1
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Suzuki Y, Ishiyama K, Yoon DK, Takegahara-Tamakawa Y, Kondo E, Suganami M, Wada S, Miyake C, Makino A. Suppression of chloroplast triose phosphate isomerase evokes inorganic phosphate-limited photosynthesis in rice. PLANT PHYSIOLOGY 2022; 188:1550-1562. [PMID: 34893891 PMCID: PMC8896644 DOI: 10.1093/plphys/kiab576] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/14/2021] [Indexed: 05/12/2023]
Abstract
The availability of inorganic phosphate (Pi) for ATP synthesis is thought to limit photosynthesis at elevated [CO2] when Pi regeneration via sucrose or starch synthesis is limited. We report here another mechanism for the occurrence of Pi-limited photosynthesis caused by insufficient capacity of chloroplast triose phosphate isomerase (cpTPI). In cpTPI-antisense transgenic rice (Oryza sativa) plants with 55%-86% reductions in cpTPI content, CO2 sensitivity of the rate of CO2 assimilation (A) decreased and even reversed at elevated [CO2]. The pool sizes of the Calvin-Benson cycle metabolites from pentose phosphates to 3-phosphoglycerate increased at elevated [CO2], whereas those of ATP decreased. These phenomena are similar to the typical symptoms of Pi-limited photosynthesis, suggesting sufficient capacity of cpTPI is necessary to prevent the occurrence of Pi-limited photosynthesis and that cpTPI content moderately affects photosynthetic capacity at elevated [CO2]. As there tended to be slight variations in the amounts of total leaf-N depending on the genotypes, relationships between A and the amounts of cpTPI were examined after these parameters were expressed per unit amount of total leaf-N (A/N and cpTPI/N, respectively). A/N at elevated [CO2] decreased linearly as cpTPI/N decreased before A/N sharply decreased, owing to further decreases in cpTPI/N. Within this linear range, decreases in cpTPI/N by 80% led to decreases up to 27% in A/N at elevated [CO2]. Thus, cpTPI function is crucial for photosynthesis at elevated [CO2].
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Affiliation(s)
- Yuji Suzuki
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
- Author for communication:
| | - Keiki Ishiyama
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Dong-Kyung Yoon
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | | | - Eri Kondo
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Mao Suganami
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Shinya Wada
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
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2
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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3
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Hu C, Rao J, Song Y, Chan SA, Tohge T, Cui B, Lin H, Fernie AR, Zhang D, Shi J. Dissection of flag leaf metabolic shifts and their relationship with those occurring simultaneously in developing seed by application of non-targeted metabolomics. PLoS One 2020; 15:e0227577. [PMID: 31978163 PMCID: PMC6980602 DOI: 10.1371/journal.pone.0227577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/20/2019] [Indexed: 11/24/2022] Open
Abstract
Rice flag leaves are major source organs providing more than half of the nutrition needed for rice seed development. The dynamic metabolic changes in rice flag leaves and the detailed metabolic relationship between source and sink organs in rice, however, remain largely unknown. In this study, the metabolic changes of flag leaves in two japonica and two indica rice cultivars were investigated using non-targeted metabolomics approach. Principal component analysis (PCA) revealed that flag leaf metabolomes varied significantly depending on both species and developmental stage. Only a few of the metabolites in flag leaves displayed the same change pattern across the four tested cultivars along the process of seed development. Further association analysis found that levels of 45 metabolites in seeds that are associated with human nutrition and health correlated significantly with their levels in flag leaves. Comparison of metabolomics of flag leaves and seeds revealed that some flavonoids were specific or much higher in flag leaves while some lipid metabolites such as phospholipids were much higher in seeds. This reflected not only the function of the tissue specific metabolism but also the different physiological properties and metabolic adaptive features of these two tissues.
