1
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O’Lone C, Juhász A, Nye-Wood M, Moody D, Dunn H, Ral JP, Colgrave ML. Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley ( Hordeum vulgare L.). J Agric Food Chem 2024; 72:10149-10161. [PMID: 38635353 PMCID: PMC11066872 DOI: 10.1021/acs.jafc.4c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
The conversion of raw barley (Hordeum vulgare L.) to malt requires a process of controlled germination, where the grain is submerged in water to raise the moisture content to >40%. The transmembrane proteins, aquaporins, influence water uptake during the initial stage of controlled germination, yet little is known of their involvement in malting. With the current focus on sustainability, understanding the mechanisms of water uptake and usage during the initial stages of malting has become vital in improving efficient malting practices. In this study, we used quantitative proteomics analysis of two malting barley genotypes demonstrating differing water-uptake phenotypes in the initial stages of malting. Our study quantified 19 transmembrane proteins from nine families, including seven distinct aquaporin isoforms, including the plasma intrinsic proteins (PIPs) PIP1;1, PIP2;1, and PIP2;4 and the tonoplast intrinsic proteins (TIPs) TIP1;1, TIP2;3, TIP3;1, and TIP3;2. Our findings suggest that the presence of TIP1;1, TIP3;1, and TIP3;2 in the mature barley grain proteome is essential for facilitating water uptake, influencing cell turgor and the formation of large central lytic vacuoles aiding storage reserve hydrolysis and endosperm modification efficiency. This study proposes that TIP3s mediate water uptake in malting barley grain, offering potential breeding targets for improving sustainable malting practices.
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Affiliation(s)
- Clare
E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - David Moody
- InterGrain
Pty Ltd, Bibra
Lake 6163, Western Australia, Australia
| | - Hugh Dunn
- Pilot
Malting Australia, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Jean-Philippe Ral
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, St Lucia 4067, Queensland, Australia
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2
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. From grain to malt: Tracking changes of ultra-low-gluten barley storage proteins after malting. Food Chem 2024; 432:137189. [PMID: 37619393 DOI: 10.1016/j.foodchem.2023.137189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Barley (Hordeum vulgare L.) is a major cereal crop produced globally. Hordeins, the major storage proteins in barley, can trigger immune responses leading to celiac disease or symptoms associated with food allergy. Here, proteomics approaches were employed to investigate the proteome level changes of grain and malt from the malting barley cultivar, Sloop, and single-, double- and triple hordein-reduced lines. The triple hordein-reduced line is an ultra-low gluten barley cultivar, Kebari®. Using discovery proteomics, 2,688 and 3,034 proteins in the barley and malt samples were detected respectively. Through the application of targeted proteomics, a significant reduction in the quantity of B-, D-, and γ-hordeins, as well as avenin-like proteins, was observed in the ultra-low gluten malt sample. A compensation mechanism was observed evidenced by increased biosynthesis of seed storage globulins, specifically vicilin-like globulins. Overall, this study has provided insights into protein compositional changes after malting in celiac-friendly barley varieties.
