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Sheedy EM, Van de Wouw AP, Howlett BJ, May TW. Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia. Mycologia 2017; 105:547-63. [DOI: 10.3852/12-266] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Tom W. May
- Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, Victoria 3141, Australia
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Howlett BJ, Lowe RGT, Marcroft SJ, van de Wouw AP. Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease. Mycologia 2015; 107:441-51. [PMID: 25725000 DOI: 10.3852/14-317] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 11/25/2014] [Accepted: 01/25/2015] [Indexed: 11/10/2022]
Abstract
The propensity of a fungal pathogen to evolve virulence depends on features of its biology (e.g. mode of reproduction) and of its genome (e.g. amount of repetitive DNA). Populations of Leptosphaeria maculans, a pathogen of Brassica napus (canola), can evolve and overcome disease resistance bred into canola within three years of commercial release of a cultivar. Avirulence effector genes are key fungal genes that are complementary to resistance genes. In L. maculans these genes are embedded within inactivated transposable elements in genomic regions where they are readily mutated or deleted. The risk of resistance breakdown in the field can be minimised by monitoring disease severity of canola cultivars and virulence of fungal populations using high throughput molecular assays and by sowing canola cultivars with different resistance genes in subsequent years. This strategy has been exploited to avert yield losses due to blackleg disease in Australia.
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Affiliation(s)
| | - Rohan G T Lowe
- School of Botany, University of Melbourne, VIC 3010, Australia
| | - Stephen J Marcroft
- Marcroft Grains Pathology, Grains Innovation Park, Horsham, VIC 3400, Australia
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Sheedy EM, Van de Wouw AP, Howlett BJ, May TW. Population genetic structure of the ectomycorrhizal fungus Laccaria sp . A resembles that of its host tree Nothofagus cunninghamii. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Chambers K, Lowe RG, Howlett BJ, Zander M, Batley J, Van de Wouw AP, Elliott CE. Next-generation genome sequencing can be used to rapidly characterise sequences flanking T-DNA insertions in random insertional mutants of Leptosphaeria maculans. Fungal Biol Biotechnol 2014; 1:10. [PMID: 28955452 PMCID: PMC5611616 DOI: 10.1186/s40694-014-0010-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/14/2014] [Indexed: 12/05/2022] Open
Abstract
Background Banks of mutants with random insertions of T-DNA from Agrobacterium tumefaciens are often used in forward genetics approaches to identify phenotypes of interest. Upon identification of mutants of interest, the flanking sequences of the inserted T-DNA must be identified so that the mutated gene can be characterised. However, for many fungi, this task is not trivial as widely used PCR-based methods such as thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) are not successful. Findings Next-generation Illumina sequencing was used to locate T-DNA insertion sites in four mutants of Leptosphaeria maculans, a fungal plant pathogen. Sequence reads of up to 150 bp and coverage ranging from 6 to 24 times, were sufficient for identification of insertion sites in all mutants. All T-DNA border sequences were truncated to different extents. Additionally, next-generation sequencing revealed chromosomal rearrangements associated with the insertion in one of the mutants. Conclusions Next-generation sequencing is a cost-effective and rapid method of identifying sites of T-DNA insertions, and associated genomic rearrangements in Leptosphaeria maculans and potentially in other fungal species.
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Affiliation(s)
- Kylie Chambers
- School of Botany, the University of Melbourne, Parkville, 3010 Victoria Australia
| | - Rohan Gt Lowe
- School of Botany, the University of Melbourne, Parkville, 3010 Victoria Australia.,Department of Biochemistry, La Trobe University, Bundoora, 3086 Victoria Australia
| | - Barbara J Howlett
- School of Botany, the University of Melbourne, Parkville, 3010 Victoria Australia
| | - Manuel Zander
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Brisbane, 4072 Queensland Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Brisbane, 4072 Queensland Australia.,School of Plant Biology, University of Western Australia, Crawley, 6009 Western Australia Australia
| | - Angela P Van de Wouw
- School of Botany, the University of Melbourne, Parkville, 3010 Victoria Australia
| | - Candace E Elliott
- School of Botany, the University of Melbourne, Parkville, 3010 Victoria Australia
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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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Van de Wouw AP, Lowe RGT, Elliott CE, Dubois DJ, Howlett BJ. An avirulence gene, AvrLmJ1, from the blackleg fungus, Leptosphaeria maculans, confers avirulence to Brassica juncea cultivars. Mol Plant Pathol 2014; 15:523-30. [PMID: 24279453 PMCID: PMC6638781 DOI: 10.1111/mpp.12105] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The fungus Leptosphaeria maculans causes blackleg of Brassica species. Here, we report the mapping and subsequent cloning of an avirulence gene from L. maculans. This gene, termed AvrLmJ1, confers avirulence towards all three Brassica juncea cultivars tested. Analysis of RNA-seq data showed that AvrLmJ1 is housed in a region of the L. maculans genome which contains only one gene that is highly expressed in planta. The closest genes are 57 and 33 kb away and, like other avirulence genes of L. maculans, AvrLmJ1 is located within an AT-rich, gene-poor region of the genome. The encoded protein is 141 amino acids, has a predicted signal peptide and is cysteine rich. Two virulent isolates contain a premature stop codon in AvrLmJ1. Complementation of an isolate that forms cotyledonary lesions on B. juncea with the wild-type allele of AvrLmJ1 confers avirulence towards all three B. juncea cultivars tested, suggesting that the gene may confer species-specific avirulence activity.
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Sheedy EM, Van de Wouw AP, Howlett BJ, May TW. Mitochondrial microsatellite markers for the Australian ectomycorrhizal fungus Laccaria sp. A (Hydnangiaceae). Appl Plant Sci 2014; 2:apps1300086. [PMID: 25202611 PMCID: PMC4103105 DOI: 10.3732/apps.1300086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Microsatellite loci were developed for the ectomycorrhizal fungus Laccaria sp. A to investigate the population genetic structure of this fungal symbiont across its fragmented distribution in southeastern Australia. • METHODS AND RESULTS A partial genome sequence from an individual collection of Laccaria sp. A was obtained by 454 genome sequencing. Eight microsatellite markers were selected from 66 loci identified in the genome. The selected markers were highly polymorphic (4-19 alleles per locus, average 13 alleles) and amplified reproducibly from collections made across the distribution of this species. Five of these markers also amplified reproducibly in the sister species Laccaria sp. E (1). All eight of the selected microsatellite loci were from the mitochondrial genome. • CONCLUSIONS The highly polymorphic markers described here will enable population structure of Laccaria sp. A to be determined, contributing to research on mycorrhizal fungi from a novel distribution.
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Affiliation(s)
| | | | | | - Tom W. May
- Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, Victoria 3141, Australia
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Elliott CE, Callahan DL, Schwenk D, Nett M, Hoffmeister D, Howlett BJ. A gene cluster responsible for biosynthesis of phomenoic acid in the plant pathogenic fungus, Leptosphaeria maculans. Fungal Genet Biol 2013; 53:50-8. [PMID: 23396262 DOI: 10.1016/j.fgb.2013.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/20/2012] [Accepted: 01/23/2013] [Indexed: 01/08/2023]
Abstract
Phomenoic acid, a long chain aliphatic carboxylic acid is a major metabolite produced by Leptosphaeria maculans, a fungal pathogen of Brassica napus (canola). This fungus has 15 predicted polyketide synthases (PKS) and seven of them have the appropriate domains for the biosynthesis of phomenoic acid. The most highly expressed PKS gene after 7 days growth in 10% V8 juice, PKS2, was silenced and the resultant mutant produced very low levels of phomenoic acid, indicating that this PKS is involved in phomenoic acid biosynthesis. This gene is part of a co-regulated cluster of genes. Reduced expression of an adjacent gene encoding the transcriptional regulator C6TF, led to reduced expression of genes for PKS2, P450, a cytochrome P450 monoxygenase, YogA, an alcohol dehydrogenase/quinone reductase, RTA1, a lipid transport exporter superfamily member and MFS, a Major Facilitator Superfamily transporter, as well as a marked reduction in phomenoic acid production. Phomenoic acid is toxic towards another canola pathogen Leptosphaeria biglobosa 'canadensis', but not towards L. maculans and only moderately toxic towards the wheat pathogen Stagonospora nodorum. This molecule is detected in infected stems and stubble of B. napus, but biosynthesis of it does not appear to be essential for pathogenicity of L. maculans. Phomenoic acid may play a role in allowing L. maculans to outcompete other fungi in its environmental niche.
