"PP2C7s", Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases

• Published in: PloS one 2015-08, Vol.10 (8), p.e0132863-e0132863
• Main Authors: Kerk, David, Silver, Dylan, Uhrig, R Glen, Moorhead, Greg B G
• Format: Article
• Language: English
• Subjects: Algae; Arabidopsis; Arabidopsis thaliana; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Binding; Catalysis; Chlamydia; Chlorophyta - enzymology; Chlorophyta - genetics; Chloroplasts - enzymology; Dephosphorylation; Distillation; Enzymes; Eukaryotes; Evolution; Evolution, Molecular; Gene expression; Gene Expression Regulation, Plant; Gene Regulatory Networks; Gene sequencing; Gene transfer; Genes, Plant; Genetic aspects; Genomes; Genomics; Homology; Kinases; Localization; Magnesium; Magnesium - physiology; Manganese; Markov chains; Metabolism; Metal ions; Metals; Mitochondria; Mitochondria - enzymology; Molecular biology; Molecular Structure; Pathogens; Phosphatase; Phosphoprotein Phosphatases - chemistry; Phosphoprotein Phosphatases - genetics; Phosphorylation; Photosynthesis; Photosynthesis - genetics; Phylogenetics; Phylogeny; Physiological aspects; Plant Proteins - chemistry; Plant Proteins - genetics; Plant sciences; Plant tissues; Plants - enzymology; Plants - genetics; Plastids; Prokaryotes; Protein kinases; Protein Phosphatase 2C; Protein Structure, Secondary; Proteins; Sequence Alignment; Sequence Homology, Amino Acid; Starch; Starch - metabolism; Target recognition; Terminal protein; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0132863

Mg+2/Mn+2-dependent type 2C protein phosphatases (PP2Cs) are ubiquitous in eukaryotes, mediating diverse cellular signaling processes through metal ion catalyzed dephosphorylation of target proteins. We have identified a distinct PP2C sequence class ("PP2C7s") which is nearly universally distributed in Eukaryotes, and therefore apparently ancient. PP2C7s are by far most prominent and diverse in plants and green algae. Combining phylogenetic analysis, subcellular localization predictions, and a distillation of publically available gene expression data, we have traced the evolutionary trajectory of this gene family in photosynthetic eukaryotes, demonstrating two major sequence assemblages featuring a succession of increasingly derived sub-clades. These display predominant expression moving from an ancestral pattern in photosynthetic tissues toward non-photosynthetic, specialized and reproductive structures. Gene co-expression network composition strongly suggests a shifting pattern of PP2C7 gene functions, including possible regulation of starch metabolism for one homologue set in Arabidopsis and rice. Distinct plant PP2C7 sub-clades demonstrate novel amino terminal protein sequences upon motif analysis, consistent with a shifting pattern of regulation of protein function. More broadly, neither the major events in PP2C sequence evolution, nor the origin of the diversity of metal binding characteristics currently observed in different PP2C lineages, are clearly understood. Identification of the PP2C7 sequence clade has allowed us to provide a better understanding of both of these issues. Phylogenetic analysis and sequence comparisons using Hidden Markov Models strongly suggest that PP2Cs originated in Bacteria (Group II PP2C sequences), entered Eukaryotes through the ancestral mitochondrial endosymbiosis, elaborated in Eukaryotes, then re-entered Bacteria through an inter-domain gene transfer, ultimately producing bacterial Group I PP2C sequences. A key evolutionary event, occurring first in ancient Eukaryotes, was the acquisition of a conserved aspartate in classic Motif 5. This has been inherited subsequently by PP2C7s, eukaryotic PP2Cs and bacterial Group I PP2Cs, where it is crucial to the formation of a third metal binding pocket, and catalysis.