51
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McCotter SW, Horianopoulos LC, Kronstad JW. Regulation of the fungal secretome. Curr Genet 2016; 62:533-45. [DOI: 10.1007/s00294-016-0578-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 02/07/2023]
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52
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Park S, Gupta R, Krishna R, Kim ST, Lee DY, Hwang DJ, Bae SC, Ahn IP. Proteome Analysis of Disease Resistance against Ralstonia solanacearum in Potato Cultivar CT206-10. THE PLANT PATHOLOGY JOURNAL 2016; 32:25-32. [PMID: 26889112 PMCID: PMC4755672 DOI: 10.5423/ppj.oa.05.2015.0076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 10/15/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Potato is one of the most important crops worldwide. Its commercial cultivars are highly susceptible to many fungal and bacterial diseases. Among these, bacterial wilt caused by Ralstonia solanacearum causes significant yield loss. In the present study, integrated proteomics and genomics approaches were used in order to identify bacterial wilt resistant genes from Rs resistance potato cultivar CT-206-10. 2-DE and MALDI-TOF/TOF-MS analysis identified eight differentially abundant proteins including glycine-rich RNA binding protein (GRP), tomato stress induced-1 (TSI-1) protein, pathogenesis-related (STH-2) protein and pentatricopeptide repeat containing (PPR) protein in response to Rs infection. Further, semi-quantitative RT-PCR identified up-regulation in transcript levels of all these genes upon Rs infection. Taken together, our results showed the involvement of the identified proteins in the Rs stress tolerance in potato. In the future, it would be interesting to raise the transgenic plants to further validate their involvement in resistance against Rs in potato.
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Affiliation(s)
- Sangryeol Park
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - R. Krishna
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - Dong Yeol Lee
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701,
Korea
| | - Duk-ju Hwang
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Shin-Chul Bae
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Il-Pyung Ahn
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
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53
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Cho WK, Hyun TK, Kumar D, Rim Y, Chen XY, Jo Y, Kim S, Lee KW, Park ZY, Lucas WJ, Kim JY. Proteomic Analysis to Identify Tightly-Bound Cell Wall Protein in Rice Calli. Mol Cells 2015; 38:685-96. [PMID: 26194822 PMCID: PMC4546940 DOI: 10.14348/molcells.2015.0033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 12/21/2022] Open
Abstract
Rice is a model plant widely used for basic and applied research programs. Plant cell wall proteins play key roles in a broad range of biological processes. However, presently, knowledge on the rice cell wall proteome is rudimentary in nature. In the present study, the tightly-bound cell wall proteome of rice callus cultured cells using sequential extraction protocols was developed using mass spectrometry and bioinformatics methods, leading to the identification of 1568 candidate proteins. Based on bioinformatics analyses, 389 classical rice cell wall proteins, possessing a signal peptide, and 334 putative non-classical cell wall proteins, lacking a signal peptide, were identified. By combining previously established rice cell wall protein databases with current data for the classical rice cell wall proteins, a comprehensive rice cell wall proteome, comprised of 496 proteins, was constructed. A comparative analysis of the rice and Arabidopsis cell wall proteomes revealed a high level of homology, suggesting a predominant conservation between monocot and eudicot cell wall proteins. This study importantly increased information on cell wall proteins, which serves for future functional analyses of these identified rice cell wall proteins.
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Affiliation(s)
- Won Kyong Cho
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 361-763,
Korea
| | - Dhinesh Kumar
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Yeonggil Rim
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Xiong Yan Chen
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Yeonhwa Jo
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Suwha Kim
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Zee-Yong Park
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - William J. Lucas
- Department of Plant Biology, University of California, Davis, CA 95616,
USA
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
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54
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Feussner I, Polle A. What the transcriptome does not tell - proteomics and metabolomics are closer to the plants' patho-phenotype. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:26-31. [PMID: 26051215 DOI: 10.1016/j.pbi.2015.05.023] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 05/18/2023]
Abstract
The proteome and metabolome of the plant provide a wealth of additional information on plant-microbe interactions since they not only represent additional levels of regulation, but often they harbor the end products of regulatory processes. Proteomics has contributed to our understanding of plant-microbe research by increasing the spatial resolution of the analysis within the infected tissue, because components of the basal immunity were uncovered in the apoplast. Metabolomics has developed into a powerful approach to discover the role of small molecules during plant-microbe interactions in non-model plants since it does not depend on the availability of genome or transcriptome data. Moreover, novel molecules involved in systemic acquired resistance and the precursors for the formation of molecules that provide physical barriers to prevent spreading of pathogens were identified.
