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Vincent D, Bui A, Ezernieks V, Shahinfar S, Luke T, Ram D, Rigas N, Panozzo J, Rochfort S, Daetwyler H, Hayden M. A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem. Gigascience 2022; 12:giad084. [PMID: 37919977 PMCID: PMC10627334 DOI: 10.1093/gigascience/giad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Late-maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point alpha-amylase following a temperature shock during mid-grain development or prolonged cold throughout grain development, both leading to starch degradation. While the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have applied high-throughput proteomics to 4,061 wheat flours displaying a range of LMA activities. Using an array of statistical analyses to select LMA-responsive biomarkers, we have mined them using a suite of tools applicable to wheat proteins. RESULTS We observed that LMA-affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis; TCA cycle, along with DNA- and RNA- binding mechanisms; and protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as well as protein assembly via dimerisation and complexing. The secondary metabolism was also mobilized with the upregulation of phytohormones and chemical and defence responses. LMA further invoked cellular structures, including ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain storage proteins, as well as starch and other carbohydrates, with the upregulation of alpha-gliadins and starch metabolism, whereas LMW glutenin, stachyose, sucrose, UDP-galactose, and UDP-glucose were downregulated. CONCLUSIONS To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue but also the largest plant-based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses are discussed.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - AnhDuyen Bui
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Vilnis Ezernieks
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Saleh Shahinfar
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Timothy Luke
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Doris Ram
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Nicholas Rigas
- Agriculture Victoria Research, Grains Innovation Park, Horsham, VIC 3400, Australia
| | - Joe Panozzo
- Agriculture Victoria Research, Grains Innovation Park, Horsham, VIC 3400, Australia
- Centre for Agricultural Innovation, University of Melbourne, Parkville, VIC 3010, Australia
| | - Simone Rochfort
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Hans Daetwyler
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, Center Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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Si A, Sun Z, Li Z, Chen B, Gu Q, Zhang Y, Wu L, Zhang G, Wang X, Ma Z. A Genome Wide Association Study Revealed Key Single Nucleotide Polymorphisms/Genes Associated With Seed Germination in Gossypium hirsutum L. FRONTIERS IN PLANT SCIENCE 2022; 13:844946. [PMID: 35371175 PMCID: PMC8967292 DOI: 10.3389/fpls.2022.844946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/21/2022] [Indexed: 05/17/2023]
Abstract
Fast and uniform seed germination is essential to stabilize crop yields in agricultural production. It is important to understand the genetic basis of seed germination for improving the vigor of crop seeds. However, little is known about the genetic basis of seed vigor in cotton. In this study, we evaluated four seed germination-related traits of a core collection consisting of 419 cotton accessions, and performed a genome-wide association study (GWAS) to explore important loci associated with seed vigor using 3.66 million high-quality single nucleotide polymorphisms (SNPs). The results showed that four traits, including germination potential, germination rate, germination index, and vigor index, exhibited broad variations and high correlations. A total of 92 significantly associated SNPs located within or near 723 genes were identified for these traits, of which 13 SNPs could be detected in multiple traits. Among these candidate genes, 294 genes were expressed at seed germination stage. Further function validation of the two genes of higher expression showed that Gh_A11G0176 encoding Hsp70-Hsp90 organizing protein negatively regulated Arabidopsis seed germination, while Gh_A09G1509 encoding glutathione transferase played a positive role in regulating tobacco seed germination and seedling growth. Furthermore, Gh_A09G1509 might promote seed germination and seedling establishment through regulating glutathione metabolism in the imbibitional seeds. Our findings provide unprecedented information for deciphering the genetic basis of seed germination and performing molecular breeding to improve field emergence through genomic selection in cotton.