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Affiliation(s)
- Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
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3
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. Proteome Changes Resulting from Malting in Hordein-Reduced Barley Lines. J Agric Food Chem 2023; 71:14079-14091. [PMID: 37712129 PMCID: PMC10540200 DOI: 10.1021/acs.jafc.3c02292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Hordeum vulgare L., commonly known as barley, is primarily used for animal feed and malting. The major storage proteins in barley are hordeins, known triggers of celiac disease (CD). Here, sequential window acquisition of all theoretical mass spectra (SWATH)-MS proteomics was employed to investigate the proteome profile of grain and malt samples from the malting barley cultivar Sloop and single-, double-, and triple hordein-reduced lines bred in a Sloop background. Using a discovery proteomics approach, 2688 and 3034 proteins were detected from the grain and malt samples, respectively. By utilizing label-free relative quantitation through SWATH-MS, a total of 2654 proteins have been quantified from grain and malt. The comparative analyses between the barley grain and malt samples revealed that the C-hordein-reduced lines have a more significant impact on proteome level changes due to malting than B- and D-hordein-reduced lines. Upregulated proteins in C-hordein-reduced lines were primarily involved in the tricarboxylic acid cycle and fatty acid peroxidation processes to provide more energy for seed germination during malting. By applying proteomics approaches after malting in hordein-reduced barley lines, we uncovered additional changes in the proteome driven by the genetic background that were not apparent in the sound grain. Our findings offer valuable insights for barley breeders and maltsters seeking to understand and optimize the performance of gluten-free grains in malt products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
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4
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Tahmasian A, Drew R, Broadbent JA, Juhász A, Nye-Wood M, Colgrave ML. Conventional solid-state fermentation impacts the white lupin proteome reducing the abundance of allergenic peptides. Food Chem 2023; 426:136622. [PMID: 37356243 DOI: 10.1016/j.foodchem.2023.136622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 06/27/2023]
Abstract
The demand for high-quality and sustainable protein sources is on the rise. Lupin is an emerging plant-based source of protein with health-enhancing properties; however, the allergenic potential of lupins limits their widespread adoption in food products. A combination of discovery and targeted quantitative proteome measurements was used to investigate the impact of solid-state fermentation induced by Rhizopus oligosporus on the proteome composition and allergenic protein abundances of white lupin seed. In total, 1,241 proteins were uniquely identified in the fermented sample. Moreover, the effectiveness of the solid-state fermentation in reducing the abundance of the tryptic peptides derived from white lupin allergens was demonstrated. Comparably, a greater decrease was noted for the major white lupin allergen based on β-conglutin peptide abundances. Hence, conventional solid-state fermentation processing can be beneficial for reducing the potential allergenicity of lupin-based foods. This finding will open new avenues for unlocking the potential of this under-utilised legume.
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Affiliation(s)
- Arineh Tahmasian
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia; CSIRO Agriculture and Food, St. Lucia, QLD, Australia
| | - Roger Drew
- Eighth Day Foods, Coburg North, VIC, Australia
| | | | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Mitchell Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia; CSIRO Agriculture and Food, St. Lucia, QLD, Australia.
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5
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Bahmani M, Juhász A, Broadbent J, Bose U, Nye-Wood MG, Edwards IB, Colgrave ML. Proteome Phenotypes Discriminate the Growing Location and Malting Traits in Field-Grown Barley. J Agric Food Chem 2022; 70:10680-10691. [PMID: 35981222 PMCID: PMC9449971 DOI: 10.1021/acs.jafc.2c03816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Barley is one of the key cereal grains for malting and brewing industries. However, climate variability and unprecedented weather events can impact barley yield and end-product quality. The genetic background and environmental conditions are key factors in defining the barley proteome content and malting characteristics. Here, we measure the barley proteome and malting characteristics of three barley lines grown in Western Australia, differing in genetic background and growing location, by applying liquid chromatography-mass spectrometry (LC-MS). Using data-dependent acquisition LC-MS, 1571 proteins were detected with high confidence. Quantitative data acquired using sequential window acquisition of all theoretical (SWATH) MS on barley samples resulted in quantitation of 920 proteins. Multivariate analyses revealed that the barley lines' genetics and their growing locations are strongly correlated between proteins and desired traits such as the malt yield. Linking meteorological data with proteomic measurements revealed how high-temperature stress in northern regions affects seed temperature tolerance during malting, resulting in a higher malt yield. Our results show the impact of environmental conditions on the barley proteome and malt characteristics; these findings have the potential to expedite breeding programs and malt quality prediction.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - James Broadbent
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd., SABC, Loneragan Building, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
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6
