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Zhang L, Liu X, Xu L, Xie M, Yu M. Non-Targeted Metabolomics Analysis of γ-Aminobutyric Acid Enrichment in Germinated Maize Induced by Pulsed Light. Foods 2024; 13:2675. [PMID: 39272441 PMCID: PMC11395081 DOI: 10.3390/foods13172675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Pulsed light is an emerging technique in plant physiology recognized for its ability to enhance germination and accumulate γ-aminobutyric acid in maize. Pulsed light involves exposing plants to brief, high-intensity bursts of light, which can enhance photosynthesis, improve growth, and increase resistance to environmental stresses. Despite its promising potential, the specific metabolic changes leading to γ-aminobutyric acid enrichment in maize induced by pulsed light are not fully understood. This study addresses this gap by quantifying key nutrients and γ-aminobutyric acid-related compounds during maize germination and investigating the underlying mechanisms using non-targeted metabolomics. Our findings indicate that pulsed light significantly promotes maize germination and accelerates the hydrolysis of proteins, sugars, and lipids. This acceleration is likely due to the activation of enzymes involved in these metabolic pathways. Additionally, pulsed light markedly increases the content of glutamic acid and the activity of glutamate decarboxylase, which are crucial for γ-aminobutyric acid synthesis. Moreover, pulsed light significantly reduces the activity of γ-aminobutyric transaminase, thereby inhibiting γ-aminobutyric acid decomposition and resulting in a substantial increase in γ-aminobutyric acid content, with a 27.20% increase observed in germinated maize following pulsed light treatment. Metabolomic analysis further revealed enrichment of metabolic pathways associated with γ-aminobutyric acid, including amino acid metabolism, carbohydrate metabolism, plant hormone signal transduction, energy metabolism, pyrimidine metabolism, and ABC transporters. In conclusion, pulsed light is a robust and efficient method for producing sprouted maize with a high γ-aminobutyric acid content. This technique provides a novel approach for developing sprouted cereal foods with enhanced nutritional profiles, leveraging the physiological benefits of γ-aminobutyric acid, which include stress alleviation and potential health benefits for humans.
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Affiliation(s)
- Liangchen Zhang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Xiaojing Liu
- Center for Disease Control and Prevention of Liaoning Province, Shenyang 110172, China
| | - Liwei Xu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Mengxi Xie
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Miao Yu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
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Li Y, Liang Y, Liu M, Zhang Q, Wang Z, Fan J, Ruan Y, Zhang A, Dong X, Yue J, Li C. Genome-Wide Association Studies Provide Insights Into the Genetic Architecture of Seed Germination Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:930438. [PMID: 35755688 PMCID: PMC9226777 DOI: 10.3389/fpls.2022.930438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/25/2022] [Indexed: 06/01/2023]
Abstract
Seed germination is an important agronomic trait that affects crop yield and quality. Rapid and uniform seed germination traits are required in agricultural production. Although several genes are involved in seed germination and have been identified in Arabidopsis and rice, the genetic basis governing seed germination in maize remains unknown. Herein, we conducted a genome-wide association study to determine the genetic architecture of two germination traits, germination speed, and consistency, in a diverse panel. We genotyped 321 maize inbred populations with tropical, subtropical, or temperate origins using 1219401 single-nucleotide polymorphism markers. We identified 58 variants that were associated with the two traits, and 12 of these were shared between the two traits, indicating partial genetic similarity. Moreover, 36 candidate genes were involved in seed germination with functions including energy metabolism, signal transduction, and transcriptional regulation. We found that favorable variants had a greater effect on the tropical subpopulation than on the temperate. Accumulation of favorable variants shortened germination time and improved uniformity in maize inbred lines. These findings contribute significantly to understanding the genetic basis of maize seed germination and will contribute to the molecular breeding of maize seed germination.
