTC1 protein, S cerevisiae; D010749:Phosphoprotein Phosphatases; D054648:Protein Phosphatase 2; D000071636:Protein Phosphatase 2C; C442824:DUSP22 protein, human; D054637:Dual-Specificity Phosphatases; D017027:Protein Tyrosine Phosphatases