1
|
Lin A, See D, Fondrie WE, Keich U, Noble WS. Target-decoy false discovery rate estimation using Crema. Proteomics 2024; 24:e2300084. [PMID: 38380501 DOI: 10.1002/pmic.202300084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Assigning statistical confidence estimates to discoveries produced by a tandem mass spectrometry proteomics experiment is critical to enabling principled interpretation of the results and assessing the cost/benefit ratio of experimental follow-up. The most common technique for computing such estimates is to use target-decoy competition (TDC), in which observed spectra are searched against a database of real (target) peptides and a database of shuffled or reversed (decoy) peptides. TDC procedures for estimating the false discovery rate (FDR) at a given score threshold have been developed for application at the level of spectra, peptides, or proteins. Although these techniques are relatively straightforward to implement, it is common in the literature to skip over the implementation details or even to make mistakes in how the TDC procedures are applied in practice. Here we present Crema, an open-source Python tool that implements several TDC methods of spectrum-, peptide- and protein-level FDR estimation. Crema is compatible with a variety of existing database search tools and provides a straightforward way to obtain robust FDR estimates.
Collapse
Affiliation(s)
- Andy Lin
- Chemical and Biological Signatures, Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - Donavan See
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
| | | | - Uri Keich
- School of Mathematics and Statistics, University of Sydney, Sydney, Australia
| | - William Stafford Noble
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| |
Collapse
|
2
|
Kuang J, Xu K, Dang B, Zheng W, Yang X, Zhang W, Zhang J, Huang J. Interaction with wheat starch affect the aggregation behavior and digestibility of gluten proteins. Int J Biol Macromol 2023; 253:127066. [PMID: 37748592 DOI: 10.1016/j.ijbiomac.2023.127066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Understanding the interplay between gluten and wheat starch is crucial for elucidating the digestibility mechanism of gluten in wheat-based products. However, this mechanism remains under-investigated. This study sought to elucidate the influence of starch-induced protein structural modifications on gluten digestion. Our findings revealed that starch considerably enhanced gluten digestion. In the presence of starch, gluten protein digestibility increased from 10.91 % (in the control group with a gluten-to-starch ratio of 1:0) to 14.40 % (in the complex with a gluten-to-corn starch ratio of 1:1). The diminished gluten protein digestibility due to starch may be ascribed to modifications in protein configuration and aggregation behavior. Morphological studies suggested that starch not only functioned as filler particles but also diluted the gluten matrix. A protein network assessment further affirmed that both the junction density and branching rate of gluten proteins decreased notably by 29.9 % and 25.1 %, respectively. Conversely, lacunarity increased by 1.92-fold, compromising the cohesiveness and connectivity of the gluten matrix. Elevated starch concentrations suppressed the formation of disulfide bonds, impeding gluten protein aggregation. Concurrently, gluten-starch interactions were governed by hydrogen bonds and hydrophobic associations. In summary, starch augmented gluten protein digestibility by curtailing their polymerization. This revelation might offer novel perspectives on optimizing gluten protein digestion and utilization.
Collapse
Affiliation(s)
- Jiwei Kuang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China
| | - Ke Xu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, 810016, China
| | - Bin Dang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China
| | - Wancai Zheng
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China
| | - Xijuan Yang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China.
| | - Wengang Zhang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China
| | - Jie Zhang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai Province, 810016, China; Qinghai Tibetan Plateau Key Laboratory of Agricultural Product Processing, Academy of Agriculture and Forestry Sciences, Xining, Qinghai Province 810016, China
| | - Junrong Huang
- School of Food and Biological Engineering, Natural Food Macromolecule Research Center, Shaanxi University of Science and Technology, Xi'an, Shaanxi Province 710021, China.
| |
Collapse
|
3
|
Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. Food allergen detection by mass spectrometry: From common to novel protein ingredients. Proteomics 2023; 23:e2200427. [PMID: 37691088 DOI: 10.1002/pmic.202200427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
Food allergens are molecules, mainly proteins, that trigger immune responses in susceptible individuals upon consumption even when they would otherwise be harmless. Symptoms of a food allergy can range from mild to acute; this last effect is a severe and potentially life-threatening reaction. The European Union (EU) has identified 14 common food allergens, but new allergens are likely to emerge with constantly changing food habits. Mass spectrometry (MS) is a promising alternative to traditional antibody-based assays for quantifying multiple allergenic proteins in complex matrices with high sensitivity and selectivity. Here, the main allergenic proteins and the advantages and drawbacks of some MS acquisition protocols, such as multiple reaction monitoring (MRM) and data-dependent analysis (DDA) for identifying and quantifying common allergenic proteins in processed foodstuffs are summarized. Sections dedicated to novel foods like microalgae and insects as new sources of allergenic proteins are included, emphasizing the significance of establishing stable marker peptides and validated methods using database searches. The discussion involves the in-silico digestion of allergenic proteins, providing insights into their potential impact on immunogenicity. Finally, case studies focussing on microalgae highlight the value of MS as an effective analytical tool for ensuring regulatory compliance throughout the food control chain.