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Affiliation(s)
- Candace E Elliott
- School of Botany, The University of Melbourne, Victoria 3010, Australia.
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Wang Y, Song J, Wu Y, Odeph M, Liu Z, Howlett BJ, Wang S, Yang P, Yao L, Zhao L, Yang Q. Eplt4 proteinaceous elicitor produced in Pichia pastoris has a protective effect against Cercosporidium sofinum infections of soybean leaves. Appl Biochem Biotechnol 2013; 169:722-37. [PMID: 23271623 DOI: 10.1007/s12010-012-0015-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/04/2012] [Indexed: 12/27/2022]
Abstract
A complementary DNA library was constructed from the mycelium of Trichoderma asperellum T4, and a highly expressed gene fragment named EplT4 was found. In order to find a more efficient and cost-effective way of obtaining EplT4, this study attempted to produce EplT4 using a Pichia pastoris expression system. The gene encoding EplT4, with an additional 6-His tag at the C-terminus, was cloned into the yeast vector pPIC9K and expressed in the P. pastoris strain GS115 to obtaining more protein for the further research. Transformants of P. pastoris were selected by PCR analysis, and the ability to secrete high levels of the EplT4 protein was determined. The optimal conditions for induction were assayed using the shake flask method and an enzyme-linked immunosorbent assay. The yield of purified EplT4 was approximately 20 mg/L by nickel affinity chromatography and gel-filtration chromatography. Western blot and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer analysis revealed that the recombinant EplT4 was expressed in both its monomers and dimers. Soybean leaves treated with the EplT4 monomer demonstrated the induction of glucanase, chitinase III-A, cysteine proteinase inhibitor, and peroxidase genes. Early cellular events in plant defense response were also observed after incubation with EplT4. Soybean leaves protected by EplT4 against the pathogen Cercosporidium sofinum (Hara) indicated that EplT4 produced in P. pastoris was biologically active and would be potentially useful for improving food security.
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Affiliation(s)
- Yun Wang
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
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Van de Wouw AP, Howlett BJ. Estimating frequencies of virulent isolates in field populations of a plant pathogenic fungus, Leptosphaeria maculans, using high-throughput pyrosequencing. J Appl Microbiol 2012; 113:1145-53. [PMID: 22830361 DOI: 10.1111/j.1365-2672.2012.05413.x] [Citation(s) in RCA: 23] [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] [Received: 06/21/2012] [Revised: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 11/27/2022]
Abstract
AIM To develop a pyrosequencing assay to monitor the frequency of alleles of an avirulence gene, AvrLm4, in populations of sexual spores of Leptosphaeria maculans, a fungal pathogen of canola (Brassica napus). METHODS AND RESULTS The predominant mutation in AvrLm4 responsible for virulence to the corresponding resistance gene, Rlm4, is a single nucleotide polymorphism (SNP) at base 358. Pyrosequencing primers were designed to amplify a 90-bp region that included this SNP. The assay was developed and validated by analysing the frequency of AvrLm4 in isolate mixtures of different proportions. Furthermore, the frequency of avrLm4 (virulence allele) determined by pyrosequencing of populations of sexual spores was consistent with the frequency of avrLm4 determined by Sanger sequencing of the entire AvrLm4 gene from single isolates cultured from the same stubble. CONCLUSION This high-throughput assay can play an important role in predicting the risk of resistance breakdown in crops. SIGNIFICANCE AND IMPACT OF THE STUDY Similar assays can be applied to monitor frequencies of fungicide resistance in pathogens of crops and to assay diversity in microbial soil communities such as in soil samples from bat caves where white-nose syndrome has been detected.
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Affiliation(s)
- A P Van de Wouw
- School of Botany, University of Melbourne, Melbourne, Vic., Australia.
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McLean MS, Howlett BJ, Turkington TK, Platz GJ, Hollaway GJ. Spot Form of Net Blotch Resistance in a Diverse Set of Barley Lines in Australia and Canada. Plant Dis 2012; 96:569-576. [PMID: 30727433 DOI: 10.1094/pdis-06-11-0477] [Citation(s) in RCA: 4] [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] [Indexed: 06/09/2023]
Abstract
The responses of 95 barley lines and cultivars to spot form of net blotch (SFNB) caused by Pyrenophora teres f. maculata were analyzed as seedlings and adults in Australia and Canada. Cluster analyses revealed complex reaction responses. Only 2 lines (Esperance Orge 289 and TR3189) were resistant to all isolates at the seedling stage, whereas 15 lines and cultivars (81-82/033, Arimont, BYDV-018, CBSS97M00855T-B2-M1-Y1-M2-Y-1M-0Y, CI9776, Keel, Sloop, Torrens, TR326, VB0111, Yarra, VB0229, WI-2477, WI2553, and Wisconsin Pedigree) were resistant toward the two Canadian isolates and mixture of Australian isolates at the adult stages. In Australian field experiments, the effectiveness of SFNB resistance in three barley cultivars (Barque, Cowabbie, and Schooner) and one breeding line (VB9104) with a different source of resistance was tested. Barque, which possessed a resistance gene that provided complete resistance to SFNB, was the most effective and showed no effect on grain yield or quality in the presence of inoculum. Generally, cultivars with seedling or adult resistance had less disease and better grain quality than the susceptible control, Dash, but they were not as effective as Barque. A preliminary differential set of 19 barley lines and cultivars for P. teres f. maculata is proposed.
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Affiliation(s)
- Mark S McLean
- BioSciences Research, Department of Primary Industries, Horsham, VIC, 3401, Australia, and School of Botany, The University of Melbourne, VIC, 3010, Australia
| | | | - T Kelly Turkington
- Lacombe Research Centre, Agriculture and Agri-food Canada, Lacombe, AB, T4L 1W1, Canada
| | - Greg J Platz
- Department of Employment, Economic Development and Innovation, Warwick, QLD, 4370, Australia
| | - Grant J Hollaway
- BioSciences Research, Department of Primary Industries, Horsham, Australia
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Affiliation(s)
| | - Barbara J. Howlett
- School of Botany, The University of Melbourne, Victoria, Australia
- * E-mail:
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [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: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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Elliott CE, Fox EM, Jarvis RS, Howlett BJ. The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans. BMC Microbiol 2011; 11:169. [PMID: 21791055 PMCID: PMC3199737 DOI: 10.1186/1471-2180-11-169] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 05/11/2011] [Accepted: 07/26/2011] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Sirodesmin PL is a secondary metabolite toxin made by the ascomycetous plant pathogen, Leptosphaeria maculans. The sirodesmin biosynthetic genes are clustered in the genome. The key genes are a non-ribosomal peptide synthetase, sirP, and a pathway-specific transcription factor, sirZ. Little is known about regulation of sirodesmin production. RESULTS Genes involved in regulation of sirodesmin PL in L. maculans have been identified. Two hundred random insertional T-DNA mutants were screened with an antibacterial assay for ones producing low levels of sirodesmin PL. Three such mutants were isolated and each transcribed sirZ at very low levels. One of the affected genes had high sequence similarity to Aspergillus fumigatus cpcA, which regulates the cross-pathway control system in response to amino acid availability. This gene was silenced in L. maculans and the resultant mutant characterised. When amino acid starvation was artificially-induced by addition of 3-aminotriazole for 5 h, transcript levels of sirP and sirZ did not change in the wild type. In contrast, levels of sirP and sirZ transcripts increased in the silenced cpcA mutant. After prolonged amino acid starvation the silenced cpcA mutant produced much higher amounts of sirodesmin PL than the wild type. CONCLUSIONS Production of sirodesmin PL in L. maculans is regulated by the cross pathway control gene, cpcA, either directly or indirectly via the pathway-specific transcription factor, sirZ.
