Platforms for enrichment of phosphorylated proteins and peptides in proteomics

Batalha, Íris L.; Lowe, Christopher R.; Roque, Ana C. A.

doi:10.1016/j.tibtech.2011.07.004

Cited by 85 publications

(78 citation statements)

References 76 publications

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“…Several techniques were developed and applied for detecting modified proteins that are otherwise lost in the crowd of abundant proteins. Enrichment technologies make use of immunoaffinity, protein charge, or hydrophobicity [36,37]. For analysis of phosphoproteins, the anti-phosphotyrosine (Y) antibodies can be immobilized on a solid support to allow the enrichment of modified proteins from complex protein mixtures.…”

Section: Techniques For Detection Of Post-translational Modificatimentioning

confidence: 99%

“…Methods that use positively charged metal ions or metal oxides are techniques known as immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC), respectively. Combined usage of commercially available IMAC or MOAC with interaction chromatography methods can improve recovery late of modified peptides of interest in the animal research field [37]. A study relating to crop production was performed by Li et al using polymer-based metal ion affinity capture using germinating rice seeds [36].…”

Section: Techniques For Detection Of Post-translational Modificatimentioning

confidence: 99%

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Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

Hashiguchi

Komatsu

2016

Proteomes

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The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein–protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.

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Section: Techniques For Detection Of Post-translational Modificatimentioning

confidence: 99%

Section: Techniques For Detection Of Post-translational Modificatimentioning

confidence: 99%

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

Hashiguchi

Komatsu

2016

Proteomes

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“…A successful phosphoproteomics study depends not only on the selective enrichment of phosphopeptides, but also on accurate detection and quantitation of the peptides, as well as precise mapping of the phosphorylation sites. Advances in these areas have been extensively reviewed (Batalha et al, 2012; Fíla and Honys, 2012; Kline and De Luca, 2014; Silva-Sanchez et al, 2015). Most of the technologies were developed in animal and yeast systems, and subsequently applied in plants.…”

Section: Phosphoproteomics Technologiesmentioning

confidence: 99%

“…Approximately one-third of the proteins are modified by phosphorylation (Hubbard and Cohen, 1993). The kinase mediated covalent addition of a phosphate group to serine, threonine, and tyrosine residues in eukaryotes, and other amino acids such as histidine, aspartate, glutamate, lysine, arginine, and cysteine in prokaryotes and the subsequent removal of the phosphate groups by protein phosphatases constitute important signaling and regulatory mechanisms in living organisms (Batalha et al, 2012). Reversible protein phosphorylation regulates a wide range of cellular processes such as transmembrane signaling, intracellular amplification of signals, and cell-cycle control.…”

Section: Introductionmentioning

confidence: 99%

Phosphoproteomics technologies and applications in plant biology research

Silva-Sanchez

Zhang

et al. 2015

Front. Plant Sci.

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Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.

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“…The loading and washing conditions enhance specicity at the cost of inferior sensitivity plus recovery. 11 Composites exhibit properties of each component when compared to individual metal oxides. 8,9 On-going work focuses on the versatile nature of the phosphorylation/dephosphorylation process.…”

Section: Introductionmentioning

confidence: 99%

Enhanced enrichment performance of nickel oxide nanoparticles via fabrication of a nanocomposite with a graphene template

et al. 2015

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Metal oxide based nanocomposites are applied in phosphoproteomics for enrichment through the surface hydroxyl groups of metal oxides, though the role of the metal is rarely described. Using graphene as a template after modification with nickel oxide, a nanocomposite with an increased surface area is fabricated and applied to phosphopeptides. Characterisation shows a narrow size distribution of 15-20 nm, BET surface area of 179.70 m 2 g À1 and a pore volume of 0.44 cm 3 g À1 . The graphene possesses well distributed NiO nanoparticles showing selectivity up to 1000 folds of complexity with a sensitivity as low as 1 femtomole. The G-NiO nanocomposite shows a higher selectivity towards phosphopeptides compared to TiO 2 , ZrO 2 and NiO nanoparticles. The enrichment with the G-NiO nanocomposite is tested for biological samples like egg yolk, non-fat milk and human serum. Phosphopeptides having phosphorylations of up to 6 phosphate groups, derived from phosvitin and lipovitellin, are enriched in the egg yolk digest. Phosphopeptides characteristic of casein variants are enriched in the non-fat milk digest with a recovery of aS1 21.9%, aS2 30% and b-casein 20%. Phosphorylated proteins are identified in human serum through the enrichment of phosphopeptides. † Electronic supplementary information (ESI) available: Additional information regarding the preparation of the HeLa cell extract. See: Fig. S1 for phosphopeptides enrichment of b-casein, Fig. S2 for comparison to metal oxide NPs, Fig. S3 for bottom-up identication of serum phosphoproteins and Table S1 for enrichment from serum. See

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Platforms for enrichment of phosphorylated proteins and peptides in proteomics

Cited by 85 publications

References 76 publications

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

Phosphoproteomics technologies and applications in plant biology research

Enhanced enrichment performance of nickel oxide nanoparticles via fabrication of a nanocomposite with a graphene template

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