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Xia P, Zhou S, Zhao X, Zhao C. Characterization and Expression Analysis of Sugar Transporters through Partial Least Square Structural Equation Model (PLS-SEM) Revealed Their Role in Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1825. [PMID: 38999665 PMCID: PMC11243835 DOI: 10.3390/plants13131825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
Pepper (Capsicum annuum L.) is one of the most important economic crops in the world. By controlling the transport and distribution of photosynthetic products between cells and organs, sugar transporters are widely involved in growth and development, environmental adaptation, and microbial interactions. The present study was carried out at the genome-wide level to systematically characterize sugar transporters. As a result, 50 MST, 3 SUT, and 29 SWEET genes were identified and classified. The expression pattern of sugar transporters in pepper was analyzed by transcriptomic data. The expression properties of sugar transporters were further explored in pepper varieties with significant differences in weight, shape, and pungency. It was shown that the pepper sugar transporter genes had obvious spatiotemporal specific expression characteristics and exhibited variety-specific expression preferences. We focus on analyzing candidate genes that may be involved in fruit development and expansion. We further explore the response of pepper sugar transporters to adversity stress using a structural equation model. Finally, we found that the MST, SUT, and SWEET families are collectively involved in balancing pepper resistance to abiotic stress by coordinating the expression strengths of different family members. Our study may contribute to the functional study of pepper sugar transporter genes and create the prospect of utilizing sugar transporter gene resources to improve pepper variety.
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Affiliation(s)
- Pan Xia
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shiyong Zhou
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xiaoxue Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changling Zhao
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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de Aguiar ÉS, Dias AN, Sousa RM, Germano TA, de Sousa RO, Miranda RDS, Costa JH, dos Santos CP. Genome and Transcriptome Analyses of Genes Involved in Ascorbate Biosynthesis in Pepper Indicate Key Genes Related to Fruit Development, Stresses, and Phytohormone Exposures. PLANTS (BASEL, SWITZERLAND) 2023; 12:3367. [PMID: 37836106 PMCID: PMC10574469 DOI: 10.3390/plants12193367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/10/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Pepper (Capsicum annuum L.) is a vegetable consumed worldwide, primarily used for vitamin C uptake and condiment purposes. Ascorbate (Asc) is a multifunctional metabolite, acting as an antioxidant and enzymatic cofactor involved in multiple cellular processes. Nevertheless, there is no evidence about the contribution of biosynthesis pathways and regulatory mechanisms responsible for Asc reserves in pepper plants. Here, we present a genome- and transcriptome-wide investigation of genes responsible for Asc biosynthesis in pepper during fruit development, stresses, and phytohormone exposures. A total of 21 genes, scattered in ten of twelve pepper chromosomes were annotated. Gene expression analyses of nine transcriptomic experiments supported the primary role of the L-galactose pathway in the Asc-biosynthesizing process, given its constitutive, ubiquitous, and high expression profile observed in all studied conditions. However, genes from alternative pathways generally exhibited low expression or were unexpressed and appeared to play some secondary role under specific stress conditions and phytohormone treatments. Taken together, our findings provide a deeper spatio-temporal understanding of expression levels of genes involved in Asc biosynthesis, and they highlight GGP2, GME1 and 2, and GalLDH members from L-galactose pathway as promising candidates for future wet experimentation, addressing the attainment of increase in ascorbate content of peppers and other crops.
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Affiliation(s)
- Évelyn Silva de Aguiar
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
| | - Abigailde Nascimento Dias
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Raquel Mendes Sousa
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Thais Andrade Germano
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Renato Oliveira de Sousa
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
| | - Rafael de Souza Miranda
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
- Plant Science Department, Federal University of Piauí, Teresina 64049-550, Piauí, Brazil
| | - José Hélio Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Clesivan Pereira dos Santos
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
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Du K, Zhao W, Lv Z, Liu L, Ali S, Chen B, Hu W, Zhou Z, Wang Y. Auxin and abscisic acid play important roles in promoting glucose metabolism of reactivated young kernels of maize (Zea mays L.). PHYSIOLOGIA PLANTARUM 2023; 175:e14019. [PMID: 37882255 DOI: 10.1111/ppl.14019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 10/27/2023]
Abstract
In maize, young kernels that are less competitive and have poor sink activity often abort. Studies have indicated that such poor competitiveness depends, in part, on the regulation by auxin (IAA) and abscisic acid (ABA). However, the mechanisms for such effects remain unclear. We used pollination-blocking and hand-pollination treatments accompanied by multi-omics and physiological tests, to identify underlying mechanism by which IAA and ABA, along with sugar signaling affect kernel development. Results showed that preventing pollination of the primary ears reactivated kernels in the secondary ears and altered both sugar metabolism and hormone signaling pathways. This was accompanied by increased enzyme activities in carbon metabolism and concentrations of glucose and starch, as well as increased levels of IAA and decreased levels of ABA in the reactivated kernels. Positive and negative correlations were observed between IAA, ABA contents and cell wall invertase (CWIN) activity, and glucose contents, respectively. In vitro culture revealed that the expression of genes involved in glucose utilization was upregulated by IAA, but downregulated by ABA. IAA could promote the expression of ABA signaling genes ZmPP2C9 and ZmPP2C13 but downregulated the expression of Zmnced5, an ABA biosynthesis gene, and ZmSnRK2.10, which is involved in ABA signal transduction. However, these genes showed opposite trends when IAA transport was inhibited. To summarize, we suggest a regulatory model for how IAA inhibits ABA metabolism by promoting the smooth utilization of glucose in reactivated young kernels. Our findings highlight the importance of IAA in ABA signaling by regulating glucose production and transport in maize.
