1
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Kerr ED, Fox GP, Schulz BL. Proteomics and Metabolomics Reveal that an Abundant α-Glucosidase Drives Sorghum Fermentability for Beer Brewing. J Proteome Res 2023; 22:3596-3606. [PMID: 37821127 DOI: 10.1021/acs.jproteome.3c00436] [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: 10/13/2023]
Abstract
Sorghum (Sorghum bicolor), a grass native to Africa, is a popular alternative to barley for brewing beer. The importance of sorghum to beer brewing is increasing because it is a naturally gluten-free cereal, and climate change is expected to cause a reduction in the production of barley over the coming decades. However, there are challenges associated with the use of sorghum instead of barley in beer brewing. Here, we used proteomics and metabolomics to gain insights into the sorghum brewing process to advise processes for efficient beer production from sorghum. We found that during malting, sorghum synthesizes the amylases and proteases necessary for brewing. Proteomics revealed that mashing with sorghum malt required higher temperatures than barley malt for efficient protein solubilization. Both α- and β-amylase were considerably less abundant in sorghum wort than in barley wort, correlating with lower maltose concentrations in sorghum wort. However, metabolomics revealed higher glucose concentrations in sorghum wort than in barley wort, consistent with the presence of an abundant α-glucosidase detected by proteomics in sorghum malt. Our results indicate that sorghum can be a viable grain for industrial fermented beverage production, but that its use requires careful process optimization for efficient production of fermentable wort and high-quality beer.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Glen P Fox
- Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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2
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Pinto MBC, Schmidt FL, Rappsilber J, Gibson B, Wietstock PC. Addition of Hop ( Humulus Lupulus L.) Bitter Acids Yields Modification of Malt Protein Aggregate Profiles during Wort Boiling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5700-5711. [PMID: 36989404 DOI: 10.1021/acs.jafc.3c00185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Hop bitter acids are used in the brewing industry to give beer bitterness. However, much of this bitterness is lost during processing, specifically during the wort boiling step. One of the major causes might be the interaction with protein-protein complexes. Therefore, the aim of this study was to clarify the role of hop bitter acids in protein aggregate formation using a proteomic approach. The effect of hop addition on protein composition was analyzed by liquid chromatography-mass spectrometry/MS (LC-MS/MS), and further analyses were performed to characterize the wort before and after boiling. Addition of hop bitter acids yielded a change in wort protein profiles, and hop bitter acids were found to bind primarily to less abundant proteins which are not related to beer quality traits, such as foam or haze. Wort protein aggregate profiles were revealed, and findings from this study suggested the precipitation of particular proteins in the aggregates during boiling when hops were added.
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Affiliation(s)
- Mariana B C Pinto
- Fruit, Vegetable and Confectionery Products Laboratory, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato 80, 13083-862 Campinas, São Paulo, Brazil
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Flavio L Schmidt
- Fruit, Vegetable and Confectionery Products Laboratory, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato 80, 13083-862 Campinas, São Paulo, Brazil
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Brian Gibson
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Philip C Wietstock
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
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3
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Rizzo AJ, Palacios MB, Vale EM, Zelada AM, Silveira V, Burrieza HP. Snapshot of four mature quinoa ( Chenopodium quinoa) seeds: a shotgun proteomics analysis with emphasis on seed maturation, reserves and early germination. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:319-334. [PMID: 37033760 PMCID: PMC10073371 DOI: 10.1007/s12298-023-01295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/10/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Chenopodium quinoa Willd. is a crop species domesticated over 5000 years ago. This species is highly diverse, with a geographical distribution that covers more than 5000 km from Colombia to Chile, going through a variety of edaphoclimatic conditions. Quinoa grains have great nutritional quality, raising interest at a worldwide level. In this work, by using shotgun proteomics and in silico analysis, we present an overview of mature quinoa seed proteins from a physiological context and considering the process of seed maturation and future seed germination. For this purpose, we selected grains from four contrasting quinoa cultivars (Amarilla de Maranganí, Chadmo, Sajama and Nariño) with different edaphoclimatic and geographical origins. The results give insight on the most important metabolic pathways for mature quinoa seeds including: starch synthesis, protein bodies and lipid bodies composition, reserves and their mobilization, redox homeostasis, and stress related proteins like heat-shock proteins (HSPs) and late embryogenesis abundant proteins (LEAs), as well as evidence for capped and uncapped mRNA translation. LEAs present in our analysis show a specific pattern of expression matching that of other species. Overall, this work presents a complete snapshot of quinoa seeds physiological context, providing a reference point for further studies. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01295-8.
