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Ontoy JC, Ham JH. Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:1205. [PMID: 38732420 PMCID: PMC11085595 DOI: 10.3390/plants13091205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.
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Affiliation(s)
- John Christian Ontoy
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
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Dai X, Wang Y, Yu K, Zhao Y, Xiong L, Wang R, Li S. OsNPR1 Enhances Rice Resistance to Xanthomonas oryzae pv. oryzae by Upregulating Rice Defense Genes and Repressing Bacteria Virulence Genes. Int J Mol Sci 2023; 24:ijms24108687. [PMID: 37240026 DOI: 10.3390/ijms24108687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The bacteria pathogen Xanthomonas oryzae pv. oryzae (Xoo) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression of OsNPR1 significantly increases rice resistance to Xoo. Although some downstream rice genes were found to be regulated by OsNPR1, how OsNPR1 affects the interaction of rice-Xoo and alters Xoo gene expression remains unknown. In this study, we challenged the wild-type and OsNPR1-OE rice materials with Xoo and performed dual RNA-seq analyses for the rice and Xoo genomes simultaneously. In Xoo-infected OsNPR1-OE plants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand, Xoo genes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes of Xoo, including genes encoding components of type III and other secretion systems, were downregulated by OsNPR1 overexpression. Our results suggest that OsNPR1 enhances rice resistance to Xoo by bidirectionally regulating gene expression in rice and Xoo.
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Affiliation(s)
- Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yankai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaili Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yonghui Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Langyu Xiong
- Institute of Advanced Studies in Humanities and Social Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Shengben Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Liu N, Qi L, Huang M, Chen D, Yin C, Zhang Y, Wang X, Yuan G, Wang RJ, Yang J, Peng YL, Lu X. Comparative Secretome Analysis of Magnaporthe oryzae Identified Proteins Involved in Virulence and Cell Wall Integrity. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:728-746. [PMID: 34284133 PMCID: PMC9880818 DOI: 10.1016/j.gpb.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023]
Abstract
Plant fungal pathogens secrete numerous proteins into the apoplast at the plant-fungus contact sites to facilitate colonization. However, only a few secretory proteins were functionally characterized in Magnaporthe oryzae, the fungal pathogen causing rice blast disease worldwide. Asparagine-linked glycosylation 3 (Alg3) is an α-1,3-mannosyltransferase functioning in the N-glycan synthesis of N-glycosylated secretory proteins. Fungal pathogenicity and cell wall integrity are impaired in Δalg3 mutants, but the secreted proteins affected in Δalg3 mutants are largely unknown. In this study, we compared the secretomes of the wild-type strain and the Δalg3 mutant and identified 51 proteins that require Alg3 for proper secretion. These proteins were predicted to be involved in metabolic processes, interspecies interactions, cell wall organization, and response to chemicals. Nine proteins were selected for further validation. We found that these proteins were localized at the apoplastic region surrounding the fungal infection hyphae. Moreover, the N-glycosylation of these proteins was significantly changed in the Δalg3 mutant, leading to the decreased protein secretion and abnormal protein localization. Furthermore, we tested the biological functions of two genes, INV1 (encoding invertase 1, a secreted invertase) and AMCase (encoding acid mammalian chinitase, a secreted chitinase). The fungal virulence was significantly reduced, and the cell wall integrity was altered in the Δinv1 and Δamcase mutant strains. Moreover, the N-glycosylation was essential for the function and secretion of AMCase. Taken together, our study provides new insight into the role of N-glycosylated secretory proteins in fungal virulence and cell wall integrity.
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Affiliation(s)
- Ning Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Linlu Qi
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Manna Huang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Deng Chen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Changfa Yin
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Yiying Zhang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Xingbin Wang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Guixin Yuan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China,Graduate School of China Agricultural University, Beijing 100193, China
| | - Rui-Jin Wang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Xunli Lu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China,Corresponding author.
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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Wu G, Zhang Y, Wang B, Li K, Lou Y, Zhao Y, Liu F. Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. RICE (NEW YORK, N.Y.) 2021; 14:57. [PMID: 34176023 PMCID: PMC8236019 DOI: 10.1186/s12284-021-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. RESULTS Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. CONCLUSION Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.
