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Wang Y, Hao R, Guo R, Nong H, Qin Y, Dong N. Integrative Analysis of Metabolome and Transcriptome Reveals Molecular Insight into Metabolomic Variations during Hawthorn Fruit Development. Metabolites 2023; 13:metabo13030423. [PMID: 36984863 PMCID: PMC10054872 DOI: 10.3390/metabo13030423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Hawthorn (Crataegus pinnatifida var. major), a cultivated fruit tree, is native and unique to China. Its fruits have high nutritional, health, and medicinal values. However, the development and ripening process of hawthorns is accompanied by dramatic changes in flavor, aroma, and bioactive phytochemicals, which are the fundamental factors that contribute to the potential health benefits and establishment of fruit quality. Therefore, an exploration of the dynamic changes in metabolites and their regulatory networks during the development of hawthorn fruits can elucidate the formation mechanisms of active substances in hawthorn fruits. In this study, we used a broad targeted metabolomics approach to identify and analyze the dynamics of metabolites in hawthorn fruits at five developmental stages. The results revealed 998 primary and secondary metabolites that were classified into 15 categories. The accumulation levels of most sugars increased during fruit development and then accelerated at the fruit ripening stage. The accumulation levels of a few organic acids (e.g., citric acid, isocitric acid, and quinic acid) continuously increased. Many organic acids exhibited significant decreasing trends. Among the 561 secondary metabolites detected, 189 were phenolic acids and 199 were flavonoids. The levels of many flavonoids were significantly reduced at later stages of fruit development; in contrast, the levels of two anthocyanins significantly increased during fruit ripening. Correlation analysis revealed that there is a certain correlation within and between primary as well as secondary metabolites during fruit development. Furthermore, the integration of metabolomic and transcriptomic data in this study revealed that changes in the expression of some differentially expressed genes (DEGs) were associated with the accumulation of metabolites such as sugars, organic acids, and flavonoids, e.g., the upregulated expression levels of CS (citrate synthase) genes were consistent with the continued accumulation of citric acid. Overall, this study demonstrates the metabolic changes that occur during the development of hawthorn fruit, explores the molecular mechanisms that underlie metabolite changes during fruit development, and lays a strong theoretical foundation for the improvement of hawthorn fruit quality and the development of functional components.
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Gong X, Qi K, Chen J, Zhao L, Xie Z, Yan X, Khanizadeh S, Zhang S, Tao S. Multi-omics analyses reveal stone cell distribution pattern in pear fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:626-642. [PMID: 36546867 DOI: 10.1111/tpj.16073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Stone cells are the brachysclereid cells in pear (Pyrus) fruit, consisting almost entirely of lignified secondary cell walls. They are distributed mainly near the fruit core and spread radially in the whole fruit. However, the development of stone cells has not been comprehensively characterized, and little is known about the regulation of stone cell formation at the transcriptomic, proteomic, and metabolomic levels. In the present study, we performed phenomic analysis on the stone cells and their associated vascular bundles distributed near the fruit cores. Transcriptomic, proteomic, and metabolomic analyses revealed a significant positive regulation of biological processes which contribute to the lignification and lignin deposition in stone cells near the fruit core, including sucrose metabolism and phenylalanine, tyrosine, tryptophan, and phenylalanine biosynthesis. We found many metabolites generated from the phenylpropanoid pathway contributing to the cell wall formation of stone cells near the fruit core. Furthermore, we identified a key transcription factor, PbbZIP48, which was highly expressed near the fruit core and was shown to regulate lignin biosynthesis in stone cells. In conclusion, the present study provides insight into the mechanism of lignified stone cell formation near the pear fruit core at multiple levels.
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Affiliation(s)
- Xin Gong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Juanli Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liangyi Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihua Xie
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xin Yan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shahrokh Khanizadeh
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shutian Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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3
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Song J, Campbell L, Vinqvist-Tymchuk M. Application of quantitative proteomics to investigate fruit ripening and eating quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153766. [PMID: 35921768 DOI: 10.1016/j.jplph.2022.153766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.