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Affiliation(s)
- Axel Joel Rizzo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Belén Palacios
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ Brazil
| | - Alicia Mercedes Zelada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ Brazil
| | - Hernán Pablo Burrieza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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4
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Clermont K, Graham CJ, Lloyd SW, Grimm CC, Randall JJ, Mattison CP. Proteomic Analysis of Pecan ( Carya illinoinensis) Nut Development. Foods 2023; 12:foods12040866. [PMID: 36832940 PMCID: PMC9957463 DOI: 10.3390/foods12040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Pecan (Carya illinoinensis) nuts are an economically valuable crop native to the United States and Mexico. A proteomic summary from two pecan cultivars at multiple time points was used to compare protein accumulation during pecan kernel development. Patterns of soluble protein accumulation were elucidated using qualitative gel-free and label-free mass-spectrometric proteomic analyses and quantitative (label-free) 2-D gel electrophoresis. Two-dimensional (2-D) gel electrophoresis distinguished a total of 1267 protein spots and shotgun proteomics identified 556 proteins. Rapid overall protein accumulation occurred in mid-September during the transition to the dough stage as the cotyledons enlarge within the kernel. Pecan allergens Car i 1 and Car i 2 were first observed to accumulate during the dough stage in late September. While overall protein accumulation increased, the presence of histones diminished during development. Twelve protein spots accumulated differentially based on 2-D gel analysis in the weeklong interval between the dough stage and the transition into a mature kernel, while eleven protein spots were differentially accumulated between the two cultivars. These results provide a foundation for more focused proteomic analyses of pecans that may be used in the future to identify proteins that are important for desirable traits, such as reduced allergen content, improved polyphenol or lipid content, increased tolerance to salinity, biotic stress, seed hardiness, and seed viability.
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Affiliation(s)
- Kristen Clermont
- Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture, New Orleans, LA 70124, USA
- U.S. Department of Energy, Oak Ridge Institute for Science and Education, Oak Ridge, TN 20585, USA
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | | | - Steven W. Lloyd
- Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture, New Orleans, LA 70124, USA
| | - Casey C. Grimm
- Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture, New Orleans, LA 70124, USA
| | - Jennifer J. Randall
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM 88003, USA
| | - Christopher P. Mattison
- Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture, New Orleans, LA 70124, USA
- Correspondence: ; Tel.: +1-504-286-4392
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5
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Xu C, Abbas HMK, Zhan C, Huang Y, Huang S, Yang H, Wang Y, Yuan H, Luo J, Zeng X. Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration. FRONTIERS IN PLANT SCIENCE 2022; 13:1038625. [PMID: 36388537 PMCID: PMC9641248 DOI: 10.3389/fpls.2022.1038625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.
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Affiliation(s)
- Congping Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | | | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yuxiao Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sishu Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Haizhen Yang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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6
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Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196621. [PMID: 36235158 PMCID: PMC9573702 DOI: 10.3390/molecules27196621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
The control of the duration of the dormancy phase is a significant challenge in the potato industry and for seed producers. However, the proteome landscape involved in the regulation of the length of the dormancy period over potato cultivars remains largely unexplored. In this study, we performed for the first time a comparative proteome profiling of potato cultivars with differential duration of tuber dormancy. More specifically, the proteome profiling of Agata, Kennebec and Agria commercial potato varieties with short, medium and medium-long dormancy, respectively, was assessed at the endodormancy stage using high-resolution two-dimensional electrophoresis (2-DE) coupled to reversed-phase liquid chromatography–tandem mass spectrometry (LC-TripleTOF MS/MS). A total of 11 proteins/isoforms with statistically significant differential abundance among cultivars were detected on 2-DE gels and confidently identified by LC-TripleTOF MS/MS. Identified proteins have known functions related to tuber development, sprouting and the oxylipins biosynthesis pathway. Fructokinase, a mitochondrial ADP/ATP carrier, catalase isozyme 2 and heat shock 70 kDa were the proteins with the strongest response to dormancy variations. To the best of our knowledge, this study reports the first candidate proteins underlying variable dormancy length in potato cultivars.
