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Long R, Li M, Zhang T, Kang J, Sun Y, Cong L, Gao Y, Liu F, Yang Q. Comparative Proteomic Analysis Reveals Differential Root Proteins in Medicago sativa and Medicago truncatula in Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:424. [PMID: 27066057 PMCID: PMC4814493 DOI: 10.3389/fpls.2016.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/18/2016] [Indexed: 05/20/2023]
Abstract
Salt stress is an important abiotic stress that causes decreased crop yields. Root growth and plant activities are affected by salt stress through the actions of specific genes that help roots adapt to adverse environmental conditions. For a more comprehensive understanding of proteins affected by salinity, we used two-dimensional gel electrophoresis and mass spectrometry to characterize the proteome-level changes associated with salt stress response in Medicago sativa cv. Zhongmu-1 and Medicago truncatula cv. Jemalong A17 roots. Our physiological and phenotypic observations indicated that Zhongmu-1 was more salt tolerant than Jemalong A17. We identified 93 and 30 proteins whose abundance was significantly affected by salt stress in Zhongmu-1 and Jemalong A17 roots, respectively. The tandem mass spectrometry analysis of the differentially accumulated proteins resulted in the identification of 60 and 26 proteins in Zhongmu-1 and Jemalong A17 roots, respectively. Function analyses indicated molecule binding and catalytic activity were the two primary functional categories. These proteins have known functions in various molecular processes, including defense against oxidative stress, metabolism, photosynthesis, protein synthesis and processing, and signal transduction. The transcript levels of four identified proteins were determined by quantitative reverse transcription polymerase chain reaction. Our results indicate that some of the identified proteins may play key roles in salt stress tolerance.
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Affiliation(s)
- Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
| | - Mingna Li
- Department of Grass and Forage Science, College of Animal Science and Technology, China Agricultural UniversityBeijing, China
| | - Tiejun Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yan Sun
- Department of Grass and Forage Science, College of Animal Science and Technology, China Agricultural UniversityBeijing, China
| | - Lili Cong
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yanli Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fengqi Liu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural SciencesHaerbin, China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Qingchuan Yang ;
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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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Karagiannis E, Tanou G, Samiotaki M, Michailidis M, Diamantidis G, Minas IS, Molassiotis A. Comparative Physiological and Proteomic Analysis Reveal Distinct Regulation of Peach Skin Quality Traits by Altitude. FRONTIERS IN PLANT SCIENCE 2016; 7:1689. [PMID: 27891143 PMCID: PMC5102882 DOI: 10.3389/fpls.2016.01689] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
The role of environment in fruit physiology has been established; however, knowledge regarding the effect of altitude in fruit quality traits is still lacking. Here, skin tissue quality characters were analyzed in peach fruit (cv. June Gold), harvested in 16 orchards located in low (71.5 m mean), or high (495 m mean) altitutes sites. Data indicated that soluble solids concentration and fruit firmness at commercial harvest stage were unaffected by alitute. Peach grown at high-altitude environment displayed higher levels of pigmentation and specific antioxidant-related activity in their skin at the commercial harvest stage. Skin extracts from distinct developmental stages and growing altitudes exhibited different antioxidant ability against DNA strand-scission. The effects of altitude on skin tissue were further studied using a proteomic approach. Protein expression analysis of the mature fruits depicted altered expression of 42 proteins that are mainly involved in the metabolic pathways of defense, primary metabolism, destination/storage and energy. The majority of these proteins were up-regulated at the low-altitude region. High-altitude environment increased the accumulation of several proteins, including chaperone ClpC, chaperone ClpB, pyruvate dehydrogenase E1, TCP domain class transcription factor, and lipoxygenase. We also discuss the altitude-affected protein variations, taking into account their potential role in peach ripening process. This study provides the first characterization of the peach skin proteome and helps to improve our understanding of peach's response to altitude.
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Affiliation(s)
- Evangelos Karagiannis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
| | - Georgia Tanou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
| | | | - Michail Michailidis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
| | - Grigorios Diamantidis
- Laboratory of Agricultural Chemistry, Department of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
| | - Ioannis S. Minas
- Department of Horticulture and Landscape Architecture, Colorado State UniversityFort Collins, CO, USA
- Western Colorado Research Center at Orchard Mesa, Colorado State UniversityGrand Junction, CO, USA
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
- *Correspondence: Athanassios Molassiotis
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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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Li JM, Huang XS, Li LT, Zheng DM, Xue C, Zhang SL, Wu J. Proteome analysis of pear reveals key genes associated with fruit development and quality. PLANTA 2015; 241:1363-1379. [PMID: 25682102 DOI: 10.1007/s00425-015-2263-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Comparative and association analyses of the proteome and transcriptome for pear fruit development were conducted for the first time in this study. Pear fruit development involves complex physiological and biochemical processes, but there is still little knowledge available at proteomic and transcriptomic levels, which would be helpful for understanding the molecular mechanisms of fruit development and quality in pear. In our study, three important stages, including early development (S4-22), middle development (S6-27), and near ripening (S8-30), were investigated in 'Dangshansuli' by isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology, identifying a total of 1,810 proteins during pear fruit development. The association analysis of proteins and transcript expression revealed 1,724, 1,722, and 1,718 associated proteins identified in stages S4-22, S6-27, and S8-30, respectively. A total of 237, 318, and 425 unique proteins were identified as differentially expressed during S4-22 vs S6-27, S6-27 vs S8-30, S4-22 vs S8-30, respectively, and the corresponding correlation coefficients of the overall differentially expressed proteins and transcripts data were 0.6336, 0.4113, and 0.7049. The phenylpropanoid biosynthesis pathway, which is related to lignin formation of pear fruit, was identified as a significantly enriched pathway during early stages of fruit development. Finally, a total of 35 important differentially expressed proteins related to fruit quality were identified, including three proteins related to sugar formation, seven proteins related to aroma synthesis, and sixteen proteins related to the formation of lignin. In addition, qRT-PCR verification provided further evidence to support differentially expressed gene selection. This study is the first to reveal protein and associated mRNA variations in pear during fruit development and quality conformation, and identify key genes and proteins helpful for future functional genomics studies, and provides gene resources for improvement of pear quality.
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Affiliation(s)
- Jia Ming Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
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Wang WQ, Song BY, Deng ZJ, Wang Y, Liu SJ, Møller IM, Song SQ. Proteomic analysis of lettuce seed germination and thermoinhibition by sampling of individual seeds at germination and removal of storage proteins by polyethylene glycol fractionation. PLANT PHYSIOLOGY 2015; 167:1332-50. [PMID: 25736209 PMCID: PMC4378177 DOI: 10.1104/pp.15.00045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/01/2015] [Indexed: 05/09/2023]
Abstract
Germination and thermoinhibition in lettuce (Lactuca sativa 'Jianyexianfeng No. 1') seeds were investigated by a proteomic comparison among dry seeds, germinated seeds at 15°C, at 15°C after imbibition at 25°C for 48 h, or at 25°C in KNO3 (all sampled individually at germination), and ungerminated seeds at 25°C, a thermoinhibitory temperature. Before two-dimensional gel electrophoresis analysis, storage proteins (greater than 50% of total extractable protein) were removed by polyethylene glycol precipitation, which significantly improved the detection of less abundant proteins on two-dimensional gels. A total of 108 protein spots were identified to change more than 2-fold (P<0.05) in abundance in at least one germination treatment. Nineteen proteins increasing and one protein decreasing in abundance during germination had higher abundance in germinated 15°C, 15°C after imbibition at 25°C for 48 h, and 25°C in KNO3 seeds than in ungerminated 25°C seeds. Gene expression of 12 of those proteins correlated well with the protein accumulation. Methionine metabolism, ethylene production, lipid mobilization, cell elongation, and detoxification of aldehydes were revealed to be potentially related to lettuce seed germination and thermoinhibition. Accumulation of three proteins and expression of five genes participating in the mevalonate (MVA) pathway of isoprenoid biosynthesis correlated positively with seed germinability. Inhibition of this pathway by lovastatin delayed seed germination and increased the sensitivity of germination to abscisic acid. MVA pathway-derived products, cytokinins, partially reversed the lovastatin inhibition of germination and released seed thermoinhibition at 25°C. We conclude that the MVA pathway for isoprenoid biosynthesis is involved in lettuce seed germination and thermoinhibition.
