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Witte TE, Villeneuve N, Boddy CN, Overy DP. Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens. Front Microbiol 2021; 12:664276. [PMID: 33968000 PMCID: PMC8102738 DOI: 10.3389/fmicb.2021.664276] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic "crosstalk" with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies of Alternaria pathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes in Fusarium species offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.
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Affiliation(s)
- Thomas E. Witte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Villeneuve
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David P. Overy
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
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Victorin, the host-selective cyclic peptide toxin from the oat pathogen Cochliobolus victoriae, is ribosomally encoded. Proc Natl Acad Sci U S A 2020; 117:24243-24250. [PMID: 32929037 DOI: 10.1073/pnas.2010573117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The necrotrophic fungal pathogen Cochliobolus victoriae produces victorin, a host-selective toxin (HST) essential for pathogenicity to certain oat cultivars with resistance against crown rust. Victorin is a mixture of highly modified heterodetic cyclic hexapeptides, previously assumed to be synthesized by a nonribosomal peptide synthetase. Herein, we demonstrate that victorin is a member of the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Analysis of a newly generated long-read assembly of the C. victoriae genome revealed three copies of precursor peptide genes (vicA1-3) with variable numbers of "GLKLAF" core peptide repeats corresponding to the victorin peptide backbone. vicA1-3 are located in repeat-rich gene-sparse regions of the genome and are loosely clustered with putative victorin biosynthetic genes, which are supported by the discovery of compact gene clusters harboring corresponding homologs in two distantly related plant-associated Sordariomycete fungi. Deletion of at least one copy of vicA resulted in strongly diminished victorin production. Deletion of a gene encoding a DUF3328 protein (VicYb) abolished the production altogether, supporting its predicted role in oxidative cyclization of the core peptide. In addition, we uncovered a copper amine oxidase (CAO) encoded by vicK, in which its deletion led to the accumulation of new glycine-containing victorin derivatives. The role of VicK in oxidative deamination of the N-terminal glycyl moiety of the hexapeptides to the active glyoxylate forms was confirmed in vitro. This study finally unraveled the genetic and molecular bases for biosynthesis of one of the first discovered HSTs and expanded our understanding of underexplored fungal RiPPs.
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Wisecaver JH, Slot JC, Rokas A. The evolution of fungal metabolic pathways. PLoS Genet 2014; 10:e1004816. [PMID: 25474404 PMCID: PMC4256263 DOI: 10.1371/journal.pgen.1004816] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/12/2014] [Indexed: 01/07/2023] Open
Abstract
Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.
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Affiliation(s)
- Jennifer H. Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jason C. Slot
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (JCS); (AR)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (JCS); (AR)
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Wight WD, Labuda R, Walton JD. Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae. BMC Microbiol 2013; 13:165. [PMID: 23865912 PMCID: PMC3729494 DOI: 10.1186/1471-2180-13-165] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/12/2013] [Indexed: 11/23/2022] Open
Abstract
Background HC-toxin, a cyclic tetrapeptide, is a virulence determinant for the plant pathogenic fungus Cochliobolus carbonum. It was recently discovered that another fungus, Alternaria jesenskae, also produces HC-toxin. Results The major genes (collectively known as AjTOX2) involved in the biosynthesis of HC-toxin were identified from A. jesenskae by genomic sequencing. The encoded orthologous proteins share 75-85% amino acid identity, and the genes for HC-toxin biosynthesis are duplicated in both fungi. The genomic organization of the genes in the two fungi show a similar but not identical partial clustering arrangement. A set of representative housekeeping proteins show a similar high level of amino acid identity between C. carbonum and A. jesenskae, which is consistent with the close relatedness of these two genera within the family Pleosporaceae (Dothideomycetes). Conclusions This is the first report that the plant virulence factor HC-toxin is made by an organism other than C. carbonum. The genes may have moved by horizontal transfer between the two species, but it cannot be excluded that they were present in a common ancestor and lost from other species of Alternaria and Cochliobolus.
