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Xie Q, Wei B, Zhan Z, He Q, Wu K, Chen Y, Liu S, He C, Niu X, Li C, Tang C, Tao J. Arabidopsis membrane protein AMAR1 interaction with type III effector XopAM triggers a hypersensitive response. PLANT PHYSIOLOGY 2023; 193:2768-2787. [PMID: 37648267 DOI: 10.1093/plphys/kiad478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/07/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
The efficient infection of plants by the bacteria Xanthomonas campestris pv. campestris (Xcc) depends on its type III effectors (T3Es). Although the functions of AvrE family T3Es have been reported in some bacteria, the member XopAM in Xcc has not been studied. As XopAM has low sequence similarity to reported AvrE-T3Es and different reports have shown that these T3Es have different targets in hosts, we investigated the functions of XopAM in the Xcc-plant interaction. Deletion of xopAM from Xcc reduced its virulence in cruciferous crops but increased virulence in Arabidopsis (Arabidopsis thaliana) Col-0, indicating that XopAM may perform opposite functions depending on the host species. We further found that XopAM is a lipase that may target the cytomembrane and that this activity might be enhanced by its membrane-targeted protein XOPAM-ACTIVATED RESISTANCE 1 (AMAR1) in Arabidopsis Col-0. The binding of XopAM to AMAR1 induced an intense hypersensitive response that restricted Xcc proliferation. Our results showed that the roles of XopAM in Xcc infection are not the same as those of other AvrE-T3Es, indicating that the functions of this type of T3E have differentiated during long-term bacterium‒host interactions.
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Affiliation(s)
- Qingbiao Xie
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Bingzheng Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Zhaohong Zhan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiguang He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
| | - Kejian Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yu Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Shiyao Liu
- Sanya Nanfan Research Institute, Hainan University, Sanya 572024, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Sanya Nanfan Research Institute, Hainan University, Sanya 572024, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Xiaolei Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Sanya Nanfan Research Institute, Hainan University, Sanya 572024, China
| | - Chunxia Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Chaorong Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jun Tao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
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2
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Kaur A, Rana R, Bansal K, Patel HK, Sonti RV, Patil PB. Insights into the Diversity of Transcription Activator-Like Effectors in Indian Pathotype Strains of Xanthomonas oryzae pv. oryzae. PHYTOPATHOLOGY 2023; 113:953-959. [PMID: 36441870 DOI: 10.1094/phyto-08-22-0304-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a major rice pathogen, and its genome harbors extensive inter-strain and inter-lineage variations. The emergence of highly virulent pathotypes of Xoo that can overcome major resistance (R) genes deployed in rice breeding programs is a grave threat to rice cultivation. The present study reports on a long-read Oxford nanopore-based complete genomic investigation of Xoo isolates from 11 pathotypes that are reported based on their reaction toward 10 R genes. The investigation revealed remarkable variation in the genome structure in the strains belonging to different pathotypes. Furthermore, transcription activator-like effector (TALE) proteins secreted by the type III secretion system display marked variation in content, genomic location, classes, and DNA-binding domain. We also found the association of tal genes in the vicinity of regions with genome structural variations. Furthermore, in silico analysis of the genome-wide rice targets of TALEs allowed us to understand the emergence of pathotypes compatible with major R genes. Long-read, cost-effective sequencing technologies such as nanopore can be a game changer in the surveillance of major and emerging pathotypes. The resource and findings will be invaluable in the management of Xoo and in appropriate deployment of R genes in rice breeding programs.