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Affiliation(s)
- Yuntong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Qiyuan Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Ziwei Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Jinjuan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Jing Yue
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
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Zhang L, Hao N, Li W, Zhang B, Shi T, Xie M, Yu M. Effect of Ultrasonic Induction on the Main Physiological and Biochemical Indicators and γ–Aminobutyric Acid Content of Maize during Germination. Foods 2022; 11:foods11091358. [PMID: 35564080 PMCID: PMC9102003 DOI: 10.3390/foods11091358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/04/2022] Open
Abstract
Research on the nutrient content of cereal grains during germination is becoming a hot topic; however, studies on germinated maize are still scarce. This study aimed to provide a technical reference and theoretical basis for the development of functional maize health foods and to expand the application of ultrasonic technology in the production of germinated grains. In this study, the germination rate of maize was used as the evaluation index, and the ultrasonic frequency, ultrasonic temperature, and induction time were selected as the influencing factors in orthogonal experiments to determine the optimal process parameters for ultrasonic induction of maize germination (ultrasonic frequency of 45 kHz, ultrasonic temperature of 30 °C, and ultrasonic induction time of 30 min). Based on this process, the effects of ultrasonic induction on the main physiological, biochemical, and γ–aminobutyric acid contents of maize during germination were investigated. The results showed that the respiration of the ultrasonic treated maize was significantly enhanced during germination, resulting in a 27% increase in sprout length, as well as a 4.03% higher dry matter consumption rate, and a 2.11% higher starch consumption rate. Furthermore, the reducing sugar content of germinated maize increased by 22.83%, soluble protein content increased by 22.52%, and γ–aminobutyric acid content increased by 30.55% after ultrasonic induction treatment. Throughout the germination process, the glutamate acid decarboxylase activity of the ultrasonically treated maize was higher than that of the control group, indicating that ultrasonication can promote maize germination, accelerate the germination process, and shorten the enrichment time of γ–aminobutyric acid in germinated maize. The results of this study can be applied to the production of γ–aminobutyric acid enrichment in germinated maize.
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Affiliation(s)
- Liangchen Zhang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (L.Z.); (T.S.); (M.X.)
| | - Nan Hao
- Corn Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China;
| | - Wenjuan Li
- College of Food Science and Technology, Shenyang Normal University, Shenyang 110034, China; (W.L.); (B.Z.)
| | - Baiqing Zhang
- College of Food Science and Technology, Shenyang Normal University, Shenyang 110034, China; (W.L.); (B.Z.)
| | - Taiyuan Shi
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (L.Z.); (T.S.); (M.X.)
| | - Mengxi Xie
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (L.Z.); (T.S.); (M.X.)
| | - Miao Yu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (L.Z.); (T.S.); (M.X.)
- Correspondence: ; Tel./Fax: +86-159-9837-8968
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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Identification of Quantitative Trait Loci Controlling Ethylene Production in Germinating Seeds in Maize (Zea mays L.). Sci Rep 2020; 10:1677. [PMID: 32015470 PMCID: PMC6997408 DOI: 10.1038/s41598-020-58607-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/17/2020] [Indexed: 11/15/2022] Open
Abstract
Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed germination remains poorly understood. In this study, we quantified the diversity of germination among 14 inbred lines representing the parental materials corresponding to multiple recombinant inbred line (RIL) mapping populations. Quantitative trait loci (QTLs) controlling ethylene production were then identified in germinating seeds from an RIL population constructed from two parental lines showing differences in both germination speed and ethylene production during germination. To explore the possible genetic correlations of ethylene production with other traits, seed germination and seed weight were evaluated using the same batch of samples. On the basis of high-density single nucleotide polymorphism-based genetic linkage maps, we detected three QTLs for ethylene production in germinating seeds, three QTLs for seed germination, and four QTLs for seed weight, with each QTL explaining 5.8%–13.2% of the phenotypic variation of the trait. No QTLs were observed to be co-localized, suggesting that the genetic bases underlying the three traits are largely different. Our findings reveal three chromosomal regions responsible for ethylene production during seed germination, and provide a valuable reference for the future investigation of the genetic mechanism underlying the role of the stress hormone ethylene in maize germination control under unfavourable external conditions.
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Zhang B, Chen J, Zong J, Yan X, Liu J. Unbiased phosphoproteome profiling uncovers novel phosphoproteins and phosphorylation motifs in bermudagrass stolons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:92-99. [PMID: 31561202 DOI: 10.1016/j.plaphy.2019.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/21/2019] [Indexed: 05/20/2023]
Abstract
As a widely used turfgrass species, bermudagrass (Cynodon dactylon L.) can be easily propagated through colonial growth of stolons. Previous studies collectively revealed that exotic environmental factors and intrinsic hormones and genes are all involved in the differentiation, development, and diageotropical growth of stolons. However, the detailed molecular mechanism how environmental and hormone signals regulate the gene expression and biochemical activities in bermudagrass stolons remains unclear. In this study, we observed that reversible phosphorylation modification plays important roles in normal growth and physiological functions of bermudagrass stolons. LC-MS/MS analyses of the total protein extracts of bermudagrass stolons without preliminary phosphopeptide-enrichment successfully identified 646 nonredundant phosphorylation sites and 485 phosphoproteins. The phosphoproteins were significantly enriched in protein phosphorylation regulation and starch metabolism processes. Motif-X analyses further revealed that phosphoproteins containing novel phosphorylation motifs might be involved in transcription regulation of bermudagrass stolons. These results greatly expanded our understanding of the growth and development of bermudagrass stolons at the post-translational level.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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8