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Affiliation(s)
- Wanessa D Wight
- Department of Energy Plant Research Laboratory, Michigan State University, 612 Wilson Road, Room 210, East Lansing, MI 48824, USA
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Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet 2013; 9:e1003233. [PMID: 23357949 PMCID: PMC3554632 DOI: 10.1371/journal.pgen.1003233] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/14/2012] [Indexed: 11/17/2022] Open
Abstract
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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Affiliation(s)
- Bradford J. Condon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Dongliang Wu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Robin A. Ohm
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Robert Otillar
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Joel Martin
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - NurAinIzzati MohdZainudin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chunsheng Xue
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Rui Wang
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Zheng Jin Tu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Asaf Salamov
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Hui Sun
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Steve Lowry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kurt LaButti
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - James Han
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Alex Copeland
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Erika Lindquist
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kerrie Barry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Scott E. Baker
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Igor V. Grigoriev
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
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Stergiopoulos I, Collemare J, Mehrabi R, De Wit PJGM. Phytotoxic secondary metabolites and peptides produced by plant pathogenic Dothideomycete fungi. FEMS Microbiol Rev 2012; 37:67-93. [PMID: 22931103 DOI: 10.1111/j.1574-6976.2012.00349.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/01/2012] [Accepted: 07/19/2012] [Indexed: 01/25/2023] Open
Abstract
Many necrotrophic plant pathogenic fungi belonging to the class of Dothideomycetes produce phytotoxic metabolites and peptides that are usually required for pathogenicity. Phytotoxins that affect a broad range of plant species are known as non-host-specific toxins (non-HSTs), whereas HSTs affect only a particular plant species or more often genotypes of that species. For pathogens producing HSTs, pathogenicity and host specificity are largely defined by the ability to produce the toxin, while plant susceptibility is dependent on the presence of the toxin target. Non-HSTs are not the main determinants of pathogenicity but contribute to virulence of the producing pathogen. Dothideomycetes are remarkable for the production of toxins, particularly HSTs because they are the only fungal species known so far to produce them. The synthesis, regulation, and mechanisms of action of the most important HSTs and non-HSTs will be discussed. Studies on the mode of action of HSTs have highlighted the induction of programed cell death (PCD) as an important mechanism. We discuss HST-induced PCD and the plant hypersensitive response upon recognition of avirulence factors that share common pathways. In this respect, although nucleotide-binding-site-leucine-rich repeat types of resistance proteins mediate resistance against biotrophs, they can also contribute to susceptibility toward necrotrophs.
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Cornman RS, Bennett AK, Murray KD, Evans JD, Elsik CG, Aronstein K. Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis. BMC Genomics 2012; 13:285. [PMID: 22747707 PMCID: PMC3425160 DOI: 10.1186/1471-2164-13-285] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Background We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture. Results We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website. Conclusions This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.
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Jin JM, Lee S, Lee J, Baek SR, Kim JC, Yun SH, Park SY, Kang S, Lee YW. Functional characterization and manipulation of the apicidin biosynthetic pathway in Fusarium semitectum. Mol Microbiol 2010; 76:456-66. [PMID: 20233305 DOI: 10.1111/j.1365-2958.2010.07109.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Apicidin is a cyclic tetrapeptide produced by certain isolates of Fusarium semitectum and has been shown to inhibit Apicomplexan histone deacetylase. An apicidin-producing strain (KCTC16676) of the filamentous fungus was mutated using an Agrobacterium tumefaciens-mediated transformation, resulting in 24 apicidin-deficient mutants. Three of the mutants had a T-DNA insertion in a gene that encodes a non-ribosomal peptide synthetase (NRPS). Results of sequence, expression, and gene deletion analyses defined an apicidin biosynthetic gene cluster, and the NRPS gene was named as apicidin synthetase gene 1 (APS1). A 63 kb region surrounding APS1 was sequenced and analysis revealed the presence of 19 genes. All of the genes including APS1 were individually deleted to determine their roles in apicidin biosynthesis. Chemical analyses of the mutant strains showed that eight genes are required for apicidin production and were used to propose an apicidin biosynthetic pathway. The apicidin analogues apicidin E, apicidin D(2) and apicidin B were identified from chemical analysis of the mutants. The cluster gene APS2, a putative transcription factor, was shown to regulate expression of the genes in the cluster and overexpression of APS2 increased apicidin production. This study establishes the apicidin biosynthetic pathway and provides new opportunities to improve the production of apicidin and produce new analogues.
