Effect of cleavage enzyme, search algorithm and decoy database on mass spectrometric identification of wheat gluten proteins

Vensel, William H.; DuPont, Frances M.; Sloane, Stacia; Altenbach, Susan B.

doi:10.1016/j.phytochem.2011.01.002

Cited by 38 publications

(39 citation statements)

References 43 publications

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“…S2 A and B). The fluorescent spots, which were either absent or less intense in control gels, were analyzed by mass spectrometry (17). The experiment with DTT was performed in triplicate and that with Ec-NTR+NAPDH was performed once.…”

Section: Resultsmentioning

confidence: 99%

Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii

Susanti

Wong

Vensel

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Thioredoxin (Trx), a small redox protein, controls multiple processes in eukaryotes and bacteria by changing the thiol redox status of selected proteins. The function of Trx in archaea is, however, unexplored. To help fill this gap, we have investigated this aspect in methanarchaea-strict anaerobes that produce methane, a fuel and greenhouse gas. Bioinformatic analyses suggested that Trx is nearly universal in methanogens. Ancient methanogens that produce methane almost exclusively from H 2 plus CO 2 carried approximately two Trx homologs, whereas nutritionally versatile members possessed four to eight. Due to its simplicity, we studied the Trx system of Methanocaldococcus jannaschii-a deeply rooted hyperthermophilic methanogen growing only on H 2 plus CO 2 . The organism carried two Trx homologs, canonical Trx1 that reduced insulin and accepted electrons from Escherichia coli thioredoxin reductase and atypical Trx2. Proteomic analyses with air-oxidized extracts treated with reduced Trx1 revealed 152 potential targets representing a range of processes-including methanogenesis, biosynthesis, transcription, translation, and oxidative response. In enzyme assays, Trx1 activated two selected targets following partial deactivation by O 2 , validating proteomics observations: methylenetetrahydromethanopterin dehydrogenase, a methanogenesis enzyme, and sulfite reductase, a detoxification enzyme. The results suggest that Trx assists methanogens in combating oxidative stress and synchronizing metabolic activities with availability of reductant, making it a critical factor in the global carbon cycle and methane emission. Because methanogenesis developed before the oxygenation of Earth, it seems possible that Trx functioned originally in metabolic regulation independently of O 2 , thus raising the question whether a complex biological system of this type evolved at least 2.5 billion years ago. methanogenic archaea | redox regulation | hydrothermal vent | early Earth | evolution T hioredoxins (Trxs) are small (∼12-kDa) redox proteins typically bearing a characteristic Cys-Gly-Pro-Cys motif that reduce specific disulfide bonds of selected proteins (1). Reduction alters the biochemical properties of the proteins targeted-e.g., by increasing their activity or solubility (1). Trxs are found in the three domains of life: bacteria, eukarya, and archaea (2). In eukarya and bacteria, the regulatory role of Trx has been shown to span the major aspects of metabolism, including photosynthesis, biosynthesis, replication, transcription, translation, and stress response (1). Trx also acts as an electron donor for enzymes, notably ribonucleotide reductase, phosphoadenosinephosphosulfate reductase, methionine sulfoxide reductase, and peroxiredoxins (1). However, in contrast to the wealth of information for bacteria and eukaryotes, our understanding of archaeal Trx is limited to its biochemical and structural properties (3-9). Its physiological role remains a mystery.To help fill this gap, we have investigated the role of Trx in a group of a...

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Section: Resultsmentioning

confidence: 99%

Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii

Susanti

Wong

Vensel

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…The scarcity of arginine and lysine residues in gluten protein sequences makes it difficult to produce enough suitable tryptic fragments for subsequent analysis. Moreover, the many very similar proteins with repetitive sequences within each gluten protein fraction make it challenging to distinguish one group member from another 76 Proteomics was again used to elucidate why the quality of translocated genotypes varies so considerably with the finding that some cultivars show an unexpectedly high quality with respect to dough rheology and bread-making 79 .…”

Section: Proteomics and The Study Of Gluten Proteinsmentioning

confidence: 99%

“…Recently, Vensel et al76 demonstrated that combining three enzymes, two search algorithms and a specialized database, increases the number of peptides generated and the number of identified proteins.Proteomics has been employed successfully in the study of other issues related to the quality and yield of wheat grain. For example, the replacement of chromosome 1BS of wheat by the chromosome 1RS of rye (the so-called 1BL.1RS translocation) is commonly associated with decreases in bread-making quality and poor rheological characteristics 77 .…”

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confidence: 99%

One Hundred Years of Grain Omics: Identifying the Glutens That Feed the World

et al. 2013

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Glutens, the storage proteins in wheat grains, are a major source of protein in human nutrition. The protein composition of wheat has therefore been an important focus of cereal research. Proteomic tools have been used to describe the genetic diversity of wheat germplasms from different origins at the level of polymorphisms in alleles encoding glutenin and gliadin, the two main proteins of gluten. More recently, proteomics has been used to understand the impact of specific gluten proteins on wheat quality. Here we review the impact of proteomics on the study of gluten proteins as it has evolved from fractionation and electrophoretic techniques to advanced mass spectrometry. In the postgenome era, proteomics is proving to be essential in the effort to identify and understand the interactions between different gluten proteins. This is helping to fill in gaps in our knowledge of how the technological quality of wheat is determined by the interaction between genotype and environment. We also collate information on the various storage protein alleles identified and their prevalence, which makes it possible to infer the effects of wheat selection on grain protein content. We conclude by reviewing the more recent use of transgenesis aimed at improving the quality of gluten.

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“…Additionally, current sequence databases do not reflect the considerable heterogeneity that is found among individual proteins in different cultivars (Altenbach et al, 2010a,b;Mamone et al, 2005Mamone et al, , 2009. Recently, Vensel et al (2011) optimized MS/MS methods for identification of gluten proteins by digesting each protein with chymotrypsin and thermolysin in addition to trypsin, using improved search strategies for analysis of spectral data, and including cultivar-specific sequences of gluten proteins in databases searched with spectral data. These improvements made it possible to significantly increase the MS/MS coverage of individual gluten proteins and to develop a 2-DE map of wheat flour proteins in the US wheat Butte 86 in which 22 LMW-GSs, 13 ggliadins, and 23 a-gliadins were associated with specific gene sequences .…”

Section: Proteomic Analysis Of Gluten Proteinsmentioning

confidence: 99%

New insights into the effects of high temperature, drought and post-anthesis fertilizer on wheat grain development

Altenbach

2012

Journal of Cereal Science

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104

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Effect of cleavage enzyme, search algorithm and decoy database on mass spectrometric identification of wheat gluten proteins

Cited by 38 publications

References 43 publications

Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii

Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii

One Hundred Years of Grain Omics: Identifying the Glutens That Feed the World

New insights into the effects of high temperature, drought and post-anthesis fertilizer on wheat grain development

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