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Clark KJ, Feng C, Anchieta AG, Van Deynze A, Correll JC, Klosterman SJ. Dual transcriptional characterization of spinach and Peronospora effusa during resistant and susceptible race-cultivar interactions. BMC Genomics 2024; 25:937. [PMID: 39375608 PMCID: PMC11457348 DOI: 10.1186/s12864-024-10809-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 09/17/2024] [Indexed: 10/09/2024] Open
Abstract
BACKGROUND Spinach downy mildew, caused by the obligate oomycete pathogen, Peronospora effusa remains a major concern for spinach production. Disease control is predominantly based on development of resistant spinach cultivars. However, new races and novel isolates of the pathogen continue to emerge and overcome cultivar resistance. Currently there are 20 known races of P. effusa. Here we characterized the transcriptomes of spinach, Spinacia oleracea, and P. effusa during disease progression using the spinach cultivar Viroflay, the near isogenic lines NIL1 and NIL3, and P. effusa races, R13 and R19, at 24 h post inoculation and 6 days post inoculation. A total of 54 samples were collected and subjected to sequencing and transcriptomic analysis. RESULTS Differentially expressed gene (DEG) analysis in resistant spinach interactions of R13-NIL1 and R19-NIL3 revealed spinach DEGs from protein kinase-like and P-loop containing families, which have roles in plant defense. The homologous plant defense genes included but were not limited to, receptor-like protein kinases (Spiol0281C06495, Spiol06Chr21559 and Spiol06Chr24027), a BAK1 homolog (Spiol0223C05961), genes with leucine rich repeat motifs (Spiol04Chr08771, Spiol04Chr01972, Spiol05Chr26812, Spiol04Chr11049, Spiol0084S08137, Spiol03Chr20299) and ABC-transporters (Spiol02Chr28975, Spiol06Chr22112, Spiol06Chr03998 and Spiol04Chr09723). Additionally, analysis of the expression of eight homologous to previously reported downy mildew resistance genes revealed that some are differentially expressed during resistant reactions but not during susceptible reactions. Examination of P. effusa gene expression during infection of susceptible cultivars identified expressed genes present in R19 or R13 including predicted RxLR and Crinkler effector genes that may be responsible for race-specific virulence on NIL1 or NIL3 spinach hosts, respectively. CONCLUSIONS These findings deliver foundational insight to gene expression in both spinach and P. effusa during susceptible and resistant interactions and provide a library of candidate genes for further exploration and functional analysis. Such resources will be beneficial to spinach breeding efforts for disease resistance in addition to better understanding the virulence mechanisms of this obligate pathogen.
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Affiliation(s)
- Kelley J Clark
- Department of Agriculture, Agricultural Research Service, Sam Farr United States Crop Improvement and Protection Research Center, Salinas, CA, USA
- Seed Biotechnology Center, Department of Plant Sciences, University of California-Davis, Davis, CA, USA
| | - Chunda Feng
- Department of Agriculture, Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS, USA
- Department of Plant Pathology and Entomology, University of Arkansas, Fayetteville, AR, USA
| | - Amy G Anchieta
- Department of Agriculture, Agricultural Research Service, Sam Farr United States Crop Improvement and Protection Research Center, Salinas, CA, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, Department of Plant Sciences, University of California-Davis, Davis, CA, USA
| | - James C Correll
- Department of Plant Pathology and Entomology, University of Arkansas, Fayetteville, AR, USA
| | - Steven J Klosterman
- Department of Agriculture, Agricultural Research Service, Sam Farr United States Crop Improvement and Protection Research Center, Salinas, CA, USA.
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Guan Y, Gajewska J, Sobieszczuk-Nowicka E, Floryszak-Wieczorek J, Hartman S, Arasimowicz-Jelonek M. The effect of nitrosative stress on histone H3 and H4 acetylation in Phytophthora infestans life cycle. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109129. [PMID: 39288571 DOI: 10.1016/j.plaphy.2024.109129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/11/2024] [Accepted: 09/13/2024] [Indexed: 09/19/2024]
Abstract
The oomycete Phytophthora infestans is one of the most destructive phytopathogens globally. It has a proven ability to adapt to changing environments rapidly; however, molecular mechanisms responsible for host invasion and adaptation to new environmental conditions still need to be explored. The study aims to understand the epigenetic mechanisms exploited by P. infestans in response to nitrosative stress conditions created by the (micro)environment and the host plant. To characterize reactive nitrogen species (RNS)-dependent acetylation profiles in avirulent/virulent (avr/vr) P. infestans, a transient gene expression, ChIP and immunoblot analyses, and nitric oxide (NO) emission by chemiluminescence were used in combination with the pharmacological approach. Nitrosative stress increased total H3/H4 acetylation and some histone acetylation marks, mainly in sporulating hyphae of diverse (avr/vr) isolates and during potato colonization. These results correlated with transcriptional up-regulation of acetyltransferases PifHAC3 and PifHAM1, catalyzing H3K56 and H4K16 acetylation, respectively. NO or peroxynitrite-mediated changes were also associated with H3K56 and H4K16 mark deposition on the critical pathogenicity-related gene promoters (CesA1, CesA2, CesA3, sPLD-like1, Hmp1, and Avr3a) elevating their expression. Our study highlights RNS-dependent transcriptional reprogramming via histone acetylation of essential gene expression in the sporulating and biotrophic phases of plant colonization by P. infestans as a tool promoting its evolutionary plasticity.
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Affiliation(s)
- Yufeng Guan
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Joanna Gajewska
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | | | - Sjon Hartman
- Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, D-79104, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104, Freiburg, Germany
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Coles DW, Bithell SL, Jeffries T, Cuddy WS, Plett JM. Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis. FRONTIERS IN PLANT SCIENCE 2024; 15:1439020. [PMID: 39224851 PMCID: PMC11366588 DOI: 10.3389/fpls.2024.1439020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024]
Abstract
Introduction Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analyzed the transcriptome of P. medicaginis across three phases of colonization of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterization of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.
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Affiliation(s)
- Donovin W. Coles
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Sean L. Bithell
- New South Wales Department of Primary Industries, Tamworth, NSW, Australia
| | - Thomas Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - William S. Cuddy
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Jonathan M. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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Fernandes P, Pimentel D, Ramiro RS, Silva MDC, Fevereiro P, Costa RL. Dual transcriptomic analysis reveals early induced Castanea defense-related genes and Phytophthora cinnamomi effectors. FRONTIERS IN PLANT SCIENCE 2024; 15:1439380. [PMID: 39188543 PMCID: PMC11345161 DOI: 10.3389/fpls.2024.1439380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/05/2024] [Indexed: 08/28/2024]
Abstract
Phytophthora cinnamomi Rands devastates forest species worldwide, causing significant ecological and economic impacts. The European chestnut (Castanea sativa) is susceptible to this hemibiotrophic oomycete, whereas the Asian chestnuts (Castanea crenata and Castanea mollissima) are resistant and have been successfully used as resistance donors in breeding programs. The molecular mechanisms underlying the different disease outcomes among chestnut species are a key foundation for developing science-based control strategies. However, these are still poorly understood. Dual RNA sequencing was performed in C. sativa and C. crenata roots inoculated with P. cinnamomi. The studied time points represent the pathogen's hemibiotrophic lifestyle previously described at the cellular level. Phytophthora cinnamomi expressed several genes related to pathogenicity in both chestnut species, such as cell wall-degrading enzymes, host nutrient uptake transporters, and effectors. However, the expression of effectors related to the modulation of host programmed cell death (elicitins and NLPs) and sporulation-related genes was higher in the susceptible chestnut. After pathogen inoculation, 1,556 and 488 genes were differentially expressed by C. crenata and C. sativa, respectively. The most significant transcriptional changes occur at 2 h after inoculation (hai) in C. sativa and 48 hai in C. crenata. Nevertheless, C. crenata induced more defense-related genes, indicating that the resistant response to P. cinnamomi is controlled by multiple loci, including several pattern recognition receptors, genes involved in the phenylpropanoid, salicylic acid and ethylene/jasmonic acid pathways, and antifungal genes. Importantly, these results validate previously observed cellular responses for C. crenata. Collectively, this study provides a comprehensive time-resolved description of the chestnut-P. cinnamomi dynamic, revealing new insights into susceptible and resistant host responses and important pathogen strategies involved in disease development.