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Affiliation(s)
- Guichun Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yuqiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, P. R. China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Kaihuai Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Yuanlai Lou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
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Vo KTX, Rahman MM, Rahman MM, Trinh KTT, Kim ST, Jeon JS. Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update. RICE (NEW YORK, N.Y.) 2021; 14:30. [PMID: 33721115 PMCID: PMC7960847 DOI: 10.1186/s12284-021-00461-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/28/2021] [Indexed: 05/19/2023]
Abstract
Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mizanor Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Kieu Thi Thuy Trinh
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463 South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
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Zhang F, Zhang F, Huang L, Zeng D, Cruz CV, Li Z, Zhou Y. Comparative proteomic analysis reveals novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae. BMC PLANT BIOLOGY 2020; 20:563. [PMID: 33317452 PMCID: PMC7734852 DOI: 10.1186/s12870-020-02769-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/02/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Rice introgression line H471, derived from the recurrent parent Huang-Hua-Zhan (HHZ) and the donor parent PSBRC28, exhibits broad-spectrum resistance to Xoo, including to the highly virulent Xoo strain PXO99A, whereas its parents are susceptible to PXO99A. To characterize the responses to Xoo, we compared the proteome profiles of the host and pathogen in the incompatible interaction (H471 inoculated with PXO99A) and the compatible interaction (HHZ inoculated with PXO99A). RESULTS In this study, a total of 374 rice differentially abundant proteins (DAPs) and 117 Xoo DAPs were detected in the comparison between H471 + PXO99A and HHZ + PXO99A. Most of the Xoo DAPs related to pathogen virulence, including the outer member proteins, type III secretion system proteins, TonB-dependent receptors, and transcription activator-like effectors, were less abundant in the incompatible interaction than in the compatible interaction. The rice DAPs were mainly involved in secondary metabolic processes, including phenylalanine metabolism and the biosynthesis of flavonoids and phenylpropanoids. Additionally, some DAPs involved in the phenolic phytoalexin and salicylic acid (SA) biosynthetic pathways accumulated much more in H471 than in HHZ after the inoculation with PXO99A, suggesting that phytoalexin and SA productions were induced faster in H471 than in HHZ. Further analyses revealed that the SA content increased much more rapidly in H471 than in HHZ after the inoculation, suggesting that the SA signaling pathway was activated faster in the incompatible interaction than in the compatible interaction. CONCLUSIONS Overall, our results indicate that during an incompatible interaction between H471 and PXO99A, rice plants prevent pathogen invasion and also initiate multi-component defense responses that inhibit disease development.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China
- Graduate School of Chinese Academy of Agricultural Sciences, 12 Zhong-Guan-Cun Street, Beijing, 100081, China
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Dan Zeng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China
| | - Yongli Zhou
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China.
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Koduru L, Kim HY, Lakshmanan M, Mohanty B, Lee YQ, Lee CH, Lee D. Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae. MOLECULAR PLANT PATHOLOGY 2020; 21:527-540. [PMID: 32068953 PMCID: PMC7060145 DOI: 10.1111/mpp.12914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 05/29/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a vascular pathogen that causes leaf blight in rice, leading to severe yield losses. Since the usage of chemical control methods has not been very promising for the future disease management, it is of high importance to systematically gain new insights about Xoo virulence and pathogenesis, and devise effective strategies to combat the rice disease. To do this, we reconstructed a genome-scale metabolic model of Xoo (iXOO673) and validated the model predictions using culture experiments. Comparison of the metabolic architecture of Xoo and other plant pathogens indicated that the Entner-Doudoroff pathway is a more common feature in these bacteria than previously thought, while suggesting some of the unique virulence mechanisms related to Xoo metabolism. Subsequent constraint-based flux analysis allowed us to show that Xoo modulates fluxes through gluconeogenesis, glycogen biosynthesis, and degradation pathways, thereby exacerbating the leaf blight in rice exposed to nitrogenous fertilizers, which is remarkably consistent with published experimental literature. Moreover, model-based interrogation of transcriptomic data revealed the metabolic components under the diffusible signal factor regulon that are crucial for virulence and survival in Xoo. Finally, we identified promising antibacterial targets for the control of leaf blight in rice by using gene essentiality analysis.
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Affiliation(s)
- Lokanand Koduru
- Bioprocessing Technology InstituteAgency for Science, Technology and ResearchSingapore
| | - Hyang Yeon Kim
- Department of Bioscience and BiotechnologyKonkuk UniversitySeoulRepublic of Korea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology InstituteAgency for Science, Technology and ResearchSingapore
| | - Bijayalaxmi Mohanty
- Bioprocessing Technology InstituteAgency for Science, Technology and ResearchSingapore
| | - Yi Qing Lee
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and BiotechnologyKonkuk UniversitySeoulRepublic of Korea
| | - Dong‐Yup Lee
- Bioprocessing Technology InstituteAgency for Science, Technology and ResearchSingapore
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
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9
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Soni N, Swain SK, Kant R, Singh A, Ravichandran R, Verma SK, Panda PK, Suar M. Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica. Comput Biol Chem 2019; 83:107110. [PMID: 31445418 DOI: 10.1016/j.compbiolchem.2019.107110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 07/16/2019] [Accepted: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Salmonella, an Enterobacteria is a therapeutically important pathogen for the host. The advancement of genome sequencing of S. enterica serovar Enteritidis have identified a distinct ROD9 pathogenic island, imparting virulence. The occurrence of 17 ROD9 hypothetical proteins, necessitates subsequent bioinformatics approach for structural and functional aspects of protein-protein relations or networks in different pathogenic phenotypes express. A collective analysis using predictive bioinformatics tools that includes NCBI-BLASTp and BLAST2GO annotated the motif patterns and functional significance. The VFDB identified 10 virulence proteins at both genomic and metagenomic level. Phylogenetic analysis revealed a divergent and convergent relationship between 17 ROD9 and 41 SP-1 proteins. Here, combining a comprehensive approach from sequence based, motif recognitions, domain identification, virulence ability to structural modelling provides a precise function to ROD9 proteins biological network, for which no experimental information is available.