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Parra-Londono S, Fiedler K, Kavka M, Samans B, Wieckhorst S, Zacharias A, Uptmoor R. Genetic dissection of early-season cold tolerance in sorghum: genome-wide association studies for seedling emergence and survival under field and controlled environment conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:581-595. [PMID: 29147737 DOI: 10.1007/s00122-017-3021-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/10/2017] [Indexed: 05/20/2023]
Abstract
A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions. Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker-trait associations controlling temperature-related seedling establishment. A diversity set consisting of 194 biomass sorghum lines was subjected to extensive phenotyping comprising field trials and controlled environment experiments. The final emergence percentage (FEP) under field conditions was significantly reduced under cold stress. Broad-sense heritability was h 2 = 0.87 for FEP in the field and h 2 = 0.93 for seedling survival rate (SR) under controlled conditions. Correlations between FEP in the field and under controlled conditions were low; higher correlations were observed between field FEP and SR in controlled environments. Genome-wide association studies (GWAS) were conducted using 44,515 single nucleotide polymorphisms (SNPs) and revealed eight regions with suggestive marker-trait associations for FEP and SR on chromosomes SBI-01, -02, -03, -06, -09, and -10 (p < 5.7 × 10-5) and a significant association on SBI-06 for field FEP (p < 2.9 × 10-6). Although not significant under controlled conditions, SR of genotypes carrying the minor allele on the field FEP quantitative trait loci (QTL) on SBI-06 was on average 13.1% higher, while FEP under controlled conditions was on average 9.7% higher with a linearly decreasing effect with increasing temperatures (R 2 = 0.82). Promising candidate genes putatively conferring seedling cold tolerance were identified.
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Affiliation(s)
| | - Karin Fiedler
- KWS SAAT SE, Grimsehlstraße 31, 37555, Einbeck, Germany
| | - Mareike Kavka
- Chair of Agronomy, University of Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany
| | - Birgit Samans
- Department of Plant Breeding, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | | | | | - Ralf Uptmoor
- Chair of Agronomy, University of Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany.
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Zhang H, Zhou KX, Wang WQ, Liu SJ, Song SQ. Proteome analysis reveals an energy-dependent central process for Populus×canadensis seed germination. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:134-147. [PMID: 28384531 DOI: 10.1016/j.jplph.2017.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
Poplar (Populus×canadensis) seeds rapidly germinated in darkness at 10, 15, and 20°C and reached 50% seed germination after about 22, 4.5, and 3.5h, respectively. Germination of poplar seeds was markedly inhibited by abscisic acid (ABA) at 50μM and cycloheximide (CHX) at 100μM, and these inhibitive roles were temperature-dependent. In the present study, mature poplar seeds were used to investigate the differentially changed proteome of seeds germinating in water, ABA, and CHX. A total of 130 protein spots showed a significant change (1.5-fold increase/decrease, P<0.05) in abundance, and 101 protein spots were successfully identified. Most of the proteins were associated with cell defense and rescue (21%), storage proteins (21%), protein synthesis and destination (20%), metabolism (16%), and energy (14%). The germination of poplar seeds is closely related with the increase in those proteins involved in amino acid and lipid metabolism, the tricarboxylic acid cycle and pentose phosphate pathway, protein synthesis and destination, cell defense and rescue, and degradation of storage proteins. ABA and CHX inhibit the germination of poplar seeds by decreasing the protein abundance associated with protein proteolysis, protein folding, and storage proteins. We conclude that poplar seed germination is an energy-dependent active process, and is accompanied by increasing amino acid activation, protein synthesis and destination, as well as cell defense and rescue, and degradation of storage proteins.
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Affiliation(s)
- Hong Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ke-Xin Zhou
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Abstract
Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.
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Affiliation(s)
- Monika Bansal
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab.,b School of Agriculture , Lovely Professional University , Phagwara 144411 , Punjab
| | - Madhu Sharma
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Priyanka Kanwar
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Aakash Goyal
- c Biodiversity and Integrated Gene Management Program , International Center for Agriculture Research in the Dry Areas (ICARDA) , P.O.Box 6299, Rabat-Institutes, Rabat , Morocco
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11
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Abstract
Background Barley seed proteins are of prime importance to the brewing industry, human and animal nutrition and in plant breeding for cultivar identification. To obtain comprehensive proteomic data from seeds, total protein from a two-rowed (Conrad) and a six-rowed (Lacey) barley cultivar were precipitated in acetone, digested in-solution, and the resulting peptides were analyzed by nano-liquid chromatography coupled with tandem mass spectrometry. Results The raw mass spectra data searched against Uniprot’s Barley database using in-house Mascot search engine identified 1168 unique proteins. Gene Ontology (GO) analysis indicated that the majority of the seed proteins were cytosolic, with catalytic activity and associated with carbohydrate metabolism. Spectral counting analysis showed that there are 20 differentially abundant seed proteins between the two-rowed Conrad and six-rowed Lacey cultivars. Conclusion This study paves the way for the use of a top-down gel-free proteomics strategy in barley for investigating more complex traits such as malting quality. Differential abundance of hordoindoline proteins impact the seed hardness trait of barley cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3408-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ramamurthy Mahalingam
- USDA, Agricultural Research Service, Cereal Crops Research Unit, 502 Walnut Street, Madison, WI, 53726, USA.