Collapse
Affiliation(s)
- Mariachiara Bianco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Giovanni Ventura
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Cosima D Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Ilario Losito
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| |
Collapse
|
4
|
Lu Y, Ji H, Chen Y, Li Z, Timira V. A systematic review on the recent advances of wheat allergen detection by mass spectrometry: future prospects. Crit Rev Food Sci Nutr 2023; 63:12324-12340. [PMID: 35852160 DOI: 10.1080/10408398.2022.2101091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Wheat is one of the three major staple foods in the world. Although wheat is highly nutritional, it has a variety of allergenic components that are potentially fatal to humans and pose a significant hazard to the growth and consumption of wheat. Wheat allergy is a serious health problem, which is becoming more and more prevalent all over the world. To address and prevent related health risks, it is crucial to establish precise and sensitive detection and analytical methods as well as an understanding of the structure and sensitization mechanism of wheat allergens. Among various analytical tools, mass spectrometry (MS) is known to have high specificity and sensitivity. It is a promising non immune method to evaluate and quantify wheat allergens. In this article, the current research on the detection of wheat allergens based on mass spectrometry is reviewed. This review provides guidance for the further research on wheat allergen detection using mass spectrometry, and speeds up the development of wheat allergen research in China.
Collapse
Affiliation(s)
- Yingjun Lu
- College of Food Science and Technology, Shihezi University, Shihezi, Xinjiang, P.R. China
| | - Hua Ji
- College of Food Science and Technology, Shihezi University, Shihezi, Xinjiang, P.R. China
| | - Yan Chen
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), Beijing, P.R. China
| | - Zhenxing Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, P.R. China
| | - Vaileth Timira
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, P.R. China
| |
Collapse
|
5
|
Bacala R, Hatcher DW, Perreault H, Fu BX. Challenges and opportunities for proteomics and the improvement of bread wheat quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153743. [PMID: 35749977 DOI: 10.1016/j.jplph.2022.153743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.
Collapse
Affiliation(s)
- Ray Bacala
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Dave W Hatcher
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada
| | - Héléne Perreault
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Bin Xiao Fu
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; Department of Food and Human Nutritional Sciences, 209 - 35 Chancellor's Circle, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| |
Collapse
|
6
|
The Diverse Potential of Gluten from Different Durum Wheat Varieties in Triggering Celiac Disease: A Multilevel In Vitro, Ex Vivo and In Vivo Approach. Nutrients 2020; 12:nu12113566. [PMID: 33233787 PMCID: PMC7699868 DOI: 10.3390/nu12113566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 11/16/2022] Open
Abstract
The reasons behind the increasing prevalence of celiac disease (CD) worldwide are still not fully understood. This study adopted a multilevel approach (in vitro, ex vivo, in vivo) to assess the potential of gluten from different wheat varieties in triggering CD. Peptides triggering CD were identified and quantified in mixtures generated from simulated gastrointestinal digestion of wheat varieties (n = 82). Multivariate statistics enabled the discrimination of varieties generating low impact on CD (e.g., Saragolla) and high impact (e.g., Cappelli). Enrolled subjects (n = 46) were: 19 healthy subjects included in the control group; 27 celiac patients enrolled for the in vivo phase. Celiacs were divided into a gluten-free diet group (CD-GFD), and a GFD with Saragolla-based pasta group (CD-Sar). The diet was followed for 3 months. Data were compared between CD-Sar and CD-GFD before and after the experimental diet, demonstrating a limited ability of Saragolla to trigger immunity, although not comparable to a GFD. Ex vivo studies showed that Saragolla and Cappelli activated immune responses, although with great variability among patients. The diverse potential of durum wheat varieties in triggering CD immune response was demonstrated. Saragolla is not indicated for celiacs, yet it has a limited potential to trigger adverse immune response.
Collapse
|
7
|
Lakhneko O, Danchenko M, Morgun B, Kováč A, Majerová P, Škultéty Ľ. Comprehensive Comparison of Clinically Relevant Grain Proteins in Modern and Traditional Bread Wheat Cultivars. Int J Mol Sci 2020; 21:E3445. [PMID: 32414116 PMCID: PMC7279209 DOI: 10.3390/ijms21103445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is one of the most valuable cereal crops for human consumption. Its grain storage proteins define bread quality, though they may cause food intolerances or allergies in susceptible individuals. Herein, we discovered a diversity of grain proteins in three Ukrainian wheat cultivars: Sotnytsia, Panna (both modern selection), and Ukrainka (landrace). Firstly, proteins were isolated with a detergent-containing buffer that allowed extraction of various groups of storage proteins (glutenins, gliadins, globulins, and albumins); secondly, the proteome was profiled by the two-dimensional gel electrophoresis. Using multi-enzymatic digestion, we identified 49 differentially accumulated proteins. Parallel ultrahigh-performance liquid chromatography separation followed by direct mass spectrometry quantification complemented the results. Principal component analysis confirmed that differences among genotypes were a major source of variation. Non-gluten fraction better discriminated bread wheat cultivars. Various accumulation of clinically relevant plant proteins highlighted one of the modern genotypes as a promising donor for the breeding of hypoallergenic cereals.
Collapse
Affiliation(s)
- Olha Lakhneko
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska 9, 84505 Bratislava, Slovak Republic; (O.L.); (Ľ.Š.)
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Akademika Zabolotnoho 148, 03143 Kyiv, Ukraine;
| | - Maksym Danchenko
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska 9, 84505 Bratislava, Slovak Republic; (O.L.); (Ľ.Š.)
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Akademicka 2, 95007 Nitra, Slovak Republic
| | - Bogdan Morgun
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Akademika Zabolotnoho 148, 03143 Kyiv, Ukraine;
| | - Andrej Kováč
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska 9, 84510 Bratislava, Slovak Republic; (A.K.); (P.M.)
| | - Petra Majerová
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska 9, 84510 Bratislava, Slovak Republic; (A.K.); (P.M.)
| | - Ľudovit Škultéty
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska 9, 84505 Bratislava, Slovak Republic; (O.L.); (Ľ.Š.)
