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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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Xue J, Lu Z, Liu W, Wang S, Lu D, Wang X, He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:51-65. [PMID: 32661897 DOI: 10.1007/s11427-020-1699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/29/2020] [Indexed: 10/23/2022]
Abstract
The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.
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Affiliation(s)
- Jiao Xue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Dongbai Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
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Newberry E, Bhandari R, Kemble J, Sikora E, Potnis N. Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations. Environ Microbiol 2020; 22:2693-2708. [PMID: 32207218 DOI: 10.1111/1462-2920.14989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 01/12/2023]
Abstract
Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.
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Affiliation(s)
- Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Joseph Kemble
- Department of Horticulture, Auburn University, Auburn, AL, USA
| | - Edward Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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Sun H, Hao P, Gu L, Cheng S, Wang H, Wu A, Ma L, Wei H, Yu S. Pectate lyase-like Gene GhPEL76 regulates organ elongation in Arabidopsis and fiber elongation in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110395. [PMID: 32081256 DOI: 10.1016/j.plantsci.2019.110395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/02/2019] [Accepted: 12/27/2019] [Indexed: 05/08/2023]
Abstract
Pectate lyases (PELs) play important roles in plant growth and development, mainly by degrading the pectin in primary cell walls. However, the role of PELs in cotton fiber elongation, which also involves changes in cellular structure and components, is poorly understood. Therefore, we aimed to isolate and characterize GhPEL76, as we suspected it to contribute to the regulation of fiber elongation. Expression analysis (qRT-PCR) revealed that GhPEL76 is predominately expressed in cotton fiber, with significantly different expression levels in long- and short-fiber cultivars, and that GhPEL76 expression is responsive to gibberellic acid and indoleacetic acid treatment. Furthermore, GhPEL76 promoter-driven β-glucuronidase activity was detected in the roots, hypocotyls, and leaves of transgenic Arabidopsis plants, and the overexpression of GhPEL76 in transgenic Arabidopsis promoted the elongation of several organs, including petioles, hypocotyls, primary roots, and trichomes. Additionally, the virus-induced silencing of GhPEL76 in cotton reduced fiber length, and both yeast one-hybrid and transient dual-luciferase assays suggested that GhbHLH13, a bHLH transcription factor that is up-regulated during fiber elongation, activates GhPEL76 expression by binding to the G-box of the GhPEL76 promoter region. Therefore, these results suggest GhPEL76 positively regulates fiber elongation and provide a basis for future studies of cotton fiber development.
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Affiliation(s)
- Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China.
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Castro-Moretti FR, Gentzel IN, Mackey D, Alonso AP. Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions. Metabolites 2020; 10:E52. [PMID: 32013104 PMCID: PMC7074241 DOI: 10.3390/metabo10020052] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/16/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.
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Affiliation(s)
- Fernanda R. Castro-Moretti
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
| | - Irene N. Gentzel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA;
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA;
| | - Ana P. Alonso
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
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Saijo Y, Loo EPI. Plant immunity in signal integration between biotic and abiotic stress responses. THE NEW PHYTOLOGIST 2020; 225:87-104. [PMID: 31209880 DOI: 10.1111/nph.15989] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/04/2019] [Indexed: 05/20/2023]
Abstract
Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant-microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant-microbe-environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.
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Affiliation(s)
- Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eliza Po-Iian Loo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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Abstract
In the past four decades, tremendous progress has been made in understanding how plants respond to microbial colonization and how microbial pathogens and symbionts reprogram plant cellular processes. In contrast, our knowledge of how environmental conditions impact plant-microbe interactions is less understood at the mechanistic level, as most molecular studies are performed under simple and static laboratory conditions. In this review, we highlight research that begins to shed light on the mechanisms by which environmental conditions influence diverse plant-pathogen, plant-symbiont, and plant-microbiota interactions. There is a great need to increase efforts in this important area of research in order to reach a systems-level understanding of plant-microbe interactions that are more reflective of what occurs in nature.
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Affiliation(s)
- Yu Ti Cheng
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Li Zhang
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Sheng Yang He
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Plant Resilient Institute, Michigan State University, East Lansing, MI 48824, USA.
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58
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Kim JG, Mudgett MB. Tomato bHLH132 Transcription Factor Controls Growth and Defense and Is Activated by Xanthomonas euvesicatoria Effector XopD During Pathogenesis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1614-1622. [PMID: 31322482 DOI: 10.1094/mpmi-05-19-0122-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Effector-dependent manipulation of host transcription is a key virulence mechanism used by Xanthomonas species causing bacterial spot disease in tomato and pepper. Transcription activator-like (TAL) effectors employ novel DNA-binding domains to directly activate host transcription, whereas the non-TAL effector XopD uses a small ubiquitin-like modifier (SUMO) protease activity to represses host transcription. The targets of TAL and non-TAL effectors provide insight to the genes governing susceptibility and resistance during Xanthomonas infection. In this study, we investigated the extent to which the X. euvesicatoria non-TAL effector strain Xe85-10 activates tomato transcription to gain new insight to the transcriptional circuits and virulence mechanisms associated with Xanthomonas euvesicatoria pathogenesis. Using transcriptional profiling, we identified a putative basic helix-loop-helix (bHLH) transcription factor, bHLH132, as a pathogen-responsive gene that is moderately induced by microbe-associated molecular patterns and defense hormones and is highly induced by XopD during X. euvesicatoria infection. We also found that activation of bHLH132 transcription requires the XopD SUMO protease activity. Silencing bHLH132 mRNA expression results in stunted tomato plants with enhanced susceptibility to X. euvesicatoria infection. Our work suggests that bHLH132 is required for normal vegetative growth and development as well as resistance to X. euvesicatoria. It also suggests new transcription-based models describing XopD virulence and recognition in tomato.