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Affiliation(s)
- Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Ramesh V Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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3
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Kalaivanan NS, Ghoshal T, Lakshmi MA, Mondal KK, Kulshreshtha A, Singh KBM, Thakur JK, Supriya P, Bhatnagar S, Mani C. Complete genome resource unravels the close relation of an Indian Xanthomonas oryzae pv. oryzae strain IXOBB0003 with Philippines strain causing bacterial blight of rice. 3 Biotech 2023; 13:187. [PMID: 37193328 PMCID: PMC10182915 DOI: 10.1007/s13205-023-03596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen of concern for rice growers as it limits the production potential of rice varieties worldwide. Due to their high genomic plasticity, the pathogen continues to evolve, nullifying the deployed resistance mechanisms. It is pertinent to monitor the evolving Xoo population for the virulent novel stains, and the affordable sequencing technologies made the task feasible with an in-depth understanding of their pathogenesis arsenals. We present the complete genome of a highly virulent Indian Xoo strain IXOBB0003, predominantly found in northwestern parts of India, by employing next-generation sequencing and single-molecule sequencing in real-time technologies. The final genome assembly comprises 4,962,427 bp and has 63.96% GC content. The pan genome analysis reveals that strain IXOBB0003 houses total of 3655 core genes, 1276 accessory genes and 595 unique genes. Comparative analysis of the predicted gene clusters of coding sequences and protein count of strain IXOBB0003 depicts 3687 of almost 90% gene clusters shared by other Asian strains, 17 unique to IXOBB0003 and 139 CDSs of IXOBB0003 are shared with PXO99A. AnnoTALE-based studies revealed 16 TALEs conferred from the whole genome sequence. Prominent TALEs of our strain are found orthologous to TALEs of the Philippines strain PXO99A. The genomic features of Indian Xoo strain IXOBB0003 and in comparison with other Asian strains would certainly contribute significantly while formulating novel strategies for BB management. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03596-x.
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Affiliation(s)
- N. S. Kalaivanan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Thungri Ghoshal
- Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India
| | - M. Amrutha Lakshmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kalyan K. Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Kajol B. M. Singh
- National Institute of Plant Genome Research, New Delhi, 110067 India
| | - Jithendra K. Thakur
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - P. Supriya
- ICAR-National Academy of Agricultural Research Management, Hyderabad, 500030 India
| | - Seema Bhatnagar
- Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India
| | - Chandra Mani
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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4
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Song Z, Zheng J, Zhao Y, Yin J, Zheng D, Hu H, Liu H, Sun M, Ruan L, Liu F. Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen. Front Cell Infect Microbiol 2023; 13:1183416. [PMID: 37305415 PMCID: PMC10250591 DOI: 10.3389/fcimb.2023.1183416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023] Open
Abstract
The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.
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Affiliation(s)
- Zhiwei Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Huifeng Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Erkes A, Grove RP, Žarković M, Krautwurst S, Koebnik R, Morgan RD, Wilson GG, Hölzer M, Marz M, Boch J, Grau J. Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing. BMC Genomics 2023; 24:151. [PMID: 36973643 PMCID: PMC10045945 DOI: 10.1186/s12864-023-09228-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. RESULTS Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. CONCLUSIONS Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - René P Grove
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Milena Žarković
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Sebastian Krautwurst
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34090, Montpellier, France
| | | | | | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Manja Marz
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
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Taura S, Ichitani K. Chromosomal Location of xa19, a Broad-Spectrum Rice Bacterial Blight Resistant Gene from XM5, a Mutant Line from IR24. PLANTS (BASEL, SWITZERLAND) 2023; 12:602. [PMID: 36771686 PMCID: PMC9919685 DOI: 10.3390/plants12030602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Bacterial blight is an important rice disease caused by bacteria named Xanthomonas oryzae pv. oryzae (Xoo). XM5 is an Xoo resistant mutant line with the genetic background of IR24, an Indica Xoo susceptible cultivar, induced by a chemical mutagen N-methyl-N-nitrosourea (MNU). XM5 carries a recessive Xoo resistant gene, xa19. Trisomic analysis was conducted using the cross between XM5 and the trisomic series under the genetic background of IR24, showing that xa19 was located on chromosome 7. The approximate chromosomal location was found using 37 surely resistant plants in the F2 population from XM5 × Kinmaze, which was susceptible to most Japanese Xoo races. The IAS44 line carries a Japonica cultivar Asominori chromosomal segment covering the xa19 locus under the IR24 genetic background. Linkage analysis using the F2 population from the cross between XM5 and IAS44 revealed that xa19 was located within the 0.8 cM region between RM8262 and RM6728. xa19 is not allelic to the known Xoo resistant genes. However, its location suggests that it might be allelic to a lesion-mimic mutant gene spl5, some alleles of which are resistant to several Xoo races. Together with xa20 and xa42, three Xoo resistant genes were induced from IR24 by MNU. The significance of chemical mutagen as a source of Xoo resistance was discussed.