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Affiliation(s)
- Jun Song
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada.
| | - Leslie Campbell
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
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Kuang L, Chen S, Guo Y, Scheuring D, Flaishman MA, Ma H. Proteome Analysis of Vacuoles Isolated from Fig (Ficus carica L.) Flesh during Fruit Development. PLANT & CELL PHYSIOLOGY 2022; 63:785-801. [PMID: 35348748 DOI: 10.1093/pcp/pcac039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fruit flesh cell vacuoles play a pivotal role in fruit growth and quality formation. In the present study, intact vacuoles were carefully released and collected from protoplasts isolated from flesh cells at five sampling times along fig fruit development. Label-free quantification and vacuole proteomic analysis identified 1,251 proteins, 1,137 of which were recruited as differentially abundant proteins (DAPs) by fold change ≥ 1.5, P < 0.05. DAPs were assigned to 10 functional categories; among them, 238, 186, 109, 93 and 90 were annotated as metabolism, transport proteins, membrane fusion or vesicle trafficking, protein fate and stress response proteins, respectively. Decreased numbers of DAPs were uncovered along fruit development. The overall changing pattern of DAPs revealed two major proteome landscape conversions in fig flesh cell vacuoles: the first occurred when fruit developed from late-stage I to mid-stage II, and the second occurred when the fruit started ripening. Metabolic proteins related to glycosidase, lipid and extracellular proteins contributing to carbohydrate storage and vacuole expansion, and protein-degrading proteins determining vacuolar lytic function were revealed. Key tonoplast proteins contributing to vacuole expansion, cell growth and fruit quality formation were also identified. The revealed comprehensive changes in the vacuole proteome during flesh development were compared with our previously published vacuole proteome of grape berry. The information expands our knowledge of the vacuolar proteome and the protein basis of vacuole functional evolution during fruit development and quality formation.
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Affiliation(s)
- Liuqing Kuang
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing 100193, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Shangwu Chen
- College of Food Science and Nutrition Engineering, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- College of Biology Sciences, China Agricultural University, Beijing 100193, China
| | - David Scheuring
- Department of Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Moshe A Flaishman
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing 100193, China
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Li J, Zhang M, Li X, Khan A, Kumar S, Allan AC, Lin-Wang K, Espley RV, Wang C, Wang R, Xue C, Yao G, Qin M, Sun M, Tegtmeier R, Liu H, Wei W, Ming M, Zhang S, Zhao K, Song B, Ni J, An J, Korban SS, Wu J. Pear genetics: Recent advances, new prospects, and a roadmap for the future. HORTICULTURE RESEARCH 2022; 9:uhab040. [PMID: 35031796 PMCID: PMC8778596 DOI: 10.1093/hr/uhab040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".
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Affiliation(s)
- Jiaming Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xiaolong Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Awais Khan
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Satish Kumar
- Hawke’s Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand
| | - Andrew Charles Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Richard Victor Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Runze Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Mengfan Qin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Manyi Sun
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Tegtmeier
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Hainan Liu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weilin Wei
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Ming
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kejiao Zhao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiangping Ni
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianping An
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Schuyler S Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Wang P, Xuan X, Su Z, Wang W, Abdelrahman M, Jiu S, Zhang X, Liu Z, Wang X, Wang C, Fang J. Identification of miRNAs-mediated seed and stone-hardening regulatory networks and their signal pathway of GA-induced seedless berries in grapevine (V. vinifera L.). BMC PLANT BIOLOGY 2021; 21:442. [PMID: 34587914 PMCID: PMC8480016 DOI: 10.1186/s12870-021-03188-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Stone-hardening stage is crucial to the development of grape seed and berry quality. A significant body of evidence supports the important roles of MicroRNAs in grape-berry development, but their specific molecular functions during grape stone-hardening stage remain unclear. RESULTS Here, a total of 161 conserved and 85 species-specific miRNAs/miRNAs* (precursor) were identified in grape berries at stone-hardening stage using Solexa sequencing. Amongst them, 30 VvmiRNAs were stone-hardening stage-specific, whereas 52 exhibited differential expression profiles during berry development, potentially participating in the modulation of berry development as verified by their expression patterns. GO and KEGG pathway analysis showed that 13 VvmiRNAs might be involved in the regulation of embryo development, another 11 in lignin and cellulose biosynthesis, and also 28 in the modulation of hormone signaling, sugar, and proline metabolism. Furthermore, the target genes for 4 novel VvmiRNAs related to berry development were validated using RNA Ligase-Mediated (RLM)-RACE and Poly(A) Polymerase-Mediated (PPM)-RACE methods, and their cleavage mainly occurred at the 9th-11th sites from the 5' ends of miRNAs at their binding regions. In view of the regulatory roles of GA in seed embryo development and stone-hardening in grape, we investigated the expression modes of VvmiRNAs and their target genes during GA-induced grape seedless-berry development, and we validated that GA induced the expression of VvmiR31-3p and VvmiR8-5p to negatively regulate the expression levels of CAFFEOYL COENZYME A-3-O-METHYLTRANSFERASE (VvCCoAOMT), and DDB1-CUL4 ASSOCIATED FACTOR1 (VvDCAF1). The series of changes might repress grape stone hardening and embryo development, which might be a potential key molecular mechanism in GA-induced grape seedless-berry development. Finally, a schematic model of miRNA-mediated grape seed and stone-hardening development was proposed. CONCLUSION This work identified 30 stone-hardening stage-specific VvmiRNAs and 52 significant differential expression ones, and preliminary interpreted the potential molecular mechanism of GA-induced grape parthenocarpy. GA negatively manipulate the expression of VvCCoAOMT and VvDCAF1 by up-regulation the expression of VvmiR31-3p and VvmiR8-5p, thereby repressing seed stone and embryo development to produce grape seedless berries.