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7
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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8
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Warsame AO, Michael N, O’Sullivan DM, Tosi P. Seed Development and Protein Accumulation Patterns in Faba Bean ( Vicia faba, L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9295-9304. [PMID: 35862501 PMCID: PMC9354250 DOI: 10.1021/acs.jafc.2c02061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A major objective in faba bean breeding is to improve its protein quality by selecting cultivars with enhanced desirable physicochemical properties. However, the protein composition of the mature seed is determined by a series of biological processes occurring during seed growth. Thus, any attempt to explain the final seed composition must consider the dynamics of the seed proteome during seed development. Here, we investigated the proteomic profile of developing faba bean seeds across 12 growth stages from 20 days after pollination (DAP) to full maturity. We analyzed trypsin-digested total protein extracts from the seeds at different growth stages by liquid chromatography-tandem mass spectrometry (LC-MS/MS), identifying 1217 proteins. The functional clusters of these proteins showed that, in early growth stages, proteins related to cell growth, division, and metabolism were most abundant compared to seed storage proteins that began to accumulate from 45 DAP. Moreover, label-free quantification of the relative abundance of seed proteins, including important globulin proteins, revealed several distinct temporal accumulation trends among the protein classes. These results suggest that these proteins are regulated differently and require further understanding of the impact of the different environmental stresses occurring at different grain filling stages on the expression and accumulation of these seed storage proteins.
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Affiliation(s)
- Ahmed O. Warsame
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
| | - Nicholas Michael
- School
of Chemistry, Food and Pharmacy, University
of Reading, Reading RG6 6AH, U.K.
| | - Donal M. O’Sullivan
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
| | - Paola Tosi
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
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9
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Tan X, Tan X, Li E, Bai Y, Nguyen TTL, Gilbert RG. Starch molecular fine structure is associated with protein composition in chickpea seed. Carbohydr Polym 2021; 272:118489. [PMID: 34420745 DOI: 10.1016/j.carbpol.2021.118489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022]
Abstract
Chickpea (Cicer arietinum L.) seed is a nutritional food high in starch and protein. This study aims to find the relationships between the molecular fine structure of starch and the composition of storage proteins and metabolic enzymes, using different chickpea varieties. It is found that storage proteins and starch biosynthetic enzymes influence each other. The initial formation of amylopectin molecules is affected by storage proteins, as suggested by the positive correlation (p < 0.01) between the average molecular size of amylopectin and total protein content. In addition, a higher amount of seed globulin could be an indication of higher amylose content and more short - medium amylose chains (degree of polymerization, DP, 118-2000). This study might assist selection of chickpea varieties with desirable qualities, such as low starch digestibility.
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Affiliation(s)
- Xiaoyan Tan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Xinle Tan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Enpeng Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yeming Bai
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Thoa T L Nguyen
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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10
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Qin Q, Liu J, Hu S, Dong J, Yu J, Fang L, Huang S, Wang L. Comparative proteomic analysis of different barley cultivars during seed germination. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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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. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 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] [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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12
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The post-translational modification landscape of commercial beers. Sci Rep 2021; 11:15890. [PMID: 34354100 PMCID: PMC8342498 DOI: 10.1038/s41598-021-95036-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/15/2021] [Indexed: 02/02/2023] Open
Abstract
Beer is one of the most popular beverages worldwide. As a product of variable agricultural ingredients and processes, beer has high molecular complexity. We used DIA/SWATH-MS to investigate the proteomic complexity and diversity of 23 commercial Australian beers. While the overall complexity of the beer proteome was modest, with contributions from barley and yeast proteins, we uncovered a very high diversity of post-translational modifications (PTMs), especially proteolysis, glycation, and glycosylation. Proteolysis was widespread throughout barley proteins, but showed clear site-specificity. Oligohexose modifications were common on lysines in barley proteins, consistent with glycation by maltooligosaccharides released from starch during malting or mashing. O-glycosylation consistent with oligomannose was abundant on secreted yeast glycoproteins. We developed and used data analysis pipelines to efficiently extract and quantify site-specific PTMs from SWATH-MS data, and showed incorporating these features into proteomic analyses extended analytical precision. We found that the key differentiator of the beer glyco/proteome was the brewery, with beer from independent breweries having a distinct profile to beer from multinational breweries. Within a given brewery, beer styles also had distinct glyco/proteomes. Targeting our analyses to beers from a single brewery, Newstead Brewing Co., allowed us to identify beer style-specific features of the glyco/proteome. Specifically, we found that proteins in darker beers tended to have low glycation and high proteolysis. Finally, we objectively quantified features of foam formation and stability, and showed that these quality properties correlated with the concentration of abundant surface-active proteins from barley and yeast.
