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Balesdent MH, Laval V, Noah JM, Bagot P, Mousseau A, Rouxel T. Large-scale population survey of Leptosphaeria maculans in France highlights both on-going breakdowns and potentially effective resistance genes in oilseed rape. Pest Manag Sci 2024; 80:2426-2434. [PMID: 36750403 DOI: 10.1002/ps.7401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/03/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Leptosphaeria maculans, the cause of stem canker of oilseed rape, develops gene-for-gene interactions with its host and shows a high evolutionary potential to 'break down' novel resistance genes (R, Rlm) deployed in cultivars over large areas. For optimal management of R genes, updated knowledge of the population structure of the pathogen is needed. In France, large-scale surveys have been done at 10-year intervals since 2000. Here we report the characterization of a large L. maculans population collected in France in 2019-2020. RESULTS A total of 844 isolates were collected from 11 sites in ten French departments and were phenotyped for their virulence against nine Brassica napus R genes. All isolates were virulent toward Rlm2 and Rlm9. Very few isolates were avirulent on Rlm1 (1.8%) and Rlm4 (0.6%). Avirulent isolates toward Rlm7 ('AvrLm7') varied from 67% to 11.3%, depending on the site sampled, illustrating the ongoing breakdown of Rlm7. The decrease of AvrLm7 isolates (29.2% at the national level) compared to the 2010 survey (96.5%) was accompanied by an increase of avirulent isolates on Rlm3 (0% in 2010; 54% in 2019-2020). However, virulent isolates on both Rlm3 and Rlm7, previously rarely detected, were found in all sites with a frequency of 17.3%. Finally, most or all isolates were avirulent on Rlm11 (96.1%), LepR2 (RlmS, 99.8%), and Rlm6 (100%), suggesting these three genes still effectively control the disease. CONCLUSION These data will help guide strategies for breeding and deploying resistant oilseed rape varieties against L. maculans in France. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, UR Bioger, 22, Place de l'Agronomie, Palaiseau, 91120, France
| | - Valérie Laval
- Université Paris-Saclay, INRAE, UR Bioger, 22, Place de l'Agronomie, Palaiseau, 91120, France
| | - Julie Marie Noah
- Université Paris-Saclay, INRAE, UR Bioger, 22, Place de l'Agronomie, Palaiseau, 91120, France
| | - Patrick Bagot
- GEVES, Domaine de l'Anjouère, La Pouëze, 49370, Erdre en Anjou, France
| | - Arnaud Mousseau
- GEVES, Domaine de l'Anjouère, La Pouëze, 49370, Erdre en Anjou, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR Bioger, 22, Place de l'Agronomie, Palaiseau, 91120, France
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Clairet C, Gay EJ, Porquier A, Blaise F, Marais CL, Balesdent MH, Rouxel T, Soyer JL, Fudal I. Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-player game. New Phytol 2024; 242:247-261. [PMID: 38358035 DOI: 10.1111/nph.19581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Effector genes, encoding molecules involved in disease establishment, are concertedly expressed throughout the lifecycle of plant-pathogenic fungi. However, little is known about how effector gene expression is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in their regulation was recently investigated, notably establishing that the repressive histone modification H3K9me3, deposited by KMT1, was involved in several fungal species including Leptosphaeria maculans. Nevertheless, previous data suggest that a second regulatory layer, probably involving a specific transcription factor (TF), might be required. In L. maculans, a Dothideomycete causing stem canker of oilseed rape, we identified the ortholog of Pf2, a TF belonging to the Zn2Cys6 fungal-specific family, and described as essential for pathogenicity and effector gene expression. We investigated its role together with KMT1, by inactivating and over-expressing LmPf2 in a wild-type strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis and we found a major effect of LmPf2 on the induction of effector gene expression once KMT1 repression is lifted. Our results show, for the first time, a dual control of effector gene expression.
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Affiliation(s)
- Colin Clairet
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Antoine Porquier
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
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Gay EJ, Jacques N, Lapalu N, Cruaud C, Laval V, Balesdent MH, Rouxel T. Location and timing govern tripartite interactions of fungal phytopathogens and host in the stem canker species complex. BMC Biol 2023; 21:247. [PMID: 37936151 PMCID: PMC10631019 DOI: 10.1186/s12915-023-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Leptosphaeria maculans "brassicae" (Lmb) and Leptosphaeria biglobosa "brassicae" (Lbb) make up a species complex involved in the stem canker (blackleg) disease of rapeseed (Brassica napus). They coinfect rapeseed together, from the early stage of infection on leaves to the final necrotic stage at the stem base, and both perform sexual crossings on plant residues. L. biglobosa is suggested to be a potential biocontrol agent against Lmb, but there has been no mechanistic investigation of the different types of interactions that may occur between the plant and the two fungal species. RESULTS We investigated the bi- or tripartite interaction mechanisms by (i) confronting Lmb and Lbb in culture conditions or during cotyledon infection, with different timing and/or spore concentration regimes, (ii) performing RNA-Seq experiments in vitro or on the kinetics of infection of cotyledons infected by Lmb and/or Lbb to evaluate the transcriptomic activity and the plant response when both fungal species are inoculated together. Lbb infection of B. napus cotyledons was typical of a necrotrophic behavior, with a very early setup of one pathogenicity program and very limited colonization of tissues. This contrasted with the complex succession of pathogenicity programs of the hemibiotroph Lmb. During simultaneous co-infection by both species, Lmb was strongly impacted in its growth and transcriptomic dynamics both in vitro and in planta, while Lbb was unaffected by the presence of Lmb. However, the drastic inhibition of Lmb growth by Lbb was ineffective in the case of delayed inoculation with Lbb or a lower amount of spores of Lbb compared to Lmb. CONCLUSIONS Our data suggest that Lmb growth inhibition by Lbb is the result of a combination of factors that may include competition for trophic resources, the generation by Lbb of an environment unsuitable for the lifecycle of Lmb or/and the effect on Lmb of plant defense responses induced by Lbb. It indicates that growth inhibition occurs in very specific conditions (i.e., co-inoculation at the same place of an equal amount of inoculum) that are unlikely to occur in the field where their coexistence does not prevent any species from completing their life cycle.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Noémie Jacques
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Valerie Laval
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
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Talbi N, Fokkens L, Audran C, Petit‐Houdenot Y, Pouzet C, Blaise F, Gay EJ, Rouxel T, Balesdent M, Rep M, Fudal I. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes. Mol Plant Pathol 2023; 24:914-931. [PMID: 37128172 PMCID: PMC10346447 DOI: 10.1111/mpp.13338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as "cooperating proteins", able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue.