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Affiliation(s)
- Ivo Feussner
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Andrea Polle
- Georg-August University, Büsgen-Institute, Department for Forest Botany and Tree Physiology, Büsgenweg 2, 37077 Göttingen, Germany
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55
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Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
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56
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Francin-Allami M, Merah K, Albenne C, Rogniaux H, Pavlovic M, Lollier V, Sibout R, Guillon F, Jamet E, Larré C. Cell wall proteomic of Brachypodium distachyon grains: A focus on cell wall remodeling proteins. Proteomics 2015; 15:2296-306. [PMID: 25787258 DOI: 10.1002/pmic.201400485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/23/2015] [Accepted: 03/13/2015] [Indexed: 01/12/2023]
Abstract
Cell walls play key roles during plant development. Following their deposition into the cell wall, polysaccharides are continually remodeled according to the growth stage and stress environment to accommodate cell growth and differentiation. To date, little is known concerning the enzymes involved in cell wall remodeling, especially in gramineous and particularly in the grain during development. Here, we investigated the cell wall proteome of the grain of Brachypodium distachyon. This plant is a suitable model for temperate cereal crops. Among the 601 proteins identified, 299 were predicted to be secreted. These proteins were distributed into eight functional classes; the class of proteins that act on carbohydrates was the most highly represented. Among these proteins, numerous glycoside hydrolases were found. Expansins and peroxidases, which are assumed to be involved in cell wall polysaccharide remodeling, were also identified. Approximately half of the proteins identified in this study were newly discovered in grain and were not identified in the previous proteome analysis conducted using the culms and leaves of B. distachyon. Therefore, the data obtained from all organs of B. distachyon infer a global cell wall proteome consisting of 460 proteins. At present, this is the most extensive cell wall proteome of a monocot species.
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Affiliation(s)
| | - Kahina Merah
- INRA, Biopolymères Interactions Assemblages, Nantes, France.,Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | | | | | | | - Richard Sibout
- INRA, Institut Jean-Pierre Bourgin (IJPB), Saclay Plant Science, Versailles, France
| | | | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | - Colette Larré
- INRA, Biopolymères Interactions Assemblages, Nantes, France
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57
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Ceballos-Laita L, Gutierrez-Carbonell E, Lattanzio G, Vázquez S, Contreras-Moreira B, Abadía A, Abadía J, López-Millán AF. Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply. FRONTIERS IN PLANT SCIENCE 2015; 6:145. [PMID: 25852707 PMCID: PMC4364163 DOI: 10.3389/fpls.2015.00145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/23/2015] [Indexed: 05/23/2023]
Abstract
The fluid collected by direct leaf centrifugation has been used to study the proteome of the sugar beet apoplastic fluid as well as the changes induced by Fe deficiency and Fe resupply to Fe-deficient plants in the protein profile. Plants were grown in Fe-sufficient and Fe-deficient conditions, and Fe resupply was carried out with 45 μM Fe(III)-EDTA for 24 h. Protein extracts of leaf apoplastic fluid were analyzed by two-dimensional isoelectric focusing-SDS-PAGE electrophoresis. Gel image analysis revealed 203 consistent spots, and proteins in 81% of them (164) were identified by nLC-MS/MS using a custom made reference repository of beet protein sequences. When redundant UniProt entries were deleted, a non-redundant leaf apoplastic proteome consisting of 109 proteins was obtained. TargetP and SecretomeP algorithms predicted that 63% of them were secretory proteins. Functional classification of the non-redundant proteins indicated that stress and defense, protein metabolism, cell wall and C metabolism accounted for approximately 75% of the identified proteome. The effects of Fe-deficiency on the leaf apoplast proteome were limited, with only five spots (2.5%) changing in relative abundance, thus suggesting that protein homeostasis in the leaf apoplast fluid is well-maintained upon Fe shortage. The identification of three chitinase isoforms among proteins increasing in relative abundance with Fe-deficiency suggests that one of the few effects of Fe deficiency in the leaf apoplast proteome includes cell wall modifications. Iron resupply to Fe deficient plants changed the relative abundance of 16 spots when compared to either Fe-sufficient or Fe-deficient samples. Proteins identified in these spots can be broadly classified as those responding to Fe-resupply, which included defense and cell wall related proteins, and non-responsive, which are mainly protein metabolism related proteins and whose changes in relative abundance followed the same trend as with Fe-deficiency.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Elain Gutierrez-Carbonell