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Affiliation(s)
- Chaoyang Hu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Rao
- Jiangxi Cancer Hospital, Nanchang, China
| | - Yue Song
- Agilent Technologies Incorporated Company, Shanghai, China
| | - Shen-An Chan
- Agilent Technologies Incorporated Company, Shanghai, China
| | - Takayuki Tohge
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Bo Cui
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Lin
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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4
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Zhang Z, Xu M, Guo Y. Ring/U-Box Protein AtUSR1 Functions in Promoting Leaf Senescence Through JA Signaling Pathway in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:608589. [PMID: 33391323 PMCID: PMC7772223 DOI: 10.3389/fpls.2020.608589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/17/2020] [Indexed: 05/10/2023]
Abstract
Leaf senescence is regulated by a large number of internal and environmental factors. Here, we report that AtUSR1 (U-box Senescence Related 1) which encodes a plant Ring/U-box protein, is involved in age-dependent and dark-induced leaf senescence in Arabidopsis. Expression of AtUSR1 gene in leaves was up-regulated in darkness and during aging. Plants of usr1, an AtUSR1 gene knock-down mutant, showed a significant delay in age-dependent and dark-induced leaf senescence and the delayed senescence phenotype was rescued when the AtUSR1 gene was transferred back to the mutant plants. Meanwhile, overexpression of AtUSR1 caused accelerated leaf senescence. Furthermore, the role of AtUSR1 in regulating leaf senescence is related to MYC2-mediuated jasmonic acid (JA) signaling pathway. MeJA treatments promoted the accumulation of AtUSR1 transcripts and this expression activation was dependent on the function of MYC2, a key transcription factor in JA signaling. Dual-luciferase assay results indicated that MYC2 promoted the expression of AtUSR1. Overexpression of AtUSR1 in myc2 mutant plants showed precocious senescence, while myc2 mutation alone caused a delay in leaf senescence, suggesting that AtUSR1 functions downstream to MYC2 in the JA signaling pathway in promoting leaf senescence.
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5
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Gao Z, Liu Q, Zhang Y, Fang H, Zhang Y, Sinumporn S, Abbas A, Ning Y, Wang GL, Cheng S, Cao L. A proteomic approach identifies novel proteins and metabolites for lesion mimic formation and disease resistance enhancement in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110182. [PMID: 31481196 DOI: 10.1016/j.plantsci.2019.110182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/05/2019] [Accepted: 06/29/2019] [Indexed: 06/10/2023]
Abstract
Lesion mimic mutants are ideal genetic materials to study programmed cell death and defense signaling in plants. However, the molecular basis of lesion mimic formation remains largely unknown. Here, we first used a proteomic approach to identify differentially expressed proteins during dynamic lesion mimic formation in the rice oscul3a mutant, then electron microscope observation and physiological assays were used to analyze the mutant. The oscul3a mutant had disrupted cell metabolism balance, and the identified differentially expressed proteins were mainly located in the chloroplast and cytoplasm, which caused enhanced lipid metabolism, but suppressed carbon/nitrogen metabolism with reduced growth and grain quality. The oscul3a mutant had higher salicylic acid (SA) concentration in leaves, and H2O2 was shown to accumulate late in the formation of lesions. The secondary metabolite coumarin induced reactive oxygen species (ROS) and had rice blast resistance activity. Moreover, the cell death initiated lesion mimic formation of oscul3a mutant was light-sensitive, which might be associated with metabolite biosynthesis and accumulation. This study sheds light on the metabolic transition associated with cell death and defense response, which is under tight regulation by OsCUL3a and metabolism-related proteins, and the newly identified chemicals in the secondary metabolic pathway can potentially be used to control disease in crop plants.
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Affiliation(s)
- Zhiqiang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Qunen Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Hong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Yue Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Sittipun Sinumporn
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Thung Kula Ronghai Roi Et Campus, Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.
| | - Adil Abbas
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Liyong Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
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6
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Barrera NF, Melgarejo LM, Cruz-Gallego M, Cortés LJ, Guzmán F, Calvo JC. Conformationally Restricted Peptides from Rice Proteins Elicit Antibodies That Recognize the Corresponding Native Protein in ELISA Assays. Molecules 2018; 23:molecules23092262. [PMID: 30189617 PMCID: PMC6225240 DOI: 10.3390/molecules23092262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 01/13/2023] Open
Abstract
The rice hoja blanca virus (RHBV), transmitted by the planthopper insect Tagosodes orizicolus, is a disease that attacks rice and generates significant production losses in Colombia. Fedearroz 2000 and Colombia I commercial rice varieties, which have different resistance levels to the disease, were selected in this study. To identify proteins associated to the insect and virus signaling, a comparative proteomics study was performed. By comparing proteomic profiles, between virus-infected and control group plants in two-dimensional electrophoresis, proteins exhibiting significant changes in abundance were found. In another test, peptide dendrimers containing sequences conformationally restricted to α-helix from four of those rice proteins were synthesized. In the experiment, sera from mice inoculated with peptide dendrimers could recognize the corresponding native protein in ELISA assays. Reported comparative proteomic results provide new insights into the molecular mechanisms of plant response to the RHBV and comprehensive tools for the analysis of new crop varieties. Besides, results from conformational peptide dendrimer approach are promising and show that it is feasible to detect proteins as markers, and may have biological applications by decreasing the susceptibility to proteolytic degradation.