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Affiliation(s)
- Nikita Soni
- School of Biotechnology and Bioinformatics, D. Y. Patil (Deemed to be University), Navi Mumbai, India
| | | | - Ravi Kant
- University of Delhi, New Delhi, India
| | - Aditya Singh
- School of Biotechnology and Bioinformatics, D. Y. Patil (Deemed to be University), Navi Mumbai, India
| | - Rahul Ravichandran
- School of Chemical and Biotechnology, SASTRA University, Tamil Nadu, India
| | - Suresh K Verma
- Institute of Environmental Medicine (IMM), C6, Molecular Toxicology, Karolinska Institutet, Sweden
| | - Pritam Kumar Panda
- Division of Pediatric Hematology and Oncology, University Medical Center, University of Freiburg, Germany.
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, India.
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10
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Li Z, Zhang H, Li G. Characterization of phytotoxin and secreted proteins identifies of Lasiodiplodia theobromae, causes of peach gummosis. Fungal Biol 2019; 123:51-58. [PMID: 30654957 DOI: 10.1016/j.funbio.2018.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/06/2018] [Indexed: 11/18/2022]
Abstract
Lasiodiplodia theobromae, a phytopathogenic fungus that causes peach gummosis, is considered one of the major constraints to peach production worldwide. Here, we report the characteristics of toxic metabolites and the proteomics investigation of the secreted proteins of L. theobromae from its in vitro culture. The phytotoxins of L. theobromae from the culture filtrate of Richard's liquid medium showed high toxicity on peach current year shoots with large lesion diameter and high gum weight. The toxicity measurement showed that 23.6 and 21.2 mg gum were induced from peach shoots by solvent fractions of ethyl acetate and dichloromethane, respectively, with significant differences from other organic solvents. A total of 23 proteins were identified by liquid chromatography-mass spectrometry from the in vitro secretome of L. theobromae. Sequence analysis indicated that 14 proteins were extracellular proteins based on signal peptides and localization. The expression profiles of the analyzed fungal genes were significantly upregulated from 1 day postinoculation (dpi) to 2 dpi, indicating that the early stage is an important stage for the infection of L. theobromae. The present study has provided insights into the extracellular phytotoxins and secreted proteins that are possibly associated with pathogenicity of the peach gummosis.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - He Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guohuai Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Meng Q, Gupta R, Min CW, Kim J, Kramer K, Wang Y, Park SR, Finkemeier I, Kim ST. A proteomic insight into the MSP1 and flg22 induced signaling in Oryza sativa leaves. J Proteomics 2018; 196:120-130. [PMID: 29970347 DOI: 10.1016/j.jprot.2018.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/02/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Previously, we reported a novel Magnaporthe oryzae- secreted protein MSP1, which triggers cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. To investigate the MSP1 induced defense response in rice at the protein level, we employed a label-free quantitative proteomic approach, in parallel with flg22 treatment, which is a well-known elicitor. Exogenous application of MSP1 to rice leaves induced an oxidative burst, MAPK3/6 activation, and activation of pathogenesis-related genes (DUF26, PBZ, and PR-10). MaxQuant based label free proteome analysis led to the identification of 4167 protein groups of which 433 showed significant differences in response to MSP1 and/or flg22 treatment. Functional annotation of the differential proteins showed that majority of the proteins related to primary, secondary, and lipid metabolism were decreased, while proteins associated mainly with the stress response, post-translational modification and signaling were increased in abundance. Moreover, several peroxidases and receptor kinases were induced by both the elicitors, highlighting their involvement in MSP1 and flg22 induced signaling in rice. Taken together, the results reported here contribute to our understanding of MSP1 and flg22 triggered immune responses at the proteome level, thereby increasing our overall understanding of PTI signaling in rice. BIOLOGICAL SIGNIFICANCE: MSP1 is a M. oryzae secreted protein, which triggers defense responses in rice. Previous reports have shown that MSP1 is required for the pathogenicity of rice blast fungus, however, the exact mechanism of its action and its downstream targets in rice are currently unknown. Identification of the downstream targets is required in order to understand the MSP1 induced signaling in rice. Moreover, key proteins identified could also serve as potential candidates for the generation of disease resistance crops by modulating stress signaling pathways. Therefore, here we employed, for the first time, a label-free quantitative proteomic approach to investigate the MSP1 induced signaling in rice together with flg22. Functional annotation of the differential proteins showed that majority of the proteins related to primary, secondary, and lipid metabolism were decreased, while proteins related to the defense response, signaling and ROS detoxification were majorly increased. Thus, as an elicitor, recombinant MSP1 proteins could be utilized to inducing broad pathogen resistance in crops by priming the local immune responses.
