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Sun J, Li X, Qu Z, Wang H, Cheng Y, Dong S, Zhao H. Comparative proteomic analysis reveals novel insights into the continuous cropping induced response in Scrophularia ningpoensis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1832-1845. [PMID: 36271763 DOI: 10.1002/jsfa.12284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/23/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Scrophularia ningpoensis is a well-known medicinal crop. Continuous cropping seriously affects the yield and quality, but little is known about the influence of continuous cropping on metabolic pathways. In this study, the difference in protein abundance between continuous cropping and non-continuous cropping of S. ningpoensis roots was studied by proteomics, and the molecular mechanism that protects S. ningpoensis against continuous cropping was explored. RESULTS The results suggested that continuous cropping in S, ningpoensis altered the expression of proteins related to starch and sucrose metabolism, glycolysis/gluconeogenesis, pentose phosphate pathway, citric acid cycle, phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, monoterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and steroid biosynthesis. Among these processes, the most affected were phenylpropanoid biosynthesis and starch and sucrose metabolism, which may be important for continuous cropping resistance. CONCLUSION The effect of continuous cropping on S. ningpoensis was demonstrated at the proteome level in this work, and identified candidate proteins that may cause continuous cropping reactions. The paper provides the theoretical foundation and scientific reference for enhancing the continuous cropping resistance of S. ningpoensis. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jiachen Sun
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Xuejiao Li
- Endocrine and Metabolic Disease Center, Medical Key Laboratory of Hereditary Rare Diseases of Henan, Luoyang Sub-Center of National Clinical Research Center for Metabolic Diseases, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Zhuo Qu
- School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Huairui Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yao Cheng
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Shengjie Dong
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Faculty of Education and Sports, Guangdong Baiyun University, Guangzhou, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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3
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Identification of allergen encoding sequences in a novel food ingredient from Moringa oleifera leaves. Food Chem 2023; 401:134185. [DOI: 10.1016/j.foodchem.2022.134185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/12/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022]
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4
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Licaj I, Di Meo MC, Fiorillo A, Samperna S, Marra M, Rocco M. Comparative Analysis of the Response to Polyethylene Glycol-Simulated Drought Stress in Roots from Seedlings of "Modern" and "Ancient" Wheat Varieties. PLANTS (BASEL, SWITZERLAND) 2023; 12:428. [PMID: 36771510 PMCID: PMC9921267 DOI: 10.3390/plants12030428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Durum wheat is widely cultivated in the Mediterranean, where it is the basis for the production of high added-value food derivatives such as pasta. In the next few years, the detrimental effects of global climate change will represent a serious challenge to crop yields. For durum wheat, the threat of climate change is worsened by the fact that cultivation relies on a few genetically uniform, elite varieties, better suited to intensive cultivation than "traditional" ones but less resistant to environmental stress. Hence, the renewed interest in "ancient" traditional varieties are expected to be more tolerant to environmental stress as a source of genetic resources to be exploited for the selection of useful agronomic traits such as drought tolerance. The aim of this study was to perform a comparative analysis of the effect and response of roots from the seedlings of two durum wheat cultivars: Svevo, a widely cultivated elite variety, and Saragolla, a traditional variety appreciated for its organoleptic characteristics, to Polyethylene glycol-simulated drought stress. The effect of water stress on root growth was analyzed and related to biochemical data such as hydrogen peroxide production, electrolyte leakage, membrane lipid peroxidation, proline synthesis, as well as to molecular data such as qRT-PCR analysis of drought responsive genes and proteomic analysis of changes in the protein repertoire of roots from the two cultivars.
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Affiliation(s)
- Ilva Licaj
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Maria Chiara Di Meo
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Anna Fiorillo
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Simone Samperna
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Mauro Marra
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
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5
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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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Xu J, Liu S, Cai L, Wang L, Dong Y, Qi Z, Yu J, Zhou Y. SPINDLY interacts with EIN2 to facilitate ethylene signalling-mediated fruit ripening in tomato. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:219-231. [PMID: 36204970 PMCID: PMC9829397 DOI: 10.1111/pbi.13939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The post-translational modification of proteins enables cells to respond promptly to dynamic stimuli by controlling protein functions. In higher plants, SPINDLY (SPY) and SECRET AGENT (SEC) are two prominent O-glycosylation enzymes that have both unique and overlapping roles; however, the effects of their O-glycosylation on fruit ripening and the underlying mechanisms remain largely unknown. Here we report that SlSPY affects tomato fruit ripening. Using slspy mutants and two SlSPY-OE lines, we provide biological evidence for the positive role of SlSPY in fruit ripening. We demonstrate that SlSPY regulates fruit ripening by changing the ethylene response in tomato. To further investigate the underlying mechanism, we identify a central regulator of ethylene signalling ETHYLENE INSENSITIVE 2 (EIN2) as a SlSPY interacting protein. SlSPY promotes the stability and nuclear accumulation of SlEIN2. Mass spectrometry analysis further identified that SlEIN2 has two potential sites Ser771 and Thr821 of O-glycans modifications. Further study shows that SlEIN2 is essential for SlSPY in regulating fruit ripening in tomatoes. Collectively, our findings reveal a novel regulatory function of SlSPY in fruit and provide novel insights into the role of the SlSPY-SlEIN2 module in tomato fruit ripening.
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Affiliation(s)
- Jin Xu
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
| | - Sidi Liu
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
| | - Licong Cai
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
| | - Lingyu Wang
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
| | - Yufei Dong
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
| | - Zhenyu Qi
- Agricultural Experiment StationZhejiang UniversityHangzhouChina
| | - Jingquan Yu
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plants Growth and DevelopmentAgricultural Ministry of ChinaHangzhouChina
| | - Yanhong Zhou
- Department of Horticulture, Zijingang CampusZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plants Growth and DevelopmentAgricultural Ministry of ChinaHangzhouChina
- Hainan Institute, Zhejiang UniversitySanyaChina
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7
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Sang K, Li J, Qian X, Yu J, Zhou Y, Xia X. The APETALA2a/DWARF/BRASSINAZOLE-RESISTANT 1 module contributes to carotenoid synthesis in tomato fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1238-1251. [PMID: 36271694 DOI: 10.1111/tpj.16009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Ethylene (ET) signaling plays a critical role in the ripening of climacteric fruits such as tomato. Brassinosteroids (BRs) were found to promote the ripening of both climacteric and non-climacteric fruits. However, the mechanism of interaction between ET and BRs during fruit ripening is unclear. Here, we found that BR synthesis and signaling increased after the onset of fruit ripening. Overexpression of the BR synthesis gene DWARF (DWF) promotedfruit softening, lycopene synthesis and ET production, whereas defect of DWF inhibited them. BRASSINAZOLE RESISTANT 1 (BZR1) as a key component of BR signaling, enhanced fruit lycopene content by directly activating the transcription of PSY1 gene. Interestingly, the increases in BR synthesis and BZR1 protein levels were dependent on ET signaling. Knocking out the ET-induced APETALA2a (AP2a) suppressed the expression of DWF and BR accumulation. Molecular assays demonstrated that AP2a was a positive regulator of DWF expression. Furthermore, 28-homobrassinolide, a bioactive BR, partially compensated the defects of lycopene accumulation and expression of PSY1 in ap2a mutant fruits. The results demonstrated that AP2a mediated ET signaling to regulate BR synthesis and signaling. BRs played critical roles in lycopene synthesis after onset of fruit ripening.
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Affiliation(s)
- Kangqi Sang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Junjie Li
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiangjie Qian
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Agricultural Ministry of China, Hangzhou, 310058, People's Republic of China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, 572025, People's Republic of China
| | - Xiaojian Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, 572025, People's Republic of China
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8
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González-Gordo S, Rodríguez-Ruiz M, Paradela A, Ramos-Fernández A, Corpas FJ, Palma JM. Mitochondrial protein expression during sweet pepper (Capsicum annuum L.) fruit ripening: iTRAQ-based proteomic analysis and role of cytochrome c oxidase. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153734. [PMID: 35667195 DOI: 10.1016/j.jplph.2022.153734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
The physiological process of fruit ripening is associated with the late developmental stages of plants in which mitochondrial organelles play an important role in the final success of this whole process. Thus, an isobaric tag for relative and absolute quantification (iTRAQ)-based analysis was used to quantify the mitochondrial proteome in pepper fruits in this study. Analysis of both green and red pepper fruits identified a total of 2284 proteins, of which 692 were found to be significantly more abundant in unripe green fruits as compared to red fruits, while 497 showed lower levels as the ripening process proceeded. Of the total number of proteins identified, 2253 (98,6%) were found to share orthologs with Arabidopsis thaliana. Proteomic analysis identified 163 proteins which were categorized as cell components, the major part assigned to cellular, intracellular space and other subcellular locations such as cytosol, plastids and, to a lesser extent, to mitochondria. Of the 224 mitochondrial proteins detected in pepper fruits, 78 and 48 were more abundant in green and red fruits, respectively. The majority of these proteins which displayed differential abundance in both fruit types were involved in the mitochondrial electron transport chain (mETC) and the tricarboxylic acid (TCA) cycle. The abundance levels of the proteins from both pathways were higher in green fruits, except for cytochrome c (CYC2), whose abundance was significantly higher in red fruits. We also investigated cytochrome c oxidase (COX) activity during pepper fruit ripening, as well as in the presence of molecules such as nitric oxide (NO) and hydrogen peroxide (H2O2), which promote thiol-based oxidative post-translational modifications (oxiPTMs). Thus, with the aid of in vitro assays, cytochrome c oxidase (COX) activity was found to be potentially inhibited by the PTMs nitration, S-nitrosation and carbonylation. According to protein abundance data, the final segment of the mETC appears to be a crucial locus with regard to fruit ripening, but also because in this location the biosynthesis of ascorbate, an antioxidant which plays a major role in the metabolism of pepper fruits, occurs.