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Affiliation(s)
- Patrícia Fernandes
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Diana Pimentel
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
| | | | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Fevereiro
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB, Green-It Unit), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Oeiras, Portugal
- Centro de Estudos Florestais, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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Soto-Contreras A, Caamal-Chan MG, Ramírez-Mosqueda MA, Murguía-González J, Núñez-Pastrana R. Morphological and Molecular Identification of Phytophthora capsici Isolates with Differential Pathogenicity in Sechium edule. PLANTS (BASEL, SWITZERLAND) 2024; 13:1602. [PMID: 38931034 PMCID: PMC11207793 DOI: 10.3390/plants13121602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Chayote (Sechium edule) is a crop of great economic and pharmaceutical importance in Mexico. Chayote is affected by Phytophthora capsici, which causes plant wilt and fruit rot. Three isolates of P. capsici (A1-C, A2-H, and A3-O) were obtained from three producing areas in Veracruz, Mexico. Morphometric characteristics of sporangia and the colony pattern on three different media were described. They were molecularly identified by amplification of the internal transcribed spacer region (ITS) and the partial sequence of cytochrome c oxidase subunit 1 (COI), sequences that were phylogenetically analyzed. The mating type, pathogenicity in S. edule fruits, and sensitivity to metalaxyl were determined. Isolate A1-C presented the largest sporangium; all sporangia were papillated, with different morphologies and pedicel lengths. All isolates showed different colony patterns: chrysanthemum (A1-C), stellate (A2-H), and petaloid (A3-O). The topology of the phylogenetic tree was similar for the ITS region and COI gene, the sequences of the three isolates clustered with sequences of the genus Phytophthora classified in group 2b, corroborating their identity as P. capsici. The mating type of isolates A1-C and A3-O was A2 and of isolate A2-H was A1. The pathogenicity test indicated that isolate A1-C was the most virulent and with intermediate sensitivity to metalaxyl. This work suggests that P. capsici isolates from various production areas in Mexico may exhibit morphological and virulence variability.
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Affiliation(s)
- Anell Soto-Contreras
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Josefa Ortiz de Domínguez s/n, Amatlán de los Reyes 94945, Veracruz, Mexico; (A.S.-C.); (J.M.-G.)
| | - María G. Caamal-Chan
- CONAHCYT-Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Mexico;
| | - Marco A. Ramírez-Mosqueda
- Laboratorio Agrícola-Forestal, Centro Nacional de Recursos Genéticos-INIFAP, Boulevard de la Biodiversidad 400, Rancho las Cruces, Tepatitlán de Morelos 47600, Jalisco, Mexico;
| | - Joaquín Murguía-González
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Josefa Ortiz de Domínguez s/n, Amatlán de los Reyes 94945, Veracruz, Mexico; (A.S.-C.); (J.M.-G.)
| | - Rosalía Núñez-Pastrana
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Josefa Ortiz de Domínguez s/n, Amatlán de los Reyes 94945, Veracruz, Mexico; (A.S.-C.); (J.M.-G.)
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Testi S, Kuhn ML, Allasia V, Auroy P, Kong F, Peltier G, Pagnotta S, Cazareth J, Keller H, Panabières F. The Phytophthora parasitica effector AVH195 interacts with ATG8, attenuates host autophagy, and promotes biotrophic infection. BMC Biol 2024; 22:100. [PMID: 38679707 PMCID: PMC11057187 DOI: 10.1186/s12915-024-01899-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Plant pathogens secrete effector proteins into host cells to suppress immune responses and manipulate fundamental cellular processes. One of these processes is autophagy, an essential recycling mechanism in eukaryotic cells that coordinates the turnover of cellular components and contributes to the decision on cell death or survival. RESULTS We report the characterization of AVH195, an effector from the broad-spectrum oomycete plant pathogen, Phytophthora parasitica. We show that P. parasitica expresses AVH195 during the biotrophic phase of plant infection, i.e., the initial phase in which host cells are maintained alive. In tobacco, the effector prevents the initiation of cell death, which is caused by two pathogen-derived effectors and the proapoptotic BAX protein. AVH195 associates with the plant vacuolar membrane system and interacts with Autophagy-related protein 8 (ATG8) isoforms/paralogs. When expressed in cells from the green alga, Chlamydomonas reinhardtii, the effector delays vacuolar fusion and cargo turnover upon stimulation of autophagy, but does not affect algal viability. In Arabidopsis thaliana, AVH195 delays the turnover of ATG8 from endomembranes and promotes plant susceptibility to P. parasitica and the obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis. CONCLUSIONS Taken together, our observations suggest that AVH195 targets ATG8 to attenuate autophagy and prevent associated host cell death, thereby favoring biotrophy during the early stages of the infection process.
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Affiliation(s)
- Serena Testi
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
- Present Address: Station Biologique de Roscoff, UMR8227 LBI2M, CNRS-Sorbonne Unversité, 29680, Roscoff, France
| | - Marie-Line Kuhn
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - Valérie Allasia
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - Pascaline Auroy
- Aix Marseille Université, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
| | - Fantao Kong
- Aix Marseille Université, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
- Present address: School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Gilles Peltier
- Aix Marseille Université, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
| | - Sophie Pagnotta
- Université Côte d'Azur, Centre Commun de Microscopie Appliquée, 06108, Nice, France
| | - Julie Cazareth
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06903, Sophia Antipolis, France
| | - Harald Keller
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.
| | - Franck Panabières
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
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Guo Y, Krasnow CS, Hausbeck MK. Characterizing the Dynamics of Virulence and Fungicide Resistance of Phytophthora capsici in Michigan Vegetable Fields Reveals Loci Associated with Virulence. PLANT DISEASE 2024; 108:332-341. [PMID: 37656035 DOI: 10.1094/pdis-03-23-0576-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The oomycete Phytophthora capsici is a destructive pathogen infecting more than 50 plant species and is one of the most serious threats to cucurbit production. Phytophthora blight caused by Phytophthora capsici can affect all plant growth stages, and fungicides and cultural controls are used to limit losses. Dissecting pathogen virulence and fungicide resistance can provide insights into pathogenic mechanisms and inform effective management practices to control P. capsici. In this study, we assessed virulence, mefenoxam sensitivity, and genetic diversity of nine P. capsici populations collected from Cucurbitaceae, Solanaceae, and Fabaceae host families in Michigan from 2002 to 2016. We developed 992 simple sequence repeats (SSRs) in the P. capsici genome and identified 60 SSRs located within or close to RXLR-class (Arginine-any amino acid-Leucine-Arginine) effectors and 29 SSRs within or close to effector CRN (CRinkling and Necrosis) family protein, which represent 62 RXLR and 34 putative CRNs. Population structure analysis shows that mefenoxam resistance was not associated with the year of collection, host type, or location, but there were significant differences in virulence among the populations. Using the general linear model and mixed linear model-based association analyses with all effector-related SSR markers, we identified four SSR markers significantly associated with at least one of the virulence-related parameters. Of these, one (Pce_SC18) was in a predicted CRN effector and had high identity with the putative PhCRN37 effector in the pathogen Plasmopara halstedii, which can be further verified for virulence identification in P. capsici.
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Affiliation(s)
- Yufang Guo
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI
| | - Charles S Krasnow
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI
| | - Mary K Hausbeck
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI
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8
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Quesada-Ocampo LM, Parada-Rojas CH, Hansen Z, Vogel G, Smart C, Hausbeck MK, Carmo RM, Huitema E, Naegele RP, Kousik CS, Tandy P, Lamour K. Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:185-208. [PMID: 37257056 DOI: 10.1146/annurev-phyto-021622-103801] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.
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Affiliation(s)
- L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - C H Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - Z Hansen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Vogel
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - C Smart
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - M K Hausbeck
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - R M Carmo
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
| | - E Huitema
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - R P Naegele
- Sugarbeet and Bean Research Unit, USDA, ARS, East Lansing, Michigan, USA
| | - C S Kousik
- US Vegetable Laboratory, USDA, ARS, Charleston, South Carolina, USA
| | - P Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
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9
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Wang Z, Su C, Hu W, Su Q, Luan Y. The effectors of Phytophthora infestans impact host immunity upon regulation of antagonistic hormonal activities. PLANTA 2023; 258:59. [PMID: 37530861 DOI: 10.1007/s00425-023-04215-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
MAIN CONCLUSION Phytophthora infestans effectors manipulate the antagonism of host hormones to interfere with the immune response of plants at different infection stages. Phytophthora infestans (P. infestans) poses a serious threat to global crop production, and its effectors play an indispensable role in its pathogenicity. However, the function of these effectors during the switch from biotrophy to necrotrophy of P. infestans remains unclear. Further research on the effectors that manipulate the antagonistic response of host hormones is also lacking. In this study, a coexpression analysis and infection assays were performed to identify distinct gene expression changes in both P. infestans and tomato. During the switch from biotrophy to necrotrophy, P. infestans secretes three types of effectors to interfere with host salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) levels. The three aforementioned effectors also regulate the host gene expression including NPR1, TGA2.1, PDF1.2, NDR1, ERF3, NCED6, GAI4, which are involved in hormone crosstalk. The changes in plant hormones are mediated by the three types of effectors, which may accelerate infection and drive completion of the P. infestans lifecycle. Our findings provide new insight into plant‒pathogen interactions that may contribute to the prevention growth of hemibiotrophic pathogens.
