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Zeng J, Yang Q, Ran Y, Guo Y, Jiao P, Qiao D, Cao Y, Xu H. Novel extracellular lipase gene Lip1728 influences nutrient-dependent performance bacterial quorum sensing of Burkholderia pyrrocinia WZ10-3. Int J Biol Macromol 2024; 278:134299. [PMID: 39097047 DOI: 10.1016/j.ijbiomac.2024.134299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
Quorum sensing (QS) is a cellular communication mechanism in which bacteria secrete and recognize signaling molecules to regulate group behavior. Lipases provide energy for bacterial cell growth but it is unknown whether they influence nutrient-dependent QS by hydrolyzing substrate. A high-yield lipase-producing strain, Burkholderia pyrrocinia WZ10-3, was previously identified in our laboratory, but the composition of its crude enzymes was not elucidated. Here, we identified a key extracellular lipase, Lip1728, in WZ10-3, which accounts for 99 % of the extracellular lipase activity. Lip1728 prefers to hydrolyze triglycerides at sn-1,3 positions, with pNP-C16 being its optimal substrate. Lip1728 exhibited activity at pH 5.0-10.0 and regardless of the presence of metal ions. It had strong resistance to sodium dodecyl sulfate and short-chain alcohols and was activated by phenylmethanesulfonylfluoride (PMSF). Lip1728 knockout significantly affected lipid metabolism and biofilm formation in the presence of olive oil. Finally, oleic acid, a hydrolysate of Lip1728, influenced the production of the signal molecule N-acyl homoserine lactone (AHL) and biofilm formation by downregulating the AHL synthetase gene pyrI. In conclusion, Lip1728, as a key extracellular lipase in B. pyrrocinia WZ10-3, exhibits superior properties that make it suitable for biodiesel production and plays a crucial role in QS.
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Affiliation(s)
- Jie Zeng
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Qingzhuoma Yang
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yulu Ran
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yihan Guo
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Pengrui Jiao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yi Cao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| | - Hui Xu
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
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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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Sreenayana B, Mondal KK, Mathiyalagan N, Shanmugam KN, Kumar S, Shrinivas Reddy M, Mani C. Molecular characterization and evaluation of novel management options for Burkholderia glumae BG1, the causative agent of panicle blight of rice (Oryza sativa L.). Mol Biol Rep 2024; 51:519. [PMID: 38625424 DOI: 10.1007/s11033-024-09498-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Bacterial panicle blight, incited by Burkholderia glumae, has impacted rice production globally. Despite its significance, knowledge about the disease and the virulence pattern of the causal agent is very limited. Bacterial panicle blight is a major challenge in the rice-growing belts of North-western India, resulting in yield reduction. However, the management of B. glumae has become a challenge due to the lack of proper management strategies. METHODOLOGY AND RESULTS Twenty-one BG strains have been characterized using the 16S rRNA and the gyrB gene-based sequence approach in the present study. The gyrB gene-based phylogenetic analysis resulted in geographic region-specific clustering of the BG isolates. The virulence screening of twenty-one BG strains by inoculating the pathogenic bacterial suspension of 1 × 10-8 cfu/ml at the booting stage (55 DAT) revealed the variation in the disease severity and the grain yield of rice plants. The most virulent BG1 strain resulted in the highest disease incidence (82.11%) and lowest grain yield (11.12 g/plant), and the least virulent BG10 strain resulted in lowest disease incidence of 18.94% and highest grain yield (24.62 g/plant). In vitro evaluation of various biocontrol agents and nano copper at different concentrations by agar well diffusion method revealed that nano copper at 1000 mg/L inhibited the colony growth of B. glumae. Under net house conditions, nano copper at 1000 mg/L reduced the disease severity to 21.23% and increased the grain yield by 20.91% (31.76 g per plant) compared to the positive control (COC 0.25% + streptomycin 200 ppm). Remarkably, pre-inoculation with nano copper at 1000 mg/L followed by challenge inoculation with B. glumae enhanced the activity of enzymatic antioxidants viz., Phenyl ammonia-lyase (PAL), Polyphenol oxidase (PPO) and Peroxidase (POX) and non-enzymatic antioxidant phenol. Additionally, we observed a substantial transcript level upregulation of six defense-related genes to several folds viz., OsPR2, OsPR5, OsWRKY71, OsPAL1, OsAPX1, and OsPPO1 in comparison to the pathogen control and healthy control. CONCLUSIONS Overall, our study provides valuable insights into the potential and practical application of nano copper for the mitigation of bacterial panicle blight, offering promising prospects for commercial utilization in disease management.
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Affiliation(s)
- Bhaskaran Sreenayana
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Kalyan Kumar Mondal
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India.
- National Institute of Biotic Stress Management, Raipur, Chhattisgarh, India.
| | - Nivetha Mathiyalagan
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Sanjeev Kumar
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Chander Mani
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
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Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Xiao Y, Zhang S, Li H, Teng K, Wu S, Liu Y, Yu F, He Z, Li L, Li L, Meng D, Yin H, Wang Y. Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2024; 15:1325141. [PMID: 38434434 PMCID: PMC10904623 DOI: 10.3389/fpls.2024.1325141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.
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Affiliation(s)
- Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Sai Zhang
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Hongguang Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Kai Teng
- Xiangxi Tobacco Co Hunan Prov, Changsha, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yongbin Liu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Fahui Yu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Zhihong He
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Lijuan Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yujie Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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Next Generation Sequencing and Comparative Genomic Analysis Reveal Extreme Plasticity of Two Burkholderia glumae Strains HN1 and HN2. Pathogens 2022; 11:pathogens11111265. [DOI: 10.3390/pathogens11111265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Burkholderia glumae is an important rice pathogen, thus the genomic and evolutionary history may be helpful to control this notorious pathogen. Here, we present two complete genomes of the B. glumae strains HN1 and HN2, which were isolated from diseased rice seed in China. Average nucleotide identity (ANI) analysis shows greater than 99% similarity of the strains HN1 and HN2 with other published B. glumae genomes. Genomic annotation revealed that the genome of strain HN1 consists of five replicons (6,680,415 bp) with an overall G + C content of 68.06%, whereas the genome of strain HN2 comprises of three replicons (6,560,085 bp) with an overall G + C content of 68.34%. The genome of HN1 contains 5434 protein-coding genes, 351 pseudogenes, and 1 CRISPR, whereas the genome of HN2 encodes 5278 protein-coding genes, 357 pseudogenes, and 2 CRISPR. Both strains encode many pathogenic-associated genes (143 genes in HN1 vs. 141 genes in HN2). Moreover, comparative genomic analysis shows the extreme plasticity of B. glumae, which may contribute to its pathogenicity. In total, 259 single-copy genes were affected by positive selection. These genes may contribute to the adaption to different environments. Notably, six genes were characterized as virulence factors which may be an additional way to assist the pathogenicity of B. glumae.
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Current Advances in the Concept of Quorum Sensing-Based Prevention of Spoilage of Fish Products by Pseudomonads. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Microbial spoilage of fish is attributed to quorum sensing (QS)-based activities. QS is a communication process between the cells in which microorganisms secrete and sense the specific chemicals (autoinductors, AIs) that regulate proteolysis, lipolysis, and biofilm formation. These activities change the organoleptic characteristics and reduce the safety of the products. Although the microbial community of fish is diverse and may consist of a range of bacterial strains, the deterioration of fish-based products is attributed to the growth and activity of Pseudomonas spp. This work summarizes recent advancements to assess the influence of QS mechanisms on seafood spoilage by Pseudomonas spp. The quorum sensing inhibition (QSI) in the context of fish preservation has also been discussed. Detailed recognition of this phenomenon is crucial in establishing effective strategies to prevent the premature deterioration of fish-based products.
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Rosenberg T, Jiménez-Guerrero I, Tamir-Ariel D, Yarnitzky T, Burdman S. The GDSL-Lipolytic Enzyme Lip1 Is Required for Full Virulence of the Cucurbit Pathogenic Bacterium Acidovorax citrulli. Microorganisms 2022; 10:microorganisms10051016. [PMID: 35630458 PMCID: PMC9147443 DOI: 10.3390/microorganisms10051016] [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: 04/19/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
Bacterial fruit blotch caused by Acidovoraxcitrulli is a serious disease of cucurbit crops. Here we report characterization of a mutant strain of A. citrulli M6 defective in lip1, a gene encoding a lipolytic enzyme. The M6-lip1- mutant was detected in a mutant library screen aimed at identifying M6 mutants with altered levels of twitching motility. In this screen M6-lip1- was the only mutant that showed significantly larger twitching motility haloes around colonies than wild-type M6. Sequence analyses indicated that lip1 encodes a member of the GDSL family of secreted lipolytic enzymes. In line with this finding, lipolytic assays showed that the supernatants of M6-lip1- had lower lipolytic activity as compared with those of wild-type M6 and a lip1-complemented strain. The mutant was also affected in swimming motility and had compromised virulence on melon seedlings and on Nicotiana benthamiana leaves relative to wild-type and complemented strains. Lip1 contains a predicted N-terminal signal sequence for type II secretion. Evidence from our study confirms Lip1 is indeed secreted in a type II secretion-dependent manner, and this is required for full virulence of A. citrulli. To the best of our knowledge this is the first study reporting contribution of lipolytic activity to virulence of a plant-pathogenic Acidovorax species.
