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Vishwakarma G, Saini A, Bhardwaj SC, Kumar S, Das BK. Comparative transcriptomics of stem rust resistance in wheat NILs mediated by Sr24 rust resistance gene. PLoS One 2023; 18:e0295202. [PMID: 38079439 PMCID: PMC10712884 DOI: 10.1371/journal.pone.0295202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Stem rust of wheat is a deleterious fungal disease across the globe causing severe yield losses. Although, many stem rust resistance genes (Sr) are being used in wheat breeding programs, new emerging stem rust pathotypes are a challenge to important Sr genes. In recent years, multiple studies on leaf and yellow rust molecular mechanism have been done, however, for stem rust such studies are lacking. Current study investigated stem rust induced response in the susceptible wheat genotype C306 and its Near Isogenic Line (NIL) for Sr24 gene, HW2004, using microarray analysis to understand the transcriptomic differences at different stages of infection. Results showed that HW2004 has higher basal levels of several important genes involved in pathogen detection, defence, and display early activation of multiple defence mechanisms. Further Gene Ontology (GO) and pathway analysis identified important genes responsible for pathogen detection, downstream signalling cascades and transcription factors (TFs) involved in activation and mediation of defence responses. Results suggest that generation of Reactive Oxygen Species (ROS), cytoskeletal rearrangement, activation of multiple hydrolases, and lipid metabolism mediated biosynthesis of certain secondary metabolites are collectively involved in Sr24-mediated defence in HW2004, in response to stem rust infection. Novel and unannotated, but highly responsive genes were also identified, which may also contribute towards resistance phenotype. Furthermore, certain DEGs also mapped close to the Sr24-linked marker on Thinopyrum elongatum translocated fragment on wheat 3E chromosome, which advocate further investigations for better insights of the Sr24-mediated stem rust resistance.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ajay Saini
- Homi Bhabha National Institute, Mumbai, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | | | - Satish Kumar
- ICAR—Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, India
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Zhang F, Hu Z, Wu Z, Lu J, Shi Y, Xu J, Wang X, Wang J, Zhang F, Wang M, Shi X, Cui Y, Vera Cruz C, Zhuo D, Hu D, Li M, Wang W, Zhao X, Zheng T, Fu B, Ali J, Zhou Y, Li Z. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics. THE PLANT CELL 2021; 33:2538-2561. [PMID: 34467412 PMCID: PMC8408478 DOI: 10.1093/plcell/koab146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 05/15/2021] [Indexed: 05/23/2023]
Abstract
A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.
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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, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Zhiqiang Hu
- 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, Haidian District, Beijing 100081, China
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Zhichao Wu
- 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, Haidian District, Beijing 100081, China
| | - Jialing Lu
- 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, Haidian District, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Jianlong Xu
- 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, Haidian District, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, 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, Haidian District, Beijing 100081, China
| | - Mingming Wang
- 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, Haidian District, Beijing 100081, China
| | - Xiaorong Shi
- 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, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Yanru Cui
- 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, Haidian District, Beijing 100081, China
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Dalong Zhuo
- 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, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Dandan Hu
- 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, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Wensheng Wang
- 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, Haidian District, Beijing 100081, China
| | - Xiuqin Zhao
- 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, Haidian District, Beijing 100081, China
| | - Tianqing Zheng
- 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, Haidian District, Beijing 100081, China
| | - Binying Fu
- 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, Haidian District, Beijing 100081, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - 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, Haidian District, Beijing 100081, China
| | - 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, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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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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4
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TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale. Microorganisms 2021; 9:microorganisms9020315. [PMID: 33557009 PMCID: PMC7913752 DOI: 10.3390/microorganisms9020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Transcription activator-like effectors (TALEs) play a significant role for pathogenesis in several xanthomonad pathosystems. Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of Cassava Bacterial Blight (CBB), uses TALEs to manipulate host metabolism. Information about Xpm TALEs and their target genes in cassava is scarce, but has been growing in the last few years. We aimed to characterize the TALE diversity in Colombian strains of Xpm and to screen for TALE-targeted gene candidates. We selected eighteen Xpm strains based on neutral genetic diversity at a country scale to depict the TALE diversity among isolates from cassava productive regions. RFLP analysis showed that Xpm strains carry TALomes with a bimodal size distribution, and affinity-based clustering of the sequenced TALEs condensed this variability mainly into five clusters. We report on the identification of 13 novel variants of TALEs in Xpm, as well as a functional variant with 22 repeats that activates the susceptibility gene MeSWEET10a, a previously reported target of TAL20Xam668. Transcriptomics and EBE prediction analyses resulted in the selection of several TALE-targeted candidate genes and two potential cases of functional convergence. This study provides new bases for assessing novel potential TALE targets in the Xpm–cassava interaction, which could be important factors that define the fate of the infection.