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Affiliation(s)
- Satoru Taura
- Institute of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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7
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Yan F, Wang J, Zhang S, Lu Z, Li S, Ji Z, Song C, Chen G, Xu J, Feng J, Zhou X, Zhou H. CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates. PLoS Pathog 2023; 19:e1010961. [PMID: 36626407 PMCID: PMC9870152 DOI: 10.1371/journal.ppat.1010961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/23/2023] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout in Xanthomonas oryzae pv. oryzae (Xoo), one of the most important bacterial pathogens on rice, by employing the heterologous CRISPR/Cas12a from Francisella novicida and NHEJ proteins from Mycobacterium tuberculosis. FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion, and plasmid curing in the Xoo PXO99A strain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25 xop genes involved in Xoo pathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogen Pseudomonas syringae pv. tomato (Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis of Xoo.
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Affiliation(s)
- Fang Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingwen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sujie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Zhenwan Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Congfeng Song
- Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Gongyou Chen
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China,* E-mail:
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8
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Bellanger N, Dereeper A, Koebnik R. Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri—Witnesses to a Global Expansion of a Bacterial Pathogen over Time. Microorganisms 2022; 10:microorganisms10091715. [PMID: 36144317 PMCID: PMC9504256 DOI: 10.3390/microorganisms10091715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas citri pv. citri, a Gram-negative bacterium, is the causal agent of citrus canker, a significant threat to citrus production. Understanding of global expansion of the pathogen and monitoring introduction into new regions are of interest for integrated disease management at the local and global level. Genetic diversity can be assessed using genomic approaches or information from partial gene sequences, satellite markers or clustered regularly interspaced short palindromic repeats (CRISPR). Here, we compared CRISPR loci from 355 strains of X. citri pv. citri, including a sample from ancient DNA, and generated the genealogy of the spoligotypes, i.e., the absence/presence patterns of CRISPR spacers. We identified 26 novel spoligotypes and constructed their likely evolutionary trajectory based on the whole-genome information. Moreover, we analyzed ~30 additional pathovars of X. citri and found that the oldest part of the CRISPR array was present in the ancestor of several pathovars of X. citri. This work presents a framework for further analyses of CRISPR loci and allows drawing conclusions about the global spread of the citrus canker pathogen, as exemplified by two introductions in West Africa.
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9
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Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane. Appl Environ Microbiol 2022; 88:e0055022. [PMID: 35916503 PMCID: PMC9397109 DOI: 10.1128/aem.00550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.
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10
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Sanya DRA, Syed-Ab-Rahman SF, Jia A, Onésime D, Kim KM, Ahohuendo BC, Rohr JR. A review of approaches to control bacterial leaf blight in rice. World J Microbiol Biotechnol 2022; 38:113. [PMID: 35578069 DOI: 10.1007/s11274-022-03298-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 01/16/2023]
Abstract
The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
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Affiliation(s)
| | | | - Aiqun Jia
- School of Environmental & Biological Engineering, Nanjing University of Science and Technology, Xiaolingwei No. 200, Xuanwu District, 210014, Nanjing, Jiangsu, China
| | - Djamila Onésime
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kyung-Min Kim
- School of Applied BioSciences, College of Agriculture & Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-Gu, 41566, Daegu, Korea
| | - Bonaventure Cohovi Ahohuendo
- Faculty of Agricultural Sciences, University of Abomey-Calavi, 526 Recette Principale, Cotonou 01, 01 BP, Abomey-Calavi, Benin
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Eck Institute of Global Health, Environmental Change Initiative, 178 Galvin Life Science Center, 46556, Notre Dame, IN, USA
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11
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Deb S, Gokulan CG, Nathawat R, Patel HK, Sonti RV. Suppression of XopQ-XopX-induced immune responses of rice by the type III effector XopG. MOLECULAR PLANT PATHOLOGY 2022; 23:634-648. [PMID: 35150038 PMCID: PMC8995061 DOI: 10.1111/mpp.13184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/01/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Effectors that suppress effector-triggered immunity (ETI) are an essential part of the arms race in the co-evolution of bacterial pathogens and their host plants. Xanthomonas oryzae pv. oryzae uses multiple type III secretion system (T3SS) secreted effectors such as XopU, XopV, XopP, XopG, and AvrBs2 to suppress rice immune responses that are induced by the interaction of two other effectors, XopQ and XopX. Here we show that each of these five suppressors can interact individually with both XopQ and XopX. One of the suppressors, XopG, is a predicted metallopeptidase that appears to have been introduced into X. oryzae pv. oryzae by horizontal gene transfer. XopQ and XopX interact with each other in the nucleus while interaction with XopG sequesters them in the cytoplasm. The XopG E76A and XopG E85A mutants are defective in interaction with XopQ and XopX, and are also defective in suppression of XopQ-XopX-mediated immune responses. Both mutations individually affect the virulence-promoting ability of XopG. These results indicate that XopG is important for X. oryzae pv. oryzae virulence and provide insights into the mechanisms by which this protein suppresses ETI in rice.
