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Gu C, Pei MS, Guo ZH, Wu L, Qi KJ, Wang XP, Liu H, Liu Z, Lang Z, Zhang S. Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism. Genome Biol 2024; 25:70. [PMID: 38486226 PMCID: PMC10938805 DOI: 10.1186/s13059-024-03200-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved. RESULTS We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening. CONCLUSION Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.
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Affiliation(s)
- Chao Gu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mao-Song Pei
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Hua Guo
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Wu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai-Jie Qi
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue-Ping Wang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Liu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Shaoling Zhang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Ma Y, Wang C, Gao Z, Yao Y, Kang H, Du Y. VvPL15 Is the Core Member of the Pectate Lyase Gene Family Involved in Grape Berries Ripening and Softening. Int J Mol Sci 2023; 24:ijms24119318. [PMID: 37298267 DOI: 10.3390/ijms24119318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The process of ripening and softening in grape begins at veraison and is closely related to the depolymerization of pectin components. A variety of enzymes are involved in pectin metabolism and one class of enzyme, pectin lyases (PLs), have been reported to play an important role in softening in many fruits; however, little information is available on the VvPL gene family in grape. In this study, 16 VvPL genes were identified in the grape genome using bioinformatics methods. Among them, VvPL5, VvPL9, and VvPL15 had the highest expression levels during grape ripening, which suggests that these genes are involved in grape ripening and softening. Furthermore, overexpression of VvPL15 affects the contents of water-soluble pectin (WSP) and acid-soluble pectin (ASP) in the leaves of Arabidopsis and significantly changes the growth of Arabidopsis plants. The relationship between VvPL15 and pectin content was further determined by antisense expression of VvPL15. In addition, we also studied the effect of VvPL15 on fruit in transgenic tomato plants, which showed that VvPL15 accelerated fruit ripening and softening. Our results indicate that VvPL15 plays an important role in grape berry softening during ripening by depolymerizing pectin.
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Affiliation(s)
- Yuying Ma
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Chukun Wang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Zhen Gao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Hui Kang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yuanpeng Du
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
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Wang P, Wu X, Shi Z, Tao S, Liu Z, Qi K, Xie Z, Qiao X, Gu C, Yin H, Cheng M, Gu X, Liu X, Tang C, Cao P, Xu S, Zhou B, Gu T, Bian Y, Wu J, Zhang S. A large-scale proteogenomic atlas of pear. MOLECULAR PLANT 2023; 16:599-615. [PMID: 36733253 DOI: 10.1016/j.molp.2023.01.011] [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: 10/03/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Pear is an important fruit tree that is widely distributed around the world. The first pear genome map was reported from our laboratory approximately 10 years ago. To further study global protein expression patterns in pear, we generated pear proteome data based on 24 major tissues. The tissue-resolved profiles provided evidence of the expression of 17 953 proteins. We identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18 090 peptide spectra with peptide spectrum matches >1. Among the eight randomly selected new short coding open reading frames that were expressed in the style, four promoted and one inhibited the growth of pear pollen tubes. Based on gene coexpression module analysis, we explored the key genes associated with important agronomic traits, such as stone cell formation in fruits. The network regulating the synthesis of lignin, a major component of stone cells, was reconstructed, and receptor-like kinases were implicated as core factors in this regulatory network. Moreover, we constructed the online database PearEXP (http://www.peardb.org.cn) to enable access to the pear proteogenomic resources. This study provides a paradigm for in-depth proteogenomic studies of woody plants.