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Affiliation(s)
- Kang Du
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wenqing Zhao
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agricultural University, Nanjing, China
| | - Zhiwei Lv
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Lin Liu
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Saif Ali
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Binglin Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agricultural University, Nanjing, China
| | - Wei Hu
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agricultural University, Nanjing, China
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agricultural University, Nanjing, China
| | - Youhua Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agricultural University, Nanjing, China
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Heng Z, Xu X, Xu X, Li Y, Wang H, Huang W, Yan S, Li T. Integrated transcriptomic and metabolomic analysis of chili pepper fruits provides new insight into the regulation of the branched chain esters and capsaicin biosynthesis. Food Res Int 2023; 169:112856. [PMID: 37254430 DOI: 10.1016/j.foodres.2023.112856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 06/01/2023]
Abstract
Chili pepper (Capsicum spp.) is one of the world's most popular vegetables and spices. Aroma is an important quality indicator of pepper, but the nature of the related volatiles is still not clear. In this study, we investigated the fruit of two pepper varieties, one with strong fruity aroma 'CC' Capsicum chinense and one without 'TJ' Capsicum annuum at four different developmental stages using transcriptomic and metabolomic analysis. The results showed that the content of green leaf volatiles (GLVs) was higher in TJ than in CC and was higher in the young fruit stage in both varieties. GLVs content was positively correlated with the expression of 13-LOX1, 2, 5 and HPL. But the levels of branched-chain (BC) esters and capsaicin were higher in CC, and were positively correlated with the expression of IMPS4 and DADH1. Our findings shed light on the molecular mechanism of aroma biosynthesis in pepper and provide a theoretical basis for the molecular breeding of high-quality pepper fruits.
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Affiliation(s)
- Zhou Heng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Xiaowan Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Xiaomei Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Ying Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Hengming Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China.
| | - Tao Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China.
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Huang C, Li P, Yang X, Niu T, Zhao S, Yang L, Wang R, Wang Z. Integrated transcriptome and proteome analyses reveal candidate genes for ginsenoside biosynthesis in Panax japonicus C. A. Meyer. FRONTIERS IN PLANT SCIENCE 2023; 13:1106145. [PMID: 36699857 PMCID: PMC9868605 DOI: 10.3389/fpls.2022.1106145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Panax japonicus C. A. Meyer is a plant of the Araliaceae family, and its rhizomes can be used as dietary supplements. It is extremely rich in bioactive components ginsenosides with benefits to human health. However, the underlying mechanisms of ginsenosides biosynthesis in Panax japonicus remains poorly understood. Therefore, a comprehensive analysis of the metabolites, transcriptome, and proteome was conducted to investigate ginsenoside metabolism of Panax japonicus. Here, three types of ginsenosides were found to exhibited tissue-specific distribution using the liquid chromatography-mass spectrometry method. Next, differentially expressed gene analysis revealed that transcript levels of ginsenosides biosynthetic genes have significant differences between differential samples. In addition, correlation analysis showed that the ginsenosides content was closely related to the expression level of 29 cytochrome P450s and 92 Uridine diphosphate-glycosyltransferases. Finally, phylogenetic analysis was performed for the target proteins to conduct preliminary studies on their functions and classification. This study provides insight into the dynamic changes and biosynthetic pathway of ginsenosides and offers valuable information on the metabolic regulation of Panax japonicus.