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Affiliation(s)
- Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Wenyun Hu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qiao Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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10
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Krishnan P, Caseys C, Soltis N, Zhang W, Burow M, Kliebenstein DJ. Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis-Botrytis pathosystem. Genetics 2023; 224:iyad099. [PMID: 37216906 PMCID: PMC10789313 DOI: 10.1093/genetics/iyad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/30/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
Bidirectional flow of information shapes the outcome of the host-pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana. We show that genetic variation in the pathogen has a greater influence on the co-transcriptome than mutations that abolish defense signaling pathways in the host. Genome-wide association mapping using the pathogens' genetic variation and both organisms' transcriptomes allowed an assessment of how the pathogen modulates plasticity in response to the host. This showed that the differences in both organism's responses were linked to trans-expression quantitative trait loci (eQTL) hotspots within the pathogen's genome. These hotspots control gene sets in either the host or pathogen and show differential allele sensitivity to the host's genetic variation rather than qualitative host specificity. Interestingly, nearly all the trans-eQTL hotspots were unique to the host or pathogen transcriptomes. In this system of differential plasticity, the pathogen mediates the shift in the co-transcriptome more than the host.
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Affiliation(s)
- Parvathy Krishnan
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
| | - Celine Caseys
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
| | - Nik Soltis
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
| | - Wei Zhang
- Department of Botany & Plant Sciences, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Meike Burow
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
| | - Daniel J Kliebenstein
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
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11
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Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. FRONTIERS IN PLANT SCIENCE 2022; 13:980587. [PMID: 36479518 PMCID: PMC9721114 DOI: 10.3389/fpls.2022.980587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
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Affiliation(s)
| | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- LaMME, Université d'Evry Val d'Essonne, INRAE, Evry, France
| | | | | | | | | | - Ingo Hein
- Division Plant Sciences at the JHI, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute (JHI), Dundee, United Kingdom
| | - Kurt Lamour
- INRAE, GAFL, Montfavet, France
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
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12
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Vogel G, Giles G, Robbins KR, Gore MA, Smart CD. Quantitative Genetic Analysis of Interactions in the Pepper- Phytophthora capsici Pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1018-1033. [PMID: 35914305 DOI: 10.1094/mpmi-12-21-0307-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of pepper cultivars with durable resistance to the oomycete Phytophthora capsici has been challenging due to differential interactions between the species that allow certain pathogen isolates to cause disease on otherwise resistant host genotypes. Currently, little is known about the pathogen genes involved in these interactions. To investigate the genetic basis of P. capsici virulence on individual pepper genotypes, we inoculated sixteen pepper accessions, representing commercial varieties, sources of resistance, and host differentials, with 117 isolates of P. capsici, for a total of 1,864 host-pathogen combinations. Analysis of disease outcomes revealed a significant effect of inter-species genotype-by-genotype interactions, although these interactions were quantitative rather than qualitative in scale. Isolates were classified into five pathogen subpopulations, as determined by their genotypes at over 60,000 single-nucleotide polymorphisms (SNPs). While absolute virulence levels on certain pepper accessions significantly differed between subpopulations, a multivariate phenotype reflecting relative virulence levels on certain pepper genotypes compared with others showed the strongest association with pathogen subpopulation. A genome-wide association study (GWAS) identified four pathogen loci significantly associated with virulence, two of which colocalized with putative RXLR effector genes and another with a polygalacturonase gene cluster. All four loci appeared to represent broad-spectrum virulence genes, as significant SNPs demonstrated consistent effects regardless of the host genotype tested. Host genotype-specific virulence variants in P. capsici may be difficult to map via GWAS with all but excessively large sample sizes, perhaps controlled by genes of small effect or by multiple allelic variants that have arisen independently. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Garrett Giles
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Kelly R Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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13
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Yu YY, Si FJ, Wang N, Wang T, Jin Y, Zheng Y, Yang W, Luo YM, Niu DD, Guo JH, Jiang CH. Bacillus-Secreted Oxalic Acid Induces Tomato Resistance Against Gray Mold Disease Caused by Botrytis cinerea by Activating the JA/ET Pathway. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:659-671. [PMID: 36043906 DOI: 10.1094/mpmi-11-21-0289-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacillus spp. are known for their ability to control plant diseases; however, the mechanism of disease control by Bacillus spp. is still unclear. Previously, bacterial organic acids have been implicated in the process of disease suppression. We extracted the total organic acid from Bacillus cereus AR156 culture filtrate and identified oxalic acid (OA) as the programmed cell death-inducing factor. OA strongly suppressed the lesion caused by Botrytis cinerea without significant antagonism against the fungus. Low concentration of OA produced by Bacillus spp. inhibited cell death caused by high concentrations of OA in a concentration- and time-dependent manner. Pretreatment with a low concentration of OA led to higher accumulation of active oxygen-scavenging enzymes in tomato leaves and provoked the expression of defense-related genes. The activation of gene expression relied on the jasmonic acid (JA) signaling pathway but not the salicylic acid (SA) pathway. The disease suppression capacity of OA was confirmed on wild-type tomato and its SA accumulation-deficient line, while the control effect was diminished in JA synthesis-deficient mutant, suggesting that the OA-triggered resistance relied on JA and ethylene (ET) signaling transduction. OA secretion ability was widely distributed among the tested Bacillus strains and the final environmental OA concentration was under strict regulation by a pH-sensitive degradation mechanism. This study provides the first systematic analysis on the role of low-concentration OA secreted and maintained by Bacillus spp. in suppression of gray mold disease and determines the dependence of OA-mediated resistance on the JA/ET signaling pathway. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Yi-Yang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Fang-Jie Si
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ning Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ting Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Yu Jin
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Wei Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an 223300, China
| | - Yu-Ming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an 223300, China
| | - Dong-Dong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
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14
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Midgley KA, van den Berg N, Swart V. Unraveling Plant Cell Death during Phytophthora Infection. Microorganisms 2022; 10:microorganisms10061139. [PMID: 35744657 PMCID: PMC9229607 DOI: 10.3390/microorganisms10061139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/02/2023] Open
Abstract
Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, of which several hundred organisms are considered among the most devastating plant pathogens—especially members of the genus Phytophthora. Phytophthora spp. have a large repertoire of effectors that aid in eliciting a susceptible response in host plants. What is of increasing interest is the involvement of Phytophthora effectors in regulating programed cell death (PCD)—in particular, the hypersensitive response. There have been numerous functional characterization studies, which demonstrate Phytophthora effectors either inducing or suppressing host cell death, which may play a crucial role in Phytophthora’s ability to regulate their hemi-biotrophic lifestyle. Despite several advances in techniques used to identify and characterize Phytophthora effectors, knowledge is still lacking for some important species, including Phytophthora cinnamomi. This review discusses what the term PCD means and the gap in knowledge between pathogenic and developmental forms of PCD in plants. We also discuss the role cell death plays in the virulence of Phytophthora spp. and the effectors that have so far been identified as playing a role in cell death manipulation. Finally, we touch on the different techniques available to study effector functions, such as cell death induction/suppression.
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15
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Dolatabadian A, Fernando WGD. Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.
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Affiliation(s)
- Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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16
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Chickpea Roots Undergoing Colonisation by Phytophthora medicaginis Exhibit Opposing Jasmonic Acid and Salicylic Acid Accumulation and Signalling Profiles to Leaf Hemibiotrophic Models. Microorganisms 2022; 10:microorganisms10020343. [PMID: 35208798 PMCID: PMC8874544 DOI: 10.3390/microorganisms10020343] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Hemibiotrophic pathogens cause significant losses within agriculture, threatening the sustainability of food systems globally. These microbes colonise plant tissues in three phases: a biotrophic phase followed by a biotrophic-to-necrotrophic switch phase and ending with necrotrophy. Each of these phases is characterized by both common and discrete host transcriptional responses. Plant hormones play an important role in these phases, with foliar models showing that salicylic acid accumulates during the biotrophic phase and jasmonic acid/ethylene responses occur during the necrotrophic phase. The appropriateness of this model to plant roots has been challenged in recent years. The need to understand root responses to hemibiotrophic pathogens of agronomic importance necessitates further research. In this study, using the root hemibiotroph Phytophthora medicaginis, we define the duration of each phase of pathogenesis in Cicer arietinum (chickpea) roots. Using transcriptional profiling, we demonstrate that susceptible chickpea roots display some similarities in response to disease progression as previously documented in leaf plant–pathogen hemibiotrophic interactions. However, our transcriptomic results also show that chickpea roots do not conform to the phytohormone responses typically found in leaf colonisation by hemibiotrophs. We found that quantified levels of salicylic acid concentrations in root tissues decreased significantly during biotrophy while jasmonic acid concentrations were significantly induced. This study demonstrated that a wider spectrum of plant species should be investigated in the future to understand the physiological changes in plants during colonisation by soil-borne hemibiotrophic pathogens before we can better manage these economically important microbes.