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Affiliation(s)
- Jung-Gun Kim
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
| | - Mary Beth Mudgett
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
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Velásquez AC, Castroverde CDM, He SY. Plant-Pathogen Warfare under Changing Climate Conditions. Curr Biol 2019; 28:R619-R634. [PMID: 29787730 DOI: 10.1016/j.cub.2018.03.054] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Global environmental changes caused by natural and human activities have accelerated in the past 200 years. The increase in greenhouse gases is predicted to continue to raise global temperature and change water availability in the 21st century. In this Review, we explore the profound effect the environment has on plant diseases - a susceptible host will not be infected by a virulent pathogen if the environmental conditions are not conducive for disease. The change in CO2 concentrations, temperature, and water availability can have positive, neutral, or negative effects on disease development, as each disease may respond differently to these variations. However, the concept of disease optima could potentially apply to all pathosystems. Plant resistance pathways, including pattern-triggered immunity to effector-triggered immunity, RNA interference, and defense hormone networks, are all affected by environmental factors. On the pathogen side, virulence mechanisms, such as the production of toxins and virulence proteins, as well as pathogen reproduction and survival are influenced by temperature and humidity. For practical reasons, most laboratory investigations into plant-pathogen interactions at the molecular level focus on well-established pathosystems and use a few static environmental conditions that capture only a fraction of the dynamic plant-pathogen-environment interactions that occur in nature. There is great need for future research to increasingly use dynamic environmental conditions in order to fully understand the multidimensional nature of plant-pathogen interactions and produce disease-resistant crop plants that are resilient to climate change.
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Affiliation(s)
| | - Christian Danve M Castroverde
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Sheng Yang He
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA.
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60
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Uluisik S, Seymour GB. Pectate lyases: Their role in plants and importance in fruit ripening. Food Chem 2019; 309:125559. [PMID: 31679850 DOI: 10.1016/j.foodchem.2019.125559] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 11/25/2022]
Abstract
Plant cell walls are complex structures that are modified throughout development. They are a major contributor to the properties of plant structure and act as barriers against pathogens. The primary cell walls of plants are composed of polysaccharides and proteins. The polysaccharide fraction is divided into components cellulose, hemicelluloses and pectin, are all modified during fruit ripening. Pectin plays an important role in intercellular adhesion and controlling the porosity of the wall. A large number of pectin degrading enzymes have been characterised from plants and they are involved in numerous aspects of plant development. The role of pectate lyases in plant development has received little attention, probably because they are normally associated with the action of plant pathogenic organisms. However their importance in plant development and ripening is now becoming well established and new information about the role of pectate lyases in plant development forms the focus of this review.
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Affiliation(s)
- Selman Uluisik
- Burdur Mehmet Akif Ersoy University, Burdur Food Agriculture and Livestock Vocational School, 15030 Burdur, Turkey.
| | - Graham B Seymour
- Nottinham University, Division of Plant and Crop Sciences, University of Nottingham, Sutton Bonington, Loughborough LE12, UK.
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Li C, Ji C, Huguet‐Tapia JC, White FF, Dong H, Yang B. An efficient method to clone TAL effector genes from Xanthomonas oryzae using Gibson assembly. MOLECULAR PLANT PATHOLOGY 2019; 20:1453-1462. [PMID: 31414714 PMCID: PMC6792135 DOI: 10.1111/mpp.12820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transcription Activator-Like effectors (TALes) represent the largest family of type III effectors among pathogenic bacteria and play a critical role in the process of infection. Strains of Xanthomonas oryzae pv. oryzae (Xoo) and some strains of other Xanthomonas pathogens contain large numbers of TALe genes. Previous techniques to clone individual or a complement of TALe genes through conventional strategies are inefficient and time-consuming due to multiple genes (up to 29 copies) in a given genome, and technically challenging due to the repetitive sequences (up to 33 nearly identical 102-nucleotide repeats) of individual TALe genes. Thus, only a limited number of TALe genes have been molecularly cloned and characterized, and the functions of most TALe genes remain unknown. Here, we present an easy and efficient cloning technique to clone TALe genes selectively through in vitro homologous recombination and single-strand annealing, and demonstrate the feasibility of this approach with four different Xoo strains. Based on the Gibson assembly strategy, two complementary vectors with scaffolds that can preferentially capture all TALe genes from a pool of genomic fragments were designed. Both vector systems enabled cloning of a full complement of TALe genes from each of four Xoo strains and functional analysis of individual TALes in rice in approximately 1 month compared to 3 months by previously used methods. The results demonstrate a robust tool to advance TALe biology and a potential for broad usage of this approach to clone multiple copies of highly competitive DNA elements in any genome of interest.