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Affiliation(s)
- Salvador González-Gordo
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008, Granada, Spain
| | - Marta Rodríguez-Ruiz
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008, Granada, Spain
| | - Alberto Paradela
- Proteomics Core Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008, Granada, Spain
| | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008, Granada, Spain.
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9
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Choi HG, Park DY, Kang NJ. The Fruit Proteome Response to the Ripening Stages in Three Tomato Genotypes. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040553. [PMID: 35214885 PMCID: PMC8877657 DOI: 10.3390/plants11040553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 05/21/2023]
Abstract
The tomato is a horticultural crop that appears in various colors as it ripens. Differences in the proteome expression abundance of a tomato depend on its genotype and ripening stage. Thus, this study aimed to confirm the differences in changes in the proteome according to four ripening stages (green, breaker, turning, and mature) of three tomato genotypes, i.e., yellow, black, and red tomatoes, using a gel-based proteomic technique. The number of protein spots shown as two-dimensional electrophoresis (2-DE) gels differed according to tomato genotype and ripening stage. A total of 286 variant proteins were determined using matrix-assisted laser desorption-time of flight (MALDI-TOF) mass spectrometry (MS) analysis, confirming 233 identified protein functions. In three tomato genotypes in each ripening stage, grouping according to the Munich Information Center for Protein Sequences (MIPS) functional categories confirmed the variant proteins involved in the following: energy processes (21%); metabolism (20%); protein fate (15%); protein synthesis (10%); a protein with a binding function or cofactor requirement (8%); cell rescue, defense, and virulence (8%); cellular transport, transport facilitation, and transport routes (6%); the biogenesis of cellular components (5%); cell cycle and DNA processing (2%); others (5%). Among the identified protein spots in the function category, two proteins related to metabolism, four related to energy, four related to protein synthesis, and two related to interaction with the cellular environment showed significantly different changes according to the fruit color by the ripening stage. This study reveals the physiological changes in different types of tomatoes according to their ripening stage and provides information on the proteome for further improvement.
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Affiliation(s)
- Hyo-Gil Choi
- Department of Horticulture, Kongju National University, Yesan 32439, Korea;
| | - Dong-Young Park
- Department of Horticulture, Gyeongsang National University, Jinju 52828, Korea;
| | - Nam-Jun Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
- Correspondence:
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10
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Lv J, Zheng T, Song Z, Pervaiz T, Dong T, Zhang Y, Jia H, Fang J. Strawberry Proteome Responses to Controlled Hot and Cold Stress Partly Mimic Post-harvest Storage Temperature Effects on Fruit Quality. Front Nutr 2022; 8:812666. [PMID: 35242791 PMCID: PMC8887963 DOI: 10.3389/fnut.2021.812666] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
To determine the effect of different temperature on strawberry after harvest, physiological indicator analysis and proteomics analysis were conducted on ripened strawberry (“Sweet Charlie”) fruit stored at 4, 23, and 37°C for 10 or 20 days. Results showed that 4°C maintained a better visual quality of strawberry, and the weight loss and firmness remained stable within 3 days. Low temperature negatively affected anthocyanin but positively affected soluble sugars. Though anthocyanin content was higher with increasing temperature, anthocyanin synthesis related proteins were downregulated. Higher indole-acetic acid (IAA) content in seeds and lower abscisic acid (ABA) content were found in berry at 4°C. Antioxidant related proteins were upregulated during storage, showing a significant up-regulation of peroxidase (POD) at 4°C, and ascorbate-glutathione (AsA-GSH) cycle related proteins and heat shock proteins (HSPs) at 37°C. In addition, overexpressed sugar phosphate/phosphate translocator, 1-aminocyclopropane-1-carboxylate oxidase, and aquaporin PIP2-2 had a positive effect in response to low temperature stress for containing higher protopectin content and POD activity.
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Affiliation(s)
- Jinhua Lv
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zenglu Song
- College of Electrical Engineering, Nanjing Vocational University of Industry Technology, Nanjing, China
| | - Tariq Pervaiz
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yanyi Zhang
- Agricultural College, Liaocheng University, Liaocheng, China
| | - Haifeng Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Haifeng Jia
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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11
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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Gallo V, Zappettini A, Villani M, Marmiroli N, Marmiroli M. Comparative Analysis of Proteins Regulated during Cadmium Sulfide Quantum Dots Response in Arabidopsis thaliana Wild Type and Tolerant Mutants. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:615. [PMID: 33804515 PMCID: PMC7998754 DOI: 10.3390/nano11030615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022]
Abstract
In previous work, two independent Arabidopsis thaliana Ac/Ds transposon insertional mutant lines, atnp01 and atnp02, were identified that showed a higher level of tolerance than the wild type (wt) line to cadmium sulfide quantum dots (CdS QDs). The tolerance response was characterized at physiological, genetic and transcriptomic levels. In this work, a comparative analysis was performed on protein extracts from plantlets of the two mutants and of wt, each treated with 80 mg L-1 CdS QDs. A comparative protein analysis was performed by 2D-PAGE, and proteins were characterized by MALDI-TOF/TOF mass spectrometry. Of 250 proteins identified from all three lines, 98 showed significant changes in relative abundance between control and CdS QD-treated plantlets. The wt, atnp01, and atnp02 control-treated pairs respectively showed 61, 31, and 31 proteins with differential expression. The two mutants had a different response to treatment in terms of type and quantity of up- and downregulated proteins. This difference became more striking when compared to wt. A network analysis of the proteins differentially expressed in atnp01 and atnp02 included several of those encoded by putative genes accommodating the transposons, which were responsible for regulation of some proteins identified in this study. These included nifu-like protein 3 (Nfu3), involved in chloroplast assembly, elongator complex 3 (Elo3), involved in transcriptional elongation, magnesium-chelate subunit-2 (Chli2), involved in chlorophyll biosynthesis, and protein phosphatase 2C (PP2C) which mediates abiotic stress response.
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Affiliation(s)
- Valentina Gallo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
| | - Andrea Zappettini
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Marco Villani
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
- The Italian National Interuniversity Consortium for Environmental Sciences (CINSA), 43123 Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
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Kok SY, Namasivayam P, Ee GCL, Ong-Abdullah M. Comparative proteomic analysis of oil palm (Elaeis guineensis Jacq.) during early fruit development. J Proteomics 2020; 232:104052. [PMID: 33262095 DOI: 10.1016/j.jprot.2020.104052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 01/04/2023]
Abstract
To gain insights on protein changes in fruit setting and growth in oil palm, a comparative proteomic approach was undertaken to study proteome changes during its early development. The variations in the proteome at five early developmental stages were investigated via a gel-based proteomic technique. A total of 129 variant proteins were determined using mass spectrometric analysis, resulting in 80 identifications. The majority of the identified protein species were classified as energy and metabolism, stress response/defence and cell structure during early oil palm development representing potential candidates for the control of final fruit size and composition. Seven prominent protein species were then characterised using real-time polymerase chain reaction to validate the mRNA expression against the protein abundant profiles. Transcript and protein profiles were parallel across the developmental stages, but divergent expression was observed in one protein spot, indicative of possible post-transcriptional events. Our results revealed protein changes in early oil palm fruit development provide valuable information in the understanding of fruit growth and metabolism during early stages that may contribute towards improving agronomic traits. BIOLOGICAL SIGNIFICANCE: Two-dimensional gel electrophoresis coupled with mass spectrometry approach was used in this study to identify differentially expressed proteins during early oil palm fruit development. A total of 80 protein spots with significant change in abundance were successfully identified and selected genes were analysed using real time PCR to validate their expression. The dynamic changes in oil palm fruit proteome during early development were mostly active in primary and energy metabolism, stress responses, cell structure and protein metabolism. This study reveals the physiological processes during early oil palm fruit development and provides a reference proteome for further improvements in fruit quality traits.