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Affiliation(s)
- Aijun Si
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- Xingfen Wang,
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- *Correspondence: Zhiying Ma,
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Reilly A, Karki SJ, Twamley A, Tiley AMM, Kildea S, Feechan A. Isolate-Specific Responses of the Nonhost Grass Brachypodium distachyon to the Fungal Pathogen Zymoseptoria tritici Compared with Wheat. PHYTOPATHOLOGY 2021; 111:356-368. [PMID: 32720875 DOI: 10.1094/phyto-02-20-0041-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Septoria tritici blotch (STB) is an important foliar disease of wheat that is caused by the fungal pathogen Zymoseptoria tritici. The grass Brachypodium distachyon has been used previously as a model system for cereal-pathogen interactions. In this study, we examined the nonhost resistance (NHR) response of B. distachyon to two different Z. tritici isolates in comparison with wheat. These isolates vary in aggressiveness on wheat cultivar Remus, displaying significant differences in disease and pycnidia coverage. Using microscopy, we found that similar isolate-specific responses were observed for hydrogen peroxide accumulation and cell death in both wheat and B. distachyon. Despite this, induction of isolate-specific patterns of defense gene expression by Z. tritici did differ between B. distachyon and wheat. Our results suggest that expression of the phenylalanine ammonia lyase PAL gene may be important for NHR in B. distachyon, while pathogenesis-related PR genes and expression of genes regulating reactive oxygen species may be important to limit disease in wheat. Future studies of the B. distachyon-Z. tritici interaction may allow identification of conserved plant immunity targets that are responsible for the isolate-specific responses observed in both plant species.
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Affiliation(s)
- Aisling Reilly
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sujit Jung Karki
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anthony Twamley
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anna M M Tiley
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven Kildea
- Department of Crop Science, Teagasc Crops Environment and Land Use Programme, Teagasc, Oak Park, County Carlow, Ireland
| | - Angela Feechan
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Ishibashi Y, Yuasa T, Iwaya-Inoue M. Mechanisms of Maturation and Germination in Crop Seeds Exposed to Environmental Stresses with a Focus on Nutrients, Water Status, and Reactive Oxygen Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:233-257. [DOI: 10.1007/978-981-13-1244-1_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Das A, Kim DW, Khadka P, Rakwal R, Rohila JS. Unraveling Key Metabolomic Alterations in Wheat Embryos Derived from Freshly Harvested and Water-Imbibed Seeds of Two Wheat Cultivars with Contrasting Dormancy Status. FRONTIERS IN PLANT SCIENCE 2017; 8:1203. [PMID: 28747920 PMCID: PMC5506182 DOI: 10.3389/fpls.2017.01203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/26/2017] [Indexed: 05/20/2023]
Abstract
Untimely rains in wheat fields during harvest season can cause pre-harvest sprouting (PHS), which deteriorates the yield and quality of wheat crop. Metabolic homeostasis of the embryo plays a role in seed dormancy, determining the status of the maturing grains either as dormant (PHS-tolerant) or non-dormant (PHS-susceptible). Very little is known for direct measurements of global metabolites in embryonic tissues of dormant and non-dormant wheat seeds. In this study, physiologically matured and freshly harvested wheat seeds of PHS-tolerant (cv. Sukang, dormant) and PHS-susceptible (cv. Baegjoong, non-dormant) cultivars were water-imbibed, and the isolated embryos were subjected to high-throughput, global non-targeted metabolomic profiling. A careful comparison of identified metabolites between Sukang and Baegjoong embryos at 0 and 48 h after imbibition revealed that several key metabolic pathways [such as: lipids, fatty acids, oxalate, hormones, the raffinose family of oligosaccharides (RFOs), and amino acids] and phytochemicals were differentially regulated between dormant and non-dormant varieties. Most of the membrane lipids were highly reduced in Baegjoong compared to Sukang, which indicates that the cell membrane instability in response to imbibition could also be a key factor in non-dormant wheat varieties for their untimely germination. This study revealed that several key marker metabolites (e.g., RFOs: glucose, fructose, maltose, and verbascose), were highly expressed in Baegjoong after imbibition. Furthermore, the data showed that the key secondary metabolites and phytochemicals (vitexin, chrysoeriol, ferulate, salidroside and gentisic acid), with known antioxidant properties, were comparatively low at basal levels in PHS-susceptible, non-dormant cultivar, Baegjoong. In conclusion, the results of this investigation revealed that after imbibition the metabolic homeostasis of dormant wheat is significantly less affected compared to non-dormant wheat. The inferences from this study combined with proteomic and transcriptomic studies will advance the molecular understanding of the pathways and enzyme regulations during PHS.