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Affiliation(s)
- Tally Rosenberg
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (T.R.); (I.J.-G.); (D.T.-A.); (T.Y.)
| | - Irene Jiménez-Guerrero
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (T.R.); (I.J.-G.); (D.T.-A.); (T.Y.)
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Dafna Tamir-Ariel
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (T.R.); (I.J.-G.); (D.T.-A.); (T.Y.)
| | - Tali Yarnitzky
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (T.R.); (I.J.-G.); (D.T.-A.); (T.Y.)
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (T.R.); (I.J.-G.); (D.T.-A.); (T.Y.)
- Correspondence: ; Tel.: +972-8-9489369
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Wang D, Chen H, Li J, Li T, Ren L, Liu J, Shen Y. Screening and validation of quorum quenching enzyme PF2571 from Pseudomonas fluorescens strain PF08 to inhibit the spoilage of red sea bream filets. Int J Food Microbiol 2022; 362:109476. [PMID: 34798478 DOI: 10.1016/j.ijfoodmicro.2021.109476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
Bacteria are the main cause of spoilage for fish and fishery products. Through the inactivation of the quorum sensing (QS) system, quorum quenching (QQ) enzymes can block the synthesis of bacterial virulence factors and effectively inhibit bacteria-induced food spoilage. This study analyzed the changes of microbiota in red sea bream filets during refrigerated storage. The results showed a decrease in microbial diversity with storage time, with Aeromonas veronii becoming the dominant bacteria on day 4. A novel N-acyl homoserine lactones (AHL) acylase PF2571, from the screened QQ bacterium Pseudomonas fluorescens PF08, was identified and expressed in Escherichia coli to evaluate its QQ efficiency and effects on spoilage potential. Spoilage-related QS factors of A. veronii BY-8, including biofilm formation, motility, and protease, lipase, and alginate production, were inhibited by PF2571. Its inhibitory effect on red sea bream spoilage was demonstrated by the lower freshness indicators for PF2571 treated filets. Our study demonstrates the potential of the QQ enzyme for prolonging the shelf life of fish and fishery products.
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Affiliation(s)
- Dangfeng Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Haitao Chen
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jianrong Li
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresource Utilization (Dalian Minzu University), Ministry of Education, Dalian, Liaoning 116029, China
| | - Likun Ren
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin, Heilongjiang 150076, China
| | - Jingyun Liu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Yue Shen
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
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Lee HH, Lelis T, Ontoy J, Bruno J, Ham JH, Seo YS. Complete Genome Sequence Data of Four Burkholderia glumae Strains Isolated from Rice Fields in the United States. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1324-1327. [PMID: 34353115 DOI: 10.1094/mpmi-04-21-0090-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial panicle blight caused by Burkholderia glumae is a major disease in rice production worldwide. Currently, only a few whole-genome sequences of B. glumae strains isolated in the United States are available. Here, we report the complete genome sequence of four B. glumae strains, including three virulent strains (336gr-1, 411gr-6, and 957856-41-c) and the nonpathogenic strain B. glumae 257sh-1, which were isolated from rice fields in Louisiana (336gr-1, 957856-41-c, and 257sh-1) and Arkansas (411gr-6). The whole-genome sequence data of B. glumae strains will contribute to investigations of the molecular mechanism underlying bacterial pathogenicity and virulence to rice plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46247, Korea
| | - Tiago Lelis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - John Ontoy
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jobelle Bruno
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46247, Korea
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Mehta S, Chakraborty A, Roy A, Singh IK, Singh A. Fight Hard or Die Trying: Current Status of Lipid Signaling during Plant-Pathogen Interaction. PLANTS (BASEL, SWITZERLAND) 2021; 10:1098. [PMID: 34070722 PMCID: PMC8228701 DOI: 10.3390/plants10061098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 12/29/2022]
Abstract
Plant diseases pose a substantial threat to food availability, accessibility, and security as they account for economic losses of nearly $300 billion on a global scale. Although various strategies exist to reduce the impact of diseases, they can introduce harmful chemicals to the food chain and have an impact on the environment. Therefore, it is necessary to understand and exploit the plants' immune systems to control the spread of pathogens and enable sustainable agriculture. Recently, growing pieces of evidence suggest a functional myriad of lipids to be involved in providing structural integrity, intracellular and extracellular signal transduction mediators to substantial cross-kingdom cell signaling at the host-pathogen interface. Furthermore, some pathogens recognize or exchange plant lipid-derived signals to identify an appropriate host or development, whereas others activate defense-related gene expression. Typically, the membrane serves as a reservoir of lipids. The set of lipids involved in plant-pathogen interaction includes fatty acids, oxylipins, phospholipids, glycolipids, glycerolipids, sphingolipids, and sterols. Overall, lipid signals influence plant-pathogen interactions at various levels ranging from the communication of virulence factors to the activation and implementation of host plant immune defenses. The current review aims to summarize the progress made in recent years regarding the involvement of lipids in plant-pathogen interaction and their crucial role in signal transduction.
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Affiliation(s)
- Sahil Mehta
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India;
| | - Amrita Chakraborty
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic; (A.C.); (A.R.)
| | - Amit Roy
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic; (A.C.); (A.R.)
- Excelentní Tým pro Mitigaci (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India
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12
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Choi O, Lee Y, Park J, Kang B, Chun HJ, Kim MC, Kim J. A novel toxoflavin-quenching regulation in bacteria and its application to resistance cultivars. Microb Biotechnol 2021; 14:1657-1670. [PMID: 34009736 PMCID: PMC8313270 DOI: 10.1111/1751-7915.13831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/28/2022] Open
Abstract
The toxoflavin (Txn), broad host range phytotoxin produced by a variety of bacteria, including Burkholderia glumae, is a key pathogenicity factor of B. glumae in rice and field crops. Two bacteria exhibiting Txn‐degrading activity were isolated from healthy rice seeds and identified as Sphingomonas adhaesiva and Agrobacterium sp. respectively. The genes stdR and stdA, encoding proteins responsible for Txn degradation of both bacterial isolates, were identical, indicating that horizontal gene transfer occurred between microbial communities in the same ecosystem. We identified a novel Txn‐quenching regulation of bacteria, demonstrating that the LysR‐type transcriptional regulator (LTTR) StdR induces the expression of the stdA, which encodes a Txn‐degrading enzyme, in the presence of Txn as a coinducer. Here we show that the bacterial StdRTxn‐quenching regulatory system mimics the ToxRTxn‐mediated biosynthetic regulation of B. glumae. Substrate specificity investigations revealed that Txn is the only coinducer of StdR and that StdA has a high degree of specificity for Txn. Rice plants expressing StdA showed Txn resistance. Collectively, bacteria mimic the mechanism of Txn biosynthesis regulation, employ it in the development of a Txn‐quenching regulatory system and share it with neighbouring bacteria for survival in rice environments full of Txn.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, South Korea
| | - Jiyeong Park
- Department of Plant Medicine, Gyeongsang National University, Jinju, South Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, South Korea
| | - Hyun Jin Chun
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Min Chul Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, South Korea.,Division of Applied Life Science, Gyeongsang National University, Jinju, South Korea
| | - Jinwoo Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, South Korea.,Department of Plant Medicine, Gyeongsang National University, Jinju, South Korea.,Division of Applied Life Science, Gyeongsang National University, Jinju, South Korea
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13
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Myszka K, Tomaś N, Wolko Ł, Szwengiel A, Grygier A, Nuc K, Majcher M. In situ approaches show the limitation of the spoilage potential of Juniperus phoenicea L. essential oil against cold-tolerant Pseudomonas fluorescens KM24. Appl Microbiol Biotechnol 2021; 105:4255-4268. [PMID: 33988734 PMCID: PMC8140959 DOI: 10.1007/s00253-021-11338-3] [Citation(s) in RCA: 7] [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: 01/20/2021] [Revised: 04/20/2021] [Accepted: 05/07/2021] [Indexed: 12/02/2022]
Abstract
Abstract The present study aimed to elucidate the effect of subinhibitory concentrations (sub-MICs) of juniper essential oil (EO), α-pinene, and sabinene on the quorum-sensing (QS)–mediated proteolytic and lipolytic properties of Pseudomonas fluorescens KM24. These activities were verified under in situ conditions, in which sub-MICs of the agents altered the morphology of KM24 cells. RNA-Seq studies revealed key coding sequences (CDSs)/genes related to QS and the proteolytic/lipolytic activities of pseudomonads. In this work, all the examined agents decreased autoinducer synthesis and influenced the mRNA expression of the encoding acyltransferase genes lptA, lptD, and plsB. The highest reduction on the 3rd and 5th days of cultivation was observed for the genes lptD (−5.5 and −5.61, respectively) and lptA (−3.5 and −4.0, respectively) following treatment with EO. Inhibition of the lptA, lptD, and plsB genes by singular constituents of EO was on average, from −0.4 to −0.7. At 5 days of cultivation the profile of AHLs of the reference P. fluorescens KM24 strain consisted of 3-oxo-C14-HSL, 3-oxo-C6-HSL, C4-HSL, and N-[(RS)-3-hydroxybutyryl]-HSL, the concentrations of which were 0.570, 0.018, 3.744, and 0.554 μg ml−1, respectively. Independent of the incubation time, EO, α-pinene, and sabinene also suppressed the protease genes prlC (−1.5, −0.5, and −0.5, respectively) and ctpB (−1.5, −0.7, and −0.4, respectively). Lipolysis and transcription of the lipA/lipB genes were downregulated by the agents on average from −0.3 to −0.6. α-Pinene- and sabinene-rich juniper EO acts as an anti-quorum-sensing agent and can repress the spoilage phenotype of pseudomonads. Key points: Juniper EO, α-pinene, sabinene exhibited anti-QS potential toward KM24. RNA-Seq revealed key CDSs/genes related to QS/proteolytic/lipolytic activities of KM24. Agents at sub-MIC levels influenced the mRNA expression of QS/lipase/protease genes.
