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Wu Q, He Y, Cui C, Tao X, Zhang D, Zhang Y, Ying T, Li L. Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7469-7483. [PMID: 37421609 DOI: 10.1002/jsfa.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/17/2023] [Accepted: 07/08/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction. RESULTS Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups. CONCLUSION ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qiong Wu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Yanan He
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Chunxiao Cui
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Xiaoya Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Dongdong Zhang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Yurong Zhang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Li Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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Lukša J, Celitan E, Servienė E, Serva S. Association of ScV-LA Virus with Host Protein Metabolism Determined by Proteomics Analysis and Cognate RNA Sequencing. Viruses 2022; 14:v14112345. [PMID: 36366443 PMCID: PMC9697790 DOI: 10.3390/v14112345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 02/01/2023] Open
Abstract
Saccharomyces yeasts are highly dispersed in the environment and microbiota of higher organisms. The yeast killing phenotype, encoded by the viral system, was discovered to be a significant property for host survival. Minor alterations in transcription patterns underpin the reciprocal relationship between LA and M viruses and their hosts, suggesting the fine-tuning of the transcriptional landscape. To uncover the principal targets of both viruses, we performed proteomics analysis of virus-enriched subsets of host proteins in virus type-specific manner. The essential pathways of protein metabolism-from biosynthesis and folding to degradation-were found substantially enriched in virus-linked subsets. The fractionation of viruses allowed separation of virus-linked host RNAs, investigated by high-content RNA sequencing. Ribosomal RNA was found to be inherently associated with LA-lus virus, along with other RNAs essential for ribosome biogenesis. This study provides a unique portrayal of yeast virions through the characterization of the associated proteome and cognate RNAs, and offers a background for understanding ScV-LA viral infection persistency.
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Affiliation(s)
- Juliana Lukša
- Department of Biochemistry and Molecular Biology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
- Laboratory of Genetics, Nature Research Centre, LT-08412 Vilnius, Lithuania
| | - Enrika Celitan
- Department of Biochemistry and Molecular Biology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Elena Servienė
- Laboratory of Genetics, Nature Research Centre, LT-08412 Vilnius, Lithuania
| | - Saulius Serva
- Department of Biochemistry and Molecular Biology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
- Correspondence:
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Min CW, Jang JW, Lee GH, Gupta R, Yoon J, Park HJ, Cho HS, Park SR, Kwon SW, Cho LH, Jung KH, Kim YJ, Wang Y, Kim ST. TMT-based quantitative membrane proteomics identified PRRs potentially involved in the perception of MSP1 in rice leaves. J Proteomics 2022; 267:104687. [PMID: 35914717 DOI: 10.1016/j.jprot.2022.104687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 11/26/2022]
Abstract
Pathogen-associated molecular patterns (PAMPs) play a key role in triggering PAMPs triggered immunity (PTI) in plants. In the case of the rice-Magnaporthe oryzae pathosystem, fewer PAMPs and their pattern recognition receptors (PRRs) have been characterized. Recently, a M. oryzae snodprot1 homolog protein (MSP1) has been identified that functions as PAMP and triggering the PTI responses in rice. However, the molecular mechanism underlying MSP1-induced PTI is currently elusive. Therefore, we generated MSP1 overexpressed transgenic lines of rice, and a tandem mass tag (TMT)-based quantitative membrane proteomic analysis was employed to decipher the potential MSP1-induced signaling in rice using total cytosolic as well as membrane protein fractions. This approach led to the identification of 8033 proteins of which 1826 were differentially modulated in response to overexpression of MSP1 and/or exogenous jasmonic acid treatment. Of these, 20 plasma membrane-localized receptor-like kinases (RLKs) showed increased abundance in MSP1 overexpression lines. Moreover, activation of proteins related to the protein degradation and modification, calcium signaling, redox, and MAPK signaling was observed in transgenic lines expressing MSP1 in the apoplast. Taken together, our results identified potential PRR candidates involved in MSP1 recognition and suggested the overview mechanism of the MSP1-induced PTI signaling in rice leaves. SIGNIFICANCE: In plants, recognition of pathogen pathogen-derived molecules, such as PAMPs, by plant plant-derived PRRs has an essential role for in the activation of PTI against pathogen invasion. Typically, PAMPs are recognized by plasma membrane (PM) localized PRRs, however, identifying the PM-localized PRR proteins is challenging due to their low abundance. In this study, we performed an integrated membrane protein enrichment by microsomal membrane extraction (MME) method and subsequent TMT-labeling-based quantitative proteomic analysis using MSP1 overexpressed rice. Based on these results, we successfully identified various intracellular and membrane membrane-localized proteins that participated in the MSP1-induced immune response and characterized the potential PM-localized PRR candidates in rice.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Hyun Ji Park
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hye Sun Cho
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Yiming Wang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea.