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17
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Jin J, Shew HD. Impacts of Continued Exposure to a Susceptible Host Genotype on Aggressiveness of Phytophthora nicotianae Isolates Adapted to Multiple Sources of Partial Resistance. PLANT DISEASE 2022; 106:373-381. [PMID: 34282925 DOI: 10.1094/pdis-09-20-1972-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pathogen adaptation can threaten the durability of partial resistance. Mixed plantings of susceptible and partially resistant varieties may prolong the effectiveness of partial resistance, but little is known about how continued exposure to a susceptible genotype can change the aggressiveness of pathogen isolates adapted to a source of partial resistance. The objective of this study was to examine the effects of continued exposure to a highly susceptible tobacco genotype on isolates of Phytophthora nicotianae that had been adapted to partial resistance. Isolates of P. nicotianae previously adapted to two sources of partial resistance were continually exposed to either the original host of adaptation or a susceptible host. After six generations of host exposure, isolates obtained from the partially resistant and the susceptible hosts were compared for their aggressiveness on the resistant host and for differences in expression of genes associated with pathogenicity and aggressiveness. Results suggested that exposure to the susceptible tobacco genotype reduced aggressiveness of isolates adapted to partial resistance in K 326 Wz/- but not of isolates adapted to partial resistance in Fla 301. Quantification of pathogenicity-associated gene expression using qRT-PCR suggested the rapid change in aggressiveness of isolates adapted to Wz-sourced partial resistance may have resulted from modification in gene expression in multiple genes.
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Affiliation(s)
- Jing Jin
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - H David Shew
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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18
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Syed‐Ab‐Rahman SF, Arkhipov A, Wass TJ, Xiao Y, Carvalhais LC, Schenk PM. Rhizosphere bacteria induce programmed cell death defence genes and signalling in chilli pepper. J Appl Microbiol 2022; 132:3111-3124. [DOI: 10.1111/jam.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Sharifah Farhana Syed‐Ab‐Rahman
- Plant‐Microbe Interactions Laboratory School of Agriculture and Food Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Alexander Arkhipov
- Plant‐Microbe Interactions Laboratory School of Agriculture and Food Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Taylor J. Wass
- Plant‐Microbe Interactions Laboratory School of Agriculture and Food Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Yawen Xiao
- Plant‐Microbe Interactions Laboratory School of Agriculture and Food Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Lilia C. Carvalhais
- Queensland Alliance for Agriculture and Food Innovation The University of Queensland Ecosciences Precinct GPO Box 267 Queensland 4001 Australia
| | - Peer M. Schenk
- Plant‐Microbe Interactions Laboratory School of Agriculture and Food Sciences The University of Queensland Brisbane Queensland 4072 Australia
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19
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Bautista D, Guayazan-Palacios N, Buitrago MC, Cardenas M, Botero D, Duitama J, Bernal AJ, Restrepo S. Comprehensive Time-Series Analysis of the Gene Expression Profile in a Susceptible Cultivar of Tree Tomato ( Solanum betaceum) During the Infection of Phytophthora betacei. FRONTIERS IN PLANT SCIENCE 2021; 12:730251. [PMID: 34745164 PMCID: PMC8567061 DOI: 10.3389/fpls.2021.730251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/22/2021] [Indexed: 05/30/2023]
Abstract
Solanum betaceum is a tree from the Andean region bearing edible fruits, considered an exotic export. Although there has been renewed interest in its commercialization, sustainability, and disease management have been limiting factors. Phytophthora betacei is a recently described species that causes late blight in S. betaceum. There is no general study of the response of S. betaceum, particularly, in the changes in expression of pathogenesis-related genes. In this manuscript we present a comprehensive RNA-seq time-series study of the plant response to the infection of P. betacei. Following six time points of infection, the differentially expressed genes (DEGs) involved in the defense by the plant were contextualized in a sequential manner. We documented 5,628 DEGs across all time-points. From 6 to 24 h post-inoculation, we highlighted DEGs involved in the recognition of the pathogen by the likely activation of pattern-triggered immunity (PTI) genes. We also describe the possible effect of the pathogen effectors in the host during the effector-triggered response. Finally, we reveal genes related to the susceptible outcome of the interaction caused by the onset of necrotrophy and the sharp transcriptional changes as a response to the pathogen. This is the first report of the transcriptome of the tree tomato in response to the newly described pathogen P. betacei.
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Affiliation(s)
- Daniel Bautista
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Natalia Guayazan-Palacios
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Biology, University of Washington, Seattle, WA, United States
| | | | - Martha Cardenas
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - David Botero
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Department of Systems and Computing Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Adriana J. Bernal
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
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20
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Thorpe P, Vetukuri RR, Hedley PE, Morris J, Whisson MA, Welsh LRJ, Whisson SC. Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae. G3 (BETHESDA, MD.) 2021; 11:jkab282. [PMID: 34849788 PMCID: PMC8527500 DOI: 10.1093/g3journal/jkab282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/22/2021] [Indexed: 11/14/2022]
Abstract
Species of Phytophthora, plant pathogenic eukaryotic microbes, can cause disease on many tree species. Genome sequencing of species from this genus has helped to determine components of their pathogenicity arsenal. Here, we sequenced genomes for two widely distributed species, Phytophthora pseudosyringae and Phytophthora boehmeriae, yielding genome assemblies of 49 and 40 Mb, respectively. We identified more than 270 candidate disease promoting RXLR effector coding genes for each species, and hundreds of genes encoding candidate plant cell wall degrading carbohydrate active enzymes (CAZymes). These data boost genome sequence representation across the Phytophthora genus, and form resources for further study of Phytophthora pathogenesis.
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Affiliation(s)
- Peter Thorpe
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, SE-234 22, Sweden
| | - Pete E Hedley
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jenny Morris
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - Lydia R J Welsh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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21
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Wang S, Vetukuri RR, Kushwaha SK, Hedley PE, Morris J, Studholme DJ, Welsh LRJ, Boevink PC, Birch PRJ, Whisson SC. Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae. MOLECULAR PLANT PATHOLOGY 2021; 22:954-968. [PMID: 34018655 PMCID: PMC8295517 DOI: 10.1111/mpp.13072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 05/29/2023]
Abstract
Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.
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Affiliation(s)
- Shumei Wang
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
| | - Ramesh R. Vetukuri
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
| | - Sandeep K. Kushwaha
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
- National Institute of Animal BiotechnologyHyderabadIndia
| | - Pete E. Hedley
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Jenny Morris
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Lydia R. J. Welsh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Paul R. J. Birch
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
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22
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Zhou Y, Yang K, Cheng M, Cheng Y, Li Y, Ai G, Bai T, Xu R, Duan W, Peng H, Li X, Xia A, Wang Y, Jing M, Dou D, Dickman MB. Double-faced role of Bcl-2-associated athanogene 7 in plant-Phytophthora interaction. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5751-5765. [PMID: 34195821 DOI: 10.1093/jxb/erab252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Due to their sessile nature, plants must respond to various environmental assaults in a coordinated manner. The endoplasmic reticulum is a central hub for plant responses to various stresses. We previously showed that Phytophthora utilizes effector PsAvh262-mediated binding immunoglobulin protein (BiP) accumulation for suppressing endoplasmic reticulum stress-triggered cell death. As a BiP binding partner, Bcl-2-associated athanogene 7 (BAG7) plays a crucial role in the maintenance of the unfolded protein response, but little is known about its role in plant immunity. In this work, we reveal a double-faced role of BAG7 in Arabidopsis-Phytophthora interaction in which it regulates endoplasmic reticulum stress-mediated immunity oppositely in different cellular compartments. In detail, it acts as a susceptibility factor in the endoplasmic reticulum, but plays a resistance role in the nucleus against Phytophthora. Phytophthora infection triggers the endoplasmic reticulum-to-nucleus translocation of BAG7, the same as abiotic heat stress; however, this process can be prevented by PsAvh262-mediated BiP accumulation. Moreover, the immunoglobulin/albumin-binding domain in PsAvh262 is essential for both pathogen virulence and BiP accumulation. Taken together, our study uncovers a double-faced role of BAG7; Phytophthora advances its colonization in planta by utilizing an effector to detain BAG7 in the endoplasmic reticulum.