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Affiliation(s)
- Peipei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuxian Xuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziwen Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wenran Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mostafa Abdelrahman
- Department of Botany, Faculty of Sciences, Aswan University, Aswan, 81528, Egypt
- Arid Land Research Center, Tottori University, Tottori, 680-001, Japan
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xicheng Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Zhang HP, Su Y, Yu Q, Qin GH. Quantitative proteomic analysis of pear (Pyrus pyrifolia cv. "Hosui") flesh provides novel insights about development and quality characteristics of fruit. PLANTA 2021; 253:69. [PMID: 33599839 DOI: 10.1007/s00425-021-03585-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
A total of 6763 proteins were identified in the developing pear flesh, which were further screened for differentially expressed proteins related to fruit quality and ATP-binding cassette transporters. To obtain further details on changes in protein levels during fruit ripening and to identify and evaluate changes in various metabolic pathways that affect fruit quality, a proteomic method using tandem mass tags was implemented at three developmental stages in Pyrus pyrifolia cv. "Hosui" that identified 6763 proteins. Subcellular localization and Gene Ontology enrichment analysis revealed major functions of all identified proteins. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that all metabolic processes are reflected in the up- and downregulation of differentially expressed proteins during fruit development, which play predominant roles in cell division, cell expansion, and fruit ripening. Among the examined differentially expressed proteins, 160 related to fruit quality, and 14 ATP-binding cassette transporters related to fruit development were identified and analyzed. The quantitative data were validated by parallel reaction monitoring, which confirmed the reliability of the experimental results.
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Affiliation(s)
- Hu Ping Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ying Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gai Hua Qin
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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Zhou D, Zhang Q, Li P, Pan L, Tu K. Combined transcriptomics and proteomics analysis provides insight into metabolisms of sugars, organic acids and phenols in UV-C treated peaches during storage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:148-159. [PMID: 33120107 DOI: 10.1016/j.plaphy.2020.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
3Ultraviolet-C (UV-C) irradiation is known for prolonging the shelf life of many fruit by regulating different pathways. To better understand the roles of UV-C treatment in regulating the metabolic pathways in peach fruit during cold storage, transcriptomics and proteomics approaches were applied to investigate changes in peaches treated with UV-C (1.5 kJ m-2). The results showed that most differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were largely matched to carbohydrates and secondary metabolites. Further analysis found that peaches treated with UV-C exhibited higher sucrose, citric acid, malic acid, phenols, flavonoids and anthocyanins compared with untreated peaches. Proteomics and transcriptomics together indicated that changes of sugars and acids were associated with the expressions of invertase, sucrose synthase, fructokinase, malate dehydrogenase and citrate synthase. UV-C irradiation promoted the synthesis of phenols, flavonoids and anthocyanins by up-regulating expressions of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase, chalcone synthase, dihydroflavonol 4-reductase and UDP-glucose:flavonoid glucosyltransferase. In summary, this research explained the general molecular mechanism of the changes of sugars, acids and phenols in peaches in response to UV-C.
