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Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii.

Chen X, Chan WL, Zhu FY, Lo C - Proteome Sci (2014)

Bottom Line: As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution.Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants.A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China ; Wuhan Institute of Biotechnology, Wuhan, Hubei, China.

ABSTRACT

Background: Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms.

Results: In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class.

Conclusions: Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.

No MeSH data available.


Sellaginella phosphoproteins involved in photosynthesis. (A) Graphical representation of the photosynthesis machineries using the KEGG classification system. Different proteins participating in light-dependent reactions are shown. Circles filled with red color denoted phosphoproteins with confirmed phosphosites identified in this study. UniProtKB accession numbers of Selaginella proteins are shown underneath the corresponding photosynthetic proteins. (B) Alignment of the identified Selaginella photosynthesis phosphoproteins (selected regions) with orthologous sequence from Arabidopsis, rice (ORYSA) and P. patens (PHYPA). Phosphosites identified in this study and in Arabidopsis are highlighted in red and yellow, respectively. Complete alignments of these proteins are available in Additional file 6: Figure S2. Phosphorylation information for the rice and P. patens sequences is not available.
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Figure 4: Sellaginella phosphoproteins involved in photosynthesis. (A) Graphical representation of the photosynthesis machineries using the KEGG classification system. Different proteins participating in light-dependent reactions are shown. Circles filled with red color denoted phosphoproteins with confirmed phosphosites identified in this study. UniProtKB accession numbers of Selaginella proteins are shown underneath the corresponding photosynthetic proteins. (B) Alignment of the identified Selaginella photosynthesis phosphoproteins (selected regions) with orthologous sequence from Arabidopsis, rice (ORYSA) and P. patens (PHYPA). Phosphosites identified in this study and in Arabidopsis are highlighted in red and yellow, respectively. Complete alignments of these proteins are available in Additional file 6: Figure S2. Phosphorylation information for the rice and P. patens sequences is not available.

Mentions: Furthermore, we performed a close examination on the phosphorylation events in Selaginella photosynthesis-related proteins. The molecular machinery of photosynthesis has been highly conserved during plant evolution. Among our identified phosphoproteins with confirmed phosphosites, seven are involved in photosystem II (PSII) and two are involved in photosystem I (PSI) (Figure 4A). To reveal possible evolutionary significance, sequences were aligned with orthologs from Arabidopsis, rice, and Physcomitrella patens (moss), representing diverse lineages of dicot, monocot, and bryophytes, respectively (Figure 4B and Additional file6: Figure S2). In all cases, phosphorylation information is only available for the Arabidopsis proteins. Sequences of rice and moss are included for examination of phosphorylatable residues at equivalent sites.


Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii.

Chen X, Chan WL, Zhu FY, Lo C - Proteome Sci (2014)

Sellaginella phosphoproteins involved in photosynthesis. (A) Graphical representation of the photosynthesis machineries using the KEGG classification system. Different proteins participating in light-dependent reactions are shown. Circles filled with red color denoted phosphoproteins with confirmed phosphosites identified in this study. UniProtKB accession numbers of Selaginella proteins are shown underneath the corresponding photosynthetic proteins. (B) Alignment of the identified Selaginella photosynthesis phosphoproteins (selected regions) with orthologous sequence from Arabidopsis, rice (ORYSA) and P. patens (PHYPA). Phosphosites identified in this study and in Arabidopsis are highlighted in red and yellow, respectively. Complete alignments of these proteins are available in Additional file 6: Figure S2. Phosphorylation information for the rice and P. patens sequences is not available.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4022089&req=5

Figure 4: Sellaginella phosphoproteins involved in photosynthesis. (A) Graphical representation of the photosynthesis machineries using the KEGG classification system. Different proteins participating in light-dependent reactions are shown. Circles filled with red color denoted phosphoproteins with confirmed phosphosites identified in this study. UniProtKB accession numbers of Selaginella proteins are shown underneath the corresponding photosynthetic proteins. (B) Alignment of the identified Selaginella photosynthesis phosphoproteins (selected regions) with orthologous sequence from Arabidopsis, rice (ORYSA) and P. patens (PHYPA). Phosphosites identified in this study and in Arabidopsis are highlighted in red and yellow, respectively. Complete alignments of these proteins are available in Additional file 6: Figure S2. Phosphorylation information for the rice and P. patens sequences is not available.
Mentions: Furthermore, we performed a close examination on the phosphorylation events in Selaginella photosynthesis-related proteins. The molecular machinery of photosynthesis has been highly conserved during plant evolution. Among our identified phosphoproteins with confirmed phosphosites, seven are involved in photosystem II (PSII) and two are involved in photosystem I (PSI) (Figure 4A). To reveal possible evolutionary significance, sequences were aligned with orthologs from Arabidopsis, rice, and Physcomitrella patens (moss), representing diverse lineages of dicot, monocot, and bryophytes, respectively (Figure 4B and Additional file6: Figure S2). In all cases, phosphorylation information is only available for the Arabidopsis proteins. Sequences of rice and moss are included for examination of phosphorylatable residues at equivalent sites.

Bottom Line: As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution.Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants.A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China ; Wuhan Institute of Biotechnology, Wuhan, Hubei, China.

ABSTRACT

Background: Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms.

Results: In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class.

Conclusions: Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.

No MeSH data available.