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Affiliation(s)
- Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Bin-Yan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Zhi-Jun Deng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Yue Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Ian Max Møller
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (W.-Q.W., B.-Y.S., Z.-J.D., Y.W., S.-J.L., S.-Q.S.);College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China (B.-Y.S.);College of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China (Z.-J.D.); andDepartment of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark (I.M.M.)
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Yin Y, Yang R, Gu Z. Organ-specific proteomic analysis of NaCl-stressed germinating soybeans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7233-44. [PMID: 24960070 DOI: 10.1021/jf500851r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A comparative proteomic approach was employed to explore proteome expression patterns in germinating soybeans under NaCl stress and NaCl-aminoguanidine treatment. The proteins were extracted from 4-day-old germinating soybean cotyledons and noncotyledons (hypocotyl and radicle) and were separated using two-dimensional polyacrylamide gel electrophoresis. A total of 63 and 72 differentially expressed proteins were confidently identified by MALDI-TOF/TOF in the noncotyledons and cotyledons, respectively. These identified proteins were divided into ten functional groups and most of them were predicted to be cytoplasmic proteins in noncotyledons. Moreover, γ-aminobutyric acid was accumulated while the major allergen (Bd 30K protein) was reduced in the germinating soybeans. The proteins involved in energy metabolism and in protein processing in endoplasmic reticulum were enriched under NaCl stress. Meanwhile, the negative effect of stress was aggravated once polyamine degradation was inhibited. Redistribution of storage proteins under stress indicated that storage proteins might not only function as seed storage reserves but also have additional roles in plant defense.
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Affiliation(s)
- Yongqi Yin
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
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58
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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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59
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Ahmed Nasef N, Mehta S, Ferguson LR. Dietary interactions with the bacterial sensing machinery in the intestine: the plant polyphenol case. Front Genet 2014; 5:64. [PMID: 24772116 PMCID: PMC3983525 DOI: 10.3389/fgene.2014.00064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/13/2014] [Indexed: 12/20/2022] Open
Abstract
There are millions of microbes that live in the human gut. These are important in digestion as well as defense. The host immune system needs to be able to distinguish between the harmless bacteria and pathogens. The initial interaction between bacteria and the host happen through the pattern recognition receptors (PRRs). As these receptors are in direct contact with the external environment, this makes them important candidates for regulation by dietary components and therefore potential targets for therapy. In this review, we introduce some of the main PRRs including a cellular process known as autophagy, and how they function. Additionally we review dietary phytochemicals from plants which are believed to be beneficial for humans. The purpose of this review was to give a better understanding of how these components work in order to create better awareness on how they could be explored in the future.
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Affiliation(s)
- Noha Ahmed Nasef
- Department of Nutrition, Faculty of Medical and Health Sciences, University of Auckland Auckland, New Zealand
| | - Sunali Mehta
- Department of Nutrition, Faculty of Medical and Health Sciences, University of Auckland Auckland, New Zealand
| | - Lynnette R Ferguson
- Department of Nutrition, Faculty of Medical and Health Sciences, University of Auckland Auckland, New Zealand
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Wu J, Xu Z, Zhang Y, Chai L, Yi H, Deng X. An integrative analysis of the transcriptome and proteome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1651-71. [PMID: 24600016 PMCID: PMC3967095 DOI: 10.1093/jxb/eru044] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit ripening is a complex, genetically programmed process that occurs in conjunction with the differentiation of chloroplasts into chromoplasts and involves changes to the organoleptic properties of the fruit. In this study, an integrative analysis of the transcriptome and proteome was performed to identify important regulators and pathways involved in fruit ripening in a spontaneous late-ripening mutant ('Fengwan' orange, Citrus sinensis L. Osbeck) and its wild type ('Fengjie 72-1'). At the transcript level, 628 genes showed a 2-fold or more expression difference between the mutant and wild type as detected by an RNA sequencing approach. At the protein level, 130 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. A comparison of the transcriptome and proteome data revealed some aspects of the regulation of metabolism during orange fruit ripening. First, a large number of differential genes were found to belong to the plant hormone pathways and cell-wall-related metabolism. Secondly, we noted a correlation between ripening-associated transcripts and sugar metabolites, which suggests the importance of these metabolic pathways during fruit ripening. Thirdly, a number of genes showed inconsistency between the transcript and protein level, which is indicative of post-transcriptional events. These results reveal multiple ripening-associated events during citrus ripening and provide new insights into the molecular mechanisms underlying citrus ripening regulatory networks.
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Affiliation(s)
- Juxun Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhilong Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yajian Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
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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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Hyun TK, Lee S, Rim Y, Kumar R, Han X, Lee SY, Lee CH, Kim JY. De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel). PLoS One 2014; 9:e88292. [PMID: 24505466 PMCID: PMC3914977 DOI: 10.1371/journal.pone.0088292] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022] Open
Abstract
The Korean black raspberry (Rubus coreanus Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of F3'H1, DFR4 and LDOX1 resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcMCHI2 (R. coreanus Miquel chalcone flavanone isomerase 2) gene to complement Arabidopsis transparent testa 5 mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.
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Affiliation(s)
- Tae Kyung Hyun
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Sarah Lee
- Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Yeonggil Rim
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Ritesh Kumar
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Xiao Han
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Choong Hwan Lee
- Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
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Perez-Fons L, Wells T, Corol DI, Ward JL, Gerrish C, Beale MH, Seymour GB, Bramley PM, Fraser PD. A genome-wide metabolomic resource for tomato fruit from Solanum pennellii. Sci Rep 2014; 4:3859. [PMID: 24457419 PMCID: PMC3900926 DOI: 10.1038/srep03859] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 01/02/2014] [Indexed: 12/25/2022] Open
Abstract
Tomato and its processed products are one of the most widely consumed fruits. Its domestication, however, has resulted in the loss of some 95% of the genetic and chemical diversity of wild relatives. In order to elucidate this diversity, exploit its potential for plant breeding, as well as understand its biological significance, analytical approaches have been developed, alongside the production of genetic crosses of wild relatives with commercial varieties. In this article, we describe a multi-platform metabolomic analysis, using NMR, mass spectrometry and HPLC, of introgression lines of Solanum pennellii with a domesticated line in order to analyse and quantify alleles (QTL) responsible for metabolic traits. We have identified QTL for health-related antioxidant carotenoids and tocopherols, as well as molecular signatures for some 2000 compounds. Correlation analyses have revealed intricate interactions in isoprenoid formation in the plastid that can be extrapolated to other crop plants.
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Affiliation(s)
- Laura Perez-Fons
- Centre for Systems and Synthetic Biology, School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey, TW20 OEX, UK
| | - Tom Wells
- Centre for Systems and Synthetic Biology, School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey, TW20 OEX, UK
| | - Delia I Corol
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Jane L Ward
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Christopher Gerrish
- Centre for Systems and Synthetic Biology, School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey, TW20 OEX, UK
| | - Michael H Beale
- National Centre for Plant and Microbial Metabolomics, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Graham B Seymour
- Plant and Crop Science Division, University of Nottingham, Loughborough, Leicestershire, LE12 5RD, UK
| | - Peter M Bramley
- Centre for Systems and Synthetic Biology, School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey, TW20 OEX, UK
| | - Paul D Fraser
- Centre for Systems and Synthetic Biology, School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey, TW20 OEX, UK
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64
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Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis. Nat Protoc 2014; 9:362-74. [PMID: 24434803 DOI: 10.1038/nprot.2014.022] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Crop plants contain large amounts of secondary compounds that interfere with protein extraction and gel-based proteomic analysis. Thus, a protein extraction protocol that can be easily applied to various crop materials with minimal optimization is essential. Here we describe a universal protocol for total protein extraction involving trichloroacetic acid (TCA)/acetone precipitation followed by SDS and phenol extraction. Through SDS extraction, the proteins precipitated by the TCA/acetone treatment can be fully resolubilized and then further purified by phenol extraction. This protocol combines TCA/acetone precipitation, which aggressively removes nonprotein compounds, and phenol extraction, which selectively dissolves proteins, resulting in effective purification of proteins from crop tissues. This protocol can also produce high-quality protein preparations from various recalcitrant tissues, and therefore it has a wide range of applications in crop proteomic analysis. Designed to run on a small scale, this protocol can be completed within 5 h.