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| |
Collapse
|
8
|
Moosa JM, Guan S, Moran MF, Ma B. Repeat-Preserving Decoy Database for False Discovery Rate Estimation in Peptide Identification. J Proteome Res 2020; 19:1029-1036. [DOI: 10.1021/acs.jproteome.9b00555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Johra Muhammad Moosa
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo N2L 3G1, Canada
| | - Shenheng Guan
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo N2L 3G1, Canada
- Program in Cell Biology and SPARC BioCentre, Hospital for Sick Children, 686 Bay St, Toronto, Ontario M5G 0A4, Canada
| | - Michael F. Moran
- Program in Cell Biology and SPARC BioCentre, Hospital for Sick Children, 686 Bay St, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, 686 Bay St, Toronto, Ontario M5G 0A4, Canada
| | - Bin Ma
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo N2L 3G1, Canada
| |
Collapse
|
9
|
Boukid F, Prandi B, Faccini A, Sforza S. A Complete Mass Spectrometry (MS)-Based Peptidomic Description of Gluten Peptides Generated During In Vitro Gastrointestinal Digestion of Durum Wheat: Implication for Celiac Disease. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1481-1490. [PMID: 31049870 DOI: 10.1007/s13361-019-02212-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/02/2019] [Indexed: 05/29/2023]
Abstract
Resistance of gluten to gastrointestinal digestion is involved in immune-mediated adverse reactions to wheat, since several peptides produced by the incomplete digestion are able to trigger, in predisposed individuals, the immune response responsible, for instance, of celiac disease (CD) and other adverse reactions. Even if several peptides have been identified, an exhaustive description of the peptidome generated by wheat digestion is lacking. To this end, in the present work, durum wheat proteins were fractionated, digested, and then subjected to various proteomic techniques, including single stage and multiple stage mass spectrometry (MS) (SDS-PAGE, UPLC/ESI-MS, UPLC/ESI-MS/MS, and LTQ-Orbitrap). Based on SDS-PAGE, although proteins were severely degraded after in vitro gastrointestinal digestion, some differences were observed among protein profile of the different digests. Through untargeted UPLC techniques, 227 peptide sequences were identified, with only few sequences shared by the different digests. In particular, 9 gluten peptides involved in CD were identified. Based on target proteomic, the quantification of these peptides revealed significant (p ≤ 0.05) differences among the different extracts. Taken together, all the proteomic tools confirmed that gluten digestion is closely related to the matrix regardless of wheat genotype.
Collapse
Affiliation(s)
- Fatma Boukid
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 23/A, Parma, 43124, Italy
| | - Barbara Prandi
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy.
- Department of Human Sciences and Promotion of Quality of Life, Telematic University San Raffaele Roma, via Val Cannuta, 247, Rome, Italy.
| | - Andrea Faccini
- Interdepartmental Centre for Measurements, University of Parma, Parco Area Delle Scienze 23/A, 43124, Parma, Italy
| | - Stefano Sforza
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 23/A, Parma, 43124, Italy
| |
Collapse
|
10
|
Wen W, Li S, Gu Y, Wang S, Wang J. Effects of Starch on the Digestibility of Gluten under Different Thermal Processing Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7120-7127. [PMID: 31026160 DOI: 10.1021/acs.jafc.9b01063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gluten and starch are the primary ingredients of wheat. The complex reaction between gluten and starch will occur during thermal food processing, which will affect digestibility. The effects of proteins on the digestibility of starch have been reported, but the effects of starch on the digestibility of proteins have not been well-researched. In this paper, the effects of starch on gluten digestion during the heating process were studied by the gluten-starch simulated system, and it was found that starch can enhance gluten digestion. When the complex of 1:1 gluten-starch is heated at 100 °C, the digestibility of gluten is higher and more low-molecular-weight peptides are produced. Results from the digestibility and digestion peptide mapping of the gluten-starch complex at different conditions showed that the addition of starch during processing enhanced the digestion performance of gluten. Meanwhile, the secondary structure, intrinsic fluorescence, and microscopic structure of the gluten-starch complex were investigated to understand the mechanism of the enhancement. The digestion performance is related to the secondary structure variation during the thermal processing caused by the hydration increase and disulfide bond reduction. The gluten-starch complex spatial structure is looser than gluten after heating, which could expose more protease cleavage sites. These results suggest that starch can protect gluten from aggregation in water and destroy the spatial structure of gluten with the assistance of heating, exposing more cleavage sites and enhancing gluten digestion.