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5
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Jain A, Singh HB, Das S. Deciphering plant-microbe crosstalk through proteomics studies. Microbiol Res 2020; 242:126590. [PMID: 33022544 DOI: 10.1016/j.micres.2020.126590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.
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Affiliation(s)
- Akansha Jain
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
| | - Harikesh Bahadur Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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Qiu A, Lei Y, Yang S, Wu J, Li J, Bao B, Cai Y, Wang S, Lin J, Wang Y, Shen L, Cai J, Guan D, He S. CaC3H14 encoding a tandem CCCH zinc finger protein is directly targeted by CaWRKY40 and positively regulates the response of pepper to inoculation by Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2018; 19:2221-2235. [PMID: 29683552 PMCID: PMC6638151 DOI: 10.1111/mpp.12694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/27/2018] [Accepted: 04/20/2018] [Indexed: 05/10/2023]
Abstract
Tandem CCCH zinc finger (TZnF) proteins have been implicated in plant defence, but their role in pepper (Capsicum annuum) is unclear. In the present study, the role of CaC3H14, a pepper TZnF protein, in the immune response of pepper plants to Ralstonia solanacearum infection was characterized. When fused to the green fluorescent protein, CaC3H14 was localized exclusively to the nuclei in leaf cells of Nicotiana benthamiana plants transiently overexpressing CaC3H14. Transcript abundance of CaC3H14 was up-regulated by inoculation with R. solanacearum. Virus-induced silencing of CaC3H14 increased the susceptibility of the plants to R. solanacearum and down-regulated the genes associated with the hypersensitive response (HR), specifically HIR1 and salicylic acid (SA)-dependent PR1a. By contrast, silencing resulted in the up-regulation of jasmonic acid (JA)-dependent DEF1 and ethylene (ET) biosynthesis-associated ACO1. Transient overexpression of CaC3H14 in pepper triggered an intensive HR, indicated by cell death and hydrogen peroxide (H2 O2 ) accumulation, up-regulated PR1a and down-regulated DEF1 and ACO1. Ectopic overexpression of CaC3H14 in tobacco plants significantly decreased the susceptibility of tobacco plants to R. solanacearum. It also up-regulated HR-associated HSR515, immunity-associated GST1 and the SA-dependent marker genes NPR1 and PR2, but down-regulated JA-dependent PR1b and ET-dependent EFE26. The CaC3H14 promoter and was bound and its transcription was up-regulated by CaWRKY40. Collectively, these results indicate that CaC3H14 is transcriptionally targeted by CaWRKY40, is a modulator of the antagonistic interaction between SA and JA/ET signalling, and enhances the defence response of pepper plants to infection by R. solanacearum.