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Affiliation(s)
- Aayudh Das
- Department of Plant Biology, University of Vermont, BurlingtonVT, United States
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
| | - Dea-Wook Kim
- National Institute of Crop Science, Rural Development AdministrationWanju-gun, South Korea
| | - Pramod Khadka
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of TsukubaTsukuba, Japan
| | - Jai S. Rohila
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
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Yang M, Gao X, Dong J, Gandhi N, Cai H, von Wettstein DH, Rustgi S, Wen S. Pattern of Protein Expression in Developing Wheat Grains Identified through Proteomic Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:962. [PMID: 28649254 PMCID: PMC5465268 DOI: 10.3389/fpls.2017.00962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 05/22/2017] [Indexed: 05/20/2023]
Abstract
Grain development is one of the biological processes, which contributes to the final grain yield. To understand the molecular changes taking place during the early grain development, we profiled proteomes of two common wheat cultivars P271 and Chinese Spring (CS) with large and small grains, respectively at three grain developmental stages (4, 8, and 12 days post anthesis). An iTRAQ (isobaric tags for relative and absolute quantitation) based proteomics approach was used for this purpose. More than 3,600 proteins were reported to accumulate during early grain development in both wheat cultivars. Of these 3,600 proteins, 130 expressed differentially between two wheat cultivars, and 306 exhibited developmental stage-specific accumulation in either or both genotypes. Detailed bioinformatic analyses of differentially expressed proteins (DEPs) from the large- and small-grain wheat cultivars underscored the developmental differences observed between them and shed light on the molecular and cellular processes contributing to these differences. In silico localization of either or both sets of DEPs to wheat chromosomes exhibited a biased genomic distribution with chromosome 4D contributing largely to it. These results corresponded well with the earlier studies, performed in common wheat, where chromosome 4D was reported to harbor QTLs for yield contributing traits specifically grain length. Collectively, our results provide insight into the molecular processes taking place during early grain development, a knowledge, which may prove useful in improving wheat grain yield in the future.
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Affiliation(s)
- Mingming Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
| | - Xiang Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
- *Correspondence: Xiang Gao
| | - Jian Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Wheat Engineering Research Center of Shaanxi Province, Northwest A&F UniversityYangling, China
| | - Nitant Gandhi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education CenterFlorence, SC, United States
| | - Huanjie Cai
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F UniversityYangling, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F UniversityYangling, China
| | - Diter H. von Wettstein
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, United States
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education CenterFlorence, SC, United States
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, United States
- Sachin Rustgi
| | - Shanshan Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Shanshan Wen
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Hägglund P, Finnie C, Yano H, Shahpiri A, Buchanan BB, Henriksen A, Svensson B. Seed thioredoxin h. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:974-82. [PMID: 26876537 DOI: 10.1016/j.bbapap.2016.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022]
Abstract
Thioredoxins are nearly ubiquitous disulfide reductases involved in a wide range of biochemical pathways in various biological systems, and also implicated in numerous biotechnological applications. Plants uniquely synthesize an array of thioredoxins targeted to different cell compartments, for example chloroplastic f- and m-type thioredoxins involved in regulation of the Calvin-Benson cycle. The cytosolic h-type thioredoxins act as key regulators of seed germination and are recycled by NADPH-dependent thioredoxin reductase. The present review on thioredoxin h systems in plant seeds focuses on occurrence, reaction mechanisms, specificity, target protein identification, three-dimensional structure and various applications. The aim is to provide a general background as well as an update covering the most recent findings. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Per Hägglund
- Protein and Immune Systems Biology, Department of Systems Biology, Matematiktorvet, Building 301, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Christine Finnie
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 4, DK-1799 Copenhagen V, Denmark
| | - Hiroyuki Yano
- National Food Research Institute, National Agriculture and Food Research Organization, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | - Azar Shahpiri
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Bob B Buchanan
- Department of Plant and Microbial Biology, Koshland Hall 111, Berkeley, CA 94720-3102, USA
| | - Anette Henriksen
- Department of Large Protein Biophysics and Formulation, Global Research Unit, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Elektrovej, Building 375, DK-2800 Kgs. Lyngby, Denmark.