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Affiliation(s)
- Sohini Deb
- CSIR ‐ Centre for Cellular and Molecular Biology (CSIR‐CCMB)HyderabadIndia
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - C. G. Gokulan
- CSIR ‐ Centre for Cellular and Molecular Biology (CSIR‐CCMB)HyderabadIndia
| | - Rajkanwar Nathawat
- CSIR ‐ Centre for Cellular and Molecular Biology (CSIR‐CCMB)HyderabadIndia
| | - Hitendra K. Patel
- CSIR ‐ Centre for Cellular and Molecular Biology (CSIR‐CCMB)HyderabadIndia
| | - Ramesh V. Sonti
- CSIR ‐ Centre for Cellular and Molecular Biology (CSIR‐CCMB)HyderabadIndia
- Indian Institute of Science Education and Research (IISER) TirupatiTirupatiIndia
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12
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Bansal K, Kaur A, Midha S, Kumar S, Korpole S, Patil PB. Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India. Antonie van Leeuwenhoek 2021; 114:1935-1947. [PMID: 34533662 DOI: 10.1007/s10482-021-01652-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/01/2021] [Indexed: 12/01/2022]
Abstract
We report three yellow-pigmented, Gram-negative, aerobic, rod-shaped, motile bacterial isolates designated as PPL1T, PPL2, and PPL3 from healthy basmati rice seeds. Phenotypic and 16S rRNA gene sequence analysis assigned these isolates to the genus Xanthomonas. The 16S rRNA showed a 99.59% similarity with X. sacchari CFBP 4641T, a sugarcane pathogen. Further, biochemical and fatty acid analysis revealed it to be closer to X. sacchari. Still, it differed from other species in general and known rice associated species such as X. oryzae (pathogenic) and X. maliensis (non-pathogenic) in particular. Interestingly, the isolatess in this study were isolated from healthy rice plants but are closely related to species that is pathogenic and isolated from diseased sugarcane. Accordingly, in planta studies revealed that PPL1T, PPL2, and PPL3 are non-pathogenic to rice plants upon leaf inoculation. Taxonogenomic studies based on orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values with type strains of Xanthomonas species were below the recommended threshold values for species delineation. Whole genome-based phylogenomic analysis revealed that these isolates formed a distinct monophyletic clade with X. sacchari CFBP 4641T as their closest neighbour. Further, pangenome analysis revealed PPL1T, PPL2, and PPL3 isolates to comprise NRPS cluster along with a large number of unique genes associated with the novel species. Based on polyphasic and genomic approaches, a novel lineage and species associated with healthy rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (JCM 33631T = CFBP 8688T = ICMP 23426T = MTCC 12491T) and PPL2 (JCM 33632 = CFBP 8689 = ICMP 23427 = MTCC 12492) and PPL3 (JCM 33633 = CFBP 8690 = ICMP 23428 = MTCC 12493) as other strains of the species.
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Affiliation(s)
- Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Samriti Midha
- CSIR-Institute of Microbial Technology, Chandigarh, India.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Sanjeet Kumar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- CSIR-Institute of Microbial Technology, Chandigarh, India.
