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Wei L, Wang D, Gupta R, Kim ST, Wang Y. A Proteomics Insight into Advancements in the Rice-Microbe Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051079. [PMID: 36903938 PMCID: PMC10005616 DOI: 10.3390/plants12051079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 05/23/2023]
Abstract
Rice is one of the most-consumed foods worldwide. However, the productivity and quality of rice grains are severely constrained by pathogenic microbes. Over the last few decades, proteomics tools have been applied to investigate the protein level changes during rice-microbe interactions, leading to the identification of several proteins involved in disease resistance. Plants have developed a multi-layered immune system to suppress the invasion and infection of pathogens. Therefore, targeting the proteins and pathways associated with the host's innate immune response is an efficient strategy for developing stress-resistant crops. In this review, we discuss the progress made thus far with respect to rice-microbe interactions from side views of the proteome. Genetic evidence associated with pathogen-resistance-related proteins is also presented, and challenges and future perspectives are highlighted in order to understand the complexity of rice-microbe interactions and to develop disease-resistant crops in the future.
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Affiliation(s)
- Lirong Wei
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dacheng Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Yiming Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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2
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. Proteomes 2022; 10:5. [PMID: 35225985 PMCID: PMC8883913 DOI: 10.3390/proteomes10010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Affiliation(s)
- Sadegh Balotf
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
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3
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Chopra P, Chhillar H, Kim YJ, Jo IH, Kim ST, Gupta R. Phytochemistry of ginsenosides: Recent advancements and emerging roles. Crit Rev Food Sci Nutr 2021; 63:613-640. [PMID: 34278879 DOI: 10.1080/10408398.2021.1952159] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ginsenosides, a group of tetracyclic saponins, accounts for the nutraceutical and pharmaceutical relevance of the ginseng (Panax sp.) herb. Owing to the associated therapeutic potential of ginsenosides, their demand has been increased significantly in the last two decades. However, a slow growth cycle, low seed production, and long generation time of ginseng have created a gap between the demand and supply of ginsenosides. The biosynthesis of ginsenosides involves an intricate network of pathways with multiple oxidation and glycosylation reactions. However, the exact functions of some of the associated genes/proteins are still not completely deciphered. Moreover, ginsenoside estimation and extraction using analytical techniques are not feasible with high efficiency. The present review is a step forward in recapitulating the comprehensive aspects of ginsenosides including their distribution, structural diversity, biotransformation, and functional attributes in both plants and animals including humans. Moreover, ginsenoside biosynthesis in the potential plant sources and their metabolism in the human body along with major regulators and stimulators affecting ginsenoside biosynthesis have also been discussed. Furthermore, this review consolidates biotechnological interventions to enhance the biosynthesis of ginsenosides in their potential sources and advancements in the development of synthetic biosystems for efficient ginsenoside biosynthesis to meet their rising industrial demands.
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Affiliation(s)
- Priyanka Chopra
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Himanshu Chhillar
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ick Hyun Jo
- Department of Herbal Crop Research, Rural Development Administration, Eumseong, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India.,Department of Forestry, Environment, and Systems, College of Science and Technology, Kookmin University, Seoul, South Korea
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4
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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Cun Z, Zhang JY, Wu HM, Zhang L, Chen JW. High nitrogen inhibits photosynthetic performance in a shade-tolerant and N-sensitive species Panax notoginseng. PHOTOSYNTHESIS RESEARCH 2021; 147:283-300. [PMID: 33587246 DOI: 10.1007/s11120-021-00823-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/18/2021] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) is a primary factor limiting leaf photosynthesis. However, the mechanism of high-N-driven inhibition on photosynthetic efficiency and photoprotection is still unclear in the shade-tolerant and N-sensitive species such as Panax notoginseng. Leaf chlorophyll (Chl) content, Ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) activity and content, N allocation in the photosynthetic apparatus, photosynthetic performance and Chl fluorescence were comparatively analyzed in a shade-tolerant and N-sensitive species P. notoginseng grown under the levels of moderate nitrogen (MN) and high nitrogen (HN). The results showed that Rubisco content, Chl content and specific leaf nitrogen (SLN) were greater in the HN individuals. Rubisco activity, net photosynthetic rate (Anet), photosynthetic N use efficiency (PNUE), maximum carboxylation rate (Vcmax) and maximum electron transport rate (Jmax) were lower when plants were exposed to HN as compared with ones to MN. A large proportion of leaf N was allocated to the carboxylation component under the levels of MN. More N was only served as a form of N storage and not contributed to photosynthesis in HN individuals. Compared with the MN plants, the maximum quantum yield of photosystem II (Fv/Fm), non-photochemical quenching of PSII (NPQ), effective quantum yield and electron transport rate were obviously reduced in the HN plants. Cycle electron flow (CEF) was considerably enhanced in the MN individuals. There was not a significant difference in maximum photo-oxidation P700+ (Pm) between the HN and MN individuals. Most importantly, the HN individuals showed higher K phase in the fast chlorophyll fluorescence induction kinetic curve (OJIP kinetic curve) than the MN ones. The results obtained suggest that photosynthetic capacity might be primarily inhibited by the inactivated Rubisco in the HN individuals, and HN-induced depression of photoprotection might be caused by the photodamage to the donor side of PSII oxygen-evolving complex.
