Comparison of Full Versus Partial Metabolic Labeling for Quantitative Proteomics Analysis in Arabidopsis thaliana

Huttlin, Edward L.; Hegeman, Adrian D.; Harms, Amy C.; Sussman, Michael R.

doi:10.1074/mcp.m600347-mcp200

Cited by 96 publications

(124 citation statements)

References 31 publications

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“…Three of these were also identified in a study of the Arabidopsis tonoplast (Shimaoka et al, 2004). In another proteomics study, Huttlin et al (2007) identified peptides for ESM1 in the organellar fraction but other putative MyAPs in both the organellar and microsomal fractions.…”

Section: Cloning and Identification Of Mvp1 As A Myapmentioning

confidence: 94%

“…The MyAPs feature GDSLlike lipase motifs, but no lipase activity has yet been definitively established for any of the MyAPs. A number of proteomic studies have detected ESM1 in the vacuole (Carter et al, 2004;Shimaoka et al, 2004;Huttlin et al, 2007). Five other putative MyAPs were detected in vacuoles (Carter et al, 2004).…”

Section: Cloning and Identification Of Mvp1 As A Myapmentioning

confidence: 99%

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MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking

et al. 2009

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We identified an Arabidopsis (Arabidopsis thaliana) ethyl methanesulfonate mutant, modified vacuole phenotype1-1 (mvp1-1), in a fluorescent confocal microscopy screen for plants with mislocalization of a green fluorescent protein-d tonoplast intrinsic protein fusion. The mvp1-1 mutant displayed static perinuclear aggregates of the reporter protein. mvp1 mutants also exhibited a number of vacuole-related phenotypes, as demonstrated by defects in growth, utilization of stored carbon, gravitropic response, salt sensitivity, and specific susceptibility to the fungal necrotroph Alternaria brassicicola. Similarly, crosses with other endomembrane marker fusions identified mislocalization to aggregate structures, indicating a general defect in protein trafficking. Map-based cloning showed that the mvp1-1 mutation altered a gene encoding a putative myrosinase-associated protein, and glutathione S-transferase pull-down assays demonstrated that MVP1 interacted specifically with the Arabidopsis myrosinase protein, THIOGLUCOSIDE GLUCOHYDROLASE2 (TGG2), but not TGG1. Moreover, the mvp1-1 mutant showed increased nitrile production during glucosinolate hydrolysis, suggesting that MVP1 may play a role in modulation of myrosinase activity. We propose that MVP1 is a myrosinase-associated protein that functions, in part, to correctly localize the myrosinase TGG2 and prevent inappropriate glucosinolate hydrolysis that could generate cytotoxic molecules.

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Section: Cloning and Identification Of Mvp1 As A Myapmentioning

confidence: 94%

Section: Cloning and Identification Of Mvp1 As A Myapmentioning

confidence: 99%

MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking

et al. 2009

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“…Experimental data points are shown as closed circles, and the least-squares fits using eqs [13][14][15][16][17][18][19][20][21][22] Composite peaks from unlabeled and fractionally 13 C-Ile-labeled peptides resulting from pulse labeling. Experimental data points are shown as closed circles, and the least-squares fits using eqs [13][14][15][16][17][18][19][20][21][22] Composite peak from an unlabeled and fractional 13 C-Ile/ 2 H-Leu-labeled peptide resulting from pulse labeling. Experimental data points are shown as closed circles, and the least-squares fits using eqs 13-22 are shown as the solid line.…”

Section: Discussionmentioning

confidence: 99%

“…There is one isotope envelope from the unlabeled species present at the beginning of the 15 N-pulse, and a second 15 N-enriched isotope envelope from the species biosynthesized after the pulse. The observed spectrum can be expressed as the sum of the two isotope distributions for the two species (14) where B is a baseline offset, A U is the amplitude of the unlabeled distribution S U (m), and A L is the amplitude of the labeled distribution S L (m). The isotope distributions for the unlabeled and labeled species are readily calculated in the μ-domain: (15) ( 16) In order to calculate the labeled distribution, a new atom type, N* for 15 N-enriched atoms, is introduced for the labeled nitrogen atoms, and n elements is increased by one.…”

Section: Analytical Description Of a Composite Unlabeled And Fractionmentioning

confidence: 99%

Quantitative Analysis of Isotope Distributions In Proteomic Mass Spectrometry Using Least-Squares Fourier Transform Convolution

et al. 2008

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Quantitative proteomic mass spectrometry involves comparison of the amplitudes of peaks resulting from different isotope labeling patterns, including fractional atomic labeling and fractional residue labeling. We have developed a general and flexible analytical treatment of the complex isotope distributions that arise in these experiments, using Fourier transform convolution to calculate labeled isotope distributions and least-squares for quantitative comparison with experimental peaks. The degree of fractional atomic and fractional residue labeling can be determined from experimental peaks at the same time as the integrated intensity of all of the isotopomers in the isotope distribution. The approach is illustrated using data with fractional 15 N-labeling and fractional 13 C-isoleucine labeling. The least-squares Fourier transform convolution approach can be applied to many types of quantitive proteomic data, including data from stable isotope labeling by amino acids in cell culture and pulse labeling experiments.Stable isotope labeling in cells coupled with mass spectrometry has many important applications in the analysis of protein expression, modification, turnover, and metabolism. 1 Cells and organisms can be isotopically labeled by supplying labeled precursors in the form of nutrients such as amino acids, glucose, and ammonia. These labeled precursors are incorporated into proteins, whose resulting isotope labeling patterns reflect their abundance and the dynamics of protein synthesis and turnover. The era of quantitative proteomics began with experiments where mixtures of unlabeled control cells and 15 N-labeled or isotope depleted test cells were quantitatively analyzed to determine protein expression and phosphorylation levels. 2,3 More recently, the SILAC technique was developed based on specific amino acid labeling of cells for quantitative analysis of protein expression, modification, and turnover. 4-6The two basic classes of quantitative metabolic labeling approaches are the stable isotope labeling by amino acids in cell culture (SILAC) experiments and pulse labeling experiments, both of which have been implemented in a variety of ways. 7 In the SILAC method, independent samples are prepared with different labeling patterns that are mixed prior to mass spectrometry analysis. For pulse labeling experiments, labels that are added to the growth medium are taken up to metabolically label the proteome, which generates fractionally enriched proteins from a

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“…However, it works well for mammalian cell lines [113][114][115], but not so effective in autotrophic organisms such as cyanobacteria due to their ability to synthesize all amino acids [116,117]. The second primary method in stable isotope metabolic labeling relies on the introduction of a heavy isotope such as 15 N, often in the form of Na 15 NO 3 or K 15 NO 3 as a nitrogen source, is a powerful tool for the quantitative analysis in plant and bacteria [118,119]. Quantitative proteomics based on "metabolic labeling" has already been successfully used in some cyanobacterial strains [120][121][122].…”

Section: Challenge and Perspective In Ptm Proteomics Of Cyanobacteriamentioning

confidence: 99%

Proteomic analysis of post translational modifications in cyanobacteria

Xiong

Chen

2016

Journal of Proteomics

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Comparison of Full Versus Partial Metabolic Labeling for Quantitative Proteomics Analysis in Arabidopsis thaliana

Cited by 96 publications

References 31 publications

MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking

MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking

Quantitative Analysis of Isotope Distributions In Proteomic Mass Spectrometry Using Least-Squares Fourier Transform Convolution

Proteomic analysis of post translational modifications in cyanobacteria

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