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Liu C, Ding F, Hao F, Yu M, Lei H, Wu X, Zhao Z, Guo H, Yin J, Wang Y, Tang H. Reprogramming of Seed Metabolism Facilitates Pre-harvest Sprouting Resistance of Wheat. Sci Rep 2016; 6:20593. [PMID: 26860057 PMCID: PMC4748292 DOI: 10.1038/srep20593] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/07/2016] [Indexed: 12/14/2022] Open
Abstract
Pre-harvest sprouting (PHS) is a worldwide problem for wheat production and transgene antisense-thioredoxin-s (anti-trx-s) facilitates outstanding resistance. To understand the molecular details of PHS resistance, we analyzed the metabonomes of the transgenic and wild-type (control) wheat seeds at various stages using NMR and GC-FID/MS. 60 metabolites were dominant in these seeds including sugars, organic acids, amino acids, choline metabolites and fatty acids. At day-20 post-anthesis, only malate level in transgenic wheat differed significantly from that in controls whereas at day-30 post-anthesis, levels of amino acids and sucrose were significantly different between these two groups. For mature seeds, most metabolites in glycolysis, TCA cycle, choline metabolism, biosynthesis of proteins, nucleotides and fatty acids had significantly lower levels in transgenic seeds than in controls. After 30-days post-harvest ripening, most metabolites in transgenic seeds had higher levels than in controls including amino acids, sugars, organic acids, fatty acids, choline metabolites and NAD+. These indicated that anti-trx-s lowered overall metabolic activities of mature seeds eliminating pre-harvest sprouting potential. Post-harvest ripening reactivated the metabolic activities of transgenic seeds to restore their germination vigor. These findings provided essential molecular phenomic information for PHS resistance of anti-trx-s and a credible strategy for future developing PHS resistant crops.
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Affiliation(s)
- Caixiang Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Ding
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fuhua Hao
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Men Yu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,Wuhan Zhongke Metaboss Ltd, 128 Guang-Gu-Qi-Lu, Wuhan 430074, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiangyu Wu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhengxi Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongxiang Guo
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
| | - Jun Yin
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Huiru Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Developmental Biology, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200438, China
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Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
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Chen ZY, Guo XJ, Chen ZX, Chen WY, Liu DC, Zheng YL, Liu YX, Wei YM, Wang JR. Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat. BMC Genomics 2015; 16:125. [PMID: 25766308 PMCID: PMC4344791 DOI: 10.1186/s12864-015-1313-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fungal diseases, insects, drought, salinity, and cold. Transcription factors (TFs) regulate gene expression in different tissues and at various developmental stages in plants and animals, and they can be identified and classified into families according to their structural and specialized DNA-binding domains (DBDs). Transcription factors are important regulatory components of the genome, and are the main targets for engineering stress tolerance. RESULTS In total, 2407 putative TFs were identified from wheat expressed sequence tags, and then classified into 63 families by using Hmm searches against hidden Markov model (HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes in the wheat genome, a smaller proportion than those reported for other cereals in PlantTFDB V3.0 (3.33%-5.86%) and PlnTFDB (4.30%-6.46%). We assembled information from the various databases for individual TFs, including annotations and details of their developmental stage- and tissue-specific expression patterns. Based on this information, we identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, accounting for 52.22% and 45.87% of the 2407 wheat TFs, respectively. We identified 338, 269, 262, 175, 49, and 18 tissue-specific TFs in the flower, seed, root, leaf, stem, and crown, respectively. There were 100, 6, 342, 141, 390, and 278 TFs specifically expressed at the dormant seed, germinating seed, reproductive, ripening, seedling, and vegetative stages, respectively. We constructed a comprehensive database of wheat TFs, designated as WheatTFDB ( http://xms.sicau.edu.cn/wheatTFDB/ ). CONCLUSIONS Approximately 2.22% (2407 genes) of all genes in the wheat genome were identified as TFs, and were clustered into 63 TF families. We identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, based on information about their developmental- and tissue-specific expression patterns obtained from publicly available gene expression databases. The 2407 wheat TFs and their annotations are summarized in our database, WheatTFDB. These data will be useful identifying target TFs involved in the stress response at a particular stage of development.