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65
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Marondedze C, Gehring C, Thomas L. Dynamic changes in the date palm fruit proteome during development and ripening. HORTICULTURE RESEARCH 2014; 1:14039. [PMID: 26504545 PMCID: PMC4596323 DOI: 10.1038/hortres.2014.39] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/29/2014] [Accepted: 06/15/2014] [Indexed: 05/22/2023]
Abstract
Date palm (Phoenix dactylifera) is an economically important fruit tree in the Middle East and North Africa and is characterized by large cultivar diversity, making it a good model for studies on fruit development and other important traits. Here in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0.05). The identified proteins were classified into 14 functional categories. The categories with the most proteins were 'disease and defense' (16.5%) and 'metabolism' (15.4%). Twenty-nine proteins have not previously been identified in other fleshy fruits and 64 showed contrasting expression patterns in other fruits. Abundance of most proteins with a role in abiotic stress responses increased during ripening with the exception of heat shock proteins. Proteins with a role in anthocyanin biosynthesis, glycolysis, tricarboxylic acid cycle and cell wall degradation were upregulated particularly from the onset of ripening and during ripening. In contrast, expression of pentose phosphate- and photosynthesis-related proteins decreased during fruit maturation. Although date palm is considered a climacteric species, the analysis revealed downregulation of two enzymes involved in ethylene biosynthesis, suggesting an ethylene-independent ripening of 'Barhi' fruits. In summary, this proteomics study provides insights into physiological processes during date fruit development and ripening at the systems level and offers a reference proteome for the study of regulatory mechanisms that can inform molecular and biotechnological approaches to further improvements of horticultural traits including fruit quality and yield.
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Affiliation(s)
- Claudius Marondedze
- Biological and Environmental Sciences & Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Christoph Gehring
- Biological and Environmental Sciences & Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ludivine Thomas
- Bioscience and Bioengineering Core Facility, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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66
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Shi Y, Jiang L, Zhang L, Kang R, Yu Z. Dynamic changes in proteins during apple (Malus x domestica) fruit ripening and storage. HORTICULTURE RESEARCH 2014; 1:6. [PMID: 26504530 PMCID: PMC4591674 DOI: 10.1038/hortres.2014.6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 05/18/2023]
Abstract
A proteomic study, using two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight, was conducted in apple fruit (cv. 'Golden Delicious') starting at 10 days prior to harvest through 50 days in storage. Total protein was extracted using a phenol/sodium dodecyl sulfate protocol. More than 400 protein spots were detected in each gel and 55 differentially expressed proteins (p<0.05) were subjected to matrix-assisted laser desorption/ionization time-of-flight/time-of-flight analysis. Fifty-three of these proteins were finally identified using an apple expressed sequence tag database downloaded from Genome Database for Rosaceae and placed into six categories. The categories and the percentage of proteins placed in each category were stress response and defense (49.0%), energy and metabolism (34.0%), fruit ripening and senescence (5.6%), signal transduction (3.8%), cell structure (3.8%) and protein synthesis (3.8%). Proteins involved in several multiple metabolic pathways, including glycolysis, pentose-phosphate pathway, anti-oxidative systems, photosynthesis and cell wall synthesis, were downregulated, especially during the climacteric burst in respiration and during the senescent stages of fruit development. Proteins classified as allergens or involved in cell wall degradation were upregulated during the ripening process. Some protein spots exhibited a mixed pattern (increasing to maximal abundance followed by a decrease), such as 1-aminocyclopropane-1-carboxylate oxidase, L-ascorbate peroxidase and abscisic acid response proteins. The identification of differentially expressed proteins associated with physiological processes identified in the current study provides a baseline of information for understanding the metabolic processes and regulatory mechanisms that occur in climacteric apple fruit during ripening and senescence.
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Affiliation(s)
- Yun Shi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Zhang
- Suzhou Academy of Agriculture, Suzhou 215155, China
| | - Ruoyi Kang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhifang Yu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Manaa A, Faurobert M, Valot B, Bouchet JP, Grasselly D, Causse M, Ahmed HB. Effect of salinity and calcium on tomato fruit proteome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:338-52. [PMID: 23692365 DOI: 10.1089/omi.2012.0108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Salinity is a major abiotic stress that adversely affects plant growth and productivity. The physiology of the tomato in salty and nonsalty conditions has been extensively studied, providing an invaluable base to understand the responses of the plants to cultural practices. However few data are yet available at the proteomic level looking for the physiological basis of fruit development, under salt stress. Here, we report the effects of salinity and calcium on fruit proteome variations of two tomato genotypes (Cervil and Levovil). Tomato plants were irrigated with a control solution (3 dSm(-1)) or with saline solutions (Na or Ca+Na at 7.6 dSm(-1)). Tomato fruits were harvested at two ripening stages: green (14 days post-anthesis) and red ripe. Total proteins were extracted from pericarp tissue and separated by two-dimensional gel electrophoresis. Among the 600 protein spots reproducibly detected, 53 spots exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. Most of the identified proteins were involved in carbon and energy metabolism, salt stress, oxidative stress, and proteins associated with ripening process. Overall, there was a large variation on proteins abundance between the two genotypes that can be correlated to salt treatment or/and fruit ripening stage. The results showed a protective effect of calcium that limited the impact of salinization on metabolism, ripening process, and induced plant salt tolerance. Collectively, this work has improved our knowledge about salt and calcium effect on tomato fruit proteome.
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Affiliation(s)
- Arafet Manaa
- Unité d'Ecophysiologie et Nutrition des Plantes, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunisie.
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68
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Pascual L, Xu J, Biais B, Maucourt M, Ballias P, Bernillon S, Deborde C, Jacob D, Desgroux A, Faurobert M, Bouchet JP, Gibon Y, Moing A, Causse M. Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5737-52. [PMID: 24151307 PMCID: PMC3871826 DOI: 10.1093/jxb/ert349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Integrative systems biology proposes new approaches to decipher the variation of phenotypic traits. In an effort to link the genetic variation and the physiological and molecular bases of fruit composition, the proteome (424 protein spots), metabolome (26 compounds), enzymatic profile (26 enzymes), and phenotypes of eight tomato accessions, covering the genetic diversity of the species, and four of their F1 hybrids, were characterized at two fruit developmental stages (cell expansion and orange-red). The contents of metabolites varied among the genetic backgrounds, while enzyme profiles were less variable, particularly at the cell expansion stage. Frequent genotype by stage interactions suggested that the trends observed for one accession at a physiological level may change in another accession. In agreement with this, the inheritance modes varied between crosses and stages. Although additivity was predominant, 40% of the traits were non-additively inherited. Relationships among traits revealed associations between different levels of expression and provided information on several key proteins. Notably, the role of frucktokinase, invertase, and cysteine synthase in the variation of metabolites was highlighted. Several stress-related proteins also appeared related to fruit weight differences. These key proteins might be targets for improving metabolite contents of the fruit. This systems biology approach provides better understanding of networks controlling the genetic variation of tomato fruit composition. In addition, the wide data sets generated provide an ideal framework to develop innovative integrated hypothesis and will be highly valuable for the research community.