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Affiliation(s)
- Candace E Elliott
- School of Botany, the University of Melbourne, Victoria, (3010), Australia
| | - Ellen M Fox
- School of Botany, the University of Melbourne, Victoria, (3010), Australia
- Department of Sustainability and Environment, Gippsland Regional Office, (71 Hotham Street), Traralgon, Victoria (3844), Australia
| | - Renee S Jarvis
- School of Botany, the University of Melbourne, Victoria, (3010), Australia
| | - Barbara J Howlett
- School of Botany, the University of Melbourne, Victoria, (3010), Australia
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15
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Forseth RR, Fox EM, Chung D, Howlett BJ, Keller NP, Schroeder FC. Identification of cryptic products of the gliotoxin gene cluster using NMR-based comparative metabolomics and a model for gliotoxin biosynthesis. J Am Chem Soc 2011; 133:9678-81. [PMID: 21612254 DOI: 10.1021/ja2029987] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gliotoxin, a major product of the gli non-ribosomal peptide synthetase gene cluster, is strongly associated with virulence of the opportunistic human pathogen Aspergillus fumigatus. Despite identification of the gli cluster, the pathway of gliotoxin biosynthesis has remained elusive, in part because few potential intermediates have been identified. In addition, previous studies suggest that knowledge of gli-dependent metabolites is incomplete. Here we use differential analysis by 2D NMR spectroscopy (DANS) of metabolite extracts derived from gli knock-out and wild-type (WT) strains to obtain a detailed inventory of gli-dependent metabolites. DANS-based comparison of the WT metabolome with that of ΔgliZ, a knock-out strain devoid of the gene encoding the transcriptional regulator of the gli cluster, revealed nine novel gliZ-dependent metabolites including unexpected structural motifs. Their identification provides insight into gliotoxin biosynthesis and may benefit studies of the role of the gli cluster in A. fumigatus virulence. Our study demonstrates the utility of DANS for correlating gene expression and metabolite biosynthesis in microorganisms.
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Affiliation(s)
- Ry R Forseth
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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16
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Abstract
The identification of the fungal genes essential for disease underpins the development of disease control strategies. Improved technologies for gene identification and functional analyses, as well as a plethora of sequenced fungal genomes, have led to the characterization of hundreds of genes, denoted as pathogenicity genes, which are required by fungi to cause disease. We describe recent technologies applied to characterize the fungal genes involved in disease and focus on some genes that are likely to attract continuing research activity.
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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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Van de Wouw AP, Cozijnsen AJ, Hane JK, Brunner PC, McDonald BA, Oliver RP, Howlett BJ. Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathog 2010. [PMID: 21079787 DOI: 10.1071/cp16411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Brassica napus (canola) cultivars and isolates of the blackleg fungus, Leptosphaeria maculans interact in a 'gene for gene' manner whereby plant resistance (R) genes are complementary to pathogen avirulence (Avr) genes. Avirulence genes encode proteins that belong to a class of pathogen molecules known as effectors, which includes small secreted proteins that play a role in disease. In Australia in 2003 canola cultivars with the Rlm1 resistance gene suffered a breakdown of disease resistance, resulting in severe yield losses. This was associated with a large increase in the frequency of virulence alleles of the complementary avirulence gene, AvrLm1, in fungal populations. Surprisingly, the frequency of virulence alleles of AvrLm6 (complementary to Rlm6) also increased dramatically, even though the cultivars did not contain Rlm6. In the L. maculans genome, AvrLm1 and AvrLm6 are linked along with five other genes in a region interspersed with transposable elements that have been degenerated by Repeat-Induced Point (RIP) mutations. Analyses of 295 Australian isolates showed deletions, RIP mutations and/or non-RIP derived amino acid substitutions in the predicted proteins encoded by these seven genes. The degree of RIP mutations within single copy sequences in this region was proportional to their proximity to the degenerated transposable elements. The RIP alleles were monophyletic and were present only in isolates collected after resistance conferred by Rlm1 broke down, whereas deletion alleles belonged to several polyphyletic lineages and were present before and after the resistance breakdown. Thus, genomic environment and exposure to resistance genes in B. napus has affected the evolution of these linked avirulence genes in L. maculans.
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20
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Van de Wouw AP, Cozijnsen AJ, Hane JK, Brunner PC, McDonald BA, Oliver RP, Howlett BJ. Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathog 2010; 6:e1001180. [PMID: 21079787 PMCID: PMC2973834 DOI: 10.1371/journal.ppat.1001180] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [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: 03/23/2010] [Accepted: 10/06/2010] [Indexed: 11/22/2022] Open
Abstract
Brassica napus (canola) cultivars and isolates of the blackleg fungus, Leptosphaeria maculans interact in a 'gene for gene' manner whereby plant resistance (R) genes are complementary to pathogen avirulence (Avr) genes. Avirulence genes encode proteins that belong to a class of pathogen molecules known as effectors, which includes small secreted proteins that play a role in disease. In Australia in 2003 canola cultivars with the Rlm1 resistance gene suffered a breakdown of disease resistance, resulting in severe yield losses. This was associated with a large increase in the frequency of virulence alleles of the complementary avirulence gene, AvrLm1, in fungal populations. Surprisingly, the frequency of virulence alleles of AvrLm6 (complementary to Rlm6) also increased dramatically, even though the cultivars did not contain Rlm6. In the L. maculans genome, AvrLm1 and AvrLm6 are linked along with five other genes in a region interspersed with transposable elements that have been degenerated by Repeat-Induced Point (RIP) mutations. Analyses of 295 Australian isolates showed deletions, RIP mutations and/or non-RIP derived amino acid substitutions in the predicted proteins encoded by these seven genes. The degree of RIP mutations within single copy sequences in this region was proportional to their proximity to the degenerated transposable elements. The RIP alleles were monophyletic and were present only in isolates collected after resistance conferred by Rlm1 broke down, whereas deletion alleles belonged to several polyphyletic lineages and were present before and after the resistance breakdown. Thus, genomic environment and exposure to resistance genes in B. napus has affected the evolution of these linked avirulence genes in L. maculans.