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Affiliation(s)
- Nubia F Barrera
- Doctorado en Biotecnología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 224, Bogotá 110111, Colombia.
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
| | - Luz M Melgarejo
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 421, Bogotá 110111, Colombia.
| | - Maribel Cruz-Gallego
- Centro Internacional de Agricultura Tropical, CIAT, Fondo Latinoamericano para Arroz de Riego, FLAR, Palmira, Valle 763537, Colombia.
| | - Lina Jimena Cortés
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Fanny Guzmán
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Julio C Calvo
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
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7
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Velasco-Arroyo B, Diaz-Mendoza M, Gomez-Sanchez A, Moreno-Garcia B, Santamaria ME, Torija-Bonilla M, Hensel G, Kumlehn J, Martinez M, Diaz I. Silencing barley cystatins HvCPI-2 and HvCPI-4 specifically modifies leaf responses to drought stress. PLANT, CELL & ENVIRONMENT 2018; 41:1776-1790. [PMID: 29486055 DOI: 10.1111/pce.13178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/19/2018] [Accepted: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Protein breakdown and mobilization are some of the major metabolic features associated with abiotic stresses, essential for nutrient recycling and plant survival. Genetic manipulation of protease and/or protease inhibitors may contribute to modulate proteolytic processes and plant responses. The expression analysis of the whole cystatin family, inhibitors of C1A cysteine proteases, after water deprivation in barley leaves highlighted the involvement of Icy-2 and Icy-4 cystatin genes. Artificial microRNA lines independently silencing the two drought-induced cystatins were generated to assess their function in planta. Phenotype alterations at the final stages of the plant life cycle are represented by the stay-green phenotype of silenced cystatin 2 lines. Besides, the enhanced tolerance to drought and differential responses to water deprivation at the initial growing stages are observed. The mutual compensating expression of Icy-2 and Icy-4 genes in the silencing lines pointed to their cooperative role. Proteolytic patterns by silencing these cystatins were concomitant with modifications in the expression of potential target proteases, in particular, HvPap-1, HvPap-12, and HvPap-16 C1A proteases. Metabolomics analysis lines also revealed specific modifications in the accumulation of several metabolites. These findings support the use of plants with altered proteolytic regulation in crop improvement in the face of climate change.
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Affiliation(s)
- Blanca Velasco-Arroyo
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Mercedes Diaz-Mendoza
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Andrea Gomez-Sanchez
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Beatriz Moreno-Garcia
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Maria Estrella Santamaria
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Miguel Torija-Bonilla
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Goetz Hensel
- Leibniz Institut fur Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Jochen Kumlehn
- Leibniz Institut fur Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Manuel Martinez
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, 28223, Pozuelo de Alarcon, Madrid, Spain
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8
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Großkinsky DK, Syaifullah SJ, Roitsch T. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:825-844. [PMID: 29444308 DOI: 10.1093/jxb/erx333] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.
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Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Syahnada Jaya Syaifullah
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, v.v.i., Drásov, Czech Republic
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9
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Leng Y, Ye G, Zeng D. Genetic Dissection of Leaf Senescence in Rice. Int J Mol Sci 2017; 18:E2686. [PMID: 29232920 PMCID: PMC5751288 DOI: 10.3390/ijms18122686] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/04/2022] Open
Abstract
Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.