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Affiliation(s)
- Chaokang Huang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pengfei Li
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaolin Yang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tengfei Niu
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Yang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rufeng Wang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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6
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Jaiswal V, Rawoof A, Gahlaut V, Ahmad I, Chhapekar SS, Dubey M, Ramchiary N. Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F 1 hybrid. iScience 2022; 25:105318. [PMID: 36304106 PMCID: PMC9593261 DOI: 10.1016/j.isci.2022.105318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/04/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F1 hybrid and parents, and of these, 4891 DMRs showed higher methylation in F1 compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46–55% differentially expressed genes (DE-Gs) in the F1 hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65–72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F1 hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis in Capsicum. Global methylation identified significantly different proportions of mCs in hybrid Of common DMRs, 33.08% showed different methylation in hybrid from the mid-parental value Negatively correlated DEG pDMR-genes were enriched in metabolic pathways Significant higher expression of metabolites and DE-Gs were identified in the F1 hybrid
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Affiliation(s)
- Vandana Jaiswal
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Corresponding author
| | - Abdul Rawoof
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ilyas Ahmad
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sushil S. Chhapekar
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department of Horticulture, Chungnam National University, Daejeon 34134, South Korea
| | - Meenakshi Dubey
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Nirala Ramchiary
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Corresponding author
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Ge S, Qin K, Ding S, Yang J, Jiang L, Qin Y, Wang R. Gas Chromatography-Mass Spectrometry Metabolite Analysis Combined with Transcriptomic and Proteomic Provide New Insights into Revealing Cuticle Formation during Pepper Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12383-12397. [PMID: 36148491 DOI: 10.1021/acs.jafc.2c04522] [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: 06/16/2023]
Abstract
The cuticle plays an important role for the quality of pepper fruit. However, the molecular mechanism of cuticle formation in pepper fruit remains unclear. Our results showed that the wax was continuously accumulated during pepper development, while the cutin monomer first increased and then decreased. Hexadecanoic acid and 10,16-hydroxyhexadecanoic acid were the main components of wax and cutin, respectively. Combined with transcriptome and proteome, the formation patterns of wax and cutin polyester network for pepper cuticle was proposed. The 18 pairs of consistent expression genes and proteins involved in cuticle formation were revealed. Meanwhile, 12 key genes were screened from fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, fatty acid elongation, cutin, suberine, and wax biosynthesis, glycerolipid metabolism, and transport pathway. This study would provide important candidate genes and theoretical basis for the molecular mechanism of cuticle formation, which is essential for the breeding of peppers.
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Affiliation(s)
- Shuai Ge
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Keying Qin
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shenghua Ding
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jianfeng Yang
- Liuyang Hongxiu Agricultural Technology Co., Ltd., Liuyang 410300, China
| | - Liwen Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yeyou Qin
- Hunan Tantanxiang Food Biotechnology Co., Ltd., Changsha 410128, China
| | - Rongrong Wang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
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Cai Y, Xu M, Liu J, Zeng H, Song J, Sun B, Chen S, Deng Q, Lei J, Cao B, Chen C, Chen M, Chen K, Chen G, Zhu Z. Genome-wide analysis of histone acetyltransferase and histone deacetylase families and their expression in fruit development and ripening stage of pepper ( Capsicum annuum). FRONTIERS IN PLANT SCIENCE 2022; 13:971230. [PMID: 36161016 PMCID: PMC9490122 DOI: 10.3389/fpls.2022.971230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
The fruit development and ripening process involve a series of changes regulated by fine-tune gene expression at the transcriptional level. Acetylation levels of histones on lysine residues are dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which play an essential role in the control of gene expression. However, their role in regulating fruit development and ripening process, especially in pepper (Capsicum annuum), a typical non-climacteric fruit, remains to understand. Herein, we performed genome-wide analyses of the HDAC and HAT family in the pepper, including phylogenetic analysis, gene structure, encoding protein conserved domain, and expression assays. A total of 30 HAT and 15 HDAC were identified from the pepper genome and the number of gene differentiation among species. The sequence and phylogenetic analysis of CaHDACs and CaHATs compared with other plant HDAC and HAT proteins revealed gene conserved and potential genus-specialized genes. Furthermore, fruit developmental trajectory expression profiles showed that CaHDAC and CaHAT genes were differentially expressed, suggesting that some are functionally divergent. The integrative analysis allowed us to propose CaHDAC and CaHAT candidates to be regulating fruit development and ripening-related phytohormone metabolism and signaling, which also accompanied capsaicinoid and carotenoid biosynthesis. This study provides new insights into the role of histone modification mediate development and ripening in non-climacteric fruits.
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Affiliation(s)
- Yutong Cai
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Mengwei Xu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiarong Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Haiyue Zeng
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Jiali Song
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Binmei Sun
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Siqi Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qihui Deng
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jianjun Lei
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Bihao Cao
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Changming Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Muxi Chen
- Guangdong Helinong Seeds Co., Ltd., Shantou, China
| | - Kunhao Chen
- Guangdong Helinong Seeds Co., Ltd., Shantou, China
| | - Guoju Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
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9
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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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10
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Sun P, Ma Q, Zhang L. Comprehensive acetyl-proteomic analysis of Cytospora mali provides insight into its response to the biocontrol agent Bacillus velezensis L-1. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.999510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytospora mali is an important factor for apple valsa canker, and Bacillus veleznesis L-1 is an effective biocontrol agent against apple valsa canker. Quantitative acetyl-proteomics is known to regulate transcriptional activity in different organisms; limited knowledge is available for acetylation modification in C. mali, and its response to biocontrol agents. In this study, using Tandem Mass tag proteomic strategies, we identified 733 modification sites on 416 proteins in C. mali, functions of these proteins were analyzed using GO enrichment and KEGG pathway. Some lysine acetylated proteins are found to be important to the fungal pathogenicity of C. mali, and also the response of fungi to biostress. B. velezensis L-1 suppressed the C. mali QH2 by causing the energy shortage and reduced virulence. Correspondingly, the C. mali QH2 could alleviate the suppression of biostress by upregulation of autophagy, peroxidase, cytochrome P450, ABC transporter and Heat shock protein 70. In summary, our results provided the first lysine acetylome of C. mali and its response to B. velezensis L-1.