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Tahmasian A, Broadbent JA, Juhász A, Nye-Wood M, Le TT, Bose U, Colgrave ML. Evaluation of protein extraction methods for in-depth proteome analysis of narrow-leafed lupin (Lupinus angustifolius) seeds. Food Chem 2021; 367:130722. [PMID: 34375893 DOI: 10.1016/j.foodchem.2021.130722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023]
Abstract
Lupin is slated as a potential contributor towards future food security. Lupin possesses several nutritional and nutraceutical attributes, many linked to seed proteins. For in-depth characterisation of the lupin proteome, liquid chromatography-tandem mass spectrometry was used to evaluate four protein extraction procedures. The proteomes of three narrow-leafed lupin were qualitatively evaluated using protein/peptide identifications and further quantitatively assessed by data-independent proteome measurement. Each extraction buffer led to unique protein identifications; altogether yielding 2,760 protein identifications from lupin varieties. The analysis of protein abundance data highlighted distinct differences between Tris-HCl and urea extracted proteomes, while also revealing variation amongst the cultivar proteomes with the wild accession (P27255) distinctly different from the domesticated cultivars (Tanjil, Unicrop). The extraction buffer used influenced the proteome coverage, downstream functional annotation results and consequently the biological interpretation demonstrating the need to optimise and understand the impact of protein extraction conditions.
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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 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, 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 6027, Australia
| | - Thao T Le
- School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, 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 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
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14
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Rahman M, Guo Q, Baten A, Mauleon R, Khatun A, Liu L, Barkla BJ. Shotgun proteomics of Brassica rapa seed proteins identifies vicilin as a major seed storage protein in the mature seed. PLoS One 2021; 16:e0253384. [PMID: 34242257 PMCID: PMC8270179 DOI: 10.1371/journal.pone.0253384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/04/2021] [Indexed: 11/18/2022] Open
Abstract
Proteins make up a large percentage of the Brassica seed and are second only to the oil in economic importance with uses for both animal and human nutrition. The most abundant proteins reported in the seeds of Brassica are the seed storage proteins cruciferin and napin, belonging to the 12S globulin and 2S albumin families of proteins, respectively. To gain insight into the Brassica rapa seed proteome and to confirm the presence and relative quantity of proteins encoded by candidate seed storage genes in the mature seed, shotgun proteomics was carried out on protein extracts from seeds of B. rapa inbred line R-o-18. Following liquid chromatography tandem mass spectrometry, a total of 34016 spectra were mapped to 323 proteins, where 233 proteins were identified in 3 out of 4 biological replicates by at least 2 unique peptides. 2S albumin like napin seed storage proteins (SSPs), 11/12S globulin like cruciferin SSPs and 7S globulin like vicilin SSPs were identified in the samples, along with other notable proteins including oil body proteins, namely ten oleosins and two oil body-associated proteins. The identification of vicilin like proteins in the mature B. rapa seed represents the first account of these proteins in the Brassicaceae and analysis indicates high conservation of sequence motifs to other 7S vicilin-like allergenic proteins as well as conservation of major allergenic epitopes in the proteins. This study enriches our existing knowledge on rapeseed seed proteins and provides a robust foundation and rational basis for plant bioengineering of seed storage proteins.
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Affiliation(s)
- Mahmudur Rahman
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Qi Guo
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
- Institute of Precision Medicine & Bioinformatics, Sydney Local Health District, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Ramil Mauleon
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Amina Khatun
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Bronwyn J. Barkla
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
- * E-mail:
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15
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Barley Seeds miRNome Stability during Long-Term Storage and Aging. Int J Mol Sci 2021; 22:ijms22094315. [PMID: 33919202 PMCID: PMC8122619 DOI: 10.3390/ijms22094315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 04/18/2021] [Indexed: 12/18/2022] Open
Abstract
Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.