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Affiliation(s)
- Yang Zhou
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kun Yang
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Cheng
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Cheng
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yurong Li
- Corteva Agriscience, Johnston, IA 50131, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Gan Ai
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tian Bai
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruofei Xu
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Duan
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Xiaobo Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangdong, Guangzhou 510640, China
| | - Ai Xia
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Maofeng Jing
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Daolong Dou
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Marty B Dickman
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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23
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Mhlongo MI, Piater LA, Steenkamp PA, Labuschagne N, Dubery IA. Metabolomic Evaluation of Tissue-Specific Defense Responses in Tomato Plants Modulated by PGPR-Priming against Phytophthora capsici Infection. PLANTS 2021; 10:plants10081530. [PMID: 34451575 PMCID: PMC8400099 DOI: 10.3390/plants10081530] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the induction of an enhanced state of defense readiness. Here, untargeted ultra-high performance liquid chromatography–mass spectrometry (UHPLC–MS) and targeted ultra-high performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC–QqQ-MS) were used to investigate metabolic reprogramming in tomato plant tissues in response to priming by Pseudomonas fluorescens N04 and Paenibacillus alvei T22 against Phytophthora capsici. Roots were treated with the two PGPR strains prior to stem inoculation with Ph. capsici. Metabolites were methanol-extracted from roots, stems and leaves at two–eight days post-inoculation. Targeted analysis by UHPLC–QqQ-MS allowed quantification of aromatic amino acids and phytohormones. For untargeted analysis, UHPLC–MS data were chemometrically processed to determine signatory biomarkers related to priming against Ph. capsici. The aromatic amino acid content was differentially reprogrammed in Ps. fluorescens and Pa. alvei primed plants responding to Ph. capsici. Furthermore, abscisic acid and methyl salicylic acid were found to be major signaling molecules in the tripartite interaction. LC–MS metabolomics analysis showed time-dependent metabolic changes in the primed-unchallenged vs. primed-challenged tissues. The annotated metabolites included phenylpropanoids, benzoic acids, glycoalkaloids, flavonoids, amino acids, organic acids, as well as oxygenated fatty acids. Tissue-specific reprogramming across diverse metabolic networks in roots, stems and leaves was also observed, which demonstrated that PGPR priming resulted in modulation of the defense response to Ph. capsici infection.
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Affiliation(s)
- Msizi I. Mhlongo
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa; (M.I.M.); (L.A.P.); (P.A.S.)
| | - Lizelle A. Piater
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa; (M.I.M.); (L.A.P.); (P.A.S.)
| | - Paul A. Steenkamp
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa; (M.I.M.); (L.A.P.); (P.A.S.)
| | - Nico Labuschagne
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa;
| | - Ian A. Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa; (M.I.M.); (L.A.P.); (P.A.S.)
- Correspondence: ; Tel.: +27-11-559-2401
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24
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Thomazella DPDT, Seong K, Mackelprang R, Dahlbeck D, Geng Y, Gill US, Qi T, Pham J, Giuseppe P, Lee CY, Ortega A, Cho MJ, Hutton SF, Staskawicz B. Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. Proc Natl Acad Sci U S A 2021; 118:e2026152118. [PMID: 34215692 PMCID: PMC8271637 DOI: 10.1073/pnas.2026152118] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Plant diseases are among the major causes of crop yield losses around the world. To confer disease resistance, conventional breeding relies on the deployment of single resistance (R) genes. However, this strategy has been easily overcome by constantly evolving pathogens. Disabling susceptibility (S) genes is a promising alternative to R genes in breeding programs, as it usually offers durable and broad-spectrum disease resistance. In Arabidopsis, the S gene DMR6 (AtDMR6) encodes an enzyme identified as a susceptibility factor to bacterial and oomycete pathogens. Here, we present a model-to-crop translational work in which we characterize two AtDMR6 orthologs in tomato, SlDMR6-1 and SlDMR6-2. We show that SlDMR6-1, but not SlDMR6-2, is up-regulated by pathogen infection. In agreement, Sldmr6-1 mutants display enhanced resistance against different classes of pathogens, such as bacteria, oomycete, and fungi. Notably, disease resistance correlates with increased salicylic acid (SA) levels and transcriptional activation of immune responses. Furthermore, we demonstrate that SlDMR6-1 and SlDMR6-2 display SA-5 hydroxylase activity, thus contributing to the elucidation of the enzymatic function of DMR6. We then propose that SlDMR6 duplication in tomato resulted in subsequent subfunctionalization, in which SlDMR6-2 specialized in balancing SA levels in flowers/fruits, while SlDMR6-1 conserved the ability to fine-tune SA levels during pathogen infection of the plant vegetative tissues. Overall, this work not only corroborates a mechanism underlying SA homeostasis in plants, but also presents a promising strategy for engineering broad-spectrum and durable disease resistance in crops.
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Affiliation(s)
- Daniela Paula de Toledo Thomazella
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Rebecca Mackelprang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Douglas Dahlbeck
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Yu Geng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Upinder S Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Tiancong Qi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Julie Pham
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Priscila Giuseppe
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas SP 13083-100, Brazil
| | - Clara Youngna Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Arturo Ortega
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Samuel F Hutton
- Horticultural Sciences Department, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
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25
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Thomazella DPDT, Seong K, Mackelprang R, Dahlbeck D, Geng Y, Gill US, Qi T, Pham J, Giuseppe P, Lee CY, Ortega A, Cho MJ, Hutton SF, Staskawicz B. Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. Proc Natl Acad Sci U S A 2021; 118:2026152118. [PMID: 34215692 DOI: 10.1101/064824] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Plant diseases are among the major causes of crop yield losses around the world. To confer disease resistance, conventional breeding relies on the deployment of single resistance (R) genes. However, this strategy has been easily overcome by constantly evolving pathogens. Disabling susceptibility (S) genes is a promising alternative to R genes in breeding programs, as it usually offers durable and broad-spectrum disease resistance. In Arabidopsis, the S gene DMR6 (AtDMR6) encodes an enzyme identified as a susceptibility factor to bacterial and oomycete pathogens. Here, we present a model-to-crop translational work in which we characterize two AtDMR6 orthologs in tomato, SlDMR6-1 and SlDMR6-2. We show that SlDMR6-1, but not SlDMR6-2, is up-regulated by pathogen infection. In agreement, Sldmr6-1 mutants display enhanced resistance against different classes of pathogens, such as bacteria, oomycete, and fungi. Notably, disease resistance correlates with increased salicylic acid (SA) levels and transcriptional activation of immune responses. Furthermore, we demonstrate that SlDMR6-1 and SlDMR6-2 display SA-5 hydroxylase activity, thus contributing to the elucidation of the enzymatic function of DMR6. We then propose that SlDMR6 duplication in tomato resulted in subsequent subfunctionalization, in which SlDMR6-2 specialized in balancing SA levels in flowers/fruits, while SlDMR6-1 conserved the ability to fine-tune SA levels during pathogen infection of the plant vegetative tissues. Overall, this work not only corroborates a mechanism underlying SA homeostasis in plants, but also presents a promising strategy for engineering broad-spectrum and durable disease resistance in crops.