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Affiliation(s)
- Nacera Talbi
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
- Present address:
Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
| | - Corinne Audran
- UMR LIPMEUniversité de Toulouse, INRAE, CNRSCastanet‐TolosanFrance
| | | | - Cécile Pouzet
- FRAIB‐TRI Imaging Platform Facilities, FR AIBUniversité de Toulouse, CNRSCastanet‐TolosanFrance
| | | | - Elise J. Gay
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | | | | | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
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Gautier A, Laval V, Faure S, Rouxel T, Balesdent MH. Polymorphism of Avirulence Genes and Adaptation to Brassica Resistance Genes Is Gene-Dependent in the Phytopathogenic Fungus Leptosphaeria maculans. Phytopathology 2023; 113:1222-1232. [PMID: 36802873 DOI: 10.1094/phyto-12-22-0466-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The fungal phytopathogen Leptosphaeria maculans, which causes stem canker (blackleg) of rapeseed (Brassica napus), is mainly controlled worldwide by genetic resistance, which includes major resistance genes (Rlm). This model is one of those for which the highest number of avirulence genes (AvrLm) has been cloned. In many systems, including the L. maculans-B. napus interaction, intense use of resistance genes exerts strong selection pressure on the corresponding avirulent isolates, and the fungi may rapidly escape resistance through various molecular events which modify the avirulence genes. In the literature, the study of polymorphism at avirulence loci is often focused on single genes under selection pressure. In this study, we investigate allelic polymorphism at 11 avirulence loci in a French population of 89 L. maculans isolates collected on a trap cultivar in four geographic locations in the 2017-2018 cropping season. The corresponding Rlm genes have been (i) used for a long time, (ii) recently used, or (iii) unused in agricultural practice. The sequence data generated indicate an extreme diversity of situations. For example, genes submitted to an ancient selection may have either been deleted in populations (AvrLm1) or replaced by a single-nucleotide mutated virulent version (AvrLm2, AvrLm5-9). Genes that have never been under selection may either be nearly invariant (AvrLm6, AvrLm10A, AvrLm10B), exhibit rare deletions (AvrLm11, AvrLm14), or display a high diversity of alleles and isoforms (AvrLmS-Lep2). These data suggest that the evolutionary trajectory of avirulence/virulence alleles is gene-dependent and independent of selection pressure in L. maculans. [Formula: see text] Copyright © 2023 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)
- Angélique Gautier
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Valérie Laval
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
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Balesdent MH, Gautier A, Plissonneau C, Le Meur L, Loiseau A, Leflon M, Carpezat J, Pinochet X, Rouxel T. Twenty Years of Leptosphaeria maculans Population Survey in France Suggests Pyramiding Rlm3 and Rlm7 in Rapeseed Is a Risky Resistance Management Strategy. Phytopathology 2022; 112:PHYTO04220108R. [PMID: 35621309 DOI: 10.1094/phyto-04-22-0108-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Strategies for plant resistance gene deployment aim to preserve their durability to highly adaptable fungal pathogens. While the pyramiding of resistance genes is often proposed as an effective way to increase their durability, molecular mechanisms by which the pathogen can overcome the resistance also are important aspects to take into account. Here, we report a counterexample where pyramiding of two resistance genes of Brassica napus, Rlm3 and Rlm7, matching the Leptosphaeria maculans avirulence genes AvrLm3 and AvrLm4-7, respectively, favored the selection of double-virulent isolates. We previously demonstrated that the presence of a functional AvrLm4-7 gene in an isolate masks the Rlm3-AvrLm3 recognition. Rlm7 was massively deployed in France since 2004. L. maculans populations were surveyed on a large scale (>7,600 isolates) over a period of 20 years, and resistance gene deployment at the regional scale was determined. Mutations in isolates overcoming both resistance genes were analyzed. All data indicated that the simultaneous success of Rlm7, the deployment of varieties pyramiding Rlm3 and Rlm7, along with the decrease in areas cultivated with Rlm3 only, contributed to the success of virulent isolates toward Rlm7, and more recently to both Rlm3 and Rlm7. Experimental field assays proved that resistance gene alternation was a better strategy compared with pyramiding in this context. Our study also illustrated an unusually high sequence diversification of AvrLm3 and AvrLm4-7 under such a selection pressure, and identified a few regions of the AvrLm4-7 protein involved in both its recognition by Rlm7 and in its AvrLm3-Rlm3 masking ability. [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)
- Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, UR Bioger, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Angélique Gautier
- Université Paris-Saclay, INRAE, UR Bioger, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Clémence Plissonneau
- Université Paris-Saclay, INRAE, UR Bioger, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Loïc Le Meur
- Union Nationale des Producteurs de Pommes de Terre (UNPT), 43-45 rue de Naples F-75008, Paris, France
| | - Alizée Loiseau
- Agrosolutions, Village by CA Reims, 17 rond-point de l'Europe, 51430 Bezannes, France
| | - Martine Leflon
- Terres Inovia, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Julien Carpezat
- Terres Inovia, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Xavier Pinochet
- Terres Inovia, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR Bioger, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
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Jiquel A, Gay EJ, Mas J, George P, Wagner A, Fior A, Faure S, Balesdent M, Rouxel T. "Late" effectors from Leptosphaeria maculans as tools for identifying novel sources of resistance in Brassica napus. Plant Direct 2022; 6:e435. [PMID: 35949954 PMCID: PMC9356234 DOI: 10.1002/pld3.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The Dothideomycete Leptosphaeria maculans, causing stem canker (blackleg) of Brassica napus, secretes different cocktails of effectors at specific infection stages. Some effectors ("Late" effectors) are specifically produced during the long asymptomatic phase of stem colonization. By manipulating their expression so that they are overexpressed during cotyledon infection (OEC transformants of the fungus), we previously postulated that resistance genes operating in the stem may be involved in gene-for-gene relationship and thus contribute to quantitative disease resistance (QDR). Here, we selected 10 relevant new effector genes, and we generated OEC transformants to screen a collection of 130 B. napus genotypes, representative of the available diversity in the species. Five B. napus accessions showed a typical hypersensitive response when challenged with effectors LmSTEE98 or LmSTEE6826 at the cotyledon stage, and all belong to the semi-winter type of the diversity panel. In addition, five winter-type genotypes displayed an intermediate response to another late effector, LmSTEE7919. These new interactions now have to be genetically validated to check that they also correspond to gene-for-gene interactions. In all cases, they potentially provide novel resources, easy to breed for, and accounting for part of the quantitative resistance in a species for which we are currently facing limited resistance sources.
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Affiliation(s)
- Audren Jiquel
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
- Lidea SemencesMondonvilleFrance
| | - Elise J. Gay
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
| | | | | | | | | | | | | | - Thierry Rouxel
- INRAE, AgroParisTech, UR BIOGERUniversité Paris‐SaclayThiverval‐GrignonFrance
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022; 18:e1010664. [PMID: 35793393 PMCID: PMC9292093 DOI: 10.1371/journal.ppat.1010664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/18/2022] [Accepted: 06/10/2022] [Indexed: 12/31/2022] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3. An efficient strategy to control fungal diseases in the field is genetic control using resistant crop cultivars. Crop resistance mainly relies on gene-for-gene relationships between plant resistance (R) genes and pathogen avirulence (AVR) genes, as defined by Flor in the 1940s. However, such gene-for-gene relationships can increase in complexity over the course of plant-pathogen co-evolution. Resistance against the plant-pathogenic fungus Leptosphaeria maculans by Brassica napus and other Brassica species relies on the recognition of effector (AVR) proteins by R proteins; however, L. maculans produces an effector that suppresses a subset of these specific resistances. Using a protein structure approach, we revealed structural analogy between several of the resistance-triggering effectors, the resistance-suppressing effector, and effectors from other plant-pathogenic species in the Dothideomycetes and Sordariomycetes classes, defining a new family of effectors called LARS. Notably, cross-species expression of one LARS effector from Fulvia fulva, a pathogen of tomato, in L. maculans resulted in recognition by resistant cultivars of oilseed rape. These results highlight the need to integrate knowledge on effector structures to improve resistance management and to develop broad-spectrum resistances for multi-pathogen control of diseases.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
- * E-mail: (HVT); (IF)
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
- * E-mail: (HVT); (IF)
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022. [PMID: 35793393 DOI: 10.1101/2020.12.17.423041v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
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10
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Xiang Neik T, Ghanbarnia K, Ollivier B, Scheben A, Severn‐Ellis A, Larkan NJ, Haddadi P, Fernando DWG, Rouxel T, Batley J, Borhan HM, Balesdent M. Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2. Mol Plant Pathol 2022; 23:733-748. [PMID: 35239989 PMCID: PMC8995059 DOI: 10.1111/mpp.13194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 05/10/2023]
Abstract
Brassica napus (oilseed rape, canola) seedling resistance to Leptosphaeria maculans, the causal agent of blackleg (stem canker) disease, follows a gene-for-gene relationship. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the resistance genes RlmS and LepR2, respectively, present in B. napus 'Surpass 400'. Here we report cloning of AvrLmS and AvrLep2 using two independent methods. AvrLmS was cloned using combined in vitro crossing between avirulent and virulent isolates with sequencing of DNA bulks from avirulent or virulent progeny (bulked segregant sequencing). AvrLep2 was cloned using a biparental cross of avirulent and virulent L. maculans isolates and a classical map-based cloning approach. Taking these two approaches independently, we found that AvrLmS and AvrLep2 are the same gene. Complementation of virulent isolates with this gene confirmed its role in inducing resistance on Surpass 400, Topas-LepR2, and an RlmS-line. The gene, renamed AvrLmS-Lep2, encodes a small cysteine-rich protein of unknown function with an N-terminal secretory signal peptide, which is a common feature of the majority of effectors from extracellular fungal plant pathogens. The AvrLmS-Lep2/LepR2 interaction phenotype was found to vary from a typical hypersensitive response through intermediate resistance sometimes towards susceptibility, depending on the inoculation conditions. AvrLmS-Lep2 was nevertheless sufficient to significantly slow the systemic growth of the pathogen and reduce the stem lesion size on plant genotypes with LepR2, indicating the potential efficiency of this resistance to control the disease in the field.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Kaveh Ghanbarnia
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
- Department of Plant SciencesUniversity of ManitobaWinnipegManitobaCanada
| | | | - Armin Scheben
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Anita Severn‐Ellis
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Nicholas J. Larkan
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
- Armatus Genetics Inc.SaskatoonSaskatchewanCanada
| | - Parham Haddadi
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
| | | | - Thierry Rouxel
- Université Paris‐SaclayINRAEUR BIOGERThiverval‐GrignonFrance
| | - Jacqueline Batley
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Hossein M. Borhan
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
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11
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Degrave A, Wagner M, George P, Coudard L, Pinochet X, Ermel M, Gay EJ, Fudal I, Moreno‐Rico O, Rouxel T, Balesdent M. A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes. Mol Plant Pathol 2021; 22:1599-1612. [PMID: 34467616 PMCID: PMC8578820 DOI: 10.1111/mpp.13131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 05/19/2023]
Abstract
In many cultivated crops, sources of resistance to diseases are sparse and rely on introgression from wild relatives. Agricultural crops often are allopolyploids resulting from interspecific crosses between related species, which are sources of diversity for resistance genes. This is the case for Brassica napus (oilseed rape, canola), an interspecific hybrid between Brassica rapa (turnip) and Brassica oleracea (cabbage). B. napus has a narrow genetic basis and few effective resistance genes against stem canker (blackleg) disease, caused by the fungus Leptosphaeria maculans, are currently available. B. rapa diversity has proven to be a valuable source of resistance (Rlm, LepR) genes, while B. oleracea genotypes were mostly considered susceptible. Here we identified a new resistance source in B. oleracea genotypes from America, potentially effective against French L. maculans isolates under both controlled and field conditions. Genetic analysis of fungal avirulence and subsequent cloning and validation identified a new avirulence gene termed AvrLm14 and suggested a typical gene-for-gene interaction between AvrLm14 and the postulated Rlm14 gene. AvrLm14 shares all the usual characteristics of L. maculans avirulence genes: it is hosted in a genomic region enriched in transposable elements and heterochromatin marks H3K9me3, its expression is repressed during vegetative growth but shows a strong overexpression 5-9 days following cotyledon infection, and it encodes a small secreted protein enriched in cysteine residues with few matches in databases. Similar to the previously cloned AvrLm10-A, AvrLm14 contributes to reduce lesion size on susceptible cotyledons, pointing to a complex interplay between effectors promoting or reducing lesion development.