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Affiliation(s)
- Zhen-Yong Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
- College of Life Science, China West Normal University, Nanchong, 637009, China.
| | - Xiao-Jiang Guo
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Zhong-Xu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Wei-Ying Chen
- College of Life Science, China West Normal University, Nanchong, 637009, China.
| | - Deng-Cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - You-Liang Zheng
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Yaan, Sichuan, 625014, China.
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Haque E, Abe F, Mori M, Nanjo Y, Komatsu S, Oyanagi A, Kawaguchi K. Quantitative Proteomics of the Root of Transgenic Wheat Expressing TaBWPR-1.2 Genes in Response to Waterlogging. Proteomes 2014; 2:485-500. [PMID: 28250392 PMCID: PMC5302695 DOI: 10.3390/proteomes2040485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/20/2014] [Accepted: 10/22/2014] [Indexed: 01/05/2023] Open
Abstract
Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation and plant regeneration efficiencies and expression variability and instability. Earlier, we found two cDNAs encoding WL stress-responsive wheat pathogenesis-related proteins 1.2 (TaBWPR-1.2), TaBWPR-1.2#2 and TaBWPR-1.2#13. Using microprojectile bombardment, both cDNAs were introduced into "Bobwhite". Despite low transformation efficiency, four independent T₂ homozygous lines for each gene were isolated, where transgenes were ubiquitously and variously expressed. The highest transgene expression was obtained in Ubi:TaBWPR-1.2#2 L#11a and Ubi:TaBWPR-1.2#13 L#4a. Using quantitative proteomics, the root proteins of L#11a were analyzed to explore possible physiological pathways regulated by TaBWPR-1.2 under normal and waterlogged conditions. In L#11a, the abundance of proteasome subunit alpha type-3 decreased under normal conditions, whereas that of ferredoxin precursor and elongation factor-2 increased under waterlogged conditions in comparison with normal plants. Proteomic results suggest that L#11a is one of the engineered wheat plants where TaBWPR-1.2#2 is most probably involved in proteolysis, protein synthesis and alteration in the energy pathway in root tissues via the above proteins in order to gain metabolic adjustment to WL.
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Affiliation(s)
- Emdadul Haque
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Fumitaka Abe
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Masahiko Mori
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Yohei Nanjo
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Setsuko Komatsu
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Atsushi Oyanagi
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
| | - Kentaro Kawaguchi
- NARO Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
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12
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Guo H, Li F, Wang S, Li S, Xiao W, Liu W. Enhanced Protein Extraction from Tobacco Roots for Proteomic Analysis. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.930871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Whan A, Dielen AS, Mieog J, Bowerman AF, Robinson HM, Byrne K, Colgrave M, Larkin PJ, Howitt CA, Morell MK, Ral JP. Engineering α-amylase levels in wheat grain suggests a highly sophisticated level of carbohydrate regulation during development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5443-57. [PMID: 25053646 PMCID: PMC4157717 DOI: 10.1093/jxb/eru299] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 05/20/2023]
Abstract
Wheat starch degradation requires the synergistic action of different amylolytic enzymes. Our spatio-temporal study of wheat α-amylases throughout grain development shows that AMY3 is the most abundant isoform compared with the other known α-amylases. Endosperm-specific over-expression of AMY3 resulted in an increase of total α-amylase activity in harvested grains. Unexpectedly, increased activity did not have a significant impact on starch content or composition but led to an increase of soluble carbohydrate (mainly sucrose) in dry grain. In AMY3 overexpression lines (A3OE), germination was slightly delayed and triacylglycerol (TAG) content was increased in the endosperm of mature grain. Despite increased AMY3 transcript and protein content throughout grain development, alterations of α-amylase activity and starch granule degradation were not detected until grain maturation, suggesting a post-translational inhibition of α-amylase activity in the endosperm during the starch filling period. These findings show unexpected effects of a high level of α-amylase on grain development and composition, notably in carbon partitioning and TAG accumulation, and suggest the presence of a hitherto unknown regulatory pathway during grain filling.