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Affiliation(s)
- Yujia Leng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Dali Zeng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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10
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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11
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Cheng J, Wang L, Zeng P, He Y, Zhou R, Zhang H, Wang Z. Identification of genes involved in rice seed priming in the early imbibition stage. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:61-69. [PMID: 26833720 DOI: 10.1111/plb.12438] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/29/2016] [Indexed: 05/23/2023]
Abstract
Phase II of seed imbibition is a critical process during seed priming. To identify genes involved in rice seed priming, the altered proteins between the dry and imbibed (24 h) seeds were compared using a two-dimensional gel electrophoresis system in this study. Ten significantly changed proteins (fold change ≥ twofold; P < 0.01) were successfully identified, which could be categorised as carbohydrate and protein biosynthesis and metabolism-related, signalling-related, storage and stress-related proteins. A meta-analysis indicated that the highest expression of the identified genes was at the milk and dough stages and in the endosperm tissue. Quantitative real-time PCR analysis showed that there was significant variation in gene expression (except FAD-dependent oxidoreductase) in embryos during seed priming (0-48 h). The expression of genes associated with stress appeared at the early imbibition stage, while those associated with carbohydrate metabolism, protein synthesis and signalling increased at the late imbibition stage. Three identified proteins (glucose-1-phosphate adenylyltransferase large subunit, aminotransferase and prolamin precursor) had similar transcript and protein expression patterns in embryos. Based on phenotype and gene expression, the optimal stop time for seed priming is 24 h, when these three genes have relatively low expression, followed by significant induction during imbibition in embryos. These three genes are ideal candidate biomarkers for rice seed priming.
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Affiliation(s)
- J Cheng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - L Wang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - P Zeng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Y He
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - R Zhou
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - H Zhang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Z Wang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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12
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Gupta R, Lee SJ, Min CW, Kim SW, Park KH, Bae DW, Lee BW, Agrawal GK, Rakwal R, Kim ST. Coupling of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deep into the leaf senescence proteome of Glycine max. J Proteomics 2016; 148:65-74. [PMID: 27474340 DOI: 10.1016/j.jprot.2016.07.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
UNLABELLED Leaf senescence is the last stage of leaf development that re-mobilizes nutrients from the source to sink. Here, we have utilized the soybean as a model system to unravel senescence-associated proteins (SAPs). A comparative proteomics approach was used at two contrasting stages of leaf development, namely mature (R3) and senescent (R7). Selection criteria for these two stages were the contrasting differences in their biochemical parameters - chlorophyll, carotenoids and malondialdehyde contents. Proteome analysis involved subjecting the total leaf proteins to 15% poly-ethylene glycol (PEG) pre-fractional method to enrich the low-abundance proteins (LAPs) and their analyses by gel-based 2-DE and 1-DE shotgun proteomics approaches. 2-DE profiling of PEG-supernatant and -pellet fractions detected 153 differential spots between R3 and R7 stages, of which 102 proteins were identified. In parallel, 1-DE shotgun proteomics approach identified 598 and 534 proteins in supernatant and pellet fractions of R3 and R7 stages, respectively. MapMan and Gene Ontology analyses showed increased abundance and/or specific accumulation of proteins related to jasmonic acid biosynthesis and defense, while proteins associated with photosynthesis and ROS-detoxification were decreased during leaf senescence. These findings and the generated datasets further our understanding on leaf senescence at protein level, providing a resource for the scientific community. BIOLOGICAL SIGNIFICANCE Leaf senescence is a major biological event in the life cycle of plants that leads to the recycling of nutrients. However, the molecular mechanisms underlying leaf senescence still remain poorly understood. Here, we used a combination of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deeper into the leaf senescence proteome using soybean leaf as a model experimental material. For the identification of low-abundance proteins, polyethylene glycol (PEG) fractionation was employed and both PEG-supernatant and -pellet fractions were utilized for 2-DE and shotgun proteomic analysis. A total of 1234 (102 from 2-DE and 1132 from 1-DE shotgun proteome analysis) proteins were identified which were functionally annotated using GO and MapMan bioinformatics tools. Our results also emphasize the role of jasmonic acid in soybean leaf senescence.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Su Ji Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - So Wun Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Ki-Hun Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Dong-Won Bae
- Center for Research Facilities, Gyeongsang National University, Jinju, Republic of Korea
| | - Byong Won Lee
- Department of Functional Crops, National Institute of Crop Science (NICS), Rural Development Administration (RDA), Miryang 627-803, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies (TIAS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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13
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Wei S, Wang X, Shi D, Li Y, Zhang J, Liu P, Zhao B, Dong S. The mechanisms of low nitrogen induced weakened photosynthesis in summer maize (Zea mays L.) under field conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:118-128. [PMID: 27101123 DOI: 10.1016/j.plaphy.2016.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 05/21/2023]