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Hu L, Zhang H, Hu Z, Chin Y, Zhang X, Chen J, Hu Y. Comparative proteomics analysis of three commercial tuna species through SWATH-MS based mass spectrometry and chemometrics. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Bose U, Juhász A, Yu R, Bahmani M, Byrne K, Blundell M, Broadbent JA, Howitt CA, Colgrave ML. Proteome and Nutritional Shifts Observed in Hordein Double-Mutant Barley Lines. Front Plant Sci 2021; 12:718504. [PMID: 34567030 PMCID: PMC8458801 DOI: 10.3389/fpls.2021.718504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements; proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Ronald Yu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | | | | | | | - Michelle L. Colgrave
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
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8
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Bahmani M, O’Lone CE, Juhász A, Nye-Wood M, Dunn H, Edwards IB, Colgrave ML. Application of Mass Spectrometry-Based Proteomics to Barley Research. J Agric Food Chem 2021; 69:8591-8609. [PMID: 34319719 PMCID: PMC8389776 DOI: 10.1021/acs.jafc.1c01871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Clare E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Hugh Dunn
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd, SABC - Loneragan Building, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
- Phone: +61-7-3214-2697. . Fax: +61-7-3214-2900
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9
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Qiu W, Zhang X, Zhang H, Liang C, Xu J, Gao H, Ai L, Zhao S, Wang Y, Yang Y, Zhao X. Discrimination of meat from fur-producing and food-providing animals using mass spectrometry-based proteomics. Food Res Int 2020; 137:109446. [PMID: 33233126 DOI: 10.1016/j.foodres.2020.109446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/12/2023]
Abstract
Non-edible meat from fur-producing animals entering into meat consumption chain could pose a serious threat to public health. For the purpose of risk prevention and control of meat safety, in this study, marker peptides for discriminating non-edible meat of fur-producing animals (including fox, silver fox, blue fox, raccoon dog, ussuri raccoon dog, mink and American mink) from meat of food-providing animals (including pig, cattle, sheep and donkey) were explored by shot-gun proteomics and verified by target approach. Two mass spectrometry platforms combined with bioinformatic and chemometric tools were integratedly emloyed for method development. Meat samples were first subjected to in-solution protein digestion and the subsequently tryptic peptides were profiled and quantitated by ultra-high pressure liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF MS) with sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) mode. Candidate marker peptides screened by chemometric tools were further filtered for their biological specificity and detectability through bioinformatics analysis as well as multiple reaction monitoring (MRM) verification with UHPLC-triple quadrupole mass spectrometry (UHPLC-QQQ MS). As a result, 9 peptides, out of 104 candidates, were selected as markers for discriminating analysis, of which DQTLQEELAR was validated as primary indicator of non-edible meat from the concerned fur-producing animals. An MRM method based on the developed marker peptides for routine use was finally proposed for risk alarming of non-edible meat from fur-producing animals in food safety control.
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Affiliation(s)
- Wenfeng Qiu
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Xiaomei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China
| | - Hongwei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China.
| | - Chengzhu Liang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China
| | - Jie Xu
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Hongwei Gao
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China
| | - Lianfeng Ai
- Technology Center of Shijiazhuang Customs, Shijiazhuang, Hebei Province 050051, PR China
| | - Sa Zhao
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China
| | - Yanan Wang
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Yi Yang
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Xue Zhao
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China.
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10
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Bose U, Broadbent JA, Byrne K, Blundell MJ, Howitt CA, Colgrave ML. Proteome Analysis of Hordein-Null Barley Lines Reveals Storage Protein Synthesis and Compensation Mechanisms. J Agric Food Chem 2020; 68:5763-5775. [PMID: 32374605 DOI: 10.1021/acs.jafc.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hordeins are the major barley seed storage proteins and are elicitors of celiac disease. Attempts to reduce the hordein level in barley have been made; however, the resultant pleiotropic effects are less understood. Here, data-independent acquisition mass spectrometry was used to measure proteome-wide abundance differences between wild-type and single hordein-null barley lines. Using comparative quantitative proteomics, we detected proteome-wide changes (∼59%) as a result of the specific reduction in hordein proteins. The comparative analysis and functional annotation revealed an increase in non-gluten storage proteins, such as globulins and lipid transfer proteins, and proteins rich in essential amino acids in the null lines. This study yields an informative molecular portrait of the hordein-null lines and the underlying mechanisms of storage protein biosynthesis. This study indicates the extent to which protein content can be manipulated without biological consequence, and we envision its wide-scale application for studying modified crops.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Malcolm J Blundell
- CSIRO Agriculture and Food, General Post Office Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food, General Post Office Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
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11