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16
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Osama SK, Kerr ED, Yousif AM, Phung TK, Kelly AM, Fox GP, Schulz BL. Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. J Proteomics 2021; 242:104221. [PMID: 33866056 DOI: 10.1016/j.jprot.2021.104221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.
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Affiliation(s)
- Sarah K Osama
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Adel M Yousif
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Sandy Bay Campus, TAS, 7005, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Alison M Kelly
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, Qld 4350, Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Food Science and Technology, University of California Davis, CA 95616, USA.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
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17
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Gomez-Sanchez A, Santamaria ME, Gonzalez-Melendi P, Muszynska A, Matthess C, Martinez M, Diaz I. Repression of barley cathepsins, HvPap-19 and HvPap-1, differentially alters grain composition and delays germination. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3474-3485. [PMID: 33454762 DOI: 10.1093/jxb/erab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
During barley germination, cysteine proteases are essential in the mobilization of storage compounds providing peptides and amino acids to sustain embryo growth until photosynthesis is completely established. Knockdown barley plants, generated by artificial miRNA, for the cathepsins B- and F-like HvPap-19 and HvPap-1 genes, respectively, showed less cysteine protease activities and consequently lower protein degradation. The functional redundancy between proteases triggered an enzymatic compensation associated with an increase in serine protease activities in both knockdown lines, which was not sufficient to maintain germination rates and behaviour. Concomitantly, these transgenic lines showed alterations in the accumulation of protein and carbohydrates in the grain. While the total amount of protein increased in both transgenic lines, the starch content decreased in HvPap-1 knockdown lines and the sucrose concentration was reduced in silenced HvPap-19 grains. Consequently, phenotypes of HvPap-1 and HvPap-19 artificial miRNA lines showed a delay in the grain germination process. These data demonstrate the potential of exploring the properties of barley proteases for selective modification and use in brewing or in the livestock feeding industry.
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Affiliation(s)
- Andrea Gomez-Sanchez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Aleksandra Muszynska
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse, Gatersleben, Germany
| | - Christiane Matthess
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse, Gatersleben, Germany
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
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18
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Kerr ED, Caboche CH, Josh P, Schulz BL. Benchtop micro-mashing: high-throughput, robust, experimental beer brewing. Sci Rep 2021; 11:1480. [PMID: 33452289 PMCID: PMC7810850 DOI: 10.1038/s41598-020-80442-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
Brewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash, and both mash scales produced wort with equivalent fermentable sugar and free amino acid profiles. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher H Caboche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Peter Josh
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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19
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Zhang G, Zhang G, Zeng X, Xu Q, Wang Y, Yuan H, Zhang Y, Nyima T. Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:568-583. [PMID: 33371680 DOI: 10.1021/acs.jafc.0c05284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xingquan Zeng
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Qijun Xu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yulin Wang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Tashi Nyima
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
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20
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Leišová-Svobodová L, Psota V, Stočes Š, Vácha P, Kučera L. Comparative de novo transcriptome analysis of barley varieties with different malting qualities. Funct Integr Genomics 2020; 20:801-812. [PMID: 32948934 PMCID: PMC7585565 DOI: 10.1007/s10142-020-00750-z] [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: 03/02/2020] [Revised: 07/22/2020] [Accepted: 08/18/2020] [Indexed: 12/01/2022]
Abstract
Barley is one of the most important crops in the world. Barley is used as both food and feed and is important for malt production. Demands for malting quality differ among countries and customs. Malting quality is a complex characteristic involving barley genetics, the environmental conditions during barley growth, and the technological parameters of the malting process. In this study, the hypothesis was that there were no differences between two groups of barley varieties with different but defined malting qualities, which was tested using RNA sequencing during selected stages of malting. In total, 919 differentially transcribed genes between the two barley groups were identified and annotated. Differentially expressed genes (DEGs) were primarily assigned to gene ontology (GO) terms of oxidation-reduction process - oxidoreductase activity, response to stress, carbohydrate metabolic process, and proteolysis - hydrolase activity, and metal ion binding. Genes connected with the plasma membrane and its integral components also play important roles in malting quality. DEG profiles of selected genes in the three malting stages indicate a complex character of malting quality. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were identified. SNPs and indels with the best quality were used for primer design. After optimization and validation, five molecular markers were developed for use in barley breeding.