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Affiliation(s)
- Jian-Ming Jin
- Department of Agricultural Biotechnology and Centers for Fungal Pathogenesis and for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
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Slightom JL, Metzger BP, Luu HT, Elhammer AP. Cloning and molecular characterization of the gene encoding the Aureobasidin A biosynthesis complex in Aureobasidium pullulans BP-1938. Gene 2008; 431:67-79. [PMID: 19084058 DOI: 10.1016/j.gene.2008.11.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 10/21/2022]
Abstract
The gene (aba1) encoding the NRPS complex responsible for the synthesis of the cyclic peptide antibiotic Aureobasidin A (AbA) in Aureobasidium pullulans BP-1938, was cloned using a combination of PCR and library screening approaches. The aba1 gene was found to consist of a single, intronless open reading frame (ORF) of 34,980 bp, encoding an 11,659 amino acid protein with a calculated molecular mass of 1,286,254 Da. Putative promoter and translation start elements were identified upstream from the putative ATG in the aba1 gene, and a consensus poly(A) addition signal (AATAAA) was identified 191 bp downstream of the translation termination codon (TGA). As predicted by the structure AbA, the aba1 gene encodes an enzyme composed of nine biosynthetic modules, eight of which contain adenylation domains with recognizable amino acid specificity-conferring code elements, and four of which contain embedded methylation domains. The biosynthetic module located at position one in the aba1 gene lacks recognizable specificity-conferring code elements, consistent with it being responsible for incorporation of the 2-hydroxy-3-methylpentanoic acid residue at that position in AbA. An unusual feature of the aba1 gene sequence is a very high degree of shared identity among eight of the biosynthetic modules, at both the nucleotide and amino acid level. The majority of the modules share better than 70% nucleotide identity with another module in the complex, and modules with the same amino acid adenylation specificity share up to 95% identity. Insertion of a hygromycin B phosphotransferase (HPT) gene cassette in place of the module 4 sequence in aba1 resulted in a cessation of AbA production, thus validating that the isolated gene encodes the AbA biosynthesis complex.
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Affiliation(s)
- Jerry L Slightom
- AureoGen Biosciences Inc., 6475 Technology Avenue, Suite C, Kalamazoo, MI 49009, USA
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4-O-acetylation and 3-O-acetylation of trichothecenes by trichothecene 15-O-acetyltransferase encoded by Fusarium Tri3. Biosci Biotechnol Biochem 2008; 72:2485-9. [PMID: 18776660 DOI: 10.1271/bbb.80501] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the biosynthesis of Fusarium trichothecenes, the C-3 hydroxyl group of isotrichodermol must be acetylated by TRI101 for subsequent pathway genes to function. Despite the importance of this 3-O-acetylation step in biosynthesis, Tri101 is both physically and evolutionarily unrelated to other Tri genes in the trichothecene gene cluster. To gain insight into the evolutionary history of the cluster, we purified recombinant TRI3 (rTRI3), one of the two cluster gene-encoded trichothecene O-acetyltransferases, and examined to determine whether this 15-O-acetyltransferase can add an acetyl to the C-3 hydroxyl group of isotrichodermol. When a high concentration of rTRI3 was used in the assay (final concentration, 50 microM), we observed 3-O-acetylation activity against isotrichodermol that was more than 10(5) times less efficient than the known 15-O-acetylation activity against 15-deacetylcalonectrin. The rTRI3 protein also exhibited 4-O-acetylation activity when nivalenol was used as a substrate; in addition to 15-acetylnivalenol, di-acetylated derivatives, 4,15-diacetylnivalenol, and, to a lesser extent, 3,15-diacetylnivalenol, were also detected at high enzyme concentrations. The significance of the trace trichothecene 3-O-acetyltransferase activity detected in rTRI3 is discussed in relation to the evolution of the trichothecene gene cluster.
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van der Does HC, Rep M. Virulence genes and the evolution of host specificity in plant-pathogenic fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1175-82. [PMID: 17918619 DOI: 10.1094/mpmi-20-10-1175] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.