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Affiliation(s)
- Chenhao Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095Jiangsu ProvidenceP.R. China
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
| | - Chonghui Ji
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
| | | | - Frank F. White
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
| | - Hansong Dong
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095Jiangsu ProvidenceP.R. China
| | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
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Independent Evolution with the Gene Flux Originating from Multiple Xanthomonas Species Explains Genomic Heterogeneity in Xanthomonas perforans. Appl Environ Microbiol 2019; 85:AEM.00885-19. [PMID: 31375496 DOI: 10.1128/aem.00885-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022] Open
Abstract
Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria for that of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of 2 decades, including a shift in race and diversification into three phylogenetic groups driven by genome-wide homologous-recombination events derived from X. euvesicatoria In our sampling of Xanthomonas strains associated with bacterial spot disease in Alabama, we were readily able to isolate X. perforans from symptomatic pepper plants grown in several Alabama counties, indicating a recent shift in the host range of the pathogen. To investigate the diversity of these pepper-pathogenic strains and their relation to populations associated with tomatoes grown in the southeast United States, we sequenced the genomes of eight X. perforans strains isolated from tomatoes and peppers grown in Alabama and compared them with previously published genome data available from GenBank. Surprisingly, reconstruction of the X. perforans core genome revealed the presence of two novel genetic groups in Alabama that each harbored a different transcription activation-like effector (TALE). While one TALE, AvrHah1, was associated with an emergent lineage pathogenic to both tomato and pepper, the other was identified as a new class within the AvrBs3 family, here designated PthXp1, and was associated with enhanced symptom development on tomato. Examination of patterns of homologous recombination across the larger X. euvesicatoria species complex revealed a dynamic pattern of gene flow, with multiple donors of Xanthomonas spp. associated with diverse hosts of isolation.IMPORTANCE Bacterial leaf spot of tomato and pepper is an endemic plant disease with a global distribution. In this study, we investigated the evolutionary processes leading to the emergence of novel X. perforans lineages identified in Alabama. While one lineage was isolated from symptomatic tomato and pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, here designated PthXp1. Functional analysis of PthXp1 indicated that it does not induce Bs4-mediated resistance in tomato and contributes to virulence, providing an adaptive advantage to strains on tomato. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts that results in the emergence of novel pathogen lineages and associated phenotypes, including host range.
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Xanthomonas translucens commandeers the host rate-limiting step in ABA biosynthesis for disease susceptibility. Proc Natl Acad Sci U S A 2019; 116:20938-20946. [PMID: 31575748 PMCID: PMC6800315 DOI: 10.1073/pnas.1911660116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pathogenic bacteria acquire new virulence strategies for exploiting their hosts. This work reveals that the bacterial wheat pathogen Xanthomonas translucens uses a transcription activation-like (TAL) effector to promote virulence by directly activating the host gene 9-cis-epoxycarotenoid dioxygenase, the rate-limiting enzyme in biosynthesis of abscisic acid that is normally involved in water management within the host plant. Evolutionarily, TAL effectors are a relatively new class of virulence factors limited to a few species of pathogenic bacteria, and this work adds to the diversity of host susceptibility genes that can be exploited by pathogens through TAL effector gene function. Plants are vulnerable to disease through pathogen manipulation of phytohormone levels, which otherwise regulate development, abiotic, and biotic responses. Here, we show that the wheat pathogen Xanthomonas translucens pv. undulosa elevates expression of the host gene encoding 9-cis-epoxycarotenoid dioxygenase (TaNCED-5BS), which catalyzes the rate-limiting step in the biosynthesis of the phytohormone abscisic acid and a component of a major abiotic stress-response pathway, to promote disease susceptibility. Gene induction is mediated by a type III transcription activator-like effector. The induction of TaNCED-5BS results in elevated abscisic acid levels, reduced host transpiration and water loss, enhanced spread of bacteria in infected leaves, and decreased expression of the central defense gene TaNPR1. The results represent an appropriation of host physiology by a bacterial virulence effector.
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Shah SMA, Haq F, Ma W, Xu X, Wang S, Xu Z, Zou L, Zhu B, Chen G. Tal1 NXtc01 in Xanthomonas translucens pv. cerealis Contributes to Virulence in Bacterial Leaf Streak of Wheat. Front Microbiol 2019; 10:2040. [PMID: 31551976 PMCID: PMC6737349 DOI: 10.3389/fmicb.2019.02040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Xanthomonas translucens pv. cerealis (Xtc) causes bacterial leaf streak (BLS) of important cereal crops, including wheat (Triticum aestivum) and barley (Hordeum vulgare). Transcription activator-like effectors (TALEs) play vital roles in many plant diseases caused by Xanthomonas spp., however, TALEs have not been previously characterized in Xtc. In this study, the whole genome of NXtc01, a virulent strain of Xtc from Xinjiang, China, was sequenced and compared with genomes of other Xanthomonas spp. Xtc NXtc01 consists of a single 4,622,298 bp chromosome that encodes 4,004 genes. Alignment of the NXtc01 sequence with the draft genome of Xtc strain CFBP 2541 (United States) revealed a single giant inversion and differences in the location of two tal genes, which were designated tal1 and tal2. In NXtc01, both tal genes are located on the chromosome, whereas tal2 is plasmid-encoded in CFBP 2541. The repeat variable diresidues (RVDs) at the 12th and 13th sites within Tal2 repeat units were identical in both strains, whereas Tal1 showed differences in the third RVD. Xtc NXtc01 and CFBP 2541 encoded 35 and 33 non-TALE type III effectors (T3Es), respectively. tal1, tal2, and tal-free deletion mutants of Xtc NXtc01 were constructed and evaluated for virulence. The tal1 and tal-free deletion mutants were impaired with respect to symptom development and growth in wheat, suggesting that tal1 is a virulence factor in NXtc01. This was confirmed in gain-of-function experiments that showed the introduction of tal1, but not tal2, restored virulence to the tal-free mutant. Furthermore, we generated a hrcC deletion mutant of NXtc01; the hrcC mutant was non-pathogenic on wheat and unable to elicit a hypersensitive response in the non-host Nicotiana benthamiana. Our data provide a platform for exploring the roles of both TALEs and non-TALEs in promoting BLS on wheat.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Cerutti A, Jauneau A, Laufs P, Leonhardt N, Schattat MH, Berthomé R, Routaboul JM, Noël LD. Mangroves in the Leaves: Anatomy, Physiology, and Immunity of Epithemal Hydathodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:91-116. [PMID: 31100996 DOI: 10.1146/annurev-phyto-082718-100228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydathodes are organs found on aerial parts of a wide range of plant species that provide almost direct access for several pathogenic microbes to the plant vascular system. Hydathodes are better known as the site of guttation, which is the release of droplets of plant apoplastic fluid to the outer leaf surface. Because these organs are only described through sporadic allusions in the literature, this review aims to provide a comprehensive view of hydathode development, physiology, and immunity by compiling a historic and contemporary bibliography. In particular, we refine the definition of hydathodes.We illustrate their important roles in the maintenance of plant osmotic balance, nutrient retrieval, and exclusion of deleterious chemicals from the xylem sap. Finally, we present our current understanding of the infection of hydathodes by adapted vascular pathogens and the associated plant immune responses.