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Affiliation(s)
- Ailian Qiu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yufen Lei
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Sheng Yang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Ji Wu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jiazhi Li
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Bingjin Bao
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yiting Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Song Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinhui Lin
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yuzhu Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Lei Shen
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinsen Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Deyi Guan
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Shuilin He
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
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8
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Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. pruni early leaf infection. PLoS One 2018; 13:e0196590. [PMID: 29698473 PMCID: PMC5919700 DOI: 10.1371/journal.pone.0196590] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap) is a major threat to Prunus species worldwide. The molecular mechanisms of peach resistance to Xap during early leaf infection were investigated by RNA-Seq analysis of two Prunus persica cultivars, ‘Redkist’ (resistant), and ‘JH Hale’ (susceptible) at 30 minutes, 1 and 3 hours-post-infection (hpi). Both cultivars exhibited extensive modulation of gene expression at 30 mpi, which reduced significantly at 1 hpi, increasing again at 3 hpi. Overall, 714 differentially expressed genes (DEGs) were detected in ‘Redkist’ (12% at 30 mpi and 1 hpi and 88% at 3 hpi). In ‘JH Hale’, 821 DEGs were identified (47% at 30 mpi and 1 hpi and 53% at 3 hpi). Highly up-regulated genes (fold change > 100) at 3 hpi exhibited higher fold change values in ‘Redkist’ than in ‘JH Hale’. RNA-Seq bioinformatics analyses were validated by RT-qPCR. In both cultivars, DEGs included genes with putative roles in perception, signal transduction, secondary metabolism, and transcription regulation, and there were defense responses in both cultivars, with enrichment for the gene ontology terms, ‘immune system process’, ‘defense response’, and ‘cell death’. There were particular differences between the cultivars in the intensity and kinetics of modulation of expression of genes with putative roles in transcriptional activity, secondary metabolism, photosynthesis, and receptor and signaling processes. Analysis of differential exon usage (DEU) revealed that both cultivars initiated remodeling their transcriptomes at 30 mpi; however, ‘Redkist’ exhibited alternative exon usage for a greater number of genes at every time point compared with ‘JH Hale’. Candidate resistance genes (WRKY-like, CRK-like, Copper amine oxidase-like, and TIR-NBS-LRR-like) are of interest for further functional characterization with the aim of elucidating their role in Prunus spp. resistance to Xap.
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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OxyR-regulated catalase CatB promotes the virulence in rice via detoxifying hydrogen peroxide in Xanthomonas oryzae pv. oryzae. BMC Microbiol 2016; 16:269. [PMID: 27825304 PMCID: PMC5101826 DOI: 10.1186/s12866-016-0887-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To facilitate infection, Xanthomonas oryzae pv. oryzae (Xoo), the bacterial blight pathogen of rice, needs to degrade hydrogen peroxide (H2O2) generated by the host defense response via a mechanism that is mediated by the transcriptional regulator OxyR. The catalase (CAT) gene catB has previously been shown to belong to the OxyR regulon in Xoo. However, its expression patterns and function in H2O2 detoxification and bacterial pathogenicity on rice remain to be elucidated. RESULTS The catB gene encodes a putative catalase and is highly conserved in the sequenced strains of Xanthomonas spp. β-galactosidase analysis and electrophoretic mobility shift assays (EMSA) showed that OxyR positively regulated the transcription of catB by directly binding to its promoter region. The quantitative real-time PCR (qRT-PCR) assays revealed that the expression levels of catB and oxyR were significantly induced by H2O2. Deletion of catB or oxyR drastically impaired bacterial viability in the presence of extracellular H2O2 and reduced CAT activity, demonstrating that CatB and OxyR contribute to H2O2 detoxification in Xoo. In addition, ΔcatB and ΔoxyR displayed shorter bacterial blight lesions and reduced bacterial growth in rice compared to the wild-type stain, indicating that CatB and OxyR play essential roles in the virulence of Xoo. CONCLUSIONS Transcription of catB is enhanced by OxyR in response to exogenous H2O2. CatB functions as an active catalase that is required for the full virulence of Xoo in rice.
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Müller OA, Grau J, Thieme S, Prochaska H, Adlung N, Sorgatz A, Bonas U. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses. PLoS One 2015; 10:e0136499. [PMID: 26313760 PMCID: PMC4552032 DOI: 10.1371/journal.pone.0136499] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/04/2015] [Indexed: 11/18/2022] Open
Abstract
The Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv) causes bacterial spot disease of pepper and tomato by direct translocation of type III effector proteins into the plant cell cytosol. Once in the plant cell the effectors interfere with host cell processes and manipulate the plant transcriptome. Quantitative RT-PCR (qRT-PCR) is usually the method of choice to analyze transcriptional changes of selected plant genes. Reliable results depend, however, on measuring stably expressed reference genes that serve as internal normalization controls. We identified the most stably expressed tomato genes based on microarray analyses of Xcv-infected tomato leaves and evaluated the reliability of 11 genes for qRT-PCR studies in comparison to four traditionally employed reference genes. Three different statistical algorithms, geNorm, NormFinder and BestKeeper, concordantly determined the superiority of the newly identified reference genes. The most suitable reference genes encode proteins with homology to PHD finger family proteins and the U6 snRNA-associated protein LSm7. In addition, we identified pepper orthologs and validated several genes as reliable normalization controls for qRT-PCR analysis of Xcv-infected pepper plants. The newly identified reference genes will be beneficial for future qRT-PCR studies of the Xcv-tomato and Xcv-pepper pathosystems, as well as for the identification of suitable normalization controls for qRT-PCR studies of other plant-pathogen interactions, especially, if related plant species are used in combination with bacterial pathogens.