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Affiliation(s)
| | | | - James K. Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Bentley, Western Australia, Australia
| | - Patrick C. Brunner
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Richard P. Oliver
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Bentley, Western Australia, Australia
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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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22
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Sexton AC, Minic Z, Cozijnsen AJ, Pedras MSC, Howlett BJ. Cloning, purification and characterisation of brassinin glucosyltransferase, a phytoalexin-detoxifying enzyme from the plant pathogen Sclerotinia sclerotiorum. Fungal Genet Biol 2008; 46:201-9. [PMID: 19041410 DOI: 10.1016/j.fgb.2008.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/30/2008] [Accepted: 10/31/2008] [Indexed: 01/24/2023]
Abstract
The plant-pathogenic fungus Sclerotinia sclerotiorum can detoxify cruciferous phytoalexins such as brassinin via glucosylation. Here we describe a multifaceted approach including genome mining, transcriptional induction, phytoalexin quantification, protein expression and enzyme purification that led to identification of a S. sclerotiorum glucosyltransferase that detoxifies brassinin. Transcription of this gene, denoted as brassinin glucosyltransferase 1 (SsBGT1), was induced significantly in response to the cruciferous phytoalexins camalexin, cyclobrassinin, brassilexin, brassinin and 3-phenylindole, a camalexin analogue. This gene was also up-regulated during infection of Brassica napus leaves. Levels of brassinin decreased significantly between 48 and 72h post-inoculation, with a concomitant increase in levels of 1-beta-d-glucopyranosylbrassinin, the product of the reaction catalysed by SsBGT1. These findings strongly implicate the involvement of this gene during infection of B. napus. This gene was cloned and expressed in Saccharomyces cerevisiae. The purified recombinant enzyme was able to glucosylate brassinin and two other phytoalexins, albeit much less effectively. This is the first report of a fungal gene involved in detoxification of plant defence molecules via glucosylation.
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Fox EM, Howlett BJ. Secondary metabolism: regulation and role in fungal biology. Curr Opin Microbiol 2008; 11:481-7. [PMID: 18973828 DOI: 10.1016/j.mib.2008.10.007] [Citation(s) in RCA: 296] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/01/2008] [Accepted: 10/01/2008] [Indexed: 11/26/2022]
Abstract
Filamentous fungi produce a diverse array of secondary metabolites--small molecules that are not necessary for normal growth or development. Secondary metabolites have a tremendous impact on society; some are exploited for their antibiotic and pharmaceutical activities, others are involved in disease interactions with plants or animals. The availability of fungal genome sequences has led to an enhanced effort at identifying biosynthetic genes for these molecules. Genes that regulate production of secondary metabolites have been identified and a link between secondary metabolism, light and sexual/asexual reproduction established. However, the role of secondary metabolites in the fungi that produce them remains a mystery. Many of these fungi live saprophytically in the soil and such molecules may provide protection against other inhabitants in this ecological niche.
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Affiliation(s)
- Ellen M Fox
- School of Botany, The University of Melbourne, Victoria, 3010, Australia
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24
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Elliott CE, Howlett BJ. Mutation of a gene in the fungus Leptosphaeria maculans allows increased frequency of penetration of stomatal apertures of Arabidopsis thaliana. Mol Plant 2008; 1:471-481. [PMID: 19825554 DOI: 10.1093/mp/ssn014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Leptosphaeria maculans, a pathogen of Brassica napus, is unable to invade most wild-type accessions of Arabidopsis thaliana, although several mutants are susceptible. The infection pathway of L. maculans via a non-invasive inoculation method on A. thaliana lms1 (undefined), pmr4-1 (defective in callose deposition), and pen1-1 and pen2-1 (defective in non-host responses to several pathogens) mutants is described. On wild types Col-0 and Ler-0, hyphae are generally arrested at stomatal apertures. A T-DNA insertional mutant of L. maculans (A22) that penetrates stomatal apertures of Col-0 and Ler-0 five to seven times more often than the wild-type isolate is described. The higher penetration frequency of isolate A22 is associated with an increased hypersensitive response, which includes callose deposition. Complementation analysis showed that the phenotype of this isolate is due to T-DNA insertion in an intronless gene denoted as ipa (increased penetration on Arabidopsis). This gene is predicted to encode a protein of 702 amino acids with best matches to hypothetical proteins in other filamentous ascomycetes. The ipa gene is expressed in the wild-type isolate at low levels in culture and during infection of A. thaliana and B. napus.
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Affiliation(s)
- Candace E Elliott
- School of Botany, The University of Melbourne, Melbourne, Vic 3010, Australia
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25
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Fox EM, Gardiner DM, Keller NP, Howlett BJ. A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans. Fungal Genet Biol 2008; 45:671-82. [PMID: 18023597 PMCID: PMC2399893 DOI: 10.1016/j.fgb.2007.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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: 08/27/2007] [Revised: 10/11/2007] [Accepted: 10/11/2007] [Indexed: 01/07/2023]
Abstract
A gene, sirZ, encoding a Zn(II)(2)Cys(6) DNA binding protein is present in a cluster of genes responsible for the biosynthesis of the epipolythiodioxopiperazine (ETP) toxin, sirodesmin PL in the ascomycete plant pathogen, Leptosphaeria maculans. RNA-mediated silencing of sirZ gives rise to transformants that produce only residual amounts of sirodesmin PL and display a decrease in the transcription of several sirodesmin PL biosynthetic genes. This indicates that SirZ is a major regulator of this gene cluster. Proteins similar to SirZ are encoded in the gliotoxin biosynthetic gene cluster of Aspergillus fumigatus (gliZ) and in an ETP-like cluster in Penicillium lilacinoechinulatum (PlgliZ). Despite its high level of sequence similarity to gliZ, PlgliZ is unable to complement the gliotoxin-deficiency of a mutant of gliZ in A. fumigatus. Putative binding sites for these regulatory proteins in the promoters of genes in these clusters were predicted using bioinformatic analysis. These sites are similar to those commonly bound by other proteins with Zn(II)(2)Cys(6) DNA binding domains.
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Affiliation(s)
- Ellen M. Fox
- School of Botany, The University of Melbourne, Vic, 3010 Australia, Corresponding author. Phone: +61 3 8344-5056 Fax: +61 3 9347-5460, E-mail address: (E. Fox)
| | | | - Nancy P. Keller
- Department of Plant Pathology, University of Wisconsin-Madison, Wisconsin, 53706 USA
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Lambou K, Tharreau D, Kohler A, Sirven C, Marguerettaz M, Barbisan C, Sexton AC, Kellner EM, Martin F, Howlett BJ, Orbach MJ, Lebrun MH. Fungi have three tetraspanin families with distinct functions. BMC Genomics 2008; 9:63. [PMID: 18241352 PMCID: PMC2278132 DOI: 10.1186/1471-2164-9-63] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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: 09/06/2007] [Accepted: 02/03/2008] [Indexed: 01/16/2023] Open
Abstract
Background Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have been identified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea, Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third family of tetraspanins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of these genes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results The exhaustive search for tetraspanins in fungal genomes reveals that higher fungi (basidiomycetes and ascomycetes) contain three families of tetraspanins (Pls1, Tsp2 and Tsp3) with different distribution amongst phyla. Pls1 is found in ascomycetes and basidiomycetes, whereas Tsp2 is restricted to basidiomycetes and Tsp3 to ascomycetes. A unique copy of each of PLS1 and TSP3 was found in ascomycetes in contrast to TSP2, which has several paralogs in the basidiomycetes, Coprinus cinereus and Laccaria bicolor. A tetraspanin-like family (Tpl1) was also identified in ascomycetes. Transcriptional analyses in various tissues of L. bicolor and M. grisea showed that PLS1 and TSP2 are expressed in all tissues in L. bicolor and that TSP3 and TPL1 are overexpressed in the sexual fruiting bodies (perithecia) and mycelia of M. grisea, suggesting that these genes are not pseudogenes. Phenotypic analysis of gene replacementmutants Δtsp3 and Δtpl1 of M. grisea revealed a reduction of the pathogenicity only on rice, in contrast to Δpls1 mutants, which are completely non-pathogenic on barley and rice. Conclusion A new tetraspanin family (Tsp3) and a tetraspanin-like protein family (Tpl1) have been identified in fungi. Functional analysis by gene replacement showed that these proteins, as well as Pls1, are involved in the infection process of the plant pathogenic fungus M. grisea. The next challenge will be to decipher the role(s) of tetraspanins in a range of symbiotic, saprophytic and human pathogenic fungi.