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Affiliation(s)
- Dandan Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qin Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengxia Li
- Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, PR China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210095, Jiangsu, PR China
| | - Leiqing Pan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kang Tu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Zhang Z, Xia B, Li Y, Lin Y, Xie J, Wu P, Lin L, Liao D. Comparative proteomic analysis of Prunella vulgaris L. spica ripening. J Proteomics 2020; 232:104028. [PMID: 33129985 DOI: 10.1016/j.jprot.2020.104028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
Prunella vulgaris L., better known as 'self-heal', has been extensively used in the traditional system of medicines. To reveal the regulatory mechanism of its development, TMT-based quantitative proteome analysis was performed in the Prunella vulgaris L. spica before and during ripening (Group A and Group B, respectively). This analysis resulted in the identification of 7655 proteins, of which 1910 showed differential abundance between the two groups. Pronounced changes in the proteomic profile included the following: 1) Stress-responsive proteins involved in protecting cells and promoting fruit ripening and seed development were highly abundant during ripening. 2) The degradation of chlorophyll, inhibition of chlorophyll biosynthesis and increased abundance of transketolase occurred simultaneously in the spica of Prunella vulgaris L., resulting in the spica changing color from green to brownish red. 3) The abundance of protein species related to phenylpropanoid biosynthesis mainly increased during ripening, while flavonoid and terpenoid backbone biosynthesis mostly occurred before ripening. SIGNIFICANCE: This study establishes a link between protein profiles and mature phenotypes, which will help to improve our understanding of the molecular mechanisms involved in the maturation of Prunella vulgaris L. at the proteome level and reveal the scientific connotation for the best time to harvest Prunella vulgaris L. This work provides a scientific basis for the production of high-quality medicinal Prunella vulgaris L., as well as a typical demonstration of molecular research used for the harvest period of traditional Chinese medicine. BIOLOGICAL SIGNIFICANCE: This work provided a comprehensive overview on the functional protein profile changes of Prunella vulgaris L. spica at different growing stages, as well as the scientific rationale of Prunella vulgaris L. harvested in summer after brownish red, thus laid an intriguing stepping stone for elucidating the molecular mechanisms of quality development.
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Affiliation(s)
- Zhimin Zhang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Bohou Xia
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Yamei Li
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Yan Lin
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Jingchen Xie
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Ping Wu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Limei Lin
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Duanfang Liao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; Collaborative Innovation Center for the Protection, Utilization of Chinese Herbal Medicine Resources in Hunan Province, Hunan University of Chinese Medicine, Changsha 410208, China.
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Lü J, Tao X, Yao G, Zhang S, Zhang H. Transcriptome Analysis of Low- and High-Sucrose Pear Cultivars Identifies Key Regulators of Sucrose Biosynthesis in Fruits. PLANT & CELL PHYSIOLOGY 2020; 61:1493-1506. [PMID: 32396606 DOI: 10.1093/pcp/pcaa068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Sucrose accumulation is one of the important factors that determine fruit enlargement and quality. Evaluation of the sugar profile of 105 pear cultivars revealed low-sucrose and high-sucrose (HS) types of pear fruits. To better understand the molecular mechanisms governing the sucrose content of pear fruits, this study performed transcriptome analysis during fruit development using low-sucrose 'Korla' fragrant pear and HS 'Hosui' pear, and a coexpression module uniquely associated with the control of high-sucrose accumulation was identified by weighted gene coexpression network analysis. These results suggested that there are seven candidate genes encoding key enzymes (fructokinase, glucose-6-phosphate isomerase, sucrose phosphate synthase and sucrose synthase) involved in sucrose biosynthesis and several transcription factors (TFs) whose expression patterns correlate with those of genes associated with sucrose biosynthesis. This correlation was confirmed by linear regression analysis between predicted gene expression and sucrose content in different pear cultivars during fruit development. This study provides insight into the molecular mechanism underlying differences in sucrose content across pear cultivars and presents candidate structural genes and TFs that could play important roles in regulating carbohydrate partitioning and sucrose accumulation.
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Affiliation(s)
- Jiahong Lü
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Gaifang Yao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huping Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. Sci Rep 2019; 9:18922. [PMID: 31831861 PMCID: PMC6908688 DOI: 10.1038/s41598-019-55287-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023] Open
Abstract
Japanese pear (Pyrus pyrifolia) is a major fruit tree in the family Rosaceae and is bred for fruit production. To promote the development of breeding strategies and molecular research for Japanese pear, we sequenced the transcripts of Japanese pear variety 'Hosui'. To exhaustively collect information of total gene expression, RNA samples from various organs and stages of Japanese pear were sequenced by three technologies, single-molecule real-time (SMRT) sequencing, 454 pyrosequencing, and Sanger sequencing. Using all those reads, we determined comprehensive reference sequences of Japanese pear. Then, their protein sequences were predicted, and biological functional annotations were assigned. Finally, we developed a web database, TRANSNAP (http://plantomics.mind.meiji.ac.jp/nashi), which is the first web resource of Japanese pear omics information. This database provides highly reliable information via a user-friendly web interface: the reference sequences, gene functional annotations, and gene expression profiles from microarray experiments. In addition, based on sequence comparisons among Japanese, Chinese and European pears, similar protein sequences among the pears and species-specific proteins in Japanese pear can be quickly and efficiently identified. TRANSNAP will aid molecular research and breeding in Japanese pear, and its information is available for comparative analysis among other pear species and families.
