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Abstract
Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.
Highlights
Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell
For two types of eukaryotic bacterial-like phosphoprotein phosphatases (PPPs) investigated here (SLPs and RLPHs), a well-supported group of sequences from a-Proteobacteria lies in close association in phylogenetic trees
The most straightforward interpretation of this observation is that these bacteriallike PPP genes entered eukaryotes very early in their history, with the advent of mitochondria
Summary
Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Utilizing a number of in silico bioinformatic techniques and available sequenced genomes, the molecular evolution of three bacterial-like PPP classes found in eukaryotes is revealed to involve ancient mitochondrial or archaeal origin plus additional possible LGT events. The large sequence collections compiled here have allowed the elucidation of two highly conserved C-terminal domain motifs, which are specific to each bacterial-like PPP class and whose differences are pronounced in photosynthetic eukaryotes. Together, these findings substantially expand our knowledge of the molecular evolution of the bacterial-like PPPs and point the way toward attractive future research avenues
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