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Affiliation(s)
- Sau-Yee Kok
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia; Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Gwendoline Cheng-Lian Ee
- Department of Chemistry, Faculty of Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
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Meena RP, Vishwakarma H, Ghosh G, Gaikwad K, Chellapilla TS, Singh MP, Padaria JC. Novel ASR isolated from drought stress responsive SSH library in pearl millet confers multiple abiotic stress tolerance in PgASR3 transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:7-19. [PMID: 32891968 DOI: 10.1016/j.plaphy.2020.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 05/09/2023]
Abstract
A genomic resource of drought stress responsive genes/ESTs was generated using Suppression Subtractive Hybridization (SSH) approach in a drought stress tolerant Pennisetum glaucum genotype 841B. Fifty five days old plants were subjected to drought stress after withholding water for different time intervals (10 days, 15 days, 20 days and 25 days). A forward subtractive cDNA library was prepared from isolated RNA of leaf tissue. Differential gene expression under drought stress was validated for selected nine contigs by RT-qPCR. A transcript homologous to Setaria italica ASR3 upregulated under drought stress was isolated from genotype 841B and characterized. Heterologous expression of PgASR3 was validated in Arabidopsis and confirmed under multiple abiotic stress conditions. A total of four independent transgenic lines overexpressing gene PgASR3 were analyzed by Southern blot at T1 stage. For drought stress tolerance, three independent lines (T2 stage) were analyzed by biochemical and physiological assays at seedling stage. The growth rate (shoot and root length) of transgenic seedlings improved as compared to WT seedling under differenct abiotic stress conditions. The three transgenic lines were also validated for drought stress tolerance and RT-qPCR analysis, at maturity stage. Under drought stress conditions, the mature transgenic lines showed higher levels of RWC, chlorophyll and proline but lower levels of MDA as compared to WT plants. PgASR3 gene isolated and validated in this study can be utilized for developing abiotic stress tolerant crops.
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Affiliation(s)
| | | | - Gourab Ghosh
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Tara Satyavathi Chellapilla
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India; Division of Genetics, IARI, Pusa Campus, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, IARI Pusa Campus, New Delhi, India
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15
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Zhang Z, Xia B, Li Y, Lin Y, Xie J, Wu P, Lin L, Liao D. Comparative proteomic analysis of Prunella vulgaris L. spica ripening. J Proteomics 2020; 232:104028. [PMID: 33129985 DOI: 10.1016/j.jprot.2020.104028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
Prunella vulgaris L., better known as 'self-heal', has been extensively used in the traditional system of medicines. To reveal the regulatory mechanism of its development, TMT-based quantitative proteome analysis was performed in the Prunella vulgaris L. spica before and during ripening (Group A and Group B, respectively). This analysis resulted in the identification of 7655 proteins, of which 1910 showed differential abundance between the two groups. Pronounced changes in the proteomic profile included the following: 1) Stress-responsive proteins involved in protecting cells and promoting fruit ripening and seed development were highly abundant during ripening. 2) The degradation of chlorophyll, inhibition of chlorophyll biosynthesis and increased abundance of transketolase occurred simultaneously in the spica of Prunella vulgaris L., resulting in the spica changing color from green to brownish red. 3) The abundance of protein species related to phenylpropanoid biosynthesis mainly increased during ripening, while flavonoid and terpenoid backbone biosynthesis mostly occurred before ripening. SIGNIFICANCE: This study establishes a link between protein profiles and mature phenotypes, which will help to improve our understanding of the molecular mechanisms involved in the maturation of Prunella vulgaris L. at the proteome level and reveal the scientific connotation for the best time to harvest Prunella vulgaris L. This work provides a scientific basis for the production of high-quality medicinal Prunella vulgaris L., as well as a typical demonstration of molecular research used for the harvest period of traditional Chinese medicine. BIOLOGICAL SIGNIFICANCE: This work provided a comprehensive overview on the functional protein profile changes of Prunella vulgaris L. spica at different growing stages, as well as the scientific rationale of Prunella vulgaris L. harvested in summer after brownish red, thus laid an intriguing stepping stone for elucidating the molecular mechanisms of quality development.
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Affiliation(s)
- Zhimin Zhang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Bohou Xia
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Yamei Li
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Yan Lin
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Jingchen Xie
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Ping Wu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Limei Lin
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Duanfang Liao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China.
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Tartaglia M, Arena S, Scaloni A, Marra M, Rocco M. Biochar Administration to San Marzano Tomato Plants Cultivated Under Low-Input Farming Increases Growth, Fruit Yield, and Affects Gene Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1281. [PMID: 32973840 PMCID: PMC7481538 DOI: 10.3389/fpls.2020.01281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Biochar is a rich-carbon charcoal obtained by pyrolysis of biomasses, which was used since antiquity as soil amendant. Its storage in soils was demonstrated contributing to abate the effects of climate changes by sequestering carbon, also providing bioenergy, and improving soil characteristics and crop yields. Despite interest in this amendant, there is still poor information on its effects on soil fertility and plant growth. Considerable variation in the plant response has been reported, depending on biomass source, pyrolysis conditions, crop species, and cultivation practices. Due to these conflicting evidences, this work was aimed at studying the effects of biochar from pyrolyzed wood at 550°C, containing 81.1% carbon and 0.91% nitrogen, on growth and yield of tomato plants experiencing low-input farming conditions. San Marzano ecotype from Southern Italy was investigated, due to its renowned quality and adaptability to sustainable farming practices. Biochar administration improved vegetative growth and berry yield, while affecting gene expression and protein repertoire in berries. Different enzymes of carbon metabolism and photosynthesis were over-represented, whereas various stress-responsive and defense proteins were down-represented. Molecular results are here discussed in relation to estimated agronomic parameters to provide a rationale justifying the growth-promoting effect of this soil amendant.
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Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Mauro Marra
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, Benevento, Italy
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Lee MY, Seo HS, Singh D, Lee SJ, Lee CH. Unraveling dynamic metabolomes underlying different maturation stages of berries harvested from Panax ginseng. J Ginseng Res 2020; 44:413-423. [PMID: 32372863 PMCID: PMC7195594 DOI: 10.1016/j.jgr.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Ginseng berries (GBs) show temporal metabolic variations among different maturation stages, determining their organoleptic and functional properties. METHODS We analyzed metabolic variations concomitant to five different maturation stages of GBs including immature green (IG), mature green (MG), partially red (PR), fully red (FR), and overmature red (OR) using mass spectrometry (MS)-based metabolomic profiling and multivariate analyses. RESULTS The partial least squares discriminant analysis score plot based on gas chromatography-MS datasets highlighted metabolic disparity between preharvest (IG and MG) and harvest/postharvest (PR, FR, and OR) GB extracts along PLS1 (34.9%) with MG distinctly segregated across PLS2 (18.2%). Forty-three significantly discriminant primary metabolites were identified encompassing five developmental stages (variable importance in projection > 1.0, p < 0.05). Among them, most amino acids, organic acids, 5-C sugars, ethanolamines, purines, and palmitic acid were detected in preharvest GB extracts, whereas 6-C sugars, phenolic acid, and oleamide levels were distinctly higher during later maturation stages. Similarly, the partial least squares discriminant analysis based on liquid chromatography-MS datasets displayed preharvest and harvest/postharvest stages clustered across PLS1 (11.1 %); however, MG and PR were separated from IG, FR, and OR along PLS2 (5.6 %). Overall, 24 secondary metabolites were observed significantly discriminant (variable importance in projection > 1.0, p < 0.05), with most displaying higher relative abundance during preharvest stages excluding ginsenosides Rg1 and Re. Furthermore, we observed strong positive correlations between total flavonoid and phenolic metabolite contents in GB extracts and antioxidant activity. CONCLUSION Comprehending the dynamic metabolic variations associated with GB maturation stages rationalize their optimal harvest time per se the related agroeconomic traits.
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Affiliation(s)
- Mee Youn Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Han Sol Seo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | | | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
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Tang H, Zhang X, Gong B, Yan Y, Shi Q. Proteomics and metabolomics analysis of tomato fruit at different maturity stages and under salt treatment. Food Chem 2019; 311:126009. [PMID: 31887558 DOI: 10.1016/j.foodchem.2019.126009] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 11/25/2022]
Abstract
Proteomics and metabolomics were used to study the changes in proteins and metabolites in tomato fruits at different ripening stages and the effect of salt treatment on fruit quality. The results showed 2607 and 153 differentially expressed proteins in ripe fruits compared with mature green fruits and in NaCl-treated ripe fruits compared with control ripe fruits, respectively. KEGG analysis indicated that these proteins were mainly involved in photosynthesis, pentose and glucuronate interconversions in different ripening stages of fruits, and salt-induced proteins were involved in flavonoid biosynthesis and linoleic acid metabolism. A series of metabolites, including carbohydrates and amino acids showed significantly different accumulations between ripe and mature green fruits and between salt-treated and control fruits. Combined analysis explored glycine, L-alanine, D-xylose and sucrose and some proteins involved in multiple metabolic pathways under salt conditions. Their interactions might affect fruit development and fruit quality under salt treatment.
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Affiliation(s)
- Huimeng Tang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 2018, PR China
| | - Xu Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 2018, PR China
| | - Biao Gong
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 2018, PR China
| | - Yanyan Yan
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 2018, PR China
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 2018, PR China.