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Affiliation(s)
- Aude Cerutti
- LIPM, Université de Toulouse, INRA and CNRS and Université Paul Sabatier, F-31326 Castanet-Tolosan, France;
| | - Alain Jauneau
- Plateforme Imagerie, Institut Fédératif de Recherche 3450, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA and AgroParisTech and CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - Nathalie Leonhardt
- Laboratoire de Biologie du Développement des Plantes, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Aix-Marseille Université and Commissariat à l'Energie Atomique et aux Energies Alternatives and CNRS, UMR 7265, F-13108 Saint Paul-Les-Durance, France
| | - Martin H Schattat
- Department of Plant Physiology, Institute for Biology, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Richard Berthomé
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Jean-Marc Routaboul
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Laurent D Noël
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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Cox KL, Babilonia K, Wheeler T, He P, Shan L. Return of old foes - recurrence of bacterial blight and Fusarium wilt of cotton. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:95-103. [PMID: 31075542 DOI: 10.1016/j.pbi.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/11/2019] [Accepted: 03/25/2019] [Indexed: 05/28/2023]
Abstract
Bacterial blight of cotton, caused by Xanthomonas citri subsp. malvacearum, and Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum, contribute cotton losses worldwide. Resurgences of these diseases in the United States were reported in recent years. There is a pressing need to understand pathogenicity and host responses to the pathogens and develop effective strategies for disease prevention and management. Here, we discuss the current status of bacterial blight and Fusarium wilt of cotton in the field as well as the knowledge of cotton resistance and susceptibility to these pathogens. In addition, we aim to provide insights into how these diseases are recurring and possible methods to use current technologies for biological control of these pathogens.
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Affiliation(s)
- Kevin L Cox
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, AgriLife Research, Texas A&M University, College Station, TX 77843, USA
| | - Kevin Babilonia
- Institute for Plant Genomics and Biotechnology, AgriLife Research, Texas A&M University, College Station, TX 77843, USA; Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Terry Wheeler
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA; Texas A&M AgriLife Research, Lubbock, TX 79403, USA
| | - Ping He
- Institute for Plant Genomics and Biotechnology, AgriLife Research, Texas A&M University, College Station, TX 77843, USA; Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Libo Shan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, AgriLife Research, Texas A&M University, College Station, TX 77843, USA; Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA.
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLoS Comput Biol 2019; 15:e1007206. [PMID: 31295249 PMCID: PMC6650089 DOI: 10.1371/journal.pcbi.1007206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/23/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria secrete transcription activator-like effectors (TALEs) into host cells, where they act as transcriptional activators on plant target genes to support bacterial virulence. TALEs have a unique modular DNA-binding domain composed of tandem repeats. Two amino acids within each tandem repeat, termed repeat-variable diresidues, bind to contiguous nucleotides on the DNA sequence and determine target specificity. In this paper, we propose a novel approach for TALE target prediction to identify potential virulence targets. Our approach accounts for recent findings concerning TALE targeting, including frame-shift binding by repeats of aberrant lengths, and the flexible strand orientation of target boxes relative to the transcription start of the downstream target gene. The computational model can account for dependencies between adjacent RVD positions. Model parameters are learned from the wealth of quantitative data that have been generated over the last years. We benchmark the novel approach, termed PrediTALE, using RNA-seq data after Xanthomonas infection in rice, and find an overall improvement of prediction performance compared with previous approaches. Using PrediTALE, we are able to predict several novel putative virulence targets. However, we also observe that no target genes are predicted by any prediction tool for several TALEs, which we term orphan TALEs for this reason. We postulate that one explanation for orphan TALEs are incomplete gene annotations and, hence, propose to replace promoterome-wide by genome-wide scans for target boxes. We demonstrate that known targets from promoterome-wide scans may be recovered by genome-wide scans, whereas the latter, combined with RNA-seq data, are able to detect putative targets independent of existing gene annotations.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
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Zhang L, Chen L, Dong H. Plant Aquaporins in Infection by and Immunity Against Pathogens - A Critical Review. FRONTIERS IN PLANT SCIENCE 2019; 10:632. [PMID: 31191567 PMCID: PMC6546722 DOI: 10.3389/fpls.2019.00632] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/26/2019] [Indexed: 05/18/2023]
Abstract
Plant aquaporins (AQPs) of the plasma membrane intrinsic protein (PIP) family face constant risk of hijack by pathogens aiming to infect plants. PIPs can also be involved in plant immunity against infection. This review will utilize two case studies to discuss biochemical and structural mechanisms that govern the functions of PIPs in the regulation of plant infection and immunity. The first example concerns the interaction between rice Oryza sativa and the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). To infect rice, Xoo uses the type III (T3) secretion system to secrete the proteic translocator Hpa1, and Hpa1 subsequently mediates the translocation of T3 effectors secreted by this system. Once shifted from bacteria into rice cells, effectors exert virulent or avirulent effects depending on the susceptibility of the rice varieties. The translocator function of Hpa1 requires cooperation with OsPIP1;3, the rice interactor of Hpa1. This role of OsPIP1;3 is related to regulatory models of effector translocation. The regulatory models have been proposed as, translocon-dependent delivery, translocon-independent pore formation, and effector endocytosis with membrane protein/lipid trafficking. The second case study includes the interaction of Hpa1 with the H2O2 transport channel AtPIP1;4, and the associated consequence for H2O2 signal transduction of immunity pathways in Arabidopsis thaliana, a non-host of Xoo. H2O2 is generated in the apoplast upon induction by a pathogen or microbial pattern. H2O2 from this source translocates quickly into Arabidopsis cells, where it interacts with pathways of intracellular immunity to confer plant resistance against diseases. To expedite H2O2 transport, AtPIP1;4 must adopt a specific conformation in a number of ways, including channel width extension through amino acid interactions and selectivity for H2O2 through amino acid protonation and tautomeric reactions. Both topics will reference relevant studies, conducted on other organisms and AQPs, to highlight possible mechanisms of T3 effector translocation currently under debate, and highlight the structural basis of AtPIP1;4 in H2O2 transport facilitated by gating and trafficking regulation.
