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

Kerk D, Silver D, Uhrig RG, Moorhead GB - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
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.

No MeSH data available.


Phylogenetic orthogonal tree depicting interrelationships between representative PP2C7 sequences from plants, green algae, and fungi.Inference of unrooted phylogenetic trees was performed as outlined in “Materials and Methods.” A typical example is shown. The most crucial nodes are labeled. Node support values with the four inference methods (PhyML [aBayes], RAxML [RBS], MrBayes [PP], PhyloBayes_MPI [PP]) are tabulated in the Figure, separated by slashes (“/”). Support values for all trees are summarized in Table N in S1 File. Predicted in silico subcellular localizations are represented as follows: Ch, chloroplast; Cy, cytosol; M, mitochondria; S, signal peptide; Unk (unknown), sequence fragment lacking native amino terminus. Sequences used in phylogenetic tree generation are listed in Table A in S1 File, while compiled in silico subcellular localization data can be found in Table B in S1 File (non-photosynthetic organisms) and Table F in S1 File (photosynthetic organisms). * = Three algal sequences included in this cluster.
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pone.0132863.g003: Phylogenetic orthogonal tree depicting interrelationships between representative PP2C7 sequences from plants, green algae, and fungi.Inference of unrooted phylogenetic trees was performed as outlined in “Materials and Methods.” A typical example is shown. The most crucial nodes are labeled. Node support values with the four inference methods (PhyML [aBayes], RAxML [RBS], MrBayes [PP], PhyloBayes_MPI [PP]) are tabulated in the Figure, separated by slashes (“/”). Support values for all trees are summarized in Table N in S1 File. Predicted in silico subcellular localizations are represented as follows: Ch, chloroplast; Cy, cytosol; M, mitochondria; S, signal peptide; Unk (unknown), sequence fragment lacking native amino terminus. Sequences used in phylogenetic tree generation are listed in Table A in S1 File, while compiled in silico subcellular localization data can be found in Table B in S1 File (non-photosynthetic organisms) and Table F in S1 File (photosynthetic organisms). * = Three algal sequences included in this cluster.

Mentions: Structure-guided alignments were made from sets of PP2C sequences with solved structures using the 3DCOMB function of the RaptorX server ([38, 39]; http://raptorx.uchicago.edu/DeepAlign/submit/). Solved structures used were: ((1A6Q, 2P8E, 2I0O, 2IQ1 –eukaryotic PP2Cs); (1TXO, 2PK0, 2JFR, 2J82 –bacterial Group I); (3ES2, 3W40, 3ZT9 –bacterial Group II)). Additional sequences (eukaryotic PP2C7s) were added with the sequence to profile function of ClustalO [40, 41] at the Mobyle Portal (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-sequence). Alignments were then visualized and hand-edited within GeneDoc ([42]; http://www.nrbsc.org/gfx/genedoc/). In some instances local sequence regions were further aligned using a regional re-alignment capability of MAFFT (Ruby script kindly supplied by Dr. Kazutaka Katoh, modified for Windows by Justin Kerk) (http://mafft.cbrc.jp/alignment/software/regionalrealignment.html) using the following parameters (treeoption—6merpair; realign—localpair—maxiterate 100—bl 45—op 3.0). Phylogenetic trees were inferred as detailed below. This procedure formed the basis for the alignment corresponding to the phylogenetic trees presented in Figs 1, 2 and 3 (Fig A in S2 File (Panel 1)), and the alignment in Fig 7. A large alignment consisting of eukaryotic PP2C7, bacterial Group II, bacterial Group I and the PP2C sets from human and Arabidopsis was initially constructed by MAFFT ([43]; http://mafft.cbrc.jp/alignment/server/), using the BLOSUM45 scoring matrix, and the E-INS-I option (multiple conserved domains and long gaps). Editing of this alignment within GeneDoc was guided by the previous structure-guided alignments detailed above. At some points in the editing process the above cited MAFFT regional realignment procedure was also used. This procedure formed the basis for the alignment in Fig A in S2 File (Panel 4) (corresponding to the phylogenetic tree presented as Fig 6). Finally, large sets of bacterial Group II PP2Cs (GNG2s), with either PP2C7s or eukaryotic PP2Cs, were aligned with MAFFT, using the BLOSUM45 scoring matrix with the E-INS-I option, and manually edited within GeneDoc. In order to decrease the computational load during tree inference, the bacterial Group II component of these alignments was pruned to sequences sharing 80% identity or less, using the ExPasy “Decrease Redundancy” tool (http://web.expasy.org/decrease_redundancy/). This procedure formed the basis for the alignments in Fig A of S2 File (Panels 2, 3, and 5) (corresponding to the phylogenetic trees presented as Figs 4, 5, and Fig E in S2 File.). As necessary during this multiple sequence alignment work, files were interconverted between various formats using the online format converters at either the Mobyle Portal (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::squizz_convert), or the Phylogeny.fr site (http://www.phylogeny.fr/version2_cgi/data_converter.cgi).