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11338-3.
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Affiliation(s)
- Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, PL-60,627, Poznan, Poland.
| | - Natalia Tomaś
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, PL-60,627, Poznan, Poland
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, PL-60-632, Poznan, Poland
| | - Artur Szwengiel
- Department of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznan, Poland
| | - Anna Grygier
- Department of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznan, Poland
| | - Katarzyna Nuc
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, PL-60-632, Poznan, Poland
| | - Małgorzata Majcher
- Department of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznan, Poland
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14
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Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. Appl Environ Microbiol 2021; 87:AEM.02348-20. [PMID: 33741619 DOI: 10.1128/aem.02348-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
Burkholderia encompasses a group of ubiquitous Gram-negative bacteria that includes numerous saprophytes as well as species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored, redox-active secondary metabolites called phenazines. Phenazines contribute to competitiveness, biofilm formation, and virulence in the opportunistic pathogen Pseudomonas aeruginosa, but knowledge of their diversity, biosynthesis, and biological functions in Burkholderia is lacking. In this study, we screened publicly accessible genome sequence databases and identified phenazine biosynthesis genes in multiple strains of the Burkholderia cepacia complex, some isolates of the B. pseudomallei clade, and the plant pathogen B. glumae We then focused on B. lata ATCC 17760 to reveal the organization and function of genes involved in the production of dimethyl 4,9-dihydroxy-1,6-phenazinedicarboxylate. Using a combination of isogenic mutants and plasmids carrying different segments of the phz locus, we characterized three novel genes involved in the modification of the phenazine tricycle. Our functional studies revealed a connection between the presence and amount of phenazines and the dynamics of biofilm growth in flow cell and static experimental systems but at the same time failed to link the production of phenazines with the capacity of Burkholderia to kill fruit flies and rot onions.IMPORTANCE Although the production of phenazines in Burkholderia was first reported almost 70 years ago, the role these metabolites play in the biology of these economically important microorganisms remains poorly understood. Our results revealed that the phenazine biosynthetic pathway in Burkholderia has a complex evolutionary history, which likely involved horizontal gene transfers among several distantly related groups of organisms. The contribution of phenazines to the formation of biofilms suggests that Burkholderia, like fluorescent pseudomonads, may benefit from the unique redox-cycling properties of these versatile secondary metabolites.
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15
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Choi O, Kim S, Kang B, Lee Y, Bae J, Kim J. Genetic Diversity and Distribution of Korean Isolates of Burkholderia glumae. PLANT DISEASE 2021; 105:1398-1407. [PMID: 33325743 DOI: 10.1094/pdis-08-20-1795-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Burkholderia glumae causes panicle blight of rice (grain rot in Japan and Korea), and the severity of damage is increasing worldwide. During 2017 and 2018, 137 isolates of B. glumae were isolated from symptomatic grain rot of rice cultivated in paddy fields throughout South Korea. Genetic diversity of the isolates was determined using transposase-based PCR (Tnp-PCR) genomic fingerprinting. All 138 isolates, including the B. glumae BGR1 strain, produced toxoflavin in various amounts, and 17 isolates produced an unidentified purple or orange pigment on Luria-Bertani medium and casamino acid-peptone-glucose medium, respectively, at 28°C. Transposase-based PCR genomic fingerprinting was performed using a novel primer designed based on transposase (tnp) gene sequences located at the ends of the toxoflavin efflux transporter operon; this method provided reliable and reproducible results. Through Tnp-PCR genomic fingerprinting, the genetic groups of Korean B. glumae isolates were divided into 11 clusters and three divisions. The Korean B. glumae isolates were mainly grouped in division I (73%). Interestingly, most of the pigment-producing isolates were grouped in divisions II and III; of these, 10 were grouped in cluster VIII, which comprised 67% of this cluster. Results of a phylogenetic analysis based on tofI and hrpB gene sequences were consistent with classification by Tnp-PCR genomic fingerprinting. The BGR1 strain did not belong to any of the clusters, indicating that this strain does not exhibit the typical genetic representation of B. glumae. B. glumae isolates showed diversity in the use of carbon and nitrogen sources, but no correlation with genetic classification by PCR fingerprinting was found. This is the first study to analyze the geographical distribution and genetic diversity of Korean B. glumae isolates.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seunghoe Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juyoung Bae
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinwoo Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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16
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Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208. Pathogens 2021; 10:pathogens10020087. [PMID: 33498266 PMCID: PMC7909282 DOI: 10.3390/pathogens10020087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/01/2022] Open
Abstract
Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.
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17
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Valette M, Rey M, Doré J, Gerin F, Wisniewski-Dyé F. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2537-2551. [PMID: 33424163 PMCID: PMC7772126 DOI: 10.1007/s12298-020-00911-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere bacteria, whether phytopathogenic or phytobeneficial, are thought to be perceived by the plant as a threat. Plant Growth-Promoting Rhizobacteria (PGPR), such as many strains of the Azospirillum genus known as the main phytostimulator of cereals, cooperate with host plants and favorably affect their growth and health. An earlier study of rice root transcriptome, undertaken with two rice cultivars and two Azospirillum strains, revealed a strain-dependent response during the rice-Azospirillum association and showed that only a few genes, including some implicated in plant defense, were commonly regulated in all tested conditions. Here, a set of genes was selected from previous studies and their expression was monitored by qRT-PCR in rice roots inoculated with ten PGPR strains isolated from various plants and belonging to various genera (Azospirillum, Herbaspirillum, Paraburkholderia). A common expression pattern was highlighted for four genes that are proposed to be markers of the rice-PGPR interaction: two genes involved in diterpenoid phytoalexin biosynthesis (OsDXS3 and OsDTC2) and one coding for an uncharacterized protein (Os02g0582900) were significantly induced by PGPR whereas one defense-related gene encoding a pathogenesis-related protein (PR1b, Os01g0382000) was significantly repressed. Interestingly, exposure to a rice bacterial pathogen also triggered the expression of OsDXS3 while the expression of Os02g0582900 and PR1b was down-regulated, suggesting that these genes might play a key role in rice-bacteria interactions. Integration of these results with previous data led us to propose that the jasmonic acid signaling pathway might be triggered in rice roots upon inoculation with PGPR.
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Affiliation(s)
- Marine Valette
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Marjolaine Rey
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Jeanne Doré
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Gerin
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Wisniewski-Dyé
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
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18
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Ortega L, Walker KA, Patrick C, Wamishe Y, Rojas A, Rojas CM. Harnessing Pseudomonas protegens to Control Bacterial Panicle Blight of Rice. PHYTOPATHOLOGY 2020; 110:1657-1667. [PMID: 32852258 DOI: 10.1094/phyto-02-20-0045-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial panicle blight of rice is a seedborne disease caused by the bacterium Burkholderia glumae. This disease has affected rice production worldwide and its effects are likely to become more devastating with the continuous increase in global temperatures, especially during the growing season. The bacterium can cause disease symptoms in different tissues and at different developmental stages. In reproductive stages, the bacterium interferes with grain development in the panicles and, as a result, directly affects rice yield. Currently, there are no methods to control the disease because chemical control is not effective and completely resistant cultivars are not available. Thus, a promising approach is the use of antagonistic microorganisms. In this work, we identified one strain of Pseudomonas protegens and one strain of B. cepacia with antimicrobial activity against B. glumae in vitro and in planta. We further characterized the antimicrobial activity of P. protegens and found that this activity is associated with bacterial secretions. Cell-free secretions from P. protegens inhibited the growth of B. glumae in vitro and also prevented B. glumae from causing disease in rice. Although the specific molecules associated with these activities have not been identified, these findings suggest that the secreted fractions from P. protegens could be harnessed as biopesticides to control bacterial panicle blight of rice.