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Affiliation(s)
- Alex Whan
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Anne-Sophie Dielen
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jos Mieog
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Andrew F Bowerman
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Hannah M Robinson
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Keren Byrne
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Animal, Food and Health Sciences, St Lucia, Queensland, Australia
| | - Michelle Colgrave
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Animal, Food and Health Sciences, St Lucia, Queensland, Australia
| | - Philip J Larkin
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601 Australia
| | - Crispin A Howitt
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Matthew K Morell
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Jean-Philippe Ral
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia.
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Valdés A, Simó C, Ibáñez C, García-Cañas V. Foodomics strategies for the analysis of transgenic foods. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Li X, Bai T, Li Y, Ruan X, Li H. Proteomic analysis of Fusarium oxysporum f. sp. cubense tropical race 4-inoculated response to Fusarium wilts in the banana root cells. Proteome Sci 2013; 11:41. [PMID: 24070062 PMCID: PMC3850410 DOI: 10.1186/1477-5956-11-41] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/22/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Fusarium wilt of banana is one of the most destructive diseases in the world. This disease has caused heavy losses in major banana production areas. Except for molecular breeding methods based on plant defense mechanisms, effective methods to control the disease are still lacking. Dynamic changes in defense mechanisms between susceptible, moderately resistant, and highly resistant banana and Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4) at the protein level remain unknown. This research reports the proteomic profile of three banana cultivars in response to Foc4 and transcriptional levels correlated with their sequences for the design of disease control strategies by molecular breeding. RESULTS Thirty-eight differentially expressed proteins were identified to function in cell metabolism. Most of these proteins were positively regulated after Foc4 inoculation. These differentially regulated proteins were found to have important functions in banana defense response. Functional categories implicated that these proteins were associated with pathogenesis-related (PR) response; isoflavonoid, flavonoid, and anthocyanin syntheses; cell wall strengthening; cell polarization; reactive oxygen species production and scavenging; jasmonic acid-, abscisic acid-, and auxin-mediated signaling conduction; molecular chaperones; energy; and primary metabolism. By comparing the protein profiles of resistant and susceptible banana cultivars, many proteins showed obvious distinction in their defense mechanism functions. PR proteins in susceptible 'Brazil' were mainly involved in defense. The proteins related to PR response, cell wall strengthening and antifungal compound synthesis in moderately resistant 'Nongke No.1' were mainly involved in defense. The proteins related to PR response, cell wall strengthening, and antifungal compound synthesis in highly resistant 'Yueyoukang I' were mainly involved in defense. 12 differentially regulated genes were selected to validate through quantitative real time PCR method. Quantitative RT-PCR analyses of these selected genes corroborate with their respective protein abundance after pathogen infection. CONCLUSIONS This report is the first to use proteomic profiling to study the molecular mechanism of banana roots infected with Foc4. The differentially regulated proteins involved in different defense pathways are likely associated with different resistant levels of the three banana cultivars.