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Affiliation(s)
- Karine Lambou
- UMR 5240 CNRS-UCB-INSA-Bayer CropScience, Microbiologie, Adaptation et Pathogénie, Bayer CropScience, 14-20 rue Pierre Baizet, 69263 Lyon Cedex 09, France.
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Elliott CE, Gardiner DM, Thomas G, Cozijnsen A, VAN DE Wouw A, Howlett BJ. Production of the toxin sirodesmin PL by Leptosphaeria maculans during infection of Brassica napus. Mol Plant Pathol 2007; 8:791-802. [PMID: 20507539 DOI: 10.1111/j.1364-3703.2007.00433.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
SUMMARY Sirodesmin PL is a non-host-selective phytotoxin produced by Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus). Previous studies have shown that sirodesmin PL biosynthesis involves a cluster of 18 co-regulated genes and that disruption of the two-module non-ribosomal peptide synthetase gene (sirP) in this cluster prevents the production of sirodesmin PL. Loss of sirodesmin PL did not affect the growth or fertility of the sirP mutant in vitro, but this mutant had less antibacterial and antifungal activity than the wild-type. When the sirP mutant was inoculated on to cotyledons of B. napus, it caused similar-sized lesions on cotyledons as the wild-type isolate, but subsequently caused fewer lesions and was half as effective as the wild-type in colonizing stems, as shown by quantitative PCR analyses. However, no significant difference was observed in size of lesions when either wild-type or mutant isolates were injected directly into the stem. The expression of two cluster genes, sirP and an ABC transporter, sirA, was studied in planta. Fungal isolates containing fusions of the green fluorescent protein gene with the promoters of these genes fluoresced after 10 days post-inoculation (dpi). Transcripts of sirP and sirA were detected after 11 dpi in cotyledons by reverse transcriptase PCR, and expression of both genes increased dramatically in stem tissue. This expression pattern was consistent with the distribution of sirodesmin PL in planta as revealed by mass spectrometry experiments.
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Affiliation(s)
- Candace E Elliott
- School of Botany, The University of Melbourne, Victoria 3010 Australia
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Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, Nierman WC, Howlett BJ. Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol Biol 2007; 7:174. [PMID: 17897469 PMCID: PMC2045112 DOI: 10.1186/1471-2148-7-174] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [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: 02/28/2007] [Accepted: 09/26/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genes responsible for biosynthesis of fungal secondary metabolites are usually tightly clustered in the genome and co-regulated with metabolite production. Epipolythiodioxopiperazines (ETPs) are a class of secondary metabolite toxins produced by disparate ascomycete fungi and implicated in several animal and plant diseases. Gene clusters responsible for their production have previously been defined in only two fungi. Fungal genome sequence data have been surveyed for the presence of putative ETP clusters and cluster data have been generated from several fungal taxa where genome sequences are not available. Phylogenetic analysis of cluster genes has been used to investigate the assembly and heredity of these gene clusters. RESULTS Putative ETP gene clusters are present in 14 ascomycete taxa, but absent in numerous other ascomycetes examined. These clusters are discontinuously distributed in ascomycete lineages. Gene content is not absolutely fixed, however, common genes are identified and phylogenies of six of these are separately inferred. In each phylogeny almost all cluster genes form monophyletic clades with non-cluster fungal paralogues being the nearest outgroups. This relatedness of cluster genes suggests that a progenitor ETP gene cluster assembled within an ancestral taxon. Within each of the cluster clades, the cluster genes group together in consistent subclades, however, these relationships do not always reflect the phylogeny of ascomycetes. Micro-synteny of several of the genes within the clusters provides further support for these subclades. CONCLUSION ETP gene clusters appear to have a single origin and have been inherited relatively intact rather than assembling independently in the different ascomycete lineages. This progenitor cluster has given rise to a small number of distinct phylogenetic classes of clusters that are represented in a discontinuous pattern throughout ascomycetes. The disjunct heredity of these clusters is discussed with consideration to multiple instances of independent cluster loss and lateral transfer of gene clusters between lineages.
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Affiliation(s)
- Nicola J Patron
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- School of Botany, the University of Melbourne, Victoria 3010, Australia
| | - Ross F Waller
- School of Botany, the University of Melbourne, Victoria 3010, Australia
| | - Anton J Cozijnsen
- School of Botany, the University of Melbourne, Victoria 3010, Australia
| | - David C Straney
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Donald M Gardiner
- School of Botany, the University of Melbourne, Victoria 3010, Australia
- CSIRO Plant Industry, 306 Carmody Rd, St Lucia, QLD 4072, Australia
| | - William C Nierman
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 USA, and The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, Washington, DC 20037, USA
| | - Barbara J Howlett
- School of Botany, the University of Melbourne, Victoria 3010, Australia
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Hayden HL, Cozijnsen AJ, Howlett BJ. Microsatellite and Minisatellite Analysis of Leptosphaeria maculans in Australia Reveals Regional Genetic Differentiation. Phytopathology 2007; 97:879-87. [PMID: 18943938 DOI: 10.1094/phyto-97-7-0879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
ABSTRACT The population genetic structure of the fungal pathogen Leptosphaeria maculans was determined in Australia using six microsatellite and two minisatellite markers. Ascospores were sampled from Brassica napus stubble in disease nurseries and commercial fields in different sites over 2 years. The 13 subpopulations of L. maculans exhibited high gene (H = 0.393 to 0.563) and genotypic diversity, with 357 haplotypes identified among 513 isolates. Although the majority of genetic variation was distributed within subpopulations (85%), 10% occurred between the regions of eastern and Western Australia, and 5% within regions. F(ST) analysis of subpopulation pairs also showed the east-west genetic differentiation, whereas factorial correspondence analysis separated Western Australian subpopulations from eastern ones. Bayesian model-based population structure analyses of multilocus haplotypes inferred three distinct populations, one in Western Australia and an admixture of two in eastern Australia. These two regions are separated by 1,200 km of arid desert that may act as a natural barrier to gene flow, resulting in differentiation by random genetic drift. The genetic differentiation of L. maculans isolates between eastern and Western Australia means that these regions can be treated as different management units, and reinforces the need for widespread disease nurseries in each region to screen breeding lines against a range of genetic and pathogenic populations of L. maculans.
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Abstract
The genome sequence of a second plant pathogenic fungus is now available, revealing unique gene clusters encoding secretory proteins that are induced during infection and regulate pathogenesis. Gene clusters play important roles in pathogenic fungi, yet their evolution and maintenance remain a mystery.
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Affiliation(s)
- Barbara J Howlett
- School of Botany, The University of Melbourne, Victoria 3010, Australia.
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Abstract
Infection of Brassica napus cotyledons and leaves by germinating ascospores of Leptosphaeria maculans leads to production of leaf lesions followed by stem cankers (blackleg). Leptosphaeria maculans also causes root rot but the pathway of infection has not been described. An L. maculans isolate expressing green fluorescent protein (GFP) was applied to the petiole of B. napus plants. Hyphal growth was followed by fluorescence microscopy and by culturing of sections of plant tissue on growth media. Leptosphaeria maculans grew within stem and hypocotyl tissue during the vegetative stages of plant growth, and proliferated into the roots within xylem vessels at the onset of flowering. Hyphae grew in all tissues in the stem and hypocotyl, but were restricted mainly to xylem tissue in the root. Leptosphaeria maculans also infected intact roots when inoculum was applied directly to them and hyphae entered at sites of lateral root emergence. Hyphal entry may occur at other sites but the mechanism is uncertain as penetration structures were not observed. Infection of B. napus roots by L. maculans can occur via above- and below-ground sources of inoculum, but the relative importance of the infection pathways under field conditions is unknown.