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Affiliation(s)
- Laura Ortega
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Katherine A Walker
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Casey Patrick
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Yeshi Wamishe
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR 72160, U.S.A
| | - Alejandro Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Clemencia M Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
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Mirghasempour A, Glick BR, Hou Y, Huang S. A system to study the expression of phytopathogenic genes encoded by Burkholderia glumae. Arch Microbiol 2020; 203:383-387. [PMID: 32785734 DOI: 10.1007/s00203-020-01986-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022]
Abstract
Rice is often infected by bacterial panicle blight disease caused by Burkholderia glumae. Since most studies have assessed the transcriptome of the plant when it is exposed to bacteria, the gene expression of the phytopathogenic bacteria have not been well elaborated during the infection process or in the host cell. Recently, a few researches were conducted to evaluate the in vivo transcriptome of bacteria during the infective process. Most bacterial cells do not express genes involved in pathogenicity in culture medium making it difficult to investigate gene expression of bacterial cells in plant cells. Here, we sought a simulated patho-system that would allow bacterial cells to express their pathogenic genes. Thus, rice root exudates (RE) and bacterial N-acyl homoserine lactone (AHL) were used and their effects on bacterial gene expression were assessed. Transcription patterns of B. glumae virulence determinants showed that enrichment medium (LB + RE + C8-HSL) could significantly induce virulence factor genes compared with Luria Bertani (LB; control) medium. The data indicate that the artificial environment is similar to the real patho-system, and that this induced maximum relevant gene expression. In this model system, bacterial gene expression changes are traceable in the infection process. Bacterial cells exposed to either an artificial environment or LB + RE + C8-HSL behaved similarly to the natural environment in situ.
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Affiliation(s)
- A Mirghasempour
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - B R Glick
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Y Hou
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - S Huang
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China.
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20
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Peng J, Lelis T, Chen R, Barphagha I, Osti S, Ham JH. tepR encoding a bacterial enhancer-binding protein orchestrates the virulence and interspecies competition of Burkholderia glumae through qsmR and a type VI secretion system. MOLECULAR PLANT PATHOLOGY 2020; 21:1042-1054. [PMID: 32608174 PMCID: PMC7368122 DOI: 10.1111/mpp.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/23/2020] [Accepted: 05/04/2020] [Indexed: 05/05/2023]
Abstract
The pathogenesis of the rice pathogenic bacterium Burkholderia glumae is under the tight regulation of the tofI/tofR quorum-sensing (QS) system. tepR, encoding a group I bacterial enhancer-binding protein, negatively regulates the production of toxoflavin, the phytotoxin acting as a major virulence factor in B. glumae. In this study, through a transcriptomic analysis, we identified the genes that were modulated by tepR and/or the tofI/tofR QS system. More than half of the differentially expressed genes, including the genes for the biosynthesis and transport of toxoflavin, were significantly more highly expressed in the ΔtepR mutant but less expressed in the ΔtofI-tofR (tofI/tofR QS-defective) mutant. In consonance with the transcriptome data, other virulence-related functions of B. glumae, extracellular protease activity and flagellum-dependent motility, were also negatively regulated by tepR, and this negative regulatory function of tepR was dependent on the IclR-type transcriptional regulator gene qsmR. Likewise, the ΔtepR mutant exhibited a higher level of heat tolerance in congruence with the higher transcription levels of heat shock protein genes in the mutant. Interestingly, tepR also exhibited its positive regulatory function on a previously uncharacterized type VI secretion system (denoted as BgT6SS-1). The survival of the both ΔtepR and ΔtssD (BgT6SS-1-defective) mutants was significantly compromised compared to the wild-type parent strain 336gr-1 in the presence of the natural rice-inhabiting bacterium, Pantoea sp. RSPAM1. Taken together, this study revealed pivotal regulatory roles of tepR in orchestrating multiple biological functions of B. glumae, including pathogenesis, heat tolerance, and bacterial interspecies competition.
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Affiliation(s)
- Jingyu Peng
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMI48824USA
| | - Tiago Lelis
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Tropical Research and Education CenterInstitute of Food and Agriculture SciencesUniversity of FloridaHomesteadFLUSA
| | - Ruoxi Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
1501 Capitol AvenueSacramentoCA95814USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Surendra Osti
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Agricultural Economics and AgribusinessLouisiana State UniversityBaton RougeLA70803USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
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21
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Wang S, Nie W, Gong Q, Lee Y, Shui H, Chen G, Zhu B. Complete Genomic Data of Burkholderia glumae Strain GX Associated with Bacterial Panicle Blight of Rice in China. PLANT DISEASE 2020; 104:1578-1580. [PMID: 32282280 DOI: 10.1094/pdis-10-19-2265-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Burkholderia glumae is a seedborne pathogen causing bacterial panicle blight of rice. Here, we report the complete genome of B. glumae strain GX, which represents the first whole-genome sequence of an isolate from China. The assembled genome consisted of five contigs, with two circular chromosomes of 3,712,850 and 2,750,046 bp and three plasmids of 201,571, 105,587, and 96,100 bp. This complete genome will provide a valuable resource for further studies on bacterial panicle blight worldwide.
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Affiliation(s)
- Sai Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Wenhan Nie
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Qiang Gong
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Yaohui Lee
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Hanxia Shui
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
| | - Bo Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai 200240, China
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22
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Hussain A, Shahbaz M, Tariq M, Ibrahim M, Hong X, Naeem F, Khalid Z, Raza HMZ, Bo Z, Bin L. Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin. Comput Biol Chem 2020; 86:107245. [PMID: 32172200 DOI: 10.1016/j.compbiolchem.2020.107245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/29/2022]
Abstract
Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70-100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, β-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.
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Affiliation(s)
- Annam Hussain
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Maham Shahbaz
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Maria Tariq
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Muhammad Ibrahim
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Xianxian Hong
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Faryal Naeem
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Zunera Khalid
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Hafiz Muhammad Zeeshan Raza
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Zhu Bo
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Li Bin
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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23
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Valette M, Rey M, Gerin F, Comte G, Wisniewski-Dyé F. A common metabolomic signature is observed upon inoculation of rice roots with various rhizobacteria. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:228-246. [PMID: 30920733 DOI: 10.1111/jipb.12810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/20/2019] [Indexed: 05/21/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR), whose growth is stimulated by root exudates, are able to improve plant growth and health. Among those, bacteria of the genus Azospirillum were shown to affect root secondary metabolite content in rice and maize, sometimes without visible effects on root architecture. Transcriptomic studies also revealed that expression of several genes involved in stress and plant defense was affected, albeit with fewer genes when a strain was inoculated onto its original host cultivar. Here, we investigated, via a metabolic profiling approach, whether rice roots responded differently and with gradual intensity to various PGPR, isolated from rice or not. A common metabolomic signature of nine compounds was highlighted, with the reduced accumulation of three alkylresorcinols and increased accumulation of two hydroxycinnamic acid amides (HCAA), identified as N-p-coumaroylputrescine and N-feruloylputrescine. This was accompanied by the increased transcription of two genes involved in the N-feruloylputrescine biosynthetic pathway. Interestingly, exposure to a rice bacterial pathogen triggered a reduced accumulation of these HCAA in roots, a result contrasting with previous reports of increased HCAA content in leaves upon pathogen infection. Accumulation of HCAA, that are potential antimicrobial compounds, might be considered as a primary reaction of plant to bacterial perception.