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13
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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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14
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Castillo AI, Almeida RPP. Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen. G3-GENES GENOMES GENETICS 2021; 11:6170658. [PMID: 33715000 PMCID: PMC8495750 DOI: 10.1093/g3journal/jkab076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022]
Abstract
Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
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15
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Shami A, Mostafa M, Abd-Elsalam KA. CRISPR applications in plant bacteriology: today and future perspectives. CRISPR AND RNAI SYSTEMS 2021:551-577. [DOI: 10.1016/b978-0-12-821910-2.00011-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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16
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain. Front Microbiol 2020; 11:579504. [PMID: 33193207 PMCID: PMC7610140 DOI: 10.3389/fmicb.2020.579504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) constrains production in major rice growing countries of Asia. Xoo injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” (S) genes that are important for disease. The bacterial blight resistance gene xa5, which reduces TALE activity generally, has been widely deployed. However, strains defeating xa5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major S gene SWEET11 strongly enough to be effective even when diminished by xa5. The findings suggest international migration of the xa5-compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Prasanta K Dash
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gouri S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jagjeet S Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K Singh
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
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17
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Deb S, Ghosh P, Patel HK, Sonti RV. Interaction of the Xanthomonas effectors XopQ and XopX results in induction of rice immune responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:332-350. [PMID: 32654337 DOI: 10.1111/tpj.14924] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Xanthomonas oryzae pv. oryzae uses several type III secretion system (T3SS) secreted effectors, namely XopN, XopQ, XopX and XopZ, to suppress rice immune responses that are induced following treatment with cell wall degrading enzymes. Here we show that a T3SS secreted effector XopX interacts with two of the eight rice 14-3-3 proteins. Mutants of XopX that are defective in 14-3-3 binding are also defective in suppression of immune responses, suggesting that interaction with 14-3-3 proteins is required for suppression of host innate immunity. However, Agrobacterium-mediated delivery of both XopQ and XopX into rice cells results in induction of rice immune responses. These immune responses are not observed when either protein is individually delivered into rice cells. XopQ-XopX-induced rice immune responses are not observed with a XopX mutant that is defective in 14-3-3 binding. Yeast two-hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays indicate that XopQ and XopX interact with each other. A screen for Xanthomonas effectors that can suppress XopQ-XopX-induced rice immune responses led to the identification of five effectors, namely XopU, XopV, XopP, XopG and AvrBs2, that could individually suppress these immune responses. These results suggest a complex interplay of Xanthomonas T3SS effectors in suppression of both pathogen-triggered immunity and effector-triggered immunity to promote virulence on rice.
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Affiliation(s)
- Sohini Deb
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
| | - Palash Ghosh
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
| | - Ramesh V Sonti
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
- National Institute of Plant Genome Research, New Delhi, 110067, India
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18
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Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS. Intra-regional diversity of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing. J Appl Microbiol 2020; 130:1259-1272. [PMID: 32767623 DOI: 10.1111/jam.14813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
AIM To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India. METHODS AND RESULTS A total of 27 yellow-pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible-rice cultivar, C14-8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes-VI and -VII were highly virulent, whereas the pathotype-I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal-complexes (CC). While CC-I comprised of isolates from Andaman Island, the CC-II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans-boundary pathogen introduction and a consequent intra-regional diversification on these islands due to the deployment of different rice cultivars in different regions. CONCLUSIONS Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans-boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R-genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands SIGNIFICANCE AND IMPACT OF THE STUDY: Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host-mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi-gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.
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Affiliation(s)
- K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - A Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - K Manigundan
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - G S Laha
- Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - R Velazhahan
- Center for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - R Singh
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - I S Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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19
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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20
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Joshi JB, Arul L, Ramalingam J, Uthandi S. Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management. J Biosci 2020. [DOI: 10.1007/s12038-020-00085-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Dixit S, Singh UM, Singh AK, Alam S, Venkateshwarlu C, Nachimuthu VV, Yadav S, Abbai R, Selvaraj R, Devi MN, Ramayya PJ, Badri J, Ram T, Lakshmi J, Lakshmidevi G, Lrk JV, Padmakumari AP, Laha GS, Prasad MS, Seetalam M, Singh VK, Kumar A. Marker Assisted Forward Breeding to Combine Multiple Biotic-Abiotic Stress Resistance/Tolerance in Rice. RICE (NEW YORK, N.Y.) 2020; 13:29. [PMID: 32472217 PMCID: PMC7260318 DOI: 10.1186/s12284-020-00391-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/12/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17), gall midge (GM) (Gm4, Gm8) and QTLs for drought tolerance (qDTY1.1 and qDTY3.1) through marker-assisted forward breeding (MAFB) approach. RESULT Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23-26%). Out of these, three ILs viz., IL1 (Pi9+ Xa4+ xa5+ Xa21+ Bph17+ Gm8+ qDTY1.1+ qDTY3.1), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY1.1+ qDTY3.1) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY1.1+ qDTY3.1) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty. CONCLUSION The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha- 1 under drought condition, without adverse effect on grain quality traits under non-stress.