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Affiliation(s)
- Qingfeng Meng
- Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea.
| | - Chul Woo Min
- Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea
| | - Jongyun Kim
- Division of Biotechnology, Korea University, Seoul 02841, South Korea
| | - Katharina Kramer
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Germany
| | - Yiming Wang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Sang-Ryeol Park
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, South Korea
| | - Iris Finkemeier
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Germany; Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang 627-706, South Korea.
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12
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Assis RDAB, Polloni LC, Patané JSL, Thakur S, Felestrino ÉB, Diaz-Caballero J, Digiampietri LA, Goulart LR, Almeida NF, Nascimento R, Dandekar AM, Zaini PA, Setubal JC, Guttman DS, Moreira LM. Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. Sci Rep 2017; 7:16133. [PMID: 29170530 PMCID: PMC5700972 DOI: 10.1038/s41598-017-16325-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023] Open
Abstract
The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria.
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Affiliation(s)
- Renata de A B Assis
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | | | - José S L Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Shalabh Thakur
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | - Érica B Felestrino
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Julio Diaz-Caballero
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | | | - Luiz Ricardo Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Nalvo F Almeida
- School of Computing, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, MS, Brazil
| | - Rafael Nascimento
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Paulo A Zaini
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil.,Department of Plant Sciences, University of California, Davis, CA, USA
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | - Leandro Marcio Moreira
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil. .,Department of Biological Science, Institute of Exact and Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
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13
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Label-free quantitative secretome analysis of Xanthomonas oryzae pv. oryzae highlights the involvement of a novel cysteine protease in its pathogenicity. J Proteomics 2017; 169:202-214. [DOI: 10.1016/j.jprot.2017.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/23/2017] [Accepted: 02/14/2017] [Indexed: 11/24/2022]
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14
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Lee SE, Gupta R, Jayaramaiah RH, Lee SH, Wang Y, Park SR, Kim ST. Global Transcriptome Profiling of Xanthomonas oryzae pv. oryzae under in planta Growth and in vitro Culture Conditions. THE PLANT PATHOLOGY JOURNAL 2017; 33:458-466. [PMID: 29018309 PMCID: PMC5624488 DOI: 10.5423/ppj.oa.04.2017.0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 05/29/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is a major threat to rice productivity. Here, we performed RNA-Seq based transcriptomic analysis of Xoo transcripts isolated under in planta growth (on both susceptible and resistant hosts) and in vitro culture conditions. Our in planta extraction method resulted in successful enrichment of Xoo cells and provided RNA samples of high quality. A total of 4,619 differentially expressed genes were identified between in planta and in vitro growth conditions. The majority of the differentially expressed genes identified under in planta growth conditions were related to the nutrient transport, protease activity, stress tolerance, and pathogenicity. Among them, over 1,300 differentially expressed genes were determined to be secretory, including 184 putative type III effectors that may be involved in Xoo pathogenicity. Expression pattern of some of these identified genes were further validated by semi-quantitative RT-PCR. Taken together, these results provide a transcriptome overview of Xoo under in planta and in vitro growth conditions with a focus on its pathogenic processes, deepening our understanding of the behavior and pathogenicity of Xoo.