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Lexhaller B, Ludwig C, Scherf KA. Identification of Isopeptides Between Human Tissue Transglutaminase and Wheat, Rye, and Barley Gluten Peptides. Sci Rep 2020; 10:7426. [PMID: 32367038 PMCID: PMC7198585 DOI: 10.1038/s41598-020-64143-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/09/2020] [Indexed: 01/28/2023] Open
Abstract
Celiac disease (CD) is a chronic immune-mediated enteropathy of the small intestine, which is triggered by the ingestion of storage proteins (gluten) from wheat, rye, and barley in genetically predisposed individuals. Human tissue transglutaminase (TG2) plays a central role in the pathogenesis of CD, because it is responsible for specific gluten peptide deamidation and covalent crosslinking, resulting in the formation of Nε-(γ-glutamyl)-lysine isopeptide bonds. The resulting TG2-gluten peptide complexes are assumed to cause the secretion of anti-TG2 autoantibodies, but the underlying mechanisms are only partly known. To gain more insight into the structures of these complexes, the aim of our study was to identify TG2-gluten isopeptides. With the use of discovery-driven as well as targeted nanoscale liquid chromatography tandem mass spectrometry, we detected 29 TG2-gluten isopeptides in total, involving seven selected TG2 lysine residues (K205, K265, K429, K468, K590, K600, K677). Several gluten peptides carried known B-cell epitopes and/or T-cell epitopes, either intact 9-mer core regions or partial sequences, as well as sequences bearing striking similarities to already known epitopes. These novel insights into the molecular structures of TG2-gluten peptide complexes may help clarify their physiological relevance in the initiation of CD autoimmunity and the role of anti-TG2 autoantibodies.
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Affiliation(s)
- Barbara Lexhaller
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany. .,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany.
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Sun R, Hunter C, Chen C, Ge W, Morrice N, Liang S, Zhu T, Yuan C, Ruan G, Zhang Q, Cai X, Yu X, Chen L, Dai S, Luan Z, Aebersold R, Zhu Y, Guo T. Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS. J Proteome Res 2020; 19:2732-2741. [PMID: 32053377 DOI: 10.1021/acs.jproteome.9b00671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We reported and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in preclassified clinical specimens. The method uses a 15 min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration, and OpenSWATH software for data analysis. We applied the method to a cohort containing 204 FFPE tissue samples from 58 prostate cancer patients and 10 benign prostatic hyperplasia patients. Altogether we identified 27,975 proteotypic peptides and 4037 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with a 2 h gradient, we found 3800 proteins were quantified by the two methods on two different instruments with relatively high consistency (r = 0.77). The accelerated method consumed only 17% instrument time, while quantifying 80% of proteins compared to the 2 h gradient SWATH. Although the missing value rate increased by 20%, batch effects reduced by 21%. 75 deregulated proteins measured by the accelerated method were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, and the results exhibited high quantitative consistency with the 15 min SWATH method (r = 0.89) in the same sample set. We further verified the applicability of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n = 154). Altogether, the results showed that the 15 min gradient microflow SWATH accelerated large-scale data acquisition by 6 times, reduced batch effect by 21%, introduced 20% more missing values, and exhibited comparable ability to separate disease groups.
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Affiliation(s)
- Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | | | | | - Weigang Ge
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | | | - Shuang Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Tiansheng Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Chunhui Yuan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Guan Ruan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xiaoyan Yu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shaozheng Dai
- School of Computer Science and Engineering, Beihang University, Beijing 100083, China
| | - Zhongzhi Luan
- School of Computer Science and Engineering, Beihang University, Beijing 100083, China
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8049 Zurich, Switzerland.,Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
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Lexhaller B, Colgrave ML, Scherf KA. Characterization and Relative Quantitation of Wheat, Rye, and Barley Gluten Protein Types by Liquid Chromatography-Tandem Mass Spectrometry. Front Plant Sci 2019; 10:1530. [PMID: 31921226 PMCID: PMC6923249 DOI: 10.3389/fpls.2019.01530] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/01/2019] [Indexed: 05/24/2023]
Abstract
The consumption of wheat, rye, and barley may cause adverse reactions to wheat such as celiac disease, non-celiac gluten/wheat sensitivity, or wheat allergy. The storage proteins (gluten) are known as major triggers, but also other functional protein groups such as α-amylase/trypsin-inhibitors or enzymes are possibly harmful for people suffering of adverse reactions to wheat. Gluten is widely used as a collective term for the complex protein mixture of wheat, rye or barley and can be subdivided into the following gluten protein types (GPTs): α-gliadins, γ-gliadins, ω5-gliadins, ω1,2-gliadins, high- and low-molecular-weight glutenin subunits of wheat, ω-secalins, high-molecular-weight secalins, γ-75k-secalins and γ-40k-secalins of rye, and C-hordeins, γ-hordeins, B-hordeins, and D-hordeins of barley. GPTs isolated from the flours are useful as reference materials for clinical studies, diagnostics or in food analyses and to elucidate disease mechanisms. A combined strategy of protein separation according to solubility