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Odriozola I, Rasmussen JA, Gilbert MTP, Limborg MT, Alberdi A. A practical introduction to holo-omics. CELL REPORTS METHODS 2024; 4:100820. [PMID: 38986611 PMCID: PMC11294832 DOI: 10.1016/j.crmeth.2024.100820] [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: 12/14/2023] [Revised: 04/17/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.
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Affiliation(s)
- Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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2
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Lim S, Kwon HJ, Jeong DG, Nie H, Lee S, Ko SR, Lee KS, Ryu YB, Mason HS, Kim HS, Shin AY, Kwon SY. Enhanced binding and inhibition of SARS-CoV-2 by a plant-derived ACE2 protein containing a fused mu tailpiece. Biotechnol J 2024; 19:e2300319. [PMID: 37853601 DOI: 10.1002/biot.202300319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Infectious diseases such as Coronavirus disease 2019 (COVID-19) and Middle East respiratory syndrome (MERS) present an increasingly persistent crisis in many parts of the world. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The angiotensin-converting enzyme 2 (ACE2) is a crucial cellular receptor for SARS-CoV-2 infection. Inhibition of the interaction between SARS-CoV-2 and ACE2 has been proposed as a target for the prevention and treatment of COVID-19. We produced four recombinant plant-derived ACE2 isoforms with or without the mu tailpiece (μ-tp) of immunoglobulin M (IgM) and the KDEL endoplasmic reticulum retention motif in a plant expression system. The plant-derived ACE2 isoforms bound whole SARS-CoV-2 virus and the isolated receptor binding domains of SARS-CoV-2 Alpha, Beta, Gamma, Delta, and Omicron variants. Fusion of μ-tp and KDEL to the ACE2 protein (ACE2 μK) had enhanced binding activity with SARS-CoV-2 in comparison with unmodified ACE2 protein derived from CHO cells. Furthermore, the plant-derived ACE2 μK protein exhibited no cytotoxic effects on Vero E6 cells and effectively inhibited SARS-CoV-2 infection. The efficient and rapid scalability of plant-derived ACE2 μK protein offers potential for the development of preventive and therapeutic agents in the early response to future viral outbreaks.
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Affiliation(s)
- Sohee Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Dae Gwin Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Hualin Nie
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Kyu-Sun Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Young Bae Ryu
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Hugh S Mason
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute at ASU, Tempe, Arizona, USA
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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Gupta R, Min CW, Park SR, Kim ST. Label-free proteome data of susceptible and resistant rice cultivars in response to Xanthomonas oryzae pv. oryzae inoculation. Data Brief 2022; 41:107890. [PMID: 35198671 PMCID: PMC8842008 DOI: 10.1016/j.dib.2022.107890] [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: 01/06/2022] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Here we report the data associated with the article: "Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae" [1]. Bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice across the globe; however, the underlying molecular mechanism of rice-Xoo interaction is currently not well understood. In this manuscript, we report the proteome profiles of rice leaves generated using a label-free quantitative proteomic analysis using QExactive™ Orbitrap High-Resolution Mass Spectrometer, MapMan, and rice interactome viewer [1].
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Affiliation(s)
- Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Sang-Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
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Lee H, Seo Y, Lee JH, Lee SE, Oh S, Kim J, Jung S, Kim H, Park H, Kim S, Mang H, Choi D. Plasma membrane-localized plant immune receptor targets H + -ATPase for membrane depolarization to regulate cell death. THE NEW PHYTOLOGIST 2022; 233:934-947. [PMID: 34632584 PMCID: PMC9298278 DOI: 10.1111/nph.17789] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
The hypersensitive response (HR) is a robust immune response mediated by nucleotide-binding, leucine-rich repeat receptors (NLRs). However, the early molecular event that links activated NLRs to cell death is unclear. Here, we demonstrate that NLRs target plasma membrane H+ -ATPases (PMAs) that generate electrochemical potential, an essential component of living cells, across the plasma membrane. CCA 309, an autoactive N-terminal domain of a coiled-coil NLR (CNL) in pepper, is associated with PMAs. Silencing or overexpression of PMAs reversibly affects cell death induced by CCA 309 in Nicotiana benthamiana. CCA 309-induced extracellular alkalization causes plasma membrane depolarization, followed by cell death. Coimmunoprecipitation analyses suggest that CCA 309 inhibits PMA activation by preoccupying the dephosphorylated penultimate threonine residue of PMA. Moreover, pharmacological experiments using fusicoccin, an irreversible PMA activator, showed that inhibition of PMAs contributes to CNL-type (but not Toll interleukin-1 receptor NLR-type) resistance protein-induced cell death. We suggest PMAs as primary targets of plasma membrane-associated CNLs leading to HR-associated cell death by disturbing the electrochemical gradient across the membrane. These results provide new insight into NLR-mediated cell death in plants, as well as innate immunity in higher eukaryotes.