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Affiliation(s)
- H Charlotte van der Does
- Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, The Netherlands
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Chen H, Lee MH, Daub ME, Chung KR. Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae. Mol Microbiol 2007; 64:755-70. [PMID: 17462021 DOI: 10.1111/j.1365-2958.2007.05689.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a core gene cluster, comprised of eight genes (designated CTB1-8), and associated with cercosporin toxin production in Cercospora nicotianae. Sequence analysis identified 10 putative open reading frames (ORFs) flanking the previously characterized CTB1 and CTB3 genes that encode, respectively, the polyketide synthase and a dual methyltransferase/monooxygenase required for cercosporin production. Expression of eight of the genes was co-ordinately induced under cercosporin-producing conditions and was regulated by the Zn(II)Cys(6) transcriptional activator, CTB8. Expression of the genes, affected by nitrogen and carbon sources and pH, was also controlled by another transcription activator, CRG1, previously shown to regulate cercosporin production and resistance. Disruption of the CTB2 gene encoding a methyltransferase or the CTB8 gene yielded mutants that were completely defective in cercosporin production and inhibitory expression of the other CTB cluster genes. Similar 'feedback' transcriptional inhibition was observed when the CTB1, or CTB3 but not CTB4 gene was inactivated. Expression of four ORFs located on the two distal ends of the cluster did not correlate with cercosporin biosynthesis and did not show regulation by CTB8, suggesting that the biosynthetic cluster was limited to CTB1-8. A biosynthetic pathway and a regulatory network leading to cercosporin formation are proposed.
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Affiliation(s)
- Huiqin Chen
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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Turgeon BG, Baker SE. Genetic and Genomic Dissection of the Cochliobolus heterostrophus Tox1 Locus Controlling Biosynthesis of the Polyketide Virulence Factor T‐toxin. FUNGAL GENOMICS 2007; 57:219-61. [PMID: 17352906 DOI: 10.1016/s0065-2660(06)57006-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fungal pathogenesis to plants is an intricate developmental process requiring biological components found in most fungi, as well as factors that are unique to fungal taxa that participate in particular fungus-plant interactions. The host-selective polyketide toxin known as T-toxin produced by Cochliobolus heterostrophus race T, a highly virulent pathogen of maize, is an intriguing example of the latter type of virulence determinant. The Tox1 locus, which controls biosynthesis of T-toxin, originally defined as a single genetic locus, it is, in fact, two exceedingly complex loci on two chromosomes that are reciprocally translocated with respect to their counterparts in weakly pathogenic race O. Race O lacks the Tox1 locus and does not produce T-toxin. Highly virulent race T was first recognized when it caused an epidemic of Southern Corn Leaf Blight, which devastated the US corn crop in 1970. The evolutionary origin of the Tox1 locus remains unknown.
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Affiliation(s)
- B Gillian Turgeon
- Department of Plant Pathology, Cornell University Ithaca, New York 14853, USA
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Hoffmeister D, Keller NP. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 2007; 24:393-416. [PMID: 17390002 DOI: 10.1039/b603084j] [Citation(s) in RCA: 378] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the literature on the enzymes, genes, and whole gene clusters underlying natural product biosyntheses and their regulation in filamentous fungi. We have included literature references from 1958, yet the majority of citations are between 1995 and the present. A total of 295 references are cited.
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Affiliation(s)
- Dirk Hoffmeister
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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15
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Abstract
HC-toxin is a cyclic tetrapeptide of structure cyclo(D-Pro-L-Ala-D-Ala-L-Aeo), where Aeo stands for 2-amino-9,10-epoxi-8-oxodecanoic acid. It is a determinant of specificity and virulence in the interaction between the producing fungus, Cochliobolus carbonum, and its host, maize. HC-toxin qualifies as one of the few microbial secondary metabolites whose ecological function in nature is understood. Reaction to C. carbonum and to HC-toxin is controlled in maize by the Hm1 and Hm2 loci. These loci encode HC-toxin reductase, which detoxifies HC-toxin by reducing the 8-carbonyl group of Aeo. HC-toxin is an inhibitor of histone deacetylases (HDACs) in many organisms, including plants, insects, and mammals, but why inhibition of HDACs during infection by C. carbonum leads to disease is not understood. The genes for HC-toxin biosynthesis (collectively known as the TOX2 locus) are loosely clustered over >500 kb in C. carbonum. All of the known TOX2 genes are present in multiple, functional copies and are absent from natural toxin non-producing isolates. The central enzyme in HC-toxin biosynthesis is a 570-kDa non-ribosomal synthetase encoded by a 15.7-kb open reading frame. Other genes known to be required for HC-toxin encode alpha and beta subunits of fatty acid synthase, which are presumed to contribute to the synthesis of Aeo; a pathway-specific transcription factor; an efflux carrier; a predicted branched-chain amino acid aminotransferase; and an alanine racemase.