followed by preparative reversed-phase high-performance liquid chromatography was employed to purify the GPTs according to hydrophobicity. Due to the heterogeneity of gluten proteins and their partly polymeric nature, it is a challenge to obtain highly purified GPTs with only one protein group. Therefore, it is essential to characterize and identify the proteins and their proportions in each GPT. In this study, the complexity of gluten from wheat, rye, and barley was demonstrated by identification of the individual proteins employing an undirected proteomics strategy involving liquid chromatography-tandem mass spectrometry of tryptic and chymotryptic hydrolysates of the GPTs. Different protein groups were obtained and the relative composition of the GPTs was revealed. Multiple reaction monitoring liquid chromatography-tandem mass spectrometry was used for the relative quantitation of the most abundant gluten proteins. These analyses also allowed the identification of known wheat allergens and celiac disease-active peptides. Combined with functional assays, these findings may shed light on the mechanisms of gluten/wheat-related disorders and may be useful to characterize reference materials for analytical or diagnostic assays more precisely.
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Affiliation(s)
- Barbara Lexhaller
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Michelle L. Colgrave
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Katharina A. Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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15
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Li Y, Lammi C, Boschin G, Arnoldi A, Aiello G. Recent Advances in Microalgae Peptides: Cardiovascular Health Benefits and Analysis. J Agric Food Chem 2019; 67:11825-11838. [PMID: 31588750 DOI: 10.1021/acs.jafc.9b03566] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There is now great interest in food protein hydrolysates and food-derived peptides, because they may provide numerous health benefits. Among other foodstuffs, microalgae appear to be sustainable sources of proteins and bioactive peptides that can be exploited in foods and functional formulations. This review considers protein hydrolysates and individual peptides that may be relevant in cardiovascular disease prevention because they mimic the functions of mediators involved in pathologic processes that represent relevant risk factors for cardiovascular disease development, such as hypercholesterolemia, hypertension, diabetes, inflammation, and oxidative status. Some of these peptides are also multifunctional (i.e., they offer more than one benefit). Moreover, the most efficient techniques for protein extraction and hydrolyzation are commented on, as well as the best methodologies for high-throughput detection and quantification. Finally, current challenges and critical issues are discussed.
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Affiliation(s)
- Yuchen Li
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Carmen Lammi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Giovanna Boschin
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Anna Arnoldi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Gilda Aiello
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
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Tanner G, Juhász A, Florides CG, Nye-Wood M, Békés F, Colgrave ML, Russell AK, Hardy MY, Tye-Din JA. Preparation and Characterization of Avenin-Enriched Oat Protein by Chill Precipitation for Feeding Trials in Celiac Disease. Front Nutr 2019; 6:162. [PMID: 31681788 PMCID: PMC6803533 DOI: 10.3389/fnut.2019.00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022] Open
Abstract
The safety of oats for people with celiac disease remains unresolved. While oats have attractive nutritional properties that can improve the quality and palatability of the restrictive, low fiber gluten-free diet, rigorous feeding studies to address their safety in celiac disease are needed. Assessing the oat prolamin proteins (avenins) in isolation and controlling for gluten contamination and other oat components such as fiber that can cause non-specific effects and symptoms is crucial. Further, the avenin should contain all reported immunogenic T cell epitopes, and be deliverable at a dose that enables biological responses to be correlated with clinical effects. To date, isolation of a purified food-grade avenin in sufficient quantities for feeding studies has not been feasible. Here, we report a new gluten isolation technique that enabled 2 kg of avenin to be extracted from 400 kg of wheat-free oats under rigorous gluten-free and food grade conditions. The extract consisted of 85% protein of which 96% of the protein was avenin. The concentration of starch (1.8% dry weight), β-glucan (0.2% dry weight), and free sugars (1.8% dry weight) were all low in the final avenin preparation. Other sugars including oligosaccharides, small fructans, and other complex sugars were also low at 2.8% dry weight. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the proteins in these preparations showed they consisted only of oat proteins and were uncontaminated by gluten containing cereals including wheat, barley or rye. Proteomic analysis of the avenin enriched samples detected more avenin subtypes and fewer other proteins compared to samples obtained using other extraction procedures. The identified proteins represented five main groups, four containing known immune-stimulatory avenin peptides. All five groups were identified in the 50% (v/v) ethanol extract however the group harboring the epitope DQ2.5-ave-1b was less represented. The avenin-enriched protein fractions were quantitatively collected by reversed phase HPLC and analyzed by MALDI-TOF mass spectrometry. Three reverse phase HPLC peaks, representing ~40% of the protein content, were enriched in proteins containing DQ2.5-ave-1a epitope. The resultant high quality avenin will facilitate controlled and definitive feeding studies to establish the safety of oat consumption by people with celiac disease.
