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Lelis TDP, Bruno J, Padilla J, Barphagha I, Ontoy J, Ham JH. qsmR encoding an IclR-family transcriptional factor is a core pathogenic determinant of Burkholderia glumae beyond the acyl-homoserine lactone-mediated quorum-sensing system. PLoS Pathog 2024; 20:e1011862. [PMID: 39361719 DOI: 10.1371/journal.ppat.1011862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 09/20/2024] [Indexed: 10/05/2024] Open
Abstract
The plant pathogenic bacterium Burkholderia glumae causes bacterial panicle blight (BPB) in rice-growing areas worldwide. It has been widely accepted that an acyl-homoserine lactone (AHL)-type quorum sensing (QS) system encoded by tofI and tofR genes (TofIR QS) is a key regulatory mechanism underlying the bacterial pathogenesis of B. glumae. In addition, qsmR, which encodes an IclR-family regulatory protein, has been considered an important part of TofIR QS. However, the present study with three strains of B. glumae representing different pathogenic strains revealed that this currently accepted paradigm should be modified. We characterized the regulatory function of TofIR QS and qsmR in three different strains of B. glumae, 336gr-1 (virulent), 411gr-6 (hypervirulent) and 257sh-1 (avirulent). In 336gr-1, both TofIR QS and qsmR were critical for the pathogenesis, being consistent with previous studies. However, in the hypervirulent strain 411gr-6, TofIR QS only partially contributes to the virulence, whereas qsmR was critical for pathogenesis like in 336gr-1. Furthermore, we found that a single nucleotide polymorphism causing T50K substitution in the qsmR coding sequence was the cause of the non-pathogenic trait of the naturally avirulent strain 257sh-1. Subsequent analyses of gene expression and transcriptome revealed that TofIR QS is partially controlled by qsmR at the transcriptional level in both virulent strains. Further genetic tests of additional B. glumae strains showed that 11 out of 20 virulent strains retained the ability to produce toxoflavin even after removing the tofI/tofM/tofR QS gene cluster like 411gr-6. In contrast, all the virulent strains tested lost the ability to produce toxoflavin almost completely upon deletion of the qsmR gene. Taking these results together, qsmR, rather than TofIR QS, is a master regulator that determines the pathogenic trait of B. glumae thus a more appropriate pathogen target for successful management of BPB.
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Affiliation(s)
- Tiago De Paula Lelis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Jobelle Bruno
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Jonas Padilla
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - John Ontoy
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
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Valdez-Nuñez RA, Ramos-Luna LC, Meza-Catalán PP, Asencios-Sifuentes NR, Ocaña-Rodriguez AW, Chávez-Galarza JC, Sandoval-Vergara AN, Béna G. Genetic Diversity and Virulence of Phytopathogenic Burkholderia glumae Strains Isolated from Rice Cultivars in Valleys of the High Jungle of Perú. PLANT DISEASE 2024; 108:2376-2388. [PMID: 38386299 DOI: 10.1094/pdis-09-23-1823-re] [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: 02/23/2024]
Abstract
Burkholderia glumae causes bacterial leaf blight in rice, and its global spread has been exacerbated by climate change. To understand the genetic diversity and virulence of B. glumae strains isolated from rice cultivars in Perú, 47 isolates were obtained from infected rice fields, all belonging to B. glumae, and confirmed by recA and toxB sequences. The BOX-PCR typing group has 38 genomic profiles, and these turn into seven variable number tandem repeats (VNTR) haplotypes. There was no correlation between clustering and geographical origin. Nineteen strains were selected for phenotypic characterization and virulence, using both the maceration level of the onion bulb proxy and inoculation of seeds of two rice cultivars. Several strains produced pigments other than toxoflavin, which correlated with onion bulb maceration. In terms of virulence at the seed level, all strains produced inhibition at the root and coleoptile level, but the severity of symptoms varied significantly between strains, revealing significant differences in pathogenicity. There is no correlation between maceration and virulence scores, probably reflecting different virulence mechanisms depending on the host infection stage. This is the first study to evaluate the VNTR diversity and virulence of Peruvian strains of B. glumae in two commercial cultivars.