Collapse
Affiliation(s)
- Wenjun Wen
- State Key Laboratory of Food Nutrition and Safety , Tianjin University of Science & Technology , 29 Thirteenth Road , Tianjin Economy and Technology Development Area, Tianjin 300457 , People's Republic of China
| | - Shijie Li
- State Key Laboratory of Food Nutrition and Safety , Tianjin University of Science & Technology , 29 Thirteenth Road , Tianjin Economy and Technology Development Area, Tianjin 300457 , People's Republic of China
| | - Ying Gu
- State Key Laboratory of Food Nutrition and Safety , Tianjin University of Science & Technology , 29 Thirteenth Road , Tianjin Economy and Technology Development Area, Tianjin 300457 , People's Republic of China
| | - Shuo Wang
- Medical College , Nankai University , 38 Tongyan Road , Jinnan District, Tianjin 300350 , People's Republic of China
| | - Junping Wang
- State Key Laboratory of Food Nutrition and Safety , Tianjin University of Science & Technology , 29 Thirteenth Road , Tianjin Economy and Technology Development Area, Tianjin 300457 , People's Republic of China
| |
Collapse
|
11
|
Alves TO, D’Almeida CTS, Scherf KA, Ferreira MSL. Modern Approaches in the Identification and Quantification of Immunogenic Peptides in Cereals by LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2019; 10:1470. [PMID: 31798614 PMCID: PMC6868032 DOI: 10.3389/fpls.2019.01470] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 10/22/2019] [Indexed: 05/17/2023]
Abstract
Celiac disease (CD) is an immunogenic disorder that affects the small intestine. It is caused by the ingestion of gluten, a protein network formed by prolamins and glutelins from cereals such as wheat, barley, rye and, possibly, oats. For predisposed people, gluten presents epitopes able to stimulate T-cells causing symptoms like nausea, vomiting, diarrhea, among others unrelated to the gastrointestinal system. The only treatment for CD is to maintain a gluten-free diet, not exceeding 20 mg/kg of gluten, what is generally considered the safe amount for celiacs. Due to this context, it is very important to identify and quantify the gluten content of food products. ELISA is the most commonly used method to detect gluten traces in food. However, by detecting only prolamins, the results of ELISA tests may be underestimated. For this reason, more reliable and sensitive assays are needed to improve gluten quantification. Because of high sensitivity and the ability to detect even trace amounts of peptides in complex matrices, the most promising approaches to verify the presence of gluten peptides in food are non-immunological techniques, like liquid chromatography coupled to mass spectrometry. Different methodologies using this approach have been developed and described in the last years, ranging from non-targeted and exploratory analysis to targeted and specific methods depending on the purpose of interest. Non-targeted analyses aim to define the proteomic profile of the sample, while targeted analyses allow the search for specific peptides, making it possible to quantify them. This review aims to gather and summarize the main proteomic techniques used in the identification and quantitation of gluten peptides related to CD-activity and gluten-related allergies.
Collapse
Affiliation(s)
- Thais O. Alves
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
| | - Carolina T. S. D’Almeida
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
| | - Katharina A. Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Mariana S. L. Ferreira
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
- *Correspondence: Mariana S. L. Ferreira,
| |
Collapse
|
12
|
Immunogenic and allergenic profile of wheat flours from different technological qualities revealed by ion mobility mass spectrometry. J Food Compost Anal 2018. [DOI: 10.1016/j.jfca.2018.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
13
|
Victorio VCM, Souza GH, Santos MCB, Vega AR, Cameron L, Ferreira MSL. Differential expression of albumins and globulins of wheat flours of different technological qualities revealed by nanoUPLC-UDMSE. Food Chem 2018; 239:1027-1036. [DOI: 10.1016/j.foodchem.2017.07.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/30/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022]
|
14
|
Nunes-Miranda JD, Bancel E, Viala D, Chambon C, Capelo JL, Branlard G, Ravel C, Igrejas G. Wheat glutenin: the “tail” of the 1By protein subunits. J Proteomics 2017; 169:136-142. [DOI: 10.1016/j.jprot.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/03/2017] [Accepted: 05/18/2017] [Indexed: 10/19/2022]
|
15
|
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] [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.
Collapse
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
| |
Collapse
|
16
|
Genome-wide analysis of complex wheat gliadins, the dominant carriers of celiac disease epitopes. Sci Rep 2017; 7:44609. [PMID: 28300172 PMCID: PMC5353739 DOI: 10.1038/srep44609] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/09/2017] [Indexed: 01/08/2023] Open
Abstract
Gliadins, specified by six compound chromosomal loci (Gli-A1/B1/D1 and Gli-A2/B2/D2) in hexaploid bread wheat, are the dominant carriers of celiac disease (CD) epitopes. Because of their complexity, genome-wide characterization of gliadins is a strong challenge. Here, we approached this challenge by combining transcriptomic, proteomic and bioinformatic investigations. Through third-generation RNA sequencing, full-length transcripts were identified for 52 gliadin genes in the bread wheat cultivar Xiaoyan 81. Of them, 42 were active and predicted to encode 25 α-, 11 γ-, one δ- and five ω-gliadins. Comparative proteomic analysis between Xiaoyan 81 and six newly-developed mutants each lacking one Gli locus indicated the accumulation of 38 gliadins in the mature grains. A novel group of α-gliadins (the CSTT group) was recognized to contain very few or no CD epitopes. The δ-gliadins identified here or previously did not carry CD epitopes. Finally, the mutant lacking Gli-D2 showed significant reductions in the most celiac-toxic α-gliadins and derivative CD epitopes. The insights and resources generated here should aid further studies on gliadin functions in CD and the breeding of healthier wheat.