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Affiliation(s)
- Laura Pascual
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Jiaxin Xu
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
- Northwest A&F University, College of Horticulture, Yang Ling, Shaanxin 712100, PR China
| | - Benoît Biais
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Mickaël Maucourt
- Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | | | - Stéphane Bernillon
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Catherine Deborde
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Daniel Jacob
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Aurore Desgroux
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Mireille Faurobert
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Yves Gibon
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Annick Moing
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Mathilde Causse
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
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Sebastiana M, Figueiredo A, Monteiro F, Martins J, Franco C, Coelho AV, Vaz F, Simões T, Penque D, Pais MS, Ferreira S. A possible approach for gel-based proteomic studies in recalcitrant woody plants. SPRINGERPLUS 2013; 2:210. [PMID: 23724367 PMCID: PMC3663981 DOI: 10.1186/2193-1801-2-210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/04/2013] [Indexed: 12/26/2022]
Abstract
Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more efficient for woody recalcitrant plant gel-based proteomics. Grapevine leaves, pine needles and cork oak ectomycorrhizal roots were used to represent woody plant species and tissues. The phenol protocol produced higher quality 2-DE gels, with increased number of resolved spots, better spot focusing and representation of all molecular mass and isoelectric point ranges tested. In order to test the compatibility of the phenol extracted proteomes with protein identification several spots were excised from the phenol gels and analyzed by mass spectrometry (MALDI-TOF/TOF). Regardless the incomplete genome/protein databases for the plant species under analysis, 49 proteins were identified by Peptide Mass Fingerprint (PMF). Proteomic data have been deposited to the ProteomeXchange with identifier PXD000224. Our results demonstrate the complexity of protein extraction from woody plant tissues and the suitability of the phenol protocol for obtaining high quality protein extracts for efficient 2-DE separation and downstream applications such as protein identification by mass spectrometry.
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Affiliation(s)
- Mónica Sebastiana
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Andreia Figueiredo
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Filipa Monteiro
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Joana Martins
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Catarina Franco
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Ana Varela Coelho
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Fátima Vaz
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Tânia Simões
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Deborah Penque
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Maria Salomé Pais
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Sílvia Ferreira
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
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70
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Racchi ML. Antioxidant Defenses in Plants with Attention to Prunus and Citrus spp. Antioxidants (Basel) 2013; 2:340-69. [PMID: 26784469 PMCID: PMC4665512 DOI: 10.3390/antiox2040340] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/08/2013] [Accepted: 10/28/2013] [Indexed: 12/13/2022] Open
Abstract
This short review briefly introduces the formation of reactive oxygen species (ROS) as by-products of oxidation/reduction (redox) reactions, and the ways in which the antioxidant defense machinery is involved directly or indirectly in ROS scavenging. Major antioxidants, both enzymatic and non enzymatic, that protect higher plant cells from oxidative stress damage are described. Biochemical and molecular features of the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) are discussed because they play crucial roles in scavenging ROS in the different cell compartments and in response to stress conditions. Among the non enzymatic defenses, particular attention is paid to ascorbic acid, glutathione, flavonoids, carotenoids, and tocopherols. The operation of ROS scavenging systems during the seasonal cycle and specific developmental events, such as fruit ripening and senescence, are discussed in relation to the intense ROS formation during these processes that impact fruit quality. Particular attention is paid to Prunus and Citrus species because of the nutritional and antioxidant properties contained in these commonly consumed fruits.
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Affiliation(s)
- Milvia Luisa Racchi
- Department of Agri-Food Production and Environmental Sciences, Section of Agricultural Genetics-DISPAA, University of Florence, via Maragliano 77, Firenze 50144, Italy.
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71
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Aizat WM, Able JA, Stangoulis JCR, Able AJ. Proteomic analysis during capsicum ripening reveals differential expression of ACC oxidase isoform 4 and other candidates. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1115-1128. [PMID: 32481179 DOI: 10.1071/fp12330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/14/2013] [Indexed: 06/11/2023]
Abstract
Capsicum (Capsicum annuum L.) is categorised as a non-climacteric fruit that exhibits limited ethylene production during ripening and the molecular mechanisms associated with this process are poorly understood. A proteomic approach was used to identify the differentially expressed proteins during various ripening stages (Green (G), Breaker Red 1 (BR1) and Light Red (LR)) and the genes associated with their synthesis. From 2D gel electrophoresis (2DGE), seven protein spots were identified as selectively present either in G or BR1 and are involved in carbon metabolism, colour and fruit development, protein synthesis and chaperones or biosynthesis of amino acids and polyamines. One candidate of interest, 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) is known to be involved in ethylene biosynthesis and was only present in BR1 and is related to the tomato ACO isoform 4 (LeACO4) and hence named CaACO4. CaACO4 RNA expression as well as total ACO protein expression in multiple stages of ripening (G, Breaker (B), BR1, Breaker Red 2 (BR2), LR and Deep Red (DR)) corresponded to the 2DGE protein spot abundance in breaker stages. Our findings highlight the involvement of the ethylene pathway in non-climacteric fruit ripening.
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Affiliation(s)
- Wan M Aizat
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
| | - James C R Stangoulis
- School of Biological Science, Flinders University, Bedford Park, SA 5042, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
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72
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Zhu W, Zhang E, Li H, Chen X, Zhu F, Hong Y, Liao B, Liu S, Liang X. Comparative proteomics analysis of developing peanut aerial and subterranean pods identifies pod swelling related proteins. J Proteomics 2013; 91:172-87. [DOI: 10.1016/j.jprot.2013.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/29/2013] [Accepted: 07/01/2013] [Indexed: 11/15/2022]
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73
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Alberton D, Müller-Santos M, Brusamarello-Santos LCC, Valdameri G, Cordeiro FA, Yates MG, de Oliveira Pedrosa F, de Souza EM. Comparative Proteomics Analysis of the Rice Roots Colonized by Herbaspirillum seropedicae Strain SmR1 Reveals Induction of the Methionine Recycling in the Plant Host. J Proteome Res 2013; 12:4757-68. [DOI: 10.1021/pr400425f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Dayane Alberton
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Marcelo Müller-Santos
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | | | - Glaucio Valdameri
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Fabio Aparecido Cordeiro
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Marshall Geoffrey Yates
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
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74
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Xu J, Pascual L, Aurand R, Bouchet JP, Valot B, Zivy M, Causse M, Faurobert M. An extensive proteome map of tomato (Solanum lycopersicum
) fruit pericarp. Proteomics 2013; 13:3059-63. [DOI: 10.1002/pmic.201200438] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 05/16/2013] [Accepted: 07/20/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Jiaxin Xu
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
- College of Horticulture; Northwest A&F University; Yang Ling P. R. China
| | - Laura Pascual
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
| | - Rémy Aurand
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
- INRA; UR1115 Plantes et Systèmes de Culture Horticoles; Avignon France
| | - Jean-Paul Bouchet
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
| | - Benoît Valot
- INRA/Université Paris-Sud/CNRS; Plateforme d'Analyse Protéomique de Paris Sud-Ouest; UMR 0320/UMR 8120 de Génétique Végétale Gif-sur-Yvette France
| | - Michel Zivy
- INRA/Université Paris-Sud/CNRS; Plateforme d'Analyse Protéomique de Paris Sud-Ouest; UMR 0320/UMR 8120 de Génétique Végétale Gif-sur-Yvette France
| | - Mathilde Causse
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
| | - Mireille Faurobert
- INRA, UR1052; Unité de Génétique et Amélioration des Fruits et Légumes; Montfavet France
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D'Amato A, Esteve C, Fasoli E, Citterio A, Righetti PG. Proteomic analysis ofLycium barbarum(Goji) fruit via combinatorial peptide ligand libraries. Electrophoresis 2013. [DOI: 10.1002/elps.201200643] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alfonsina D'Amato
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Clara Esteve
- Department of Analytical Chemistry; Faculty of Chemistry; University of Alcalá; Alcalá de Henares; Madrid; Spain
| | - Elisa Fasoli
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Attilio Citterio
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Pier Giorgio Righetti
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
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76
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Ruiz-May E, Rose JKC. Progress toward the tomato fruit cell wall proteome. FRONTIERS IN PLANT SCIENCE 2013; 4:159. [PMID: 23755055 PMCID: PMC3665905 DOI: 10.3389/fpls.2013.00159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 05/09/2013] [Indexed: 05/09/2023]
Abstract
The plant cell wall (CW) compartment, or apoplast, is host to a highly dynamic proteome, comprising large numbers of both enzymatic and structural proteins. This reflects its importance as the interface between adjacent cells and the external environment, the presence of numerous extracellular metabolic and signaling pathways, and the complex nature of wall structural assembly and remodeling during cell growth and differentiation. Tomato fruit ontogeny, with its distinct phases of rapid growth and ripening, provides a valuable experimental model system for CW proteomic studies, in that it involves substantial wall assembly, remodeling, and coordinated disassembly. Moreover, diverse populations of secreted proteins must be deployed to resist microbial infection and protect against abiotic stresses. Tomato fruits also provide substantial amounts of biological material, which is a significant advantage for many types of biochemical analyses, and facilitates the detection of lower abundance proteins. In this review, we describe a variety of orthogonal techniques that have been applied to identify CW localized proteins from tomato fruit, including approaches that: target the proteome of the CW and the overlying cuticle; functional "secretome" screens; lectin affinity chromatography; and computational analyses to predict proteins that enter the secretory pathway. Each has its merits and limitations, but collectively they are providing important insights into CW proteome composition and dynamics, as well as some potentially controversial issues, such as the prevalence of non-canonical protein secretion.