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Affiliation(s)
- Marine Valette
- Université de Lyon, Université Lyon1, Ecologie Microbienne, CNRS UMR-5557, INRA UMR-1418, VetAgroSup, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Marjolaine Rey
- Université de Lyon, Université Lyon1, Ecologie Microbienne, CNRS UMR-5557, INRA UMR-1418, VetAgroSup, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Florence Gerin
- Université de Lyon, Université Lyon1, Ecologie Microbienne, CNRS UMR-5557, INRA UMR-1418, VetAgroSup, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Gilles Comte
- Université de Lyon, Université Lyon1, Ecologie Microbienne, CNRS UMR-5557, INRA UMR-1418, VetAgroSup, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Florence Wisniewski-Dyé
- Université de Lyon, Université Lyon1, Ecologie Microbienne, CNRS UMR-5557, INRA UMR-1418, VetAgroSup, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
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24
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Elshafie HS, Devescovi G, Venturi V, Camele I, Bufo SA. Study of the Regulatory Role of N-Acyl Homoserine Lactones Mediated Quorum Sensing in the Biological Activity of Burkholderia gladioli pv. agaricicola Causing Soft Rot of Agaricus spp. Front Microbiol 2019; 10:2695. [PMID: 31849865 PMCID: PMC6895463 DOI: 10.3389/fmicb.2019.02695] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/06/2019] [Indexed: 01/22/2023] Open
Abstract
Many Burkholderia spp. produce in vitro secondary metabolites with relevant biological activities and potential practical applications. Burkholderia gladioli pv. agaricicola (Bga) possess promising biological activities regulated by N-Acyl homoserine lactones (N.AHLs) based quorum sensing (QS) mechanism. In the current study, N.AHLs-deficient (ICMP11096glad-I) and N.AHLs-complemented (ICMP11096glad-IR) mutants were constructed in which the gene coding for AHL synthase was inactivated by allelic exchange in glad I mutant strain. The aims of this research were to (i) assess the antagonistic activity of the wild type (WT) and the glad-I mutant of Bga against Bacillus megaterium (G+ve) and Escherichia coli (G-ve), (ii) screen their hydrolytic enzymes and hemolytic substances, (iii) monitor the pathogenic effect against Agaricus bisporus, and finally (iv) analyze the bioactive secondary metabolites produced by WT and mutant strain using high performance liquid chromatography (HPLC). Results showed that N.AHLs-deficient mutant exhibited high reduction of antagonistic activity against the tested microorganisms and notable reduction of chitinolytic, proteolytic and glucanolytic activities and complete absence of hemolytic activity, and the glad-IR complemented mutant was able to regain the major part of these activities. Furthermore, N.AHLs-deficient mutant strain was unable to degrade flesh cubes pseudo-tissues of A. bisporus. On the other hand, the virulence effect of complemented mutant was like to the parental WT strain. HPLC analysis revealed that some of the single components produced by WT strain were absent in N.AHLs-deficient mutant and others were highly reduced. The out-findings of the current research gave a spot into the regulatory role of N.AHLs and QS phenomenon in the biological activity of Bga bacterium.
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Affiliation(s)
- Hazem S Elshafie
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giulia Devescovi
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Sabino A Bufo
- Department of Science, University of Basilicata, Potenza, Italy.,Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
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25
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Ashitha A, Midhun S, Sunil M, Nithin T, Radhakrishnan E, Mathew J. Bacterial endophytes from Artemisia nilagirica (Clarke) Pamp., with antibacterial efficacy against human pathogens. Microb Pathog 2019; 135:103624. [DOI: 10.1016/j.micpath.2019.103624] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/03/2019] [Accepted: 07/16/2019] [Indexed: 11/17/2022]
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26
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Pan Y, Wang Y, Yan X, Liu C, Wu B, He X, Liang Y. Quorum Quenching Enzyme APTM01, an Acylhomoserine-Lactone Acylase from Marine Bacterium of Pseudoalteromonas tetraodonis Strain MQS005. Curr Microbiol 2019; 76:1387-1397. [PMID: 31292680 DOI: 10.1007/s00284-019-01739-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/04/2019] [Indexed: 10/26/2022]
Abstract
Quorum sensing is a system of stimuli and response correlated to population density and involves in pathogen infection, colonization, and pathogenesis. Quorum quenching enzymes as quorum sensing inhibitors have been identified in a number of bacteria and been used to control by triggering the pathogenic phenotype. The marine bacteria of Pseudoalteromonas had wide activity of degrading AHLs as a type of signal molecule associated with quorum sensing. We screened many Pseudoalteromonas strains in large scale to explore genes of quorum quenching enzymes from the China seas by whole-genome sequencing rather than genomic library construction. Nine target strains were obtained and an acylases gene APTM01 from the strain MQS005 belonging to PvdQ type on sub-branch in phylogenetic tree. And the heterogenous host containing the vector with target gene could degrade C10-HSL, C12-HSL and OC12-HSL. The obtained AHL acylase gene would be a candidate quorum quenching gene to apply in some fields. We identified that the strains of Pseudoalteromonas have wide AHL-degrading ability depending on quorum quenching. The strains would be a resource to explore new quorum quenching enzymes.
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Affiliation(s)
- Yonglong Pan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanbo Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Life Sciences, Jilin University, Changchun, 130012, Jilin, People's Republic of China
| | - Xiaoqing Yan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chunhua Liu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Binbin Wu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xinping He
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yan Liang
- University of Electronic Science and Technology of China, Chengdu, Sichuan, People's Republic of China. .,Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China.
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27
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Lelis T, Peng J, Barphagha I, Chen R, Ham JH. The Virulence Function and Regulation of the Metalloprotease Gene prtA in the Plant-Pathogenic Bacterium Burkholderia glumae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:841-852. [PMID: 30694091 DOI: 10.1094/mpmi-11-18-0312-r] [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: 05/25/2023]
Abstract
Bacterial panicle blight caused by Burkholderia glumae is a major bacterial disease of rice. Our preliminary RNA-seq study showed that a serine metalloprotease gene, prtA, is regulated in a similar manner to the genes for the biosynthesis and transport of toxoflavin, which is a known major virulence factor of B. glumae. prtA null mutants of the virulent strain B. glumae 336gr-1 did not show a detectable extracellular protease activity, indicating that prtA is the solely responsible gene for the extracellular protease activity detected from this bacterium. In addition, inoculation of rice panicles with the prtA mutants resulted in a significant reduction of disease severity compared with the wild-type parent strain, suggesting the requirement of prtA for the full virulence of B. glumae. A double mutant deficient in both serine metalloprotease and toxoflavin (ΔtoxA/prtA-) exhibited a further numeric but not statistically significant decrease of disease development compared with the ΔtoxA strain. Both the prtA-driven extracellular protease activity and the toxoflavin production were dependent on both the tofI/tofR quorum-sensing and the global regulatory gene qsmR, indicating the important roles of the two global regulatory factors for the bacterial pathogenesis by this pathogen.
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Affiliation(s)
- Tiago Lelis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jingyu Peng
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Ruoxi Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
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28
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Torres M, Dessaux Y, Llamas I. Saline Environments as a Source of Potential Quorum Sensing Disruptors to Control Bacterial Infections: A Review. Mar Drugs 2019; 17:md17030191. [PMID: 30934619 PMCID: PMC6471967 DOI: 10.3390/md17030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Saline environments, such as marine and hypersaline habitats, are widely distributed around the world. They include sea waters, saline lakes, solar salterns, or hypersaline soils. The bacteria that live in these habitats produce and develop unique bioactive molecules and physiological pathways to cope with the stress conditions generated by these environments. They have been described to produce compounds with properties that differ from those found in non-saline habitats. In the last decades, the ability to disrupt quorum-sensing (QS) intercellular communication systems has been identified in many marine organisms, including bacteria. The two main mechanisms of QS interference, i.e., quorum sensing inhibition (QSI) and quorum quenching (QQ), appear to be a more frequent phenomenon in marine aquatic environments than in soils. However, data concerning bacteria from hypersaline habitats is scarce. Salt-tolerant QSI compounds and QQ enzymes may be of interest to interfere with QS-regulated bacterial functions, including virulence, in sectors such as aquaculture or agriculture where salinity is a serious environmental issue. This review provides a global overview of the main works related to QS interruption in saline environments as well as the derived biotechnological applications.
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Affiliation(s)
- Marta Torres
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain.
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, 18100 Granada, Spain.
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain.
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, 18100 Granada, Spain.
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29
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Mannaa M, Park I, Seo YS. Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species. Int J Mol Sci 2018; 20:E121. [PMID: 30598000 PMCID: PMC6337347 DOI: 10.3390/ijms20010121] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022] Open
Abstract
The members of the Burkholderia genus are characterized by high versatility and adaptability to various ecological niches. With the availability of the genome sequences of numerous species of Burkholderia, many studies have been conducted to elucidate the unique features of this exceptional group of bacteria. Genomic and metabolic plasticity are common among Burkholderia species, as evidenced by their relatively large multi-replicon genomes that are rich in insertion sequences and genomic islands and contain a high proportion of coding regions. Such unique features could explain their adaptability to various habitats and their versatile lifestyles, which are reflected in a multiplicity of species including free-living rhizospheric bacteria, plant endosymbionts, legume nodulators, and plant pathogens. The phytopathogenic Burkholderia group encompasses several pathogens representing threats to important agriculture crops such as rice. Contrarily, plant-beneficial Burkholderia have also been reported, which have symbiotic and growth-promoting roles. In this review, the taxonomy of Burkholderia is discussed emphasizing the recent updates and the contributions of genomic studies to precise taxonomic positioning. Moreover, genomic and functional studies on Burkholderia are reviewed and insights are provided into the mechanisms underlying the virulence and benevolence of phytopathogenic and plant-beneficial Burkholderia, respectively, on the basis of cutting-edge knowledge.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - Inmyoung Park
- Department of Oriental Food and Culinary Arts, Youngsan University, Busan 48015, Korea.