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Affiliation(s)
- Susan J Sprague
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
- School of Botany, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michelle Watt
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Barbara J Howlett
- School of Botany, University of Melbourne, Parkville, VIC 3010, Australia
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Affiliation(s)
- Adrienne C Sexton
- School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
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Sexton AC, Whitten AR, Howlett BJ. Population structure of Sclerotinia sclerotiorum in an Australian canola field at flowering and stem-infection stages of the disease cycle. Genome 2006; 49:1408-15. [PMID: 17426756 DOI: 10.1139/g06-101] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Populations of the ascomycete pathogen Sclerotinia sclerotiorum sampled from a canola field were analysed using microsatellite markers. Fifty isolates were collected from ascospore-infested canola petals and, later in the season, another 55 isolates were obtained from stem lesions; these isolates were used to compare inoculum and disease-causing populations. Fifty-five unique haplotypes were identified, with gene diversity ranging from 0.40 to 0.71. Genotypic diversity was higher in the inoculum population than it had been in the previous year, but analysis of molecular variance (AMOVA) showed that less than 10% of the variation was attributable to differences between the 2 years. Genotypic disequilibrium measures were consistent with the occurrence of both clonal reproduction and out-crossing. There was no significant population subdivision between the ascospore and stem-lesion populations, as measured with fixation indices (RST= 0.015, p = 0.90) and AMOVA, suggesting that there are no genetically defined subgroups of isolates more likely to proceed from petal colonization to cause stem infection. This might be because S. sclerotiorum possesses wide-ranging pathogenicity mechanisms that account for the lack of host specificity observed to date.
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Affiliation(s)
- Adrienne C Sexton
- School of Botany, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Abstract
Fungal pathogens derive nutrition from the plants they invade. Some fungi can subvert plant defence responses such as programmed cell death to provide nutrition for their growth and colonisation. Secondary metabolite toxins produced by fungi often play a role in triggering these responses. Knowledge of the biosynthesis of these toxins, and the availability of fungal genome sequences and gene disruption techniques, allows the development of tools for experiments aimed at discovering the role of such toxins in triggering plant cell death and plant disease.
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Affiliation(s)
- Barbara J Howlett
- School of Botany, The University of Melbourne, 3010 Victoria, Australia.
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Sexton AC, Cozijnsen AJ, Keniry A, Jewell E, Love CG, Batley J, Edwards D, Howlett BJ. Comparison of transcription of multiple genes at three developmental stages of the plant pathogen Sclerotinia sclerotiorum. FEMS Microbiol Lett 2006; 258:150-60. [PMID: 16630270 DOI: 10.1111/j.1574-6968.2006.00212.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ascomycete Sclerotinia sclerotiorum is a plant pathogen with a very broad host range. In order to identify and characterize genes involved in S. sclerotiorum infection of Brassica napus (canola), expressed sequence tags (ESTs) were examined from libraries prepared from three tissues: complex appressorium (infection cushions), mycelia grown on agar and lesions formed on leaves of B. napus. A high proportion of genes (68%) had not been previously reported for S. sclerotiorum in public gene or EST databases. The types of novel genes identified in the infection cushion library highlights the functional specificity of these structures and similarities to appressoria in other fungal pathogens. Quantitative real-time PCR was used to analyse tissue specificity and timing of transcription of genes with best matches to MAS3 (appressoria-associated protein from Magnaporthe grisea), cellobiohydrolase I, oxaloacetate acetylhydrolase, metallothionein, pisatin demethylase, and an unknown gene with orthologs in fungal pathogens but not in saprophytic fungi.
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Affiliation(s)
- Adrienne C Sexton
- School of Botany, The University of Melbourne, Parkville, VIC, Australia.
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Elliott CE, Howlett BJ. Overexpression of a 3-ketoacyl-CoA thiolase in Leptosphaeria maculans causes reduced pathogenicity on Brassica napus. Mol Plant Microbe Interact 2006; 19:588-96. [PMID: 16776292 DOI: 10.1094/mpmi-19-0588] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Agrobacterium tumefaciens-mediated random mutagenesis was used to generate insertional mutants of the fungus Leptosphaeria maculans. Of 91 transformants screened, only one (A3) produced lesions of reduced size on cotyledons of canola (Brassica napus). Genes flanking the T-DNA insertion had the best matches to an alcohol dehydrogenase class 4 (ADH4)-like gene (Adh4L) and a 3-ketoacyl-CoA thiolase gene (Thiol) and were expressed in mutant A3 in vitro and in planta at significantly higher levels than in the wild type. This is the first report of a T-DNA insertion in fungi causing increased gene expression. Transformants of the wild-type isolate expressing both Adh4L and Thiol under the control of a heterologous promoter had similar pathogenicity to mutant A3. Ectopic expression of only thiolase resulted in loss of pathogenicity, suggesting that thiolase overexpression was primarily responsible for the reduced pathogenicity of the A3 isolate. The thiolase gene encoded a functional protein, as shown by assays in which a nontoxic substrate (2, 4 dichlorophenoxybutyric acid) was converted to a toxic product. The use of a translational fusion with a reporter gene showed thiolase expressed in organelles that are most likely peroxisomes.
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Affiliation(s)
- Candace E Elliott
- School of Botany, The University of Melbourne, Victoria, 3010 Australia
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Sprague SJ, Marcroft SJ, Hayden HL, Howlett BJ. Major Gene Resistance to Blackleg in Brassica napus Overcome Within Three Years of Commercial Production in Southeastern Australia. Plant Dis 2006; 90:190-198. [PMID: 30786411 DOI: 10.1094/pd-90-0190] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The infection by Leptosphaeria maculans of Brassica napus cultivars with major gene resistance derived from Brassica rapa subsp. sylvestris was studied in southeastern Australia. Following the commercial release of these cultivars in Australia in 2000, plants with stem cankers were first reported in 2002 at two geographically isolated regions in South Australia and New South Wales. In 2003, this study showed that the major gene resistance had been overcome in an area of approximately 50,000 ha in South Australia and in two fields in New South Wales (0.5 and 30 ha). There was no relationship between disease severity and incidence in 2003 and the proximity to the sites where resistance breakdown occurred in 2002. At some locations, the frequency of isolates able to overcome the B. rapa subsp. sylvestris-derived resistance had increased between 2002 and 2003. Isolates cultured from canola cultivars with either B. rapa subsp. sylvestris-derived resistance or polygenic resistance showed host specificity when inoculated onto cultivars with B. rapa subsp. sylvestris-derived or polygenic resistance, respectively. The most likely cause of the resistance breakdown was the rapid increase in frequency of L. maculans isolates virulent on this particular resistance source. The selection pressure leading to this increased frequency was probably mediated by the planting of cultivars harboring the major resistance gene in the same locations for a 3-year period, and the ability of the pathogen to produce large numbers of asexual and sexual spores.