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Affiliation(s)
- Peng Wang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Wu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zebin Shi
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shutian Tao
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhe Liu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Gu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyu Cheng
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyu Gu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Liu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Tang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Cao
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | | | | | - Tingting Gu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangyang Bian
- College of Life Sciences, Northwest University, Xi'an 710127, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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Shi Y, Li BJ, Su G, Zhang M, Grierson D, Chen KS. Transcriptional regulation of fleshy fruit texture. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1649-1672. [PMID: 35731033 DOI: 10.1111/jipb.13316] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/22/2022] [Indexed: 05/24/2023]
Abstract
Fleshy fruit texture is a critically important quality characteristic of ripe fruit. Softening is an irreversible process which operates in most fleshy fruits during ripening which, together with changes in color and taste, contributes to improvements in mouthfeel and general attractiveness. Softening results mainly from the expression of genes encoding enzymes responsible for cell wall modifications but starch degradation and high levels of flavonoids can also contribute to texture change. Some fleshy fruit undergo lignification during development and post-harvest, which negatively affects eating quality. Excessive softening can also lead to physical damage and infection, particularly during transport and storage which causes severe supply chain losses. Many transcription factors (TFs) that regulate fruit texture by controlling the expression of genes involved in cell wall and starch metabolism have been characterized. Some TFs directly regulate cell wall targets, while others act as part of a broader regulatory program governing several aspects of the ripening process. In this review, we focus on advances in our understanding of the transcriptional regulatory mechanisms governing fruit textural change during fruit development, ripening and post-harvest. Potential targets for breeding and future research directions for the control of texture and quality improvement are discussed.
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Affiliation(s)
- Yanna Shi
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Bai-Jun Li
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Guanqing Su
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Mengxue Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Donald Grierson
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Kun-Song Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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Wang L, Xu Z, Yin W, Xu K, Wang S, Shang Q, Sa W, Liang J, Wang L. Genome-wide analysis of the Thaumatin-like gene family in Qingke ( Hordeum vulgare L. var. nudum) uncovers candidates involved in plant defense against biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:912296. [PMID: 36061804 PMCID: PMC9428612 DOI: 10.3389/fpls.2022.912296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Thaumatin-like proteins (TLPs) participate in the defense responses of plants as well as their growth and development processes, including seed germination. Yet the functioning of TLP family genes, in addition to key details of their encoded protein products, has not been thoroughly investigated for Qingke (Hordeum vulgare L. var. nudum). Here, a total of 36 TLP genes were identified in the genome of Qingke via HMM profiling. Of them, 25 TLPs contained a signal peptide at the N-terminus, with most proteins predicted to localize in the cytoplasm or outer membrane. Sequence alignment and motif analysis revealed that the five REDDD residues required for β-1,3-glucanase activity were conserved in 21 of the 36 Qingke TLPs. Phylogenetically, the TLPs in plants are clustered in 10 major groups. Our analysis of gene structure did not detect an intron in 15 Qingke TLPs whereas the other 21 did contain 1-7 introns. A diverse set of cis-acting motifs were found in the promoters of the 36 TLPs, including elements related to light, hormone, and stress responses, growth and development, circadian control, and binding sites of transcription factors, thus suggesting a multifaceted role of TLPs in Qingke. Expression analyses revealed the potential involvement of TLPs in plant defense against biotic and abiotic stresses. Taken together, the findings of this study deepen our understanding of the TLP family genes in Qingke, a staple food item in Tibet, which could strengthen future investigations of protein function in barley and its improved genetic engineering.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Zepeng Xu
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Wei Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Kai Xu
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Shuai Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qianhan Shang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Sa
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Li Wang
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
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Liu J, Ma Q, Liu D, Meng C, Hu Z, Ma L. Identification of the cell wall proteins associated with the softening of Lycium barbarum L. fruit by using iTRAQ technology. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100110. [PMID: 35586663 PMCID: PMC9108469 DOI: 10.1016/j.fochms.2022.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
This was the first proteomic study on the cell walls of Lycium barbarum L. during fruit softening. A total of 258 differentially expressed proteins (DEPs) from the cell walls were identified between pre- and post-climacteric stages. Softening of Lycium barbarum L. fruit was accompanied by degradation of cell wall materials. DEPs promote cell wall polysaccharide degradation by driving energy metabolism.
