Phosphoproteomics technologies and applications in plant biology research

Li, Jinna; Silva-Sanchez, Cecilia; Zhang, Tong; Chen, Sixue; Li, Haiying

doi:10.3389/fpls.2015.00430

Cited by 37 publications

(31 citation statements)

References 69 publications

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“…Quantitative phosphoproteomics, as a tool to capture the dynamics and specificity of protein phosphorylation, can be used to compare different physiological and developmental states (for recent reviews, see Li et al, 2015;Silva-Sanchez et al, 2015). Mutants in protein kinase activity have also been employed (Nukarinen et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

et al. 2017

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SummaryConjugation of the small ubiquitin‐related modifier (SUMO) to protein substrates has an impact on stress responses and on development. We analyzed the proteome and phosphoproteome of mutants in this pathway. The mutants chosen had defects in SUMO ligase SIZ1, which catalyzes attachment of single SUMO moieties onto substrates, and in ligases PIAL1 and PIAL2, which are known to form SUMO chains. A total of 2657 proteins and 550 phosphopeptides were identified and quantified. Approximately 40% of the proteins and 20% of the phosphopeptides showed differences in abundance in at least one of the analyzed genotypes, demonstrating the influence of SUMO conjugation on protein abundance and phosphorylation. The data show that PIAL1 and PIAL2 are integral parts of the SUMO conjugation system with an impact on stress response, and confirm the involvement of SIZ1 in plant defense. We find a high abundance of predicted SUMO attachment sites in phosphoproteins (70% versus 40% in the total proteome), suggesting convergence of phosphorylation and sumoylation signals onto a set of common targets.

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Section: Introductionmentioning

confidence: 99%

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

et al. 2017

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“…Hydroxyapatite (HAP) resin has a similar affinity for phosphopeptides under non-acidic conditions but can be applied to complex samples 11 . The structure of HAP is close to the chemical structure of natural bones or coral and can therefore be used at physiological pH to bind phosphate, although HAP is sensitive to degradation under acid conditions and its use is not advised for standard acid elution 12 .…”

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confidence: 99%

A non-acidic method using hydroxyapatite and phosphohistidine monoclonal antibodies allows enrichment of phosphopeptides containing non-conventional phosphorylations for mass spectrometry analysis

Adam

Fuhs

Meisenhelder

et al. 2019

Preprint

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Four types of phosphate-protein linkage generate nine different phosphoresidues in living organisms. Histidine phosphorylation is a long-time established but largely unexplored post-translational modification, mainly because of the acid-lability of the phosphoramidate bonds. This lability means that standard phosphoproteomic methods used for conventional phosphate esters (phospho-Ser/Thr/Tyr) must be modified to analyze proteins containing the phosphoramidate-amino acids -phospho-His/Arg/Lys. We show that a non-acidic method allows enrichment of non-conventional phosphoresiduecontaining peptides from tryptic digests of human cell lines, using hydroxyapatite binding and/or immobilized 1-pHis and 3-pHis monoclonal antibodies for enrichment. 425 unique non-conventional phosphorylation sites (i.e. pHis, pLys and pArg) were detected with a high probability of localization by LC-MS/MS analysis and identified using a customized MaxQuant configuration, contributing to a new era of study in post-translational modification and cell signaling in humans. This is the first fully non-acidic method for phosphopeptide enrichment which uses immunoaffinity purification and remains compatible with mass spectrometry analysis for a wider coverage of potential protein phosphorylation events. Introduction:Phosphoproteomics has contributed to tremendous progress in the field of life science and revealed the extensive use of phosphorylation as one of the most important post-translational modifications in eukaryotic organisms. The identification and characterization of phosphorylation sites has been revolutionized by mass spectrometry (MS) with faster and more sensitive instruments. Progress in phosphosite-mapping with tandem mass spectrometry (MS/MS) has allowed improved localization and phosphorylation assignment to a single residue with high confidence. The development of bioinformatics tools for large-scale phosphoproteome data analysis was an equally important step and permitted the integration of different parameters searching for complex combinatorial possibilities 1,2 .Up until now, only one class of phosphate-bond containing phosphoamino acid, corresponding to the conventional serine, threonine and tyrosine phosphorylation (phosphate-ester or O-phosphate) has been systematically considered for phosphorylation site searching. But nine out of the 20 amino acids have the

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“…Protein phosphorylation is the most common mechanism of signal and because of that, phosphoproteomics is the immediate strategy to be employed. Silva-Sanchez et al [108] and Li et al [29] have summarized the current methodologies used in extracting, enriching, and fractionating phosphoproteins, and in their MS analyses for identification, quantitation, and phosphorylation site mapping, conclude on cross-talk between different PTMs (phosphorylation, glycosylation, and redox modifications) and data validation. They provided a list of phosphoproteins, softwares, and databases.…”

Section: From Proteomics To Biologymentioning

confidence: 99%

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

et al. 2016

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The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.

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Phosphoproteomics technologies and applications in plant biology research

Cited by 37 publications

References 69 publications

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

A non-acidic method using hydroxyapatite and phosphohistidine monoclonal antibodies allows enrichment of phosphopeptides containing non-conventional phosphorylations for mass spectrometry analysis

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

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