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77
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Expression of three β-type carbonic anhydrases in tomato fruits. Mol Biol Rep 2013; 40:4189-96. [DOI: 10.1007/s11033-013-2498-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
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78
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Pedreschi R, Lurie S, Hertog M, Nicolaï B, Mes J, Woltering E. Post-harvest proteomics and food security. Proteomics 2013; 13:1772-83. [PMID: 23483703 DOI: 10.1002/pmic.201200387] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 11/11/2012] [Indexed: 12/12/2022]
Abstract
To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.
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Affiliation(s)
- Romina Pedreschi
- Food & Biobased Research Centre, Wageningen University, Wageningen, The Netherlands.
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79
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Kilambi HV, Kumar R, Sharma R, Sreelakshmi Y. Chromoplast-specific carotenoid-associated protein appears to be important for enhanced accumulation of carotenoids in hp1 tomato fruits. PLANT PHYSIOLOGY 2013; 161:2085-101. [PMID: 23400702 PMCID: PMC3613478 DOI: 10.1104/pp.112.212191] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/09/2013] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) high-pigment mutants with lesions in diverse loci such as DNA Damage-Binding Protein1 (high pigment1 [hp1]), Deetiolated1 (hp2), Zeaxanthin Epoxidase (hp3), and Intense pigment (Ip; gene product unknown) exhibit increased accumulation of fruit carotenoids coupled with an increase in chloroplast number and size. However, little is known about the underlying mechanisms exaggerating the carotenoid accumulation and the chloroplast number in these mutants. A comparison of proteome profiles from the outer pericarp of hp1 mutant and wild-type (cv Ailsa Craig) fruits at different developmental stages revealed at least 72 differentially expressed proteins during ripening. Hierarchical clustering grouped these proteins into three clusters. We found an increased abundance of chromoplast-specific carotenoid-associated protein (CHRC) in hp1 fruits at red-ripe stage that is also reflected in its transcript level. Western blotting using CHRC polyclonal antibody from bell pepper (Capsicum annuum) revealed a 2-fold increase in the abundance of CHRC protein in the red-ripe stage of hp1 fruits compared with the wild type. CHRC levels in hp2 were found to be similar to that of hp1, whereas hp3 and Ip showed intermediate levels to those in hp1, hp2, and wild-type fruits. Both CHRC and carotenoids were present in the isolated plastoglobules. Overall, our results suggest that loss of function of DDB1, DET1, Zeaxanthin Epoxidase, and Ip up-regulates CHRC levels. Increase in CHRC levels may contribute to the enhanced carotenoid content in these high-pigment fruits by assisting in the sequestration and stabilization of carotenoids.
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Affiliation(s)
- Himabindu Vasuki Kilambi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Rakesh Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Rameshwar Sharma
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Yellamaraju Sreelakshmi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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80
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Konozy EHE, Rogniaux H, Causse M, Faurobert M. Proteomic analysis of tomato (Solanum lycopersicum) secretome. JOURNAL OF PLANT RESEARCH 2013; 126:251-266. [PMID: 22892874 DOI: 10.1007/s10265-012-0516-4 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/02/2012] [Indexed: 05/27/2023]
Abstract
In fleshy fruits, fruit texture features are mainly related to chemical and mechanical properties of the cell wall. The description of tomato fruit cell wall proteome is a first step in the process of linking tomato genetic variability to fruit texture phenotypes. In this study, the proteome of 3 ripe tomato fruit lines with contrasted texture traits were studied. Weakly bound and soluble proteins were extracted from cell wall of the three cultivars using both destructive and non-destructive methods, respectively. Wall proteins were separated on 1D-PAGE, bands were excised and identified by LC-MS/MS. The software SignalP which searches for the leader peptide was used to discriminate between protein with or without signal peptide. In combine, seventy-five different cell wall proteins were recorded for both weakly bound and soluble cell wall fractions. The major identified functions included several proteins acting on polysaccharides, proteins involved in "lipid metabolism", proteins having interacting domain, "oxido-reductases" and "proteases" whose putative roles in ripe fruit cell wall is discussed. Several proteins with no obvious signal peptide, however, with accumulating supportive evidences to be bona fide wall proteins, were also identified. Some variations in protein repertories were observed among the lines, demonstrating the possibility to characterize cell wall protein genetic variability by such in muro proteome analyses.
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Affiliation(s)
- Emadeldin H E Konozy
- Unité de Génétique et Amélioration des Fruits et Légumes, INRA, BP 94, 84143 Montfavet, France.
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81
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Konozy EHE, Rogniaux H, Causse M, Faurobert M. Proteomic analysis of tomato (Solanum lycopersicum) secretome. JOURNAL OF PLANT RESEARCH 2013; 126:251-66. [PMID: 22892874 DOI: 10.1007/s10265-012-0516-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/02/2012] [Indexed: 05/19/2023]
Abstract
In fleshy fruits, fruit texture features are mainly related to chemical and mechanical properties of the cell wall. The description of tomato fruit cell wall proteome is a first step in the process of linking tomato genetic variability to fruit texture phenotypes. In this study, the proteome of 3 ripe tomato fruit lines with contrasted texture traits were studied. Weakly bound and soluble proteins were extracted from cell wall of the three cultivars using both destructive and non-destructive methods, respectively. Wall proteins were separated on 1D-PAGE, bands were excised and identified by LC-MS/MS. The software SignalP which searches for the leader peptide was used to discriminate between protein with or without signal peptide. In combine, seventy-five different cell wall proteins were recorded for both weakly bound and soluble cell wall fractions. The major identified functions included several proteins acting on polysaccharides, proteins involved in "lipid metabolism", proteins having interacting domain, "oxido-reductases" and "proteases" whose putative roles in ripe fruit cell wall is discussed. Several proteins with no obvious signal peptide, however, with accumulating supportive evidences to be bona fide wall proteins, were also identified. Some variations in protein repertories were observed among the lines, demonstrating the possibility to characterize cell wall protein genetic variability by such in muro proteome analyses.
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Affiliation(s)
- Emadeldin H E Konozy
- Unité de Génétique et Amélioration des Fruits et Légumes, INRA, BP 94, 84143 Montfavet, France.