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11
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Chen X, Han J, Wang S. Integrated evolutionary analysis reveals the resistance risk to antimicrobial peptides in Staphylococcus aureus. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Zou W, Zhao C, Zhang X, Jin C, Jiang K, Zhou Q. Mitigation Effects and Associated Mechanisms of Environmentally Relevant Thiols on the Phytotoxicity of Molybdenum Disulfide Nanosheets. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9556-9568. [PMID: 35576172 DOI: 10.1021/acs.est.1c08534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Thorough investigations of the environmental fate and risks are necessary for the safe application of engineered nanomaterials. Nevertheless, the current understanding of potential transformations of MoS2 (an intensively studied two-dimensional nanosheet) upon interactions with ubiquitous environmentally relevant thiols (ERTs) in water is limited. This study revealed that two ERTs, l-cysteine and mercaptoacetic acid, could modify MoS2 by covalently grafting thiol groups on S atoms of 1T phases, improving the colloidal persistence and chemical stability of MoS2. Compared with the pristine form, MoS2-thiols with higher dispersity exhibited significantly mitigated envelopment and ultrastructural damage to microalgae. MoS2-triggered growth inhibition, upregulation of reactive oxygen species, photosynthetic injury, and metabolic perturbation in algae were remarkably attenuated by ERTs. The diminished capability for MoS2 to generate reactive intermediates and glutathione oxidation driven by ERTs caused the weakness of oxidative stress and negative effects. Additionally, molecular dynamics simulations demonstrated that ERTs altered the extent of the influence of MoS2 on the secondary structures and functions of adsorbed intracellular proteins, which also contributed to the lower phytotoxicity of MoS2. Our findings provide evidence for the crucial role of specific organic ligands in the risk of MoS2 in aquatic environments.
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Affiliation(s)
- Wei Zou
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Chenxu Zhao
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Xingli Zhang
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Caixia Jin
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Kai Jiang
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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13
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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14
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Yan H, Nie Y, Cui K, Sun J. Integrative Transcriptome and Metabolome Profiles Reveal Common and Unique Pathways Involved in Seed Initial Imbibition Under Artificial and Natural Salt Stresses During Germination of Halophyte Quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:853326. [PMID: 35498713 PMCID: PMC9039654 DOI: 10.3389/fpls.2022.853326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 05/31/2023]
Abstract
Salt stress is a major environmental factor that seriously restricts quinoa seed germination. However, the key regulatory mechanisms underlying the effect of salt stress on the initial imbibition stage of quinoa seeds are unclear. In this study, dry seeds (0 h) and imbibed (8 h) seeds with 450 mM NaCl (artificial salt) and 100% brackish water of Yellow River Estuary (BW, natural salt) were used to assess the key salt responses based on germination, transcriptome, and metabolome analyses. The results indicated that the capacity of germinating seeds to withstand these two salt stresses was similar due to the similarities in the germination percentage, germination index, mean germination time, and germination phenotypes. Combined omics analyses revealed that the common and unique pathways were induced by NaCl and BW. Starch and sucrose metabolism were the only commonly enriched pathways in which the genes were significantly changed. Additionally, amino sugar and nucleotide sugar metabolism, and ascorbate and aldarate metabolism were preferably enriched in the NaCl group. However, glutathione metabolism tended to enrich in the BW group where glutathione peroxidase, peroxiredoxin 6, and glutathione S-transferase were significantly regulated. These findings suggest that the candidates involved in carbohydrate metabolism and antioxidant defense can regulate the salt responses of seed initial imbibition, which provide valuable insights into the molecular mechanisms underlying the effect of artificial and natural salt stresses.
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Affiliation(s)
| | | | | | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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15
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Momo J, Kumar A, Islam K, Ahmad I, Rawoof A, Ramchiary N. A comprehensive update on Capsicum proteomics: Advances and future prospects. J Proteomics 2022; 261:104578. [DOI: 10.1016/j.jprot.2022.104578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 10/18/2022]
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16
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Ye Z, Yu J, Yan W, Zhang J, Yang D, Yao G, Liu Z, Wu Y, Hou X. Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera. HORTICULTURE RESEARCH 2021; 8:157. [PMID: 34193845 PMCID: PMC8245520 DOI: 10.1038/s41438-021-00591-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.
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Affiliation(s)
- Zhouchen Ye
- College of Horticulture, Hainan University, Haikou, China
| | - Jing Yu
- College of Horticulture, Hainan University, Haikou, China
| | - Wuping Yan
- College of Horticulture, Hainan University, Haikou, China
| | - Junfeng Zhang
- College of Horticulture, Hainan University, Haikou, China
| | - Dongmei Yang
- College of Horticulture, Hainan University, Haikou, China
| | - Guanglong Yao
- College of Horticulture, Hainan University, Haikou, China
| | - Zijin Liu
- College of Horticulture, Hainan University, Haikou, China
| | - Yougen Wu
- College of Horticulture, Hainan University, Haikou, China.