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Mitochondrial Proteome Studies in Seeds during Germination. Proteomes 2016; 4:proteomes4020019. [PMID: 28248229 PMCID: PMC5217346 DOI: 10.3390/proteomes4020019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 01/25/2023] Open
Abstract
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination.
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Xu HH, Liu SJ, Song SH, Wang RX, Wang WQ, Song SQ. Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:219-42. [PMID: 27035683 DOI: 10.1016/j.plaphy.2016.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 05/09/2023]
Abstract
Seed germination is a complex trait which is influenced by many genetic, endogenous and environmental factors, but the key event(s) associated with seed germination are still poorly understood. In present study, the non-dormant cultivated rice Yannong S and the dormant Dongxiang wild rice seeds were used as experimental materials, we comparatively investigated the water uptake, germination time course, and the differential proteome of the effect of embryo and endosperm on germination of these two types of seeds. A total of 231 and 180 protein spots in embryo and endosperm, respectively, showed a significant change in abundance during germination. We observed that the important proteins associated with seed germination included those involved in metabolism, energy production, protein synthesis and destination, storage protein, cell growth and division, signal transduction, cell defense and rescue. The contribution of embryo and endosperm to seed germination is different. In embryo, the proteins involved in amino acid activation, sucrose cleavage, glycolysis, fermentation and protein synthesis increased; in endosperm, the proteins involved in sucrose cleavage and glycolysis decreased, and those with ATP and CoQ synthesis and proteolysis increased. Our results provide some new knowledge to understand further the mechanism of seed germination.
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Affiliation(s)
- Heng-Heng Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shun-Hua Song
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Rui-Xia Wang
- College of Life Science, Linyi University, Linyi 276005, China
| | - Wei-Qing Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Ning DL, Liu KH, Liu CC, Liu JW, Qian CR, Yu Y, Wang YF, Wang YC, Wang BC. Large-scale comparative phosphoprotein analysis of maize seedling leaves during greening. PLANTA 2016; 243:501-517. [PMID: 26497871 DOI: 10.1007/s00425-015-2420-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
MAIN CONCLUSION : Large-scale comparative phosphoprotein analysis in maize seedlings reveals a complicated molecular regulation mechanism at the phosphoproteomic level during de-etiolation. In the present study we report a phosphoproteomic study conducted on Zea mays etiolated leaves harvested at three time points during greening (etiolated seedlings and seedlings exposed to light for 6 or 12 h). We identified a total of 2483 phosphopeptides containing 2389 unambiguous phosphosites from 1339 proteins. The abundance of nearly 692 phosphorylated peptides containing 783 phosphosites was reproducible and profiled with high confidence among treatments. Comparisons with other large-scale phosphoproteomic studies revealed that 473 of the phosphosites are novel to this study. Of the 783 phosphosites identified, 171, 79, and 138 were identified in 0, 6, and 12 h samples, respectively, which suggest that regulation of phosphorylation plays important roles during maize seedling de-etiolation. Our experimental methods included enrichment of phosphoproteins, allowing the identification of a great number of low abundance proteins, such as transcription factors, protein kinases, and photoreceptors. Most of the identified phosphoproteins were involved in gene transcription, post-transcriptional regulation, or signal transduction, and only a few were involved in photosynthesis and carbon metabolism. It is noteworthy that tyrosine phosphorylation and calcium signaling pathways might play important roles during maize seedling de-etiolation. Taken together, we have elucidated a new level of complexity in light-induced reversible protein phosphorylation during maize seedling de-etiolation.