Collapse
|
17
|
Bromilow SNL, Gethings LA, Langridge JI, Shewry PR, Buckley M, Bromley MJ, Mills ENC. Comprehensive Proteomic Profiling of Wheat Gluten Using a Combination of Data-Independent and Data-Dependent Acquisition. FRONTIERS IN PLANT SCIENCE 2017; 7:2020. [PMID: 28119711 PMCID: PMC5223596 DOI: 10.3389/fpls.2016.02020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 05/24/2023]
Abstract
Wheat is the most important food crop in the world, the unique physiochemical properties of wheat gluten enabling a diverse range of food products to be manufactured. However, genetic and environmental factors affect the technological properties of gluten in unpredictable ways. Although newer proteomic methods have the potential to offer much greater levels of information, it is the older gel-based methods that remain most commonly used to identify compositional differences responsible for the variation in gluten functionality, in part due to the nature of their primary sequences. A combination of platforms were investigated for comprehensive gluten profiling: a QTOF with a data independent schema, which incorporated ion mobility (DIA-IM-MS) and a data dependent acquisition (DDA) workflow using a linear ion trap quadrupole (LTQ) instrument. In conjunction with a manually curated gluten sequence database a total of 2736 gluten peptides were identified with only 157 peptides identified by both platforms. These data showed 127 and 63 gluten protein accessions to be inferred with a minimum of one and three unique peptides respectively. Of the 63 rigorously identified proteins, 26 were gliadin species (4 ω-, 14 α-, and 8 γ-gliadins) and 37 glutenins (including 29 LMW glutenin and 8 HMW glutenins). Of the HMW glutenins, three were 1Dx type and five were 1Bx type illustrating the challenge of unambiguous identification of highly polymorphic proteins without cultivar specific gene sequences. The capacity of the platforms to sequence longer peptides was crucial to achieving the number of identifications, the combination of QTOF-LTQ technology being more important than extraction method to obtain a comprehensive profile. Widespread glutamine deamidation, a post-translational modification, was observed adding complexity to an already highly polymorphic mixture of proteins, with numerous insertions, deletions and substitutions. The data shown is the most comprehensive and detailed proteomic profile of gluten to date.
Collapse
Affiliation(s)
- Sophie N. L. Bromilow
- Faculty of Biology, Medicine and Health, Infection, Immunity and Respiratory Medicine, Manchester Academic Health Sciences Centre, Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | | | | | | | - Michael Buckley
- School of Chemistry, Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | | | - E. N. Clare Mills
- Faculty of Biology, Medicine and Health, Infection, Immunity and Respiratory Medicine, Manchester Academic Health Sciences Centre, Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| |
Collapse
|
18
|
Lee JY, Kang CS, Beom HR, Jang YR, Altenbach SB, Lim SH, Kim YM, Park CS. Characterization of a wheat mutant missing low-molecular-weight glutenin subunits encoded by the B-genome. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
19
|
Defining the wheat gluten peptide fingerprint via a discovery and targeted proteomics approach. J Proteomics 2016; 147:156-168. [PMID: 26994601 DOI: 10.1016/j.jprot.2016.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 11/24/2022]
Abstract
UNLABELLED Accurate, reliable and sensitive detection methods for gluten are required to support current EU regulations. The enforcement of legislative levels requires that measurement results are comparable over time and between methods. This is not a trivial task for gluten which comprises a large number of protein targets. This paper describes a strategy for defining a set of specific analytical targets for wheat gluten. A comprehensive proteomic approach was applied by fractionating wheat gluten using RP-HPLC (reversed phase high performance liquid chromatography) followed by a multi-enzymatic digestion (LysC, trypsin and chymotrypsin) with subsequent mass spectrometric analysis. This approach identified 434 peptide sequences from gluten. Peptides were grouped based on two criteria: unique to a single gluten protein sequence; contained known immunogenic and toxic sequences in the context of coeliac disease. An LC-MS/MS method based on selected reaction monitoring (SRM) was developed on a triple quadrupole mass spectrometer for the specific detection of the target peptides. The SRM based screening approach was applied to gluten containing cereals (wheat, rye, barley and oats) and non-gluten containing flours (corn, soy and rice). A unique set of wheat gluten marker peptides were identified and are proposed as wheat specific markers. SIGNIFICANCE The measurement of gluten in processed food products in support of regulatory limits is performed routinely. Mass spectrometry is emerging as a viable alternative to ELISA based methods. Here we outline a set of peptide markers that are representative of gluten and consider the end user's needs in protecting those with coeliac disease. The approach taken has been applied to wheat but can be easily extended to include other species potentially enabling the MS quantification of different gluten containing species from the identified markers.
Collapse
|
20
|
Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in food proteomics: a tutorial. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:768-784. [PMID: 25230173 DOI: 10.1002/jms.3374] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 06/03/2023]
Abstract
In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed.
Collapse
Affiliation(s)
- Vincenzo Cunsolo
- Department of Chemical Sciences, University of Catania, Viale A. Doria, 6, I-95125, Catania, Italy
| | | | | | | |
Collapse
|
21
|
Fiedler KL, McGrath SC, Callahan JH, Ross MM. Characterization of grain-specific peptide markers for the detection of gluten by mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5835-5844. [PMID: 24866027 DOI: 10.1021/jf500997j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Global and targeted mass spectrometry-based proteomic approaches were developed to discover, evaluate, and apply gluten peptide markers to detect low parts per million (ppm) wheat contamination of oats. Prolamins were extracted from wheat, barley, rye, and oat flours and then reduced, alkylated, and digested with chymotrypsin. The resulting peptides were subjected to LC-MS/MS analysis and database matching. No peptide markers common to wheat, barley, and rye were identified that could be used for global gluten detection. However, many grain-specific peptide markers were identified, and a set of these markers was selected for gluten detection and grain differentiation. Wheat flour was spiked into gluten-free oat flour at concentrations of 1-100,000 ppm and analyzed to determine the lowest concentration at which the wheat "contaminant" could be confidently detected in the mixture. The same 2D ion trap instrument that was used for the global proteomics approach was used for the targeted proteomics approach, providing a seamless transition from target discovery to application. A powerful, targeted MS/MS method enabled detection of two wheat peptide markers at the 10 ppm wheat flour-in-oat flour concentration. Because gluten comprises approximately 10% of wheat flour protein, the reported wheat gluten-specific peptides can enable detection of approximately 1 ppm of wheat gluten in oats.