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Li J, Chen S, Qiu RS, Zhang LZ, Chen Y, Zheng X, Li TT, Zhao LH, Zhang ZK. Functional analysis of the nonstructural protein NSs of tomato zonate spot virus. PLoS One 2022; 17:e0262194. [PMID: 35073345 PMCID: PMC8786149 DOI: 10.1371/journal.pone.0262194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/20/2021] [Indexed: 11/19/2022] Open
Abstract
Tomato zonate spot virus (TZSV), a member of the genus orthotospovirus, causes severe damage to vegetables and ornamental crops in southwest China. The NSs protein is an RNA silencing suppressor in various orthotospovirus like TZSV, but its mechanism and role in virus infection are poorly understood. Here, we observed that an NSs-GFP fusion protein was transiently expressed on the plasma membrane and Golgi bodies in Nicotiana benthamiana plants. The TZSV NSs gene was silenced and infiltrated into N. benthamiana and N. tabacum cv. K326. RT-qPCR and Indirect enzyme-linked immunosorbent assay (ID-ELISA) showed that the transcription and the protein expression of the NSs gene were inhibited by more than 90.00%, and the symptoms on silenced plants were alleviated. We also found that the expression of the Zingipain-2-like gene significantly decreased when the NSs gene was silenced, resulting in co-localization of the NSs-GFP and the Zingipain-2-like-mCherry fusion protein. The findings of this study provide new insights into the mechanism of silencing suppression by NSs, as well as its effect on systemic virus infection, and also support the theory of disease resistance breeding and control and prevention of TZSV in the field.
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Affiliation(s)
- Jing Li
- Life Science College, Southwest Forestry University, Kunming, China
| | - Si Chen
- Life Science College, Southwest Forestry University, Kunming, China
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Run-Shuang Qiu
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Li-Zhen Zhang
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yue Chen
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xue Zheng
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ting-Ting Li
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Li-Hua Zhao
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Zhong-Kai Zhang
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
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Nguyen TV, Gupta R, Annas D, Yoon J, Kim YJ, Lee GH, Jang JW, Park KH, Rakwal R, Jung KH, Min CW, Kim ST. An Integrated Approach for the Efficient Extraction and Solubilization of Rice Microsomal Membrane Proteins for High-Throughput Proteomics. FRONTIERS IN PLANT SCIENCE 2021; 12:723369. [PMID: 34567038 PMCID: PMC8460067 DOI: 10.3389/fpls.2021.723369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
The preparation of microsomal membrane proteins (MPs) is critically important to microsomal proteomics. To date most research studies have utilized an ultracentrifugation-based approach for the isolation and solubilization of plant MPs. However, these approaches are labor-intensive, time-consuming, and unaffordable in certain cases. Furthermore, the use of sodium dodecyl sulfate (SDS) and its removal prior to a mass spectrometry (MS) analysis through multiple washing steps result in the loss of proteins. To address these limitations, this study introduced a simple micro-centrifugation-based MP extraction (MME) method from rice leaves, with the efficacy of this approach being compared with a commercially available plasma membrane extraction kit (PME). Moreover, this study assessed the subsequent solubilization of isolated MPs in an MS-compatible surfactant, namely, 4-hexylphenylazosulfonate (Azo) and SDS using a label-free proteomic approach. The results validated the effectiveness of the MME method, specifically in the enrichment of plasma membrane proteins as compared with the PME method. Furthermore, the findings showed that Azo demonstrated several advantages over SDS in solubilizing the MPs, which was reflected through a label-free quantitative proteome analysis. Altogether, this study provided a relatively simple and rapid workflow for the efficient extraction of MPs with an Azo-integrated MME approach for bottom-up proteomics.