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Affiliation(s)
| | - Vratislav Psota
- Research Institute of Brewing and Malting, Analytical Testing Laboratory - Malting Institute Brno, Mostecká 971/7, 614 00, Brno, Czech Republic
| | - Štěpán Stočes
- SEQme s.r.o., Dlouhá 176 26301, Dobříš, Czech Republic
| | - Petr Vácha
- SEQme s.r.o., Dlouhá 176 26301, Dobříš, Czech Republic
| | - Ladislav Kučera
- Crop Research Institute, Drnovská, 507 161 06, Prague 6, Czech Republic
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21
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Kim S, Cheong K, Park J, Kim M, Kim J, Seo M, Chae GY, Jang MJ, Mang H, Kwon S, Kim Y, Koo N, Min CW, Kim K, Oh N, Kim K, Jeon J, Kim H, Lee Y, Sohn KH, McCann HC, Ye S, Kim ST, Park K, Lee Y, Choi D. TGFam-Finder: a novel solution for target-gene family annotation in plants. THE NEW PHYTOLOGIST 2020; 227:1568-1581. [PMID: 32392385 PMCID: PMC7496378 DOI: 10.1111/nph.16645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jieun Park
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Myung‐Shin Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jihyun Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Min‐Ki Seo
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Geun Young Chae
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Min Jeong Jang
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Hyunggon Mang
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Sun‐Ho Kwon
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Yong‐Min Kim
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Namjin Koo
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Cheol Woo Min
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kwang‐Soo Kim
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Nuri Oh
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Ki‐Tae Kim
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Yoon‐Young Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey University AucklandAuckland0632New Zealand
| | - Sang‐Kyu Ye
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Sun Tae Kim
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kyung‐Soon Park
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Yong‐Hwan Lee
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Doil Choi
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
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22
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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23
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372,10.13140/rg.2.1.1233.5760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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24
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Mahalingam R. Analysis of the Barley Malt Rootlet Proteome. Int J Mol Sci 2019; 21:E179. [PMID: 31887991 PMCID: PMC6981388 DOI: 10.3390/ijms21010179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022] Open
Abstract
Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.
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25
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Sano N, Takebayashi Y, To A, Mhiri C, Rajjou LC, Nakagami H, Kanekatsu M. Shotgun Proteomic Analysis Highlights the Roles of Long-Lived mRNAs and De Novo Transcribed mRNAs in Rice Seeds upon Imbibition. PLANT & CELL PHYSIOLOGY 2019; 60:2584-2596. [PMID: 31373371 DOI: 10.1093/pcp/pcz152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/27/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, proteins are translated not only from mRNAs newly transcribed upon imbibition but also from long-lived mRNAs that are synthesized during seed maturation and stored in the mature dry seeds. To clarify the distinct roles of proteins translated from long-lived mRNAs and de novo transcribed mRNAs in germinating rice embryos, proteome analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) combining the use of a transcriptional inhibitor was performed. We observed that α-amanitin significantly represses transcription in germinating embryos; nevertheless, the embryos could germinate, albeit slowly. The proteomic analysis revealed that a total of 109 proteins were translated from long-lived mRNAs associated with germination as well as 222 proteins whose expression were dependent on de novo transcription upon imbibition. Transcriptomic datasets available in public databases demonstrated that mRNAs of the 222 proteins notably increased during germination while those of the 109 proteins highly accumulated in dry embryos and constitutively expressed upon imbibition. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of the 109 proteins from long-lived mRNAs are implicated in energy production such as glycolysis or annotated as nucleotide binding proteins, while the 222 proteins are involved in pathways such as pyruvate metabolism and TCA cycle following glycolysis, and momilactones biosynthesis. We propose that long-lived mRNAs support initial energy production and activation of translational machinery upon imbibition whereas de novo transcription accelerates the energy production after glycolysis, which enables rice seeds to germinate vigorously.