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Affiliation(s)
- Daniela Paula de Toledo Thomazella
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Rebecca Mackelprang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Douglas Dahlbeck
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Yu Geng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Upinder S Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Tiancong Qi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Julie Pham
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Priscila Giuseppe
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas SP 13083-100, Brazil
| | - Clara Youngna Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Arturo Ortega
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
| | - Samuel F Hutton
- Horticultural Sciences Department, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Innovative Genomics Institute, University of California, Berkeley, CA 94704
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26
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de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
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27
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Stam R, Motion GB, Martinez-Heredia V, Boevink PC, Huitema E. A Conserved Oomycete CRN Effector Targets Tomato TCP14-2 to Enhance Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:309-318. [PMID: 33258418 DOI: 10.1094/mpmi-06-20-0172-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora spp. secrete vast arrays of effector molecules during infection to aid in host colonization. The crinkling and necrosis (CRN) protein family forms an extensive repertoire of candidate effectors that accumulate in the host nucleus to perturb processes required for immunity. Here, we show that CRN12_997 from Phytophthora capsici binds a TCP transcription factor, SlTCP14-2, to inhibit its immunity-associated activity against Phytophthora spp. Coimmunoprecipitation and bimolecular fluorescence complementation studies confirm a specific CRN12_997-SlTCP14-2 interaction in vivo. Coexpression of CRN12_997 specifically counteracts the TCP14-enhanced immunity phenotype, suggesting that CRN mediated perturbation of SlTCP14-2 function. We show that SlTCP14-2 associates with nuclear chromatin and that CRN12_997 diminishes SlTCP14-2 DNA binding. Collectively, our data support a model in which SlTCP14-2 associates with chromatin to enhance immunity. The interaction between CRN12_997 and SlTCP14-2 reduces DNA binding of the immune regulator. We propose that the modulation of SlTCP14-2 chromatin affinity, caused by CRN12-997, enhances susceptibility to P. capsici.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Graham B Motion
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Victor Martinez-Heredia
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Edgar Huitema
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
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28
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Fernandes P, Machado H, Silva MDC, Costa RL. A Histopathological Study Reveals New Insights Into Responses of Chestnut ( Castanea spp.) to Root Infection by Phytophthora cinnamomi. PHYTOPATHOLOGY 2021; 111:345-355. [PMID: 32755337 DOI: 10.1094/phyto-04-20-0115-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The European chestnut (Castanea sativa) is threatened by the hemibiotrophic oomycete Phytophthora cinnamomi, the causal agent of ink disease. Chestnut species have different susceptibility levels to P. cinnamomi, with the Asian species (C. crenata; C. mollissima) exhibiting the highest level of resistance. A histological approach was used to study the responses exhibited by susceptible and resistant chestnut genotypes by characterizing the early stages of P. cinnamomi infection and the cellular responses it induces in roots. C. sativa (susceptible) and C. crenata (resistant) plantlets were inoculated with a P. cinnamomi virulent isolate with a zoospore suspension or by direct contact with mycelia agar pieces. Root samples were collected at 0.5, 3.5, 24, 48, and 72 h after inoculation (hai) for microscopic observations. Penetration was observed in both species at 0.5 and 3.5 hai with mycelium and zoospore inoculations, respectively. In both inoculation methods, following penetration into the rhizodermis, P. cinnamomi hyphae grew inter- and intracellularly through the cortex and into the vascular cylinder. C. crenata cells displayed a delay in the pattern of infection by having fewer cell layers colonized compared with C. sativa. At 72 hai, the collapse of the first layers of C. sativa cortical cells was observed, indicating the beginning of necrotrophy. C. crenata was able to respond more efficiently to P. cinnamomi than C. sativa by restricting the pathogen's growth area through the early activation of resistance responses such as callose deposition around some intracellular hyphae, hypersensitive response-like cell death, cell wall thickening, and accumulation of phenolic-like compounds.
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Affiliation(s)
- Patrícia Fernandes
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Quinta do Marquês, Oeiras 2780-157, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (Green-it Unit), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Machado
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Quinta do Marquês, Oeiras 2780-157, Portugal
| | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras 2784-505, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa 1349-017, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Quinta do Marquês, Oeiras 2780-157, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa 1349-017, Portugal
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29
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Concurrent Metabolic Profiling and Quantification of Aromatic Amino Acids and Phytohormones in Solanum lycopersicum Plants Responding to Phytophthora capsici. Metabolites 2020; 10:metabo10110466. [PMID: 33207638 PMCID: PMC7696014 DOI: 10.3390/metabo10110466] [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: 10/09/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/05/2023] Open
Abstract
Pathogenic microorganisms account for large production losses in the agricultural sector. Phytophthora capsici is an oomycete that causes blight and fruit rot in important crops, especially those in the Solanaceae family. P. capsici infection is difficult to control due to genetic diversity, arising from sexual reproduction, and resistant spores that remain dormant in soil. In this study, the metabolomics of tomato plants responding to infection by P. capsici were investigated. Non-targeted metabolomics, based on liquid chromatography coupled to mass spectrometry (LC-MS), were used with multivariate data analyses to investigate time-dependent metabolic reprogramming in the roots, stems, and leaves of stem-infected plants, over an 8 day period. In addition, phytohormones and amino acids were determined using quantitative LC-MS. Methyl salicylate and 1-aminocyclopropane-1-carboxylate were detected as major signalling molecules in the defensive response to P. capsici. As aromatic amino acid precursors of secondary metabolic pathways, both phenylalanine and tryptophan showed a continuous increase over time in all tissues, whereas tyrosine peaked at day 4. Non-targeted metabolomic analysis revealed phenylpropanoids, benzoic acids, glycoalkaloids, flavonoids, amino acids, organic acids, and fatty acids as the major classes of reprogrammed metabolites. Correlation analysis showed that metabolites derived from the same pathway, or synthesised by different pathways, could either have a positive or negative correlation. Furthermore, roots, stems, and leaves showed contrasting time-dependent metabolic reprogramming, possibly related to the biotrophic vs. necrotrophic life-stages of the pathogen, and overlapping biotic and abiotic stress signaling. As such, the targeted and untargeted approaches complemented each other, to provide a detailed view of key time-dependent metabolic changes, occurring in both the asymptomatic and symptomatic stages of infection.
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Boevink PC, Birch PRJ, Turnbull D, Whisson SC. Devastating intimacy: the cell biology of plant-Phytophthora interactions. THE NEW PHYTOLOGIST 2020; 228:445-458. [PMID: 32394464 PMCID: PMC7540312 DOI: 10.1111/nph.16650] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/15/2020] [Indexed: 05/07/2023]
Abstract
An understanding of the cell biology underlying the burgeoning molecular genetic and genomic knowledge of oomycete pathogenicity is essential to gain the full context of how these pathogens cause disease on plants. An intense research focus on secreted Phytophthora effector proteins, especially those containing a conserved N-terminal RXLR motif, has meant that most cell biological studies into Phytophthora diseases have focussed on the effectors and their host target proteins. While these effector studies have provided novel insights into effector secretion and host defence mechanisms, there remain many unanswered questions about fundamental processes involved in spore biology, host penetration and haustorium formation and function.
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Affiliation(s)
- Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Dionne Turnbull
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Stephen C. Whisson
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
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Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit. BMC Genomics 2020; 21:628. [PMID: 32917129 PMCID: PMC7488727 DOI: 10.1186/s12864-020-07040-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/31/2020] [Indexed: 11/10/2022] Open
Abstract
Background Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms are largely uncharacterized. In cucumber, rapidly growing fruit are highly susceptible to Phytophthora capsici but become resistant as they complete exponential growth. We previously demonstrated that ARR is associated with the fruit peel and identified gene expression and metabolomic changes potentially functioning as preformed defenses. Results Here, we compare the response to infection in fruit at resistant and susceptible ages using microscopy, quantitative bioassays, and weighted gene co-expression analyses. We observed strong transcriptional changes unique to resistant aged fruit 2–4 h post inoculation (hpi). Microscopy and bioassays confirmed this early response, with evidence of pathogen death and infection failure as early as 4 hpi and cessation of pathogen growth by 8–10 hpi. Expression analyses identified candidate genes involved in conferring the rapid response including those encoding transcription factors, hormone signaling pathways, and defenses such as reactive oxygen species metabolism and phenylpropanoid biosynthesis. Conclusion The early pathogen death and rapid defense response in resistant-aged fruit provide insight into potential mechanisms for ARR, implicating both pre-formed biochemical defenses and developmentally regulated capacity for pathogen recognition as key factors shaping age-related resistance.
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Cheng W, Jiang Y, Peng J, Guo J, Lin M, Jin C, Huang J, Tang W, Guan D, He S. The transcriptional reprograming and functional identification of WRKY family members in pepper's response to Phytophthora capsici infection. BMC PLANT BIOLOGY 2020; 20:256. [PMID: 32493221 PMCID: PMC7271409 DOI: 10.1186/s12870-020-02464-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plant transcription factors (TFs) are key transcriptional regulators to manipulate the regulatory network of host immunity. However, the globally transcriptional reprogramming of plant TF families in response to pathogens, especially between the resistant and susceptible host plants, remains largely unknown. RESULTS Here, we performed time-series RNA-seq from a resistant pepper line CM334 and a susceptible pepper line EC01 upon challenged with Phytophthora capsici, and enrichment analysis indicated that WRKY family most significantly enriched in both CM334 and EC01. Interestingly, we found that nearly half of the WRKY family members were significantly up-regulated, whereas none of them were down-regulated in the two lines. These induced WRKY genes were greatly overlapped between CM334 and EC01. More strikingly, most of these induced WRKY genes were expressed in time-order patterns, and could be mainly divided into three subgroups: early response (3 h-up), mid response (24 h-up) and mid-late response (ML-up) genes. Moreover, it was found that the responses of these ML-up genes were several hours delayed in EC01. Furthermore, a total of 19 induced WRKY genes were selected for functional identification by virus-induced gene silencing. The result revealed that silencing of CaWRKY03-6, CaWRKY03-7, CaWRKY06-5 or CaWRKY10-4 significantly increase the susceptibility to P. capsici both in CM334 and EC01, indicating that they might contribute to pepper's basal defense against P. capsici; while silencing of CaWRKY08-4 and CaWRKY01-10 significantly impaired the disease resistance in CM334 but not in EC01, suggesting that these two WRKY genes are prominent modulators specifically in the resistant pepper plants. CONCLUSIONS These results considerably extend our understanding of WRKY gene family in pepper's resistance against P. capsici and provide potential applications for genetic improvement against phytophthora blight.