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Giuseppe Lattanzio
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Saul Vázquez
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Bruno Contreras-Moreira
- Laboratory of Computational and Structural Biology, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
- Fundación ARAIDZaragoza, Spain
| | - Anunciación Abadía
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Javier Abadía
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Ana-Flor López-Millán
- Plant Stress Physiology Group, Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
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58
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Fang X, Chen J, Dai L, Ma H, Zhang H, Yang J, Wang F, Yan C. Proteomic dissection of plant responses to various pathogens. Proteomics 2015; 15:1525-43. [DOI: 10.1002/pmic.201400384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/28/2014] [Accepted: 01/12/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Xianping Fang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jianping Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Liangying Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
| | - Huasheng Ma
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Fang Wang
- Laboratory of Biotechnology; Institute of Biotechnology; Ningbo Academy of Agricultural Sciences; Ningbo P. R. China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
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59
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Gupta R, Lee SE, Agrawal GK, Rakwal R, Park S, Wang Y, Kim ST. Understanding the plant-pathogen interactions in the context of proteomics-generated apoplastic proteins inventory. FRONTIERS IN PLANT SCIENCE 2015; 6:352. [PMID: 26082784 PMCID: PMC4451336 DOI: 10.3389/fpls.2015.00352] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/03/2015] [Indexed: 05/14/2023]
Abstract
The extracellular space between cell wall and plasma membrane acts as the first battle field between plants and pathogens. Bacteria, fungi, and oomycetes that colonize the living plant tissues are encased in this narrow region in the initial step of infection. Therefore, the apoplastic region is believed to be an interface which mediates the first crosstalk between host and pathogen. The secreted proteins and other metabolites, derived from both host and pathogen, interact in this apoplastic region and govern the final relationship between them. Hence, investigation of protein secretion and apoplastic interaction could provide a better understanding of plant-microbe interaction. Here, we are briefly discussing the methods available for the isolation and normalization of the apoplastic proteins, as well as the current state of secretome studies focused on the in-planta interaction between the host and the pathogen.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - So Eui Lee
- 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 (GRADE), Academy Private LimitedBirgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education (GRADE), Academy Private LimitedBirgunj, Nepal
- Organization for Educational Initiatives, University of TsukubaTsukuba, Japan
- Faculty of Health and Sport Sciences, Tsukuba International Academy for Sport Studies, University of TsukubaTsukuba, Japan
| | - Sangryeol Park
- Bio-crop Development Division, National Academy of Agricultural Science, Rural Development AdministrationJeonju, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Sun Tae Kim, Department of Plant Bioscience, Pusan National University, Miryang 627-706, South Korea
| | - Sun T. Kim
- 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 Research, Carl-von-Linne weg 10, Cologne 50829, Germany
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60
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Wang Y, Kwon SJ, Wu J, Choi J, Lee YH, Agrawal GK, Tamogami S, Rakwal R, Park SR, Kim BG, Jung KH, Kang KY, Kim SG, Kim ST. Transcriptome Analysis of Early Responsive Genes in Rice during Magnaporthe oryzae Infection. THE PLANT PATHOLOGY JOURNAL 2014; 30:343-54. [PMID: 25506299 PMCID: PMC4262287 DOI: 10.5423/ppj.oa.06.2014.0055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/25/2014] [Accepted: 07/30/2014] [Indexed: 05/04/2023]
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10) by RT-PCR, and phytoalexins (sakuranetin and momilactone A) with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05) in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.
