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1.
ACS Synth Biol ; 12(4): 1133-1145, 2023 04 21.
Article En | MEDLINE | ID: mdl-36987837

Agroclavine, which has anti-depressant activity and anti-Alzheimer effects, is the raw material used to synthesize ergo-based drugs. Although the production of agroclavine from Saccharomyces cerevisiae is possible, its yield is exceptionally low. The current study proposes a modular compartmentalization strategy for identifying and modifying the bottleneck step in agroclavine overproduction. The agroclavine synthetic pathway was reconstituted in yeast, and the best combination of Claviceps fusiformis EasA with Claviceps purpurea EasD/EasG was identified. According to the data on the expression and subcellular localization of agroclavine pathway proteins, the whole pathway was divided into two modules by chanoclavine-I. Separate enzyme distribution within the downstream module and low expression of DmaW and EasE in the upstream module were identified as the bottleneck steps in the pathway. The pathway efficiency was enhanced 2.06-fold when the downstream module was entirely anchored to the endoplasmic reticulum compartment. Increasing NADPH supply by overexpressing POS5 further improved the agroclavine yield by 27.4%. Altering the intracellular localization of DmaW from the peroxisome to the endoplasmic reticulum (ER) not only improved protein expression but also accelerated the accumulation of agroclavine by 59.9%. Integration of all modified modules into the host chromosome resulted in an improved yield of agroclavine at 101.6 mg/L with flask fermentation (a 241-fold improvement over the initial strain) and ultimately produced 152.8 mg/L of agroclavine on fed-batch fermentation. The current study unlocked the potential of S. cerevisiae in the advanced biosynthesis of ergot alkaloids. It also provides a promising strategy to reconstitute compartmentalized pathways.


Ergot Alkaloids , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Ergot Alkaloids/genetics , Phosphotransferases (Alcohol Group Acceptor) , Mitochondrial Proteins , Saccharomyces cerevisiae Proteins/genetics
2.
BMC Res Notes ; 15(1): 183, 2022 May 18.
Article En | MEDLINE | ID: mdl-35585609

OBJECTIVE: The fungus Metarhizium brunneum produces ergot alkaloids of the lysergic acid amide class, most abundantly lysergic acid α-hydroxyethylamide (LAH). Genes for making ergot alkaloids are clustered in the genomes of producers. Gene clusters of LAH-producing fungi contain an α/ß hydrolase fold protein-encoding gene named easP whose presence correlates with LAH production but whose contribution to LAH synthesis in unknown. We tested whether EasP contributes to LAH accumulation through gene knockout studies. RESULTS: We knocked out easP in M. brunneum via a CRISPR/Cas9-based approach, and accumulation of LAH was reduced to less than half the amount observed in the wild type. Because LAH accumulation was reduced and not eliminated, we identified and mutated the only close homolog of easP in the M. brunneum genome, a gene we named estA. An easP/estA double mutant did not differ from the easP mutant in lysergic acid amide accumulation, indicating estA had no role in the pathway. We conclude EasP contributes to LAH accumulation but is not absolutely required. Either a gene encoding redundant function and lacking sequence identity with easP resides outside the ergot alkaloid synthesis gene cluster, or EasP plays an accessory role in the synthesis of LAH.


Ergot Alkaloids , Metarhizium , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Lysergic Acid Diethylamide/analogs & derivatives , Metarhizium/genetics , Metarhizium/metabolism
3.
J Am Chem Soc ; 144(12): 5485-5493, 2022 03 30.
Article En | MEDLINE | ID: mdl-35302734

Ergopeptines constitute one of the representative classes of ergoline alkaloids and carry a tripeptide extension on the lysergic acid core. In the current study, we discovered and structurally characterized newly isolated ergopeptine-like compounds named lentopeptins from a filamentous fungus Aspergillus lentulus, a close relative of A. fumigatus. Interestingly, in lentopeptins, the common lysergic acid moiety of ergopeptines is replaced by a cinnamic acid moiety at the N-terminus of the peptide segment. Moreover, lentopeptins lack the C-terminal proline residue necessary for the spontaneous cyclization of the peptide extension. Herein, we report the atypical lentopeptin biosynthetic pathway identified through targeted deletion of the len cluster biosynthetic genes predicted from the genome sequence. Further in vitro characterizations of the thiolation-terminal condensation-like (T-CT) didomain of the nonribosomal peptide synthetase LenA and its site-specific mutants revealed the mechanism of peptide release via diketopiperazine formation, an activity previously unreported for CT domains. Most intriguingly, in vitro assays of the cytochrome P450 LenC illuminated the unique mechanisms to generate two diastereomeric products. Lentopeptin A forms via a stereospecific hydroxylation, followed by a spontaneous bicyclic lactam core formation, while lentopeptin B is produced through an initial dehydrogenation, followed by a bicyclic lactam core formation and stereospecific hydration. Our results showcase how nature exploits common biosynthetic enzymes to forge new complex natural products effectively (213/250).