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Affiliation(s)
- Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, 221006, India
| | - Arun Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Shamshad Alam
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Challa Venkateshwarlu
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Shailesh Yadav
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ramchander Selvaraj
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - M Nagamallika Devi
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Jyothi Badri
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - T Ram
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Jhansi Lakshmi
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - G Lakshmidevi
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Jai Vidhya Lrk
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | | | - G S Laha
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - M S Prasad
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Malathi Seetalam
- Professor Jayashankar Telangana State Agricultural University (PJTSAU), RARS, Warangal, India
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India.
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, 221006, India.
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22
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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23
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Bansal K, Kumar S, Patil PB. Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus. mSphere 2020; 5:e00087-20. [PMID: 32295869 PMCID: PMC7160680 DOI: 10.1128/msphere.00087-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/18/2020] [Indexed: 01/24/2023] Open
Abstract
Xanthomonas species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of Xanthomonas following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, Xanthomonas sontii, from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic Xanthomonas arboricola species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., type 1 secretion system [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and rpf gene cluster) and adaptation (i.e., gum, iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a Xanthomonas community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus XanthomonasIMPORTANCEXanthomonas citri is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, Xanthomonas is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a Xanthomonas community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic Xanthomonas strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of Xanthomonas from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.
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Affiliation(s)
- Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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24
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The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae. ISME JOURNAL 2019; 14:492-505. [PMID: 31666657 PMCID: PMC6976662 DOI: 10.1038/s41396-019-0545-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 11/15/2022]
Abstract
The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv. oryzae (Xoo) collected in the Philippines in a span of 40 years. After the deployment of Xa4 in the early 1960s, the emergence of virulent pathogen groups was associated with the increasing adoption of rice varieties carrying Xa4, which reached 80% of the total planted area. Whole genomes analysis of a representative sample suggested six major pathogen groups with distinctive signatures of selection in genes related to secretion system, cell-wall degradation, lipopolysaccharide production, and detoxification of host defense components. Association genetics also suggested that each population might evolve different mechanisms to adapt to Xa4. Interestingly, we found evidence of strong selective sweep affecting several populations in the mid-1980s, suggesting a major bottleneck that coincides with the peak of Xa4 deployment in the archipelago. Our study highlights how modern agricultural practices facilitate the adaptation of pathogens to overcome the effects of standard crop improvement efforts.
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25
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Kaur A, Bansal K, Kumar S, Sonti RV, Patil PB. Complete genome dynamics of a dominant-lineage strain of Xanthomonas oryzae pv. oryzae harbouring a novel plasmid encoding a type IV secretion system. Access Microbiol 2019; 1:e000063. [PMID: 32974563 PMCID: PMC7472545 DOI: 10.1099/acmi.0.000063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/27/2019] [Indexed: 11/29/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen causing bacterial blight disease in rice. Population genomic studies have revealed that rampant inter-strain rather than inter-lineage differences are contributing to the evolutionary success of this pathogen. Here, we report the complete genome sequence of BXO1, a strain of Xoo belonging to a dominant lineage from India. A complete genome-based investigation revealed the presence of two plasmids, pBXO1-1 (66.7 kb) and pBXO1-2 (25.6 kb). The pBXO1-1 plasmid encodes 71 genes, 38 of which encode hypothetical proteins of unknown function. However, these hypothetical genes possess atypical GC content, pointing towards their acquisition and movement through horizontal gene transfer. Interestingly, pBXO1-2 encodes a type IV secretion system (T4SS), which is known to play an important role in the conjugative transfer of genetic material, and also provides fitness to pathogenic bacteria for their enhanced survival. Neither plasmid has been reported previously in any other complete Xoo genome published to date. Our analysis also revealed that the pBXO1-2 plasmid is present in Xanthomonas albilineans str. GPE PC73, which is known to cause leaf scald, a lethal disease in sugarcane. Our complete genome sequence analysis of BXO1 has provided us with detailed insights into the two novel strain-specific plasmids, in addition to decoding their functional capabilities, which were not assessable when using the draft genome sequence of the strain. Overall, our study has revealed the mobility of a novel T4SS in two pathogenic species of Xanthomonas that infect the vascular tissues of two economically important monocot plants, i.e. rice and sugarcane.
