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

TitlePhosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii.
Authors
Issue Date2014
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.proteomesci.com/home/
Citation
Proteome Science, 2014, v. 12, article no. 16 How to Cite?
AbstractBACKGROUND: 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.
Persistent Identifierhttp://hdl.handle.net/10722/201565
ISSN
2015 Impact Factor: 1.746
2015 SCImago Journal Rankings: 0.683
PubMed Central ID

 

DC FieldValueLanguage
dc.contributor.authorChen, Xen_US
dc.contributor.authorChan, WLen_US
dc.contributor.authorZhu, FYen_US
dc.contributor.authorLo, CSCen_US
dc.date.accessioned2014-08-21T07:30:26Z-
dc.date.available2014-08-21T07:30:26Z-
dc.date.issued2014en_US
dc.identifier.citationProteome Science, 2014, v. 12, article no. 16en_US
dc.identifier.issn1477-5956-
dc.identifier.urihttp://hdl.handle.net/10722/201565-
dc.description.abstractBACKGROUND: 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.-
dc.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.proteomesci.com/home/-
dc.relation.ispartofProteome Scienceen_US
dc.rightsProteome Science. Copyright © BioMed Central Ltd.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titlePhosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii.en_US
dc.typeArticleen_US
dc.identifier.emailLo, CSC: clivelo@hkucc.hku.hken_US
dc.identifier.authorityLo, CSC=rp00751en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1477-5956-12-16-
dc.identifier.pmid24628833-
dc.identifier.pmcidPMC4022089-
dc.identifier.hkuros234680en_US
dc.identifier.volume12en_US
dc.publisher.placeUnited Kingdom-

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