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Affiliation(s)
| | - Marine Wagner
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | - Laurent Coudard
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | - Xavier Pinochet
- TERRES INOVIA, campus INRA Agro ParisTechThiverval‐GrignonFrance
| | - Magali Ermel
- INRAE, Institut Agro, Univ Rennes, IGEPPLe RheuFrance
| | - Elise J. Gay
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | - Isabelle Fudal
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | - Thierry Rouxel
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
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12
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Jiquel A, Gervais J, Geistodt‐Kiener A, Delourme R, Gay EJ, Ollivier B, Fudal I, Faure S, Balesdent M, Rouxel T. A gene-for-gene interaction involving a 'late' effector contributes to quantitative resistance to the stem canker disease in Brassica napus. New Phytol 2021; 231:1510-1524. [PMID: 33621369 PMCID: PMC8360019 DOI: 10.1111/nph.17292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/19/2023]
Abstract
The control of stem canker disease of Brassica napus (rapeseed), caused by the fungus Leptosphaeria maculans is based largely on plant genetic resistance: single-gene specific resistance (Rlm genes) or quantitative, polygenic, adult-stage resistance. Our working hypothesis was that quantitative resistance partly obeys the gene-for-gene model, with resistance genes 'recognizing' fungal effectors expressed during late systemic colonization. Five LmSTEE (stem-expressed effector) genes were selected and placed under the control of the AvrLm4-7 promoter, an effector gene highly expressed at the cotyledon stage of infection, for miniaturized cotyledon inoculation test screening of a gene pool of 204 rapeseed genotypes. We identified a rapeseed genotype, 'Yudal', expressing hypersensitive response to LmSTEE98. The LmSTEE98-RlmSTEE98 interaction was further validated by inactivation of the LmSTEE98 gene with a CRISPR-Cas9 approach. Isolates with mutated versions of LmSTEE98 induced more severe stem symptoms than the wild-type isolate in 'Yudal'. This single-gene resistance was mapped in a 0.6 cM interval of the 'Darmor_bzh' × 'Yudal' genetic map. One typical gene-for-gene interaction contributes partly to quantitative resistance when L. maculans colonizes the stems of rapeseed. With numerous other effectors specific to stem colonization, our study provides a new route for resistance gene discovery, elucidation of quantitative resistance mechanisms and selection for durable resistance.
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Affiliation(s)
- Audren Jiquel
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Euralis Semences6 Chemin des PanedautesMondonville31700France
| | - Julie Gervais
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Aude Geistodt‐Kiener
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Université Paris‐SaclayRoute de l'Orme aux MerisiersSaint‐Aubin91190France
| | | | - Elise J. Gay
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
- Université Paris‐SaclayRoute de l'Orme aux MerisiersSaint‐Aubin91190France
| | - Bénédicte Ollivier
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Isabelle Fudal
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | | | - Marie‐Hélène Balesdent
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- INRAEAgroParisTechUMR BIOGERUniversité Paris‐SaclayAvenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
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13
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Soyer JL, Clairet C, Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal I. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Res 2021; 29:219-236. [PMID: 34018080 PMCID: PMC8159818 DOI: 10.1007/s10577-021-09658-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
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Affiliation(s)
- Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Colin Clairet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
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14
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Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T, Balesdent MH. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol 2021; 19:55. [PMID: 33757516 PMCID: PMC7986464 DOI: 10.1186/s12915-021-00989-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. RESULTS We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. CONCLUSION This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Juliette Linglin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Levrel
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Jocelyne Lemoine
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Regine Delourme
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
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15
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Petit-Houdenot Y, Degrave A, Meyer M, Blaise F, Ollivier B, Marais CL, Jauneau A, Audran C, Rivas S, Veneault-Fourrey C, Brun H, Rouxel T, Fudal I, Balesdent MH. A two genes - for - one gene interaction between Leptosphaeria maculans and Brassica napus. New Phytol 2019; 223:397-411. [PMID: 30802965 DOI: 10.1111/nph.15762] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 02/18/2019] [Indexed: 05/26/2023]
Abstract
Interactions between Leptosphaeria maculans, causal agent of stem canker of oilseed rape, and its Brassica hosts are models of choice to explore the multiplicity of 'gene-for-gene' complementarities and how they diversified to increased complexity in the course of plant-pathogen co-evolution. Here, we support this postulate by investigating the AvrLm10 avirulence that induces a resistance response when recognized by the Brassica nigra resistance gene Rlm10. Using genome-assisted map-based cloning, we identified and cloned two AvrLm10 candidates as two genes in opposite transcriptional orientation located in a subtelomeric repeat-rich region of the genome. The AvrLm10 genes encode small secreted proteins and show expression profiles in planta similar to those of all L. maculans avirulence genes identified so far. Complementation and silencing assays indicated that both genes are necessary to trigger Rlm10 resistance. Three assays for protein-protein interactions showed that the two AvrLm10 proteins interact physically in vitro and in planta. Some avirulence genes are recognized by two distinct resistance genes and some avirulence genes hide the recognition specificities of another. Our L. maculans model illustrates an additional case where two genes located in opposite transcriptional orientation are necessary to induce resistance. Interestingly, orthologues exist for both L. maculans genes in other phytopathogenic species, with a similar genome organization, which may point to an important conserved effector function linked to heterodimerization of the two proteins.
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Affiliation(s)
- Yohann Petit-Houdenot
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Alexandre Degrave
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Michel Meyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Françoise Blaise
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Bénédicte Ollivier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Claire-Line Marais
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Alain Jauneau
- Plateforme Imagerie, Pôle de Biotechnologie Végétale, Fédération de Recherche 3450, Castanet-Tolosan, F-31326, France
| | - Corinne Audran
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Claire Veneault-Fourrey
- Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, INRA, UMR 1136, INRA-Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, F-54280, France
- Laboratoire d'Excellence ARBRE, Faculté des Sciences et Technologies, UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Université de Lorraine, Vandoeuvre les Nancy, F-54506, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Marie-Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
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16
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Abstract
In the version of this Review Article originally published, parentheses were misplaced and the longitudinal and transverse speeds were inverted in two expressions for Poisson's ratio in Box 2; the expressions should have read, respectively, ν = (3B/G - 2)/(6B/G + 2) and ν = [½(Vl/Vt)2 - 1]/[(Vl/Vt)2 - 1].
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Affiliation(s)
- G N Greaves
- Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ, UK.
- Institute of Mathematics and Physics, Aberystwyth University, Aberystwyth, SY23 3BZ, UK.
| | - A L Greer
- Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - R S Lakes
- Department of Engineering Physics, Department of Materials Science, University of Wisconsin-Madison, Wisconsin, 53706-1687, USA
| | - T Rouxel
- Applied Mechanics Laboratory, LARMAUR ERL-CNRS 6274, Université Rennes 1, 35042, Rennes cedex, France
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17
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Dean RA, Rouxel T. Host-Microbe Interactions: Fungi Vol 46. Curr Opin Microbiol 2018; 46:iii-v. [PMID: 30553294 DOI: 10.1016/j.mib.2018.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralph A Dean
- William Neil Reynolds Distinguished Professor, Department of Entomology and Plant Pathology, North Carolina State University, 851 Main Campus Drive, Raleigh NC 27606, USA.
| | - Thierry Rouxel
- Research Director, UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France.
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18
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Dutreux F, Da Silva C, d'Agata L, Couloux A, Gay EJ, Istace B, Lapalu N, Lemainque A, Linglin J, Noel B, Wincker P, Cruaud C, Rouxel T, Balesdent MH, Aury JM. De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing. Sci Data 2018; 5:180235. [PMID: 30398473 PMCID: PMC6219404 DOI: 10.1038/sdata.2018.235] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/13/2018] [Indexed: 01/11/2023] Open
Abstract
Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance.