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Affiliation(s)
- So Eui Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463,
Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463,
Korea
| | - Ramesha H. Jayaramaiah
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463,
Korea
| | - Seo Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463,
Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linneweg 10, Cologne 50829,
Germany
| | - Sang-Ryeol Park
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54875,
Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463,
Korea
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15
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Integrating cell biology and proteomic approaches in plants. J Proteomics 2017; 169:165-175. [DOI: 10.1016/j.jprot.2017.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/29/2017] [Accepted: 04/18/2017] [Indexed: 11/22/2022]
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16
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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17
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Santos C, Maximiano MR, Ribeiro DG, Oliveira-Neto OB, Murad AM, Franco OL, Mehta A. Differential accumulation ofXanthomonas campestrispv.campestrisproteins during the interaction with the host plant: Contributions of an in vivo system. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Cristiane Santos
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
- Centro de Analises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília DF Brazil
| | - Mariana R. Maximiano
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
- Universidade Federal de Juiz de Fora; MG Brazil
| | - Daiane G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
- Universidade Paulista; Brasília DF Brazil
| | | | - André M. Murad
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
| | - Octávio L. Franco
- Centro de Analises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília DF Brazil
- Universidade Federal de Juiz de Fora; MG Brazil
- S-Inova, Pós-Graduação em Biotecnologia; Universidade Católica Dom Bosco; Campo Grande MS Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
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18
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Chen JY, Xiao HL, Gui YJ, Zhang DD, Li L, Bao YM, Dai XF. Characterization of the Verticillium dahliae Exoproteome Involves in Pathogenicity from Cotton-Containing Medium. Front Microbiol 2016; 7:1709. [PMID: 27840627 PMCID: PMC5083787 DOI: 10.3389/fmicb.2016.01709] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022] Open
Abstract
Verticillium wilt, caused by the Verticillium dahliae phytopathogen, is a devastating disease affecting many economically important crops. Previous studies have shown that the exoproteome of V. dahliae plays a significant role in this pathogenic process, but the components and mechanisms that underlie this remain unclear. In this study, the exoproteome of V. dahliae was induced in a cotton-containing C’zapek-Dox (CCD) medium and quantified using the high-throughput isobaric tag technique for relative and absolute quantification (iTRAQ). Results showed that the abundance of 271 secreted proteins was affected by the CCD medium, of which 172 contain typical signal peptides generally produced by the Golgi/endoplasmic reticulum (ER). These enhanced abundance proteins were predominantly enriched in carbohydrate hydrolases; 126 were classified as carbohydrate-active (CAZymes) and almost all were significantly up-regulated in the CCD medium. Results showed that CAZymes proteins 30 and 22 participate in pectin and cellulose degradation pathways, corresponding with the transcription levels of several genes encoded plant cell wall degradation enzyme activated significantly during cotton infection. In addition, targeted deletion of two pectin lyase genes (VdPL3.1 and VdPL3.3) impaired wilt virulence to cotton. This study demonstrates that the V. dahliae exoproteome plays a crucial role in the development of symptoms of wilting and necrosis, predominantly via the pathogenic mechanisms of plant cell wall degradation as part of host plant infection.
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Affiliation(s)
- Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Hong-Li Xiao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Lei Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yu-Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
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19
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Haddadi P, Ma L, Wang H, Borhan MH. Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. MOLECULAR PLANT PATHOLOGY 2016; 17:1196-210. [PMID: 26679637 PMCID: PMC6638455 DOI: 10.1111/mpp.12356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/18/2015] [Accepted: 12/11/2015] [Indexed: 05/08/2023]
Abstract
Molecular interaction between the causal agent of blackleg disease, Leptosphaeria maculans (Lm), and its host, Brassica napus, is largely unknown. We applied a deep RNA-sequencing approach to gain insight into the pathogenicity mechanisms of Lm and the defence response of B. napus. RNA from the infected susceptible B. napus cultivar Topas DH16516, sampled at 2-day intervals (0-8 days), was sequenced and used for gene expression profiling. Patterns of gene expression regulation in B. napus showed multifaceted defence responses evident by the differential expression of genes encoding the pattern recognition receptor CERK1 (chitin elicitor receptor kinase 1), receptor like proteins and WRKY transcription factors. The up-regulation of genes related to salicylic acid and jasmonic acid at the initial and late stages of infection, respectively, provided evidence for the biotrophic and necrotrophic life stages of Lm during the infection of B. napus cotyledons. Lm transition from biotrophy to necrotropy was also supported by the expression function of Lm necrosis and ethylene-inducing (Nep-1)-like peptide. Genes encoding polyketide synthases and non-ribosomal peptide synthetases, with potential roles in pathogenicity, were up-regulated at 6-8 days after inoculation. Among other plant defence-related genes differentially regulated in response to Lm infection were genes involved in the reinforcement of the cell wall and the production of glucosinolates. Dual RNA-sequencing allowed us to define the Lm candidate effectors expressed during the infection of B. napus. Several candidate effectors suppressed Bax-induced cell death when transiently expressed in Nicotiana benthamaina leaves.