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Affiliation(s)
- Zhu Cun
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jin-Yan Zhang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Min Wu
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Ling Zhang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Wen Chen
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China.
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Shin J, Marx H, Richards A, Vaneechoutte D, Jayaraman D, Maeda J, Chakraborty S, Sussman M, Vandepoele K, Ané JM, Coon J, Roy S. A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. Nucleic Acids Res 2021; 49:e3. [PMID: 33219668 PMCID: PMC7797074 DOI: 10.1093/nar/gkaa1041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 09/19/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022] Open
Abstract
Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.
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Affiliation(s)
- Junha Shin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Harald Marx
- Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alicia Richards
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junko Maeda
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sanhita Chakraborty
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
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7
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Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples. Pathogens 2020; 9:pathogens9110966. [PMID: 33228257 PMCID: PMC7699591 DOI: 10.3390/pathogens9110966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 12/03/2022] Open
Abstract
Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us to substantially simplify the sample preparation by removing any other precipitation steps and to detect viral proteins from samples, even with less than 0.2 g of leaf tissue, by a medium resolution nanoLC-ESI-Q-TOF. The presence of capsid proteins or polyproteins of fourteen important viruses from seven different families (Geminiviridae, Luteoviridae, Bromoviridae, Caulimoviridae, Virgaviridae, Potyviridae, and Secoviridae) isolated from ten different economically important plant hosts was confirmed through many identified pathogen-specific peptides from a protein database of host proteins and potential pathogen proteins assembled separately for each host and based on existing online plant virus pathogen databases. The presented extraction protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein confirmation method that proved to be effective at identifying virus strains (as demonstrated for PPV, WDV) and distinct disease species of BYDV, as well as putative new viral protein sequences from single-plant-leaf tissue samples. Data are available via ProteomeXchange with identifier PXD022456.
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8
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Jiang MC, Hu CC, Hsu WL, Hsu TL, Lin NS, Hsu YH. Fusion of a Novel Native Signal Peptide Enhanced the Secretion and Solubility of Bioactive Human Interferon Gamma Glycoproteins in Nicotiana benthamiana Using the Bamboo Mosaic Virus-Based Expression System. FRONTIERS IN PLANT SCIENCE 2020; 11:594758. [PMID: 33281853 PMCID: PMC7688984 DOI: 10.3389/fpls.2020.594758] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/23/2020] [Indexed: 05/31/2023]
Abstract
Plant viruses may serve as expression vectors for the efficient production of pharmaceutical proteins in plants. However, the downstream processing and post-translational modifications of the target proteins remain the major challenges. We have previously developed an expression system derived from Bamboo mosaic virus (BaMV), designated pKB19, and demonstrated its applicability for the production of human mature interferon gamma (mIFNγ) in Nicotiana benthamiana. In this study, we aimed to enhance the yields of soluble and secreted mIFNγ through the incorporation of various plant-derived signal peptides. Furthermore, we analyzed the glycosylation patterns and the biological activity of the mIFNγ expressed by the improved pKB19 expression system in N. benthamiana. The results revealed that the fusion of a native N. benthamiana extensin secretory signal (SSExt) to the N-terminal of mIFNγ (designated SSExt mIFNγ) led to the highest accumulation level of protein in intracellular (IC) or apoplast washing fluid (AWF) fractions of N. benthamiana leaf tissues. The addition of 10 units of 'Ser-Pro' motifs of hydroxyproline-O-glycosylated peptides (HypGPs) at the C-terminal end of SSExt mIFNγ (designated SSExt mIFNγ(SP)10) increased the solubility to nearly 2.7- and 1.5-fold higher than those of mIFNγ and SSExt mIFNγ, respectively. The purified soluble SSExt mIFNγ(SP)10 protein was glycosylated with abundant complex-type N-glycan attached to residues N56 and N128, and exhibited biological activity against Sindbis virus and Influenza virus replication in human cell culture systems. In addition, suspension cell cultures were established from transgenic N. benthamiana, which produced secreted SSExt mIFNγ(SP)10 protein feasible for downstream processing. These results demonstrate the applicability of the BaMV-based vector systems as a useful alternative for the production of therapeutic proteins, through the incorporation of appropriate fusion tags.