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Affiliation(s)
- Fabien Dutreux
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Corinne Da Silva
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Léo d'Agata
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Arnaud Couloux
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Elise J Gay
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Benjamin Istace
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Arnaud Lemainque
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Juliette Linglin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Benjamin Noel
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissarait à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
| | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91057 Evry, France
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19
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Fudal I, Balesdent MH, Rouxel T. Effector Biology in Fungal Pathogens of Nonmodel Crop Plants. Trends Plant Sci 2018; 23:753-755. [PMID: 30041914 DOI: 10.1016/j.tplants.2018.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The recent finding of a novel fungal strategy to manipulate salicylic acid (SA) in a nonmodel plant pathogen interaction not only establishes the universality of the strategy to ensure the success of biotrophs and hemibiotrophs, but also illustrates current limitations and challenges to identify targets of fungal effector in crop plants.
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Affiliation(s)
- Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France.
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20
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Plissonneau C, Rouxel T, Chèvre A, Van De Wouw AP, Balesdent M. One gene-one name: the AvrLmJ1 avirulence gene of Leptosphaeria maculans is AvrLm5. Mol Plant Pathol 2018; 19:1012-1016. [PMID: 28661570 PMCID: PMC6638039 DOI: 10.1111/mpp.12574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 05/05/2023]
Abstract
Leptosphaeria maculans, the causal agent of blackleg disease, interacts with Brassica napus (oilseed rape, canola) and other Brassica hosts in a gene-for-gene manner. The avirulence gene AvrLmJ1 has been cloned previously and shown to interact with an unidentified Brassica juncea resistance gene. In this study, we show that the AvrLmJ1 gene maps to the same position as the AvrLm5 locus. Furthermore, isolates complemented with the AvrLmJ1 locus confer avirulence towards B. juncea genotypes harbouring Rlm5. These findings demonstrate that AvrLmJ1 is AvrLm5 and highlight the need for shared resources to characterize accurately avirulence and/or resistance genes.
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Affiliation(s)
- Clémence Plissonneau
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
| | | | | | - Marie‐Hélène Balesdent
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
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21
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Soyer JL, Balesdent MH, Rouxel T, Dean RA. To B or not to B: a tale of unorthodox chromosomes. Curr Opin Microbiol 2018; 46:50-57. [PMID: 29579575 DOI: 10.1016/j.mib.2018.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Jessica L Soyer
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | - Ralph A Dean
- Center for Integrated Fungal Research, North Carolina State University & Department of Entomology and Plant Pathology, North Carolina State University, United States.
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22
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Gervais J, Plissonneau C, Linglin J, Meyer M, Labadie K, Cruaud C, Fudal I, Rouxel T, Balesdent M. Different waves of effector genes with contrasted genomic location are expressed by Leptosphaeria maculans during cotyledon and stem colonization of oilseed rape. Mol Plant Pathol 2017; 18:1113-1126. [PMID: 27474899 PMCID: PMC6638281 DOI: 10.1111/mpp.12464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Leptosphaeria maculans, the causal agent of stem canker disease, colonizes oilseed rape (Brassica napus) in two stages: a short and early colonization stage corresponding to cotyledon or leaf colonization, and a late colonization stage during which the fungus colonizes systemically and symptomlessly the plant during several months before stem canker appears. To date, the determinants of the late colonization stage are poorly understood; L. maculans may either successfully escape plant defences, leading to stem canker development, or the plant may develop an 'adult-stage' resistance reducing canker incidence. To obtain an insight into these determinants, we performed an RNA-sequencing (RNA-seq) pilot project comparing fungal gene expression in infected cotyledons and in symptomless or necrotic stems. Despite the low fraction of fungal material in infected stems, sufficient fungal transcripts were detected and a large number of fungal genes were expressed, thus validating the feasibility of the approach. Our analysis showed that all avirulence genes previously identified are under-expressed during stem colonization compared with cotyledon colonization. A validation RNA-seq experiment was then performed to investigate the expression of candidate effector genes during systemic colonization. Three hundred and seven 'late' effector candidates, under-expressed in the early colonization stage and over-expressed in the infected stems, were identified. Finally, our analysis revealed a link between the regulation of expression of effectors and their genomic location: the 'late' effector candidates, putatively involved in systemic colonization, are located in gene-rich genomic regions, whereas the 'early' effector genes, over-expressed in the early colonization stage, are located in gene-poor regions of the genome.
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Affiliation(s)
- Julie Gervais
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Clémence Plissonneau
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Juliette Linglin
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Michel Meyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Karine Labadie
- CEA‐Institut de Génomique, GENOSCOPECentre National de SéquençageEvry CedexFrance
| | - Corinne Cruaud
- CEA‐Institut de Génomique, GENOSCOPECentre National de SéquençageEvry CedexFrance
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Marie‐Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
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23
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Möncke D, Kamitsos EI, Palles D, Limbach R, Winterstein-Beckmann A, Honma T, Yao Z, Rouxel T, Wondraczek L. Transition and post-transition metal ions in borate glasses: Borate ligand speciation, cluster formation, and their effect on glass transition and mechanical properties. J Chem Phys 2017; 145:124501. [PMID: 27782649 DOI: 10.1063/1.4962323] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A series of transition and post-transition metal ion (Mn, Cu, Zn, Pb, Bi) binary borate glasses was studied with special consideration of the cations impact on the borate structure, the cations cross-linking capacity, and more generally, structure-property correlations. Infrared (IR) and Raman spectroscopies were used for the structural characterization. These complementary techniques are sensitive to the short-range order as in the differentiation of tetrahedral and trigonal borate units or regarding the number of non-bridging oxygen ions per unit. Moreover, vibrational spectroscopy is also sensitive to the intermediate-range order and to the presence of superstructural units, such as rings and chains, or the combination of rings. In order to clarify band assignments for the various borate entities, examples are given from pure vitreous B2O3 to meta-, pyro-, ortho-, and even overmodified borate glass compositions. For binary metaborate glasses, the impact of the modifier cation on the borate speciation is shown. High field strength cations such as Zn2+ enhance the disproportionation of metaborate to polyborate and pyroborate units. Pb2+ and Bi3+ induce cluster formation, resulting in PbOn- and BiOn-pseudophases. Both lead and bismuth borate glasses show also a tendency to stabilize very large superstructural units in the form of diborate polyanions. Far-IR spectra reflect on the bonding states of modifier cations in glasses. The frequency of the measured cation-site vibration band was used to obtain the average force constant for the metal-oxygen bonding, FM-O. A linear correlation between glass transition temperature (Tg) and FM-O was shown for the metaborate glass series. The mechanical properties of the glasses also correlate with the force constant FM-O, though for cations of similar force constant the fraction of tetrahedral borate units (N4) strongly affects the thermal and mechanical properties. For paramagnetic Cu- and Mn-borate glasses, N4 was determined from the IR spectra after deducing the relative absorption coefficient of boron tetrahedral versus boron trigonal units, α = α4/α3, using NMR literature data of the diamagnetic glasses.
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Affiliation(s)
- D Möncke
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Fraunhoferstraße 6, 07743 Jena, Germany
| | - E I Kamitsos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - D Palles
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - R Limbach
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Fraunhoferstraße 6, 07743 Jena, Germany
| | - A Winterstein-Beckmann
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Fraunhoferstraße 6, 07743 Jena, Germany
| | - T Honma
- Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Japan
| | - Z Yao
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Fraunhoferstraße 6, 07743 Jena, Germany
| | - T Rouxel
- Institute of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - L Wondraczek
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Fraunhoferstraße 6, 07743 Jena, Germany
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24
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Rouxel T, Balesdent MH. Life, death and rebirth of avirulence effectors in a fungal pathogen of Brassica crops, Leptosphaeria maculans. New Phytol 2017; 214:526-532. [PMID: 28084619 DOI: 10.1111/nph.14411] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
Contents 526 I. 526 II. 527 III. 527 IV. 529 V. 529 VI. 530 VII. 530 531 References 531 SUMMARY: In agricultural systems, major (R) genes for resistance in plants exert strong selection pressure on cognate/corresponding avirulence effector genes of phytopathogens. However, a complex interplay often exists between trade-offs linked to effector function and the need to escape R gene recognition. Here, using the Leptosphaeria maculans-oilseed rape pathosystem we review evolution of effectors submitted to multiple resistance gene selection. Characteristics of this pathosystem include a crop in which resistance genes have been deployed intensively resulting in 'boom and bust' cycles; a fungal pathogen with a high adaptive potential in which seven avirulence genes are cloned and for which population surveys have been coupled with molecular analysis of events responsible for virulence. The mode of evolution of avirulence genes, all located in dispensable parts of the 'two-speed' genome, is a highly dynamic gene-specific process. In some instances, avirulence genes are readily deleted under selection. However, others, even when located in the most plastic genome regions, undergo only limited point mutations or their avirulence phenotype is 'camouflaged' by another avirulence gene. Thus, while hundreds of effector genes are present, some effectors are likely to have an important and nonredundant function, suggesting functional redundancy and dispensability of effectors might not be the rule.