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Affiliation(s)
- Parham Haddadi
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Lisong Ma
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Haiyan Wang
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Agricultural University of Hebei, Baoding, China, 071001
| | - M Hossein Borhan
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
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Analysis of the Proteins Secreted from the Oryza meyeriana Suspension-Cultured Cells Induced by Xanthomonas oryzae pv. oryzae. PLoS One 2016; 11:e0154793. [PMID: 27196123 PMCID: PMC4873123 DOI: 10.1371/journal.pone.0154793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/19/2016] [Indexed: 01/18/2023] Open
Abstract
Oryza meyeriana, a wild species of rice from China, shows high resistance to Xanthomonas oryzae pv. oryzae (Xoo), the cause of rice bacterial blight, one of the most serious rice pathogens. To better understand the resistance mechanism, a proteomic study was conducted to identify changes in the proteins secreted in embryo cell suspension cultures in response to Xoo. After two-dimensional difference gel electrophoresis (2D-DIGE), 72 differentially expressed protein spots corresponding to 34 proteins were identified by Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry. Of the 34 proteins, 10 were up regulated and 24 down regulated. The secreted proteins identified were predicted to be involved in various biological processes, including signal transduction, defense, ROS and cell wall modification. 77% of the 34 proteins were predicted to have a signal peptide by Signal P. Quantitative Real-Time PCR showed that transcript levels of 14 secreted proteins were not well correlated with secreted protein levels. Peroxidase activity was up regulated in both O. meyriana and susceptible rice but was about three times higher in O. meyeriana. This suggests that peroxidases may play an important role in the early response to Xoo in O. meyeriana. These results not only provide a better understanding of the resistance mechanism of O. meyeriana, but have implications for studies of the interactions between other plants and their pathogens.
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Ferreira RM, Moreira LM, Ferro JA, Soares MR, Laia ML, Varani AM, de Oliveira JC, Ferro MIT. Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis. PeerJ 2016; 4:e1734. [PMID: 26925342 PMCID: PMC4768671 DOI: 10.7717/peerj.1734] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/02/2016] [Indexed: 11/20/2022] Open
Abstract
Citrus canker is a major disease affecting citrus production in Brazil. It's mainly caused by Xanthomonas citri subsp. citri strain 306 pathotype A (Xac). We analysed the differential expression of proteins secreted by wild type Xac and an asymptomatic mutant for hrpB4 (ΔhrpB4) grown in Nutrient Broth (NB) and a medium mimicking growth conditions in the plant (XAM1). This allowed the identification of 55 secreted proteins, of which 37 were secreted by both strains when cultured in XAM1. In this secreted protein repertoire, the following stand out: Virk, Polyphosphate-selective porin, Cellulase, Endoglucanase, Histone-like protein, Ribosomal proteins, five hypothetical proteins expressed only in the wild type strain, Lytic murein transglycosylase, Lipoprotein, Leucyl-tRNA synthetase, Co-chaperonin, Toluene tolerance, C-type cytochrome biogenesis membrane protein, Aminopeptidase and two hypothetical proteins expressed only in the ΔhrpB4 mutant. Furthermore, Peptidoglycan-associated outer membrane protein, Regulator of pathogenicity factor, Outer membrane proteins, Endopolygalacturonase, Chorismate mutase, Peptidyl-prolyl cis-trans isomerase and seven hypothetical proteins were detected in both strains, suggesting that there was no relationship with the secretion mediated by the type III secretory system, which is not functional in the mutant strain. Also worth mentioning is the Elongation factor Tu (EF-Tu), expressed only the wild type strain, and Type IV pilus assembly protein, Flagellin (FliC) and Flagellar hook-associated protein, identified in the wild-type strain secretome when grown only in NB. Noteworthy, that FliC, EF-Tu are classically characterized as PAMPs (Pathogen-associated molecular patterns), responsible for a PAMP-triggered immunity response. Therefore, our results highlight proteins potentially involved with the virulence. Overall, we conclude that the use of secretome data is a valuable approach that may bring more knowledge of the biology of this important plant pathogen, which ultimately can lead to the establishment of new strategies to combat citrus canker.