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Liu SJ, Xu HH, Wang WQ, Li N, Wang WP, Møller IM, Song SQ. A proteomic analysis of rice seed germination as affected by high temperature and ABA treatment. PHYSIOLOGIA PLANTARUM 2015; 154:142-161. [PMID: 25270993 DOI: 10.1111/ppl.12292] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 09/07/2014] [Accepted: 09/09/2014] [Indexed: 06/03/2023]
Abstract
Seed germination is a critical phase in the plant life cycle, but the specific events associated with seed germination are still not fully understood. In this study, we used two-dimensional gel electrophoresis followed by mass spectrometry to investigate the changes in the proteome during imbibition of Oryza sativa seeds at optimal temperature with or without abscisic acid (ABA) and high temperature (germination thermoinhibition) to further identify and quantify key proteins required for seed germination. A total of 121 protein spots showed a significant change in abundance (1.5-fold increase/decrease) during germination under all conditions. Among these proteins, we found seven proteins specifically associated with seed germination including glycosyl hydrolases family 38 protein, granule-bound starch synthase 1, Os03g0842900 (putative steroleosin-B), N-carbamoylputrescine amidase, spermidine synthase 1, tubulin α-1 chain and glutelin type-A; and a total of 20 imbibition response proteins involved in energy metabolism, cell growth, cell defense and storage proteins. High temperature inhibited seed germination by decreasing the abundance of proteins involved in methionine metabolism, amino acid biosynthesis, energy metabolism, reserve degradation, protein folding and stress responses. ABA treatment inhibited germination and decreased the abundance of proteins associated with methionine metabolism, energy production and cell division. Our results show that changes in many biological processes including energy metabolism, protein synthesis and cell defense and rescue occurred as a result of all treatments, while enzymes involved in methionine metabolism and weakening of cell wall specifically accumulated when the seeds germinated at the optimal temperature.
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Affiliation(s)
- Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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16
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Abstract
Cereals are the most important crop plant supplying staple food throughout the world. The economic importance and continued breeding of crop plants such as rice, maize, wheat, or barley require a detailed scientific understanding of adaptive and developmental processes. Protein phosphorylation is one of the most important regulatory posttranslational modifications and its analysis allows deriving functional and regulatory principles in plants. This minireview summarizes the current knowledge of phosphoproteomic studies in cereals.
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Affiliation(s)
- Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China,
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Romero-Rodríguez MC, Abril N, Sánchez-Lucas R, Jorrín-Novo JV. Multiplex staining of 2-DE gels for an initial phosphoproteome analysis of germinating seeds and early grown seedlings from a non-orthodox specie: Quercus ilex L. subsp. ballota [Desf.] Samp. FRONTIERS IN PLANT SCIENCE 2015; 6:620. [PMID: 26322061 PMCID: PMC4531236 DOI: 10.3389/fpls.2015.00620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/27/2015] [Indexed: 05/08/2023]
Abstract
As a preliminary step in the phosphoproteome analysis of germinating seeds (0 and 24 h after seed imbibition) and early grown seedlings (216 h after seed imbibition) from a non-orthodox sp. Quercus ilex, a multiplex (SYPRO-Ruby and Pro-Q DPS) staining of high-resolution 2-DE gels was used. By using this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status. This simple approach could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein candidates. While 482 spots were visualized with SYPRO-Ruby, 222 were with Pro-Q DPS. Statistically significant differences in spot intensity were observed among samples, these corresponding to 85 SYPRO-Ruby-, 20 Pro-Q-DPS-, and 35 SYPRO-Ruby and Pro-Q-DPS-stained spots. Fifty-five phosphoprotein candidates showing qualitative or quantitative differences between samples were subjected to MALDI-TOF-TOF MS analysis, with 20 of them being identified. Identified proteins belonged to five different functional categories, namely: carbohydrate and amino acid metabolism, defense, protein folding, and oxidation-reduction processes. With the exception of a putative cyclase, the other 19 proteins had at least one orthologous phosphoprotein in Arabidopsis thaliana, Medicago truncatula, N. tabacum, and Glycine max. Out of the 20 identified, seven showed differences in intensity in Pro-Q-DPS but not in SYPRO-Ruby-stained gels, including enzymes of the glycolysis and amino acid metabolism. This bears out that theory the regulation of these enzymes occurs at the post-translational level by phosphorylation with no changes at the transcriptional or translational level. This is different from the mechanism reported in orthodox seeds, in which concomitant changes in abundance and phosphorylation status have been observed for these enzymes.
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Affiliation(s)
- M. Cristina Romero-Rodríguez
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de AsunciónSan Lorenzo, Paraguay
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
| | - Jesús V. Jorrín-Novo
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
- *Correspondence: Jesús V. Jorrín-Novo, Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, Ed. Severo Ochoa, Planta Baja, 14071 Cordoba, Spain
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Xiang Y, Nakabayashi K, Ding J, He F, Bentsink L, Soppe WJJ. Reduced Dormancy5 encodes a protein phosphatase 2C that is required for seed dormancy in Arabidopsis. THE PLANT CELL 2014; 26:4362-75. [PMID: 25415980 PMCID: PMC4277229 DOI: 10.1105/tpc.114.132811] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Seed dormancy determines germination timing and contributes to crop production and the adaptation of natural populations to their environment. Our knowledge about its regulation is limited. In a mutagenesis screen of a highly dormant Arabidopsis thaliana line, the reduced dormancy5 (rdo5) mutant was isolated based on its strongly reduced seed dormancy. Cloning of RDO5 showed that it encodes a PP2C phosphatase. Several PP2C phosphatases belonging to clade A are involved in abscisic acid signaling and control seed dormancy. However, RDO5 does not cluster with clade A phosphatases, and abscisic acid levels and sensitivity are unaltered in the rdo5 mutant. RDO5 transcript could only be detected in seeds and was most abundant in dry seeds. RDO5 was found in cells throughout the embryo and is located in the nucleus. A transcriptome analysis revealed that several genes belonging to the conserved PUF family of RNA binding proteins, in particular Arabidopsis PUMILIO9 (APUM9) and APUM11, showed strongly enhanced transcript levels in rdo5 during seed imbibition. Further transgenic analyses indicated that APUM9 reduces seed dormancy. Interestingly, reduction of APUM transcripts by RNA interference complemented the reduced dormancy phenotype of rdo5, indicating that RDO5 functions by suppressing APUM transcript levels.