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Affiliation(s)
- Thierry Rouxel
- UMR Bioger, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Marie-Hélène Balesdent
- UMR Bioger, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France
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25
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Plissonneau C, Blaise F, Ollivier B, Leflon M, Carpezat J, Rouxel T, Balesdent MH. Unusual evolutionary mechanisms to escape effector-triggered immunity in the fungal phytopathogen Leptosphaeria maculans. Mol Ecol 2017; 26:2183-2198. [PMID: 28160497 DOI: 10.1111/mec.14046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 01/17/2017] [Indexed: 12/18/2022]
Abstract
Leptosphaeria maculans is the fungus responsible for the stem canker disease of oilseed rape (Brassica napus). AvrLm3 and AvrLm4-7, two avirulence effector genes of L. maculans, are involved in an unusual relationship: AvrLm4-7 suppresses the Rlm3-mediated resistance. Here, we assessed AvrLm3 polymorphism in a collection of 235 L. maculans isolates. No field isolates exhibited deletion or inactivating mutations in AvrLm3, as observed for other L. maculans avirulence genes. Eleven isoforms of the AvrLm3 protein were found. In isolates virulent towards both Rlm3 and Rlm7 (a3a7), the loss of the Rlm3-mediated resistance response was due to two distinct mechanisms. First, when AvrLm4-7 was inactivated (deletion or inactivating mutations), amino acid substitutions in AvrLm3 generated virulent isoforms of the protein. Second, when only point mutations were observed in AvrLm4-7, a3a7 isolates still contained an avirulent allele of AvrLm3. Directed mutagenesis confirmed that some point mutations in AvrLm4-7 were sufficient for the fungus to escape Rlm7-mediated resistance while maintaining the suppression of the AvrLm3 phenotype. Signatures of positive selection were also identified in AvrLm3. The complex evolutionary mechanisms enabling L. maculans to escape Rlm3-mediated resistance while preserving AvrLm3 integrity, along with observed reduced aggressiveness of isolates silenced for AvrLm3, serves to emphasize the importance of this effector in pathogenicity towards B. napus. While the common response to resistance gene pressure is local selection of isolates depleted in the cognate avirulence gene, this example contributes to complexify the gene-for-gene concept of plant-pathogen evolution with a 'camouflaged' model allowing retention of nondispensable avirulence effectors.
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Affiliation(s)
- C Plissonneau
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France.,Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - F Blaise
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - B Ollivier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - M Leflon
- Terres Inovia, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - J Carpezat
- Terres Inovia, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - T Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - M-H Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
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26
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Meyer M, Bourras S, Gervais J, Labadie K, Cruaud C, Balesdent MH, Rouxel T. Impact of biotic and abiotic factors on the expression of fungal effector-encoding genes in axenic growth conditions. Fungal Genet Biol 2016; 99:1-12. [PMID: 28034799 DOI: 10.1016/j.fgb.2016.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/15/2016] [Accepted: 12/22/2016] [Indexed: 12/31/2022]
Abstract
In phytopathogenic fungi, the expression of hundreds of small secreted protein (SSP)-encoding genes is induced upon primary infection of plants while no or a low level of expression is observed during vegetative growth. In some species such as Leptosphaeria maculans, this coordinated in-planta upregulation of SSP-encoding genes expression relies on an epigenetic control but the signals triggering gene expression in-planta are unknown. In the present study, biotic and abiotic factors that may relieve suppression of SSP-encoding gene expression during axenic growth of L. maculans were investigated. Some abiotic factors (temperature, pH) could have a limited effect on SSP gene expression. In contrast, two types of cellular stresses induced by antibiotics (cycloheximide, phleomycin) activated strongly the transcription of SSP genes. A transcriptomic analysis to cycloheximide exposure revealed that biological processes such as ribosome biosynthesis and rRNA processing were induced whereas important metabolic pathways such as glycogen and nitrogen metabolism, glycolysis and tricarboxylic acid cycle activity were down-regulated. A quantitatively different expression of SSP-encoding genes compared to plant infection was also detected. Interestingly, the same physico-chemical parameters as those identified here for L. maculans effectors were identified to regulate positively or negatively the expression of bacterial effectors. This suggests that apoplastic phytopathogens may react to similar physiological parameters for regulation of their effector genes.
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Affiliation(s)
- Michel Meyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
| | - Salim Bourras
- Université Paris-Sud, 91400 Orsay, France; Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Julie Gervais
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Karine Labadie
- Centre National de Séquençage, CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Corinne Cruaud
- Centre National de Séquençage, CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Marie-Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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27
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Nováková M, Šašek V, Trdá L, Krutinová H, Mongin T, Valentová O, Balesdent MH, Rouxel T, Burketová L. Leptosphaeria maculans effector AvrLm4-7 affects salicylic acid (SA) and ethylene (ET) signalling and hydrogen peroxide (H2 O2 ) accumulation in Brassica napus. Mol Plant Pathol 2016; 17:818-31. [PMID: 26575525 PMCID: PMC6638468 DOI: 10.1111/mpp.12332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 05/03/2023]
Abstract
To achieve host colonization, successful pathogens need to overcome plant basal defences. For this, (hemi)biotrophic pathogens secrete effectors that interfere with a range of physiological processes of the host plant. AvrLm4-7 is one of the cloned effectors from the hemibiotrophic fungus Leptosphaeria maculans 'brassicaceae' infecting mainly oilseed rape (Brassica napus). Although its mode of action is still unknown, AvrLm4-7 is strongly involved in L. maculans virulence. Here, we investigated the effect of AvrLm4-7 on plant defence responses in a susceptible cultivar of B. napus. Using two isogenic L. maculans isolates differing in the presence of a functional AvrLm4-7 allele [absence ('a4a7') and presence ('A4A7') of the allele], the plant hormone concentrations, defence-related gene transcription and reactive oxygen species (ROS) accumulation were analysed in infected B. napus cotyledons. Various components of the plant immune system were affected. Infection with the 'A4A7' isolate caused suppression of salicylic acid- and ethylene-dependent signalling, the pathways regulating an effective defence against L. maculans infection. Furthermore, ROS accumulation was decreased in cotyledons infected with the 'A4A7' isolate. Treatment with an antioxidant agent, ascorbic acid, increased the aggressiveness of the 'a4a7' L. maculans isolate, but not that of the 'A4A7' isolate. Together, our results suggest that the increased aggressiveness of the 'A4A7' L. maculans isolate could be caused by defects in ROS-dependent defence and/or linked to suppressed SA and ET signalling. This is the first study to provide insights into the manipulation of B. napus defence responses by an effector of L. maculans.
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Affiliation(s)
- Miroslava Nováková
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Vladimír Šašek
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Trdá
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Krutinová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Thomas Mongin
- INRA, UMR INRA-AgroParisTech 1290 Bioger, Avenue Lucien Brétignières, Thiverval-Grignon, France
| | - Olga Valentová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Marie-HelEne Balesdent
- INRA, UMR INRA-AgroParisTech 1290 Bioger, Avenue Lucien Brétignières, Thiverval-Grignon, France
| | - Thierry Rouxel
- INRA, UMR INRA-AgroParisTech 1290 Bioger, Avenue Lucien Brétignières, Thiverval-Grignon, France
| | - Lenka Burketová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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28
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Plissonneau C, Daverdin G, Ollivier B, Blaise F, Degrave A, Fudal I, Rouxel T, Balesdent MH. A game of hide and seek between avirulence genes AvrLm4-7 and AvrLm3 in Leptosphaeria maculans. New Phytol 2016; 209:1613-24. [PMID: 26592855 DOI: 10.1111/nph.13736] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/27/2015] [Indexed: 05/02/2023]
Abstract
Extending the durability of plant resistance genes towards fungal pathogens is a major challenge. We identified and investigated the relationship between two avirulence genes of Leptosphaeria maculans, AvrLm3 and AvrLm4-7. When an isolate possesses both genes, the Rlm3-mediated resistance of oilseed rape (Brassica napus) is not expressed due to the presence of AvrLm4-7 but virulent isolates toward Rlm7 recover the AvrLm3 phenotype. Combining genetic and genomic approaches (genetic mapping, RNA-seq, BAC (bacterial artificial chromosome) clone sequencing and de novo assembly) we cloned AvrLm3, a telomeric avirulence gene of L. maculans. AvrLm3 is located in a gap of the L. maculans reference genome assembly, is surrounded by repeated elements, encodes for a small secreted cysteine-rich protein and is highly expressed at early infection stages. Complementation and silencing assays validated the masking effect of AvrLm4-7 on AvrLm3 recognition by Rlm3 and we showed that the presence of AvrLm4-7 does not impede AvrLm3 expression in planta. Y2H assays suggest the absence of physical interaction between the two avirulence proteins. This unusual interaction is the basis for field experiments aiming to evaluate strategies that increase Rlm7 durability.