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Affiliation(s)
- Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Present address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ramesh V Sonti
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.,DBT- National Institute of Plant Genome Research, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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26
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Liu F, McDonald M, Schwessinger B, Joe A, Pruitt R, Erickson T, Zhao X, Stewart V, Ronald PC. Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:656-672. [PMID: 30773771 PMCID: PMC6637879 DOI: 10.1111/mpp.12783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.
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Affiliation(s)
- Furong Liu
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Megan McDonald
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Anna Joe
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Teresa Erickson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Valley Stewart
- Department of Microbiology & Molecular GeneticsUniversity of CaliforniaDavisCA95616USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
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27
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da Silva Xavier A, de Almeida JCF, de Melo AG, Rousseau GM, Tremblay DM, de Rezende RR, Moineau S, Alfenas‐Zerbini P. Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex. MOLECULAR PLANT PATHOLOGY 2019; 20:223-239. [PMID: 30251378 PMCID: PMC6637880 DOI: 10.1111/mpp.12750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR-Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR-Cas systems in plant-pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR-Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR-Cas types I-E and II-C were found, with I-E being the most common. The presence of the same CRISPR-Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I-E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage-insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR-Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer-protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR-Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy.
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Affiliation(s)
- André da Silva Xavier
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Juliana Cristina Fraleon de Almeida
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Alessandra Gonçalves de Melo
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Rafael Reis de Rezende
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Poliane Alfenas‐Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
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28
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate. Front Microbiol 2018; 9:2703. [PMID: 30483230 PMCID: PMC6243107 DOI: 10.3389/fmicb.2018.02703] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/23/2018] [Indexed: 01/03/2023] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host "susceptibility" (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harboring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.
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Affiliation(s)
- Sara C. D. Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Prasanta K. Dash
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Gouri S. Laha
- Department of Plant Pathology, Indian Institute of Rice Research (ICAR), Hyderabad, India
| | - Jagjeet S. Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K. Singh
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Kuldeep Singh
- National Bureau of Plant Genetic Resources (ICAR), New Delhi, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
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29
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Kumar Verma R, Samal B, Chatterjee S. Xanthomonas oryzae pv. oryzae chemotaxis components and chemoreceptor Mcp2 are involved in the sensing of constituents of xylem sap and contribute to the regulation of virulence-associated functions and entry into rice. MOLECULAR PLANT PATHOLOGY 2018; 19:2397-2415. [PMID: 30011125 PMCID: PMC6638100 DOI: 10.1111/mpp.12718] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/08/2018] [Accepted: 06/17/2018] [Indexed: 05/26/2023]
Abstract
The Xanthomonas group of phytopathogens causes several economically important diseases in crops. In the bacterial pathogen of rice, Xanthomonas oryzae pv. oryzae (Xoo), it has been proposed that chemotaxis may play a role in the entry and colonization of the pathogen inside the host. However, components of the chemotaxis system, including the chemoreceptors involved, and their role in entry and virulence, are not well defined. In this study, we show that Xoo displays a positive chemotaxis response to components of rice xylem sap-glutamine, xylose and methionine. In order to understand the role of chemotaxis components involved in the promotion of chemotaxis, entry and virulence, we performed detailed deletion mutant analysis. Analysis of mutants defective in chemotaxis components, flagellar biogenesis, expression analysis and assays of virulence-associated functions indicated that chemotaxis-mediated signalling in Xoo is involved in the regulation of several virulence-associated functions, such as motility, attachment and iron homeostasis. The ∆cheY1 mutant of Xoo exhibited a reduced expression of genes involved in motility, adhesins, and iron uptake and metabolism. We show that the expression of Xoo chemotaxis and motility components is induced under in planta conditions and is required for entry, colonization and virulence. Furthermore, deletion analysis of a putative chemoreceptor mcp2 gene revealed that chemoreceptor Mcp2 is involved in the sensing of xylem sap and constituents of xylem exudate, including methionine, serine and histidine, and plays an important role in epiphytic entry and virulence. This is the first report of the role of chemotaxis in the virulence of this important group of phytopathogens.