Excessive softening of Lycium barbarum L. (LBL) fruit can limit the storage and transportation of fresh fruit. To better understand the underlying molecular mechanisms of fruit softening in LBL, changes in the pre-climacteric (S1) and post-climacteric (S2) proteomes were investigated by iTRAQ methods. The 14-fold reduction in S2 fruit firmness compared to S1 was accompanied by increased espiratory intensity and degradation of cell wall components. A total of 258 differentially expressed proteins (DEPs) were identified, which were mainly associated with photosynthesis, carbohydrate, amino acids and fatty acids metabolism. From the functional proteomic analysis, enhanced energy metabolisms, such as glycolysis/gluconeogenesis and citrate cycle (TCA cycle) contributed to cell wall degradation and conversion to substrates for respiratory metabolism, leading to fruit softening. These findings have provided new insights into the molecular pathways associated with fruit softening in LBL and the bioinformatics analyses provided insightful information for further transcriptional studies.
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Choi HR, Baek MW, Jeong CS, Tilahun S. Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene. Curr Issues Mol Biol 2022; 44:2593-2613. [PMID: 35735618 PMCID: PMC9221576 DOI: 10.3390/cimb44060177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality.
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Affiliation(s)
- Han Ryul Choi
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Min Woo Baek
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Cheon Soon Jeong
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
| | - Shimeles Tilahun
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon 24341, Korea
- Department of Horticulture and Plant Sciences, Jimma University, Jimma 378, Ethiopia
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
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Comparative Proteomic Analysis of Wild-type and a SlETR-3 (Nr) Mutant Reveals an Ethylene-Induced Physiological Regulatory Network in Fresh-Cut Tomatoes. Food Res Int 2022; 161:111491. [DOI: 10.1016/j.foodres.2022.111491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022]
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Lewis RW, Okubara PA, Sullivan TS, Madden BJ, Johnson KL, Charlesworth MC, Fuerst EP. Proteome-Wide Response of Dormant Caryopses of the Weed, Avena fatua, After Colonization by a Seed-Decay Isolate of Fusarium avenaceum. PHYTOPATHOLOGY 2022; 112:1103-1117. [PMID: 35365054 DOI: 10.1094/phyto-06-21-0234-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Promoting seed decay is an ecological approach to reducing weed persistence in the soil seedbank. Previous work demonstrated that Fusarium avenaceum F.a.1 decays dormant Avena fatua (wild oat) caryopses and induces several defense enzyme activities in vitro. The objectives of this study were to obtain a global perspective of proteins expressed after F.a.1-caryopsis colonization by conducting proteomic evaluations on (i) leachates, soluble extrinsic (seed-surface) proteins released upon washing caryopses in buffer and (ii) proteins extracted from whole caryopses; interactions with aluminum (Al) were also evaluated in the latter study because soil acidification and associated metal toxicity are growing problems. Of the 119 leachate proteins classified as defense/stress, 80 were induced or repressed. Defense/stress proteins were far more abundant in A. fatua (35%) than in F.a.1 (12%). Avena defense/stress proteins were also the most highly regulated category, with 30% induced and 35% repressed by F.a.1. Antifungal proteins represented 36% of Avena defense proteins and were the most highly regulated, with 36% induced and 37% repressed by F.a.1. These results implicate selective regulation of Avena defense proteins by F.a.1. Fusarium proteins were also highly abundant in the leachates, with 10% related to pathogenicity, 45% of which were associated with host cell wall degradation. In whole caryopsis extracts, fungal colonization generally resulted in induction of a similar set of Avena proteins in the presence and absence of Al. Results advance the hypothesis that seed decay pathogens elicit intricate and dynamic biochemical responses in dormant seeds.