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Comparative Proteomic Analysis on Fruit Ripening Processes in Two Varieties of Tropical Mango (Mangifera indica). Protein J 2019; 38:704-715. [DOI: 10.1007/s10930-019-09868-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Li L, Wu Q, Wang Y, Aghdam MS, Ban Z, Zhang X, Lu H, Li D, Yan J, Limwachiranon J, Luo Z. Systematically quantitative proteomics and metabolite profiles offer insight into fruit ripening behavior in Fragaria × ananassa. RSC Adv 2019; 9:14093-14108. [PMID: 35519301 PMCID: PMC9064045 DOI: 10.1039/c9ra00549h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/28/2019] [Indexed: 11/21/2022] Open
Abstract
Profound metabolic and proteomic changes involved in the primary and the secondary metabolism are required for the ripeness of fleshy fruit such as strawberries (Fragaria × ananassa). Here we present the quantitative proteomic profiling in parallel with metabolic and transcriptional profiling at five developmental stages of strawberry fruit ripening, and correlations between changes in representative metabolites and the abundance of related proteins were analyzed. Hierarchical clustering analysis of the quantitative proteomic profiling identified 143 proteins in strawberry fruit across five developmental stages. Meanwhile, both protein abundance and gene expression spanned a wide range of roles, such as the primary and the secondary metabolism, defense system, and response to stress stimuli. The decreased abundance of proteins contributed to the carbohydrate metabolism and the up-regulated expression of secondary biosynthetic proteins was found to be positively correlated with the accumulation of primary and secondary metabolites during strawberry development. Moreover, with the same annotations and high homology, the gene function of key genes involved in primary and secondary metabolism (FaTPI, FaPAL, FaMDH and FaME) was confirmed in Nicotiana via the transient expression assay, which provides further evidence for the role of those genes in metabolism of strawberry fruit. The results of the present study may serve as an important resource for the functional analysis of the proteome and offer new perspectives on regulation of fruit quality. Proteome and metabolite profiles of fruit ripening behavior in Fragaria × ananassa Duch. ‘Benihoppe’.![]()
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Minas IS, Tanou G, Krokida A, Karagiannis E, Belghazi M, Vasilakakis M, Papadopoulou KK, Molassiotis A. Ozone-induced inhibition of kiwifruit ripening is amplified by 1-methylcyclopropene and reversed by exogenous ethylene. BMC PLANT BIOLOGY 2018; 18:358. [PMID: 30558543 PMCID: PMC6296049 DOI: 10.1186/s12870-018-1584-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/30/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Understanding the mechanisms involved in climacteric fruit ripening is key to improve fruit harvest quality and postharvest performance. Kiwifruit (Actinidia deliciosa cv. 'Hayward') ripening involves a series of metabolic changes regulated by ethylene. Although 1-methylcyclopropene (1-MCP, inhibitor of ethylene action) or ozone (O3) exposure suppresses ethylene-related kiwifruit ripening, how these molecules interact during ripening is unknown. RESULTS Harvested 'Hayward' kiwifruits were treated with 1-MCP and exposed to ethylene-free cold storage (0 °C, RH 95%) with ambient atmosphere (control) or atmosphere enriched with O3 (0.3 μL L- 1) for up to 6 months. Their subsequent ripening performance at 20 °C (90% RH) was characterized. Treatment with either 1-MCP or O3 inhibited endogenous ethylene biosynthesis and delayed fruit ripening at 20 °C. 1-MCP and O3 in combination severely inhibited kiwifruit ripening, significantly extending fruit storage potential. To characterize ethylene sensitivity of kiwifruit following 1-MCP and O3 treatments, fruit were exposed to exogenous ethylene (100 μL L- 1, 24 h) upon transfer to 20 °C following 4 and 6 months of cold storage. Exogenous ethylene treatment restored ethylene biosynthesis in fruit previously exposed in an O3-enriched atmosphere. Comparative proteomics analysis showed separate kiwifruit ripening responses, unraveled common 1-MCP- and O3-dependent metabolic pathways and identified specific proteins associated with these different ripening behaviors. Protein components that were differentially expressed following exogenous ethylene exposure after 1-MCP or O3 treatment were identified and their protein-protein interaction networks were determined. The expression of several kiwifruit ripening related genes, such as 1-aminocyclopropane-1-carboxylic acid oxidase (ACO1), ethylene receptor (ETR1), lipoxygenase (LOX1), geranylgeranyl diphosphate synthase (GGP1), and expansin (EXP2), was strongly affected by O3, 1-MCP, their combination, and exogenously applied ethylene. CONCLUSIONS Our findings suggest that the combination of 1-MCP and O3 functions as a robust repressive modulator of kiwifruit ripening and provide new insight into the metabolic events underlying ethylene-induced and ethylene-independent ripening outcomes.
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Affiliation(s)
- Ioannis S. Minas
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
- Department of Horticulture and Landscape Architecture, Colorado State University, 301 University Avenue, Fort Collins, CO 80523 USA
| | - Georgia Tanou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
- Institute of Soil and Water Resources, ELGO-DEMETER, 57001 Thessaloniki, Greece
| | - Afroditi Krokida
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maya Belghazi
- UMR 7286 - CRN2M, Centre d’ Analyses Protéomiques de Marseille (CAPM), CNRS, Aix-Marseille Université, Marseille, France
| | - Miltiadis Vasilakakis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Kalliope K. Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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Marmiroli M, Mussi F, Imperiale D, Marmiroli N. Target proteins reprogrammed by As and As + Si treatments in Solanum lycopersicum L. fruit. BMC PLANT BIOLOGY 2017; 17:210. [PMID: 29157202 PMCID: PMC5696772 DOI: 10.1186/s12870-017-1168-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/10/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arsenic is an important contaminant of many arable soils worldwide, while silicon, one of the most abundant elements in the earth's crust, interacts with As in the context of plant metabolism. As toxicity results largely from its stimulation of reactive oxygen species, and it is believed that Si can mitigate this process through reduction of the level of oxidative stress. Experiments targeting the proteomic impact of exposure to As and Si have to date largely focused on analyses of root, shoot and seed of a range of mainly non-solanaceous species, thus it remains unclear whether oxidative stress is the most important manifestation of As toxicity in Solanum lycopersicum fruit which during ripening go through drastic physiological and molecular readjustments. The role of Si also needs to be re-evaluated. RESULTS A comparison was drawn between the proteomic responses to As and As + Si treatments of the fruit of two tomato cultivars (cvs. Aragon and Gladis) known to contrast for their ability to take up these elements and to translocate them into fruits. Treatments were applied at the beginning of the red ripening stage, and the fruit proteomes were captured after a 14 day period of exposure. For each cultivar, a set of differentially abundant fruit proteins (from non-treated and treated plants) were isolated by 2DGE and identified using mass spectrometry. In the fruit of cv. Aragon, the As treatment reprogrammed proteins largely involved in transcription regulation (growth- regulating factor 9-like), and cell structure (actin-51), while in the cv. Gladis, the majority of differentially expressed proteins were associated with protein ubiquitination and proteolysis (E3 ubiquitin protein, and hormones (1-aminocyclopropane 1-carboxylase). CONCLUSIONS The present experiments were intended to establish whether Si supplementation can be used to reverse the proteomic disturbance induced by the As treatment; this reprogram was only partial and more effective in the fruit of cv. Gladis than in that of cv. Aragon. Proteins responsible for the protection of the fruits' quality in the face of As-induced stress were identified. Moreover, supplementation with Si seemed to limit to a degree the accumulation of As in the tomato fruit of cv. Aragon.
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Affiliation(s)
- Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Francesca Mussi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Davide Imperiale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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Salzano AM, Sobolev A, Carbone V, Petriccione M, Renzone G, Capitani D, Vitale M, Minasi P, Pasquariello MS, Novi G, Zambrano N, Scortichini M, Mannina L, Scaloni A. A proteometabolomic study of Actinidia deliciosa fruit development. J Proteomics 2017; 172:11-24. [PMID: 29133123 DOI: 10.1016/j.jprot.2017.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Anatoly Sobolev
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy
| | - Paola Minasi
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marco Scortichini
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy; Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy.
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - 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, 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
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Gao Z, Zhang C, Luo M, Wu Y, Duan S, Li J, Wang L, Song S, Xu W, Wang S, Zhang C, Ma C. Proteomic analysis of pear (Pyrus pyrifolia) ripening process provides new evidence for the sugar/acid metabolism difference between core and mesocarp. Proteomics 2017; 16:3025-3041. [PMID: 27688055 DOI: 10.1002/pmic.201600108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 08/22/2016] [Accepted: 09/28/2016] [Indexed: 01/27/2023]
Abstract
Pears are one of the most popular nutrient-rich fruits in the world. The pear core and mesocarp have significantly different metabolism, although they display similar profiles. Most strikingly, the core is more acidic in taste. Our results showed that there is more titrated acid but lower total soluble solids in the core compared to the mesocarp, and the content of citric acid was more than 17-fold higher in the core compared to the mesocarp at the ripening stage. Proteomics was used to investigate the difference between core and mesocarp tissues during "Cuiguan" pear ripening. Fifty-four different protein expression patterns were identified in the core and mesocarp. In general, common variably expressed proteins between the core and mesocarp were associated with important physiological processes, such as glycolysis, pyruvate metabolic processes, and oxidative stress. Further, protein level associated qRT-PCR verification revealed a higher abundance of fructose-bisphosphate aldolase and NADP-dependent malic enzymes, which may play a role in the low acid content in the mesocarp, whereas a higher abundance of disulfide isomerase-like 2-2 and calcium-dependent lipid-binding in the core may explain why it is less prone to accumulate sugar. The different levels of a few typical ROS scavenger enzymes suggested that oxidative stress is higher in the core than in the mesocarp. This study provides the first characterization of the pear core proteome and a description of its variation compared to the mesocarp during ripening.