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Affiliation(s)
- Renzo A Valdez-Nuñez
- Departamento Académico de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
- Biotechnology Research Laboratory, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
| | - Lucero C Ramos-Luna
- Biotechnology Research Laboratory, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
| | - Patricia P Meza-Catalán
- Biotechnology Research Laboratory, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
| | | | - Angel W Ocaña-Rodriguez
- Departamento Académico de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
| | - Julio C Chávez-Galarza
- Departamento Académico de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de Barranca, Barranca 15169, Lima, Perú
| | - Ana N Sandoval-Vergara
- Departamento Académico Agrosilvopastoril, Universidad Nacional de San Martín, Tarapoto, Perú
| | - Gilles Béna
- IRD, CIRAD, INRAe, Institut Agro, PHIM (Plant Health Institute of Montpellier), University of Montpellier, Montpellier, France
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Fang Y, Ding D, Gu Y, Jia Q, Zheng Q, Qian Q, Wang Y, Rao Y, Mao Y. Identification of QTLs Conferring Resistance to Bacterial Diseases in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2853. [PMID: 37571006 PMCID: PMC10421440 DOI: 10.3390/plants12152853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
Bacterial panicle blight, bacterial leaf streak, and bacterial brown stripe are common bacterial diseases in rice that represent global threats to stable rice yields. In this study, we used the rice variety HZ, Nekken and their 120 RIL population as experimental materials. Phenotypes of the parents and RILs were quantitatively analyzed after inoculation with Burkholderia glumae, Xanthomonas oryzae pv. oryzicola, and Acidovorax avenae subsp. avenae. Genetic SNP maps were also constructed and used for QTL mapping of the quantitative traits. We located 40 QTL loci on 12 chromosomes. The analysis of disease resistance-related candidate genes in the QTL regions with high LOD value on chromosomes 1, 3, 4, and 12 revealed differential expression before and after treatment, suggesting that the identified genes mediated the variable disease resistance profiles of Huazhan and Nekken2. These results provide an important foundation for cloning bacterial-resistant QTLs of panicle blight, leaf streak, and brown stripe in rice.
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Affiliation(s)
- Yuan Fang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Y.F.); (D.D.); (Y.G.); (Q.J.)
| | - Di Ding
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Y.F.); (D.D.); (Y.G.); (Q.J.)
| | - Yujia Gu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Y.F.); (D.D.); (Y.G.); (Q.J.)
| | - Qiwei Jia
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Y.F.); (D.D.); (Y.G.); (Q.J.)
| | - Qiaolin Zheng
- Ball Horticultural Company, West Chicago, IL 60606, USA;
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; (Q.Q.); (Y.W.)
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; (Q.Q.); (Y.W.)
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Y.F.); (D.D.); (Y.G.); (Q.J.)
| | - Yijian Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; (Q.Q.); (Y.W.)
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Jungkhun N, Gomes de Farias AR, Watcharachaiyakup J, Kositcharoenkul N, Ham JH, Patarapuwadol S. Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight. Pathogens 2022; 11:pathogens11060676. [PMID: 35745530 PMCID: PMC9228322 DOI: 10.3390/pathogens11060676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen.
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Affiliation(s)
- Nootjarin Jungkhun
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Rice Department, Chiang Rai Rice Research Center, Phan, Chiang Rai 57120, Thailand
| | | | - Jutatape Watcharachaiyakup
- Center for Agricultural Biotechnology, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand
| | - Nuttima Kositcharoenkul
- Department of Agriculture, Plant Pathology Research Group, Plant Protection Research and Development Office, Bangkok 10900, Thailand;
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA;
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Center for Agricultural Biotechnology, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Correspondence:
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