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Affiliation(s)
- Jonathan D Walton
- Department of Energy Plant Research Laboratory, Michigan State University, E. Lansing, MI 48824, USA.
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Keller NP, Turner G, Bennett JW. Fungal secondary metabolism — from biochemistry to genomics. Nat Rev Microbiol 2005; 3:937-47. [PMID: 16322742 DOI: 10.1038/nrmicro1286] [Citation(s) in RCA: 1059] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Much of natural product chemistry concerns a group of compounds known as secondary metabolites. These low-molecular-weight metabolites often have potent physiological activities. Digitalis, morphine and quinine are plant secondary metabolites, whereas penicillin, cephalosporin, ergotrate and the statins are equally well known fungal secondary metabolites. Although chemically diverse, all secondary metabolites are produced by a few common biosynthetic pathways, often in conjunction with morphological development. Recent advances in molecular biology, bioinformatics and comparative genomics have revealed that the genes encoding specific fungal secondary metabolites are clustered and often located near telomeres. In this review, we address some important questions, including which evolutionary pressures led to gene clustering, why closely related species produce different profiles of secondary metabolites, and whether fungal genomics will accelerate the discovery of new pharmacologically active natural products.
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Affiliation(s)
- Nancy P Keller
- University of Wisconsin-Madison, Department of Plant Pathology, 882 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706, USA.
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17
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Abstract
Fungal secondary metabolites are of intense interest to humankind due to their pharmaceutical (antibiotics) and/or toxic (mycotoxins) properties. In the past decade, tremendous progress has been made in understanding the genes that are associated with production of various fungal secondary metabolites. Moreover, the regulatory mechanisms controlling biosynthesis of diverse groups of secondary metabolites have been unveiled. In this review, we present the current understanding of the genetic regulation of secondary metabolism from clustering of biosynthetic genes to global regulators balancing growth, sporulation, and secondary metabolite production in selected fungi with emphasis on regulation of metabolites of agricultural concern. Particularly, the roles of G protein signaling components and developmental regulators in the mycotoxin sterigmatocystin biosynthesis in the model fungus Aspergillus nidulans are discussed in depth.
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Affiliation(s)
- Jae-Hyuk Yu
- Department of Food Microbiology and Toxicology, University of Wisconsin, Madison, Wisconsin 53706, USA.
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18
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Temporini ED, VanEtten HD. An analysis of the phylogenetic distribution of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis. Curr Genet 2004; 46:29-36. [PMID: 15118835 DOI: 10.1007/s00294-004-0506-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Revised: 02/03/2004] [Accepted: 02/04/2004] [Indexed: 11/25/2022]
Abstract
The filamentous fungus Nectria haematococca mating population VI (MPVI) contains a cluster of genes required to cause disease on pea. This cluster of pea pathogenicity genes (the PEP cluster) is located on a supernumerary chromosome that is dispensable for normal growth in culture. The genes in the PEP cluster have a different G+C content and codon usage compared with the genes located on the other chromosomes and a non-homogeneous distribution within the species. These features suggest that the PEP cluster may have been acquired by N. haematococca MPVI through horizontal gene transfer (HGT). In this work, we show that homologues of the PEP genes are present in another pea pathogen, Fusarium oxysporum f. sp. pisi, but are not common among fungi that are phylogenetically closely related to N. haematococca MPVI. This phylogenetic discontinuity supports the hypothesis that the PEP cluster originated by HGT. Our analysis has also determined that homologues for all the PEP genes are present in Neocosmospora boniensis. A molecular characterization of the PEP homologues in this fungus shows that they are organized as a cluster, which has a different physical organization from the PEP cluster in N. haematococca. In addition, although no reports have been found to show that N. boniensis is a naturally occurring pea pathogen, we show here that this species is able to cause disease on pea.
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Affiliation(s)
- Esteban D Temporini
- Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Forbes Building, Room 204, Tucson, AZ 85721, USA.