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Affiliation(s)
- Naoto Sano
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Alexandra To
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Loï C Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, Germany
| | - Motoki Kanekatsu
- Department of Plant Production, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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26
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Kerr ED, Phung TK, Caboche CH, Fox GP, Platz GJ, Schulz BL. The intrinsic and regulated proteomes of barley seeds in response to fungal infection. Anal Biochem 2019; 580:30-35. [PMID: 31181183 DOI: 10.1016/j.ab.2019.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 01/14/2023]
Abstract
Barley is an important cereal grain used for beer brewing, animal feed, and human food consumption. Fungal disease can impact barley production, as it causes substantial yield loss and lowers seed quality. We used sequential window acquisition of all theoretical ions mass spectrometry (SWATH-MS) to measure and quantify the relative abundance of proteins within seeds of different barley varieties under various fungal pathogen burdens (ProteomeXchange Datasets PXD011303 and PXD014093). Fungal burden in the leaves and stems of barley resulted in changes to the seed proteome. However, these changes were minimal and showed substantial variation among barley samples infected with different pathogens. The limited effect of intrinsic disease resistance on the seed proteome is consistent with the main mediators of disease resistance being present in the leaves and stems of the plant. The seeds of barley varieties accredited for use as malt had higher levels of proteins associated with starch synthesis and beer quality. The proteomic workflows developed and implemented here have potential application in quality control, breeding and processing of barley, and other agricultural products.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Christopher H Caboche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Glen P Fox
- Centre for Nutrition and Food Sciences, Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Greg J Platz
- Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, 4370, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia; Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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27
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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] [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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28
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Chen D, Chen P, Cheng Y, Peng P, Liu J, Ma Y, Liu Y, Ruan R. Deoxynivalenol Decontamination in Raw and Germinating Barley Treated by Plasma-Activated Water and Intense Pulsed Light. FOOD BIOPROCESS TECH 2018. [DOI: 10.1007/s11947-018-2206-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Mahalingam R. Temporal Analyses of Barley Malting Stages Using Shotgun Proteomics. Proteomics 2018; 18:e1800025. [DOI: 10.1002/pmic.201800025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/08/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Ramamurthy Mahalingam
- United States Department of Agriculture; Agricultural Research Service; Cereal Crops Research Unit; 502 Walnut Street 53726 Madison WI USA
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30
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Proteomic analysis and food-grade enzymes of Moringa oleifer Lam. a Lam. flower. Int J Biol Macromol 2018; 115:883-890. [DOI: 10.1016/j.ijbiomac.2018.04.109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/28/2018] [Accepted: 04/21/2018] [Indexed: 01/28/2023]
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31
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Shabrangy A, Roustan V, Reipert S, Weidinger M, Roustan PJ, Stoger E, Weckwerth W, Ibl V. Using RT-qPCR, Proteomics, and Microscopy to Unravel the Spatio-Temporal Expression and Subcellular Localization of Hordoindolines Across Development in Barley Endosperm. FRONTIERS IN PLANT SCIENCE 2018; 9:775. [PMID: 29951075 PMCID: PMC6008550 DOI: 10.3389/fpls.2018.00775] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/22/2018] [Indexed: 05/20/2023]
Abstract
Hordeum vulgare (barley) hordoindolines (HINs), HINa, HINb1, and HINb2, are orthologous proteins of wheat puroindolines (PINs) that are small, basic, cysteine-rich seed-specific proteins and responsible for grain hardness. Grain hardness is, next to its protein content, a major quality trait. In barley, HINb is most highly expressed in the mid-stage developed endosperm and is associated with both major endosperm texture and grain hardness. However, data required to understand the spatio-temporal dynamics of HIN transcripts and HIN protein regulation during grain filling processes are missing. Using reverse transcription quantitative PCR (RT-qPCR) and proteomics, we analyzed HIN transcript and HIN protein abundance from whole seeds (WSs) at four [6 days after pollination (dap), 10, 12, and ≥20 dap] as well as from aleurone, subaleurone, and starchy endosperm at two (12 and ≥20 dap) developmental stages. At the WS level, results from RT-qPCR, proteomics, and western blot showed a continuous increase of HIN transcript and HIN protein abundance across these four developmental stages. Miroscopic studies revealed HIN localization mainly at the vacuolar membrane in the aleurone, at protein bodies (PBs) in subaleurone and at the periphery of starch granules in the starchy endosperm. Laser microdissetion (LMD) proteomic analyses identified HINb2 as the most prominent HIN protein in starchy endosperm at ≥20 dap. Additionally, our quantification data revealed a poor correlation between transcript and protein levels of HINs in subaleurone during development. Here, we correlated data achieved by RT-qPCR, proteomics, and microscopy that reveal different expression and localization pattern of HINs in each layer during barley endosperm development. This indicates a contribution of each tissue to the regulation of HINs during grain filling. The effect of the high protein abundance of HINs in the starchy endosperm and their localization at the periphery of starch granules at late development stages at the cereal-based end-product quality is discussed. Understanding the spatio-temporal regulated HINs is essential to improve barley quality traits for high end-product quality, as hard texture of the barley grain is regulated by the ratio between HINb/HINa.
