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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.


The GO annotation distribution of Selaginella whole proteins (before IMAC enrichment) and phosphoproteins in the categories of (A) cellular component, (B) molecular function and (C) biological processes.
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Figure 2: The GO annotation distribution of Selaginella whole proteins (before IMAC enrichment) and phosphoproteins in the categories of (A) cellular component, (B) molecular function and (C) biological processes.

Mentions: To understand the functional distribution of the unique Selaginella phosphoproteins identified in this study, their cellular localization, molecular function, and biological processes were analyzed and compared with those of 2400 Selaginella proteins identified after LC-MS/MS analysis of PEG-fractionated samples without the IMAC enrichment procedure. Based on the comparison of Gene Ontology (GO) term annotations (Figure 2), the 3 most over-represented categories for the identified phosphoproteins in each GO vocabulary are: nucleus, plasma membrane and cytosol for “cellular component”; DNA/RNA binding, kinase activity, and transferase activity for “molecular function”; protein modification, phosphorus metabolic process, and transcription for “biological process”.


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

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

The GO annotation distribution of Selaginella whole proteins (before IMAC enrichment) and phosphoproteins in the categories of (A) cellular component, (B) molecular function and (C) biological processes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The GO annotation distribution of Selaginella whole proteins (before IMAC enrichment) and phosphoproteins in the categories of (A) cellular component, (B) molecular function and (C) biological processes.
Mentions: To understand the functional distribution of the unique Selaginella phosphoproteins identified in this study, their cellular localization, molecular function, and biological processes were analyzed and compared with those of 2400 Selaginella proteins identified after LC-MS/MS analysis of PEG-fractionated samples without the IMAC enrichment procedure. Based on the comparison of Gene Ontology (GO) term annotations (Figure 2), the 3 most over-represented categories for the identified phosphoproteins in each GO vocabulary are: nucleus, plasma membrane and cytosol for “cellular component”; DNA/RNA binding, kinase activity, and transferase activity for “molecular function”; protein modification, phosphorus metabolic process, and transcription for “biological process”.

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.