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Zheng Q, Song J, Campbell-Palmer L, Thompson K, Li L, Walker B, Cui Y, Li X. A proteomic investigation of apple fruit during ripening and in response to ethylene treatment. J Proteomics 2013; 93:276-94. [PMID: 23435059 DOI: 10.1016/j.jprot.2013.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 01/23/2023]
Abstract
UNLABELLED A proteomic approach employing a two dimensional electrophoresis (2-DE) technique with SYPRO Ruby, a fluorescent stain with improved sensitivity and quantitative accuracy, was performed to separate the total proteins from apple fruit at different stages of ripening and senescence. After imaging and statistical analyses were performed on 2340 spots, a total of 316 spots, or approximately 13.5% of the total protein population, was found to be significantly changed in this study. Of the 316 proteins, 219 spots were only present at a specific ripening stage, while 97 spots were significantly different (p<0.05) throughout fruit ripening and in response to ethylene treatment. From 316 candidate spots, 221 proteins were further identified by liquid chromatography and mass spectrometry analysis with protein sequence and express sequence tag (EST) data searching. Analysis and identification of proteins revealed that apple fruit ripening is associated with increase of abundance of many proteins with functions such as ethylene production, antioxidation and redox, carbohydrate metabolism, oxidative stress, energy, and defense response. Ethylene treatment increased a group of unique proteins that were not present during normal fruit ripening and have not been previously reported. It also reduced some proteins involved in primary metabolism, including those of the last few steps of the glycolytic pathway. This study demonstrated the complexity and dynamic changes of protein profiles of apple fruit during ripening and in response to exogenous ethylene treatment. Identifying and tracking protein changes may allow us to better understand the mechanism of ripening in climacteric fruit. BIOLOGICAL SIGNIFICANCE Postharvest physiology and biochemistry has been conducted on apple fruit for many years. Ethylene plays an important role in ripening and senescence in many climacteric fruit. However, little information is available at the proteome level to investigate fruit ripening and effect of ethylene treatment. The significance of this paper is that it is the first study employing 2-DE and fluorescent dye in the investigation of the apple fruit ripening and influence of ethylene treatment. It reveals some significant biological changes in association with these events and demonstrates significant changed proteins under these conditions. Therefore, our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. Through the function analysis, those significantly changed proteins are also analyzed. These findings from this paper provide not only proteome information on fruit ripening, but also pave the ground for further quantitative studies using SMR to investigate certain proteins and pathways under the hypothesis involved in fruit ripening. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Qifa Zheng
- Agriculture and Agri-Food Canada, Atlantic Food and Horticulture Research Centre, 32 Main St., Kentville, NS., Canada B4N 1J5
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83
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Bianco L, Alagna F, Baldoni L, Finnie C, Svensson B, Perrotta G. Proteome regulation during Olea europaea fruit development. PLoS One 2013; 8:e53563. [PMID: 23349718 PMCID: PMC3547947 DOI: 10.1371/journal.pone.0053563] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Widespread in the Mediterranean basin, Olea europaea trees are gaining worldwide popularity for the nutritional and cancer-protective properties of the oil, mechanically extracted from ripe fruits. Fruit development is a physiological process with remarkable impact on the modulation of the biosynthesis of compounds affecting the quality of the drupes as well as the final composition of the olive oil. Proteomics offers the possibility to dig deeper into the major changes during fruit development, including the important phase of ripening, and to classify temporal patterns of protein accumulation occurring during these complex physiological processes. METHODOLOGY/PRINCIPAL FINDINGS In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three different developmental stages were separated on 2-DE and subjected to image analysis. 247 protein spots were revealed as differentially accumulated. Proteins were identified from a total of 121 spots and discussed in relation to olive drupe metabolic changes occurring during fruit development. In order to evaluate if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies. CONCLUSIONS/SIGNIFICANCE This study identifies a number of proteins responsible for quality traits of cv. Coratina, with particular regard to proteins associated to the metabolism of fatty acids, phenolic and aroma compounds. Proteins involved in fruit photosynthesis have been also identified and their pivotal contribution in oleogenesis has been discussed. To date, this study represents the first characterization of the olive fruit proteome during development, providing new insights into fruit metabolism and oil accumulation process.
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Affiliation(s)
- Linda Bianco
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), TRISAIA Research Center, Rotondella (Matera), Italy
| | | | | | - Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Gaetano Perrotta
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), TRISAIA Research Center, Rotondella (Matera), Italy
- * E-mail:
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84
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Chan Z. Proteomic responses of fruits to environmental stresses. FRONTIERS IN PLANT SCIENCE 2013; 3:311. [PMID: 23335934 PMCID: PMC3541545 DOI: 10.3389/fpls.2012.00311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/24/2012] [Indexed: 05/18/2023]
Abstract
Fruits and vegetables are extremely susceptible to decay and easily lose commercial value after harvest. Different strategies have been developed to control postharvest decay and prevent quality deterioration during postharvest storage, including cold storage, controlled atmosphere (CA), and application of biotic and abiotic stimulus. In this review, mechanisms related to protein level responses of host side and pathogen side were characterized. Protein extraction protocols have been successfully developed for recalcitrant, low protein content fruit tissues. Comparative proteome profiling and functional analysis revealed that defense related proteins, energy metabolism, and antioxidant pathway played important roles in fruits in response to storage conditions and exogenous elicitor treatments. Secretome of pathogenic fungi has been well-investigated and the results indicated that hydrolytic enzymes were the key virulent factors for the pathogen infection. These protein level changes shed new light on interaction among fruits, pathogens, and environmental conditions. Potential postharvest strategies to reduce risk of fruit decay were further proposed based on currently available proteomic data.
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
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85
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D'Ambrosio C, Arena S, Rocco M, Verrillo F, Novi G, Viscosi V, Marra M, Scaloni A. Proteomic analysis of apricot fruit during ripening. J Proteomics 2013. [DOI: 10.1016/j.jprot.2012.11.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gest N, Gautier H, Stevens R. Ascorbate as seen through plant evolution: the rise of a successful molecule? JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:33-53. [PMID: 23109712 DOI: 10.1093/jxb/ers297] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ascorbate is a widespread and efficient antioxidant that has multiple functions in plants, traditionally associated with the reactions of photosynthesis. This review aims to look at ascorbate from an evolutionary perspective. Cyanobacteria, algae, and bryophytes contain lower concentrations of ascorbate than higher plants, where the molecule accumulates in high concentrations in both photosynthetic and non-photosynthetic organs and tissues. This increase in ascorbate concentration is paralleled by an increase in the number of isoforms of ascorbate peroxidase and the ascorbate regenerating enzymes mono- and dehydroascorbate reductase. One way of understanding the rise in ascorbate concentrations is to consider ascorbate as a molecule among others that has been subject to selection pressures during evolution, due to its cost or benefit for the cell and the organism. Ascorbate has a low cost in terms of synthesis and toxicity, and its benefits include protection of the glutathione pool and proper functioning of a range of enzymes. The hypothesis presented here is that these features would have favoured increasing roles for the molecule in the development and growth of multicellular organisms. This review then focuses on this diversity of roles for ascorbate in both photosynthetic and non-photosynthetic tissues of higher plants, including fruits and seeds, as well as further functions the molecule may possess by looking at other species. The review also highlights one of the trade-offs of domestication, which has often reduced or diluted ascorbate content in the quest for increased fruit growth and yield, with unknown consequences for the corresponding functional diversity, particularly in terms of stress resistance and adaptive responses to the environment.
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Affiliation(s)
- Noé Gest
- INRA, UR1052, Génétique et amélioration des fruits et légumes, Domaine St Maurice, 84143 Montfavet, France
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Fabi JP, Seymour GB, Graham NS, Broadley MR, May ST, Lajolo FM, Cordenunsi BR, Oliveira do Nascimento JR. Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray. BMC PLANT BIOLOGY 2012; 12:242. [PMID: 23256600 PMCID: PMC3562526 DOI: 10.1186/1471-2229-12-242] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/17/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. RESULTS Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development. CONCLUSION The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.