Abstract
Soil nitrogen (N) shortage is a problem which affects many developing nations. Crops grown with low soil N levels show a marked decrease in the rate of photosynthesis and this deficiency reduces crop yield significantly. Therefore, developing a better understanding of the mechanisms by which low N levels cause decreased photosynthesis is crucial for maize agriculture. To better understand this process, we assessed the responses of photosynthesis traits and enzymatic activities in the summer maize cultivar Denghai 618 under field conditions with and without the use of N fertilisers. We measured photosynthesis parameters, and compared proteome compositions to identify the mechanisms of physiological and biochemical adaptations to N deficiency in maize. We observed that parameters that indicated the rate of photosynthesis decreased significantly under N deficiency, and this response was associated with leaf senescence. Moreover, we identified 37 proteins involved in leaf photosynthesis, and found that N deficiency significantly affected light-dependent and light-independent reactions in maize leaf photosynthesis. Although further analysis is required to fully elucidate the roles of these proteins in the response to N deficiency, our study identified candidate proteins which may be involved in the regulatory mechanisms involved in reduced photosynthesis under low N conditions in maize.
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Affiliation(s)
- Shanshan Wei
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Xiangyu Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Deyang Shi
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Yanhong Li
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Peng Liu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Bin Zhao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Shuting Dong
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China.
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14
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Yamaoka C, Suzuki Y, Makino A. Differential Expression of Genes of the Calvin-Benson Cycle and its Related Genes During Leaf Development in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:115-124. [PMID: 26615032 DOI: 10.1093/pcp/pcv183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
To understand how the machinery for photosynthetic carbon assimilation is formed and maintained during leaf development, changes in the mRNA levels of the Calvin-Benson cycle enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase and two key enzymes for sucrose synthesis were determined in rice (Oryza sativa L.). According to the patterns of changes in the mRNA levels, these genes were categorized into three groups. Group 1 included most of the genes involved in the carboxylation and reduction phases of the Calvin-Benson cycle, as well as three genes in the regeneration phase. The mRNA levels increased and reached maxima during leaf expansion and then rapidly declined, although there were some variations in the residual mRNA levels in senescent leaves. Group 2 included a number of genes involved in the regeneration phase, one gene in the reduction phase of the Calvin-Benson cycle and one gene in sucrose synthesis. The mRNA levels increased and almost reached maxima before full expansion and then gradually declined. Group 3 included Rubisco activase, one gene involved in the regeneration phase and one gene in sucrose synthesis. The overall pattern was similar to that in group 2 genes except that the mRNA levels reached maxima after the stage of full expansion. Thus, genes of the Calvin-Benson cycle and its related genes were differentially expressed during leaf development in rice, suggesting that such differential gene expression is necessary for formation and maintenance of the machinery of photosynthetic carbon assimilation.
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Affiliation(s)
- Chihiro Yamaoka
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Yuji Suzuki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
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15
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Havé M, Leitao L, Bagard M, Castell JF, Repellin A. Protein carbonylation during natural leaf senescence in winter wheat, as probed by fluorescein-5-thiosemicarbazide. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:973-9. [PMID: 25683278 DOI: 10.1111/plb.12315] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/19/2015] [Indexed: 05/08/2023]
Abstract
Leaf senescence is characterised by a massive degradation of proteins in order to recycle nitrogen to other parts of the plant, such as younger leaves or developing grain/seed. Protein degradation during leaf senescence is a highly regulated process and it is suggested that proteins to be degraded are marked by an oxidative modification (carbonylation) that makes them more susceptible to proteolysis. However, there is as yet no evidence of an increase in protein carbonylation level during natural leaf senescence. The aim of our study was thus to monitor protein carbonylation level during the process of natural senescence in the flag leaf of field-grown winter wheat plants. For this purpose, we adapted a fluorescence-based method using fluorescein-5-thiosemicarbazide (FTC) as a probe for detecting protein carbonyl derivatives. As used for the first time on plant material, this method allowed the detection of both quantitative and qualitative modifications in protein carbonyl levels during the last stages of wheat flag leaf development. The method described herein represents a convenient, sensitive and reproducible alternative to the commonly used 2,4-dinitrophenylhydrazine (DNPH)-based method. In addition, our analysis revealed changes in protein carbonylation level during leaf development that were associated with qualitative changes in protein abundance and carbonylation profiles. In the senescing flag leaf, protein carbonylation increased concomitantly with a stimulation of endoproteolytic activity and a decrease in protein content, which supports the suggested relationship between protein oxidation and proteolysis during natural leaf senescence.