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Affiliation(s)
- Ricky W Lewis
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Patricia A Okubara
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Benjamin J Madden
- Mayo Clinic Medical Genome Facility, Proteomics Core, Rochester, MN 55905
| | - Kenneth L Johnson
- Mayo Clinic Medical Genome Facility, Proteomics Core, Rochester, MN 55905
| | | | - E Patrick Fuerst
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
- Western Wheat Quality Laboratory, Washington State University, Pullman, WA 99164
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Xiao L, Liang H, Jiang G, Ding X, Liu X, Sun J, Jiang Y, Song L, Duan X. Proteome-wide identification of non-histone lysine methylation in tomato during fruit ripening. J Adv Res 2022; 42:177-188. [PMID: 36513412 PMCID: PMC9788949 DOI: 10.1016/j.jare.2022.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Histone and non-histone methylations are important post-translational modifications in plants. Histone methylation plays a crucial role in regulating chromatin structure and gene expression. However, the involvement of non-histone methylation in plant biological processes remains largely unknown. METHODS The methylated substrates and methylation sites during tomato fruit ripening were identified by LC-MS/MS. Bioinformatics of lysine methylated proteins was conducted to analyze the possible role of methylated proteins. The effects of methylation modification on protein functions were preliminarily investigated by site-directed mutation simulation. RESULTS A total of 241 lysine methylation (mono-, di- and trimethylation) sites in 176 proteins were identified with two conserved methylation motifs: xxxxxxExxx_K_xxxExxxxxx and xxxxxxExxx_K_xxxxxxxxxx. These methylated proteins were mainly related to fruit ripening and senescence, oxidation reduction process, signal transduction, stimulus and stress responses, and energy metabolism. Three representative proteins, thioredoxin (Trx), glutathione S-transferase T1 (GST T1), and NADH dehydrogenase (NOX), were selected to investigate the effect of methylation modifications on protein activity. Mimicking demethylation led to decreased Trx activity but increased GST T1 and NOX activities. In addition, RT-qPCR exhibited that the expression of many genes that encode proteins subjected to methylation was upregulated during fruit ripening. CONCLUSION Our study suggests that tomato fruit ripening undergo non-histone lysine methylation, which may participate in the regulation of fruit ripening. It is the first report of methyl proteome profiling of non-histone lysine in horticultural crops.
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Affiliation(s)
- Lu Xiao
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China,Key Laboratory of Testing and Evaluation for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Hanzhi Liang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoxiang Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuncheng Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jian Sun
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an 311300, Zhejiang Province, China,Corresponding authors at: Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (X. Duan).
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China,Corresponding authors at: Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (X. Duan).
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11
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Changes in Homogalacturonan Metabolism in Banana Peel during Fruit Development and Ripening. Int J Mol Sci 2021; 23:ijms23010243. [PMID: 35008668 PMCID: PMC8745247 DOI: 10.3390/ijms23010243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023] Open
Abstract
Though numerous studies have focused on the cell wall disassembly of bananas during the ripening process, the modification of homogalacturonan (HG) during fruit development remains exclusive. To better understand the role of HGs in controlling banana fruit growth and ripening, RNA-Seq, qPCR, immunofluorescence labeling, and biochemical methods were employed to reveal their dynamic changes in banana peels during these processes. Most HG-modifying genes in banana peels showed a decline in expression during fruit development. Four polygalacturonase and three pectin acetylesterases showing higher expression levels at later developmental stages than earlier ones might be related to fruit expansion. Six out of the 10 top genes in the Core Enrichment Gene Set were HG degradation genes, and all were upregulated after softening, paralleled to the significant increase in HG degradation enzyme activities, decline in peel firmness, and the epitope levels of 2F4, CCRC-M38, JIM7, and LM18 antibodies. Most differentially expressed alpha-1,4-galacturonosyltransferases were upregulated by ethylene treatment, suggesting active HG biosynthesis during the fruit softening process. The epitope level of the CCRC-M38 antibody was positively correlated to the firmness of banana peel during fruit development and ripening. These results have provided new insights into the role of cell wall HGs in fruit development and ripening.