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Affiliation(s)
- Oliver A. Müller
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute for Informatics, Department of Bioinformatics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Heike Prochaska
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Norman Adlung
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anika Sorgatz
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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12
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Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection. Sci Rep 2015; 5:12165. [PMID: 26184504 PMCID: PMC4505318 DOI: 10.1038/srep12165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/12/2015] [Indexed: 01/12/2023] Open
Abstract
Rice bacterial blight (BB) is a devastating rice disease. The Xa21 gene confers a broad and persistent resistance against BB. We introduced Xa21 into Oryza sativa L ssp indica (rice 9311), through multi-generation backcrossing, and generated a nearly isogenic, blight-resistant 9311/Xa21 rice. Using next-generation sequencing, we profiled the transcriptomes of both varieties before and within four days after infection of bacterium Xanthomonas oryzae pv. oryzae. The identified differentially expressed (DE) genes and signaling pathways revealed insights into the functions of Xa21. Surprisingly, before infection 1,889 genes on 135 of the 316 signaling pathways were DE between the 9311/Xa21 and 9311 plants. These Xa21-mediated basal pathways included mainly those related to the basic material and energy metabolisms and many related to phytohormones such as cytokinin, suggesting that Xa21 triggered redistribution of energy, phytohormones and resources among essential cellular activities before invasion. Counter-intuitively, after infection, the DE genes between the two plants were only one third of that before the infection; other than a few stress-related pathways, the affected pathways after infection constituted a small subset of the Xa21-mediated basal pathways. These results suggested that Xa21 primed critically important genes and signaling pathways, enhancing its resistance against bacterial infection.
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Datta A, Ghosh A, Airoldi C, Sperandeo P, Mroue KH, Jiménez-Barbero J, Kundu P, Ramamoorthy A, Bhunia A. Antimicrobial Peptides: Insights into Membrane Permeabilization, Lipopolysaccharide Fragmentation and Application in Plant Disease Control. Sci Rep 2015; 5:11951. [PMID: 26144972 PMCID: PMC4491704 DOI: 10.1038/srep11951] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/09/2015] [Indexed: 11/09/2022] Open
Abstract
The recent increase in multidrug resistance against bacterial infections has become a major concern to human health and global food security. Synthetic antimicrobial peptides (AMPs) have recently received substantial attention as potential alternatives to conventional antibiotics because of their potent broad-spectrum antimicrobial activity. These peptides have also been implicated in plant disease control for replacing conventional treatment methods that are polluting and hazardous to the environment and to human health. Here, we report de novo design and antimicrobial studies of VG16, a 16-residue active fragment of Dengue virus fusion peptide. Our results reveal that VG16KRKP, a non-toxic and non-hemolytic analogue of VG16, shows significant antimicrobial activity against Gram-negative E. coli and plant pathogens X. oryzae and X. campestris, as well as against human fungal pathogens C. albicans and C. grubii. VG16KRKP is also capable of inhibiting bacterial disease progression in plants. The solution-NMR structure of VG16KRKP in lipopolysaccharide features a folded conformation with a centrally located turn-type structure stabilized by aromatic-aromatic packing interactions with extended N- and C-termini. The de novo design of VG16KRKP provides valuable insights into the development of more potent antibacterial and antiendotoxic peptides for the treatment of human and plant infections.