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Affiliation(s)
- M Havé
- UMR 1392 iEES Paris, équipe IPE, Université Paris Est-Créteil, Créteil, France
| | - L Leitao
- UMR 1392 iEES Paris, équipe IPE, Université Paris Est-Créteil, Créteil, France
| | - M Bagard
- UMR 1392 iEES Paris, équipe IPE, Université Paris Est-Créteil, Créteil, France
| | - J-F Castell
- UMR 1091 EGC, AgroParisTech, Thiverval-Grignon, France
| | - A Repellin
- UMR 1392 iEES Paris, équipe IPE, Université Paris Est-Créteil, Créteil, France
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16
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Ling Q, Jarvis P. Functions of plastid protein import and the ubiquitin-proteasome system in plastid development. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:939-48. [PMID: 25762164 DOI: 10.1016/j.bbabio.2015.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 02/05/2023]
Abstract
Plastids, such as chloroplasts, are widely distributed endosymbiotic organelles in plants and algae. Apart from their well-known functions in photosynthesis, they have roles in processes as diverse as signal sensing, fruit ripening, and seed development. As most plastid proteins are produced in the cytosol, plastids have developed dedicated translocon machineries for protein import, comprising the TOC (translocon at the outer envelope membrane of chloroplasts) and TIC (translocon at the inner envelope membrane of chloroplasts) complexes. Multiple lines of evidence reveal that protein import via the TOC complex is actively regulated, based on the specific interplay between distinct receptor isoforms and diverse client proteins. In this review, we summarize recent advances in our understanding of protein import regulation, particularly in relation to control by the ubiquitin-proteasome system (UPS), and how such regulation changes plastid development. The diversity of plastid import receptors (and of corresponding preprotein substrates) has a determining role in plastid differentiation and interconversion. The controllable turnover of TOC components by the UPS influences the developmental fate of plastids, which is fundamentally linked to plant development. Understanding the mechanisms by which plastid protein import is controlled is critical to the development of breakthrough approaches to increase the yield, quality and stress tolerance of important crop plants, which are highly dependent on plastid development. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Paul Jarvis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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17
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Hu J, Rampitsch C, Bykova NV. Advances in plant proteomics toward improvement of crop productivity and stress resistancex. FRONTIERS IN PLANT SCIENCE 2015; 6:209. [PMID: 25926838 PMCID: PMC4396383 DOI: 10.3389/fpls.2015.00209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/16/2015] [Indexed: 05/14/2023]
Abstract
Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.
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Affiliation(s)
- Junjie Hu
- Department of Biology, Memorial University of Newfoundland, St. John’sNL, Canada
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Christof Rampitsch
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Natalia V. Bykova
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
- *Correspondence: Natalia V. Bykova, Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
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18
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Zhang N, Chen F, Huo W, Cui D. Proteomic analysis of middle and late stages of bread wheat (Triticum aestivum L.) grain development. FRONTIERS IN PLANT SCIENCE 2015; 6:735. [PMID: 26442048 PMCID: PMC4569854 DOI: 10.3389/fpls.2015.00735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/29/2015] [Indexed: 05/20/2023]
Abstract
Proteomic approaches were applied in four grain developmental stages of the Chinese bread wheat Yunong 201 and its ethyl methanesulfonate (EMS) mutant line Yunong 3114. 2-DE and tandem MALDI-TOF/TOF-MS analyzed proteome characteristics during middle and late grain development of the Chinese bread wheat Yunong 201 and its EMS mutant line Yunong 3114 with larger grain sizes. We identified 130 differentially accumulated protein spots representing 88 unique proteins, and four main expression patterns displayed a dynamic description of middle and late grain formation. Those identified protein species participated in eight biochemical processes: stress/defense, carbohydrate metabolism, protein synthesis/assembly/degradation, storage proteins, energy production and transportation, photosynthesis, transcription/translation, signal transduction. Comparative proteomic characterization demonstrated 12 protein spots that co-accumulated in the two wheat cultivars with different expression patterns, and six cultivar-specific protein spots including serpin, small heat shock protein, β-amylase, α-amylase inhibitor, dimeric α-amylase inhibitor precursor, and cold regulated protein. These cultivar-specific protein spots possibly resulted in differential yield-related traits of the two wheat cultivars. Our results provide valuable information for dissection of molecular and genetics basis of yield-related traits in bread wheat and the proteomic characterization in this study could also provide insights in the biology of middle and late grain development.