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Affiliation(s)
- Yiming Wang
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Soon Jae Kwon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-706, Republic of Korea
| | - Jingni Wu
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- GRADE Academy Pvt. Ltd., Adarsh Nagar-13, Main Road, Birgunj, Nepal
| | - Shigeru Tamogami
- Laboratory of Biologically Active Compounds, Department of Biological Production, Akita Prefectural University, Akita 010-0195, Japan
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- GRADE Academy Pvt. Ltd., Adarsh Nagar-13, Main Road, Birgunj, Nepal
- Organization for Educational Initiatives, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
| | - Sang-Ryeol Park
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Suwon 441-707, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Suwon 441-707, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Kyu Young Kang
- Plant Molecular Biology and Biotechnology Research Center/Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Sang Gon Kim
- Plant Molecular Biology and Biotechnology Research Center/Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, 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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61
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Kim JY, Wu J, Kwon SJ, Oh H, Lee SE, Kim SG, Wang Y, Agrawal GK, Rakwal R, Kang KY, Ahn IP, Kim BG, Kim ST. Proteomics of rice and Cochliobolus miyabeanus
fungal interaction: Insight into proteins at intracellular and extracellular spaces. Proteomics 2014; 14:2307-18. [DOI: 10.1002/pmic.201400066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/16/2014] [Accepted: 07/17/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Jin Yeong Kim
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Jingni Wu
- Department of Plant Microbe Interactions; Max-Planck Institute for Plant Breeding Research; Cologne Germany
| | - Soon Jae Kwon
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Haram Oh
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - So Eui Lee
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Sang Gon Kim
- National Institute of Crop Science; Rural Development Administration; Suwon South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions; Max-Planck Institute for Plant Breeding Research; Cologne Germany
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Pvt. Ltd; Birgunj Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Pvt. Ltd; Birgunj Nepal
- Organization for Educational Initiatives; University of Tsukuba; Tsukuba Ibaraki Japan
- Department of Anatomy I; Showa University School of Medicine; Shinagawa Tokyo Japan
| | - Kyu Young Kang
- Division of Applied Life Science; Gyeongsang National University; Jinju South Korea
| | - Il-Pyung Ahn
- Molecular Breeding division; National Academy of Agricultural Science, RDA; Suwon South Korea
| | - Beom-Gi Kim
- Molecular Breeding division; National Academy of Agricultural Science, RDA; Suwon 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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62
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Albenne C, Canut H, Hoffmann L, Jamet E. Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways? Proteomes 2014; 2:224-242. [PMID: 28250379 PMCID: PMC5302738 DOI: 10.3390/proteomes2020224] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/16/2022] Open
Abstract
Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components.
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Affiliation(s)
- Cécile Albenne
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Hervé Canut
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Laurent Hoffmann
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Elisabeth Jamet
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
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Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R. Rice proteomics: a model system for crop improvement and food security. Proteomics 2014; 14:593-610. [PMID: 24323464 DOI: 10.1002/pmic.201300388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/24/2013] [Accepted: 11/07/2013] [Indexed: 12/14/2022]
Abstract
Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.
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Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
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Delaunois B, Jeandet P, Clément C, Baillieul F, Dorey S, Cordelier S. Uncovering plant-pathogen crosstalk through apoplastic proteomic studies. FRONTIERS IN PLANT SCIENCE 2014; 5:249. [PMID: 24917874 PMCID: PMC4042593 DOI: 10.3389/fpls.2014.00249] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/15/2014] [Indexed: 05/14/2023]
Abstract
Plant pathogens have evolved by developing different strategies to infect their host, which in turn have elaborated immune responses to counter the pathogen invasion. The apoplast, including the cell wall and extracellular space outside the plasma membrane, is one of the first compartments where pathogen-host interaction occurs. The plant cell wall is composed of a complex network of polysaccharides polymers and glycoproteins and serves as a natural physical barrier against pathogen invasion. The apoplastic fluid, circulating through the cell wall and intercellular spaces, provides a means for delivering molecules and facilitating intercellular communications. Some plant-pathogen interactions lead to plant cell wall degradation allowing pathogens to penetrate into the cells. In turn, the plant immune system recognizes microbial- or damage-associated molecular patterns (MAMPs or DAMPs) and initiates a set of basal immune responses, including the strengthening of the plant cell wall. The establishment of defense requires the regulation of a wide variety of proteins that are involved at different levels, from receptor perception of the pathogen via signaling mechanisms to the strengthening of the cell wall or degradation of the pathogen itself. A fine regulation of apoplastic proteins is therefore essential for rapid and effective pathogen perception and for maintaining cell wall integrity. This review aims to provide insight into analyses using proteomic approaches of the apoplast to highlight the modulation of the apoplastic protein patterns during pathogen infection and to unravel the key players involved in plant-pathogen interaction.