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Affiliation(s)
- Rafael M. Ferreira
- Departamento de Tecnologia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas—Núcleo de Pesquisas em Ciências Biológicas-NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Jesus A. Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | - Marcia R.R. Soares
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Instituto de Química, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo L. Laia
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | - Julio C.F. de Oliveira
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Maria Ines T. Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
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Chen X, Deng Z, Yu C, Yan C, Chen J. Secretome analysis of rice suspension-cultured cells infected by Xanthomonas oryzae pv.oryza (Xoo). Proteome Sci 2016; 14:2. [PMID: 26839515 PMCID: PMC4735954 DOI: 10.1186/s12953-016-0091-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/17/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Rice bacterial blight (BB) caused by Xanthomonas oryzae pv.oryzae (Xoo) is one of the most devastating bacterial diseases in rice-growing regions worldwide. The rice-Xoo interaction is a classical model for studying the interaction between plants and pathogens. Secreted proteins play important roles in plant-bacterial interactions, but are poorly studied in the rice-Xoo system. Rice cv. Nipponbare is highly susceptible to Xoo. Here, we used two-dimensional difference gel electrophoresis (2D-DIGE) coupled with MALDI-TOF/TOF mass spectrometry (MS), to investigate secreted proteins in Nipponbare embryo cell suspension culture infected by Xoo. RESULTS A total of 32 protein spots changed significantly (p < 0.05) by more than 1.5 fold in gel intensity after Xoo inoculation, and were identified by MS. They represent protein products of 11 unique genes, seven from rice and four from Xoo. Of the rice proteins, six up-regulated proteins are involved in cell wall modification, the TCA cycle, glycolysis and redox, while a down-regulated protein, CHIT16, is involved in plant defense. Quantitative Real-Time PCR showed that transcript levels were not correlated with secreted protein levels. Of the Xoo proteins, three of them were possibly located in the extracellular space as shown by transient expression assays in rice protoplasts. Two of the Xoo proteins were previously reported to be likely involved in pathogenicity, and the third gene, Xoo3654, is likely a negative regulator of Xoo virulence as its overexpression reduced Xoo pathogenicity in our study. CONCLUSION Among the secreted proteins that responded to Xoo inoculation, we identified rice proteins involved in cell defense and Xoo proteins involved in pathogenicity. Our study also showed that Xoo3654 (X2) protein is likely a novel negative regulator of Xoo virulence. These results not only help us better understand the interaction between susceptible rice and Xoo, but also serve as a reference for studying the interaction between other plants and their pathogens.
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Affiliation(s)
- Xian Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ; State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Zhiping Deng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Chulang Yu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
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Lonjon F, Turner M, Henry C, Rengel D, Lohou D, van de Kerkhove Q, Cazalé AC, Peeters N, Genin S, Vailleau F. Comparative Secretome Analysis of Ralstonia solanacearum Type 3 Secretion-Associated Mutants Reveals a Fine Control of Effector Delivery, Essential for Bacterial Pathogenicity. Mol Cell Proteomics 2015; 15:598-613. [PMID: 26637540 DOI: 10.1074/mcp.m115.051078] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/21/2022] Open
Abstract
Ralstonia solanacearum, the causal agent of bacterial wilt, exerts its pathogenicity through more than a hundred secreted proteins, many of them depending directly on the functionality of a type 3 secretion system. To date, only few type 3 effectors have been identified as required for bacterial pathogenicity, notably because of redundancy among the large R. solanacearum effector repertoire. In order to identify groups of effectors collectively promoting disease on susceptible hosts, we investigated the role of putative post-translational regulators in the control of type 3 secretion. A shotgun secretome analysis with label-free quantification using tandem mass spectrometry was performed on the R. solanacearum GMI1000 strain. There were 228 proteins identified, among which a large proportion of type 3 effectors, called Rip (Ralstonia injected proteins). Thanks to this proteomic approach, RipBJ was identified as a new effector specifically secreted through type 3 secretion system and translocated into plant cells. A focused Rip secretome analysis using hpa (hypersensitive response and pathogenicity associated) mutants revealed a fine secretion regulation and specific subsets of Rips with different secretion patterns. We showed that a set of Rips (RipF1, RipW, RipX, RipAB, and RipAM) are secreted in an Hpa-independent manner. We hypothesize that these Rips could be preferentially involved in the first stages of type 3 secretion. In addition, the secretion of about thirty other Rips is controlled by HpaB and HpaG. HpaB, a candidate chaperone was shown to positively control secretion of numerous Rips, whereas HpaG was shown to act as a negative regulator of secretion. To evaluate the impact of altered type 3 effectors secretion on plant pathogenesis, the hpa mutants were assayed on several host plants. HpaB was required for bacterial pathogenicity on multiple hosts whereas HpaG was found to be specifically required for full R. solanacearum pathogenicity on the legume plant Medicago truncatula.