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Affiliation(s)
- Wei Cheng
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Jiang
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiangtao Peng
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jianwen Guo
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Menglan Lin
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chengting Jin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jinfeng Huang
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weiqi Tang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Deyi Guan
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shuilin He
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Escudero-Martinez C, Rodriguez PA, Liu S, Santos PA, Stephens J, Bos JIB. An aphid effector promotes barley susceptibility through suppression of defence gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2796-2807. [PMID: 31989174 PMCID: PMC7210766 DOI: 10.1093/jxb/eraa043] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/27/2020] [Indexed: 05/21/2023]
Abstract
Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While 'omics' approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extend efforts to characterize aphid effectors with regard to their role in promoting susceptibility to the R. padi-barley interaction. We selected three R. padi effectors based on sequence similarity to previously characterized Myzus persicae effectors and assessed their subcellular localization, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating that this effector enhances susceptibility by suppressing plant defences in barley. Our data suggest that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.
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Affiliation(s)
- Carmen Escudero-Martinez
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | - Patricia A Rodriguez
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
- Helmholtz Zentrum München, Institute of Network Biology (INET), Munich, Germany
| | - Shan Liu
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pablo A Santos
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Jorunn I B Bos
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
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Abstract
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland.
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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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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Evangelisti E, Yunusov T, Shenhav L, Schornack S. N-acetyltransferase AAC(3)-I confers gentamicin resistance to Phytophthora palmivora and Phytophthora infestans. BMC Microbiol 2019; 19:265. [PMID: 31775609 PMCID: PMC6882347 DOI: 10.1186/s12866-019-1642-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
Background Oomycetes are pathogens of mammals, fish, insects and plants, and the potato late blight agent Phytophthora infestans and the oil palm and cocoa infecting pathogen Phytophthora palmivora cause economically impacting diseases on a wide range of crop plants. Increasing genomic and transcriptomic resources and recent advances in oomycete biology demand new strategies for genetic modification of oomycetes. Most oomycete transformation procedures rely on geneticin-based selection of transgenic strains. Results We established N-acetyltransferase AAC(3)-I as a gentamicin-based selectable marker for oomycete transformation without interference with existing geneticin resistance. Strains carrying gentamicin resistance are fully infectious in plants. We further demonstrate the usefulness of this new antibiotic selection to super-transform well-characterized, already fluorescently-labelled P. palmivora strains and provide a comprehensive protocol for maintenance and zoospore electro-transformation of Phytophthora strains to aid in plant-pathogen research. Conclusions N-acetyltransferase AAC(3)-I is functional in Phytophthora oomycetes. In addition, the substrate specificity of the AAC(3)-I enzyme allows for re-transformation of geneticin-resistant strains. Our findings and resources widen the possibilities to study oomycete cell biology and plant-oomycete interactions.
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Affiliation(s)
| | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Liron Shenhav
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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39
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Balint‐Kurti P. The plant hypersensitive response: concepts, control and consequences. MOLECULAR PLANT PATHOLOGY 2019; 20:1163-1178. [PMID: 31305008 PMCID: PMC6640183 DOI: 10.1111/mpp.12821] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The hypersensitive defence response is found in all higher plants and is characterized by a rapid cell death at the point of pathogen ingress. It is usually associated with pathogen resistance, though, in specific situations, it may have other consequences such as pathogen susceptibility, growth retardation and, over evolutionary timescales, speciation. Due to the potentially severe costs of inappropriate activation, plants employ multiple mechanisms to suppress inappropriate activation of HR and to constrain it after activation. The ubiquity of this response among higher plants despite its costs suggests that it is an extremely effective component of the plant immune system.
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Affiliation(s)
- Peter Balint‐Kurti
- Plant Science Research UnitUSDA‐ARSRaleighNCUSA
- Department of Entomology and Plant PathologyNC State UniversityRaleighNC27695‐7613USA
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40
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Galeano Garcia P, Zimmermann BH, Carazzone C. Hydrophilic Interaction Liquid Chromatography Coupled to Mass Spectrometry and Multivariate Analysis of the De Novo Pyrimidine Pathway Metabolites. Biomolecules 2019; 9:biom9080328. [PMID: 31370321 PMCID: PMC6722987 DOI: 10.3390/biom9080328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
In this study, we describe the optimization of a Hydrophilic Interaction Liquid Chromatography coupled to mass spectrometry (HILIC-MS) method for the evaluation of 14 metabolites related to the de novo synthesis of pyrimidines (dnSP) while using multivariate analysis, which is the metabolic pathway for pyrimidine nucleotide production. A multivariate design was used to set the conditions of the column temperature, flow of the mobile phase, additive concentration, gradient rate, and pH of the mobile phase in order to attain higher peak resolution and ionization efficiency in shorter analysis times. The optimization process was carried out while using factorial fractional designs, Box–Behnken design and central composite design while using two zwitterionic columns, ZIC-p-HILIC and ZIC-HILIC, polymeric, and silica-based columns, respectively. The factors were evaluated while using resolution (R), retention factor (k), efficiency of the column (N), and peak height (h) as the response variables. The best optimized conditions were found with the ZIC-p-HILIC column: elution gradient rate 2 min, pH 7.0, temperature 45 °C, mobile phase flow of 0.35 mL min−1, and additive (ammonium acetate) concentration of 6 mM. The total analysis time was 28 min. The ZIC-p-HILIC LC-MS method yielded satisfactory results for linearity of calibration curves, limit of detection (LOD), and limit of quantification (LOQ). The method has been shown to be appropriate for the analysis of dnSP on samples of tomato plants that were infected with Phytophthora infestans.
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Affiliation(s)
- Paula Galeano Garcia
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
- "Grupo de Investigación en Productos Naturales Amazónicos", Facultad de Ciencias Básicas, Universidad de la Amazonia, Florencia 180002, Colombia.
| | - Barbara H Zimmermann
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 111711, Colombia
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
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Li Q, Ai G, Shen D, Zou F, Wang J, Bai T, Chen Y, Li S, Zhang M, Jing M, Dou D. A Phytophthora capsici Effector Targets ACD11 Binding Partners that Regulate ROS-Mediated Defense Response in Arabidopsis. MOLECULAR PLANT 2019; 12:565-581. [PMID: 30703564 DOI: 10.1016/j.molp.2019.01.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 01/20/2019] [Accepted: 01/20/2019] [Indexed: 05/24/2023]
Abstract
Reactive oxygen species (ROS) play a vital role in plant immune response, but the genes involved in the regulation of ROS are scantily reported. Phytophthora pathogens produce a large number of effectors to promote infection, but the modes of action adopted are largely unknown. Here, we report that RxLR207 could activate ROS-mediated cell death in Nicotiana benthamiana and was essential for virulence of P. capsici. We found that this effector targeted BPA1 (binding partner of ACD11) and four members of BPLs (BPA1-Like proteins) in Arabidopsis, and the bpa1 and bpl mutants had enhanced ROS accumulation and cell death under biotic or abiotic stresses. Furthermore, we showed that BPA1 and several BPLs functioned redundantly in plant immunity to P. capsici. We discovered that BPA1 and all six BPLs interacted with ACD11, and stabilization of ACD11 was impaired in the bpa1, bpl2, bpl3, and bpl4 mutants. RxLR207 could promote the degradation of BPA1, BPL1, BPL2, and BPL4 to disrupt ACD11 stabilization in a 26S proteasome-dependent manner. Taken together, these findings indicate the important roles of Arabidopsis BPA1 and its homologs in ROS homeostasis and defense response, highlighting the usefulness of a pathogen effector-directed approach as a promising strategy for the discovery of novel plant immune regulators.
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Affiliation(s)
- Qi Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Gan Ai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fen Zou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ji Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Bai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanyu Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shutian Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
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Thilliez GJA, Armstrong MR, Lim T, Baker K, Jouet A, Ward B, van Oosterhout C, Jones JDG, Huitema E, Birch PRJ, Hein I. Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. THE NEW PHYTOLOGIST 2019; 221:1634-1648. [PMID: 30288743 PMCID: PMC6492278 DOI: 10.1111/nph.15441] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 05/11/2023]
Abstract
The oomycete pathogens Phytophthora infestans and P. capsici cause significant crop losses world-wide, threatening food security. In each case, pathogenicity factors, called RXLR effectors, contribute to virulence. Some RXLRs are perceived by resistance proteins to trigger host immunity, but our understanding of the demographic processes and adaptive evolution of pathogen virulence remains poor. Here, we describe PenSeq, a highly efficient enrichment sequencing approach for genes encoding pathogenicity determinants which, as shown for the infamous potato blight pathogen Phytophthora infestans, make up < 1% of the entire genome. PenSeq facilitates the characterization of allelic diversity in pathogen effectors, enabling evolutionary and population genomic analyses of Phytophthora species. Furthermore, PenSeq enables the massively parallel identification of presence/absence variations and sequence polymorphisms in key pathogen genes, which is a prerequisite for the efficient deployment of host resistance genes. PenSeq represents a cost-effective alternative to whole-genome sequencing and addresses crucial limitations of current plant pathogen population studies, which are often based on selectively neutral markers and consequently have limited utility in the analysis of adaptive evolution. The approach can be adapted to diverse microbes and pathogens.