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Affiliation(s)
- João Paulo Fabi
- University of São Paulo, Department of Food Science and Experimental Nutrition, FCF, São Paulo, Brazil
| | - Graham B Seymour
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, LE12 5RD, UK
| | - Neil S Graham
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, LE12 5RD, UK
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, LE12 5RD, UK
| | - Sean T May
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, LE12 5RD, UK
| | - Franco Maria Lajolo
- University of São Paulo, Department of Food Science and Experimental Nutrition, FCF, São Paulo, Brazil
- University of São Paulo, – NAPAN – Food and Nutrition Research Center, São Paulo, Brazil
| | - Beatriz Rosana Cordenunsi
- University of São Paulo, Department of Food Science and Experimental Nutrition, FCF, São Paulo, Brazil
- University of São Paulo, – NAPAN – Food and Nutrition Research Center, São Paulo, Brazil
| | - João Roberto Oliveira do Nascimento
- University of São Paulo, Department of Food Science and Experimental Nutrition, FCF, São Paulo, Brazil
- University of São Paulo, – NAPAN – Food and Nutrition Research Center, São Paulo, Brazil
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Marjanović M, Stikić R, Vucelić-Radović B, Savić S, Jovanović Z, Bertin N, Faurobert M. Growth and proteomic analysis of tomato fruit under partial root-zone drying. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:343-56. [PMID: 22702247 DOI: 10.1089/omi.2011.0076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The effects of partial root-zone drying (PRD) on tomato fruit growth and proteome in the pericarp of cultivar Ailsa Craig were investigated. The PRD treatment was 70% of water applied to fully irrigated (FI) plants. PRD reduced the fruit number and slightly increased the fruit diameter, whereas the total fruit fresh weight (FW) and dry weight (DW) per plant did not change. Although the growth rate was higher in FI than in PRD fruits, the longer period of cell expansion resulted in bigger PRD fruits. Proteins were extracted from pericarp tissue at two fruit growth stages (15 and 30 days post-anthesis [dpa]), and submitted to proteomic analysis including two-dimensional gel electrophoresis and mass spectrometry for identification. Proteins related to carbon and amino acid metabolism indicated that slower metabolic flux in PRD fruits may be the cause of a slower growth rate compared to FI fruits. The increase in expression of the proteins related to cell wall, energy, and stress defense could allow PRD fruits to increase the duration of fruit growth compared to FI fruits. Upregulation of some of the antioxidative enzymes during the cell expansion phase of PRD fruits appears to be related to their role in protecting fruits against the mild stress induced by PRD.
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Affiliation(s)
- Milena Marjanović
- Department of Agrochemistry and Plant Physiology, Faculty of Agriculture, Institute of Food Technology and Biochemistry, University of Belgrade, Belgrade, Serbia
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Sade D, Eybishtz A, Gorovits R, Sobol I, Czosnek H. A developmentally regulated lipocalin-like gene is overexpressed in Tomato yellow leaf curl virus-resistant tomato plants upon virus inoculation, and its silencing abolishes resistance. PLANT MOLECULAR BIOLOGY 2012; 80:273-87. [PMID: 22843056 DOI: 10.1007/s11103-012-9946-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 07/17/2012] [Indexed: 05/21/2023]
Abstract
To discover genes involved in tomato resistance to Tomato yellow leaf curl virus (TYLCV), we previously compared cDNA libraries from susceptible (S) and resistant (R) tomato lines. Among the genes preferentially expressed in R plants and upregulated by TYLCV infection was a gene encoding a lipocalin-like protein. This gene was termed Solanum lycopersicum virus resistant/susceptible lipocalin (SlVRSLip). The SlVRSLip structural gene sequence of R and S plants was identical. SlVRSLip was expressed in leaves during a 15-day window starting about 40 days after sowing (20 days after planting). SlVRSLip was upregulated by Bemisia tabaci (the TYLCV vector) feeding on R plant leaves, and even more strongly upregulated following whitefly-mediated TYLCV inoculation. Silencing of SlVRSLip in R plants led to the collapse of resistance upon TYLCV inoculation and to a necrotic response along the stem and petioles accompanied by ROS production. Contrary to previously identified tomato lipocalin gene DQ222981, SlVRSLip was not regulated by cold, nor was it regulated by heat or salt. The expression of SlVRSLip was inhibited in R plants in which the hexose transporter gene LeHT1 was silenced. In contrast, the expression of LeHT1 was not inhibited in SlVRSLip-silenced R plants. Hence, in the hierarchy of the gene network conferring TYLCV resistance, SlVRSLip is downstream of LeHT1. Silencing of another gene involved in resistance, a Permease-I like protein, did not affect the expression of SlVRSLip and LeHT1; expression of the Permease was not affected by silencing SlVRSLip or LeHT1, suggesting that it does not belong to the same network. The triple co-silencing of SlVRSLip, LeHT1 and Permease provoked an immediate cessation of growth of R plants upon infection and the accumulation of large amounts of virus. SlVRSLip is the first lipocalin-like gene shown to be involved in resistance to a plant virus.
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Affiliation(s)
- Dagan Sade
- The Otto Warburg Minerva Center for Agricultural Biotechnology, Institute of Plant Science and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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Barsan C, Zouine M, Maza E, Bian W, Egea I, Rossignol M, Bouyssie D, Pichereaux C, Purgatto E, Bouzayen M, Latché A, Pech JC. Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components. PLANT PHYSIOLOGY 2012; 160:708-25. [PMID: 22908117 PMCID: PMC3461550 DOI: 10.1104/pp.112.203679] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/16/2012] [Indexed: 05/18/2023]
Abstract
A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.
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Affiliation(s)
| | | | | | | | - Isabel Egea
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Michel Rossignol
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - David Bouyssie
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Carole Pichereaux
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Eduardo Purgatto
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Mondher Bouzayen
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Alain Latché
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Jean-Claude Pech
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
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91
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Lu HC, Lin JH, Chua ACN, Chung TY, Tsai IC, Tzen JTC, Chou WM. Cloning and expression of pathogenesis-related protein 4 from jelly fig (Ficus awkeotsang Makino) achenes associated with ribonuclease, chitinase and anti-fungal activities. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 56:1-13. [PMID: 22579939 DOI: 10.1016/j.plaphy.2012.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Accepted: 04/11/2012] [Indexed: 05/16/2023]
Abstract
A cDNA fragment (FaPR4) encoding a class I pathogenesis-related protein 4 (PR-4) from Ficus awkeotsang was obtained by PCR cloning. Plant PR-4s were grouped into class I and II, differing by the presence of ChtBD and hinge. The predicted mature FaPR4 comprises N-terminal chitin-binding domain (ChtBD), hinge, Barwin domain and C-terminal extension. FaPR4-C, an N-terminal truncated form of FaPR4, was designed to mimic the structural feature of class II PR-4s. FaPR4 and FaPR4-C were over-expressed in yeast Pichia pastoris, and both recombinants exhibited RNase and anti-fungal activities. To our knowledge, it is the first report that FaPR4, a member of class I PR-4s has RNase activity as class II. FaPR4 possesses better anti-fungal activities toward Fusarium oxysporum and Sclerotium rolfsii than FaPR4-C. Heat-treated FaPR4 remained RNase and anti-fungal activities; while heat-treated FaPR4-C lost those activities. Therefore, ChtBD of FaPR4 may not only contribute to its anti-fungal but also improve the thermal stability of protein. It also implied the correlation of RNase activity with anti-fungal activity of FaPR4-C. Furthermore, FaPR4 was detected to have weak but significant chitinase activity, and its chitinase activity was reduced after heat treatment. The chitinase activity by FaPR4-C was much lower than FaPR4.
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Affiliation(s)
- Hsi-Chi Lu
- Department of Food Science, Tunghai University, Taichung 407, Taiwan, ROC
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92
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Marondedze C, Thomas LA. Apple hypanthium firmness: new insights from comparative proteomics. Appl Biochem Biotechnol 2012; 168:306-26. [PMID: 22733236 DOI: 10.1007/s12010-012-9774-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 06/10/2012] [Indexed: 01/09/2023]
Abstract
Fruit firmness constitutes an important textural property and is one of the key parameters for estimating ripening and shelf life, which has a major impact on commercialization. In order to decipher the mechanisms related to firmness of apples (Malus × domestica Borkh.), two-dimensional gel electrophoresis (2-DE) was used to compare the total proteome of high and low firmness phenotypes from apple hypanthia of a 'Golden Delicious' × 'Dietrich' population. A total of 36 differentially regulated protein spots were positively identified by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and then validated against the Malus expressed sequence tags (EST) database. The findings of this study indicated a lower expression of ethylene biosynthesis related proteins in the high firmness phenotype, which could be linked to the slowing down of the ripening and softening processes. The reduced accumulation of proteins involved in ethylene biosynthesis juxtaposed to the upregulation of a transposase and a GTP-binding protein in the high firmness phenotype. The results also showed higher expression of cytoskeleton proteins in the high firmness phenotype compared to the low firmness phenotype, which play a role in maintaining cell structure and possibly fruit integrity. Finally, a number of proteins involved in detoxification and defense were expressed in fruit hypanthium. This proteomic study provides a contribution towards a better understanding of regulatory networks involved in fruit hypanthium firmness and/or softening, which could be instrumental in the development of improved fruit quality.