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Liu X, Inlow M, VanEtten HD. Expression profiles of pea pathogenicity ( PEP) genes in vivo and in vitro, characterization of the flanking regions of the PEP cluster and evidence that the PEP cluster region resulted from horizontal gene transfer in the fungal pathogen Nectria haematococca. Curr Genet 2003; 44:95-103. [PMID: 12925899 DOI: 10.1007/s00294-003-0428-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2003] [Revised: 06/30/2003] [Accepted: 07/05/2003] [Indexed: 11/25/2022]
Abstract
A cluster of pathogenicity genes ( PEP1, PEP2, PDA1, PEP5), termed the pea pathogenicity ( PEP) cluster and located on a 1.6-Mb conditionally dispensable (CD) chromosome, was identified in the fungal pathogen Nectria haematococca. Studies determined that the expression of PDA1 is induced in both infected pea tissues and in vitro by the phytoalexin pisatin. The present study reports the use of real-time quantitative RT-PCR to monitor the expression of each PEP gene and PDA1. In mycelia actively growing in culture, the mRNA levels of PEP1, PEP5 and PDA1 were very low and the PEP2 transcript was undetectable. In planta, PDA1 and PEP2 were strongly induced, while PEP1 and PEP5 were moderately induced. Starvation slightly enhanced the expression of PEP1, PDA1 and PEP5, while the expression of PEP2 remained undetectable. Exposure to pisatin in culture stimulated the expression of PDA1 and each PEP gene to a similar level as occurred in planta. In addition, all four pathogenicity genes displayed similar temporal patterns of expression in planta and in vitro, consistent with a coordinated regulation of these genes by pisatin during pea pathogenesis. In the flanking regions of the PEP cluster, six open reading frames (ORFs) were identified and all were expressed during infection of pea. Comparison of the codon preferences of these ORFs and seven additional genes from CD chromosomes with the codon preferences of 21 genes from other chromosomes revealed there is a codon bias that correlates with the source of the genes. This difference in codon bias is consistent with the hypothesis that genes on the CD chromosome have a different origin from genes of normal chromosomes, suggesting that horizontal gene transfer may have played a role in the evolution of pathogenesis in N. haematococca.
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Affiliation(s)
- Xiaoguang Liu
- Department of Plant Pathology, University of Arizona, Tucson, AZ 85721, USA
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Proctor RH, Brown DW, Plattner RD, Desjardins AE. Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis. Fungal Genet Biol 2003; 38:237-49. [PMID: 12620260 DOI: 10.1016/s1087-1845(02)00525-x] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fumonisins are mycotoxins produced by the maize pathogen Gibberella moniliformis and are associated with cancer in rodents. In this study, we determined the nucleotide sequence of a 75-kb region of G. moniliformis DNA and identified 18 heretofore undescribed genes flanking a cluster of five previously identified fumonisin biosynthetic (FUM) genes. Ten of the newly identified genes downstream of the cluster were coregulated with FUM genes and exhibited patterns of expression that were correlated with fumonisin production. BLASTX analyses indicated that the predicted functions of proteins encoded by the 10 genes were consistent with activities expected for fumonisin biosynthesis or self-protection. These data indicate that the 10 newly identified genes and the previously identified FUM genes constitute a fumonisin biosynthetic gene cluster. Disruption of two of the new genes, encoding longevity assurance factors, had no apparent effect on fumonisin production, but disruption of a third, encoding an ABC transporter, had a subtle effect on ratios of fumonisins produced.
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Affiliation(s)
- Robert H Proctor
- US Department of Agriculture, National Center for Agricultural Utilization Research, Agriculture Research Service, 1815 North University St., Peoria, IL 61604, USA.