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Institute of Plasma Engineering, Nanjing, China.
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17
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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18
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Huang X, Hou Z. Label-free quantitative proteomics analysis of jujube ( Ziziphus jujuba Mill.) during different growth stages. RSC Adv 2021; 11:22106-22119. [PMID: 35480818 PMCID: PMC9034241 DOI: 10.1039/d1ra02989d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.
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Affiliation(s)
- Xiaoli Huang
- College of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences) No. 3501 Daxue Road, Changqing District Ji'nan Shandong Province 250353 P. R. China +86 531 89631191 +86 188 66151356
| | - Zhaohua Hou
- College of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences) No. 3501 Daxue Road, Changqing District Ji'nan Shandong Province 250353 P. R. China +86 531 89631191 +86 188 66151356
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19
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RNA seq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16. BMC Genomics 2021; 22:444. [PMID: 34126926 PMCID: PMC8204557 DOI: 10.1186/s12864-021-07756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 and ATG16. However, the functions of these two core ATG proteins still need further elucidation. Here, we applied RNAseq and tandem mass tag (TMT) proteomic approaches to identify differentially expressed genes (DEGs) and proteins (DEPs) in Dictyostelium discoideum ATG9‾, ATG16‾ and ATG9‾/16‾ strains in comparison to AX2 wild-type cells. RESULT In total, we identified 332 (279 up and 53 down), 639 (487 up and 152 down) and 260 (114 up and 146 down) DEGs and 124 (83 up and 41 down), 431 (238 up and 193 down) and 677 (347 up and 330 down) DEPs in ATG9‾, ATG16‾ and ATG9‾/16‾ strains, respectively. Thus, in the single knock-out strains, the number of DEGs was higher than the number of DEPs while in the double knock-out strain the number of DEPs was higher. Comparison of RNAseq and proteomic data further revealed, that only a small proportion of the transcriptional changes were reflected on the protein level. Gene ontology (GO) analysis revealed an enrichment of DEPs involved in lipid metabolism and oxidative phosphorylation. Furthermore, we found increased expression of the anti-oxidant enzymes glutathione reductase (gsr) and catalase A (catA) in ATG16‾ and ATG9‾/16‾ cells, respectively, indicating adaptation to excess reactive oxygen species (ROS). CONCLUSIONS Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells. Our results suggest, that most changes in protein abundance were not caused by transcriptional changes, but were rather due to changes in protein homeostasis. In particular, knock-out of atg9 and/or atg16 appears to cause dysregulation of lipid metabolism and oxidative phosphorylation.
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Wang F, Ge S, Xu X, Xing Y, Du X, Zhang X, Lv M, Liu J, Zhu Z, Jiang Y. Multiomics Analysis Reveals New Insights into the Apple Fruit Quality Decline under High Nitrogen Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5559-5572. [PMID: 33945277 DOI: 10.1021/acs.jafc.1c01548] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Excessive application of nitrogen (N) fertilizer is common in Chinese apple production. High N reduced the contents of soluble sugar and total flavonoids by 16.05 and 19.01%, respectively, resulting in poor fruit quality. Moreover, high N increased the total N and decreased the total C and C/N ratio of apple fruits. On the basis of the transcriptomic, proteomic, and metabolomic analyses, the global network was revealed. High N inhibited the accumulation of carbohydrates (sucrose, glucose, and trehalose) and flavonoids (rhamnetin-3-O-rutinoside, rutin, and trihydroxyisoflavone-7-O-galactoside) in fruits, and more C skeletons were used to synthesize amino acids and their derivatives (especially low C/N ratio, e.g., arginine) to be transferred to N metabolism. This study revealed new insights into the decline in soluble sugar and flavonoids caused by high N, and hub genes (MD07G1172700, MD05G1222800, MD16G1227200, MD01G1174400, and MD02G1207200) and hub proteins (PFK, gapN, and HK) were obtained.
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Affiliation(s)
- Fen Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Shunfeng Ge
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xinxiang Xu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yue Xing
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xin Du
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xin Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Mengxue Lv
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jingquan Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Zhanling Zhu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yuanmao Jiang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
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21
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Tartaglia M, Sciarrillo R, Zuzolo D, Amoresano A, Illiano A, Pinto G, Jorrín-Novo JV, Guarino C. Why Consumers Prefer Green Friariello Pepper: Changes in the Protein and Metabolite Profiles Along the Ripening. FRONTIERS IN PLANT SCIENCE 2021; 12:668562. [PMID: 33995464 PMCID: PMC8121147 DOI: 10.3389/fpls.2021.668562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Fruit ripening is a physiologically complex process altering texture, color, flavor, nutritional value, and aroma. However, some fruits are consumed at an early stage of ripening due to the very peculiar characteristics varying during ripening. An example is a particular ecotype of pepper, the Friariello pepper, among the most important representatives of Campania (Southern Italy) agro-alimentary culture. In this study, for the first time, the physiological variations during Friariello ripening (green, veraison, and fully ripe) were evaluated by hyphenated mass spectrometric techniques in a proteomic and metabolomic approach. We found that Lutein and Thaumatin are particularly abundant in the green Friariello. Friariello at an early stage of ripening, is rich in volatile compounds like butanol, 1 3 5-cycloheptatriene, dimethylheptane, α-pinene, furan-2-penthyl, ethylhexanol, 3-carene, detected by gas chromatography-mass spectrometry (GC-MS) analysis, which give it the peculiar fresh and pleasant taste. The detected features of Friariello may justify its preferential consumption in the early ripening stage and outline new knowledge aimed at preserving specific agro-cultural heritage.