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Affiliation(s)
- Truong Van Nguyen
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of General Education, College of General Education, Kookmin University, Seoul, South Korea
| | - Dicky Annas
- Department of Chemistry, Pusan National University, Busan, South Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Department of Life Science & Environmental Biochemistry, Pusan National University, Miryang, South Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Kang Hyun Park
- Department of Chemistry, Pusan National University, Busan, South Korea
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
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Mouden S, Leiss KA. Host plant resistance to thrips (Thysanoptera: Thripidae) - current state of art and future research avenues. CURRENT OPINION IN INSECT SCIENCE 2021; 45:28-34. [PMID: 33278641 DOI: 10.1016/j.cois.2020.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 05/27/2023]
Abstract
Integrated Pest Management (IPM) is endorsed as the future standard for crop protection worldwide. This holistic concept integrates preventative and curative measures amongst which host plant resistance (HPR) plays an essential role. Up to now HPR has been a somewhat under-utilized tool in pest management due to widespread use of pesticides and technological hindrance. Thrips are key pests in agriculture and horticulture worldwide. Here we provide an overview on the current status of research on constitutive and induced HPR including thrips-host relationships and thrips as virus vectors. We stress modulation of plant defense responses by abiotic and biotic elicitors to increase HPR and provide an outlook on the increasing potential of HPR inspired by the fast advancement of -omics techniques.
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Affiliation(s)
- Sanae Mouden
- Wageningen University & Research, Business Unit Horticulture, Violierenweg 1, 2665 MV Bleiswijk, The Netherlands
| | - Kirsten A Leiss
- Wageningen University & Research, Business Unit Horticulture, Violierenweg 1, 2665 MV Bleiswijk, The Netherlands.
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Riyazuddin R, Verma R, Singh K, Nisha N, Keisham M, Bhati KK, Kim ST, Gupta R. Ethylene: A Master Regulator of Salinity Stress Tolerance in Plants. Biomolecules 2020; 10:E959. [PMID: 32630474 PMCID: PMC7355584 DOI: 10.3390/biom10060959] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Salinity stress is one of the major threats to agricultural productivity across the globe. Research in the past three decades, therefore, has focused on analyzing the effects of salinity stress on the plants. Evidence gathered over the years supports the role of ethylene as a key regulator of salinity stress tolerance in plants. This gaseous plant hormone regulates many vital cellular processes starting from seed germination to photosynthesis for maintaining the plants' growth and yield under salinity stress. Ethylene modulates salinity stress responses largely via maintaining the homeostasis of Na+/K+, nutrients, and reactive oxygen species (ROS) by inducing antioxidant defense in addition to elevating the assimilation of nitrates and sulfates. Moreover, a cross-talk of ethylene signaling with other phytohormones has also been observed, which collectively regulate the salinity stress responses in plants. The present review provides a comprehensive update on the prospects of ethylene signaling and its cross-talk with other phytohormones to regulate salinity stress tolerance in plants.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary;
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6720 Szeged, Hungary
| | - Radhika Verma
- Department of Biotechnology, Visva-Bharati Central University, Santiniketan, West Bengal 731235, India;
| | - Kalpita Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh 201312, India;
| | - Nisha Nisha
- Department of Integrated Plant Protection, Plant Protection Institute, Faculty of Horticultural Sciences, Szent István University, Páter Károly utca 1, H-2100 Gödöllo, Hungary;
| | - Monika Keisham
- Department of Botany, University of Delhi, New Delhi 110007, India;
| | - Kaushal Kumar Bhati
- Louvain Institute of Biomolecular Science, Catholic University of Louvain, B-1348 Louvain-la-Neuve, Belgium;
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
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Min CW, Park J, Bae JW, Agrawal GK, Rakwal R, Kim Y, Yang P, Kim ST, Gupta R. In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells 2020; 9:E1517. [PMID: 32580392 PMCID: PMC7349688 DOI: 10.3390/cells9061517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Jin Woo Bae
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 3058574, Japan
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
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