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Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
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Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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14
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Hu Y, Zhu YF, Guo AX, Jia XM, Cheng L, Zhao T, Wang YX. Transcriptome analysis in Malus halliana roots in response to iron deficiency reveals insight into sugar regulation. Mol Genet Genomics 2018; 293:1523-1534. [PMID: 30101382 DOI: 10.1007/s00438-018-1479-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/06/2018] [Indexed: 12/15/2022]
Abstract
Iron (Fe) deficiency is a frequent nutritional problem limiting apple production in calcareous soils. The utilization of rootstock that is resistant to Fe deficiency is an effective way to solve this problem. Malus halliana is an Fe deficiency-tolerant rootstock; however, few molecular studies have been conducted on M. halliana. In the present work, a transcriptome analysis was combined with qRT-PCR and sugar measurements to investigate Fe deficiency responses in M. halliana roots at 0 h (T1), 12 h (T2) and 72 h (T3) after Fe deficiency stress. Total of 2473, 661, and 776 differentially expressed genes (DEGs) were identified in the pairs of T2 vs. T1, T3 vs. T1, and T3 vs. T2, respectively. Several DEGs were enriched in the photosynthesis, glycolysis and gluconeogenesis, tyrosine metabolism and fatty acid degradation pathways. The glycolysis and photosynthesis pathways were upregulated under Fe deficiency. In this experiment, sucrose accumulated in Fe-deficient roots and leaves. However, the glucose content significantly decreased in the roots, while the fructose content significantly decreased in the leaves. Additionally, 15 genes related to glycolysis and sugar synthesis and sugar transport were selected to validate the accuracy of the transcriptome data by qRT-PCR. Overall, these results indicated that sugar synthesis and metabolism in the roots were affected by Fe deficiency. Sugar regulation is a way by which M. halliana responds to Fe deficiency stress.
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Affiliation(s)
- Ya Hu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China.,Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000, China
| | - Yan-Fang Zhu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China
| | - Ai-Xia Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China
| | - Xu-Mei Jia
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China
| | - Li Cheng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China
| | - Tong Zhao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China
| | - Yan-Xiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730000, China.
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Salzano AM, Sobolev A, Carbone V, Petriccione M, Renzone G, Capitani D, Vitale M, Minasi P, Pasquariello MS, Novi G, Zambrano N, Scortichini M, Mannina L, Scaloni A. A proteometabolomic study of Actinidia deliciosa fruit development. J Proteomics 2017; 172:11-24. [PMID: 29133123 DOI: 10.1016/j.jprot.2017.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Anatoly Sobolev
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy
| | - Paola Minasi
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marco Scortichini
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy; Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy.
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Simpson CG, Cullen DW, Hackett CA, Smith K, Hallett PD, McNicol J, Woodhead M, Graham J. Mapping and expression of genes associated with raspberry fruit ripening and softening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:557-572. [PMID: 27942774 DOI: 10.1007/s00122-016-2835-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/26/2016] [Indexed: 05/24/2023]
Abstract
QTL mapping identifies a range of underlying and unrelated genes with apparent roles in raspberry fruit ripening and softening that show characteristic developing fruit expression profiles. Fruit softening is an important agronomical trait that involves a complex interaction of plant cell processes. We have used both qualitative and quantitative scoring of fruit firmness, length, mass, and resistance to applied force to identify QTL in a raspberry mapping population. QTLs were located primarily on linkage group (LG) 3 with other significant loci on LG 1 and LG 5 and showed mostly additive effects between the two parents. The expression of key genes that underlie these QTLs with roles in cell-wall solubility, water uptake, polyamine synthesis, transcription, and cell respiration was tested across five stages of fruit development, from immature green to red ripe fruit, using real-time RT-qPCR. Gene expression patterns showed variable expression patterns across fruit development with a highly significant positive and negative correlation between genes, supporting precise regulation of expression of different cell processes throughout raspberry fruit development. Variable timing in expression was also found in some genes at different fruit development stages between soft and firm cultivars. Multiple processes have a role to play in fruit softening and this will require development of multiple marker combinations to genes that characterise raspberry fruit softening.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Danny W Cullen
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Kay Smith
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul D Hallett
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, UK
| | - Mary Woodhead
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Julie Graham
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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17
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Shiratake K, Suzuki M. Omics studies of citrus, grape and rosaceae fruit trees. BREEDING SCIENCE 2016; 66:122-38. [PMID: 27069397 PMCID: PMC4780796 DOI: 10.1270/jsbbs.66.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/06/2023]
Abstract
Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.
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Affiliation(s)
- Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
- Corresponding author (e-mail: )
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
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