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
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30
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Pedraza LA, Bautista J, Uribe-Vélez D. Seed-born Burkholderia glumae Infects Rice Seedling and Maintains Bacterial Population during Vegetative and Reproductive Growth Stage. THE PLANT PATHOLOGY JOURNAL 2018; 34:393-402. [PMID: 30369849 PMCID: PMC6200043 DOI: 10.5423/ppj.oa.02.2018.0030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/05/2018] [Accepted: 05/25/2018] [Indexed: 05/31/2023]
Abstract
Rice world production is affected due to the growing impact of diseases such as bacterial panicle blight, produced by Burkholderia glumae. The pathogen-induced symptoms include seedling rot, grain rot and leaf-sheath browning in rice plants. It is currently recognized the entrance of this pathogen to the plant, from infected seeds and from environmental sources of the microorganism. However, it is still not fully elucidated the dynamics and permanence of the pathogen in the plant, from its entry until the development of disease symptoms in seedlings or panicles. In this work it was evaluated the infection of B. glumae rice plants, starting from inoculated seeds and substrates, and its subsequent monitoring after infection. Various organs of the plant during the vegetative stage and until the beginning of the reproductive stage, were evaluated. In both inoculation models, the bacteria was maintained in the plant as an endophyte between 1 × 101 and 1 × 105 cfu of B. glumae.g-1 of plant throughout the vegetative stage. An increase of bacterial population towards initiation of the panicle was observed, and in the maturity of the grain, an endophyte population was identified in the flag leaf at 1 × 106 cfu of B. glumae.g-1 fresh weight of rice plant, conducting towards the symptoms of bacterial panicle blight. The results found, suggest that B. glumae in rice plants developed from infected seeds or from the substrate, can colonize seedlings, establishing and maintaining a bacterial population over time, using rice plants as habitat to survive endophyticly until formation of bacterial panicle blight symptoms.
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Affiliation(s)
- Luz Adriana Pedraza
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
| | - Jessica Bautista
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
| | - Daniel Uribe-Vélez
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
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31
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Patel HK, Ferrante P, Xianfa M, Javvadi SG, Subramoni S, Scortichini M, Venturi V. Identification of Loci of Pseudomonas syringae pv. actinidiae Involved in Lipolytic Activity and Their Role in Colonization of Kiwifruit Leaves. PHYTOPATHOLOGY 2017; 107:645-653. [PMID: 28112597 DOI: 10.1094/phyto-10-16-0360-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial canker disease caused by Pseudomonas syringae pv. actinidiae, an emerging pathogen of kiwifruit plants, has recently brought about major economic losses worldwide. Genetic studies on virulence functions of P. syringae pv. actinidiae have not yet been reported and there is little experimental data regarding bacterial genes involved in pathogenesis. In this study, we performed a genetic screen in order to identify transposon mutants altered in the lipolytic activity because it is known that mechanisms of regulation, production, and secretion of enzymes often play crucial roles in virulence of plant pathogens. We aimed to identify the set of secretion and global regulatory loci that control lipolytic activity and also play important roles in in planta fitness. Our screen for altered lipolytic activity phenotype identified a total of 58 Tn5 transposon mutants. Mapping all these Tn5 mutants revealed that the transposons were inserted in genes that play roles in cell division, chemotaxis, metabolism, movement, recombination, regulation, signal transduction, and transport as well as a few unknown functions. Several of these identified P. syringae pv. actinidiae Tn5 mutants, notably the functions affected in phosphomannomutase AlgC, lipid A biosynthesis acyltransferase, glutamate-cysteine ligase, and the type IV pilus protein PilI, were also found affected in in planta survival and/or growth in kiwifruit plants. The results of the genetic screen and identification of novel loci involved in in planta fitness of P. syringae pv. actinidiae are presented and discussed.
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Affiliation(s)
- Hitendra Kumar Patel
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Patrizia Ferrante
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Meng Xianfa
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Sree Gowrinadh Javvadi
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Sujatha Subramoni
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Marco Scortichini
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
| | - Vittorio Venturi
- First, third, fourth, fifth, and seventh authors: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; second and sixth authors: Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy; and sixth author: Research Unit for Fruit Trees, Council for Agricultural Research and Economics, Caserta, Italy
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32
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Melanson RA, Barphagha I, Osti S, Lelis TP, Karki HS, Chen R, Shrestha BK, Ham JH. Identification of new regulatory genes involved in the pathogenic functions of the rice-pathogenic bacterium Burkholderia glumae. MICROBIOLOGY-SGM 2017; 163:266-279. [PMID: 28036242 DOI: 10.1099/mic.0.000419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia glumae is an emerging plant-pathogenic bacterium that causes disease in rice in several of the major rice-producing areas throughout the world. In the southern United States, B. glumae is the major causal agent of bacterial panicle blight of rice and has caused severe yield losses in recent decades. Despite its importance, few management options are available for diseases caused by B. glumae, and knowledge of how this pathogen causes disease is limited. In an effort to identify novel factors that contribute to the pathogenicity of B. glumae, random mutagenesis using the miniTn5gus transposon was performed on two strains of B. glumae. Resultant mutants were screened in the laboratory for altered phenotypes in various known or putative virulence factors, including toxoflavin, lipase and extracellular polysaccharides. Mutants that exhibited altered phenotypes compared to their parent strain were selected and subsequently characterized using a PCR-based method to identify the approximate location of the transposon insertion. Altogether, approximately 20 000 random mutants were screened and 51 different genes were identified as having potential involvement in the production of toxoflavin, lipase and/or extracellular polysaccharide. Especially, two regulatory genes, ntpR and tepR, encoding a LysR-type transcriptional regulator and a σ54-dependent response regulator, respectively, were discovered in this study as new negative regulatory factors for the production of toxoflavin, the major phytotoxin synthesized by B. glumae and involved in bacterial pathogenesis.
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Affiliation(s)
- Rebecca A Melanson
- Present address: Mississippi State University, Central Mississippi Research and Extension Center, 1320 Seven Springs Road, Raymond, MS 39154, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Surendra Osti
- Present address: Department of Agricultural Economics, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Tiago P Lelis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Hari S Karki
- Present address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Ruoxi Chen
- Present address: Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Bishnu K Shrestha
- Present address: Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
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Betancur LA, Naranjo-Gaybor SJ, Vinchira-Villarraga DM, Moreno-Sarmiento NC, Maldonado LA, Suarez-Moreno ZR, Acosta-González A, Padilla-Gonzalez GF, Puyana M, Castellanos L, Ramos FA. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach. PLoS One 2017; 12:e0170148. [PMID: 28225766 PMCID: PMC5321270 DOI: 10.1371/journal.pone.0170148] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022] Open
Abstract
Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities.
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Affiliation(s)
- Luz A. Betancur
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
- Universidad de Caldas. Departamento de Química. Edificio Orlando Sierra, Bloque B, Sede Palogrande Calle. Manizales, Caldas, Colombia
| | - Sandra J. Naranjo-Gaybor
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
- Universidad de las Fuerzas Armadas, ESPE Carrera de Ingeniería Agropecuaria IASA II Av. General Rumiñahui s/n, Sangolquí- Ecuador
| | - Diana M. Vinchira-Villarraga
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
| | - Nubia C. Moreno-Sarmiento
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
| | - Luis A. Maldonado
- Universidad Autónoma Metropolitana Rectoría—Secretaría General, Prolongación Canal de Miramontes, Col. Ex-hacienda San Juan de Dios, Tlalpan, México DF
| | - Zulma R. Suarez-Moreno
- Investigación y Desarrollo, Empresa Colombiana de Productos Veterinarios VECOL S.A., Bogotá D.C
| | | | - Gillermo F. Padilla-Gonzalez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do de Sao Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do Café, Ribeirão Preto–SP, Brazil
| | - Mónica Puyana
- Departamento de Ciencias Biológicas y Ambientales, Programa de Biología Marina, Universidad Jorge Tadeo Lozano, Carrera, Modulo, Oficina, Bogotá, Colombia
| | - Leonardo Castellanos
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
| | - Freddy A. Ramos
- Universidad Nacional de Colombia, Sede Bogotá, Departamento de Química, Carrera, Edificio de Química of 427, Bogotá, Colombia
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Looi HK, Toh YF, Yew SM, Na SL, Tan YC, Chong PS, Khoo JS, Yee WY, Ng KP, Kuan CS. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola. PeerJ 2017; 5:e2841. [PMID: 28149676 PMCID: PMC5274520 DOI: 10.7717/peerj.2841] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient's contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.