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Affiliation(s)
- Aritreyee Datta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Anirban Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 2016 Milano, Italy
| | - Paola Sperandeo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 2016 Milano, Italy
| | - Kamal H Mroue
- Biophysics and Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109-1055, USA
| | - Jesús Jiménez-Barbero
- 1] Infectious Diseases Program, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801A, 48160 Derio, Spain [2] IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Pallob Kundu
- Division of Plant Biology, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109-1055, USA
| | - Anirban Bhunia
- 1] Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India [2] Biophysics and Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109-1055, USA
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Shyu C, Brutnell TP. Growth-defence balance in grass biomass production: the role of jasmonates. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4165-76. [PMID: 25711704 DOI: 10.1093/jxb/erv011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Growth-defence balance is the selective partitioning of resources between biomass accumulation and defence responses. Although it is generally postulated that reallocation of limited carbon pools drives the antagonism between growth and defence, little is known about the mechanisms underlying this regulation. Jasmonates (JAs) are a group of oxylipins that are required for a broad range of responses from defence against insects to reproductive growth. Application of JAs to seedlings also leads to inhibited growth and repression of photosynthesis, suggesting a role for JAs in regulating growth-defence balance. The majority of JA research uses dicot models such as Arabidopsis and tomato, while understanding of JA biology in monocot grasses, which comprise most bioenergy feedstocks, food for human consumption, and animal feed, is limited. Interestingly, JA mutants of grasses exhibit unique phenotypes compared with well-studied dicot models. Gene expression analyses in bioenergy grasses also suggest roles for JA in rhizome development, which has not been demonstrated in Arabidopsis. In this review we summarize current knowledge of JA biology in panicoid grasses-the group that consists of the world's emerging bioenergy grasses such as switchgrass, sugarcane, Miscanthus, and sorghum. We discuss outstanding questions regarding the role of JAs in panicoid grasses, and highlight the importance of utilizing emerging grass models for molecular studies to provide a basis for engineering bioenergy grasses that can maximize biomass accumulation while efficiently defending against stress.
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Affiliation(s)
- Christine Shyu
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
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15
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Zhang F, Huang LY, Zhang F, Ali J, Cruz CV, Zhuo DL, Du ZL, Li ZK, Zhou YL. Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response. BMC Genomics 2015; 16:111. [PMID: 25765449 PMCID: PMC4349310 DOI: 10.1186/s12864-015-1329-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, the molecular mechanisms of resistance mediated by Xa39 remain unclear. In this study, the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated. RESULTS A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines' race 9b. Transcriptome profiling of H471 and its parents at 1 and 2 days post-inoculation was performed using RNA sequencing. In total, 306 differentially expressed genes (DEGs) were identified in H471 compared with its recurrent parent Huang-Hua-Zhan after inoculation with Xoo. Among them, 121 (39.5%) genes, with functional enrichments that were related to defense response, protein amino acid phosphorylation, and apoptosis, were found to be constitutively expressed. The other 185 (60.5%) genes, with GO terms that belonged to defense response, were significantly responsive to Xoo infection in H471. Ten up-regulated and 12 down-regulated genes encoding intracellular immune receptors were identified in H471 compared with Huang-Hua-Zhan. LOC_Os11g37759, which was located in the fine-mapping region harboring Xa39, is a Xa39 candidate gene. The putative BSHR-related co-regulatory networks were constructed using 33 DEGs from four functional groups, including gibberellic acid receptors and brassinosteroid regulators, which were differentially co-expressed with LOC_Os11g37759 in infected H471. Our results indicated that there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and that the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes. CONCLUSIONS The present study provides the comprehensive transcriptome profile of a rice introgression line carrying Xa39 and its parents, and identifies a set of DEGs involved in BSHR mediated by Xa39. These data provide novel insights into the regulatory networks of plant disease resistance mediated by R genes, and the identified DEGs will serve as candidates for Xa39 cloning and for further understanding the molecular mechanism of BSHR.
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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.
| | - Li-Yu 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.
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Longtou Street, North suburbs, Kunming, Yunnan, 650250, 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.
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines.