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Affiliation(s)
- Xingshen Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong 510642, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Tingting Bai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong 510642, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yunfeng Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolei Ruan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong 510642, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Huaping Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong 510642, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
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Wu L, Wang S, Chen X, Wang X, Wu L, Zu X, Chen Y. Proteomic and phytohormone analysis of the response of maize (Zea mays L.) seedlings to sugarcane mosaic virus. PLoS One 2013; 8:e70295. [PMID: 23894637 PMCID: PMC3720893 DOI: 10.1371/journal.pone.0070295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 06/22/2013] [Indexed: 12/27/2022] Open
Abstract
Background Sugarcane mosaic virus (SCMV) is an important virus pathogen in crop production, causing serious losses in grain and forage yields in susceptible cultivars. Control strategies have been developed, but only marginal successes have been achieved. For the efficient control of this virus, a better understanding of its interactions and associated resistance mechanisms at the molecular level is required. Methodology/Principal Findings The responses of resistant and susceptible genotypes of maize to SCMV and the molecular basis of the resistance were studied using a proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS) analysis. Ninety-six protein spots showed statistically significant differences in intensity after SCMV inoculation. The classification of differentially expressed proteins showed that SCMV-responsive proteins were mainly involved in energy and metabolism, stress and defense responses, and photosynthesis. Most of the proteins identified were located in chloroplasts, chloroplast membranes, and the cytoplasm. Analysis of changes in phytohormone levels after virus inoculation suggested that salicylic acid, abscisic acid, jasmonic acid, and azelaic acid may played important roles in the maize response to SCMV infection. Conclusions/Significance Among these identified proteins, 19 have not been identified previously as virus-responsive proteins, and seven were new and did not have assigned functions. These proteins may be candidate proteins for future investigation, and they may present new biological functions and play important roles in plant-virus interactions. The behavioural patterns of the identified proteins suggest the existence of defense mechanisms operating during the early stages of infection that differed in two genotypes. In addition, there are overlapping and specific phytohormone responses to SCMV infection between resistant and susceptible maize genotypes. This study may provide important insights into the molecular events during plant responses to virus infection.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Shunxi Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Xiao Chen
- Henan Province Seed Control Station, Zhengzhou, China
| | - Xintao Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Liancheng Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Xiaofeng Zu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Yanhui Chen
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
- * E-mail:
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Guo H, Wang S, Xu F, Li Y, Ren J, Wang X, Niu H, Yin J. The role of thioredoxin h in protein metabolism during wheat (Triticum aestivum L.) seed germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 67:137-143. [PMID: 23562797 DOI: 10.1016/j.plaphy.2013.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 03/05/2013] [Indexed: 06/02/2023]
Abstract
Thioredoxin h can regulate the redox environment in the cell and play an important role in the germination of cereals. In the present study, the thioredoxin s antisense transgenic wheat with down-regulation of thioredoxin h was used to study the role of thioredoxin h in protein metabolism during germination of wheat seeds, and to explore the mechanism of the thioredoxin s antisense transgenic wheat seeds having high resistance to pre-harvest sprouting. The qRT-PCR results showed that the expression of protein disulfide isomerase in the thioredoxin s antisense transgenic wheat was up-regulated, which induced easily forming glutenin macropolymers and the resistance of storage proteins to degradation. The expression of serine protease inhibitor was also up-regulated in transgenic wheat, which might be responsible for the decreased activity of thiocalsin during the germination. The expression of WRKY6 in transgenic wheat was down-regulated, which was consistent with the decreased activity of glutamine oxoglutarate aminotransferase. In transgenic wheat, the activities of glutamate dehydrogenase, glutamic pyruvic transaminase and glutamic oxaloacetic transaminase were down-regulated, indicating that the metabolism of amino acid was lower than that in wild-type wheat during seed germination. A putative model for the role of thioredoxin h in protein metabolism during wheat seed germination was proposed and discussed.