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Affiliation(s)
- Min-Chao Jiang
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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9
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Berka M, Luklová M, Dufková H, Berková V, Novák J, Saiz-Fernández I, Rashotte AM, Brzobohatý B, Černý M. Barley Root Proteome and Metabolome in Response to Cytokinin and Abiotic Stimuli. FRONTIERS IN PLANT SCIENCE 2020; 11:590337. [PMID: 33250914 PMCID: PMC7673457 DOI: 10.3389/fpls.2020.590337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Cytokinin is a phytohormone involved in the regulation of diverse developmental and physiological processes in plants. Its potential in biotechnology and for development of higher-yield and more resilient plants has been recognized, yet the molecular mechanisms behind its action are far from understood. In this report, the roots of barley seedlings were explored as a new source to reveal as yet unknown cytokinin-responsive proteins for crop improvement. Here we found significant differences reproducibly observed for 178 proteins, for which some of the revealed cytokinin-responsive pathways were confirmed in metabolome analysis, including alterations phenylpropanoid pathway, amino acid biosynthesis and ROS metabolism. Bioinformatics analysis indicated a significant overlap between cytokinin response and response to abiotic stress. This was confirmed by comparing proteome and metabolome profiles in response to drought, salinity or a period of temperature stress. The results illustrate complex abiotic stress response in the early development of model crop plant and confirm an extensive crosstalk between plant hormone cytokinin and response to temperature stimuli, water availability or salinity stress.
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Affiliation(s)
- Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Hana Dufková
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Veronika Berková
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Iñigo Saiz-Fernández
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Aaron M. Rashotte
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
- Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
- *Correspondence: Martin Černý,
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10
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Min CW, Gupta R, Agrawal GK, Rakwal R, Kim ST. Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach. Expert Rev Proteomics 2019; 16:795-804. [PMID: 31398080 DOI: 10.1080/14789450.2019.1654860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging. Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome. Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba , Tsukuba , Ibaraki , Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
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11
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Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteomics 2019; 198:1-10. [DOI: 10.1016/j.jprot.2018.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 02/03/2023]
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12
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Meng Q, Gupta R, Min CW, Kwon SW, Wang Y, Je BI, Kim YJ, Jeon JS, Agrawal GK, Rakwal R, Kim ST. Proteomics of Rice- Magnaporthe oryzae Interaction: What Have We Learned So Far? FRONTIERS IN PLANT SCIENCE 2019; 10:1383. [PMID: 31737011 PMCID: PMC6828948 DOI: 10.3389/fpls.2019.01383] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/07/2019] [Indexed: 05/21/2023]
Abstract
Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world's population. Proteomic technologies have been used as effective tools in plant-pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice-M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post-translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice-M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.
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Affiliation(s)
- Qingfeng Meng
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard, New Delhi, India
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Soon Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Byoung Il Je
- Department of Horticultural Bioscience, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- *Correspondence: Sun Tae Kim,
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Liu T, Ren T, White PJ, Cong R, Lu J. Storage nitrogen co-ordinates leaf expansion and photosynthetic capacity in winter oilseed rape. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2995-3007. [PMID: 29669007 PMCID: PMC5972566 DOI: 10.1093/jxb/ery134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/06/2018] [Indexed: 05/20/2023]
Abstract
Storage nitrogen (N) is a buffer pool for maintaining leaf growth and synthesizing photosynthetic proteins, but the dynamics of its forms within the life cycle of a single leaf and how it is influenced by N supply remain poorly understood. A field experiment was conducted to estimate the influence of N supply on leaf growth, photosynthetic characteristics, and N partitioning inthe sixth leaf of winter oilseed rape (Brassica napus L.) from emergence through senescence. Storage N content (Nstore) decreased gradually along with leaf expansion. The relative growth rate based on leaf area (RGRa) was positively correlated with Nstore during leaf expansion. The water-soluble protein form of storage N was the main N source for leaf expansion. After the leaves fully expanded, the net photosynthetic rate (An) followed a linear-plateau response to Nstore, with An stabilizing at the highest value above a threshold and declining below the threshold. Non-protein and SDS (detergent)-soluble protein forms of storage N were the main N sources for maintaining photosynthesis. For the leaf N economy, storage N is used for co-ordinating leaf expansion and photosynthetic capacity. N supply can improve Nstore, thereby promoting leaf growth and biomass.