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Affiliation(s)
| | | | | | | | | | - Sylvain Cordelier
- *Correspondence: Sylvain Cordelier, Laboratoire Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne-EA 4707, Université de Reims Champagne-Ardenne, Moulin de la Housse – BP 1039, 51687 Reims cedex 2, France e-mail:
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Lehtonen MT, Takikawa Y, Rönnholm G, Akita M, Kalkkinen N, Ahola-Iivarinen E, Somervuo P, Varjosalo M, Valkonen JPT. Protein secretome of moss plants (Physcomitrella patens) with emphasis on changes induced by a fungal elicitor. J Proteome Res 2013; 13:447-59. [PMID: 24295333 DOI: 10.1021/pr400827a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Studies on extracellular proteins (ECPs) contribute to understanding of the multifunctional nature of apoplast. Unlike vascular plants (tracheophytes), little information about ECPs is available from nonvascular plants, such as mosses (bryophytes). In this study, moss plants (Physcomitrella patens) were grown in liquid culture and treated with chitosan, a water-soluble form of chitin that occurs in cell walls of fungi and insects and elicits pathogen defense in plants. ECPs released to the culture medium were compared between chitosan-treated and nontreated control cultures using quantitative mass spectrometry (Orbitrap) and 2-DE-LC-MS/MS. Over 400 secreted proteins were detected, of which 70% were homologous to ECPs reported in tracheophyte secretomes. Bioinformatics analyses using SignalP and SecretomeP predicted classical signal peptides for secretion (37%) or leaderless secretion (27%) for most ECPs of P. patens, but secretion of the remaining proteins (36%) could not be predicted using bioinformatics. Cultures treated with chitosan contained 72 proteins not found in untreated controls, whereas 27 proteins found in controls were not detected in chitosan-treated cultures. Pathogen defense-related proteins dominated in the secretome of P. patens, as reported in tracheophytes. These results advance knowledge on protein secretomes of plants by providing a comprehensive account of ECPs of a bryophyte.
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Affiliation(s)
- Mikko T Lehtonen
- Department of Agricultural Sciences, University of Helsinki , PO Box 27, FI-00014 Helsinki, Finland
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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Choi J, Kim KT, Jeon J, Lee YH. Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes. BMC Genomics 2013; 14 Suppl 5:S7. [PMID: 24564786 PMCID: PMC3852112 DOI: 10.1186/1471-2164-14-s5-s7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In addition, many of PCWDEs are also utilized by biofuel and pulp industries. In order to develop a comparative genomics platform focused in fungal PCWDEs and provide a resource for evolutionary studies, Fungal PCWDE Database (FPDB) is constructed (http://pcwde.riceblast.snu.ac.kr/). Results In order to archive fungal PCWDEs, 22 sequence profiles were constructed and searched on 328 genomes of fungi, Oomycetes, plants and animals. A total of 6,682 putative genes encoding PCWDEs were predicted, showing differential distribution by their life styles, host ranges and taxonomy. Genes known to be involved in fungal pathogenicity, including polygalacturonase (PG) and pectin lyase, were enriched in plant pathogens. Furthermore, crop pathogens had more PCWDEs than those of rot fungi, implying that the PCWDEs analysed in this study are more needed for invading plant hosts than wood-decaying processes. Evolutionary analysis of PGs in 34 selected genomes revealed that gene duplication and loss events were mainly driven by taxonomic divergence and partly contributed by those events in species-level, especially in plant pathogens. Conclusions The FPDB would provide a fungi-specialized genomics platform, a resource for evolutionary studies of PCWDE gene families and extended analysis option by implementing Favorite, which is a data exchange and analysis hub built in Comparative Fungal Genomics Platform (CFGP 2.0; http://cfgp.snu.ac.kr/).
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Deswal R, Gupta R, Dogra V, Singh R, Abat JK, Sarkar A, Mishra Y, Rai V, Sreenivasulu Y, Amalraj RS, Raorane M, Chaudhary RP, Kohli A, Giri AP, Chakraborty N, Zargar SM, Agrawal VP, Agrawal GK, Job D, Renaut J, Rakwal R. Plant proteomics in India and Nepal: current status and challenges ahead. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:461-477. [PMID: 24431515 PMCID: PMC3781272 DOI: 10.1007/s12298-013-0198-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.
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Affiliation(s)
- Renu Deswal
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Ravi Gupta
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Vivek Dogra
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Raksha Singh
- />Department of Plant Molecular Biology, College of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jasmeet Kaur Abat
- />Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Abhijit Sarkar
- />Department of Botany, Banaras Hindu University, Varanasi, India
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Yogesh Mishra
- />Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Vandana Rai
- />National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
| | - Yelam Sreenivasulu
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Ramesh Sundar Amalraj
- />Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, India
| | - Manish Raorane
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ram Prasad Chaudhary
- />Central Department of Botany, and Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Ajay Kohli
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ashok Prabhakar Giri
- />Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
| | | | - Sajad Majeed Zargar
- />School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, 180009 Jammu and Kashmir India
| | | | - Ganesh Kumar Agrawal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Dominique Job
- />CNRS/Bayer Crop Science (UMR 5240) Joint Laboratory, Lyon, France
| | - Jenny Renaut
- />Department of Environment and Agrobiotechnologies, Centre de Recherche Public-Gabriel Lippmann, Belvaux, GD Luxembourg
| | - Randeep Rakwal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- />Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
- />Department of Anatomy I, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555 Japan
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