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Affiliation(s)
- Hong Keat Looi
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Yue Fen Toh
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Yung-Chie Tan
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Pei-Sin Chong
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Jia-Shiun Khoo
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Wai-Yan Yee
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Sian Kuan
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
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35
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Knapp A, Voget S, Gao R, Zaburannyi N, Krysciak D, Breuer M, Hauer B, Streit WR, Müller R, Daniel R, Jaeger KE. Mutations improving production and secretion of extracellular lipase by Burkholderia glumae PG1. Appl Microbiol Biotechnol 2016; 100:1265-1273. [PMID: 26476653 PMCID: PMC4717159 DOI: 10.1007/s00253-015-7041-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/15/2015] [Accepted: 09/24/2015] [Indexed: 01/05/2023]
Abstract
Burkholderia glumae is a Gram-negative phytopathogenic bacterium known as the causative agent of rice panicle blight. Strain B. glumae PG1 is used for the production of a biotechnologically relevant lipase, which is secreted into the culture supernatant via a type II secretion pathway. We have comparatively analyzed the genome sequences of B. glumae PG1 wild type and a lipase overproducing strain obtained by classical strain mutagenesis. Among a total number of 72 single nucleotide polymorphisms (SNPs) identified in the genome of the production strain, two were localized in front of the lipAB operon and were analyzed in detail. Both mutations contribute to a 100-fold overproduction of extracellular lipase in B. glumae PG1 by affecting transcription of the lipAB operon and efficiency of lipase secretion. We analyzed each of the two SNPs separately and observed a stronger influence of the promoter mutation than of the signal peptide modification but also a cumulative effect of both mutations. Furthermore, fusion of the mutated LipA signal peptide resulted in a 2-fold increase in secretion of the heterologous reporter alkaline phosphatase from Escherichia coli.
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Affiliation(s)
- Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sonja Voget
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, Germany
| | - Rong Gao
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Dagmar Krysciak
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Michael Breuer
- BASF SE, Biocatalysis and Fine Chemicals Research, Ludwigshafen, Germany
| | - Bernhard Hauer
- BASF SE, Biocatalysis and Fine Chemicals Research, Ludwigshafen, Germany
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Wolfgang R Streit
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany.
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36
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Naughton LM, An SQ, Hwang I, Chou SH, He YQ, Tang JL, Ryan RP, Dow JM. Functional and genomic insights into the pathogenesis of B
urkholderia
species to rice. Environ Microbiol 2016; 18:780-90. [DOI: 10.1111/1462-2920.13189] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Lynn M. Naughton
- School of Microbiology; Biosciences Institute; University College Cork; Cork Ireland
| | - Shi-qi An
- Division of Molecular Microbiology; College of Life Sciences; University of Dundee; Dundee UK
| | - Ingyu Hwang
- Institute of Biochemistry and Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 South Korea
| | - Shan-Ho Chou
- National Chung Hsing University Biotechnology Center; National Chung Hsing University; Taichung 40227 Taiwan
| | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources; The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering; College of Life Science and Technology; Guangxi University; 100 Daxue Road Nanning Guangxi 530004 China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources; The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering; College of Life Science and Technology; Guangxi University; 100 Daxue Road Nanning Guangxi 530004 China
| | - Robert P. Ryan
- Division of Molecular Microbiology; College of Life Sciences; University of Dundee; Dundee UK
| | - J. Maxwell Dow
- School of Microbiology; Biosciences Institute; University College Cork; Cork Ireland
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Lee J, Park J, Kim S, Park I, Seo YS. Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli. MOLECULAR PLANT PATHOLOGY 2016; 17:65-76. [PMID: 25845410 PMCID: PMC6638467 DOI: 10.1111/mpp.12262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Burkholderia gladioli is a causal agent of bacterial panicle blight and sheath/grain browning in rice in many countries. Many strains produce the yellow pigment toxoflavin, which is highly toxic to plants, fungi, animals and microorganisms. Although there have been several studies on the toxoflavin biosynthesis system of B. glumae, it is still unclear how B. gladioli activates toxoflavin biosynthesis. In this study, we explored the genomic organization of the toxoflavin system of B. gladioli and its biological functions using comparative genomic analysis between toxoflavin-producing strains (B. glumae BGR1 and B. gladioli BSR3) and a strain not producing toxoflavin (B. gladioli KACC11889). The latter exhibits normal physiological characteristics similar to other B. gladioli strains. Burkholderia gladioli KACC11889 possesses all the genes involved in toxoflavin biosynthesis, but lacks the quorum-sensing (QS) system that functions as an on/off switch for toxoflavin biosynthesis. These data suggest that B. gladioli has evolved to use the QS signalling cascade of toxoflavin production (TofI/TofR of QS → ToxJ or ToxR → tox operons) similar to that in B. glumae. However, some strains may have evolved to eliminate toxoflavin production through deletion of the QS genes. In addition, we demonstrate that the toxoflavin biosynthetic system enhances the virulence of B. gladioli. These findings provide another line of evidence supporting the differential regulation of the toxoflavin system in Burkholderia strains.
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Affiliation(s)
- Jongyun Lee
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
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Gao R, Krysciak D, Petersen K, Utpatel C, Knapp A, Schmeisser C, Daniel R, Voget S, Jaeger KE, Streit WR. Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain. Appl Environ Microbiol 2015; 81:7993-8007. [PMID: 26362987 PMCID: PMC4651095 DOI: 10.1128/aem.01043-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023] Open
Abstract
Burkholderia glumae PG1 is a soil-associated motile plant-pathogenic bacterium possessing a cell density-dependent regulation system called quorum sensing (QS). Its genome contains three genes, here designated bgaI1 to bgaI3, encoding distinct autoinducer-1 (AI-1) synthases, which are capable of synthesizing QS signaling molecules. Here, we report on the construction of B. glumae PG1 ΔbgaI1, ΔbgaI2, and ΔbgaI3 mutants, their phenotypic characterization, and genome-wide transcriptome analysis using RNA sequencing (RNA-seq) technology. Knockout of each of these bgaI genes resulted in strongly decreased motility, reduced extracellular lipase activity, a reduced ability to cause plant tissue maceration, and decreased pathogenicity. RNA-seq analysis of all three B. glumae PG1 AI-1 synthase mutants performed in the transition from exponential to stationary growth phase revealed differential expression of a significant number of predicted genes. In comparison with the levels of gene expression by wild-type strain B. glumae PG1, 481 genes were differentially expressed in the ΔbgaI1 mutant, 213 were differentially expressed in the ΔbgaI2 mutant, and 367 were differentially expressed in the ΔbgaI3 mutant. Interestingly, only a minor set of 78 genes was coregulated in all three mutants. The majority of the QS-regulated genes were linked to metabolic activities, and the most pronounced regulation was observed for genes involved in rhamnolipid and Flp pilus biosynthesis and the type VI secretion system and genes linked to a clustered regularly interspaced short palindromic repeat (CRISPR)-cas gene cluster.
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Affiliation(s)
- Rong Gao
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Dagmar Krysciak
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Katrin Petersen
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Christian Utpatel
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Christel Schmeisser
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Wolfgang R Streit
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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Lee HH, Park J, Kim J, Park I, Seo YS. Understanding the direction of evolution in Burkholderia glumae through comparative genomics. Curr Genet 2015; 62:115-23. [DOI: 10.1007/s00294-015-0523-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/02/2015] [Accepted: 10/03/2015] [Indexed: 12/11/2022]
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Seo YS, Lim JY, Park J, Kim S, Lee HH, Cheong H, Kim SM, Moon JS, Hwang I. Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts. BMC Genomics 2015; 16:349. [PMID: 25943361 PMCID: PMC4422320 DOI: 10.1186/s12864-015-1558-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/20/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages. RESULTS We first sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems. CONCLUSIONS The complete genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other animal and human Burkholderia species.
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Affiliation(s)
- Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Hoon Cheong
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon, 443-400, Republic of Korea.
| | - Sang-Mok Kim
- Yeongnam Regional Office, Animal and Plant Quarantine Agency, Busan, 600-016, Republic of Korea.
| | - Jae Sun Moon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-633, Republic of Korea.
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
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41
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Chen R, Barphagha IK, Ham JH. Identification of potential genetic components involved in the deviant quorum-sensing signaling pathways of Burkholderia glumae through a functional genomics approach. Front Cell Infect Microbiol 2015; 5:22. [PMID: 25806356 PMCID: PMC4354385 DOI: 10.3389/fcimb.2015.00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/22/2015] [Indexed: 12/21/2022] Open
Abstract
Burkholderia glumae is the chief causal agent for bacterial panicle blight of rice. The acyl-homoserine lactone (AHL)-mediated quorum-sensing (QS) system dependent on a pair of luxI and luxR homologs, tofI and tofR, is the primary cell-to-cell signaling mechanism determining the virulence of this bacterium. Production of toxoflavin, a major virulence factor of B. glumae, is known to be dependent on the tofI/tofR QS system. In our previous study, however, it was observed that B. glumae mutants defective in tofI or tofR produced toxoflavin if they grew on the surface of a solid medium, suggesting that alternative signaling pathways independent of tofI or tofR are activated in that growth condition for the production of toxoflavin. In this study, potential genetic components involved in the tofI- and tofR-independent signaling pathways for toxoflavin production were sought through screening random mini-Tn5 mutants of B. glumae to better understand the intercellular signaling pathways of this pathogen. Fifteen and three genes were initially identified as the potential genetic elements of the tofI- and tofR-independent pathways, respectively. Especially, the ORF (bglu_2g06320) divergently transcribed from toxJ, which encodes an orphan LuxR protein and controls toxoflavin biosynthesis, was newly identified in this study as a gene required for the tofR-independent toxoflavin production and named as toxK. Among those genes, flhD, dgcB, and wzyB were further studied to validate their functions in the tofI-independent toxoflavin production, and similar studies were also conducted with qsmR and toxK for their functions in the tofR-independent toxoflavin production. This work provides a foundation for future comprehensive studies of the intercellular signaling systems of B. glumae and other related pathogenic bacteria.