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Affiliation(s)
- Azita Shabrangy
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Pierre-Jean Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Verena Ibl
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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32
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Komatsu S, Hashiguchi A. Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean. Proteomes 2018; 6:E13. [PMID: 29495455 PMCID: PMC5874772 DOI: 10.3390/proteomes6010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023] Open
Abstract
Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Akiko Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan.
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33
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Roustan V, Roustan PJ, Weidinger M, Reipert S, Kapusi E, Shabrangy A, Stoger E, Weckwerth W, Ibl V. Microscopic and Proteomic Analysis of Dissected Developing Barley Endosperm Layers Reveals the Starchy Endosperm as Prominent Storage Tissue for ER-Derived Hordeins Alongside the Accumulation of Barley Protein Disulfide Isomerase (HvPDIL1-1). FRONTIERS IN PLANT SCIENCE 2018; 9:1248. [PMID: 30250475 PMCID: PMC6139375 DOI: 10.3389/fpls.2018.01248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/06/2018] [Indexed: 05/20/2023]
Abstract
Barley (Hordeum vulgare) is one of the major food sources for humans and forage sources for animal livestock. The average grain protein content (GPC) of barley ranges between 8 and 12%. Barley hordeins (i.e., prolamins) account for more than 50% of GPC in mature seeds and are important for both grain and flour quality. Barley endosperm is structured into three distinct cell layers: the starchy endosperm, which acts essentially as storage tissue for starch; the subaleurone, which is characterized by a high accumulation of seed storage proteins (SSPs); and the aleurone, which has a prominent role during seed germination. Prolamins accumulate in distinct, ER-derived protein bodies (PBs) and their trafficking route is spatio-temporally regulated. The protein disulfide isomerase (PDI) has been shown to be involved in PB formation. Here, we unravel the spatio-temporal proteome regulation in barley aleurone, subaleurone, and starchy endosperm for the optimization of end-product quality in barley. We used laser microdissection (LMD) for subsequent nanoLC-MS/MS proteomic analyses in two experiments: in Experiment One, we investigated the proteomes of dissected barley endosperm layers at 12 and at ≥20 days after pollination (DAP). We found a set of 10 proteins that were present in all tissues at both time points. Among these proteins, the relative protein abundance of D-hordein, B3-hordein and HvPDIL1-1 significantly increased in starchy endosperm between 12 and ≥20 DAP, identifying the starchy endosperm as putative major storage tissue. In Experiment Two, we specifically compared the starchy endosperm proteome at 6, 12, and ≥20 DAP. Whereas the relative protein abundance of D-hordein and B3-hordein increased between 6 and ≥20 DAP, HvPDIL1-1 increased between 6 and 12 DAP, but remained constant at ≥20 DAP. Microscopic observations showed that these relative protein abundance alterations were accompanied by additional localization of hordeins at the periphery of starch granules and a partial re-localization of HvPDIL1-1 from PBs to the periphery of starch granules. Our data indicate a spatio-temporal regulation of hordeins and HvPDIL1-1. These results are discussed in relation to the putative role of HvPDIL1-1 in end-product quality in barley.
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Affiliation(s)
- Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Pierre-Jean Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | | | - Siegfried Reipert
- Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Eszter Kapusi
- Department for Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Azita Shabrangy
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Eva Stoger
- Department for Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Verena Ibl
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- *Correspondence: Verena Ibl
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34
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Tuberosa R, Frascaroli E, Salvi S. Leveraging plant genomics for better and healthier food. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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