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

Kerk D, Silver D, Uhrig RG, Moorhead GB - PLoS ONE (2015)

Phylogenetic orthogonal tree depicting interrelationships between representative PP2C7 sequences from plants, green algae, and fungi.Inference of unrooted phylogenetic trees was performed as outlined in “Materials and Methods.” A typical example is shown. The most crucial nodes are labeled. Node support values with the four inference methods (PhyML [aBayes], RAxML [RBS], MrBayes [PP], PhyloBayes_MPI [PP]) are tabulated in the Figure, separated by slashes (“/”). Support values for all trees are summarized in Table N in S1 File. Predicted in silico subcellular localizations are represented as follows: Ch, chloroplast; Cy, cytosol; M, mitochondria; S, signal peptide; Unk (unknown), sequence fragment lacking native amino terminus. Sequences used in phylogenetic tree generation are listed in Table A in S1 File, while compiled in silico subcellular localization data can be found in Table B in S1 File (non-photosynthetic organisms) and Table F in S1 File (photosynthetic organisms). * = Three algal sequences included in this cluster.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524716&req=5

pone.0132863.g003: Phylogenetic orthogonal tree depicting interrelationships between representative PP2C7 sequences from plants, green algae, and fungi.Inference of unrooted phylogenetic trees was performed as outlined in “Materials and Methods.” A typical example is shown. The most crucial nodes are labeled. Node support values with the four inference methods (PhyML [aBayes], RAxML [RBS], MrBayes [PP], PhyloBayes_MPI [PP]) are tabulated in the Figure, separated by slashes (“/”). Support values for all trees are summarized in Table N in S1 File. Predicted in silico subcellular localizations are represented as follows: Ch, chloroplast; Cy, cytosol; M, mitochondria; S, signal peptide; Unk (unknown), sequence fragment lacking native amino terminus. Sequences used in phylogenetic tree generation are listed in Table A in S1 File, while compiled in silico subcellular localization data can be found in Table B in S1 File (non-photosynthetic organisms) and Table F in S1 File (photosynthetic organisms). * = Three algal sequences included in this cluster.
Mentions: Structure-guided alignments were made from sets of PP2C sequences with solved structures using the 3DCOMB function of the RaptorX server ([38, 39]; http://raptorx.uchicago.edu/DeepAlign/submit/). Solved structures used were: ((1A6Q, 2P8E, 2I0O, 2IQ1 –eukaryotic PP2Cs); (1TXO, 2PK0, 2JFR, 2J82 –bacterial Group I); (3ES2, 3W40, 3ZT9 –bacterial Group II)). Additional sequences (eukaryotic PP2C7s) were added with the sequence to profile function of ClustalO [40, 41] at the Mobyle Portal (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-sequence). Alignments were then visualized and hand-edited within GeneDoc ([42]; http://www.nrbsc.org/gfx/genedoc/). In some instances local sequence regions were further aligned using a regional re-alignment capability of MAFFT (Ruby script kindly supplied by Dr. Kazutaka Katoh, modified for Windows by Justin Kerk) (http://mafft.cbrc.jp/alignment/software/regionalrealignment.html) using the following parameters (treeoption—6merpair; realign—localpair—maxiterate 100—bl 45—op 3.0). Phylogenetic trees were inferred as detailed below. This procedure formed the basis for the alignment corresponding to the phylogenetic trees presented in Figs 1, 2 and 3 (Fig A in S2 File (Panel 1)), and the alignment in Fig 7. A large alignment consisting of eukaryotic PP2C7, bacterial Group II, bacterial Group I and the PP2C sets from human and Arabidopsis was initially constructed by MAFFT ([43]; http://mafft.cbrc.jp/alignment/server/), using the BLOSUM45 scoring matrix, and the E-INS-I option (multiple conserved domains and long gaps). Editing of this alignment within GeneDoc was guided by the previous structure-guided alignments detailed above. At some points in the editing process the above cited MAFFT regional realignment procedure was also used. This procedure formed the basis for the alignment in Fig A in S2 File (Panel 4) (corresponding to the phylogenetic tree presented as Fig 6). Finally, large sets of bacterial Group II PP2Cs (GNG2s), with either PP2C7s or eukaryotic PP2Cs, were aligned with MAFFT, using the BLOSUM45 scoring matrix with the E-INS-I option, and manually edited within GeneDoc. In order to decrease the computational load during tree inference, the bacterial Group II component of these alignments was pruned to sequences sharing 80% identity or less, using the ExPasy “Decrease Redundancy” tool (http://web.expasy.org/decrease_redundancy/). This procedure formed the basis for the alignments in Fig A of S2 File (Panels 2, 3, and 5) (corresponding to the phylogenetic trees presented as Figs 4, 5, and Fig E in S2 File.). As necessary during this multiple sequence alignment work, files were interconverted between various formats using the online format converters at either the Mobyle Portal (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::squizz_convert), or the Phylogeny.fr site (http://www.phylogeny.fr/version2_cgi/data_converter.cgi).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
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.

No MeSH data available.