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12
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Liu J, Liu M, Wang J, Zhang J, Miao H, Wang Z, Jia C, Zhang J, Xu B, Jin Z. Transcription factor MaMADS36 plays a central role in regulating banana fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7078-7091. [PMID: 34282447 DOI: 10.1093/jxb/erab341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Bananas are model fruits for studying starch conversion and climactericity. Starch degradation and ripening are two important biological processes that occur concomitantly in banana fruit. Ethylene biosynthesis and postharvest fruit ripening processes, i.e. starch degradation, fruit softening, and sugar accumulation, are highly correlated and thus could be controlled by a common regulatory switch. However, this switch has not been identified. In this study, we transformed red banana (Musa acuminata L.) with sense and anti-sense constructs of the MaMADS36 transcription factor gene (also MuMADS1, Ma05_g18560.1). Analysis of these lines showed that MaMADS36 interacts with 74 other proteins to form a co-expression network and could act as an important switch to regulate ethylene biosynthesis, starch degradation, softening, and sugar accumulation. Among these target genes, musa acuminata beta-amylase 9b (MaBAM9b, Ma05_t07800.1), which encodes a starch degradation enzyme, was selected to further investigate the regulatory mechanism of MaMADS36. Our findings revealed that MaMADS36 directly binds to the CA/T(r)G box of the MaBAM9b promoter to increase MaBAM9b transcription and, in turn, enzyme activity and starch degradation during ripening. These results will further our understanding of the fine regulatory mechanisms of MADS-box transcription factors in regulating fruit ripening, which can be applied to breeding programs to improve fruit shelf-life.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Mengting Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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13
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Zhang L, Wu CL, Yang P, Wang YC, Zhang LL, Yang XY. Chilling injury mechanism of hardy kiwifruit (Actinidia arguta) was revealed by proteome of label-free techniques. J Food Biochem 2021; 45:e13897. [PMID: 34390016 DOI: 10.1111/jfbc.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/25/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
Refrigeration is an important method to extend shelf life of hardy kiwifruit. However, the inappropriate storage temperature can lead to chilling injury in the fruit. We found that firmness, total soluble solids, and total polyphenolic content of the fruit exposed to 0℃ environment were apparently lower, and titratable acidity content, browning rate, weight loss rate, electrolyte leakage, proline content, and malondialdehyde content were higher obviously than 4℃. A total of 244 differentially expressed proteins were found result from differential temperatures, among which 113 were up-regulated and 131 were down-regulated. Subcellular localization results presented that the differentially expressed proteins which were affected by low temperature were located in cytoplasmic, chloroplast, nuclear, mitochondrial, plasma membrane, and extracellular. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed proteins were mainly participated in synthesis of citrate cycle, oxidative phosphorylation, fatty acid biosynthesis, and starch and sucrose metabolism. Protein-protein interaction results revealed that central proteins interaction points respectively are 30S ribosomal proteins, 30S ribosomal protein S7, chloroplastic, cell division cycle 5-like protein, 50S ribosomal protein, ribosomal protein, ribosomal protein L6 protein, and SRP54 subunit protein. The quality deviations of all identified peptides were mainly distributed within 10 ppm, and MS2 has an ideal andromeda score, with more than 87.82% peptide scores above 60 points, and the median peptide score of 99.28 points. Therefore, the results of this study provide important information for new gene revelation and gene interaction relationship in hardy kiwifruit of chilling injury. PRACTICAL APPLICATIONS: Inhibition of cold damage in hardy kiwifruit under low temperature is very important work for the development of its storage industry. However, many qualities of fruit will deteriorate after long-term cold storage and those biological activities of the fruits are regulated by proteins. It is, therefore, of great significance to reveal the key proteins caused cold damage in hardy kiwifruit. Moreover, the study results could provide a scientific information for the quality improvement and genetic modification of hardy kiwifruit.