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Affiliation(s)
- Tao Liu
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Tao Ren
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | | | - Rihuan Cong
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Jianwei Lu
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
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Nintemann SJ, Vik D, Svozil J, Bak M, Baerenfaller K, Burow M, Halkier BA. Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:2028. [PMID: 29238354 PMCID: PMC5712850 DOI: 10.3389/fpls.2017.02028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/14/2017] [Indexed: 05/20/2023]
Abstract
Within the cell, biosynthetic pathways are embedded in protein-protein interaction networks. In Arabidopsis, the biosynthetic pathways of aliphatic and indole glucosinolate defense compounds are well-characterized. However, little is known about the spatial orchestration of these enzymes and their interplay with the cellular environment. To address these aspects, we applied two complementary, untargeted approaches-split-ubiquitin yeast 2-hybrid and co-immunoprecipitation screens-to identify proteins interacting with CYP83A1 and CYP83B1, two homologous enzymes specific for aliphatic and indole glucosinolate biosynthesis, respectively. Our analyses reveal distinct functional networks with substantial interconnection among the identified interactors for both pathway-specific markers, and add to our knowledge about how biochemical pathways are connected to cellular processes. Specifically, a group of protein interactors involved in cell death and the hypersensitive response provides a potential link between the glucosinolate defense compounds and defense against biotrophic pathogens, mediated by protein-protein interactions.
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Affiliation(s)
- Sebastian J. Nintemann
- Department of Plant and Environmental Sciences, Faculty of Science, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Vik
- Department of Plant and Environmental Sciences, Faculty of Science, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
| | - Julia Svozil
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Bak
- Department of Plant and Environmental Sciences, Faculty of Science, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
| | | | - Meike Burow
- Department of Plant and Environmental Sciences, Faculty of Science, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
| | - Barbara A. Halkier
- Department of Plant and Environmental Sciences, Faculty of Science, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - 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, 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
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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16
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017; 169:125-135. [PMID: 28669816 DOI: 10.1016/j.jprot.2017.06.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023]
Abstract
Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality. BIOLOGICAL SIGNIFICANCE Controlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Seo Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Ye Eun Cheon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Won Young Han
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Jong Min Ko
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Hang Won Kang
- National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Yong Chul Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea; National Institute of Crop Science, RDA, Miryang 627-803, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; 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; 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 305-8574, Ibaraki, Japan
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea.
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17
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Min CW, Lee SH, Cheon YE, Han WY, Ko JM, Kang HW, Kim YC, Agrawal GK, Rakwal R, Gupta R, Kim ST. In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.022 pmid: 28669816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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19
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Ashwin NMR, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R. Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2017. [DOI: 10.1007/s13562-017-0402-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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20
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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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Banaei-Asl F, Farajzadeh D, Bandehagh A, Komatsu S. Comprehensive proteomic analysis of canola leaf inoculated with a plant growth-promoting bacterium, Pseudomonas fluorescens, under salt stress. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1222-1236. [DOI: 10.1016/j.bbapap.2016.04.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 04/24/2016] [Accepted: 04/28/2016] [Indexed: 01/10/2023]
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22
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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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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Advances in proteomics for production strain analysis. Curr Opin Biotechnol 2015; 35:111-7. [DOI: 10.1016/j.copbio.2015.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 11/22/2022]
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25
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López-Castillo LM, López-Arciniega JAI, Guerrero-Rangel A, Valdés-Rodríguez S, Brieba LG, García-Lara S, Winkler R. Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification. FRONTIERS IN PLANT SCIENCE 2015; 6:670. [PMID: 26379694 PMCID: PMC4553411 DOI: 10.3389/fpls.2015.00670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/13/2015] [Indexed: 05/03/2023]
Abstract
Plant peroxidases (PODs) are involved in diverse physiological processes, including defense against pathogens and insects. Contrary to their biological importance, only very few plant PODs have been proven on protein level, because their low abundance makes them difficult to detect in standard proteomics work-flows. A statistically significant positive correlation between POD activity and post-harvest insect resistance has been found for maize (Zea mays, p84C3) kernels. In combining activity-directed protein purification, genomic and proteomic tools we found that protein B6T173 (ZmPrx35) is responsible for the majority of the POD activity of the kernel. We successfully produced recombinant ZmPrx35 protein in Escherichia coli and demonstrate both, in vitro activity and the presence of a haem (heme) cofactor of the enzyme. Our findings support the screening for insect resistant maize variants and the construction of genetically optimized maize plants.
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Affiliation(s)
- Laura M. López-Castillo
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | - Janet A. I. López-Arciniega
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
| | | | | | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | | | - Robert Winkler
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- *Correspondence: Robert Winkler, Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico,
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