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Affiliation(s)
- Clémence Plissonneau
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Guillaume Daverdin
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Françoise Blaise
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Alexandre Degrave
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR INRA-AgroParisTech 1290-Bioger, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
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29
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Soyer JL, Hamiot A, Ollivier B, Balesdent MH, Rouxel T, Fudal I. The APSES transcription factor LmStuA is required for sporulation, pathogenic development and effector gene expression in Leptosphaeria maculans. Mol Plant Pathol 2015; 16:1000-5. [PMID: 25727237 PMCID: PMC6638475 DOI: 10.1111/mpp.12249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Leptosphaeria maculans causes stem canker of oilseed rape (Brassica napus). The APSES transcription factor StuA is a key developmental regulator of fungi, involved in morphogenesis, conidia production and also more recently described as required for secondary metabolite production and for effector gene expression in phytopathogenic fungi. We investigated the involvement of the orthologue of StuA in L. maculans, LmStuA, in morphogenesis, pathogenicity and effector gene expression. LmStuA is induced during mycelial growth and at 14 days after infection, corresponding to the development of pycnidia on oilseed rape leaves, consistent with the function of StuA described so far. We set up the functional characterization of LmStuA using an RNA interference approach. Silenced LmStuA transformants showed typical phenotypic defects of StuA mutants with altered growth in axenic culture and impaired conidia production and perithecia formation. Silencing of LmStuA abolished the pathogenicity of L. maculans on oilseed rape leaves and also resulted in a drastic decrease in expression of at least three effector genes during in planta infection, suggesting either that LmStuA regulates, directly or indirectly, the expression of several effector genes in L. maculans or that the infection stage in which effectors are expressed is not reached when LmStuA expression is silenced.
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Affiliation(s)
- Jessica L Soyer
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Audrey Hamiot
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
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30
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Bourras S, Rouxel T, Meyer M. Agrobacterium tumefaciens Gene Transfer: How a Plant Pathogen Hacks the Nuclei of Plant and Nonplant Organisms. Phytopathology 2015; 105:1288-1301. [PMID: 26151736 DOI: 10.1094/phyto-12-14-0380-rvw] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Agrobacterium species are soilborne gram-negative bacteria exhibiting predominantly a saprophytic lifestyle. Only a few of these species are capable of parasitic growth on plants, causing either hairy root or crown gall diseases. The core of the infection strategy of pathogenic Agrobacteria is a genetic transformation of the host cell, via stable integration into the host genome of a DNA fragment called T-DNA. This genetic transformation results in oncogenic reprogramming of the host to the benefit of the pathogen. This unique ability of interkingdom DNA transfer was largely used as a tool for genetic engineering. Thus, the artificial host range of Agrobacterium is continuously expanding and includes plant and nonplant organisms. The increasing availability of genomic tools encouraged genome-wide surveys of T-DNA tagged libraries, and the pattern of T-DNA integration in eukaryotic genomes was studied. Therefore, data have been collected in numerous laboratories to attain a better understanding of T-DNA integration mechanisms and potential biases. This review focuses on the intranuclear mechanisms necessary for proper targeting and stable expression of Agrobacterium oncogenic T-DNA in the host cell. More specifically, the role of genome features and the putative involvement of host's transcriptional machinery in relation to the T-DNA integration and effects on gene expression are discussed. Also, the mechanisms underlying T-DNA integration into specific genome compartments is reviewed, and a theoretical model for T-DNA intranuclear targeting is presented.
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Affiliation(s)
- Salim Bourras
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Thierry Rouxel
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Michel Meyer
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
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31
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Ghanbarnia K, Fudal I, Larkan NJ, Links MG, Balesdent MH, Profotova B, Fernando WGD, Rouxel T, Borhan MH. Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach. Mol Plant Pathol 2015; 16:699-709. [PMID: 25492575 PMCID: PMC6638346 DOI: 10.1111/mpp.12228] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Five avirulence genes from Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), have been identified previously through map-based cloning. In this study, a comparative genomic approach was used to clone the previously mapped AvrLm2. Given the lack of a presence-absence gene polymorphism coincident with the AvrLm2 phenotype, 36 L. maculans isolates were resequenced and analysed for single-nucleotide polymorphisms (SNPs) in predicted small secreted protein-encoding genes present within the map interval. Three SNPs coincident with the AvrLm2 phenotype were identified within LmCys1, previously identified as a putative effector-coding gene. Complementation of a virulent isolate with LmCys1, as the candidate AvrLm2 allele, restored the avirulent phenotype on Rlm2-containing B. napus lines. AvrLm2 encodes a small cysteine-rich protein with low similarity to other proteins in the public databases. Unlike other avirulence genes, AvrLm2 resides in a small GC island within an AT-rich isochore of the genome, and was never found to be deleted completely in virulent isolates.
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Affiliation(s)
- Kaveh Ghanbarnia
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | | | - Nicholas J Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Matthew G Links
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5C9
| | | | | | | | | | - M Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
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32
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Soyer JL, Rouxel T, Fudal I. Chromatin-based control of effector gene expression in plant-associated fungi. Curr Opin Plant Biol 2015; 26:51-6. [PMID: 26116976 DOI: 10.1016/j.pbi.2015.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 05/08/2023]
Abstract
Plant-associated fungi often present in their genome areas enriched in repeat sequences and effector genes, the latter being specifically induced in planta. The location of effector genes in regions enriched in repeats has been shown to have an impact on adaptability of fungi but could also provide for tight control of effector gene expression through chromatin-based regulation. The distribution of two repressive histone marks was shown to be an important regulatory layer in two fungal species with different lifestyles. Chromatin-based control of effector gene expression is likely to provide an evolutionary advantage by preventing the expression of genes not needed during vegetative growth and allow for a massive concerted expression at particular time-points of plant infection.
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Affiliation(s)
- Jessica L Soyer
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France; Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany; Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850 Thiverval-Grignon, France.
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33
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Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, Lazar N, Daverdin G, Balesdent MH, Choi DHY, Tyler BM, Rouxel T, van Tilbeurgh H, Fudal I. Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins. Plant J 2015; 83:610-24. [PMID: 26082394 DOI: 10.1111/tpj.12913] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 05/13/2023]
Abstract
The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
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Affiliation(s)
- Karine Blondeau
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Françoise Blaise
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marc Graille
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Juliette Linglin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Audrey Labarde
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Noureddine Lazar
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Guillaume Daverdin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Danielle H Y Choi
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Herman van Tilbeurgh
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
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34
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Tyler BM, Kale SD, Wang Q, Tao K, Clark HR, Drews K, Antignani V, Rumore A, Hayes T, Plett JM, Fudal I, Gu B, Chen Q, Affeldt KJ, Berthier E, Fischer GJ, Dou D, Shan W, Keller NP, Martin F, Rouxel T, Lawrence CB. Microbe-Independent Entry of Oomycete RxLR Effectors and Fungal RxLR-Like Effectors Into Plant and Animal Cells Is Specific and Reproducible. Mol Plant Microbe Interact 2015; 2015:51-56. [PMID: 27839069 DOI: 10.1094/mpmi-99-99-0002.testissue] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Brett M Tyler
- 1 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Shiv D Kale
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Qunqing Wang
- 1 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Kai Tao
- 1 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Helen R Clark
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Kelly Drews
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Vincenzo Antignani
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Amanda Rumore
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Tristan Hayes
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Jonathan M Plett
- 3 Lab of Excellence ARBRE, UMR INRA/UHP 1136, Interactions Arbres/Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France
| | - Isabelle Fudal
- 4 INRA-Bioger, Campus AgroParisTech, 78850 Thiverval-Grignon, France
| | - Biao Gu
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
- 5 College of Plant Protection and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qinghe Chen
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Katharyn J Affeldt
- 6 Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Erwin Berthier
- 6 Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Gregory J Fischer
- 6 Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Daolong Dou
- 2 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, U.S.A
- 7 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weixing Shan
- 5 College of Plant Protection and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nancy P Keller
- 6 Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Francis Martin
- 3 Lab of Excellence ARBRE, UMR INRA/UHP 1136, Interactions Arbres/Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France
| | - Thierry Rouxel
- 4 INRA-Bioger, Campus AgroParisTech, 78850 Thiverval-Grignon, France
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35
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Lowe RGT, Cassin A, Grandaubert J, Clark BL, Van de Wouw AP, Rouxel T, Howlett BJ. Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species. PLoS One 2014; 9:e103098. [PMID: 25068644 PMCID: PMC4113356 DOI: 10.1371/journal.pone.0103098] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
Leptosphaeria maculans ‘brassicae’ is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa ‘canadensis’, colonises cotyledons but causes few stem cankers. We describe the complement of genes encoding carbohydrate-active enzymes (CAZys) and peptidases of these fungi, as well as of four related plant pathogens. We also report dual-organism RNA-seq transcriptomes of these two Leptosphaeria species and B. napus during disease. During the first seven days of infection L. biglobosa ‘canadensis’, a necrotroph, expressed more cell wall degrading genes than L. maculans ‘brassicae’, a hemi-biotroph. L. maculans ‘brassicae’ expressed many genes in the Carbohydrate Binding Module class of CAZy, particularly CBM50 genes, with potential roles in the evasion of basal innate immunity in the host plant. At this time, three avirulence genes were amongst the top 20 most highly upregulated L. maculans ‘brassicae’ genes in planta. The two fungi had a similar number of peptidase genes, and trypsin was transcribed at high levels by both fungi early in infection. L. biglobosa ‘canadensis’ infection activated the jasmonic acid and salicylic acid defence pathways in B. napus, consistent with defence against necrotrophs. L. maculans ‘brassicae’ triggered a high level of expression of isochorismate synthase 1, a reporter for salicylic acid signalling. L. biglobosa ‘canadensis’ infection triggered coordinated shutdown of photosynthesis genes, and a concomitant increase in transcription of cell wall remodelling genes of the host plant. Expression of particular classes of CAZy genes and the triggering of host defence and particular metabolic pathways are consistent with the necrotrophic lifestyle of L. biglobosa ‘canadensis’, and the hemibiotrophic life style of L. maculans ‘brassicae’.