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Affiliation(s)
- Greg Tanner
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | | | | | | | | | - Amy K Russell
- Immunology Division, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melinda Y Hardy
- Immunology Division, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jason A Tye-Din
- Immunology Division, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Gastroenterology, The Royal Melbourne Hospital, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
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17
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Tanner GJ, Colgrave ML, Blundell MJ, Howitt CA, Bacic A. Hordein Accumulation in Developing Barley Grains. Front Plant Sci 2019; 10:649. [PMID: 31156692 PMCID: PMC6532529 DOI: 10.3389/fpls.2019.00649] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/30/2019] [Indexed: 05/14/2023]
Abstract
The temporal pattern of accumulation of hordein storage proteins in developing barley grains was studied by enzyme-linked immunosorbent assay (ELISA), western blot and liquid chromatography tandem mass spectrometry (LC-MS/MS). Hordein accumulation was compared to the pattern seen for two abundant control proteins, serpin Z4 (an early accumulator) and lipid transferase protein (LTP1, a late accumulator). Hordeins were detected from 6 days post-anthesis (DPA) and peaked at 30 DPA. Changes in fresh weight indicate that desiccation begins at 20 DPA and by 37 DPA fresh weight had decreased by 35%. ELISA analysis of hordein content, expressed on a protein basis, increased to a maximum at 30 DPA followed by a 17% decrease by 37 DPA. The accumulation of 39 tryptic and 29 chymotryptic hordein peptides representing all classes of hordein was studied by LC-MS/MS. Most peptides increased to a maximum at 30 DPA, and either remained at the maximum or did not decrease significantly. Only five tryptic peptides, members of the related B1- and γ1-hordeins decreased significantly by 21-51% at 37 DPA. Thus, the concentration of some specific peptides was reduced while remaining members of the same family were not affected. The N-terminal signal region was removed by proteolysis during co-translation. In addition to a suite of previously characterized hordeins, two novel barley B-hordein isoforms mapping to wheat low molecular weight glutenins (LMW-GS-like B-hordeins), and two avenin-like proteins (ALPs) sharing homology with wheat ALPs, were identified. These identified isoforms have not previously been mapped in the barley genome. Cereal storage proteins provide significant nutritional content for human consumption and seed germination. In barley, the bulk of the storage proteins comprise the hordein family and the final hordein concentration affects the quality of baked and brewed products. It is therefore important to study the accumulation of hordeins as this knowledge may assist plant breeding for improved health outcomes (by minimizing triggering of detrimental immune responses), nutrition and food processing properties.