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Affiliation(s)
- Liyuan Zhang
- Plant Immunity Research Group, National Key Laboratory of Crop Science, Department of Plant Pathology, Shandong Agricultural University, Tai’an, China
| | - Lei Chen
- Plant Immunity Research Group, National Key Laboratory of Crop Science, Department of Plant Pathology, Shandong Agricultural University, Tai’an, China
| | - Hansong Dong
- Plant Immunity Research Group, National Key Laboratory of Crop Science, Department of Plant Pathology, Shandong Agricultural University, Tai’an, China
- Plant Immunity Laboratory, Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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Roach R, Mann R, Gambley CG, Chapman T, Shivas RG, Rodoni B. Genomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli. BMC Genomics 2019; 20:310. [PMID: 31014247 PMCID: PMC6480910 DOI: 10.1186/s12864-019-5600-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/12/2019] [Indexed: 01/03/2023] Open
Abstract
Background The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity. Results Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads. Conclusions The phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5600-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R Roach
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, Australia. .,Agriculture Victoria Research Division, Department of Economic Development, Jobs, Transport & Resources, AgriBio, La Trobe University, Bundoora, Victoria, 3083, Australia.
| | - R Mann
- Agriculture Victoria Research Division, Department of Economic Development, Jobs, Transport & Resources, AgriBio, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - C G Gambley
- Department of Agriculture and Fisheries, Applethorpe Research Facility, Applethorpe, QLD, Australia
| | - T Chapman
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - R G Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - B Rodoni
- Agriculture Victoria Research Division, Department of Economic Development, Jobs, Transport & Resources, AgriBio, La Trobe University, Bundoora, Victoria, 3083, Australia
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71
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Gentzel I, Giese L, Zhao W, Alonso AP, Mackey D. A Simple Method for Measuring Apoplast Hydration and Collecting Apoplast Contents. PLANT PHYSIOLOGY 2019; 179:1265-1272. [PMID: 30824565 PMCID: PMC6446764 DOI: 10.1104/pp.18.01076] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/21/2019] [Indexed: 05/23/2023]
Abstract
The plant leaf apoplast is a dynamic environment subject to a variety of both internal and external stimuli. In addition to being a conduit for water vapor and gas exchange involved in transpiration and photosynthesis, the apoplast also accumulates many nutrients transported from the soil as well as those produced through photosynthesis. The internal leaf also provides a protective environment for endophytic and pathogenic microbes alike. Given the diverse array of physiological processes occurring in the apoplast, it is expedient to develop methods to study its contents. Many established methods rely on vacuum infiltration of an apoplast wash solution followed by centrifugation. In this study, we describe a refined method optimized for maize (Zea mays) seedling leaves, which not only provides a simple procedure for obtaining apoplast fluid, but also allows direct calculation of apoplast hydration at the time of harvest for every sample. In addition, we describe an abbreviated method for estimating apoplast hydration if the full apoplast extraction is not necessary. Finally, we show the applicability of this optimized apoplast extraction procedure for plants infected with the maize pathogen Pantoea stewartii ssp stewartii, including the efficient isolation of bacteria previously residing in the apoplast. The approaches to establishing this method should make it generally applicable to other types of plants.
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Affiliation(s)
- Irene Gentzel
- Translational Plant Sciences Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Laura Giese
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210
| | - Wanying Zhao
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210
| | - Ana Paula Alonso
- BioDiscovery Institute, University of North Texas, Denton, Texas 76201
- Department of Biological Sciences, University of North Texas, Denton, Texas 76201
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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Mücke S, Reschke M, Erkes A, Schwietzer CA, Becker S, Streubel J, Morgan RD, Wilson GG, Grau J, Boch J. Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs. FRONTIERS IN PLANT SCIENCE 2019; 10:162. [PMID: 30858855 PMCID: PMC6397873 DOI: 10.3389/fpls.2019.00162] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/29/2019] [Indexed: 05/12/2023]
Abstract
Rice-pathogenic Xanthomonas oryzae bacteria cause severe harvest loss and challenge a stable food supply. The pathogen virulence relies strongly on bacterial TALE (transcription activator-like effector) proteins that function as transcriptional activators inside the plant cell. To understand the plant targets of TALEs, we determined the genome sequences of the Indian X. oryzae pv. oryzae (Xoo) type strain ICMP 3125T and the strain PXO142 from the Philippines. Their complete TALE repertoire was analyzed and genome-wide TALE targets in rice were characterized. Integrating computational target predictions and rice transcriptomics data, we were able to verify 12 specifically induced target rice genes. The TALEs of the Xoo strains were reconstructed and expressed in a TALE-free Xoo strain to attribute specific induced genes to individual TALEs. Using reporter assays, we could show that individual TALEs act directly on their target promoters. In particular, we show that TALE classes assigned by AnnoTALE reflect common target genes, and that TALE classes of Xoo and the related pathogen X. oryzae pv. oryzicola share more common target genes than previously believed. Taken together, we establish a detailed picture of TALE-induced plant processes that significantly expands our understanding of X. oryzae virulence strategies and will facilitate the development of novel resistances to overcome this important rice disease.