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Affiliation(s)
| | - Feng Chen
- *Correspondence: Feng Chen, Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
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19
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Ma C, Zhou J, Chen G, Bian Y, Lv D, Li X, Wang Z, Yan Y. iTRAQ-based quantitative proteome and phosphoprotein characterization reveals the central metabolism changes involved in wheat grain development. BMC Genomics 2014; 15:1029. [PMID: 25427527 PMCID: PMC4301063 DOI: 10.1186/1471-2164-15-1029] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/10/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is an economically important grain crop. Two-dimensional gel-based approaches are limited by the low identification rate of proteins and lack of accurate protein quantitation. The recently developed isobaric tag for relative and absolute quantitation (iTRAQ) method allows sensitive and accurate protein quantification. Here, we performed the first iTRAQ-based quantitative proteome and phosphorylated proteins analyses during wheat grain development. RESULTS The proteome profiles and phosphoprotein characterization of the metabolic proteins during grain development of the elite Chinese bread wheat cultivar Yanyou 361 were studied using the iTRAQ-based quantitative proteome approach, TiO2 microcolumns, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Among 1,146 non-redundant proteins identified, 421 showed at least 2-fold differences in abundance, and they were identified as differentially expressed proteins (DEPs), including 256 upregulated and 165 downregulated proteins. Of the 421 DEPs, six protein expression patterns were identified, most of which were up, down, and up-down expression patterns. The 421 DEPs were classified into nine functional categories mainly involved in different metabolic processes and located in the membrane and cytoplasm. Hierarchical clustering analysis indicated that the DEPs involved in starch biosynthesis, storage proteins, and defense/stress-related proteins significantly accumulated at the late grain development stages, while those related to protein synthesis/assembly/degradation and photosynthesis showed an opposite expression model during grain development. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 12 representative genes encoding different metabolic proteins showed certain transcriptional and translational expression differences during grain development. Phosphorylated proteins analyses demonstrated that 23 DEPs such as AGPase, sucrose synthase, Hsp90, and serpins were phosphorylated in the developing grains and were mainly involved in starch biosynthesis and stress/defense. CONCLUSIONS Our results revealed a complex quantitative proteome and phosphorylation profile during wheat grain development. Numerous DEPs are involved in grain starch and protein syntheses as well as adverse defense, which set an important basis for wheat yield and quality. Particularly, some key DEPs involved in starch biosynthesis and stress/defense were phosphorylated, suggesting their roles in wheat grain development.