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Affiliation(s)
- Yong Xiang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kazumi Nakabayashi
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jia Ding
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Fei He
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Zhang M, Ma CY, Lv DW, Zhen SM, Li XH, Yan YM. Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions. J Proteome Res 2014; 13:4281-97. [PMID: 25145454 DOI: 10.1021/pr500400t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance.
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Affiliation(s)
- Ming Zhang
- College of Life Science, Capital Normal University , 100048 Beijing, China
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20
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Han C, Wang K, Yang P. Gel-based comparative phosphoproteomic analysis on rice embryo during germination. PLANT & CELL PHYSIOLOGY 2014; 55:1376-94. [PMID: 24793751 DOI: 10.1093/pcp/pcu060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, ChinaUniversity of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, China
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21
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Han C, Yin X, He D, Yang P. Analysis of proteome profile in germinating soybean seed, and its comparison with rice showing the styles of reserves mobilization in different crops. PLoS One 2013; 8:e56947. [PMID: 23460823 PMCID: PMC3584108 DOI: 10.1371/journal.pone.0056947] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/16/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Seed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date. RESULTS Proteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds. CONCLUSIONS This study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojian Yin
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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22
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Pechanova O, Takáč T, Šamaj J, Pechan T. Maize proteomics: An insight into the biology of an important cereal crop. Proteomics 2013. [DOI: 10.1002/pmic.201200275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Olga Pechanova
- Mississippi State Chemical Laboratory; Mississippi State University; Mississippi State; MS; USA
| | - Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station,; Mississippi State University; Mississippi State; MS; USA
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Xu H, Zhang W, Gao Y, Zhao Y, Guo L, Wang J. Proteomic analysis of embryo development in rice (Oryza sativa). PLANTA 2012; 235:687-701. [PMID: 22015996 DOI: 10.1007/s00425-011-1535-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/04/2011] [Indexed: 05/26/2023]
Abstract
Although embryo development is a major subject in plant growth and development research, a number of aspects of the mechanism of this development process remain unknown. Rice (Oryza sativa) is an excellent monocot plant model for studying embryogenesis with a known genome sequence. Here, we conducted proteomic analysis of embryo development in rice (O. sativa L. ssp. indica cv. 9311). The aim was to investigate and characterize the changes in the protein expression profile during embryo development. For this purpose, the proteome of developing embryos was characterized by two-dimensional gel electrophoresis and nano liquid chromatography/mass spectrometry/mass spectrometry. Proteomic analyses identified 275 differentially expressed proteins throughout the 5 sequential developmental stages from 5 to 30 days after pollination. Most of these proteins were classified into eight functional categories: metabolism, protein synthesis/destination, disease and defense, transporter, transcription, signal transduction, cell growth/division, and storage proteins, which were involved in different cellular and metabolic processes. Hierarchical clustering analyses of protein expression profiles showed that highly expressed proteins in early stages were involved in metabolism, protein synthesis/destination, and most of the other cellular functions, whereas the proteins highly expressed in later stages functioned in the desiccation and dormancy of the embryo.