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Affiliation(s)
- Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia-Alice Schwietzer
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Jana Streubel
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | | | | | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
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Naves ER, de Ávila Silva L, Sulpice R, Araújo WL, Nunes-Nesi A, Peres LEP, Zsögön A. Capsaicinoids: Pungency beyond Capsicum. TRENDS IN PLANT SCIENCE 2019; 24:109-120. [PMID: 30630668 DOI: 10.1016/j.tplants.2018.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/22/2018] [Accepted: 11/09/2018] [Indexed: 05/08/2023]
Abstract
Capsaicinoids are metabolites responsible for the appealing pungency of Capsicum (chili pepper) species. The completion of the Capsicum annuum genome has sparked new interest into the development of biotechnological applications involving the manipulation of pungency levels. Pungent dishes are already part of the traditional cuisine in many countries, and numerous health benefits and industrial applications are associated to capsaicinoids. This raises the question of how to successfully produce more capsaicinoids, whose biosynthesis is strongly influenced by genotype-environment interactions in fruits of Capsicum. In this Opinion article we propose that activating the capsaicinoid biosynthetic pathway in a more amenable species such as tomato could be the next step in the fascinating story of pungent crops.
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Affiliation(s)
- Emmanuel Rezende Naves
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lucas de Ávila Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Ronan Sulpice
- Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre (PABC) and Ryan Institute, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lázaro E P Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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Zhang D, Tian C, Yin K, Wang W, Qiu JL. Postinvasive Bacterial Resistance Conferred by Open Stomata in Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:255-266. [PMID: 30124364 DOI: 10.1094/mpmi-06-18-0162-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Stomata are leaf pores that regulate gas exchange and water transpiration in response to environmental cues. They also function in innate immunity by limiting pathogen entry through actively closing in so-called stomatal defense. However, roles of stomata in plant disease resistance are not fully elucidated, especially in monocots. Here, we report that non-race specific resistance of the rice abscisic acid-deficient mutant Osaba1 to Xanthomonas oryzae pv. oryzae is due to increased stomatal conductance. Reducing stomatal conductance in the Osaba1 mutant increases its susceptibility to X. oryzae pv. oryzae. Artificial opening of stomata in wild-type plants leads to enhanced resistance to X. oryzae pv. oryzae. The rice mutant es1-1 with constitutively higher stomatal conductance exhibits strong resistance to X. oryzae pv. oryzae. Additionally, Osaba1 and es1-1 are resistant to X. oryzae pv. oryzicola. The data support that open stomata confer postinvasive resistance against bacterial pathogens in rice, and such resistance probably results from decreased leaf water potential. Our findings reveal a novel role of stomata in plant immunity through modulation of leaf water status, which provides physiological insight into the interactions between plant, pathogen, and environment.
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Affiliation(s)
- Dandan Zhang
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and
- 2 University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caijuan Tian
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and
| | - Kangquan Yin
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and
| | - Wenyi Wang
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and
| | - Jin-Long Qiu
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and
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El Kasmi F, Horvath D, Lahaye T. Microbial effectors and the role of water and sugar in the infection battle ground. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:98-107. [PMID: 29597139 DOI: 10.1016/j.pbi.2018.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Phytopathogenic microbes multiply in the apoplast-a plant's intercellular spaces-of infected plants, and hence their success relies on the conditions in this habitat. Despite being extracellular parasites, most microbes translocate effectors into host cells that promote disease by acting inside cells. Initial studies suggested that effectors act predominantly as suppressors of plant immunity. These pioneering studies were trend-setting, causing a strong bias in the functional investigation of effectors. Yet, recent studies on bacterial model pathogens have identified effectors that promote disease by causing either increased sugar or water levels in the apoplast. These studies are likely to initiate a new era of effector research that will clarify the disease-promoting rather than defense-suppressing function of effectors, a molecular rather than genetic distinction.
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Affiliation(s)
- Farid El Kasmi
- ZMBP-Plant Physiology, University of Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Diana Horvath
- 2Blades Foundation, Suite 1901, 1630 Chicago Avenue, Evanston, IL 60201, USA
| | - Thomas Lahaye
- ZMBP-General Genetics, University of Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany.
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Shrestha A, Khan A, Dey N. cis-trans Engineering: Advances and Perspectives on Customized Transcriptional Regulation in Plants. MOLECULAR PLANT 2018; 11:886-898. [PMID: 29859265 DOI: 10.1016/j.molp.2018.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 05/03/2023]
Abstract
Coordinated transcriptional control employing synthetic promoters and transcription factors (TFs) can be used to achieve customized regulation of gene expression in planta. Synthetic promoter technology has yielded a series of promoters with modified cis-regulatory elements that provide useful tools for efficient modulation of gene expression. In addition, the use of zinc fingers (ZFs), transcription activator-like effectors (TALEs), and catalytically inactive clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (dCas9) has made it feasible to engineer TFs that can produce targeted gene expression regulation; these approaches are particularly effective when artificial TFs are coupled with transcriptional activators or repressors. This review focuses on strategies used to engineer both promoters and TFs in the context of targeted transcriptional regulation. We also discuss the creation of synthetic inducible platforms, which can be used to impart stress tolerance to plants. We propose that combinatorial "cis-trans engineering" using a CRISPR-dCas9-based bipartite module could be used to regulate the expression of multiple target genes. This approach provides an attractive tool for introduction of specific qualitative traits into plants, thus enhancing their overall environmental adaptability.
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Affiliation(s)
- Ankita Shrestha
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Ahamed Khan
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India.