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Affiliation(s)
- S J Sprague
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601 and School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - S J Marcroft
- Marcroft Grains Pathology, Grains Innovation Park, Horsham, Victoria 3400, Australia
| | - H L Hayden
- School of Botany, The University of Melbourne, Australia
| | - B J Howlett
- School of Botany, The University of Melbourne, Australia
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Voigt K, Cozijnsen AJ, Kroymann J, Pöggeler S, Howlett BJ. Phylogenetic relationships between members of the crucifer pathogenic Leptosphaeria maculans species complex as shown by mating type (MAT1-2), actin, and β-tubulin sequences. Mol Phylogenet Evol 2005; 37:541-57. [PMID: 16122948 DOI: 10.1016/j.ympev.2005.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 06/21/2005] [Accepted: 07/11/2005] [Indexed: 11/25/2022]
Abstract
The dothideomycetous fungus Leptosphaeria maculans comprises a complex of species differing in specificity and pathogenicity on Brassica napus. Twenty-eight isolates were investigated and compared to 20 other species of the Pleosporales order. Sequences of the mating type MAT1-2 (23), fragments of actin (48) and beta-tubulin (45) genes were determined and used for phylogenetic analyses inferred by maximum parsimony, distance, maximum likelihood, and Bayesian approaches. These different approaches using single genes essentially confirmed findings using concatanated sequences. L. maculans formed a monophyletic group separate from Leptosphaeria biglobosa. The L. biglobosa clade encompasses five sub-clades; this finding is consistent with classification made previously on the basis of internal-transcribed sequences of the ribosomal DNA repeat. The propensity for purifying and neutral evolution of the three genes was determined using sliding window analysis, a technique not previously applied to genes of filamentous fungi. For members of the L. maculans species complex, this approach showed that in comparison to actin and beta-tubulin, exonic sequences of MAT1-2 were more diverse and appeared to evolve at a faster rate. However, different regions of MAT1-2 displayed different degrees of sequence conservation. The more conserved upstream region (including the High Mobility Group domain) may be better suited for interspecies differentiation, while the more diverse downstream region is more appropriate for intraspecies comparisons.
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Affiliation(s)
- Kerstin Voigt
- Lehrstuhl für Allgemeine Mikrobiologie and Mikrobengenetik,Pilz-Referenz-Zentrum, Friedrich-Schiller-Universität Jena, Neugasse 24, 07743 Jena, Germany
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Hayden HL, Howlett BJ. Genetic structure of a population of the fungus Leptosphaeria maculans in a disease nursery of Brassica napus in Australia. Curr Genet 2005; 48:142-9. [PMID: 16032414 DOI: 10.1007/s00294-005-0006-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/10/2005] [Accepted: 06/12/2005] [Indexed: 10/25/2022]
Abstract
Microsatellite, minisatellite and mating type markers were used to determine the genetic structure of the fungus Leptosphaeria maculans within a disease nursery, where Brassica napus lines were screened for resistance to blackleg disease under high inoculum pressure. Fungal isolates were collected from pseudothecia in infected stubble and pycnidia within cotyledon lesions on seedlings within the nursery. Genetic diversity was high with gene diversity at H=0.700 across four polymorphic loci, and genotypic diversity at D=0.993. Among the 159 isolates analysed, 102 multilocus genotypes were identified. The even distribution of mating type idiomorphs MAT1-1 and MAT1-2 and gametic equilibrium within the population provided further evidence of random mating. Genetic diversity was distributed on a very fine scale in the disease nursery. The majority of genetic diversity (67%) was distributed among conidia within a lesion or among ascospores from a piece of stubble, while the remainder (33%) was distributed within lesions on seedlings or different stubble pieces. There were no among-group differences between samples from stubble and seedlings. This is consistent with the low level of genetic differentiation between the ascospore and conidia samples (F (ST)=0.017) indicating that all isolates of L. maculans from the disease nursery most likely belong to one population, and that ascospores form the primary inoculum in the disease nursery.
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Affiliation(s)
- Helen L Hayden
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Gardiner DM, Howlett BJ. Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster ofAspergillus fumigatus. FEMS Microbiol Lett 2005; 248:241-8. [PMID: 15979823 DOI: 10.1016/j.femsle.2005.05.046] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 05/14/2005] [Accepted: 05/25/2005] [Indexed: 11/29/2022] Open
Abstract
Gliotoxin is a secondary metabolite produced by several fungi including the opportunistic animal pathogen Aspergillus fumigatus. It is a member of the epipolythiodioxopiperazine (ETP) class of toxins characterised by a disulphide bridged cyclic dipeptide. A putative cluster of 12 genes involved in gliotoxin biosynthesis has been identified in A. fumigatus by a comparative genomics approach based on homology to genes from the sirodesmin (another ETP) biosynthetic gene cluster of Leptosphaeria maculans. The physical limits of the cluster in A. fumigatus have been defined by bioinformatics and by identifying the genes that are co-regulated and whose timing of expression correlates with the production of gliotoxin in culture.
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Gardiner DM, Waring P, Howlett BJ. The epipolythiodioxopiperazine (ETP) class of fungal toxins: distribution, mode of action, functions and biosynthesis. Microbiology (Reading) 2005; 151:1021-1032. [PMID: 15817772 DOI: 10.1099/mic.0.27847-0] [Citation(s) in RCA: 312] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epipolythiodioxopiperazines (ETPs) are toxic secondary metabolites made only by fungi. The best-known ETP is gliotoxin, which appears to be a virulence factor associated with invasive aspergillosis of immunocompromised patients. The toxicity of ETPs is due to the presence of a disulphide bridge, which can inactivate proteins via reaction with thiol groups, and to the generation of reactive oxygen species by redox cycling. With the availability of complete fungal genome sequences and efficient gene-disruption techniques for fungi, approaches are now feasible to delineate biosynthetic pathways for ETPs and to gain insights into the evolution of such gene clusters.
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Affiliation(s)
- Donald M Gardiner
- School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Paul Waring
- School of Chemistry, Australian National University, ACT 0200, Australia
| | - Barbara J Howlett
- School of Botany, The University of Melbourne, Victoria 3010, Australia
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Abstract
Sirodesmin PL is a phytotoxin produced by the fungus Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus). This phytotoxin belongs to the epipolythiodioxopiperazine (ETP) class of toxins produced by fungi including mammalian and plant pathogens. We report the cloning of a cluster of genes with predicted roles in the biosynthesis of sirodesmin PL and show via gene disruption that one of these genes (encoding a two-module non-ribosomal peptide synthetase) is essential for sirodesmin PL biosynthesis. Of the nine genes in the cluster tested, all are co-regulated with the production of sirodesmin PL in culture. A similar cluster is present in the genome of the opportunistic human pathogen Aspergillus fumigatus and is most likely responsible for the production of gliotoxin, which is also an ETP. Homologues of the genes in the cluster were also identified in expressed sequence tags of the ETP producing fungus Chaetomium globosum. Two other fungi with publicly available genome sequences, Magnaporthe grisea and Fusarium graminearum, had similar gene clusters. A comparative analysis of all four clusters is presented. This is the first report of the genes responsible for the biosynthesis of an ETP.
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Affiliation(s)
- Donald M Gardiner
- School of Botany, The University of Melbourne, Victoria, Australia 3010.
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Gardiner DM, Jarvis RS, Howlett BJ. The ABC transporter gene in the sirodesmin biosynthetic gene cluster of Leptosphaeria maculans is not essential for sirodesmin production but facilitates self-protection. Fungal Genet Biol 2005; 42:257-63. [PMID: 15707846 DOI: 10.1016/j.fgb.2004.12.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 11/26/2004] [Accepted: 12/03/2004] [Indexed: 11/26/2022]
Abstract
Epipolythiodioxopiperazine toxins are secreted by a range of fungi, including Leptosphaeria maculans, which produces sirodesmin, and Aspergillus fumigatus, which produces gliotoxin. The L. maculans biosynthetic gene cluster for sirodesmin includes an ABC transporter gene, sirA. Disruption of this gene led to increased secretion of sirodesmin into the medium and an altered ratio of sirodesmin to its immediate precursor. The transcription pattern of a peptide synthetase that catalyses an early step in sirodesmin biosynthesis was elevated in the sirA mutant by 47% over a 7-day period. This was consistent with the finding that the transporter mutant had elevated sirodesmin levels. Despite increased production of sirodesmin, the sirA mutant was more sensitive to both sirodesmin and gliotoxin. The putative gliotoxin transporter gene, gliA, (a major facilitator superfamily transporter) from A. fumigatus complemented the tolerance of the L. maculans sirA mutant to gliotoxin, but not to sirodesmin. The results indicate that SirA contributes to self-protection against sirodesmin in L. maculans and suggest a transporter other than SirA is primarily responsible for efflux of endogenously produced sirodesmin.
