Fungal secondary metabolism — from biochemistry to genomics
TL;DR: Questions are addressed, 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.
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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DSM1, Delft University of Technology2, University of Nottingham3, Technical University of Denmark4, Wageningen University and Research Centre5, University of Sheffield6, Utrecht University7, Biomax Informatics AG8, CLC bio9, University of Liverpool10, Ghent University11, University of Manchester12, University of Provence13, University of Groningen14, Pasteur Institute15, University of Amsterdam16, University of Angers17, Leiden University18, Radboud University Nijmegen19, University of Szeged20
TL;DR: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid, and the sequenced genome revealed a large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors.
Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
1,161 citations
Cites background from "Fungal secondary metabolism — from ..."
...Secondary metabolism and safety Among the secondary metabolites produced by filamentous fungi, mycotoxins are most relevant from a safety point of vie...
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Institut national de la recherche agronomique1, Broad Institute2, Wageningen University and Research Centre3, University of Salamanca4, University of Provence5, Utrecht University6, University of Nottingham7, SupAgro8, Kaiserslautern University of Technology9, University of Toronto10, La Trobe University11, University of Lyon12, Tel Aviv University13, National University of Mar del Plata14, Landcare Research15, University of Nice Sophia Antipolis16, University of Paris-Sud17, University of La Laguna18, University of Melbourne19, Agro ParisTech20, Andrés Bello National University21, University of Exeter22, Plant & Food Research23, Hebrew University of Jerusalem24, University of Florida25, Texas A&M University26
TL;DR: Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.
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.
855 citations
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...Generally in fungi, all genes from a SM cluster are involved in the same metabolic pathway and are co-regulated [111,113,114]....
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...cinerea, we searched the genomes for genes encoding key enzymes such as NRPS (non-ribosomal peptide synthetase), PKS (polyketide synthase), TS (terpene synthase) and DMATS (dimethylallyl tryptophane synthase), which are essential for the biosynthesis of peptides, polyketides, terpenes and alkaloids, respectively [111]....
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Max Planck Society1, University of Salamanca2, University of Kentucky3, Centraalbureau voor Schimmelcultures4, University of California, Davis5, Agricultural Research Organization, Volcani Center6, University of Cologne7, Broad Institute8, GATC Biotech9, Seoul National University10, United States Department of Agriculture11, University of Massachusetts Amherst12, DuPont Pioneer13, Centre national de la recherche scientifique14, Texas A&M University15, University of Erlangen-Nuremberg16, Kyoto Prefectural University17, Institut national de la recherche agronomique18, West Virginia University19, RWTH Aachen University20, University of Wisconsin-Madison21, National Center for Agricultural Utilization Research22, University of Florida23, Michigan State University24, Kyoto University25
TL;DR: Findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
Abstract: Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
753 citations
TL;DR: In this article, the authors identified the heterotrimeric velvet complex VelB/VeA/LaeA connecting light-responding developmental regulation and control of secondary metabolism in Aspergillus nidulans.
Abstract: Differentiation and secondary metabolism are correlated processes in fungi that respond to light. In Aspergillus nidulans, light inhibits sexual reproduction as well as secondary metabolism. We identified the heterotrimeric velvet complex VelB/VeA/LaeA connecting light-responding developmental regulation and control of secondary metabolism. VeA, which is primarily expressed in the dark, physically interacts with VelB, which is expressed during sexual development. VeA bridges VelB to the nuclear master regulator of secondary metabolism, LaeA. Deletion of either velB or veA results in defects in both sexual fruiting-body formation and the production of secondary metabolites.
721 citations
TL;DR: This Review discusses the strategies that have been developed in bacteria and fungi to identify and induce the expression of silent BGCs, and briefly summarize methods for the isolation and structural characterization of their metabolic products.