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Affiliation(s)
- Chaoying Ma
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Jianwen Zhou
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Guanxing Chen
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yanwei Bian
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Dongwen Lv
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Xiaohui Li
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Zhimin Wang
- />College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100094 China
| | - Yueming Yan
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
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20
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Dong M, Gu J, Zhang L, Chen P, Liu T, Deng J, Lu H, Han L, Zhao B. Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification. J Proteomics 2014; 109:382-99. [DOI: 10.1016/j.jprot.2014.07.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/27/2014] [Accepted: 07/04/2014] [Indexed: 01/30/2023]
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21
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Guo Y. Towards systems biological understanding of leaf senescence. PLANT MOLECULAR BIOLOGY 2013; 82:519-28. [PMID: 23065109 DOI: 10.1007/s11103-012-9974-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 09/20/2012] [Indexed: 05/22/2023]
Abstract
The application of systems biology approaches has greatly facilitated the process of deciphering the molecular mechanisms underlying leaf senescence. Analyses of the leaf senescence transcriptome have identified some of the major biochemical events during senescence including protein degradation and nutrient remobilization. Proteomic studies have confirmed these findings and have suggested up-regulated energy metabolism during leaf senescence which might be important for cell viability maintenance. As a critical part of systems biology, studies involving transcription regulation networking and senescence-inducing signaling have deepened our understanding on the molecular regulation of leaf senescence. The important next steps towards a systems biological understanding of leaf senescence will be discussed.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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22
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Misyura M, Colasanti J, Rothstein SJ. Physiological and genetic analysis of Arabidopsis thaliana anthocyanin biosynthesis mutants under chronic adverse environmental conditions. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:229-40. [PMID: 23162120 PMCID: PMC3528034 DOI: 10.1093/jxb/ers328] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Anthocyanin production is a characteristic response of flowering plants to unfavourable environmental conditions. The potential roles of flavonoids and anthocyanins in plant growth were investigated by growing Arabidopsis thaliana anthocyanin production mutants (transparent testa) under limiting nitrogen and high light conditions. Inability to produce kaempferol or subsequent intermediate compounds by some transparent testa lines was correlated with less biomass accumulation in mature plants compared with wild-type control plants under all growth conditions tested. However, under both limiting nitrogen and high light chronic stress conditions, mutant lines defective in later steps of the anthocyanin production pathway produced the same or more biomass than wild-type plants. No difference in senescence between transparent testa and wild-type plants was found using chlorophyll catabolism and SAG12 expression measurements, and no mutants were impaired in the ability to remobilize nutrients from the vegetative to reproductive tissues. Moreover, the absence of anthocyanin and/or upstream flavonoids does not affect the ability of plants to respond to limiting nitrogen by reducing photosynthetic capacity. These results support a role for kaempferol and quercetin accumulation in normal plant growth and development. Further, the absence of anthocyanins has no effect on plant growth under the chronic stress conditions tested.
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Affiliation(s)
- Maksym Misyura
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone rd. E, Guelph, ON N1G 2W1, Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone rd. E, Guelph, ON N1G 2W1, Canada
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone rd. E, Guelph, ON N1G 2W1, Canada
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23
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Albumin and globulin dynamics during grain development of elite Chinese wheat cultivar Xiaoyan 6. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2012.08.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012. [PMID: 22900893 DOI: 10.86/1471-2229-12-147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012; 12:147. [PMID: 22900893 PMCID: PMC3480910 DOI: 10.1186/1471-2229-12-147] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 08/16/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Dongwen Lv
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xing Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
| | | | - Pei Ge
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
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Zhang C, Yin Y, Zhang A, Lu Q, Wen X, Zhu Z, Zhang L, Lu C. Comparative proteomic study reveals dynamic proteome changes between superhybrid rice LYP9 and its parents at different developmental stages. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:387-98. [PMID: 22209166 DOI: 10.1016/j.jplph.2011.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/11/2011] [Accepted: 11/12/2011] [Indexed: 05/05/2023]
Abstract
Heterosis is a common phenomenon in which the hybrids exhibit superior agronomic performance than either inbred parental lines. Although hybrid rice is one of the most successful apotheoses in crops utilizing heterosis, the molecular mechanisms underlying rice heterosis remain elusive. To gain a better understanding of the molecular mechanisms of rice heterosis, comparative leaf proteomic analysis between a superhybrid rice LYP9 and its parental cultivars 9311 and PA64s at tillering, flowering and grain-filling stages were carried out. A total of 384 differentially expressed proteins (DP) were detected and 297 DP were identified, corresponding to 222 unique proteins. As DP were divided into those between the parents (DP(PP)) and between the hybrid and its parents (DP(HP)), the comparative results demonstrate that proteins in the categories of photosynthesis, glycolysis, and disease/defense were mainly enriched in DP. Moreover, the number of identified DP(HP) involved in photosynthesis, glycolysis, and disease/defense increased at flowering and grain-filling stages as compared to that at the tillering stage. Most of the up-regulated DP(HP) involved in the three categories showed greater expression in LYP9 at flowering and grain-filling stages than at the tillering stage. In addition, CO(2) assimilation rate and apparent quantum yield of photosynthesis also showed a greater increase in LYP9 at flowering and grain-filling stages than at the tillering stage. These results suggest that the proteins involved in photosynthesis, glycolysis, and disease/defense as well as their dynamic regulation at different developmental stages may be responsible for heterosis in rice.
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Affiliation(s)
- Chunyan Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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