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Affiliation(s)
- Zhen Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Chengjun Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Meng Luo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yusen Wu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shuyan Duan
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Jiefa Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P. R. China
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Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N, Chakraborty S. Proteometabolomic Study of Compatible Interaction in Tomato Fruit Challenged with Sclerotinia rolfsii Illustrates Novel Protein Network during Disease Progression. FRONTIERS IN PLANT SCIENCE 2016; 7:1034. [PMID: 27507973 PMCID: PMC4960257 DOI: 10.3389/fpls.2016.01034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/30/2016] [Indexed: 05/27/2023]
Abstract
Fruit is an assimilator of metabolites, nutrients, and signaling molecules, thus considered as potential target for pathogen attack. In response to patho-stress, such as fungal invasion, plants reorganize their proteome, and reconfigure their physiology in the infected organ. This remodeling is coordinated by a poorly understood signal transduction network, hormonal cascades, and metabolite reallocation. The aim of the study was to explore organ-based proteomic alterations in the susceptibility of heterotrophic fruit to necrotrophic fungal attack. We conducted time-series protein profiling of Sclerotinia rolfsii invaded tomato (Solanum lycopersicum) fruit. The differential display of proteome revealed 216 patho-stress responsive proteins (PSRPs) that change their abundance by more than 2.5-fold. Mass spectrometric analyses led to the identification of 56 PSRPs presumably involved in disease progression; regulating diverse functions viz. metabolism, signaling, redox homeostasis, transport, stress-response, protein folding, modification and degradation, development. Metabolome study indicated differential regulation of organic acid, amino acids, and carbohydrates paralleling with the proteomics analysis. Further, we interrogated the proteome data using network analysis that identified two significant functional protein hubs centered around malate dehydrogenase, T-complex protein 1 subunit gamma, and ATP synthase beta. This study reports, for the first-time, kinetically controlled patho-stress responsive protein network during post-harvest storage in a sink tissue, particularly fruit and constitute the basis toward understanding the onset and context of disease signaling and metabolic pathway alterations. The network representation may facilitate the prioritization of candidate proteins for quality improvement in storage organ.
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Muneer S, Ko CH, Wei H, Chen Y, Jeong BR. Physiological and Proteomic Investigations to Study the Response of Tomato Graft Unions under Temperature Stress. PLoS One 2016; 11:e0157439. [PMID: 27310261 PMCID: PMC4911148 DOI: 10.1371/journal.pone.0157439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/31/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Grafting is an established practice for asexual propagation in horticultural and agricultural crops. The study on graft unions has become of interest for horticulturists using proteomic and genomic techniques to observe transfer of genetic material and signal transduction pathways from root to shoot and shoot to root. Another reason to study the graft unions was potentially to observe resistance against abiotic stresses. Using physiological and proteomic analyses, we investigated graft unions (rootstock and scions) of tomato genotypes exposed to standard-normal (23/23 and 25/18°C day/night) and high-low temperatures (30/15°C day/night). RESULTS Graft unions had varied responses to the diverse temperatures. High-low temperature, but not standard-normal temperature, induced the production of reactive oxygen species (ROS) in the form of H2O2 and O2-1 in rootstock and scions. However, the expression of many cell protection molecules was also induced, including antioxidant enzymes and their immunoblots, which also show an increase in their activities such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). The graft interfaces thus actively defend against stress by modifying their physiological and proteomic responses to establish a new cellular homeostasis. As a result, many proteins for cellular defense were regulated in graft unions under diverse temperature, in addition to the regulation of photosynthetic proteins, ion binding/transport proteins, and protein synthesis. Moreover, biomass, hardness, and vascular transport activity were evaluated to investigate the basic connectivity between rootstock and scions. CONCLUSIONS Our study provides physiological evidence of the grafted plants' response to diverse temperature. Most notably, our study provides novel insight into the mechanisms used to adapt the diverse temperature in graft unions (rootstock/scion).
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Affiliation(s)
- Sowbiya Muneer
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Chung Ho Ko
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Hao Wei
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Yuze Chen
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Byoung Ryong Jeong
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660–701, Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju, 660–701, Korea
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George DS, Razali Z, Santhirasegaram V, Somasundram C. Effect of postharvest ultraviolet-C treatment on the proteome changes in fresh cut mango (Mangifera indica L. cv. Chokanan). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:2851-2860. [PMID: 26350493 DOI: 10.1002/jsfa.7454] [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: 07/22/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Postharvest treatments of fruits using techniques such as ultraviolet-C have been linked with maintenance of the fruit quality as well as shelf-life extension. However, the effects of this treatment on the quality of fruits on a proteomic level remain unclear. This study was conducted in order to understand the response of mango fruit to postharvest UV-C irradiation. RESULTS Approximately 380 reproducible spots were detected following two-dimensional gel electrophoresis. Through gel analysis, 24 spots were observed to be differentially expressed in UV-C treated fruits and 20 were successfully identified via LCMS/MS. Postharvest UV-C treatment resulted in degradative effects on these identified proteins of which 40% were related to stress response, 45% to energy and metabolism and 15% to ripening and senescence. In addition, quality and shelf-life analysis of control and irradiated mangoes was evaluated. UV-C was found to be successful in retention of quality and extension of shelf-life up to 15 days. Furthermore, UV-C was also successful in increasing antioxidants (total flavonoid, reducing power and ABTS scavenging activity) in mangoes. CONCLUSION This study provides an overview of the effects of UV-C treatment on the quality of mango on a proteomic level as well as the potential of this treatment in shelf-life extension of fresh-cut fruits. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Dominic Soloman George
- Institute of Biological Sciences & Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Zuliana Razali
- Institute of Biological Sciences & Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vicknesha Santhirasegaram
- Institute of Biological Sciences & Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Chandran Somasundram
- Institute of Biological Sciences & Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
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Li L, Li D, Luo Z, Huang X, Li X. Proteomic Response and Quality Maintenance in Postharvest Fruit of Strawberry (Fragaria × ananassa) to Exogenous Cytokinin. Sci Rep 2016; 6:27094. [PMID: 27250251 PMCID: PMC4890429 DOI: 10.1038/srep27094] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/10/2016] [Indexed: 01/08/2023] Open
Abstract
The limitations in current understanding of the molecular mechanisms underlying fruit response to the application of plant growth regulators have increasingly become major challenges in improvement of crop quality. This study aimed to evaluate the response of strawberry to the preharvest application of exogenous cytokinin known as forchlorfenuron (CPPU). Postharvest internal and physiological quality attributes were characterized following storage under different conditions. Hierarchical clustering analysis via a label-free proteomic quantitative approach identified a total of 124 proteins in strawberries across all treatments. The expression profiles of both proteins and genes spanned the ranged role of cytokinin involved in primary and secondary metabolism, stress response, and so on. Eighty-eight proteins and fifty-six proteins were significantly regulated immediately at harvest and after storage, respectively. In general, the glycolysis in strawberry was only regulated by CPPU before storage; in addition to the accelerated photosynthesis and acid metabolism, CPPU application maintained higher capacity of resistance in strawberry to stress stimuli after storage, in comparison to control. Nevertheless, the volatile biosynthesis in strawberry has been suppressed by exogenous CPPU. Novel cytokinin response proteins and processes were identified in addition to the main transcriptomic expression to gain insights into the phytohormone control of fruit postharvest quality.
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Affiliation(s)
- Li Li
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Dongdong Li
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xinhong Huang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xihong Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
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Li T, Zhang J, Zhu H, Qu H, You S, Duan X, Jiang Y. Proteomic Analysis of Differentially Expressed Proteins Involved in Peel Senescence in Harvested Mandarin Fruit. FRONTIERS IN PLANT SCIENCE 2016; 7:725. [PMID: 27303420 PMCID: PMC4885882 DOI: 10.3389/fpls.2016.00725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/11/2016] [Indexed: 05/15/2023]
Abstract
Mandarin (Citrus reticulata), a non-climacteric fruit, is an economically important fruit worldwide. The mechanism underlying senescence of non-climacteric fruit is poorly understood. In this study, a gel-based proteomic study followed by LC-ESI-MS/MS analysis was carried out to investigate the proteomic changes involved in peel senescence in harvested mandarin "Shatangju" fruit stored for 18 days. Over the course of the storage period, the fruit gradually senesced, accompanied by a decreased respiration rate and increased chlorophyll degradation and disruption of membrane integrity. Sixty-three proteins spots that showed significant differences in abundance were identified. The up-regulated proteins were mainly associated with cell wall degradation, lipid degradation, protein degradation, senescence-related transcription factors, and transcription-related proteins. In contrast, most proteins associated with ATP synthesis and scavenging of reactive oxygen species were significantly down-regulated during peel senescence. Three thioredoxin proteins and three Ca(2+) signaling-related proteins were significantly up-regulated during peel senescence. It is suggested that mandarin peel senescence is associated with energy supply efficiency, decreased antioxidant capability, and increased protein and lipid degradation. In addition, activation of Ca(2+) signaling and transcription factors might be involved in cell wall degradation and primary or secondary metabolism.