Abstract: Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
692 citations
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Washington University in St. Louis1, J. Craig Venter Institute2, Wellcome Trust Sanger Institute3, University of Manchester4, Complutense University of Madrid5, Tohoku University6, University of Nottingham7, Tulane University8, University of Kentucky9, Max Planck Society10, Spanish National Research Council11, University of Salamanca12, University of São Paulo13, Innsbruck Medical University14, University of Wisconsin-Madison15, University of Tokyo16, Nagoya University17, National Institute of Advanced Industrial Science and Technology18, Pasteur Institute19, University of Texas MD Anderson Cancer Center20, University of Idaho21, University of Lausanne22, University of Göttingen23, Tokyo University of Agriculture and Technology24, University of Sheffield25, Broad Institute26
TL;DR: The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus and revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype.
Abstract: Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.
1,356 citations
Broad Institute1, J. Craig Venter Institute2, Stanford University3, Oregon Health & Science University4, University of Glasgow5, Genetic Information Research Institute6, Institut Universitaire de France7, University of Kentucky8, University of Nebraska–Lincoln9, University of Göttingen10, Pasteur Institute11, University of São Paulo12, Texas A&M University13, Wellcome Trust Sanger Institute14, John Innes Centre15, University of Wisconsin-Madison16, Max Planck Society17, University of Oregon18, University of Nottingham19, Spanish National Research Council20, Ohio State University21, University of Georgia22, Tokyo Institute of Technology23, National Institute of Advanced Industrial Science and Technology24, George Washington University25, University of Manchester26, University of Liverpool27, University of Melbourne28, Karlsruhe Institute of Technology29, University of Idaho30
TL;DR: The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution, and a comparative study with Aspergillus fumigatus and As pergillus oryzae, used in the production of sake, miso and soy sauce, provides new insight into eukaryotic genome evolution and gene regulation.
Abstract: The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
1,297 citations
National Institute of Advanced Industrial Science and Technology1, National Institute of Technology and Evaluation2, Intec, Inc.3, Tohoku University4, University of Tokyo5, Nagoya University6, Tokyo University of Agriculture and Technology7, University of Manchester8, Broad Institute9, George Washington University10, Agricultural Research Service11, University of Nottingham12, Tulane University13, J. Craig Venter Institute14, Kikkoman15, Kyushu University16, Nara Institute of Science and Technology17
TL;DR: Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
Abstract: The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
1,149 citations
TL;DR: In the case of the filamentous fungus Aspergillus nidulans, the only described work that genetically links the sporulation of this fungus to the production of the mycotoxin sterigmatocystin through a shared G-protein signaling pathway is reviewed.
Abstract: Filamentous fungi are unique organisms-rivaled only by actinomycetes and plants-in producing a wide range of natural products called secondary metabolites. These compounds are very diverse in structure and perform functions that are not always known. However, most secondary metabolites are produced after the fungus has completed its initial growth phase and is beginning a stage of development represented by the formation of spores. In this review, we describe secondary metabolites produced by fungi that act as sporogenic factors to influence fungal development, are required for spore viability, or are produced at a time in the life cycle that coincides with development. We describe environmental and genetic factors that can influence the production of secondary metabolites. In the case of the filamentous fungus Aspergillus nidulans, we review the only described work that genetically links the sporulation of this fungus to the production of the mycotoxin sterigmatocystin through a shared G-protein signaling pathway.
967 citations
TL;DR: In Saccharopolyspora erythraea, the genes that govern synthesis of the polyketide portion of the macrolide antibiotic erythyromycin are organized in six repeated units that encode fatty acid synthase (FAS)-like activities, and each repeated unit is designated a module, and two modules are contained in a single open reading frame.
Abstract: In Saccharopolyspora erythraea, the genes that govern synthesis of the polyketide portion of the macrolide antibiotic erythromycin are organized in six repeated units that encode fatty acid synthase (FAS)-like activities. Each repeated unit is designated a module, and two modules are contained in a single open reading frame. A model for the synthesis of this complex polyketide is proposed, where each module encodes a functional synthase unit and each synthase unit participates specifically in one of the six FAS-like elongation steps required for formation of the polyketide. In addition, genetic organization and biochemical order of events appear to be colinear. Evidence for the model is provided by construction of a selected mutant and by isolation of a polyketide of predicted structure.
874 citations