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Affiliation(s)
- Lei Zhang
- Department of Food Engineering, School of Food Engineering, Jilin Agriculture and Technology University, Jilin, PR China
| | - Chun-Ling Wu
- Department of Food Science, Forest College, Bei Hua University, Jilin, PR China
| | - Ping Yang
- Department of Food Engineering, School of Food Engineering, Jilin Agriculture and Technology University, Jilin, PR China
| | - Ying-Chen Wang
- Department of Food Engineering, School of Food Engineering, Jilin Agriculture and Technology University, Jilin, PR China
| | - Lu-Lu Zhang
- Department of Food Science, Forest College, Bei Hua University, Jilin, PR China
| | - Xi-Yue Yang
- Department of Food Engineering, School of Food Engineering, Jilin Agriculture and Technology University, Jilin, PR China
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14
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Niu J, Sun Z, Shi Y, Huang K, Zhong Y, Chen J, Chen J, Luan M. Comparative Analysis of Akebia trifoliata Fruit Softening at Different Flesh Ripening Stages Using Tandem Mass Tag Technology. Front Nutr 2021; 8:684271. [PMID: 34291071 PMCID: PMC8287030 DOI: 10.3389/fnut.2021.684271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
Owing to its medicinal and high nutritional values, Akebia trifoliata can be considered as a new type of medicinal and edible homologous resources, and it has begun to be widely cultivated in many areas of China. Over-softening of fruit would affect the sensorial quality, utilization rate, and consumer acceptance of the fruit postharvest. However, fruit softening has not been characterized and the molecular mechanism underlying A. trifoliata fruit softening during ripening remains unclear. A comparative proteomic analysis was performed on the fruit at three developmental stages using tandem mass tag technology. In total, 2,839 proteins and 302 differentially abundant proteins (DAPs) were identified. Bioinformatics analysis indicated that most DAPs were implicated in oxidoreductase activity, protein domain-specific binding and pyruvate metabolism. Moreover, 29 DAPs associated with cell wall metabolism, plant hormone, and stress and defense response pathways were validated using quantitative PCR. Notably, pectinesterase, pectate lyase, and β-galactosidase, which are involved in cell wall degradation, as well as gibberellin regulated protein, cysteine protease, thaumatin-like protein and heat shock proteins which is involved in plant hormone, and stress and defense response, were significantly up-regulated in softening fruit compared with the levels in non-softening fruit. This indicated that they might play key roles in A. trifoliata fruit softening. Our findings will provide new insights into potential genes influencing fruit softening traits of A. trifoliata, which will help to develop strategies to improve fruit quality and reduce softening-related losses.
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Affiliation(s)
- Juan Niu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Zhimin Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Yaliang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Kunyong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Yicheng Zhong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Jing Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Jianhua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Changsha, China
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15
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Minamikawa MF, Kunihisa M, Noshita K, Moriya S, Abe K, Hayashi T, Katayose Y, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Iwata H. Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study. HORTICULTURE RESEARCH 2021; 8:49. [PMID: 33642580 PMCID: PMC7917097 DOI: 10.1038/s41438-021-00485-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 05/21/2023]
Abstract
Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F1 individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.
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Affiliation(s)
- Mai F Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Koji Noshita
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shigeki Moriya
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Kazuyuki Abe
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yuichi Katayose
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Toshimi Matsumoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Chikako Nishitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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16
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Tian X, Zhu L, Yang N, Song J, Zhao H, Zhang J, Ma F, Li M. Proteomics and Metabolomics Reveal the Regulatory Pathways of Ripening and Quality in Post-Harvest Kiwifruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:824-835. [PMID: 33410682 DOI: 10.1021/acs.jafc.0c05492] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the metabolic modulation of major quality traits during ripening is critical for fruit quality improvement in kiwifruits. Here, integrated proteomic and metabolomic profiling was undertaken to comprehensively examine the dynamics of kiwifruit ripening. This data set presents a global view of the critical pathways involved in fruit ripening, and the contributions of key events to the regulation of kiwifruit ripening and softening, amino acid metabolism, balance in sugar accumulation and organic acid metabolism, glycolysis, and tricarboxylic acid (TCA) pathways were discussed. We suggested key enzymes for starch synthesis and degradation, including AGPase, SS, and SBE, especially for BMY, which was considered a key enzyme for starch degradation. In addition, our analysis implicated the key enzymes ACO4 and ACS9 in ethylene synthesis and the aspartate aminotransferase ASP3 in the conversion of amino acids. These results provide new insights into the modulation of fruit ripening, metabolism, and quality in post-harvest kiwifruits.