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Affiliation(s)
- Claudius Marondedze
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville 7535, Cape Town, South Africa.
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93
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Ré MD, Gonzalez C, Sdrigotti MA, Sorrequieta A, Valle EM, Boggio SB. Ripening tomato fruit after chilling storage alters protein turnover. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:1490-6. [PMID: 22162046 DOI: 10.1002/jsfa.4732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/29/2011] [Accepted: 10/01/2011] [Indexed: 05/14/2023]
Abstract
BACKGROUND Tomato fruit is of prime importance owing to its qualities for human nutrition and its economic value. In order to extend its commercial life, it is harvested at mature but unripe stages and stored at low temperatures. The goal of this work was to study the influence of harvest and chilling storage of mature green tomato fruit (cv. Micro-Tom) on the protein pattern, amino acid content and protease activity during fruit ripening. RESULTS Fruits were sampled during ripening in three different conditions: 1, on the vine; 2, off the vine; 3, off the vine after 4 weeks at 4 °C. During all fruit ripening conditions, protein level decreased while amino acid content increased. Chilling storage of mature green fruit led to a reduction in protein content. Ripening off the vine (conditions 2 and 3) resulted in a threefold increase in red fruit amino acid levels when compared with red fruit on the vine. Protease activities (autoproteolytic, azocaseinolytic and gelatinolytic) were detected in all fruits evaluated and were differently affected by ripening stage, ripening conditions and the presence of specific inhibitors. CONCLUSION Harvest and chilling storage increased endogenous substrate proteolysis, azocaseinolytic activity and free amino acid levels, which could be related to fruit quality.
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Affiliation(s)
- Martín D Ré
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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94
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Pan Z, Zeng Y, An J, Ye J, Xu Q, Deng X. An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits. J Proteomics 2012; 75:2670-84. [DOI: 10.1016/j.jprot.2012.03.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/21/2012] [Accepted: 03/14/2012] [Indexed: 12/23/2022]
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95
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2D-DIGE analysis of mango (Mangifera indica L.) fruit reveals major proteomic changes associated with ripening. J Proteomics 2012; 75:3331-41. [PMID: 22504795 DOI: 10.1016/j.jprot.2012.03.047] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/16/2012] [Accepted: 03/26/2012] [Indexed: 11/23/2022]
Abstract
A comparative proteomic investigation between the pre-climacteric and climacteric mango fruits (cv. Keitt) was performed to identify protein species with variable abundance during ripening. Proteins were phenol-extracted from fruits, cyanine-dye-labeled, and separated on 2D gels at pH 4-7. Total spot count of about 373 proteins spots was detected in each gel and forty-seven were consistently different between pre-climacteric and climacteric fruits and were subjected to LC-MS/MS analysis. Functional classification revealed that protein species involved in carbon fixation and hormone biosynthesis decreased during ripening, whereas those related to catabolism and the stress-response, including oxidative stress and abiotic and pathogen defense factors, accumulated. In relation to fruit quality, protein species putatively involved in color development and pulp softening were also identified. This study on mango proteomics provides an overview of the biological processes that occur during ripening.
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96
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Huerta-Ocampo JÁ, Osuna-Castro JA, Lino-López GJ, Barrera-Pacheco A, Mendoza-Hernández G, De León-Rodríguez A, Barba de la Rosa AP. Proteomic analysis of differentially accumulated proteins during ripening and in response to 1-MCP in papaya fruit. J Proteomics 2012; 75:2160-9. [DOI: 10.1016/j.jprot.2012.01.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 02/03/2023]
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97
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Minas IS, Tanou G, Belghazi M, Job D, Manganaris GA, Molassiotis A, Vasilakakis M. Physiological and proteomic approaches to address the active role of ozone in kiwifruit post-harvest ripening. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2449-64. [PMID: 22268155 PMCID: PMC3346216 DOI: 10.1093/jxb/err418] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/12/2011] [Accepted: 11/21/2011] [Indexed: 05/18/2023]
Abstract
Post-harvest ozone application has recently been shown to inhibit the onset of senescence symptoms on fleshy fruit and vegetables; however, the exact mechanism of action is yet unknown. To characterize the impact of ozone on the post-harvest performance of kiwifruit (Actinidia deliciosa cv. 'Hayward'), fruits were cold stored (0 °C, 95% relative humidity) in a commercial ethylene-free room for 1, 3, or 5 months in the absence (control) or presence of ozone (0.3 μl l(-1)) and subsequently were allowed to ripen at a higher temperature (20 °C), herein defined as the shelf-life period, for up to 12 days. Ozone blocked ethylene production, delayed ripening, and stimulated antioxidant and anti-radical activities of fruits. Proteomic analysis using 1D-SDS-PAGE and mass spectrometry identified 102 kiwifruit proteins during ripening, which are mainly involved in energy, protein metabolism, defence, and cell structure. Ripening induced protein carbonylation in kiwifruit but this effect was depressed by ozone. A set of candidate kiwifruit proteins that are sensitive to carbonylation was also discovered. Overall, the present data indicate that ozone improved kiwifruit post-harvest behaviour, thus providing a first step towards understanding the active role of this molecule in fruit ripening.
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Affiliation(s)
- Ioannis S. Minas
- School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Georgia Tanou
- School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maya Belghazi
- Centre d’Analyse Protéomique de Marseille, Institut Fédératif de Recherche Jean Roche, F–13916 Marseille cedex 20, France
| | - Dominique Job
- CNRS-Bayer CropScience Joint Laboratory (UMR 5240), Bayer CropScience, F–69263 Lyon cedex 9, France
| | - George A. Manganaris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603 Lemesos, Cyprus
| | - Athanassios Molassiotis
- School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Miltiadis Vasilakakis
- School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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98
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Qin G, Wang Y, Cao B, Wang W, Tian S. Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:243-55. [PMID: 22098335 DOI: 10.1111/j.1365-313x.2011.04861.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The MADS box transcription factor RIN is a global regulator of fruit ripening. However, the direct targets modulated by RIN and the mechanisms underlying the transcriptional regulation remain largely unknown. Here we identified 41 protein spots representing 35 individual genes as potential targets of RIN by comparative proteomic analysis of a rin mutant in tomato fruits. Gene expression analysis showed that the mRNA level of 26 genes correlated well with the protein level. After examining the promoter regions of the candidate genes, a variable number of RIN binding sites were found. Five genes (E8, TomloxC, PNAE, PGK and ADH2) were identified as novel direct targets of RIN by chromatin immunoprecipitation. The results of a gel mobility shift assay confirmed the direct binding of RIN to the promoters of these genes. Of the direct target genes, TomloxC and ADH2, which encode lipoxygenase (LOX) and alcohol dehydrogenase, respectively, are critical for the production of characteristic tomato aromas derived from LOX pathway. Further study indicated that RIN also directly regulates the expression of HPL, which encodes hydroperoxide lyase, another rate-limiting enzyme in the LOX pathway. Loss of function of RIN causes de-regulation of the LOX pathway, leading to a specific defect in the generation of aroma compounds derived from this pathway. These results indicate that RIN modulates aroma formation by direct and rigorous regulation of expression of genes in the LOX pathway. Taken together, our findings suggest that the regulatory effect of RIN on fruit ripening is achieved by targeting specific molecular pathways.
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Affiliation(s)
- Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Haidian District, Beijing 100093, China.
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99
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Cui K, He CY, Zhang JG, Duan AG, Zeng YF. Temporal and Spatial Profiling of Internode Elongation-Associated Protein Expression in Rapidly Growing Culms of Bamboo. J Proteome Res 2012; 11:2492-507. [DOI: 10.1021/pr2011878] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Cui
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s
Republic of China
| | - Cai-yun He
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Jian-guo Zhang
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Ai-guo Duan
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Yan-fei Zeng
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
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100
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Nilo P. R, Campos-Vargas R, Orellana A. Assessment of Prunus persica fruit softening using a proteomics approach. J Proteomics 2012; 75:1618-38. [DOI: 10.1016/j.jprot.2011.11.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 12/23/2022]
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