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Affiliation(s)
- Raj Kumar Verma
- Centre for DNA Fingerprinting and DiagnosticsUppal RoadHyderabad500039India
- Graduate StudiesManipal Academy of Higher EducationMangaluruKarnataka576104India
| | - Biswajit Samal
- Centre for DNA Fingerprinting and DiagnosticsUppal RoadHyderabad500039India
- Graduate StudiesManipal Academy of Higher EducationMangaluruKarnataka576104India
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Intracellular Fate of Universally Labelled 13C Isotopic Tracers of Glucose and Xylose in Central Metabolic Pathways of Xanthomonas oryzae. Metabolites 2018; 8:metabo8040066. [PMID: 30326608 PMCID: PMC6316632 DOI: 10.3390/metabo8040066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022] Open
Abstract
The goal of this study is to map the metabolic pathways of poorly understood bacterial phytopathogen, Xanthomonas oryzae (Xoo) BXO43 fed with plant mimicking media XOM2 containing glutamate, methionine and either 40% [13C₅] xylose or 40% [13C₆] glucose. The metabolic networks mapped using the KEGG mapper and the mass isotopomer fragments of proteinogenic amino acids derived from GC-MS provided insights into the activities of Xoo central metabolic pathways. The average 13C in histidine, aspartate and other amino acids confirmed the activities of PPP, the TCA cycle and amino acid biosynthetic routes, respectively. The similar labelling patterns of amino acids (His, Ala, Ser, Val and Gly) from glucose and xylose feeding experiments suggests that PPP would be the main metabolic route in Xoo. Owing to the lack of annotated gene phosphoglucoisomerase in BXO43, the 13C incorporation in alanine could not be attributed to the competing pathways and hence warrants additional positional labelling experiments. The negligible presence of 13C incorporation in methionine brings into question its potential role in metabolism and pathogenicity. The extent of the average 13C labelling in several amino acids highlighted the contribution of pre-existing pools that need to be accounted for in 13C-flux analysis studies. This study provided the first qualitative insights into central carbon metabolic pathway activities in Xoo.
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Jibrin MO, Potnis N, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Jones JB, Goss EM. Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans. Appl Environ Microbiol 2018; 84:e00136-18. [PMID: 29678917 PMCID: PMC6007113 DOI: 10.1128/aem.00136-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/06/2018] [Indexed: 01/23/2023] Open
Abstract
Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.
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Affiliation(s)
- Mustafa O Jibrin
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Pamela D Roberts
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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Abstract
Durable disease resistance is a key component of global food security, and combining resistance genes into "pyramids" is an important way to increase durability of resistance. The mechanisms by which pyramids impart durability are not well known. The traditional view of resistance pyramids considers the use of major resistance gene (R-gene) combinations deployed against pathogens that are primarily asexual. Interestingly, published examples of the successful use of pyramids in the traditional sense are rare. In contrast, most published descriptions of durable pyramids in practice are for cereal rusts, and tend to indicate an association between durability and cultivars combining major R-genes with incompletely expressed, adult plant resistance genes. Pyramids have been investigated experimentally for a diversity of pathogens, and many reduce disease levels below that of the single best gene. Resistance gene combinations have been identified through phenotypic reactions, molecular markers, and challenge against effector genes. As resistance genes do not express equally in all genetic backgrounds, however, a combination of genetic information and phenotypic analyses provide the ideal scenario for testing of putative pyramids. Not all resistance genes contribute equally to pyramids, and approaches have been suggested to identify the best genes and combinations of genes for inclusion. Combining multiple resistance genes into a single plant genotype quickly is a challenge that is being addressed through alternative breeding approaches, as well as through genomics tools such as resistance gene cassettes and gene editing. Experimental and modeling tests of pyramid durability are in their infancy, but have promise to help direct future studies of pyramids. Several areas for further work on resistance gene pyramids are suggested.
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Affiliation(s)
- Christopher C Mundt
- Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis 97331-2902
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