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Affiliation(s)
- Gaetan J. A. Thilliez
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Miles R. Armstrong
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
| | - Tze‐Yin Lim
- Information and Computational SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Katie Baker
- Information and Computational SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Agathe Jouet
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7GJUK
| | - Ben Ward
- The Earlham InstituteNorwich Research ParkNorwichNR4 7UHUK
| | | | | | - Edgar Huitema
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Ingo Hein
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
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43
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Microarrays for High-Throughput Gene Expression Analysis of Barley. Methods Mol Biol 2018. [PMID: 30460566 DOI: 10.1007/978-1-4939-8944-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Microarrays remain an extremely robust and cost-efficient technology for transcriptome analysis. A custom Agilent microarray has been designed from the predicted gene transcripts of the barley genome reference. Here, we describe total RNA extraction, fluorescent labeling, hybridization, and image analysis of barley arrays. Quality control measures are detailed, along with recommendations for downstream data analysis.
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44
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Armitage AD, Lysøe E, Nellist CF, Lewis LA, Cano LM, Harrison RJ, Brurberg MB. Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLoS One 2018; 13:e0202305. [PMID: 30278048 PMCID: PMC6168125 DOI: 10.1371/journal.pone.0202305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.
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Affiliation(s)
| | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
| | | | | | - Liliana M. Cano
- University of Florida, UF/IFAS Indian River Research and Education Center, Fort Pierce, Florida, United States of America
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - May B. Brurberg
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
- Norwegian University of Life Sciences (NMBU), Department of Plant Sciences, Ås, Norway
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45
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Langner T, Kamoun S, Belhaj K. CRISPR Crops: Plant Genome Editing Toward Disease Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:479-512. [PMID: 29975607 DOI: 10.1146/annurev-phyto-080417-050158] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.
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Affiliation(s)
- Thorsten Langner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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46
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Global gene expression profiling for fruit organs and pathogen infections in the pepper, Capsicum annuum L. Sci Data 2018; 5:180103. [PMID: 29870035 PMCID: PMC5987667 DOI: 10.1038/sdata.2018.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023] Open
Abstract
Hot pepper (Capsicum annuum) is one of the most consumed vegetable crops in the world and useful to human as it has many nutritional and medicinal values. Genomic resources of pepper are publically available since the pepper genomes have been completed and massive data such as transcriptomes have been deposited. Nevertheless, global transcriptome profiling is needed to identify molecular mechanisms related to agronomic traits in pepper, but limited analyses are published. Here, we report the comprehensive analysis of pepper transcriptomes during fruit ripening and pathogen infection. For the ripening, transcriptome data were obtained from placenta and pericarp at seven developmental stages. To reveal global transcriptomic landscapes during infection, leaves at six time points post-infection by one of three pathogens (Phytophthora infestans, Pepper mottle virus, and Tobacco mosaic virus P0 strain) were profiled. The massive parallel transcriptome profiling in this study will serve as a valuable resource for detection of molecular networks of fruit development and disease resistance in Capsicum annuum.
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47
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Pham J, Stam R, Heredia VM, Csukai M, Huitema E. An NMRA-Like Protein Regulates Gene Expression in Phytophthora capsici to Drive the Infection Cycle on Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:665-677. [PMID: 29419371 DOI: 10.1094/mpmi-07-17-0193-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phytophthora spp. cause devastating disease epidemics on important crop plants and pose a grave threat to global crop production. Critically, Phytophthora pathogens represent a distinct evolutionary lineage in which pathogenicity has been acquired independently. Therefore, there is an urgent need to understand and disrupt the processes that drive infection if we aspire to defeat oomycete pathogens in the field. One area that has received little attention thus far in this respect is the regulation of Phytophthora gene expression during infection. Here, we characterize PcNMRAL1 (Phyca11_505845), a homolog of the Aspergillus nidulans nitrogen metabolite repression regulator NMRA and demonstrate a role for this protein in progression of the Phytophthora capsici infection cycle. PcNmrAL1 is coexpressed with the biotrophic marker gene PcHmp1 (haustorial membrane protein 1) and, when overexpressed, extends the biotrophic infection stage. Microarray analyses revealed that PcNmrAL1 overexpression in P. capsici leads to large-scale transcriptional changes during infection and in vitro. Importantly, detailed analysis reveals that PcNmrAL1 overexpression induces biotrophy-associated genes while repressing those associated with necrotrophy. In addition to factors controlling transcription, translation, and nitrogen metabolism, PcNMRAL1 helps regulate the expression of a considerable effector repertoire in P. capsici. Our data suggests that PcNMRAL1 is a transcriptional regulator that mediates the biotrophy to necrotrophy transition. PcNMRAL1 represents a novel factor that may drive the Phytophthora disease cycle on crops. This study provides the first insight into mechanisms that regulate infection-related processes in Phytophthora spp. and provides a platform for further studies aimed at disabling pathogenesis and preventing crop losses.
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Affiliation(s)
- Jasmine Pham
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Remco Stam
- 3 School for Life Sciences, Weihenstephan Technische Universität München, Freising, Germany; and
| | | | - Michael Csukai
- 4 Syngenta, Jealott's Hill International Research Centre, Bracknell, U.K
| | - Edgar Huitema
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
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48
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Carella P, Gogleva A, Tomaselli M, Alfs C, Schornack S. Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage. Proc Natl Acad Sci U S A 2018; 115:E3846-E3855. [PMID: 29615512 DOI: 10.1101/188912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
The expansion of plants onto land was a formative event that brought forth profound changes to the earth's geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora.
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Affiliation(s)
- Philip Carella
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Anna Gogleva
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Marta Tomaselli
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Carolin Alfs
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
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49
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Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage. Proc Natl Acad Sci U S A 2018; 115:E3846-E3855. [PMID: 29615512 PMCID: PMC5910834 DOI: 10.1073/pnas.1717900115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the importance of liverworts as the earliest diverging land plant lineage to support fungal symbiosis, it is unknown whether filamentous pathogens can establish intracellular interactions within living cells of these nonvascular plants. Here, we demonstrate that an oomycete pathogen invades Marchantia polymorpha and related liverworts to form intracellular infection structures inside cells of the photosynthetic layer. Plants lacking this tissue layer display enhanced resistance to infection, revealing an architectural susceptibility factor in complex thalloid liverworts. Moreover, we show that dedicated host cellular trafficking proteins are recruited to pathogen interfaces within liverwort cells, supporting the idea that intracellular responses to microbial invasion originated in nonvascular plants. The expansion of plants onto land was a formative event that brought forth profound changes to the earth’s geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora.
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50
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Lanver D, Müller AN, Happel P, Schweizer G, Haas FB, Franitza M, Pellegrin C, Reissmann S, Altmüller J, Rensing SA, Kahmann R. The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis. THE PLANT CELL 2018; 30:300-323. [PMID: 29371439 PMCID: PMC5868686 DOI: 10.1105/tpc.17.00764] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/20/2017] [Accepted: 01/24/2018] [Indexed: 05/19/2023]
Abstract
The maize smut fungus Ustilago maydis is a model organism for elucidating host colonization strategies of biotrophic fungi. Here, we performed an in depth transcriptional profiling of the entire plant-associated development of U. maydis wild-type strains. In our analysis, we focused on fungal metabolism, nutritional strategies, secreted effectors, and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy, and induction of tumors. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen assimilation are important virulence factors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules. While known components of the b-mating type cascade emerged as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role for leaf tumor formation and effector gene expression for one of these transcription factors.
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Affiliation(s)
- Daniel Lanver
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - André N Müller
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Petra Happel
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Gabriel Schweizer
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Fabian B Haas
- Philipps Universität Marburg, Fb17 Biologie, AG Zellbiologie der Pflanzen, 35043 Marburg, Germany
| | - Marek Franitza
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Clément Pellegrin
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Stefan A Rensing
- Philipps Universität Marburg, Fb17 Biologie, AG Zellbiologie der Pflanzen, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Regine Kahmann
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
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