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Affiliation(s)
- Taotao Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Jingying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Hong Zhu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Hongxia Qu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Shulin You
- Zhangzhou Xiangcheng District Agricultural BureauFujian, China
| | - Xuewu Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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Quantitative proteomics and phosphoproteomics of sugar beet monosomic addition line M14 in response to salt stress. J Proteomics 2016; 143:286-297. [PMID: 27233743 DOI: 10.1016/j.jprot.2016.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 12/18/2022]
Abstract
UNLABELLED Salinity is a major abiotic stress affecting plant growth, development and agriculture productivity. Understanding the molecular mechanisms of salt stress tolerance will provide valuable information for effective crop engineering and breeding. Sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. and Beta corolliflora Zoss exhibits tolerance to salt stress. In this study, the changes in the M14 proteome and phosphoproteome induced by salt stress were analyzed. We report the characteristics of the M14 plants under 0, 200, and 400mM NaCl using label-free quantitative proteomics approaches. Protein samples were subjected to total proteome profiling using LC-MS/MS and phosphopeptide enrichment to identify phosphopeptides and phosphoproteins. A total of 2182 proteins were identified and 114 proteins showed differential levels under salt stress. Interestingly, 189 phosphoproteins exhibited significant changes at the phosphorylation level under salt stress. Several signaling components associated with salt stress were found, e.g. 14-3-3 and mitogen-activated protein kinases (MAPK). Fifteen differential phosphoproteins and proteins involved in signal transduction were tested at the transcriptional level. The results revealed the short-term salt responsive mechanisms of the special sugar beet M14 line using label-free quantitative phosphoproteomics. BIOLOGICAL SIGNIFICANCE Sugar beet monosomic addition line M14 is a special germplasm with salt stress tolerance. Analysis of the M14 proteome and phosphoproteome under salt stress has provided insight into specific response mechanisms underlying salt stress tolerance. Reversible protein phosphorylation regulates a wide range of cellular processes such as transmembrane signaling, intracellular amplification of signals, and cell-cycle control. This study has identified significantly changed proteins and phosphoproteins, and determined their potential relevance to salt stress response. The knowledge gained can be potentially applied to improving crop salt tolerance.
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Ma R, Sun L, Chen X, Mei B, Chang G, Wang M, Zhao D. Proteomic Analyses Provide Novel Insights into Plant Growth and Ginsenoside Biosynthesis in Forest Cultivated Panax ginseng (F. Ginseng). FRONTIERS IN PLANT SCIENCE 2016; 7:1. [PMID: 26858731 PMCID: PMC4726751 DOI: 10.3389/fpls.2016.00001] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/05/2016] [Indexed: 05/18/2023]
Abstract
F. Ginseng (Panax ginseng) is planted in the forest to enhance the natural ginseng resources, which have an immense medicinal and economic value. The morphology of the cultivated plants becomes similar to that of wild growing ginseng (W. Ginseng) over the years. So far, there have been no studies highlighting the physiological or functional changes in F. Ginseng and its wild counterparts. In the present study, we used proteomic technologies (2DE and iTRAQ) coupled to mass spectrometry to compare W. Ginseng and F. Ginseng at various growth stages. Hierarchical cluster analysis based on protein abundance revealed that the protein expression profile of 25-year-old F. Ginseng was more like W. Ginseng than less 20-year-old F. Ginseng. We identified 192 differentially expressed protein spots in F. Ginseng. These protein spots increased with increase in growth years of F. Ginseng and were associated with proteins involved in energy metabolism, ginsenosides biosynthesis, and stress response. The mRNA, physiological, and metabolic analysis showed that the external morphology, protein expression profile, and ginsenoside synthesis ability of the F. Ginseng increased just like that of W. Ginseng with the increase in age. Our study represents the first characterization of the proteome of F. Ginseng during development and provides new insights into the metabolism and accumulation of ginsenosides.
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Affiliation(s)
- Rui Ma
- Jilin Technology Innovation Center for Chinese Medicine Biotechnology, College of Chemistry and Biology, Beihua UniversityJilin, China
- Ginseng Research Center, Changchun University of Chinese MedicineChangchun, China
| | - Liwei Sun
- Jilin Technology Innovation Center for Chinese Medicine Biotechnology, College of Chemistry and Biology, Beihua UniversityJilin, China
- *Correspondence: Liwei Sun
| | - Xuenan Chen
- Ginseng Research Center, Changchun University of Chinese MedicineChangchun, China
- The first affiliated hospital to Changchun University of Chinese MedicineChangchun, China
| | - Bing Mei
- Ginseng Research Center, Changchun University of Chinese MedicineChangchun, China
| | - Guijuan Chang
- Ginseng Research Center, Changchun University of Chinese MedicineChangchun, China
| | - Manying Wang
- Jilin Technology Innovation Center for Chinese Medicine Biotechnology, College of Chemistry and Biology, Beihua UniversityJilin, China
| | - Daqing Zhao
- Ginseng Research Center, Changchun University of Chinese MedicineChangchun, China
- Daqing Zhao
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Chen YY, Zhang ZH, Zhong CY, Song XM, Lin QH, Huang CM, Huang RH, Chen W. Functional analysis of differentially expressed proteins in Chinese bayberry ( Myrica rubra Sieb. et Zucc.) fruits during ripening. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.
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Miguel A, de Vega-Bartol J, Marum L, Chaves I, Santo T, Leitão J, Varela MC, Miguel CM. Characterization of the cork oak transcriptome dynamics during acorn development. BMC PLANT BIOLOGY 2015; 15:158. [PMID: 26109289 PMCID: PMC4479327 DOI: 10.1186/s12870-015-0534-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/26/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. RESULTS A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. CONCLUSIONS To our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.
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Affiliation(s)
- Andreia Miguel
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José de Vega-Bartol
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Liliana Marum
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- KLÓN, Innovative Technologies from Cloning, Biocant Park, Núcleo 4, Lote 4A, 3060-197, Cantanhede, Portugal.
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tatiana Santo
- Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal.
| | - José Leitão
- Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal.
| | - Maria Carolina Varela
- INIAV- Instituto Nacional de Investigação Agrária e Veterinária, IP, Quinta do, Marquês, Oeiras, 2780-159, Portugal.
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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Lomaglio T, Rocco M, Trupiano D, De Zio E, Grosso A, Marra M, Delfine S, Chiatante D, Morabito D, Scippa GS. Effect of short-term cadmium stress on Populus nigra L. detached leaves. JOURNAL OF PLANT PHYSIOLOGY 2015; 182:40-8. [PMID: 26047071 DOI: 10.1016/j.jplph.2015.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 05/09/2023]
Abstract
Pollution by toxic metals, accumulating into soils as result of human activities, is a worldwide major concern in industrial countries. Plants exhibit different degrees of tolerance to heavy metals, as a consequence of their ability to exclude or accumulate them in particular tissues, organs or sub-cellular compartments. Molecular information about cellular processes affected by heavy metals is still largely incomplete. As a fast-growing, highly tolerant perennial plant species, poplar has become a model for environmental stress response investigations. To study the short-term effects of cadmium accumulation in leaves, we analyzed photosystem II (PSII) quantum yield, hydrogen peroxide (H2O2) generation, hormone levels variation, as well as proteome profile alteration of 50μM CdSO4 vacuum-infiltrated poplar (Populus nigra L.) detached leaves. Cadmium management brought about an early and sustained production of hydrogen peroxide, an increase of abscisic acid, ethylene and gibberellins content, as well as a decrease in cytokinins and auxin levels, whereas photosynthetic electron transport was unaffected. Proteomic analysis revealed that twenty-one proteins were differentially induced in cadmium-treated leaves. Identification of fifteen polypeptides allowed to ascertain that most of them were involved in stress response while the remaining ones were involved in photosynthetic carbon metabolism and energy production.