Alkaloids , Ergot Alkaloids , Lysergic Acid , Biosynthetic Pathways , Ergot Alkaloids/chemistry , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Lactams , Lysergic Acid/chemistry , Lysergic Acid/metabolism , Peptides/metabolism
4.
Metab Eng ; 69: 198-208, 2022 01.
Article En | MEDLINE | ID: mdl-34902590

Privileged ergot alkaloids (EAs) produced by the fungal genus Claviceps are used to treat a wide range of diseases. However, their use and research have been hampered by the challenging genetic engineering of Claviceps. Here we systematically refactored and rationally engineered the EA biosynthetic pathway in heterologous host Aspergillus nidulans by using a Fungal-Yeast-Shuttle-Vector protocol. The obtained strains allowed the production of diverse EAs and related intermediates, including prechanoclavine (PCC, 333.8 mg/L), chanoclavine (CC, 241.0 mg/L), agroclavine (AC, 78.7 mg/L), and festuclavine (FC, 99.2 mg/L), etc. This fungal platform also enabled the access to the methyl-oxidized EAs (MOEAs), including elymoclavine (EC), lysergic acid (LA), dihydroelysergol (DHLG), and dihydrolysergic acid (DHLA), by overexpressing a P450 enzyme CloA. Furthermore, by optimizing the P450 electron transfer (ET) pathway and using multi-copy of cloA, the titers of EC and DHLG have been improved by 17.3- and 9.4-fold, respectively. Beyond our demonstration of A. nidulans as a robust platform for EA overproduction, our study offers a proof of concept for engineering the eukaryotic P450s-contained biosynthetic pathways in a filamentous fungal host.


Claviceps , Ergot Alkaloids , Biosynthetic Pathways/genetics , Claviceps/genetics , Claviceps/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Saccharomyces cerevisiae/metabolism
5.
Toxins (Basel) ; 13(12)2021 12 02.
Article En | MEDLINE | ID: mdl-34941699

Research into ergot alkaloid production in major cereal cash crops is crucial for furthering our understanding of the potential toxicological impacts of Claviceps purpurea upon Canadian agriculture and to ensure consumer safety. An untargeted metabolomics approach profiling extracts of C. purpurea sclerotia from four different grain crops separated the C. purpurea strains into two distinct metabolomic classes based on ergot alkaloid content. Variances in C. purpurea alkaloid profiles were correlated to genetic differences within the lpsA gene of the ergot alkaloid biosynthetic gene cluster from previously published genomes and from newly sequenced, long-read genome assemblies of Canadian strains. Based on gene cluster composition and unique polymorphisms, we hypothesize that the alkaloid content of C. purpurea sclerotia is currently undergoing adaptation. The patterns of lpsA gene diversity described in this small subset of Canadian strains provides a remarkable framework for understanding accelerated evolution of ergot alkaloid production in Claviceps purpurea.


Claviceps/genetics , Ergot Alkaloids/biosynthesis , Mycotoxins/chemistry , Canada , Claviceps/metabolism , Edible Grain/microbiology , Ergot Alkaloids/genetics , Genetic Variation , Mycotoxins/genetics , Secale/microbiology , Triticale/microbiology , Triticum/microbiology
6.
Toxins (Basel) ; 13(2)2021 02 16.
Article En | MEDLINE | ID: mdl-33669319

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala-a triploid hybrid species-were 196 kb (EAS1) and 75 kb (EAS2), and the E. hybrida EAS cluster was 83 kb. As a CRISPR-based approach to target these clusters, the fungi were transformed with ribonucleoprotein (RNP) complexes of modified Cas9 nuclease (Cas9-2NLS) and pairs of single guide RNAs (sgRNAs), plus a transiently selected plasmid. In E. coenophiala, the procedure generated deletions of EAS1 and EAS2 separately, as well as both clusters simultaneously. The technique also gave deletions of the EAS cluster in E. hybrida and of individual alkaloid biosynthesis genes (dmaW and lolC) that had previously proved difficult to delete in E. coenophiala. Thus, this facile CRISPR RNP approach readily generates non-transgenic endophytes without toxin genes for use in research and forage cultivar improvement.