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Fungal Pathogenicity Genes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1874-5334(03)80012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
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Rose MS, Yun SH, Asvarak T, Lu SW, Yoder OC, Turgeon BG. A decarboxylase encoded at the Cochliobolus heterostrophus translocation-associated Tox1B locus is required for polyketide (T-toxin) biosynthesis and high virulence on T-cytoplasm maize. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:883-893. [PMID: 12236595 DOI: 10.1094/mpmi.2002.15.9.883] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Genes at two unlinked loci (Tox1A and Tox1B) are required for production of the polyketide T-toxin by Cochliobolus heterostrophus race T, a pathogenic fungus that requires T-toxin for high virulence to maize with T-cytoplasm. Previous work indicated that Tox1A encodes a polyketide synthase (PKS1) required for T-toxin biosynthesis and for high virulence. To identify genes at Tox1B, a wild-type race T cDNA library was screened for genes missing in the genome of a Tox1B deletion mutant. The library was probed, first with a 415-kb NotI restriction fragment from the genome of the Tox1B mutant, then with the corresponding 560-kb fragment from the genome of wild type. Two genes, DEC1 (similar to acetoacetate decarboxylase-encoding genes) and RED1 (similar to genes encoding members of the medium-chain dehydrogenase/reductase superfamily), were recovered. Targeted disruption of DEC1 drastically reduced both T-toxin production and virulence of race T to T-cytoplasm maize, whereas specific inactivation of RED1 had no apparent effect on T-toxin production (as determined by bioassay) or on virulence. DEC1 and RED1 map within 1.5 kb of each other on Tox1B chromosome 6;12 and are unique to the genome of race T, an observation consistent with the hypothesis that these genes were acquired by C. heterostrophus via a horizontal transfer event.
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Affiliation(s)
- Mark S Rose
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
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Baidyaroy D, Brosch G, Graessle S, Trojer P, Walton JD. Characterization of inhibitor-resistant histone deacetylase activity in plant-pathogenic fungi. EUKARYOTIC CELL 2002; 1:538-47. [PMID: 12456002 PMCID: PMC118000 DOI: 10.1128/ec.1.4.538-547.2002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HC-toxin, a cyclic peptide made by the filamentous fungus Cochliobolus carbonum, is an inhibitor of histone deacetylase (HDAC) from many organisms. It was shown earlier that the HDAC activity in crude extracts of C. carbonum is relatively insensitive to HC-toxin as well as to the chemically unrelated HDAC inhibitors trichostatin and D85, whereas the HDAC activity of Aspergillus nidulans is sensitive (G. Brosch et al., Biochemistry 40:12855-12863, 2001). Here we report that HC-toxin-resistant HDAC activity was present in other, but not all, plant-pathogenic Cochliobolus species but not in any of the saprophytic species tested. The HDAC activities of the fungi Alternaria brassicicola and Diheterospora chlamydosporia, which also make HDAC inhibitors, were resistant. The HDAC activities of all C. carbonum isolates tested, except one non-toxin-producing isolate, were resistant. In a cross between a sensitive isolate and a resistant isolate, resistance genetically cosegregated with HC-toxin production. When fractionated by anion-exchange chromatography, extracts of resistant and sensitive isolates and species had two peaks of HDAC activity, one that was fully HC-toxin resistant and a second that was larger and sensitive. The first peak was consistently smaller in extracts of sensitive fungi than in resistant fungi, but the difference appeared to be insufficiently large to explain the differential sensitivities of the crude extracts. Differences in mRNA expression levels of the four known HDAC genes of C. carbonum did not account for the observed differences in HDAC activity profiles. When mixed together, resistant extracts protected extracts of sensitive C. carbonum but did not protect other sensitive Cochlibolus species or Neurospora crassa. Production of this extrinsic protection factor was dependent on TOXE, the transcription factor that regulates the HC-toxin biosynthetic genes. The results suggest that C. carbonum has multiple mechanisms of self-protection against HC-toxin.
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Affiliation(s)
- Dipnath Baidyaroy
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
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Wolpert TJ, Dunkle LD, Ciuffetti LM. Host-selective toxins and avirulence determinants: what's in a name? ANNUAL REVIEW OF PHYTOPATHOLOGY 2002; 40:251-85. [PMID: 12147761 DOI: 10.1146/annurev.phyto.40.011402.114210] [Citation(s) in RCA: 214] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Host-selective toxins, a group of structurally complex and chemically diverse metabolites produced by plant pathogenic strains of certain fungal species, function as essential determinants of pathogenicity or virulence. Investigations into the molecular and biochemical responses to these disease determinants reveal responses typically associated with host defense and incompatibility induced by avirulence determinants. The characteristic responses that unify these disparate disease phenotypes are numerous, yet the evidence implicating a causal relationship of these responses, whether induced by host-selective toxins or avirulence factors, in determining the consequences of the host-pathogen interaction is equivocal. This review summarizes some examples of the action of host-selective toxins to illustrate the similarity in responses with those to avirulence determinants.
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Affiliation(s)
- Thomas J Wolpert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331, USA.
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