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Affiliation(s)
- Tonia Lomaglio
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche Italy
| | - Mariapina Rocco
- Dipartimento per la Biologia, Geologia e l'Ambiente, Università del Sannio, Benevento, Italy
| | - Dalila Trupiano
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche Italy
| | - Elena De Zio
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche Italy
| | - Alessandro Grosso
- Dipartimento di Biologia, Università di Roma Tor Vergata, Roma, Italy
| | - Mauro Marra
- Dipartimento di Biologia, Università di Roma Tor Vergata, Roma, Italy
| | - Sebastiano Delfine
- Dipartimento di Agricoltura, Ambientee Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Donato Chiatante
- Dipartimento di Biotecnologia e Scienze della Vita, Università dell' Insubria, Varese, Italy
| | - Domenico Morabito
- Université d'Orléans, INRA, LBLGC, EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures, Orléans, France
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Li X, Bi Y, Wang J, Dong B, Li H, Gong D, Zhao Y, Tang Y, Yu X, Shang Q. BTH treatment caused physiological, biochemical and proteomic changes of muskmelon (Cucumis melo L.) fruit during ripening. J Proteomics 2015; 120:179-93. [DOI: 10.1016/j.jprot.2015.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
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40
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Li L, Luo Z, Huang X, Zhang L, Zhao P, Ma H, Li X, Ban Z, Liu X. Label-free quantitative proteomics to investigate strawberry fruit proteome changes under controlled atmosphere and low temperature storage. J Proteomics 2015; 120:44-57. [PMID: 25753123 DOI: 10.1016/j.jprot.2015.02.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED To elucidate the mechanisms contributing to fruit responses to senescence and stressful environmental stimuli under low temperature (LT) and controlled atmosphere (CA) storage, a label-free quantitative proteomic investigation was conducted in strawberry (Fragaria ananassa, Duch. cv. 'Akihime'). Postharvest physiological quality traits including firmness, total soluble solids, total acidity, ascorbic acid and volatile production were characterized following storage under different conditions. The observed post-storage protein expression profiles may be associated with delayed senescence features in strawberry. A total of 454 proteins were identified in differentially treated strawberry fruits. Quantitative analysis, using normalized spectral counts, revealed 73 proteins common to all treatments, which formed three clusters in a hierarchical clustering analysis. The proteins spanned a range of functions in various metabolic pathways and networks involved in carbohydrate and energy metabolism, volatile biosynthesis, phenylpropanoid activity, stress response and protein synthesis, degradation and folding. After CA and LT storage, 16 (13) and 11 (17) proteins, respectively, were significantly increased (decreased) in abundance, while expression profile of 12 proteins was significantly changed by both CA and LT. To summarize, the differential variability of abundance in strawberry proteome, working in a cooperative manner, provided an overview of the biological processes that occurred during CA and LT storage. BIOLOGICAL SIGNIFICANCE Controlled atmosphere storage at an optimal temperature is regarded to be an effective postharvest technology to delay fruit senescence and maintain fruit quality during shelf life. Nonetheless, little information on fruit proteomic changes under controlled atmosphere and/or low temperature storage is available. The significance of this paper is that it is the first study employing a label-free approach in the investigation of strawberry fruit response to controlled atmosphere and cold storage. Changes in postharvest physiological quality traits including volatile production, firmness, ascorbic acid, soluble solids and total acidity were also characterized. Significant biological changes associated with senescence were revealed and differentially abundant proteins under various storage conditions were identified. Proteomic profiles were linked to physiological aspects of strawberry fruit senescence in order to provide new insights into possible regulation mechanisms. Findings from this study not only provide proteomic information on fruit regulation, but also pave the way for further quantitative studies at the transcriptomic and metabolomic levels.
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Affiliation(s)
- Li Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zisheng Luo
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Xinhong Huang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Lu Zhang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Pengyu Zhao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hongyuan Ma
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xihong Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Zhaojun Ban
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Cooperatives, Jinan, Shandong 250014, PR China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, PR China
| | - Xia Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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Lee JJ, Kim YH, Kwak YS, An JY, Kim PJ, Lee BH, Kumar V, Park KW, Chang ES, Jeong JC, Lee HS, Kwak SS. A comparative study of proteomic differences between pencil and storage roots of sweetpotato (Ipomoea batatas (L.) Lam.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 87:92-101. [PMID: 25562766 DOI: 10.1016/j.plaphy.2014.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 05/25/2023]
Abstract
Fibrous roots of sweetpotato (Ipomoea batatas (L.) Lam.) usually develop into both pencil and storage roots. To understand protein function in root development, a proteomic analysis was conducted on the pencil and storage roots of the light orange-fleshed sweetpotato cultivar, Yulmi. Two-dimensional gel electrophoresis showed that expression of 30 protein spots differed between pencil and storage roots: 15 proteins were up-regulated or expressed in pencil roots and 15 in storage roots. Differentially expressed proteins spots were investigated using matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 10 proteins from pencil roots were identified as binding protein isoform A, catechol oxidase, peroxidases, ascorbate peroxidase, endochitinase, flavanone 3-hydroxylase and unknown proteins. Of the proteins up-regulated in, or restricted to, storage roots, 13 proteins were identified as protein disulfide isomerase, anionic peroxidase, putative ripening protein, sporamin B, sporamin A and sporamin A precursor. An analysis of enzyme activity revealed that catechol oxidase and peroxidase as the first and last enzymes of the lignin biosynthesis pathway, and ascorbate peroxidase had higher activities in pencil than in storage roots. The total concentration of phenolic compounds was also far higher in pencil than in storage roots, and lignin accumulated only in pencil roots. These results provide important insight into sweetpotato proteomics, and imply that lignin biosynthesis and stress-related proteins are up-regulated or uniquely expressed in pencil roots. The results indicate that the reduction of carbon flow toward phenylpropanoid biosynthesis and its delivery to carbohydrate metabolism is a major event in storage root formation.
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Affiliation(s)
- Jeung Joo Lee
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, College of Education, IALS, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Youn-Sig Kwak
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jae Young An
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Pil Joo Kim
- Division of Applied Life Science (BK21 Program), IALS, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Byung Hyun Lee
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Kee Woong Park
- Department of Crop Science, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Eun Sil Chang
- Gyeongsangnam-do Agricultural Research & Extension Services, Jinju 660-985, Republic of Korea
| | - Jae Cheol Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea.
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Samperi R, Capriotti AL, Cavaliere C, Colapicchioni V, Chiozzi RZ, Laganà A. Food Proteins and Peptides. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00006-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Golan I, Dominguez PG, Konrad Z, Shkolnik-Inbar D, Carrari F, Bar-Zvi D. Tomato ABSCISIC ACID STRESS RIPENING (ASR) gene family revisited. PLoS One 2014; 9:e107117. [PMID: 25310287 PMCID: PMC4195575 DOI: 10.1371/journal.pone.0107117] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/12/2014] [Indexed: 01/10/2023] Open
Abstract
Tomato ABSCISIC ACID RIPENING 1 (ASR1) was the first cloned plant ASR gene. ASR orthologs were then cloned from a large number of monocot, dicot and gymnosperm plants, where they are mostly involved in response to abiotic (drought and salinity) stress and fruit ripening. The tomato genome encodes five ASR genes: ASR1, 2, 3 and 5 encode low-molecular-weight proteins (ca. 110 amino acid residues each), whereas ASR4 encodes a 297-residue polypeptide. Information on the expression of the tomato ASR gene family is scarce. We used quantitative RT-PCR to assay the expression of this gene family in plant development and in response to salt and osmotic stresses. ASR1 and ASR4 were the main expressed genes in all tested organs and conditions, whereas ASR2 and ASR3/5 expression was two to three orders of magnitude lower (with the exception of cotyledons). ASR1 is expressed in all plant tissues tested whereas ASR4 expression is limited to photosynthetic organs and stamens. Essentially, ASR1 accounted for most of ASR gene expression in roots, stems and fruits at all developmental stages, whereas ASR4 was the major gene expressed in cotyledons and young and fully developed leaves. Both ASR1 and ASR4 were expressed in flower organs, with ASR1 expression dominating in stamens and pistils, ASR4 in sepals and petals. Steady-state levels of ASR1 and ASR4 were upregulated in plant vegetative organs following exposure to salt stress, osmotic stress or the plant abiotic stress hormone abscisic acid (ABA). Tomato plants overexpressing ASR1 displayed enhanced survival rates under conditions of water stress, whereas ASR1-antisense plants displayed marginal hypersensitivity to water withholding.
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Affiliation(s)
- Ido Golan
- Department of Life Sciences and Doris and Bertie Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pia Guadalupe Dominguez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Zvia Konrad
- Department of Life Sciences and Doris and Bertie Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Doron Shkolnik-Inbar
- Department of Life Sciences and Doris and Bertie Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Dudy Bar-Zvi
- Department of Life Sciences and Doris and Bertie Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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Vitale A, Rocco M, Arena S, Giuffrida F, Cassaniti C, Scaloni A, Lomaglio T, Guarnaccia V, Polizzi G, Marra M, Leonardi C. Tomato susceptibility to Fusarium crown and root rot: effect of grafting combination and proteomic analysis of tolerance expression in the rootstock. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 83:207-216. [PMID: 25173633 DOI: 10.1016/j.plaphy.2014.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
Grafting can enhance the tolerance of vegetable crops to soilborne diseases. The aim of this study was to investigate whether different tomato scion-rootstock combinations may affect the plant susceptibility to Fusarium oxysporum f. sp. radicis-lycopersici (FORL), the causal agent of crown and root rot. A proteomic approach was used to investigate whenever the protein repertoire of the rootstock can be modified by FORL infection, in relation to cultivar susceptibility/tolerance to the disease. To this purpose, plants of tomato hybrids with different vigor, "Costoluto Genovese" (less vigorous) and "Kadima" (more vigorous), were grafted onto "Cuore di Bue" and "Natalia" hybrids, sensitive and tolerant versus FORL infections, respectively. Disease symptoms, plant biomasses, and protein expression patterns were evaluated 45 days after FORL inoculation. The extent of vascular discoloration caused by FORL in tomato plants grafted on "Natalia" rootstock (0.12-0.37 cm) was significantly lower than that of plants grafted on sensitive "Cuore di Bue" (1.75-6.50 cm). FORL symptoms significantly differed between "Costoluto Genovese" and "Kadima" scions only when grafted on sensitive rootstock. Shoot FW of non-inoculated "Kadima"/"Cuore di Bue" combination was 35% lower than "Kadima"/"Natalia", whereas no difference was manifested in inoculated plants. Shoot FW of inoculated "Costoluto Genovese"/"Cuore di Bue" combination was decreased of 39%, whereas that of "Costoluto Genovese"/"Natalia" of 11%, compared to control plants. Proteomic results showed a higher representation of proteins associated with pathogen infection in the tolerant rootstock, compared to the sensitive one, meaning a direct involvement of plant defence mechanisms in the tomato response to the pathogen challenge.