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Affiliation(s)
- Hongxiang Guo
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China; College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Shaoxin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Fangfang Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yongchun Li
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiangping Ren
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiang Wang
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongbin Niu
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Yin
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
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Bykova NV, Rampitsch C. Modulating protein function through reversible oxidation: Redox-mediated processes in plants revealed through proteomics. Proteomics 2013. [PMID: 23197359 DOI: 10.1002/pmic.201200270] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
It has been clearly demonstrated that plants redox control can be exerted over virtually every cellular metabolic pathway affecting metabolic homeostasis and energy balance. Therefore, a tight link exists between cellular/compartmental steady-state redox level and cellular metabolism. Proteomics offers a powerful new way to characterize the response and regulation of protein oxidation in different cell types and in relation to cellular metabolism. Compelling evidence revealed in proteomics studies suggests the integration of the redox network with other cellular signaling pathways such as Ca(2+) and/or protein phosphorylation, jasmonic, salicylic, abscisic acids, ethylene, and other phytohormones. Here we review progress in using the various proteomics techniques and approaches to answer biological questions arising from redox signaling and from changes in redox status of the cell. The focus is on reversible redox protein modifications and on three main processes, namely oxidative and nitrosative stress, defense against pathogens, cellular redox response and regulation, drawing on examples from plant redox proteomics studies.
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Affiliation(s)
- Natalia V Bykova
- Cereal Research Centre, Agriculture and AgriFood Canada, 195 Dafoe Road, Winnipeg, Manitoba, Canada.
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Abstract
To gain insights into the protein dynamics during seed development, a proteomic study on the developing Brassica campestri L. seeds with embryos in different embryogenesis stages was carried out. The seed proteins at 10, 16, 20, 25 and 35 DAP (days after pollination), respectively, were separated using two-dimensional gel electrophoresis and identities of 209 spots with altered abundance were determined by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). These proteins were classified into 16 groups according to their functions. The most abundant proteins were related to primary metabolism, indicating the heavy demand of materials for rapid embryo growth. Besides, the high amount of proteins involved in protein processing and destination indicated importance of protein renewal during seed development. The remaining were those participated in oxidation/detoxification, energy, defense, transcription, protein synthesis, transporter, cell structure, signal transduction, secondary metabolism, transposition, DNA repair, storage and so on. Protein abundance profiles of each functional class were generated and hierarchical cluster analysis established 8 groups of dynamic patterns. Our results revealed novel characters of protein dynamics in seed development in Brassica campestri L. and provided valuable information about the complex process of seed development in plants.
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Affiliation(s)
- Wenlan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Yi Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hong Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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He T, Song B, Liu J, Chen X, Ou Y, Lin Y, Zhang H, Xie C. A new isoform of thioredoxin h group in potato, SbTRXh1, regulates cold-induced sweetening of potato tubers by adjusting sucrose content. PLANT CELL REPORTS 2012; 31:1463-1471. [PMID: 22527194 DOI: 10.1007/s00299-012-1261-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 03/21/2012] [Accepted: 04/02/2012] [Indexed: 05/31/2023]
Abstract
UNLABELLED In order to study the molecular mechanism of the cold-induced sweetening (CIS) of potato tubers, a novel isoform of thioredoxin h group, SbTRXh1, which was up-regulated early in the 4 °C storage of CIS-resistant potato (Solanum berthaultii) tubers, was cloned in present research. The genetic transformation of over-expression (OE) and RNA interference (RNAi) of SbTRXh1 into potato cv. E-Potato 3 (E3) was carried out to clarify its function in CIS regulation. The results showed that the transcripts of SbTRXh1 in either OE- or RNAi-tubers were strongly induced in 4 °C storage and quantitatively related to the reducing sugar (RS) accumulation, indicating that SbTRXh1 is involved in the CIS process of potato tubers. Regression analysis between the transcripts and protein contents of SbTRXh1 showed a very significant logarithmic relationship implying that the expression of SbTRXh1 may be mainly regulated at transcriptional level. Further monitoring the variation of the sugar contents in cold-stored tubers demonstrated a linear relationship between RS and sucrose (Suc). Thus, it can be inferred that SbTRXh1 may function in the Suc-RS pathway for CIS regulation of potato tubers. KEY MESSAGE SbTRXh1 is primarily demonstrated to be involved in the regulation of cold-induced sweetening (CIS) of potato tubers, and it may function in the Suc-RS pathway for CIS regulation.
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Affiliation(s)
- Tianjiu He
- National Centre for Vegetable Improvement-Central China, Key Laboratory of Horticultural Plant Biology-Huazhong Agricultural University, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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