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Affiliation(s)
- Hong Xu
- Key Laboratory of MOE for Plant Development Biology, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Yin C, Teng Y, Luo Y, Christie P. Proteomic response of wheat embryos to fosthiazate stress in a protected vegetable soil. J Environ Sci (China) 2012; 24:1843-1853. [PMID: 23520855 DOI: 10.1016/s1001-0742(11)61013-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A proteomic analysis of wheat defense response induced by the widely used organophosphorus nematicide fosthiazate is reported. Seed germination and two-dimensional gel electrophoresis (2-DE) experiments were performed using a Chinese wheat cultivar, Zhenmai No. 5. Root and shoot elongation decreased but thiobarbituric acid reactive substances (TBARS) content in embryos increased with increasing pesticide concentration. More than 1000 protein spots were reproducibly detected in each silver-stained gel. Thirty-seven protein spots with at least 2-fold changes were identified using MALDI-TOF MS/MS analysis. Of these, 24 spots were up-regulated and 13 were down-regulated. Proteins identified included some well-known classical stress responsive proteins under abiotic or biotic stresses as well as some unusual responsive proteins. Ten responsive proteins were reported for the first time at the proteomic level, including fatty acyl CoA reductase, dihydrodipicolinate synthase, DEAD-box ATPase-RNA-helicase, fimbriata-like protein, waxy B1, rust resistance kinase Lr10, putative In2.1 protein, retinoblastoma-related protein 1, pollen allergen-like protein and S-adenosyl-L-methionine:phosphoethanolamine N-methyltransferase. The proteins identified were involved in several processes such as metabolism, defense/detoxification, cell structure/cell growth, signal transduction/transcription, photosynthesis and energy. Seven candidate proteins were further analyzed at the mRNA level by RT-PCR to compare transcript and protein accumulation patterns, revealing that not all the genes were correlated well with the protein level. Identification of these responsive proteins may provide new insight into the molecular basis of the fosthiazate-stress response in the early developmental stages of plants and may be useful in stress monitoring or stress-tolerant crop breeding for environmentally friendly agricultural production.
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Affiliation(s)
- Chunyan Yin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, Job C, Job D. Seed germination and vigor. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:507-33. [PMID: 22136565 DOI: 10.1146/annurev-arplant-042811-105550] [Citation(s) in RCA: 473] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Germination vigor is driven by the ability of the plant embryo, embedded within the seed, to resume its metabolic activity in a coordinated and sequential manner. Studies using "-omics" approaches support the finding that a main contributor of seed germination success is the quality of the messenger RNAs stored during embryo maturation on the mother plant. In addition, proteostasis and DNA integrity play a major role in the germination phenotype. Because of its pivotal role in cell metabolism and its close relationships with hormone signaling pathways regulating seed germination, the sulfur amino acid metabolism pathway represents a key biochemical determinant of the commitment of the seed to initiate its development toward germination. This review highlights that germination vigor depends on multiple biochemical and molecular variables. Their characterization is expected to deliver new markers of seed quality that can be used in breeding programs and/or in biotechnological approaches to improve crop yields.
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Affiliation(s)
- Loïc Rajjou
- CNRS-Bayer CropScience Joint Laboratory, UMR 5240, Bayer CropScience, Lyon Cedex 9, France.
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Liu CC, Liu CF, Wang HX, Shen ZY, Yang CP, Wei ZG. Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar. BMC PLANT BIOLOGY 2011; 11:158. [PMID: 22074553 PMCID: PMC3234192 DOI: 10.1186/1471-2229-11-158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 11/11/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear. RESULTS We used mass spectrometry combined with TiO₂ phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (Populus simonii × P. nigra). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in Arabidopsis, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in Arabidopsis, indicating that regulatory mechanisms are well conserved between poplar and Arabidopsis. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues. CONCLUSIONS This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.
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Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
- Laboratory for Chemical Defence and Microscale Analysis, P.O. Box 3, Zhijiang 443200, China
| | - Chang-Fu Liu
- Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning 110866, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, 27 Taiping Road, Beijing 100850, China
| | - Zhi-Ying Shen
- Daqing Branch, Harbin Medical University, Daqing 163319, China
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
| | - Zhi-Gang Wei
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
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Finnie C, Sultan A, Grasser KD. From protein catalogues towards targeted proteomics approaches in cereal grains. PHYTOCHEMISTRY 2011; 72:1145-1153. [PMID: 21134685 DOI: 10.1016/j.phytochem.2010.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 05/27/2023]
Abstract
Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain proteomes, mostly derived using 2D-gel based technologies, have been described and hundreds of proteins identified. However, very little is still known about post-translational modifications, subcellular proteomes, and protein-protein interactions in cereal grains. Development of techniques for improved extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets of proteins. These "next-generation" proteomics studies will vastly increase our depth of knowledge about the processes controlling cereal grain development, nutritional and processing characteristics.
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Affiliation(s)
- Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Bldg 224, DK-2800 Kgs. Lyngby, Denmark.