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Denancé N, Szurek B, Doyle EL, Lauber E, Fontaine-Bodin L, Carrère S, Guy E, Hajri A, Cerutti A, Boureau T, Poussier S, Arlat M, Bogdanove AJ, Noël LD. Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire. THE NEW PHYTOLOGIST 2018; 219:391-407. [PMID: 29677397 DOI: 10.1111/nph.15148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
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Affiliation(s)
- Nicolas Denancé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Erin L Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Doane University, Crete, NE, 68333, USA
| | - Emmanuelle Lauber
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | | | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Endrick Guy
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Ahmed Hajri
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Aude Cerutti
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Tristan Boureau
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Stéphane Poussier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Matthieu Arlat
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Adam J Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
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78
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Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice. PLoS Pathog 2018; 14:e1007092. [PMID: 29864161 PMCID: PMC6037387 DOI: 10.1371/journal.ppat.1007092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 07/09/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022] Open
Abstract
Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9–16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3Δ1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3Δ1, validating OsERF#123 as a new, bacterial blight S gene. The ability of most Xanthomonas plant pathogenic bacteria to infect their hosts relies on the action of a specific family of proteins called TAL effectors, which are transcriptional activators injected into the plant by the bacteria. TAL effectors enter the plant cell nucleus and bind to the promoters of specific plant genes. Genes that when induced can benefit pathogen multiplication or disease development are called susceptibility (S) genes. Here, we perform a comparative analysis of the TAL effector repertoires of three strains of X. oryzae pv. oryzae, which causes bacterial leaf blight of rice, a major yield constraint in this staple crop. Using sequencing of entire genomes, we compared the large repertoires of TAL effectors in three African Xoo strains which form a genetic lineage distinct from Asian strains. We assessed the individual contribution to pathogen virulence of 13 TAL effector variants represented in the three strains, and identified one that makes a major contribution. By combining host transcriptome profiling and TAL effector binding sites prediction, we identified two targets of this TAL effector that function as S genes, one previously identified, and one, new S gene. We validated the new S gene by functional characterization using designer TAL effectors. Both S genes encode transcription factors and can therefore be considered as susceptibility hubs for pathogen manipulation of the host transcriptome. Our results provide new insights into the diversified strategies underlying the roles of TAL effectors in promoting plant disease.
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Abstract
Pseudomonas syringae is one of the best-studied plant pathogens and serves as a model for understanding host-microorganism interactions, bacterial virulence mechanisms and host adaptation of pathogens as well as microbial evolution, ecology and epidemiology. Comparative genomic studies have identified key genomic features that contribute to P. syringae virulence. P. syringae has evolved two main virulence strategies: suppression of host immunity and creation of an aqueous apoplast to form its niche in the phyllosphere. In addition, external environmental conditions such as humidity profoundly influence infection. P. syringae may serve as an excellent model to understand virulence and also of how pathogenic microorganisms integrate environmental conditions and plant microbiota to become ecologically robust and diverse pathogens of the plant kingdom.
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80
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Duan S, Jia H, Pang Z, Teper D, White F, Jones J, Zhou C, Wang N. Functional characterization of the citrus canker susceptibility gene CsLOB1. MOLECULAR PLANT PATHOLOGY 2018; 19:1908-1916. [PMID: 29461671 PMCID: PMC6638005 DOI: 10.1111/mpp.12667] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/29/2018] [Accepted: 02/16/2018] [Indexed: 05/08/2023]
Abstract
Xanthomonas citri ssp. citri (Xcc) is an important plant-pathogenic bacterium that causes citrus canker disease worldwide. PthA, a transcriptional activator-like (TAL) effector, directs the expression of the canker susceptibility gene CsLOB1. Here, we report our recent progress in the functional characterization of CsLOB1. Subcellular localization analysis of CsLOB1 protein in citrus protoplast revealed that CsLOB1 is primarily localized in the nucleus. We showed that CsLOB1 expression driven by dexamethasone (DEX) in CsLOB1-GR transgenic plants is associated with pustule formation following treatment with DEX. Pustule formation was not observed in DEX-treated wild-type plants and in non-treated CsLOB1-GR transgenic plants. Water soaking is typically associated with symptoms of citrus canker. Weaker water soaking was observed with pustule formation in CsLOB1-GR transgenic plants following DEX treatment. When CsLOB1-GR-transgenic Duncan grapefruit leaves were inoculated with Xcc306ΔpthA4 and treated with DEX, typical canker symptoms, including hypertrophy, hyperplasia and water soaking symptoms, were observed on DEX-treated transgenic plant leaves, but not on mock-treated plants. Twelve citrus genes that are induced by PthA4 are also stimulated by the DEX-induced expression of CsLOB1. As CsLOB1 acts as a transcriptional factor, we identified putative targets of CsLOB1 via bioinformatic and electrophoretic mobility shift assays. Cs2g20600, which encodes a zinc finger C3HC4-type RING finger protein, has been identified to be a direct target of CsLOB1. This study advances our understanding of the function of CsLOB1 and the molecular mechanism of how Xcc causes canker symptoms via CsLOB1.