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Affiliation(s)
- Xiaocheng Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nanxiang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianyu Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haiyan Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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17
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Xiao S, Liu L, Zhang Y, Sun H, Zhang K, Bai Z, Dong H, Liu Y, Li C. Tandem mass tag-based (TMT) quantitative proteomics analysis reveals the response of fine roots to drought stress in cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2020; 20:328. [PMID: 32652934 PMCID: PMC7353779 DOI: 10.1186/s12870-020-02531-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Fine roots are the central part of the root system that contributes to plant water and nutrient uptake. However, the mechanisms underlying the response of cotton fine roots to soil drought remains unclear. To elucidate the proteomic changes in fine roots of cotton plants under drought stress, 70-75% and 40-45% soil relative water content treatments were imposed on control (CK) and drought stress (DS) groups, respectively. Then, tandem mass tags (TMT) technology was used to determine the proteome profiles of fine root tissue samples. RESULTS Drought significantly decreased the value of average root diameter of cotton seedlings, whereas the total root length and the activities of antioxidases were increased. To study the molecular mechanisms underlying drought response further, the proteome differences between tissues under CK and DS treatments were compared pairwise at 0, 30, and 45 DAD (days after drought stress). In total, 118 differentially expressed proteins (DEPs) were up-regulated and 105 were down-regulated in the 'DS30 versus CK30' comparison; 662 DEPs were up-regulated, and 611 were down-regulated in the 'DS45 versus CK45' comparison. The functions of these DEPs were classified according to their pathways. Under early stage drought (30 DAD), some DEPs involved in the 'Cutin, suberin, and wax synthesis' pathway were up-regulated, while the down-regulated DEPs were mainly enriched within the 'Monoterpenoid biosynthesis' pathway. Forty-five days of soil drought had a greater impact on DEPs involved in metabolism. Many proteins involving 'Carbohydrate metabolism,' 'Energy metabolism,' 'Fatty acid metabolism,' 'Amino acid metabolism,' and 'Secondary metabolite biosynthesis' were identified as DEPs. Additionally, proteins related to ion transport, stress/defense, and phytohormones were also shown to play roles in determining the fine root growth of cotton plants under drought stress. CONCLUSIONS Our study identified potential biological pathways and drought-responsive proteins related to stress/defense responses and plant hormone metabolism under drought stress. Collectively, our results provide new insights for further improving drought tolerance in cotton and other crops.
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Affiliation(s)
- Shuang Xiao
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Liantao Liu
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Yongjiang Zhang
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Hongchun Sun
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Ke Zhang
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Zhiying Bai
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Hezhong Dong
- Cotton Research Center/ Key Laboratory of Cotton Breeding and Cultivation in Huang-huai-hai Plain, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Yuchun Liu
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China
| | - Cundong Li
- College of Agronomy, Hebei Agricultural University/ State Key Laboratory of North China Crop Improvement and Regulation / Key Laboratory of Crop Growth Regulation of HeBei Province, Baoding, 071001, Hebei, China.
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Duan J, Dong W, Xie L, Fan S, Xu Y, Li Y. Integrative proteomics-metabolomics strategy reveals the mechanism of hepatotoxicity induced by Fructus Psoraleae. J Proteomics 2020; 221:103767. [DOI: 10.1016/j.jprot.2020.103767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/11/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
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