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Affiliation(s)
- Donald M Gardiner
- School of Botany, The University of Melbourne, Vic. 3010, Australia.
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Sexton AC, Howlett BJ. Microsatellite markers reveal genetic differentiation among populations of Sclerotinia sclerotiorum from Australian canola fields. Curr Genet 2004; 46:357-65. [PMID: 15549318 DOI: 10.1007/s00294-004-0543-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/27/2004] [Accepted: 09/30/2004] [Indexed: 10/26/2022]
Abstract
Eight microsatellite markers were applied to 154 Sclerotinia sclerotiorum isolates from four Australian canola fields, to determine the extent of genetic variation and differentiation in populations of this pathogen. A total of 82 different haplotypes were identified and in each population many haplotypes were unique. Mycelial compatibility grouping, a phenotypic marker system controlled by multiple loci, was often associated with groups of identical or closely related microsatellite haplotypes. Genotypic diversity ranged from 36% to 80% of maximum in the four populations, and gene diversity ranged from 0.23 to 0.79. Genotypic disequilibrium analyses on each of the four populations suggested that both clonal and sexual reproduction contributed to population structure. Analyses based on genetic diversity and fixation indices demonstrated a moderate to high level of differentiation (R(ST)=0.16-0.33, F(ST)=0.18-0.23) between populations from New South Wales and those from Victoria. Despite this genetic diversity, most isolates did not vary in virulence on canola leaves.
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Affiliation(s)
- Adrienne C Sexton
- School of Botany, The University of Melbourne, Parkville, VIC 3010, Australia.
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Gardiner DM, Howlett BJ. Negative selection using thymidine kinase increases the efficiency of recovery of transformants with targeted genes in the filamentous fungus Leptosphaeria maculans. Curr Genet 2004; 45:249-55. [PMID: 14749893 DOI: 10.1007/s00294-004-0488-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 12/09/2003] [Accepted: 01/05/2004] [Indexed: 11/27/2022]
Abstract
A vector system was constructed that is designed to decrease the number of transformants required to be screened when looking for gene disruption events in filamentous fungi. This vector was used to mutate two genes, an ATP-binding cassette transporter ( LmABCt4) and a two-component histidine kinase gene ( LmHK1) in the ascomycete Leptosphaeria maculans. The system uses the thymidine kinase gene from the herpes simplex virus as a negative selectable marker. Thymidine kinase expression is regulated by the TrpC regulatory elements from Aspergillus nidulans and should be applicable to other ascomycetous fungi. When thymidine kinase is expressed in the presence of particular thymidine analogues, these analogues are converted to toxic compounds which kill the cell. We also report the transformation of L. maculans using Agrobacterium tumefaciens-mediated DNA delivery.
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Affiliation(s)
- Donald M Gardiner
- School of Botany, The University of Melbourne, 3010, Melbourne, Victoria, Australia.
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Cozijnsen AJ, Howlett BJ. Characterisation of the mating-type locus of the plant pathogenic ascomycete Leptosphaeria maculans. Curr Genet 2003; 43:351-7. [PMID: 12679880 DOI: 10.1007/s00294-003-0391-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2002] [Revised: 02/17/2003] [Accepted: 03/03/2003] [Indexed: 11/29/2022]
Abstract
The nucleotide sequences of regions containing the mating-type locus of the plant-pathogenic ascomycete Leptosphaeria maculans are described. The MAT1-1 gene is 1,368 bp, encoding a predicted protein of 441 amino acids, with a 45-bp intron. The MAT1-2 gene is 1,246 bp, encoding a predicted protein of 397 amino acids, with a 55-bp intron. This latter gene is 334 bp downstream of a small open reading frame (32 amino acids) with four amino acids in identical positions to those in the high mobility group binding domain of the MAT1-2 genes. The DNA lyase and anaphase promoting complex genes are 3' of the MAT gene, whilst a gene denoted ORF1 in Cochliobolus heterostrophus and the GTPase activating protein are present 5' of MAT. The transcriptional patterns of genes within and flanking the L. maculans MAT locus are determined. The MAT transcripts are about twice the length of the gene. The ORF1 transcript is 1.2 kb in the MAT1-1 isolate and 1.0 kb in the MAT1-2 isolate; and probes cross-hybridise weakly. A mating-type PCR assay with three nucleotide primers is developed for L. maculans.
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Affiliation(s)
- Anton J Cozijnsen
- School of Botany, The University of Melbourne, 3010 Victoria, Australia
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Idnurm A, Howlett BJ. Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans. Fungal Genet Biol 2003; 39:31-7. [PMID: 12742061 DOI: 10.1016/s1087-1845(02)00588-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Restriction enzyme mediated insertional mutagenesis using a plasmid, pUCATPH, that confers hygromycin resistance, generated loss-of-pathogenicity mutants of Leptosphaeria maculans, the fungus that causes blackleg disease of Brassica napus. Of 516 L. maculans transformants analysed, 12 were pathogenicity mutants. When eight of these mutants were crossed to an isolate that attacks B. napus, cosegregation of pUCATPH sequences and loss of pathogenicity was not observed, suggesting that these mutations were not linked to plasmid sequences. In seven of eight crosses analysed, progeny with the hygromycin resistance gene were hygromycin-sensitive. Sequence analysis of an amplified fragment of pUCATPH in six clones derived from one 'silenced' progeny showed mutation of GC to AT on one DNA strand, reminiscent of repeat-induced point mutation (RIP) in Neurospora crassa. One loss-of-pathogenicity mutant had pUCATPH inserted in the promoter of a gene with an open reading frame of 529 amino acids that had no database match. Reintroduction of a wild-type copy of the gene to this mutant restored the ability to form lesions on cotyledons of B. napus.
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Affiliation(s)
- Alexander Idnurm
- School of Botany, The University of Melbourne, Vic. 3010, Australia
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Abstract
Analysis of sterols in mycelia of the ascomycete, Leptosphaeria maculans by gas chromatography-mass spectrometry revealed that ergosterol comprised 95% of the total sterols, with eight other sterols comprising the remaining 5%. Six of these latter sterols were putative precursors of ergosterol and their presence suggested a pathway for ergosterol biosynthesis in this fungus. Ergosterol biosynthesis in fungi is inhibited by the triazole antifungal agent flutriafol. When L. maculans was grown in the presence of flutriafol, ergosterol content decreased while two 14 alpha-methylated sterols, 24-methylene dihydrolanosterol and obtusifoliol, accumulated.
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Affiliation(s)
- K M Griffiths
- School of Botany, the University of Melbourne 3010, Victoria, Australia
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Griffiths KM, Howlett BJ. Transcription of sterol Delta(5,6)-desaturase and sterol 14alpha-demethylase is induced in the plant pathogenic ascomycete, Leptosphaeria maculans, during treatment with a triazole fungicide. FEMS Microbiol Lett 2002; 217:81-7. [PMID: 12445649 DOI: 10.1111/j.1574-6968.2002.tb11459.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Two genes whose derived amino acid sequences closely resemble the ergosterol biosynthetic enzymes, sterol Delta(5,6)-desaturase (erg3) and sterol 14alpha-demethylase (erg11), were cloned from the plant pathogenic fungus Leptosphaeria maculans. Transcript levels of both these genes increased following exposure of L. maculans to the triazole fungicide, flutriafol, which specifically inhibits the ergosterol biosynthetic pathway. This induction may be due to a decrease in ergosterol content or to abnormal levels of the ergosterol precursor, 24-methylene dihydrolanosterol.
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