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28
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Arc E, Galland M, Cueff G, Godin B, Lounifi I, Job D, Rajjou L. Reboot the system thanks to protein post-translational modifications and proteome diversity: How quiescent seeds restart their metabolism to prepare seedling establishment. Proteomics 2011; 11:1606-18. [DOI: 10.1002/pmic.201000641] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 12/05/2010] [Accepted: 01/07/2011] [Indexed: 11/12/2022]
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Takáč T, Pechan T, Samaj J. Differential proteomics of plant development. J Proteomics 2011; 74:577-88. [PMID: 21315196 DOI: 10.1016/j.jprot.2011.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmental processes, which substantially changes the view on functional classification of these proteins. Next, it is noteworthy that proteomics helped to recognize some metabolic and housekeeping proteins as important signaling inducers of developmental pathways. Further, cell division and elongation are dependent on proteins involved in membrane trafficking and cytoskeleton dynamics. These protein groups are less prevalently represented in studies concerning cell differentiation and organ formation, which do not target primarily cell division. The synthesis of new proteins, generally observed during developmental processes, is followed by active protein folding. In this respect, disulfide isomerase was found to be commonly up-regulated during several developmental processes. The future progress in plant proteomics requires new and/or complementary approaches including cell fractionation, specific chemical treatments, molecular cloning and subcellular localization of proteins combined with more sensitive methods for protein detection and identification.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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Bi YD, Wang HX, Lu TC, Li XH, Shen Z, Chen YB, Wang BC. Large-scale analysis of phosphorylated proteins in maize leaf. PLANTA 2011; 233:383-92. [PMID: 21053013 DOI: 10.1007/s00425-010-1291-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 10/04/2010] [Indexed: 05/08/2023]
Abstract
Phosphorylation is an ubiquitous regulatory mechanism governing the activity, subcellular localization, and intermolecular interactions of proteins. To identify a broad range of phosphoproteins from Zea mays, we enriched phosphopeptides from Zea mays leaves using titanium dioxide microcolumns and then extensively fractionated and identified the phosphopeptides by mass spectrometry. A total of 165 unique phosphorylation sites with a putative role in biological processes were identified in 125 phosphoproteins. Most of these proteins are involved in metabolism, including carbohydrate and protein metabolism. We identified novel phosphorylation sites on translation initiation factors, splicing factors, nucleolar RNA helicases, and chromatin-remodeling proteins such as histone deacetylases. Intriguingly, we also identified phosphorylation sites on several proteins associated with photosynthesis, and we speculate that these sites may be involved in carbohydrate metabolism or electron transport. Among these phosphoproteins, phosphoenolpyruvate carboxylase and NADH: nitrate reductase (NR) which catalyzes the rate-limiting and regulated step in the pathway of inorganic nitrogen assimilation were identified. A conserved phosphorylation site was found in the cytochrome b5 heme-binding domain of NADH: nitrate reductase, suggesting that NADH: nitrate reductase is phosphorylated by the same protein kinase or highly related kinases. These data demonstrate that the pathways that regulate diverse processes in plants are major targets of phosphorylation.
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Affiliation(s)
- Ying-Dong Bi
- Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Ministry of Education and School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin 150040, People's Republic of China
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Yuan HM, Li KL, Ni RJ, Guo WD, Shen Z, Yang CP, Wang BC, Liu GF, Guo CH, Jiang J. A systemic proteomic analysis of Populus chloroplast by using shotgun method. Mol Biol Rep 2010; 38:3045-54. [DOI: 10.1007/s11033-010-9971-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
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Liu CC, Lu TC, Li HH, Wang HX, Liu GF, Ma L, Yang CP, Wang BC. Phosphoproteomic identification and phylogenetic analysis of ribosomal P-proteins in Populus dormant terminal buds. PLANTA 2010; 231:571-581. [PMID: 20072825 DOI: 10.1007/s00425-009-1037-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Accepted: 10/02/2009] [Indexed: 05/28/2023]
Abstract
To better understand the role that reversible phosphorylation plays in woody plant ribosomal P-protein function, we initiated a phosphoproteomic investigation of P-proteins from Populus dormant terminal buds. Using gel-free (in-solution) protein digestion and phosphopeptide enrichment combined with a nanoUPLC-ESI-MS/MS strategy, we identified six phosphorylation sites on eight P-proteins from Populus dormant terminal buds. Among these, six Ser sites and one Thr site were identified in the highly conserved C-terminal region of eight P-proteins of various P-protein subfamilies, including two P0, two P1, three P2 and one P3 protein. Among these, the Thr site was shown to be novel and has not been identified in any other organisms. Sequence analysis indicated that the phosphothreonine sites identified in the C-terminus of Ptr RPP2A exclusively occurred in woody species of Populus, etc. The identified phosphopeptides shared a common phosphorylation motif of (S/T)XX(D/E) and may be phosphorylated in vivo by casein kinase 2 as suggested by using Scansite analysis. Furthermore, phylogenetic analysis suggested that divergence of P2 also occurred in Populus, including type I and type II. To the best of our knowledge, this is the first systematic phosphoproteomic and phylogenetic analysis of P-proteins in woody plants, the results of which will provide a wealth of resources for future understanding and unraveling of the regulatory mechanisms of Populus P-protein phosphorylation during the maintenance of dormancy.
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Affiliation(s)
- Chang-Cai Liu
- Education Ministry Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Northeast Forestry University, 26 Hexing Road, 150040 Harbin, People's Republic of China
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