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Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Daniela Zuzolo
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Anna Illiano
- CEINGE Advanced Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Jesús V. Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, UCO-CeiA3, Córdoba, Spain
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, Benevento, Italy
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22
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Liu N, Qin L, Mazhar M, Miao S. Integrative transcriptomic-proteomic analysis revealed the flavor formation mechanism and antioxidant activity in rice-acid inoculated with Lactobacillus paracasei and Kluyveromyces marxianus. J Proteomics 2021; 238:104158. [PMID: 33631365 DOI: 10.1016/j.jprot.2021.104158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/18/2022]
Abstract
In the study on fermented acid rice soup (rice-acid) inoculated with L. paracasei H4-11 and K. marxianus L1-1, the concentrations of main flavor components on the third day of fermentation were significantly higher than those on the first day. Transcriptome analysis and proteome analysis based on RNA sequencing and 4D label-free proteomic techniques were combined to provide new insights into the molecular mechanisms of flavor characteristics and antioxidant activity of the two strains during the development of rice-acid. The key up-regulated genes and proteins in L. paracasei and K. marxianus L1-1, which were involved in flavor formation and antioxidant activity in rice-acid development, were different. The KEGG pathways involving the up-regulated genes and proteins in L. paracasei included starch and sucrose metabolism, pyruvate metabolism, amino sugar, and nucleotide sugar metabolism, and glycolysis/guconeogenesis. The KEGG pathways involving the up-regulated genes and proteins in K. marxianus L1-1 mainly included glycolysis/gluconeogenesis, TCA cycle, pyruvate metabolism, and other pathways related to antioxidant capacity. We successfully identified key genes and proteins associated with the metabolism and accumulation of flavor components and antioxidant activity. These findings provide new insights into the molecular mechanisms of flavor formation in co-cultivation with L. paracasei and K. marxianus. SIGNIFICANCE: It is anticipated that this study would provide us an insight into the mechanisms of flavor components accumulation and antioxidant activity of acid rice soup in China's minority areas. Importantly, this research provides the foundation of biological and chemical analysis for the application of the co-culture of L. paracasei H4-11 and K. marxianus in non-dairy products.
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Affiliation(s)
- Na Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Likang Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
| | - Muhammad Mazhar
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Song Miao
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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Zou W, Li X, Li C, Sun Y, Zhang X, Jin C, Jiang K, Zhou Q, Hu X. Influence of Size and Phase on the Biodegradation, Excretion, and Phytotoxicity Persistence of Single-Layer Molybdenum Disulfide. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12295-12306. [PMID: 32852947 DOI: 10.1021/acs.est.0c02642] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The increasing applications of single-layer molybdenum disulfide (SLMoS2) pose great potential risks associated with environmental exposure. This study found that metallic-phase SLMoS2 with nanoscale (N-1T-SLMoS2, ∼400 nm) and microscale (M-1T-SLMoS2, ∼3.6 μm) diameters at 10-25 mg/L induced significant algal growth inhibition (maximum 72.7 and 74.6%, respectively), plasmolysis, and oxidative damage, but these alterations were recoverable. Nevertheless, membrane permeability, chloroplast damage, and chlorophyll biosynthesis reduction were persistent. By contrast, the growth inhibition (maximum 55.3%) and adverse effects of nano-sized semiconductive-phase SLMoS2 (N-2H-SLMoS2, ∼400 nm) were weak and easily alleviated after 96 h of recovery. N-1T-SLMoS2 (0.011 μg/h) and N-2H-SLMoS2 (0.008 μg/h) were quickly biodegraded to soluble Mo compared with M-1T-SLMoS2 (0.004 μg/h) and excreted by algae. Incomplete biodegradation of SLMoS2 (26.8-43.9%) did not significantly mitigate its toxicity. Proteomics and metabolomics indicated that the downregulation of proteins (50.7-99.2%) related to antioxidants and photosynthesis and inhibition of carbon fixation and carbohydrate metabolism contributed to the persistent phytotoxicity. These findings highlight the roles and mechanisms of the size and phase in the persistent phytotoxicity of SLMoS2, which has potential implications for risk assessment and environmental applications of nanomaterials.
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Affiliation(s)
- Wei Zou
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Xinyu Li
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Chonghao Li
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Yuanyuan Sun
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Xingli Zhang
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Caixia Jin
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Kai Jiang
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Normal University, Xinxiang 453007, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Chen J, Gao G, Chen P, Chen K, Wang X, Bai L, Yu C, Zhu A. Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie ( Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation. PLANTS 2020; 9:plants9101267. [PMID: 32992865 PMCID: PMC7650756 DOI: 10.3390/plants9101267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 11/21/2022]
Abstract
Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.