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Affiliation(s)
- Gregory J. Tanner
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Michelle L. Colgrave
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, St Lucia, QLD, Australia
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Malcolm J. Blundell
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Crispin A. Howitt
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Antony Bacic
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
- La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora, VIC, Australia
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Bose U, Broadbent JA, Byrne K, Hasan S, Howitt CA, Colgrave ML. Optimisation of protein extraction for in-depth profiling of the cereal grain proteome. J Proteomics 2019; 197:23-33. [DOI: 10.1016/j.jprot.2019.02.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
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Geisslitz S, Ludwig C, Scherf KA, Koehler P. Targeted LC-MS/MS Reveals Similar Contents of α-Amylase/Trypsin-Inhibitors as Putative Triggers of Nonceliac Gluten Sensitivity in All Wheat Species except Einkorn. J Agric Food Chem 2018; 66:12395-12403. [PMID: 30365312 DOI: 10.1021/acs.jafc.8b04411] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amylase/trypsin-inhibitors (ATIs) are putative triggers of nonceliac gluten sensitivity, but contents of ATIs in different wheat species were not available. Therefore, the predominant ATIs 0.19 + 0.53, 0.28, CM2, CM3, and CM16 in eight cultivars each of common wheat, durum wheat, spelt, emmer, and einkorn grown under the same environmental conditions were quantitated by targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) and stable isotope dilution assays using specific marker peptides as internal standards. The results were compared to a label-free untargeted LC-MS/MS analysis, in which protein concentrations were determined by intensity based absolute quantitation. Both approaches yielded similar results. Spelt and emmer had higher ATI contents than common wheat, with durum wheat in between. Only three of eight einkorn cultivars contained ATIs in very low concentrations. The distribution of ATI types was characteristic for hexaploid, tetraploid, and diploid wheat species and suitable as species-specific fingerprint. The results point to a better tolerability of einkorn for NCGS patients, because of very low total ATI contents.
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Affiliation(s)
- Sabrina Geisslitz
- Leibniz-Institute for Food Systems Biology at the Technical of University Munich , Lise-Meitner-Straße 34 , 85354 Freising , Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry , Gregor-Mendel-Straße 4 , 85354 Freising , Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical of University Munich , Lise-Meitner-Straße 34 , 85354 Freising , Germany
| | - Peter Koehler
- Biotask AG , Schelztorstraße 54-56 , 73728 Esslingen am Neckar , Germany
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21
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Fenaille F, Barbier Saint-Hilaire P, Rousseau K, Junot C. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand? J Chromatogr A 2017; 1526:1-12. [PMID: 29074071 DOI: 10.1016/j.chroma.2017.10.043] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
Abstract
Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.
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Affiliation(s)
- François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Pierre Barbier Saint-Hilaire
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Kathleen Rousseau
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France.
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Huang R, Chen Z, He L, He N, Xi Z, Li Z, Deng Y, Zeng X. Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application. Theranostics 2017; 7:3559-3572. [PMID: 28912895 PMCID: PMC5596443 DOI: 10.7150/thno.20797] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests. It can also aid in elucidating the molecular mechanisms underlying cancer. In this review, we discuss MS principles and instrumentation as well as approaches in MS-based proteomics, which have been employed in the development of potential biomarkers. Furthermore, the challenges in validation of MS biomarkers for their use in clinical practice are also reviewed.
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Affiliation(s)
- Rongrong Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongsi Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lei He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Zhijiang Xi
- School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Zhiyang Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Xin Zeng
- Nanjing Maternity and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
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Colgrave ML, Byrne K, Howitt CA. Food for thought: Selecting the right enzyme for the digestion of gluten. Food Chem 2017; 234:389-397. [PMID: 28551252 DOI: 10.1016/j.foodchem.2017.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 12/24/2022]
Abstract
Gluten describes a complex mixture of proteins found in wheat, rye, barley and oats that pose a health risk to people affected by conditions such as coeliac disease and non-coeliac gluten sensitivity. Complete digestion of gluten proteins is of critical importance during quantitative analysis. To this end, chymotrypsin was investigated for its ability to efficiently and reproducibly digest specific classes of gluten in barley. Using proteomics a chymotryptic peptide marker panel was elucidated and subjected to relative quantification using LC-MRM-MS. Thorough investigation of peptide markers revealed robust and reproducible quantification with CVs <15% was possible, however a greater proportion of non-specific cleavage variants were observed relative to trypsin. The selected peptide markers were assessed to ensure their efficient liberation from their parent proteins. While trypsin remains the preferred enzyme for quantification of the avenin-like A proteins, the B-, D- and γ-hordeins, chymotrypsin was the enzyme of choice for the C-hordeins.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
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