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Affiliation(s)
- Fabien Lonjon
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Marie Turner
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Céline Henry
- ¶PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - David Rengel
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - David Lohou
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Quitterie van de Kerkhove
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Anne-Claire Cazalé
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Nemo Peeters
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Stéphane Genin
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Fabienne Vailleau
- From the ‡INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France; §CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France; ‖Université de Toulouse; INP; ENSAT; 18 chemin de Borde Rouge, Castanet Tolosan, 31326, France
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24
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Whitworth DE, Morgan BH. Synergism Between Bacterial GAPDH and OMVs: Disparate Mechanisms but Co-Operative Action. Front Microbiol 2015; 6:1231. [PMID: 26617577 PMCID: PMC4637417 DOI: 10.3389/fmicb.2015.01231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/20/2015] [Indexed: 01/06/2023] Open
Affiliation(s)
- David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Bethan H Morgan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
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25
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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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26
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Chow V, Shantharaj D, Guo Y, Nong G, Minsavage GV, Jones JB, Preston JF. Xylan utilization regulon in Xanthomonas citri pv. citri Strain 306: gene expression and utilization of oligoxylosides. Appl Environ Microbiol 2015; 81:2163-72. [PMID: 25595763 PMCID: PMC4345395 DOI: 10.1128/aem.03091-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/08/2015] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas citri pv. citri strain 306 (Xcc306), a causative agent of citrus canker, produces endoxylanases that catalyze the depolymerization of cell wall-associated xylans. In the sequenced genomes of all plant-pathogenic xanthomonads, genes encoding xylanolytic enzymes are clustered in three adjacent operons. In Xcc306, these consecutive operons contain genes encoding the glycoside hydrolase family 10 (GH10) endoxylanases Xyn10A and Xyn10C, the agu67 gene, encoding a GH67 α-glucuronidase (Agu67), the xyn43E gene, encoding a putative GH43 α-l-arabinofuranosidase, and the xyn43F gene, encoding a putative β-xylosidase. Recombinant Xyn10A and Xyn10C convert polymeric 4-O-methylglucuronoxylan (MeGXn) to oligoxylosides methylglucuronoxylotriose (MeGX3), xylotriose (X3), and xylobiose (X2). Xcc306 completely utilizes MeGXn predigested with Xyn10A or Xyn10C but shows little utilization of MeGXn. Xcc306 with a deletion in the gene encoding α-glucuronidase (Xcc306 Δagu67) will not utilize MeGX3 for growth, demonstrating the role of Agu67 in the complete utilization of GH10-digested MeGXn. Preferential growth on oligoxylosides compared to growth on polymeric MeGXn indicates that GH10 xylanases, either secreted by Xcc306 in planta or produced by the plant host, generate oligoxylosides that are processed by Xyn10 xylanases and Agu67 residing in the periplasm. Coordinate induction by oligoxylosides of xyn10, agu67, cirA, the tonB receptor, and other genes within these three operons indicates that they constitute a regulon that is responsive to the oligoxylosides generated by the action of Xcc306 GH10 xylanases on MeGXn. The combined expression of genes in this regulon may allow scavenging of oligoxylosides derived from cell wall deconstruction, thereby contributing to the tissue colonization and/or survival of Xcc306 and, ultimately, to plant disease.
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Affiliation(s)
- V Chow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - D Shantharaj
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Y Guo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - G Nong
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - G V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - J B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - J F Preston
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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27
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Escobar-Tovar L, Guzmán-Quesada M, Sandoval-Fernández JA, Gómez-Lim MA. Comparative analysis of the in vitro and in planta secretomes from Mycosphaerella fijiensis isolates. Fungal Biol 2015; 119:447-70. [PMID: 25986542 DOI: 10.1016/j.funbio.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 01/09/2023]
Abstract
Black Sigatoka, a devastating disease of bananas and plantains worldwide, is caused by the fungus Mycosphaerella fijiensis. Several banana cultivars such as 'Yangambi Km 5' and Calcutta IV, have been known to be resistant to the fungus, but the resistance has been broken in 'Yangambi Km 5' in Costa Rica. Since the resistance of this variety still persists in Mexico, the aim of this study was to compare the in vitro and in planta secretomes from two avirulent and virulent M. fijiensis isolates using proteomics and bioinformatics approaches. We aimed to identify differentially expressed proteins in fungal isolates that differ in pathogenicity and that might be responsible for breaking the resistance in 'Yangambi Km 5'. We were able to identify 90 protein spots in the secretomes of fungal isolates encoding 42 unique proteins and 35 differential spots between them. Proteins involved in carbohydrate transport and metabolism were more prevalent. Several proteases, pathogenicity-related, ROS detoxification and unknown proteins were also highly or specifically expressed by the virulent isolate in vitro or during in planta infection. An unknown protein representing a virulence factor candidate was also identified. These results demonstrated that the secretome reflects major differences between both M. fijiensis isolates.
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Affiliation(s)
- Lina Escobar-Tovar
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, 36821, Irapuato, Guanajuato, Mexico
| | - Mauricio Guzmán-Quesada
- Dirección de Investigaciones, Sección de Fitopatología, Corporación Bananera Nacional, 390-7210, La Rita, Guápiles, Costa Rica
| | - Jorge A Sandoval-Fernández
- Dirección de Investigaciones, Sección de Fitopatología, Corporación Bananera Nacional, 390-7210, La Rita, Guápiles, Costa Rica
| | - Miguel A Gómez-Lim
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, 36821, Irapuato, Guanajuato, Mexico.
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28
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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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29
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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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30
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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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31
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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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Xu S, Luo J, Pan X, Liang X, Wu J, Zheng W, Chen C, Hou Y, Ma H, Zhou M. Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1660-70. [DOI: 10.1016/j.bbapap.2013.05.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
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