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Affiliation(s)
- Alessandro Vitale
- Department of Agri-food and Environmental Systems Management, University of Catania, Catania 95123, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
| | - Simona Arena
- Proteomics & Mass Spectrometry Laboratory, National Research Council, Naples 80147, Italy
| | - Francesco Giuffrida
- Department of Agricultural and Food Science, University of Catania, Catania 95123, Italy
| | - Carla Cassaniti
- Department of Agricultural and Food Science, University of Catania, Catania 95123, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, National Research Council, Naples 80147, Italy
| | - Tonia Lomaglio
- Department of Biosciences and Territory, University of Molise, Pesche, IS 86170, Italy
| | - Vladimiro Guarnaccia
- Department of Agri-food and Environmental Systems Management, University of Catania, Catania 95123, Italy
| | - Giancarlo Polizzi
- Department of Agri-food and Environmental Systems Management, University of Catania, Catania 95123, Italy
| | - Mauro Marra
- Department of Biology, University of Rome "Tor Vergata", Rome 00133, Italy.
| | - Cherubino Leonardi
- Department of Agricultural and Food Science, University of Catania, Catania 95123, Italy
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Liu X, Zhai R, Feng W, Zhang S, Wang Z, Qiu Z, Zhang J, Ma F, Xu L. Proteomic analysis of 'Zaosu' pear (Pyrus bretschneideri Rehd.) and its early-maturing bud sport. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:120-35. [PMID: 24908513 DOI: 10.1016/j.plantsci.2014.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/13/2014] [Accepted: 04/16/2014] [Indexed: 05/09/2023]
Abstract
Maturation of fruits involves a series of physiological, biochemical, and organoleptic changes that eventually make fleshy fruits attractive, palatable, and nutritional. In order to understand the mature mechanism of the early-maturing bud sport of 'Zaosu' pear, we analyzed the differences of proteome expression between the both pears in different mature stages by the methods of a combination of two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Seventy-five differential expressed protein spots (p<0.05) were obtained between 'Zaosu' pear and its early-maturing bud sport, but only sixty-eight were demonstratively identified in the database of NCBI and uniprot. The majority of proteins were linked to metabolism, energy, stress response/defense and cell structure. Additionally, our data confirmed an increase of proteins related to cell-wall modification, oxidative stress and pentose phosphate metabolism and a decrease of proteins related to photosynthesis and glycolysis during the development process of both pears, but all these proteins increased or decreased faster in the early-maturing bud sport. This comparative analysis between both pears showed that these proteins were closely associated with maturation and could provide more detailed characteristics of the maturation process of both pears.
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Affiliation(s)
- Xueting Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Wenting Feng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Shiwei Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Zhigang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Zonghao Qiu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Junke Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingfei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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Bastías A, Yañez M, Osorio S, Arbona V, Gómez-Cadenas A, Fernie AR, Casaretto JA. The transcription factor AREB1 regulates primary metabolic pathways in tomato fruits. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2351-63. [PMID: 24659489 PMCID: PMC4036503 DOI: 10.1093/jxb/eru114] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Tomato fruit development is regulated both by the action of plant hormones and by tight genetic control. Recent studies suggest that abscisic acid (ABA) signalling may affect different aspects of fruit maturation. Previously, it was shown that SlAREB1, an ABA-regulated transcription factor involved in stress-induced responses, is expressed in seeds and in fruit tissues in tomato. Here, the role of SlAREB1 in regulating the expression of genes relevant for primary metabolic pathways and affecting the metabolic profile of the fruit was investigated using transgenic tomato lines. Metabolite profiling using gas chromatography-time of flight mass spectrometry (GC-TOF-MS) and non-targeted liquid chromatography-mass spectrometry (LC-MS) was performed on pericarp tissue from fruits harvested at three stages of fruit development. Principal component analysis of the data could distinguish the metabolite profiles of non-transgenic fruits from those that overexpress and down-regulate SlAREB1. Overexpression of SlAREB1 resulted in increased content of organic acids, hexoses, hexose-phosphates, and amino acids in immature green, mature green, and red ripe fruits, and these modifications correlated with the up-regulation of enzyme-encoding genes involved in primary carbohydrate and amino acid metabolism. A non-targeted LC-MS analysis indicated that the composition of secondary metabolites is also affected in transgenic lines. In addition, gene expression data revealed that some genes associated with fruit ripening are also up-regulated in SlAREB1-overexpressing lines compared with wild-type and antisense lines. Taken together, the results suggest that SlAREB1 participates in the regulation of the metabolic programming that takes place during fruit ripening and that may explain part of the role of ABA in fruit development in tomato.
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Affiliation(s)
- Adriana Bastías
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Mónica Yañez
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Sonia Osorio
- Max-Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Campus Riu Sec, 12071 Castelló de la Plana, Spain
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Campus Riu Sec, 12071 Castelló de la Plana, Spain
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany
| | - José A Casaretto
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
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Zhao X, Han F, Shen S. Proteomics study of the effects of high pigment-1 on plastid differentiation during the ripening of tomato fruits. CHINESE SCIENCE BULLETIN-CHINESE 2014. [DOI: 10.1007/s11434-014-0141-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wu HX, Jia HM, Ma XW, Wang SB, Yao QS, Xu WT, Zhou YG, Gao ZS, Zhan RL. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits. J Proteomics 2014; 105:19-30. [PMID: 24704857 DOI: 10.1016/j.jprot.2014.03.030] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. BIOLOGICAL SIGNIFICANCE Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Hong-xia Wu
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Hui-min Jia
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Xiao-wei Ma
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Song-biao Wang
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Quan-sheng Yao
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Wen-tian Xu
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Yi-gang Zhou
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Zhong-shan Gao
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China.
| | - Ru-lin Zhan
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
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50
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Biais B, Bénard C, Beauvoit B, Colombié S, Prodhomme D, Ménard G, Bernillon S, Gehl B, Gautier H, Ballias P, Mazat JP, Sweetlove L, Génard M, Gibon Y. Remarkable reproducibility of enzyme activity profiles in tomato fruits grown under contrasting environments provides a roadmap for studies of fruit metabolism. PLANT PHYSIOLOGY 2014; 164:1204-21. [PMID: 24474652 PMCID: PMC3938614 DOI: 10.1104/pp.113.231241] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/28/2014] [Indexed: 05/18/2023]
Abstract
To assess the influence of the environment on fruit metabolism, tomato (Solanum lycopersicum 'Moneymaker') plants were grown under contrasting conditions (optimal for commercial, water limited, or shaded production) and locations. Samples were harvested at nine stages of development, and 36 enzyme activities of central metabolism were measured as well as protein, starch, and major metabolites, such as hexoses, sucrose, organic acids, and amino acids. The most remarkable result was the high reproducibility of enzyme activities throughout development, irrespective of conditions or location. Hierarchical clustering of enzyme activities also revealed tight relationships between metabolic pathways and phases of development. Thus, cell division was characterized by high activities of fructokinase, glucokinase, pyruvate kinase, and tricarboxylic acid cycle enzymes, indicating ATP production as a priority, whereas cell expansion was characterized by enzymes involved in the lower part of glycolysis, suggesting a metabolic reprogramming to anaplerosis. As expected, enzymes involved in the accumulation of sugars, citrate, and glutamate were strongly increased during ripening. However, a group of enzymes involved in ATP production, which is probably fueled by starch degradation, was also increased. Metabolites levels seemed more sensitive than enzymes to the environment, although such differences tended to decrease at ripening. The integration of enzyme and metabolite data obtained under contrasting growth conditions using principal component analysis suggests that, with the exceptions of alanine amino transferase and glutamate and malate dehydrogenase and malate, there are no links between single enzyme activities and metabolite time courses or levels.
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Affiliation(s)
- Benoît Biais
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Camille Bénard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Bertrand Beauvoit
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Sophie Colombié
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Duyên Prodhomme
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Guillaume Ménard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Stéphane Bernillon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Bernadette Gehl
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Hélène Gautier
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Patricia Ballias
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Jean-Pierre Mazat
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Lee Sweetlove
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
| | - Michel Génard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, F–33883 Villenave d’Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- University of Bordeaux, Département Sciences de la Vie et de la Santé, F–33076 Bordeaux cedex, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., J.-P.M., Y.G.)
- Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique—Bordeaux, F–33883 Villenave d'Ornon, France (B.Bi., C.B., B.Be., S.C., D.P., G.M., S.B., P.B., Y.G.)
- Institut National de la Recherche Agronomique, Unité de Recherche 1115 Plantes et Systèmes de culture Horticoles, F–84914 Avignon cedex 9, France (C.B., H.G., M.G.); and
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (B.G., L.S.)
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