Collapse
Affiliation(s)
- Katherine L Fiedler
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, Maryland 20740, United States
| | | | | | | |
Collapse
|
22
|
Egidi E, Sestili F, Janni M, D’Ovidio R, Lafiandra D, Ceriotti A, Vensel WH, Kasarda DD, Masci S. An asparagine residue at the N-terminus affects the maturation process of low molecular weight glutenin subunits of wheat endosperm. BMC PLANT BIOLOGY 2014; 14:64. [PMID: 24629124 PMCID: PMC4004387 DOI: 10.1186/1471-2229-14-64] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/07/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Wheat glutenin polymers are made up of two main subunit types, the high- (HMW-GS) and low- (LMW-GS) molecular weight subunits. These latter are represented by heterogeneous proteins. The most common, based on the first amino acid of the mature sequence, are known as LMW-m and LMW-s types. The mature sequences differ as a consequence of three extra amino acids (MET-) at the N-terminus of LMW-m types. The nucleotide sequences of their encoding genes are, however, nearly identical, so that the relationship between gene and protein sequences is difficult to ascertain.It has been hypothesized that the presence of an asparagine residue in position 23 of the complete coding sequence for the LMW-s type might account for the observed three-residue shortened sequence, as a consequence of cleavage at the asparagine by an asparaginyl endopeptidase. RESULTS We performed site-directed mutagenesis of a LMW-s gene to replace asparagine at position 23 with threonine and thus convert it to a candidate LMW-m type gene. Similarly, a candidate LMW-m type gene was mutated at position 23 to replace threonine with asparagine. Next, we produced transgenic durum wheat (cultivar Svevo) lines by introducing the mutated versions of the LMW-m and LMW-s genes, along with the wild type counterpart of the LMW-m gene.Proteomic comparisons between the transgenic and null segregant plants enabled identification of transgenic proteins by mass spectrometry analyses and Edman N-terminal sequencing. CONCLUSIONS Our results show that the formation of LMW-s type relies on the presence of an asparagine residue close to the N-terminus generated by signal peptide cleavage, and that LMW-GS can be quantitatively processed most likely by vacuolar asparaginyl endoproteases, suggesting that those accumulated in the vacuole are not sequestered into stable aggregates that would hinder the action of proteolytic enzymes. Rather, whatever is the mechanism of glutenin polymer transport to the vacuole, the proteins remain available for proteolytic processing, and can be converted to the mature form by the removal of a short N-terminal sequence.
Collapse
Affiliation(s)
| | | | - Michela Janni
- DAFNE, Tuscia University, Viterbo, Italy
- Present address: Institute of Plant Genetics (IGV), CNR, Via Amendola 165/A, 70126 Bari, Italy
| | | | | | | | | | | | | |
Collapse
|
23
|
Vensel WH, Tanaka CK, Altenbach SB. Protein composition of wheat gluten polymer fractions determined by quantitative two-dimensional gel electrophoresis and tandem mass spectrometry. Proteome Sci 2014; 12:8. [PMID: 24517725 PMCID: PMC4016294 DOI: 10.1186/1477-5956-12-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/23/2014] [Indexed: 11/10/2022] Open
Abstract
Background Certain wheat gluten proteins form large protein polymers that are extractable in 0.5% SDS only after sonication. Although there is a strong relationship between the amounts of these polymers in the flour and bread-making quality, the protein components of these polymers have not been thoroughly investigated. Results Flour proteins from the US bread wheat Butte 86 were extracted in 0.5% SDS using a two-step procedure with and without sonication. Proteins were further separated by size exclusion chromatography (SEC) into monomeric and polymeric fractions and analyzed by quantitative two-dimensional gel electrophoresis (2-DE). When proteins in select 2-DE spots were identified by tandem mass spectrometry (MS/MS), overlapping spots from the different protein fractions often yielded different identifications. Most high-molecular-weight glutenin subunits (HMW-GS) and low-molecular-weight glutenin subunits (LMW-GS) partitioned into the polymer fractions, while most gliadins were found in the monomer fractions. The exceptions were alpha, gamma and omega gliadins containing odd numbers of cysteine residues. These proteins were detected in all fractions, but comprised the largest proportion of the SDS-extractable polymer fraction. Several types of non-gluten proteins also were found in the polymer fractions, including serpins, triticins and globulins. All three types were found in the largest proportions in the SDS-extractable polymer fraction. Conclusions This is the first study to report the accumulation of gliadins containing odd numbers of cysteine residues in the SDS-extractable glutenin polymer fraction, supporting the hypothesis that these gliadins serve as chain terminators of the polymer chains. These data make it possible to formulate hypotheses about how protein composition influences polymer size and structure and provide a foundation for future experiments aimed at determining how environment affects glutenin polymer distribution. In addition, the analysis revealed additional layers of complexity to the wheat flour proteome that should be considered when evaluating quantitative 2-DE data.