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines.
| | - Da-Long Zhuo
- 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.
| | - Zheng-Lin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beichen West Road, Chaoyang District, Beijing, 100029, China.
| | - Zhi-Kang 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.
| | - Yong-Li 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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16
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Dang TT, Shimatani Z, Kawano Y, Terada R, Shimamoto K. Gene editing a constitutively active OsRac1 by homologous recombination-based gene targeting induces immune responses in rice. PLANT & CELL PHYSIOLOGY 2013; 54:2058-70. [PMID: 24158358 DOI: 10.1093/pcp/pct147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
OsRac1 is a member of the plant small GTPase Rac/Rop family and plays a key role in rice immunity. The constitutively active (CA) G19V mutation of OsRac1 was previously shown to induce reactive oxygen species production, phytoalexin synthesis and defense gene activation, leading to resistance to rice blast infection. To study further the effect of the G19V mutation in disease resistance, we introduced a single base substitution by gene targeting and removed the selectable marker using Cre-loxP site-specific recombination. The CA-OsRac1 gene generated by gene targeting was termed CA-gOsRac1. The G19V mutation was transferred from a targeting vector to the OsRac1 locus and stably transmitted to the next generation. In the leaf blade of homozygous CA-gOsRac1 plants, mutant transcript levels were much lower than in those of wild-type plants. In contrast, mutant transcripts in roots, leaf sheaths and panicles were more abundant than those in leaf blades. However, upon chitin treatment, the expression of defense-related genes PAL1 and PBZ1 in the cell culture was greater in the mutants compared with wild-type plants. Furthermore, induction of hypersensitive response (HR)-like cell death was observed in the leaf sheaths of mutant plants infected with a compatible race of rice blast fungus. In the CA-gOsRac1 plants, a number of genes previously shown to be induced by Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae (Xoo) infection were induced in the leaf sheath without pathogen infection. These results suggest that gene targeting will provide mutations useful for gene function studies and crop improvement.
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Affiliation(s)
- Thu Thi Dang
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
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17
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Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS One 2013; 8:e68464. [PMID: 23869221 PMCID: PMC3711819 DOI: 10.1371/journal.pone.0068464] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/30/2013] [Indexed: 11/19/2022] Open
Abstract
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.
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Affiliation(s)
- Alvaro L. Pérez-Quintero
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Luis M. Rodriguez-R
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Alexis Dereeper
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Camilo López
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Ralf Koebnik
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Boris Szurek
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Sebastien Cunnac
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- * E-mail: .
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Xu J, Audenaert K, Hofte M, De Vleesschauwer D. Abscisic Acid Promotes Susceptibility to the Rice Leaf Blight Pathogen Xanthomonas oryzae pv oryzae by Suppressing Salicylic Acid-Mediated Defenses. PLoS One 2013; 8:e67413. [PMID: 23826294 PMCID: PMC3694875 DOI: 10.1371/journal.pone.0067413] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/17/2013] [Indexed: 11/26/2022] Open
Abstract
The plant hormone abscisic acid (ABA) is involved in a wide variety of plant processes, including the initiation of stress-adaptive responses to various environmental cues. Recently, ABA also emerged as a central factor in the regulation and integration of plant immune responses, although little is known about the underlying mechanisms. Aiming to advance our understanding of ABA-modulated disease resistance, we have analyzed the impact, dynamics and interrelationship of ABA and the classic defense hormone salicylic acid (SA) during progression of rice infection by the leaf blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). Consistent with ABA negatively regulating resistance to Xoo, we found that exogenously administered ABA renders rice hypersusceptible to infection, whereas chemical and genetic disruption of ABA biosynthesis and signaling, respectively, led to enhanced Xoo resistance. In addition, we found successful Xoo infection to be associated with extensive reprogramming of ABA biosynthesis and response genes, suggesting that ABA functions as a virulence factor for Xoo. Interestingly, several lines of evidence indicate that this immune-suppressive effect of ABA is due at least in part to suppression of SA-mediated defenses that normally serve to limit pathogen growth. Resistance induced by the ABA biosynthesis inhibitor fluridone, however, appears to operate in a SA-independent manner and is likely due to induction of non-specific physiological stress. Collectively, our findings favor a scenario whereby virulent Xoo hijacks the rice ABA machinery to cause disease and highlight the importance of ABA and its crosstalk with SA in shaping the outcome of rice-Xoo interactions.
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Affiliation(s)
- Jing Xu
- Laboratory of Phytopathology, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Phytopathology, Ghent University, Ghent, Belgium
- Faculty of Applied Bioscience Engineering, Ghent University College, Ghent, Belgium
| | - Monica Hofte
- Laboratory of Phytopathology, Ghent University, Ghent, Belgium
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