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Affiliation(s)
- Ruoxi Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center Baton Rouge, LA, USA
| | - Inderjit K Barphagha
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center Baton Rouge, LA, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center Baton Rouge, LA, USA
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Chaudhary R, Atamian HS, Shen Z, Briggs SP, Kaloshian I. Potato Aphid Salivary Proteome: Enhanced Salivation Using Resorcinol and Identification of Aphid Phosphoproteins. J Proteome Res 2015; 14:1762-78. [DOI: 10.1021/pr501128k] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Zhouxin Shen
- Division
of Biological Sciences, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Steven P. Briggs
- Division
of Biological Sciences, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
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Nascimento FX, Hasegawa K, Mota M, Vicente CSL. Bacterial role in pine wilt disease development - review and future perspectives. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:51-63. [PMID: 25139220 DOI: 10.1111/1758-2229.12202] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/14/2014] [Indexed: 05/02/2023]
Abstract
Mutualistic and beneficial relationships between nematodes and bacteria are highly present in nature, mostly occurring because of nutritional dependence and pathogen protection, and intrinsically related with the environment, the ecological conditions and the nematode life stages. Thirty-four years have passed since the first hypothesis suggesting a bacterial role in pine wilt disease (PWD), associated with the pinewood nematode (PWN), Bursaphelenchus xylophilus. In 1980, researchers reported that bacteria associated with the PWN could produce toxins that lead to PWD development in pine seedlings. It was also suggested a double vector system for PWD, where bacteria were vectored by the PWN and the PWN vectored by an insect from the Monochamus genus. Presently, the specific involvement of bacteria in such complex disease is still controversial, even though the increased number of studies focused on the potential bacteria role has increased considerably. This review is an up-to-date comprehensive perspective and brings new insights on the role of PWN-associated bacteria in PWD.
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Affiliation(s)
- Francisco X Nascimento
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal
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Karki HS, Ham JH. The roles of the shikimate pathway genes, aroA and aroB, in virulence, growth and UV tolerance of Burkholderia glumae strain 411gr-6. MOLECULAR PLANT PATHOLOGY 2014; 15:940-7. [PMID: 24754446 PMCID: PMC6638700 DOI: 10.1111/mpp.12147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, which is a growing disease problem for rice growers worldwide. In our previous study, some B. glumae strains showed pigmentation phenotypes producing at least two (yellow-green and purple) pigment compounds in casein-peptone-glucose agar medium. The B. glumae strains LSUPB114 and LSUPB116 are pigment-deficient mutant derivatives of the virulent and pigment-proficient strain 411gr-6, having mini-Tn5gus insertions in aroA encoding 3-phosphoshikimate 1-carboxyvinyltransferase and aroB encoding 3-dehydroquinate synthase, respectively. Both enzymes are known to be involved in the shikimate pathway, which leads to the synthesis of aromatic amino acids. Here, we demonstrate that aroA and aroB are required for normal virulence in rice and onion, growth in M9 minimal medium and tolerance to UV light, but are dispensable for the production of the phytotoxin toxoflavin. These results suggest that the shikimate pathway is involved in bacterial pathogenesis by B. glumae without a significant role in the production of toxoflavin, a major virulence factor of this pathogen.
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Affiliation(s)
- Hari Sharan Karki
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
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Magbanua ZV, Arick M, Buza T, Hsu CY, Showmaker KC, Chouvarine P, Deng P, Peterson DG, Lu S. Transcriptomic dissection of the rice-Burkholderia glumae interaction. BMC Genomics 2014; 15:755. [PMID: 25183458 PMCID: PMC4165909 DOI: 10.1186/1471-2164-15-755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/26/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. RESULTS Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction. CONCLUSION Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication.
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Affiliation(s)
- Zenaida V Magbanua
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Mark Arick
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Teresia Buza
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
- />CVM Basic Science Department, Mississippi State University, Mississippi, MS 39762 USA
| | - Chuan-Yu Hsu
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Kurt C Showmaker
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Philippe Chouvarine
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
- />Pediatric, Pneumology and Neonatology, Hanover Medical School, Hanover, Lower Saxony, D-30625 Germany
| | - Peng Deng
- />Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762 USA
| | - Daniel G Peterson
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Shien Lu
- />Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762 USA
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Kim S, Park J, Lee J, Shin D, Park DS, Lim JS, Choi IY, Seo YS. Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses. Gene 2014; 547:77-85. [PMID: 24949534 DOI: 10.1016/j.gene.2014.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 11/15/2022]
Abstract
Burkholderia glumae is a causal agent of rice grain and sheath rot. Similar to other phytopathogens, B. glumae adapts well to the host environment and controls its biology to induce diseases in the host plant; however, its molecular mechanisms are not yet fully understood. To gain a better understating of the actual physiological changes that occur in B. glumae during infection, we analyzed B. glumae transcriptome from infected rice tissues using an RNA-seq technique. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2653 transcripts that were significantly altered. We then performed KEGG pathway and module enrichment of the DEGs. Interestingly, most genes involved bacterial chemotaxis-mediated motility, ascorbate and trehalose metabolisms, and sugar transporters including l-arabinose and d-xylose were found to be highly enriched. The in vivo transcriptional profiling of pathogenic B. glumae will facilitate elucidation of unknown plant-pathogenic bacteria interactions, as well as the overall infection processes.
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Affiliation(s)
- Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Jongyun Lee
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Dongjin Shin
- Department of Functional Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Gyeongnam, 627-803, Republic of Korea
| | - Dong-Soo Park
- Department of Functional Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Gyeongnam, 627-803, Republic of Korea
| | - Jong-Sung Lim
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Ik-Young Choi
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea.
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Abstract
Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.
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Affiliation(s)
- Darren Soanes
- Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom;
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Bravo-Ruiz G, Ruiz-Roldán C, Roncero MIG. Lipolytic system of the tomato pathogen Fusarium oxysporum f. sp. lycopersici. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1054-1067. [PMID: 23718123 DOI: 10.1094/mpmi-03-13-0082-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The lipolytic profile of Fusarium oxysporum f. sp lycopersici was studied by in silico search and biochemical enzyme activity analyses. Twenty-five structural secreted lipases were predicted based on the conserved pentapeptide Gly-X-Ser-X-Gly-, characteristic of fungal lipases, and secretion signal sequences. Moreover, a predicted lipase regulatory gene was identified in addition to the previously characterized ctf1. The transcription profile of thirteen lipase genes during tomato plant colonization revealed that lip1, lip3, and lip22 were highly induced between 21 and 96 h after inoculation. Deletion mutants in five lipase genes (lip1, lip2, lip3, lip5, and lip22) and in the regulatory genes ctf1 and ctf2 as well as a Δctf1Δctf2 double mutant were generated. Quantitative reverse transcription-polymerase chain reaction expression analyses of structural lipase genes in the Δctf1, Δctf2, and Δctf1Δctf2 mutants indicated the existence of a complex lipase regulation network in F. oxysporum. The reduction of total lipase activity, as well as the severely reduced virulence of the Δctf1, Δctf2, and Δctf1Δctf2 mutants, provides evidence for an important role of the lipolytic system of this fungus in pathogenicity.
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Kim S, Park J, Kim JH, Lee J, Bang B, Hwang I, Seo YS. RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing. THE PLANT PATHOLOGY JOURNAL 2013; 29:249-59. [PMID: 25288952 PMCID: PMC4174805 DOI: 10.5423/ppj.oa.04.2013.0044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 05/16/2013] [Accepted: 05/16/2013] [Indexed: 05/31/2023]
Abstract
Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin biosynthesis and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNAseq of the wild-type B. glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::Ω) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::Ω). A comparison of gene expression profiling among the wild-type BGR1 and the two mutants before and after QS onset as well as gene ontology (GO) enrichment analysis from differential expressed genes (DEGs) revealed that genes involved in motility were highly enriched in TofI-dependent DEGs, whereas genes for transport and DNA polymerase were highly enriched in QsmR-dependent DEGs. Further, a combination of pathways with these DEGs and phenotype analysis of mutants pointed to a couple of metabolic processes, which are dependent on QS in B. glumae, that were directly or indirectly related with bacterial motility. The consistency of observed bacterial phenotypes with GOs or metabolic pathways in QS-regulated genes implied that integration RNAseq with GO enrichment or pathways would be useful to study bacterial physiology and phenotypes.
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Affiliation(s)
- Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
| | - Ji Hyeon Kim
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
| | - Jongyun Lee
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
| | - Bongjun Bang
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 609-735, Korea
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