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Affiliation(s)
- Jikang Chen
- Longping Branch, Graduate School of Hunan University, Changsha 410082, China;
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Lianyang Bai
- Longping Branch, Graduate School of Hunan University, Changsha 410082, China;
- Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
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25
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Zhang Y, Yao W, Wang F, Su Y, Zhang D, Hu S, Zhang X. AGC protein kinase AGC1-4 mediates seed size in Arabidopsis. PLANT CELL REPORTS 2020; 39:825-837. [PMID: 32219503 DOI: 10.1007/s00299-020-02533-z] [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: 01/11/2020] [Accepted: 03/13/2020] [Indexed: 05/14/2023]
Abstract
AGC1-4 kinase plays a crucial role in the regulation of seeds by mediating cell proliferation and embryo development in Arabidopsis. Seed size is a crucial factor to influence final seed yield in plants. However, the molecular mechanisms that set final seed size still need to be investigated. Here, we identified a novel AGC protein kinase AGC1-4, which encodes a serine-threonine kinase, belongs to the AGC VIIIa subfamily. The seeds of agc1-4 mutant were significantly larger than that in the wild type. Overexpression of the AGC1-4 gene reduced seed size. Regulation of AGC1-4 seed size is dependent on embryonic cell number. To further determine AGC1-4 functions in seed size, we analyzed AGC1-4 phosphoproteins using label-free quantitative phosphoproteomics coupled to the transcriptome of agc1-4 using RNA sequencing (RNA-seq). The RNA-seq analysis showed 1611 differentially expressed genes (DEGs), which cover a wide range of functions, such as cell cycle and embryo development. The 262 unique phosphoproteins were detected by phosphoproteomics analysis. The differentially phosphorylated proteins were involved in cell cycle and post-embryo development. Overlay of the RNA-seq and phosphoproteomics results demonstrated AGC1-4 as an important factor that influences seed size by mediating cell proliferation and embryo development. The results in this study provide novel data on the serine-threonine kinase AGC1-4 mediating seed size in Arabidopsis.
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Affiliation(s)
- Yuying Zhang
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Wangjinsong Yao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Dajian Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Shengwu Hu
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, 712100, China.
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
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Huang D, Wang Y, Lv J, Yan Y, Hu Y, Liu C, Zhang F, Wang J, Hao D. Proteomic profiling analysis of postmenopausal osteoporosis and osteopenia identifies potential proteins associated with low bone mineral density. PeerJ 2020; 8:e9009. [PMID: 32328356 PMCID: PMC7164430 DOI: 10.7717/peerj.9009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Postmenopausal osteoporosis (PMOP) is a major global public health concern and older women are more susceptible to experiencing fragility fractures. Our study investigated the associations between circulating proteins with bone mineral density (BMD) in postmenopausal women with or without low BMD (osteoporosis and osteopenia) using a tandem mass tag (TMT) labeling proteomic experiment and parallel reaction monitoring testing. Across all plasma samples, we quantitatively measured 1,092 proteins, and the OP and normal control (NC) samples were differentiated by principal component analysis and a partial least squares-discrimination analysis model based on the protein profiling data. The differentially abundant proteins between the low BMD and NC samples mostly exhibited binding, molecular function regulator, transporter and molecular transducer activity, and were involved in metabolic and cellular processes, stimulus response, biological regulation, immune system processes and so forth. TMT analysis and RRM validation indicated that the expression of protein Lysozyme C (P61626) was negatively related to BMD, while the expression of proteins Glucosidase (A0A024R592) and Protein disulfideisomerase A5 (Q14554) was positively related to BMD values. Collectively, our results suggest that postmenopausal women with low BMD have a different proteomic profile or signature. Protein alterations may play an important role in the pathogenesis of PMOP, and they may act as novel biomarkers and targets of therapeutic agents for this disease.
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Affiliation(s)
- Dageng Huang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an, China
| | - Jing Lv
- Clinical Laboratory of Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yuzhu Yan
- Clinical Laboratory of Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Ya Hu
- Department of Physiology, Hunan Polytechnic of Environment and Biology, Hengyang, China
| | - Cuicui Liu
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jihan Wang
- Clinical Laboratory of Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dingjun Hao
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
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Liu Z, Lv J, Liu Y, Wang J, Zhang Z, Chen W, Song J, Yang B, Tan F, Zou X, Ou L. Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction. Int J Mol Sci 2020; 21:ijms21061962. [PMID: 32183026 PMCID: PMC7139842 DOI: 10.3390/ijms21061962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022] Open
Abstract
Limited knowledge is available for phosphorylation modifications in pepper (Capsicum annuum L.), especially in pepper fruit development. In this study, we conducted the first comprehensive phosphoproteomic analysis of pepper fruit at four development stage by Tandem Mass Tag proteomic approaches. A total of 2639 unique phosphopeptides spanning 1566 proteins with 4150 nonredundant sites of phosphorylation were identified, among which 2327 peptides in 1413 proteins were accurately quantified at four different stages. Mature Green (MG) to breaker stage showed the largest number of differentially expressed phosphoproteins and the number of downregulated phosphoproteins was significantly higher than that of upregulated after MG stage. Twenty seven phosphorylation motifs, including 22 pSer motifs and five pThr motifs and 85 kinase including 28 serine/threonine kinases, 14 receptor protein kinases, six mitogen-activated protein kinases, seven calcium-dependent protein kinases, two casein kinases, and some other kinases were quantified. Then the dynamic changes of phosphorylated proteins in ethylene and abscisic acid signaling transduction pathways during fruit development were analyzed. Our results provide a cascade of phosphoproteins and a regulatory network of phosphorylation signals, which help to further understand the mechanism of phosphorylation in pepper fruit development.