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Affiliation(s)
- Rohan G. T. Lowe
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Cassin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Bethany L. Clark
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Barbara J. Howlett
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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Grandaubert J, Balesdent MH, Rouxel T. [Transposable elements reshaping genomes and favouring the evolutionary and adaptive potential of fungal phytopathogens]. Biol Aujourdhui 2014; 207:277-290. [PMID: 24594576 DOI: 10.1051/jbio/2013026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 06/03/2023]
Abstract
Phytopathogenic fungi are a major threat for global food security and show an extreme plasticity in pathogenicity behaviours. They often have a high adaptive potential allowing them to rapidly counteract the control methods used by men in agrosystems. In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. Our model is the evolutionary series Leptosphaeria maculans-Leptosphaeria biglobosa, encompassing five distinct entities, whose conspecificity or heterospecificity status is unclear, and which all are pathogens of cruciferous plants. They however differ by their host range and pathogenicity. Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). Whether the genome invasion contributed to speciation is still unclear to-date but there is a coincidence between this burst of TEs and divergence between two species. This TE burst contributed to diversification of effector proteins and thus to generation of novel pathogenic specificities. In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host.
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Tyler BM, Kale SD, Wang Q, Tao K, Clark HR, Drews K, Antignani V, Rumore A, Hayes T, Plett JM, Fudal I, Gu B, Chen Q, Affeldt KJ, Berthier E, Fischer GJ, Dou D, Shan W, Keller NP, Martin F, Rouxel T, Lawrence CB. Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible. Mol Plant Microbe Interact 2013; 26:611-6. [PMID: 23550528 PMCID: PMC3994703 DOI: 10.1094/mpmi-02-13-0051-ia] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent reexamination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells concluded that the RxLR domains of Phytophthora infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and nonhost plant and animal cells. Here, we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells and also into wheat leaf cells, at levels well above background nonspecific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the seven different labs that coauthored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected by Wawra et al. (2013).
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Affiliation(s)
- Brett M Tyler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
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Balesdent MH, Fudal I, Ollivier B, Bally P, Grandaubert J, Eber F, Chèvre AM, Leflon M, Rouxel T. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. New Phytol 2013; 198:887-898. [PMID: 23406519 DOI: 10.1111/nph.12178] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/10/2013] [Indexed: 05/02/2023]
Abstract
Phytopathogenic fungi frequently contain dispensable chromosomes, some of which contribute to host range or pathogenicity. In Leptosphaeria maculans, the stem canker agent of oilseed rape (Brassica napus), the minichromosome was previously suggested to be dispensable, without evidence for any role in pathogenicity. Using genetic and genomic approaches, we investigated the inheritance and molecular determinant of an L. maculans-Brassica rapa incompatible interaction. Single gene control of the resistance was found, while all markers located on the L. maculans minichromosome, absent in the virulent parental isolate, co-segregated with the avirulent phenotype. Only one candidate avirulence gene was identified on the minichromosome, validated by complementation experiments and termed AvrLm11. The minichromosome was frequently lost following meiosis, but the frequency of isolates lacking it remained stable in field populations sampled at a 10-yr time interval, despite a yearly sexual stage in the L. maculans life cycle. This work led to the cloning of a new 'lost in the middle of nowhere' avirulence gene of L. maculans, interacting with a B. rapa resistance gene termed Rlm11 and introgressed into B. napus. It demonstrated the dispensability of the L. maculans minichromosome and suggested that its loss generates a fitness deficit.
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Affiliation(s)
- Marie-Hélène Balesdent
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Pascal Bally
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Jonathan Grandaubert
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Frédérique Eber
- INRA, UMR1349 IGEPP, BP35327, F-35653, Le Rheu Cedex, France
| | | | - Martine Leflon
- CETIOM, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- INRA, UR1290 BIOGER, Avenue Lucien Brétignières, BP 01, F-78850, Thiverval-Grignon, France
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Rouxel T, Balesdent MH. From model to crop plant-pathogen interactions: cloning of the first resistance gene to Leptosphaeria maculans in Brassica napus. New Phytol 2013; 197:356-358. [PMID: 23253328 DOI: 10.1111/nph.12099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Thierry Rouxel
- INRA-Bioger, Av. Lucien Brétignières, 78850, Thiverval-Grignon, France
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Daverdin G, Rouxel T, Gout L, Aubertot JN, Fudal I, Meyer M, Parlange F, Carpezat J, Balesdent MH. Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLoS Pathog 2012; 8:e1003020. [PMID: 23144620 PMCID: PMC3493481 DOI: 10.1371/journal.ppat.1003020] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 09/24/2012] [Indexed: 11/21/2022] Open
Abstract
Modern agriculture favours the selection and spread of novel plant diseases. Furthermore, crop genetic resistance against pathogens is often rendered ineffective within a few years of its commercial deployment. Leptosphaeria maculans, the cause of phoma stem canker of oilseed rape, develops gene-for-gene interactions with its host plant, and has a high evolutionary potential to render ineffective novel sources of resistance in crops. Here, we established a four-year field experiment to monitor the evolution of populations confronted with the newly released Rlm7 resistance and to investigate the nature of the mutations responsible for virulence against Rlm7. A total of 2551 fungal isolates were collected from experimental crops of a Rlm7 cultivar or a cultivar without Rlm7. All isolates were phenotyped for virulence and a subset was genotyped with neutral genetic markers. Virulent isolates were investigated for molecular events at the AvrLm4-7 locus. Whilst virulent isolates were not found in neighbouring crops, their frequency had reached 36% in the experimental field after four years. An extreme diversity of independent molecular events leading to virulence was identified in populations, with large-scale Repeat Induced Point mutations or complete deletion of AvrLm4-7 being the most frequent. Our data suggest that increased mutability of fungal genes involved in the interactions with plants is directly related to their genomic environment and reproductive system. Thus, rapid allelic diversification of avirulence genes can be generated in L. maculans populations in a single field provided that large population sizes and sexual reproduction are favoured by agricultural practices.
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Affiliation(s)
| | - Thierry Rouxel
- INRA, UR 1290 Bioger, Campus AgroParisTech, Thiverval-Grignon, France
| | - Lilian Gout
- INRA, UR 1290 Bioger, Campus AgroParisTech, Thiverval-Grignon, France
- AgroParisTech, Campus AgroParisTech, Thiverval-Grignon, France
| | | | - Isabelle Fudal
- INRA, UR 1290 Bioger, Campus AgroParisTech, Thiverval-Grignon, France
| | - Michel Meyer
- INRA, UR 1290 Bioger, Campus AgroParisTech, Thiverval-Grignon, France
| | - Francis Parlange
- INRA, UR 1290 Bioger, Campus AgroParisTech, Thiverval-Grignon, France
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Rouxel T. Erratum: “Thermodynamics of viscous flow and elasticity of glass forming liquids in the glass transition range” [J. Chem. Phys. 135, 184501 (2011)]. J Chem Phys 2012. [DOI: 10.1063/1.4766466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rouxel T. Thermodynamics of viscous flow and elasticity of glass forming liquids in the glass transition range. J Chem Phys 2011; 135:184501. [DOI: 10.1063/1.3656695] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
In comparing a material's resistance to distort under mechanical load rather than to alter in volume, Poisson's ratio offers the fundamental metric by which to compare the performance of any material when strained elastically. The numerical limits are set by ½ and -1, between which all stable isotropic materials are found. With new experiments, computational methods and routes to materials synthesis, we assess what Poisson's ratio means in the contemporary understanding of the mechanical characteristics of modern materials. Central to these recent advances, we emphasize the significance of relationships outside the elastic limit between Poisson's ratio and densification, connectivity, ductility and the toughness of solids; and their association with the dynamic properties of the liquids from which they were condensed and into which they melt.
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Affiliation(s)
- G N Greaves
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK.