Collapse
Affiliation(s)
- William H Vensel
- USDA-ARS, Western Regional Research Center, 800 Buchanan St, Albany, CA 94710, USA
| | - Charlene K Tanaka
- USDA-ARS, Western Regional Research Center, 800 Buchanan St, Albany, CA 94710, USA
| | - Susan B Altenbach
- USDA-ARS, Western Regional Research Center, 800 Buchanan St, Albany, CA 94710, USA
| |
Collapse
|
24
|
Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii. Proc Natl Acad Sci U S A 2014; 111:2608-13. [PMID: 24505058 DOI: 10.1073/pnas.1324240111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
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 H2 plus CO2 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 H2 plus CO2. 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 O2, 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 O2, thus raising the question whether a complex biological system of this type evolved at least 2.5 billion years ago.
Collapse
|
25
|
Pascovici D, Gardiner DM, Song X, Breen E, Solomon PS, Keighley T, Molloy MP. Coverage and Consistency: Bioinformatics Aspects of the Analysis of Multirun iTRAQ Experiments with Wheat Leaves. J Proteome Res 2013; 12:4870-81. [DOI: 10.1021/pr400531y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Dana Pascovici
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Donald M. Gardiner
- CSIRO Plant Industry, Queensland Bioscience
Precinct, 306 Carmody Road, Brisbane, QLD 4067, Australia
| | - Xiaomin Song
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Edmond Breen
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter S. Solomon
- Plant
Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Tim Keighley
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Mark P. Molloy
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
26
|
Hurkman WJ, Tanaka CK, Vensel WH, Thilmony R, Altenbach SB. Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86. Proteome Sci 2013; 11:8. [PMID: 23432757 PMCID: PMC3599944 DOI: 10.1186/1477-5956-11-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/31/2013] [Indexed: 12/04/2022] Open
Abstract
Background Flour quality is largely determined by the gluten proteins, a complex mixture of proteins consisting of high molecular weight-glutenin subunits (HMW-GS), low molecular weight-glutenin subunits (LMW-GS), and α-, γ-, and ω-gliadins. Detailed proteomic analyses of the effects of fertilizer and high temperature on individual gliadin and glutenin protein levels are needed to determine how these environmental factors influence flour quality. Results Wheat plants (Triticum aestivum L. cv. Butte 86) were grown in greenhouses under moderate and high temperature regimens with and without post-anthesis fertilizer. Quantitative two-dimensional gel electrophoresis was used to construct accumulation profiles in developing endosperm for the entire complement of gluten proteins identified previously by tandem mass spectrometry. Amounts of individual gliadins and glutenins were also determined in flour produced under each of the regimens. Under all environmental regimens, most HMW-GS, LMW-GS, γ- and ω-gliadins accumulated rapidly during early stages of grain development and leveled off during middle stages of development. A subset of LMW-GS showed a second distinct profile, accumulating throughout development, while α-gliadins showed a variety of accumulation profiles. In flour, fourteen distinct gluten proteins responded similarly to fertilizer, high temperature, and high temperature plus fertilizer. The majority of HMW-GS and ω-gliadins and some α-gliadins increased while two LMW-GS and a minor γ-gliadin decreased. Fertilizer did not influence gluten protein accumulation under high temperature conditions. Additionally, the effects of fertilizer and high temperature were not additive; very few changes were observed when plants that received fertilizer were subjected to high temperature. Conclusions Although post-anthesis temperature and fertilizer have very different effects on grain development and yield, the two treatments elicit surprisingly similar effects on the accumulation of gluten proteins. The similarity of the responses to the different treatments is likely due to source-sink activities of nitrogen reserves in the wheat plant. Because each protein that showed a response in this study is linked to a gene sequence, the work sets the stage for transgenic studies that will better elucidate the roles of specific proteins in flour quality and in the response to the environment.
Collapse
Affiliation(s)
- William J Hurkman
- U,S, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
| | | | | | | | | |
Collapse
|
27
|
Rombouts I, Lagrain B, Brunnbauer M, Delcour JA, Koehler P. Improved identification of wheat gluten proteins through alkylation of cysteine residues and peptide-based mass spectrometry. Sci Rep 2013; 3:2279. [PMID: 23880742 PMCID: PMC3721084 DOI: 10.1038/srep02279] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/09/2013] [Indexed: 11/22/2022] Open
Abstract
The concentration and composition of wheat gluten proteins and the presence, concentration and location of cysteine residues therein are important for wheat flour quality. However, it is difficult to identify gluten proteins, as they are an extremely polymorphic mixture of prolamins. We here present methods for cysteine labeling of wheat prolamins with 4-vinylpyridine (4-VP) and iodoacetamide (IDAM) which, as compared to label-free analysis, substantially improve identification of cysteine-containing peptides in enzymic prolamin digests by electrospray ionization--tandem mass spectrometry. Both chymotrypsin and thermolysin yielded cysteine-containing peptides from different gluten proteins, but more proteins could be identified after chymotryptic digestion. In addition, to the best of our knowledge, we were the first to label prolamins with isotope coded affinity tags (ICAT), which are commonly used for quantitative proteomics. However, more peptides were detected after labeling gluten proteins with 4-VP and IDAM than with ICAT.
Collapse
Affiliation(s)
- Ine Rombouts
- German Research Center for Food Chemistry, Leibniz Institute, Lise-Meitner-Strasse 34, D-85354 Freising, Germany.
| | | | | | | | | |
Collapse
|
28
|
Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in the proteome analysis of mature cereal kernels. MASS SPECTROMETRY REVIEWS 2012; 31:448-465. [PMID: 22711440 DOI: 10.1002/mas.20347] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 06/01/2023]
Abstract
In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.