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Affiliation(s)
- Zhoubin Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Yuhua Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Jing Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Jingshuang Song
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Bozhi Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Fangjun Tan
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
| | - Lijun Ou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
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28
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Liu Z, Zhao L, Zhang Q, Huo N, Shi X, Li L, Jia L, Lu Y, Peng Y, Song Y. Proteomics-Based Mechanistic Investigation of Escherichia coli Inactivation by Pulsed Electric Field. Front Microbiol 2019; 10:2644. [PMID: 31781086 PMCID: PMC6857472 DOI: 10.3389/fmicb.2019.02644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/30/2019] [Indexed: 11/21/2022] Open
Abstract
The pulsed electric field (PEF) technology has been widely applied to inactivate pathogenic bacteria in food products. Though irreversible pore formation and membrane disruption is considered to be the main contributing factor to PEF's sterilizing effects, the exact molecular mechanisms remain poorly understood. In this study, by using mass spectrometry (MS)-based label-free quantitative proteomic analysis, we compared the protein profiles of PEF-treated and untreated Escherichia coli. We identified a total of 175 differentially expressed proteins, including 52 candidates that were only detected in at least two of the three samples in one experiment group but not in the other group. Functional analysis revealed that the differential proteins were primarily involved in the regulation of cell membrane composition and integrity, stress response, as well as various metabolic processes. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis was conducted on the genes of selected differential proteins at varying PEF intensities, which were known to result in different cell killing levels. The qRT-PCR data confirmed that the proteomic results could be reliably used for further data interpretation, and that the changes in the expression levels of the differential candidates were, to a large extent, caused directly by the PEF treatment. The findings of the current study offered valuable insight into PEF-induced cell inactivation.
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Affiliation(s)
- Zhenyu Liu
- Information Science and Engineering College, Shanxi Agricultural University, Jinzhong, China
| | - Lingying Zhao
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, Columbus, OH, United States
| | - Qin Zhang
- Life Science College, Shanxi Agricultural University, Jinzhong, China
| | - Nan Huo
- Life Science College, Shanxi Agricultural University, Jinzhong, China
| | - Xiaojing Shi
- Life Science College, Shanxi Agricultural University, Jinzhong, China
| | - Linwei Li
- Information Science and Engineering College, Shanxi Agricultural University, Jinzhong, China
| | - Liyan Jia
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong, China
| | - Yuanyuan Lu
- Life Science College, Shanxi Agricultural University, Jinzhong, China
| | - Yong Peng
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, China
| | - Yanbo Song
- Life Science College, Shanxi Agricultural University, Jinzhong, China
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29
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Proteomic analysis of sheep uterus reveals its role in prolificacy. J Proteomics 2019; 210:103526. [PMID: 31605788 DOI: 10.1016/j.jprot.2019.103526] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/19/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022]
Abstract
Small Tail Han sheep have attracted attention for their high fecundity and year-round estrus. However, the molecular mechanisms of this fecundity are unknown. Polymorphism of the FecB gene has been shown to be associated with the ovulation rate and litter size in sheep. In this study, we used tandem mass tag quantitative proteomic techniques to identify the differentially abundant proteins in polytocous and monotocous Small Tail Han sheep (FecB++) uterine tissues in the follicular and luteal phases. In total, 41 and 43 differentially abundant proteins were identified in the follicular and luteal phases, respectively. Correlation analysis between the transcriptome and proteome revealed a positive correlation at the two omics levels of prolificacy. GO and KEGG pathway analyses indicated that the mRNAs and proteins upregulated in the polytocous group relative to the monotocous group are involved in sphingolipid metabolism and amino acid metabolism, and may be important in maintaining uterine functions and increasing the embryo survival rate during the estrus cycle of polytocous sheep. In conclusion, our work provides a prospective understanding of the molecular mechanism underlying the high prolificacy of Small Tail Han sheep. SIGNIFICANCE: Fecundity critically affects the profitability of sheep production, but the genetic mechanism of high-prolificacy is still unclear in sheep. We identified potential signaling pathways and differentially abundant proteins associated with reproductive performance through a combination of sheep uterus tissues proteome and transcriptome analyses. These findings will facilitate a better revealing the mechanism and provide possible targets for molecular design breeding for the formation of polytocous traits in sheep.
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