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Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin SB, Oliver RP. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 2011; 12:R45. [PMID: 21605470 PMCID: PMC3219968 DOI: 10.1186/gb-2011-12-5-r45] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 04/27/2011] [Accepted: 05/24/2011] [Indexed: 12/20/2022] Open
Abstract
Background Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa. Results These analyses identified a novel form of evolution in which genes are conserved within homologous chromosomes, but with randomized orders and orientations. This mode of evolution is designated mesosynteny, to differentiate it from micro- and macrosynteny seen in other organisms. Mesosynteny is an alternative evolutionary pathway very different from macrosyntenic conservation. Surprisingly, mesosynteny was not found in all fungal groups. Instead, mesosynteny appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes. Conclusions The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis.
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Affiliation(s)
- James K Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia
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Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GHJ, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun 2011; 2:202. [PMID: 21326234 DOI: 10.1038/ncomms1189] [Citation(s) in RCA: 317] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 01/11/2011] [Indexed: 02/06/2023] Open
Abstract
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
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Affiliation(s)
- Thierry Rouxel
- INRA-Bioger, UR1290, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon F-78850, France.
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Bally P, Grandaubert J, Rouxel T, Balesdent MH. FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets. BMC Res Notes 2010; 3:322. [PMID: 21114810 PMCID: PMC3002364 DOI: 10.1186/1756-0500-3-322] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 11/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro-and minisatellites are among the most powerful genetic markers known to date. They have been used as tools for a large number of applications ranging from gene mapping to phylogenetic studies and isolate typing. However, identifying micro-and minisatellite markers on large sequence data sets is often a laborious process. RESULTS FONZIE was designed to successively 1) perform a search for markers via the external software Tandem Repeat Finder, 2) exclude user-defined specific genomic regions, 3) screen for the size and the percent matches of each relevant marker found by Tandem Repeat Finder, 4) evaluate marker specificity (i.e., occurrence of the marker as a single copy in the genome) using BLAST2.0, 5) design minisatellite primer pairs via the external software Primer3, and 6) check the specificity of each final PCR product by BLAST. A final file returns to users all the results required to amplify markers. A biological validation of the approach was performed using the whole genome sequence of the phytopathogenic fungus Leptosphaeria maculans, showing that more than 90% of the minisatellite primer pairs generated by the pipeline amplified a PCR product, 44.8% of which showed agarose-gel resolvable polymorphism between isolates. Segregation analyses confirmed that the polymorphic minisatellites corresponded to single-locus markers. CONCLUSION FONZIE is a stand-alone and user-friendly application developed to minimize tedious manual operations, reduce errors, and speed up the search for efficient minisatellite and microsatellite markers departing from whole-genome sequence data. This pipeline facilitates the integration of data and provides a set of specific primer sequences for PCR amplification of single-locus markers. FONZIE is freely downloadable at: http://www.versailles-grignon.inra.fr/bioger/equipes/leptosphaeria_maculans/outils_d_analyses/fonzie.
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Affiliation(s)
- Pascal Bally
- Institut National de la Recherche Agronomique, UMR 1290 BIOGER, BP 01, Avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.
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Kale SD, Gu B, Capelluto DG, Dou D, Feldman E, Rumore A, Arredondo FD, Hanlon R, Fudal I, Rouxel T, Lawrence CB, Shan W, Tyler BM. External Lipid PI3P Mediates Entry of Eukaryotic Pathogen Effectors into Plant and Animal Host Cells. Cell 2010. [DOI: 10.1016/j.cell.2010.08.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kale SD, Gu B, Capelluto DGS, Dou D, Feldman E, Rumore A, Arredondo FD, Hanlon R, Fudal I, Rouxel T, Lawrence CB, Shan W, Tyler BM. External lipid PI3P mediates entry of eukaryotic pathogen effectors into plant and animal host cells. Cell 2010; 142:284-95. [PMID: 20655469 DOI: 10.1016/j.cell.2010.06.008] [Citation(s) in RCA: 291] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 03/30/2010] [Accepted: 05/10/2010] [Indexed: 10/19/2022]
Abstract
Pathogens of plants and animals produce effector proteins that are transferred into the cytoplasm of host cells to suppress host defenses. One type of plant pathogens, oomycetes, produces effector proteins with N-terminal RXLR and dEER motifs that enable entry into host cells. We show here that effectors of another pathogen type, fungi, contain functional variants of the RXLR motif, and that the oomycete and fungal RXLR motifs enable binding to the phospholipid, phosphatidylinositol-3-phosphate (PI3P). We find that PI3P is abundant on the outer surface of plant cell plasma membranes and, furthermore, on some animal cells. All effectors could also enter human cells, suggesting that PI3P-mediated effector entry may be very widespread in plant, animal and human pathogenesis. Entry into both plant and animal cells involves lipid raft-mediated endocytosis. Blocking PI3P binding inhibited effector entry, suggesting new therapeutic avenues.
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Affiliation(s)
- Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Dilmaghani A, Balesdent MH, Rouxel T, Moreno-Rico O. First Report of Leptosphaeria biglobosa (Blackleg) on Brassica oleracea (Cabbage) in Mexico. Plant Dis 2010; 94:791. [PMID: 30754331 DOI: 10.1094/pdis-94-6-0791c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Broccoli (Brassica oleracea var. italica), cauliflower (B. oleracea var. botrytis), and cabbage (B. oleracea var. capitata) have been grown in central Mexico since 1970, with 21,000 ha cropped in 2001. In contrast, areas grown with oilseed rape (B. napus) are very limited in Mexico (<8,000 ha). Blackleg, a destructive disease of B. napus in most parts of the world, was first observed in Mexico in Zacatecas and Aguascalientes in 1988 on B. oleracea, causing as much as 70% yield loss. A species complex of two closely related Dothideomycete species, Leptosphaeria maculans and L. biglobosa, is associated with this disease of crucifers (1), but leaf symptoms on susceptible plants are different, with L. maculans typically causing >15-mm pale gray lesions with numerous pycnidia, whereas L. biglobosa causes dark and smaller lesions only containing a few pycnidia. Having a similar epidemiology, both species can be present on the same plants at the same time, and symptom confusion can occur as a function of the physiological condition of the plant or expression of plant resistance responses. A total of 209 isolates from symptomatic B. oleracea leaves were collected from three fields in central states of Mexico (58 to 71 isolates per location). All leaves showed similar symptoms, including a 10- to 15-mm tissue collapse with an occasional dark margin. Cotyledons of seven B. napus differentials were inoculated with conidia of all the isolates as described by Dilmaghani et al. (1). Two hundred isolates caused tissue collapse typical of L. maculans. However, nine obtained from white cabbage in a single location in Aguascalientes caused <5-mm dark lesions. When inoculated onto cotyledons of three B. oleracea genotypes commonly grown in Mexico (cvs. Domador, Monaco, and Iron Man), the nine isolates caused a range of symptoms characterized by tissue collapse (maximum 10 to 15 mm), showing the presence of patches of black necrotic spots within the collapse. The occasional presence of a few pycnidia allowed us to reisolate the fungus for molecular identification. ITS1-5.8S-ITS2, (internal transcribed spacers and 5.8S rDNA), actin, and β-tubulin sequences were obtained as described previously (4). Multiple gene genealogies based on these sequence data showed two subclades of L. biglobosa: L. biglobosa 'occiaustralensis' (one isolate; ITS [AM410082], actin [AM410084], and β-tubulin [AM410083]) and L. biglobosa 'canadensis' (eight isolates; ITS [AJ550868], actin [AY748956], and β-tubulin [AY749004]) (3,4), which were previously described on B. napus in the United States, Canada, and Chile. To our knowledge, this is the first report of L. biglobosa in Mexico. Previously, this species has only been reported once on B. oleracea without discrimination into subclades (2). In the Aguascalientes sampling, 24% of the isolates were L. biglobosa, similar to Canadian locations where this species is still common as compared with L. maculans (1). The large proportion of sampled L. biglobosa 'canadensis', highlights the prevalence of this subclade throughout the American continent (1). References: (1) A. Dilmaghani et al. Plant Pathol. 58:1044, 2009. (2) E. Koch et al. Mol. Plant-Microbe Interact. 4:341, 1991. (3) E. Mendes-Pereira et al. Mycol Res. 107:1287, 2003. (4) L. Vincenot et al. Phytopathology 98:321, 2008.
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Affiliation(s)
- A Dilmaghani
- INRA-BIOGER 01, F-78850 Thiverval Grignon, France
| | | | - T Rouxel
- INRA-BIOGER 01, F-78850 Thiverval Grignon, France
| | - O Moreno-Rico
- Universidad Autonoma de Aguascalientes, Microbiology Department, Aguascalientes, Ags., Mexico
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Vincent D, Balesdent MH, Gibon J, Claverol S, Lapaillerie D, Lomenech AM, Blaise F, Rouxel T, Martin F, Bonneu M, Amselem J, Dominguez V, Howlett BJ, Wincker P, Joets J, Lebrun MH, Plomion C. Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 2010; 30:4118-36. [PMID: 19960477 DOI: 10.1002/elps.200900415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
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