Evolutionary Radiation Pattern of Novel Protein Phosphatases Revealed by Analysis of Protein Data from the Completely Sequenced Genomes of Humans, Green Algae, and Higher Plants

Abstract

In addition to the major serine/threonine-specific phosphoprotein phosphatase, Mg 21 -dependent phosphoprotein phosphatase, and protein tyrosine phosphatase families, there are novel protein phosphatases, including enzymes with aspartic acidbased catalysis and subfamilies of protein tyrosine phosphatases, whose evolutionary history and representation in plants is poorly characterized. We have searched the protein data sets encoded by the well-finished nuclear genomes of the higher plants Arabidopsis (Arabidopsis thaliana) and Oryza sativa, and the latest draft data sets from the tree Populus trichocarpa and the green algae Chlamydomonas reinhardtii and Ostreococcus tauri, for homologs to several classes of novel protein phosphatases. The Arabidopsis proteins, in combination with previously published data, provide a complete inventory of known types of protein phosphatases in this organism. Phylogenetic analysis of these proteins reveals a pattern of evolution where a diverse set of protein phosphatases was present early in the history of eukaryotes, and the division of plant and animal evolution resulted in two distinct sets of protein phosphatases. The green algae occupy an intermediate position, and show similarity to both plants and animals, depending on the protein. Of specific interest are the lack of cell division cycle (CDC) phosphatases CDC25 and CDC14, and the seeming adaptation of CDC14 as a protein interaction domain in higher plants. In addition, there is a dramatic increase in proteins containing RNA polymerase C-terminal domain phosphatase-like catalytic domains in the higher plants. Expression analysis of Arabidopsis phosphatase genes differentially amplified in plants (specifically the C-terminal domain phosphatase-like phosphatases) shows patterns of tissue-specific expression with a statistically significant number of correlated genes encoding putative signal transduction proteins.

Signal processing by protein tyrosine phosphorylation in plants

“…In Arabidopsis thaliana, more than 800 PKs 6 and 150 PPs 5 have been identified. Phosphorylation is mostly found on hydroxylated amino acids such as serine (Ser), threonine (Thr) and tyrosine (Tyr).…”

“…Abbreviations: PTM, post-translational modification; Ser, serine; Thr, threonine; Tyr, tyrosine; PTK, protein tyrosine kinase; Ds, dual-specificity; PTP, protein tyrosine phosphatase; MAPK, mitogen-activated protein kinase; PAO, phenylarsine oxide; TLK, tyrosine-specific protein kinase-like kinase; MS, mass spectrometry; CID, collision-induced dissociation; ECD, electron capture dissociation; ETD, electron transfer dissociation; BR, brassinosteroid; ABA, abscisic acid; SH 2 , Src homology 2 and approximately 148 PPs 5 indicating the importance of protein phosphorylation. In Arabidopsis thaliana, more than 800 PKs 6 and 150 PPs 5 have been identified.…”

Okadaic acid and microcystin insensitive PPP-family phosphatases may represent novel biotechnology targets

“…3,8 Each of these protein phosphatases are related at the primary sequence level and display a general sensitivity to an array of small molecule and protein inhibitors including only one SLP phosphatase. 6,7 Having a single SLP enzyme appears to parallel a lack of a plastid or vestigial plastid and may account for an evolutionary history that determines whether an organism has one vs. two SLPs.…”

“…1,2 In Plantae and Metazoa alike the protein phosphatases are comprised of four main classes: the phospho-protein phosphatases (PPP), Mg 2+ -dependent phospho-protein phosphatases (PPM/PP2C), phospho-tyrosine phosphatases (PTP) and Asp-based phosphatases. [3][4][5] Previous efforts to directly compare the protein phosphatase complement of A. thaliana and H. sapiens found many similarities, emphasizing the central and conserved nature of protein phosphatases across diverse eukaryotes. 3 However, this comparison also revealed a number of differences.…”

“…[3][4][5] Previous efforts to directly compare the protein phosphatase complement of A. thaliana and H. sapiens found many similarities, emphasizing the central and conserved nature of protein phosphatases across diverse eukaryotes. 3 However, this comparison also revealed a number of differences. One striking feature was the presence of PPP-family protein phosphatases in A. thaliana that were absent in H. sapiens.…”