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Affiliation(s)
- Hye‐Young Lee
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Ye‐Eun Seo
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Joo Hyun Lee
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - So Eui Lee
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Soohyun Oh
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Jihyun Kim
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Seungmee Jung
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Haeun Kim
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Hyojeong Park
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Sejun Kim
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Hyunggon Mang
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
| | - Doil Choi
- Plant Immunity Research CenterSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
- Department of Agriculture, Forestry and BioresourcesPlant Genomics and Breeding InstituteSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Korea
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Niu L, Yuan H, Gong F, Wu X, Wang W. Protein Extraction Methods Shape Much of the Extracted Proteomes. FRONTIERS IN PLANT SCIENCE 2018; 9:802. [PMID: 29946336 PMCID: PMC6005817 DOI: 10.3389/fpls.2018.00802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 05/05/2023]
Affiliation(s)
| | | | | | | | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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Gupta R, Min CW, Kramer K, Agrawal GK, Rakwal R, Park KH, Wang Y, Finkemeier I, Kim ST. A Multi-Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment. Proteomics 2018; 18:e1700366. [PMID: 29457974 DOI: 10.1002/pmic.201700366] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/11/2018] [Indexed: 11/06/2022]
Abstract
Phytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low-abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label-free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross-talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Katharina Kramer
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry, Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
- Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Ki-Hun Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Iris Finkemeier
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
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Gupta R, Lee SJ, Min CW, Kim SW, Park KH, Bae DW, Lee BW, Agrawal GK, Rakwal R, Kim ST. Coupling of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deep into the leaf senescence proteome of Glycine max. J Proteomics 2016; 148:65-74. [PMID: 27474340 DOI: 10.1016/j.jprot.2016.07.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
UNLABELLED Leaf senescence is the last stage of leaf development that re-mobilizes nutrients from the source to sink. Here, we have utilized the soybean as a model system to unravel senescence-associated proteins (SAPs). A comparative proteomics approach was used at two contrasting stages of leaf development, namely mature (R3) and senescent (R7). Selection criteria for these two stages were the contrasting differences in their biochemical parameters - chlorophyll, carotenoids and malondialdehyde contents. Proteome analysis involved subjecting the total leaf proteins to 15% poly-ethylene glycol (PEG) pre-fractional method to enrich the low-abundance proteins (LAPs) and their analyses by gel-based 2-DE and 1-DE shotgun proteomics approaches. 2-DE profiling of PEG-supernatant and -pellet fractions detected 153 differential spots between R3 and R7 stages, of which 102 proteins were identified. In parallel, 1-DE shotgun proteomics approach identified 598 and 534 proteins in supernatant and pellet fractions of R3 and R7 stages, respectively. MapMan and Gene Ontology analyses showed increased abundance and/or specific accumulation of proteins related to jasmonic acid biosynthesis and defense, while proteins associated with photosynthesis and ROS-detoxification were decreased during leaf senescence. These findings and the generated datasets further our understanding on leaf senescence at protein level, providing a resource for the scientific community. BIOLOGICAL SIGNIFICANCE Leaf senescence is a major biological event in the life cycle of plants that leads to the recycling of nutrients. However, the molecular mechanisms underlying leaf senescence still remain poorly understood. Here, we used a combination of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deeper into the leaf senescence proteome using soybean leaf as a model experimental material. For the identification of low-abundance proteins, polyethylene glycol (PEG) fractionation was employed and both PEG-supernatant and -pellet fractions were utilized for 2-DE and shotgun proteomic analysis. A total of 1234 (102 from 2-DE and 1132 from 1-DE shotgun proteome analysis) proteins were identified which were functionally annotated using GO and MapMan bioinformatics tools. Our results also emphasize the role of jasmonic acid in soybean leaf senescence.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Su Ji Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - So Wun Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Ki-Hun Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Dong-Won Bae
- Center for Research Facilities, Gyeongsang National University, Jinju, Republic of Korea
| | - Byong Won Lee
- Department of Functional Crops, National Institute of Crop Science (NICS), Rural Development Administration (RDA), Miryang 627-803, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies (TIAS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Gupta R, Min CW, Wang Y, Kim YC, Agrawal GK, Rakwal R, Kim ST. Expect the Unexpected Enrichment of "Hidden Proteome" of Seeds and Tubers by Depletion of Storage Proteins. FRONTIERS IN PLANT SCIENCE 2016; 7:761. [PMID: 27313590 PMCID: PMC4887479 DOI: 10.3389/fpls.2016.00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Dynamic resolution of seed and tuber protein samples is highly limited due to the presence of high-abundance storage proteins (SPs). These proteins inevitably obscure the low-abundance proteins (LAPs) impeding their identification and characterization. To facilitate the detection of LAPs, several methods have been developed during the past decade, enriching the proteome with extreme proteins. Most of these methods, if not all, are based on the specific removal of SPs which ultimately magnify the proteome coverage. In this mini-review, we summarize the available methods that have been developed over the years for the enrichment of LAPs either from seeds or tubers. Incorporation of these methods during the protein extraction step will be helpful in understanding the seed/tuber biology in greater detail.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Cheol W. Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Yong C. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education, Academy Pvt. Ltd.Birgunj, Nepal
| | - Randeep Rakwal
- Global Research Arch for Developing Education, Academy Pvt. Ltd.Birgunj, Nepal
- Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies, University of TsukubaIbaraki, Japan
| | - Sun T. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
- *Correspondence: Sun T. Kim,
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