Collapse
Affiliation(s)
- Vincenzo Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | | | | | | |
Collapse
|
29
|
New insights into the effects of high temperature, drought and post-anthesis fertilizer on wheat grain development. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2011.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
30
|
Altenbach SB, Tanaka CK, Hurkman WJ, Whitehand LC, Vensel WH, Dupont FM. Differential effects of a post-anthesis fertilizer regimen on the wheat flour proteome determined by quantitative 2-DE. Proteome Sci 2011; 9:46. [PMID: 21816081 PMCID: PMC3168407 DOI: 10.1186/1477-5956-9-46] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/04/2011] [Indexed: 11/10/2022] Open
Abstract
Background Mineral nutrition during wheat grain development has large effects on wheat flour protein content and composition, which in turn affect flour quality and immunogenic potential for a commodity of great economic value. However, it has been difficult to define the precise effects of mineral nutrition on protein composition because of the complexity of the wheat flour proteome. Recent improvements in the identification of flour proteins by tandem mass spectrometry (MS/MS) and the availability of a comprehensive proteome map of flour from the US wheat Butte 86 now make it possible to document changes in the proportions of individual flour proteins that result from the application of mineral nutrition. Results Plants of Triticum aestivum 'Butte 86' were grown with or without post-anthesis fertilization (PAF) and quantitative 2-dimensional gel electrophoresis (2-DE) was used to analyze protein composition of the resulting flour. Significant changes in the proportions of 54 unique proteins were observed as a result of the treatment. Most omega-gliadins, high molecular weight glutenin subunits (HMW-GS) and serpins as well as some alpha-gliadins increased in proportion with PAF. In contrast, alpha-amylase/protease inhibitors, farinins, purinins and puroindolines decreased in proportion. Decreases were also observed in several low molecular weight glutenin subunits (LMW-GS), globulins, defense proteins and enzymes. The ratio of HMW-GS to LMW-GS in the flour increased from 0.61 to 0.95 and the ratio of gliadins to glutenins increased from 1.02 to 1.30 with PAF. Because flour protein content doubled with PAF from 7 to 14%, most protein types actually increased in absolute amount (μg/mg flour protein). Data further suggest that flour proteins change with PAF according to their content of sulfur-containing amino acids Cys + Met. Conclusions A 2-DE approach revealed changes in the wheat flour proteome due to PAF that are important for flour quality and immunogenic potential. The work forms a baseline for further studies of the effects of environmental variables on flour protein composition and provides clues about the regulation of specific flour protein genes. The study also is important for identifying targets for breeding programs and biotechnology efforts aimed at improving flour quality.
Collapse
Affiliation(s)
- Susan B Altenbach
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| | - Charlene K Tanaka
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| | - William J Hurkman
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| | - Linda C Whitehand
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| | - William H Vensel
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| | - Frances M Dupont
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710
| |
Collapse
|
31
|
Dupont FM, Vensel WH, Tanaka CK, Hurkman WJ, Altenbach SB. Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry. Proteome Sci 2011; 9:10. [PMID: 21314956 PMCID: PMC3238214 DOI: 10.1186/1477-5956-9-10] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 02/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat flour is one of the world's major food ingredients, in part because of the unique end-use qualities conferred by the abundant glutamine- and proline-rich gluten proteins. Many wheat flour proteins also present dietary problems for consumers with celiac disease or wheat allergies. Despite the importance of these proteins it has been particularly challenging to use MS/MS to distinguish the many proteins in a flour sample and relate them to gene sequences. RESULTS Grain from the extensively characterized spring wheat cultivar Triticum aestivum 'Butte 86' was milled to white flour from which proteins were extracted, then separated and quantified by 2-DE. Protein spots were identified by separate digestions with three proteases, followed by tandem mass spectrometry analysis of the peptides. The spectra were used to interrogate an improved protein sequence database and results were integrated using the Scaffold program. Inclusion of cultivar specific sequences in the database greatly improved the results, and 233 spots were identified, accounting for 93.1% of normalized spot volume. Identified proteins were assigned to 157 wheat sequences, many for proteins unique to wheat and nearly 40% from Butte 86. Alpha-gliadins accounted for 20.4% of flour protein, low molecular weight glutenin subunits 18.0%, high molecular weight glutenin subunits 17.1%, gamma-gliadins 12.2%, omega-gliadins 10.5%, amylase/protease inhibitors 4.1%, triticins 1.6%, serpins 1.6%, purinins 0.9%, farinins 0.8%, beta-amylase 0.5%, globulins 0.4%, other enzymes and factors 1.9%, and all other 3%. CONCLUSIONS This is the first successful effort to identify the majority of abundant flour proteins for a single wheat cultivar, relate them to individual gene sequences and estimate their relative levels. Many genes for wheat flour proteins are not expressed, so this study represents further progress in describing the expressed wheat genome. Use of cultivar-specific contigs helped to overcome the difficulties of matching peptides to gene sequences for members of highly similar, rapidly evolving storage protein families. Prospects for simplifying this process for routine analyses are discussed. The ability to measure expression levels for individual flour protein genes complements information gained from efforts to sequence the wheat genome and is essential for studies of effects of environment on gene expression.
Collapse
Affiliation(s)
- Frances M Dupont
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - William H Vensel
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - Charlene K Tanaka
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - William J Hurkman
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - Susan B Altenbach
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| |
Collapse
|