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Affiliation(s)
- Shuo Duan
- Citrus Research InstituteSouthwest University, Chongqing400712, China
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Hongge Jia
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Zhiqian Pang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Doron Teper
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Frank White
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
| | - Jeffrey Jones
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
| | - Changyong Zhou
- Citrus Research InstituteSouthwest University, Chongqing400712, China
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
- China‐USA Citrus Huanglongbing Joint Laboratory (A joint laboratory of The University of Florida's Institute of Food and Agricultural Sciences and Gannan Normal University)National Navel Orange Engineering Research Center, Gannan Normal UniversityGanzhouJiangxiChina
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81
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Park E, Nedo A, Caplan JL, Dinesh-Kumar SP. Plant-microbe interactions: organelles and the cytoskeleton in action. THE NEW PHYTOLOGIST 2018; 217:1012-1028. [PMID: 29250789 DOI: 10.1111/nph.14959] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/10/2017] [Indexed: 05/06/2023]
Abstract
Contents Summary 1012 I. Introduction 1012 II. The endomembrane system in plant-microbe interactions 1013 III. The cytoskeleton in plant-microbe interactions 1017 IV. Organelles in plant-microbe interactions 1019 V. Inter-organellar communication in plant-microbe interactions 1022 VI. Conclusions and prospects 1023 Acknowledgements 1024 References 1024 SUMMARY: Plants have evolved a multilayered immune system with well-orchestrated defense strategies against pathogen attack. Multiple immune signaling pathways, coordinated by several subcellular compartments and interactions between these compartments, play important roles in a successful immune response. Pathogens use various strategies to either directly attack the plant's immune system or to indirectly manipulate the physiological status of the plant to inhibit an immune response. Microscopy-based approaches have allowed the direct visualization of membrane trafficking events, cytoskeleton reorganization, subcellular dynamics and inter-organellar communication during the immune response. Here, we discuss the contributions of organelles and the cytoskeleton to the plant's defense response against microbial pathogens, as well as the mechanisms used by pathogens to target these compartments to overcome the plant's defense barrier.
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Affiliation(s)
- Eunsook Park
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Alexander Nedo
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Jeffrey L Caplan
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA
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Aung K, Jiang Y, He SY. The role of water in plant-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:771-780. [PMID: 29205604 PMCID: PMC5849256 DOI: 10.1111/tpj.13795] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 05/20/2023]
Abstract
Throughout their life plants are associated with various microorganisms, including commensal, symbiotic and pathogenic microorganisms. Pathogens are genetically adapted to aggressively colonize and proliferate in host plants to cause disease. However, disease outbreaks occur only under permissive environmental conditions. The interplay between host, pathogen and environment is famously known as the 'disease triangle'. Among the environmental factors, rainfall events, which often create a period of high atmospheric humidity, have repeatedly been shown to promote disease outbreaks in plants, suggesting that the availability of water is crucial for pathogenesis. During pathogen infection, water-soaking spots are frequently observed on infected leaves as an early symptom of disease. Recent studies have shown that pathogenic bacteria dedicate specialized virulence proteins to create an aqueous habitat inside the leaf apoplast under high humidity. Water availability in the apoplastic environment, and probably other associated changes, can determine the success of potentially pathogenic microbes. These new findings reinforce the notion that the fight over water may be a major battleground between plants and pathogens. In this article, we will discuss the role of water availability in host-microbe interactions, with a focus on plant-bacterial interactions.
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Affiliation(s)
- Kyaw Aung
- Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- For correspondence (; )
| | - Yanjuan Jiang
- Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Sheng Yang He
- Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Howard Hughes Medical Institute, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
- For correspondence (; )
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83
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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84
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Falahi Charkhabi N, Booher NJ, Peng Z, Wang L, Rahimian H, Shams-Bakhsh M, Liu Z, Liu S, White FF, Bogdanove AJ. Complete Genome Sequencing and Targeted Mutagenesis Reveal Virulence Contributions of Tal2 and Tal4b of Xanthomonas translucens pv. undulosa ICMP11055 in Bacterial Leaf Streak of Wheat. Front Microbiol 2017; 8:1488. [PMID: 28848509 PMCID: PMC5554336 DOI: 10.3389/fmicb.2017.01488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022] Open
Abstract
Bacterial leaf streak caused by Xanthomonas translucens pv. undulosa (Xtu) is an important disease of wheat (Triticum aestivum) and barley (Hordeum vulgare) worldwide. Transcription activator-like effectors (TALEs) play determinative roles in many of the plant diseases caused by the different species and pathovars of Xanthomonas, but their role in this disease has not been characterized. ICMP11055 is a highly virulent Xtu strain from Iran. The aim of this study was to better understand genetic diversity of Xtu and to assess the role of TALEs in bacterial leaf streak of wheat by comparing the genome of this strain to the recently completely sequenced genome of a U.S. Xtu strain, and to several other draft X. translucens genomes, and by carrying out mutational analyses of the TALE (tal) genes the Iranian strain might harbor. The ICMP11055 genome, including its repeat-rich tal genes, was completely sequenced using single molecule, real-time technology (Pacific Biosciences). It consists of a single circular chromosome of 4,561,583 bp, containing 3,953 genes. Whole genome alignment with the genome of the United States Xtu strain XT4699 showed two major re-arrangements, nine genomic regions unique to ICMP11055, and one region unique to XT4699. ICMP110055 harbors 26 non-TALE type III effector genes and seven tal genes, compared to 25 and eight for XT4699. The tal genes occur singly or in pairs across five scattered loci. Four are identical to tal genes in XT4699. In addition to common repeat-variable diresidues (RVDs), the tal genes of ICMP11055, like those of XT4699, encode several RVDs rarely observed in Xanthomonas, including KG, NF, Y∗, YD, and YK. Insertion and deletion mutagenesis of ICMP11055 tal genes followed by genetic complementation analysis in wheat cv. Chinese Spring revealed that Tal2 and Tal4b of ICMP11055 each contribute individually to the extent of disease caused by this strain. A largely conserved ortholog of tal2 is present in XT4699, but for tal4b, only a gene with partial, fragmented RVD sequence similarity can be found. Our results lay the foundation for identification of important host genes activated by Xtu TALEs as targets for the development of disease resistant varieties.
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Affiliation(s)
- Nargues Falahi Charkhabi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States.,Department of Plant Pathology, Tarbiat Modares UniversityTehran, Iran
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Heshmat Rahimian
- Department of Plant Protection, Sari Agricultural Science and Natural Resources UniversitySari, Iran
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, FargoND, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Frank F White
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
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