CRISPR-Cas Systems , Endophytes/genetics , Epichloe/genetics , Ergot Alkaloids/genetics , Gene Editing , Gene Knockout Techniques , Multigene Family , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/metabolism , Clustered Regularly Interspaced Short Palindromic Repeats , Endophytes/growth & development , Endophytes/metabolism , Epichloe/growth & development , Epichloe/metabolism , Ergot Alkaloids/biosynthesis , Ergot Alkaloids/toxicity , Gene Expression Regulation, Fungal , Reproduction, Asexual , Secondary Metabolism
7.
Toxins (Basel) ; 13(2)2021 01 20.
Article En | MEDLINE | ID: mdl-33498584

Epichloë endophytes are filamentous fungi (family Clavicipitaceae) that live in symbiotic associations with grasses in the sub family Poöideae. In New Zealand, E. festucae var. lolii confers significant resistance to perennial ryegrass (Lolium perenne) against insect and animal herbivory and is an essential component of pastoral agriculture, where ryegrass is a major forage species. The fungus produces in planta a range of bioactive secondary metabolites, including ergovaline, which has demonstrated bioactivity against the important pasture pest black beetle, but can also cause mammalian toxicosis. We genetically modified E. festucae var. lolii strain AR5 to eliminate key enzymatic steps in the ergovaline pathway to determine if intermediate ergot alkaloid compounds can still provide insecticidal benefits in the absence of the toxic end product ergovaline. Four genes (dmaW, easG, cloA, and lpsB) spanning the pathway were deleted and each deletion mutant was inoculated into five different plant genotypes of perennial ryegrass, which were later harvested for a full chemical analysis of the ergot alkaloid compounds produced. These associations were also used in a black beetle feeding deterrence study. Deterrence was seen with just chanoclavine present, but was cumulative as more intermediate compounds in the pathway were made available. Ergovaline was not detected in any of the deletion associations, indicating that bioactivity towards black beetle can be obtained in the absence of this mammalian toxin.


Coleoptera/physiology , Endophytes/genetics , Epichloe/genetics , Ergot Alkaloids/genetics , Gene Expression Regulation, Fungal , Lolium/microbiology , Pest Control, Biological , Animals , Endophytes/metabolism , Epichloe/metabolism , Ergot Alkaloids/biosynthesis , Ergotamines/metabolism , Gene Deletion , Herbivory , Lolium/parasitology , Symbiosis
8.
Fungal Genet Biol ; 145: 103481, 2020 12.
Article En | MEDLINE | ID: mdl-33130255

Claviceps purpurea is a plant pathogenic fungus which is still highly relevant in modern agriculture as it infects grasses such as rye and wheat. The disease caused by the consumption of contaminated grain or flour has been known since the Middle Ages and is termed ergotism. The main cause for the toxicity of this fungus is attributed to the ergot alkaloids. Apart from these alkaloids and the ergochromes known as ergot pigments, the secondary metabolism of C. purpurea is not well investigated. This study demonstrated the function of the polyketide synthase PKS7 in C. purpurea by determining the effect of its overexpression on metabolite profiles. For the first time, the depsides lecanoric acid, ethyl lecanorate, gerfelin, and C10-deoxy gerfelin were discovered as secondary metabolites of C. purpurea. Additionally, to estimate the contribution of isolated secondary metabolites to the toxic effects of C. purpurea, lecanoric acid, ethyl lecanorate, and orsellinic acid were tested on HepG2 and CCF-STTG1 cell lines. This study provides the first report on the function of C. purpurea PKS7 responsible for the production of depsides, among which lecanoric acid and ethyl lecanorate were identified as main secondary metabolites.


Claviceps/genetics , Ergot Alkaloids/biosynthesis , Polyketide Synthases/genetics , Salicylates/metabolism , Claviceps/metabolism , Edible Grain/genetics , Edible Grain/growth & development , Ergot Alkaloids/genetics , Plant Diseases/genetics , Plant Diseases/microbiology , Triticum/microbiology
9.
Mycologia ; 112(5): 974-988, 2020.
Article En | MEDLINE | ID: mdl-32936061

Four ergot species (Claviceps ripicola, C. quebecensis, C. perihumidiphila, and C. occidentalis) were recognized based on analyses of DNA sequences from multiple loci, including two housekeeping genes, RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α (TEF1-α), and a single-copy ergot alkaloid synthesis gene (easE) encoding chanoclavine I synthase oxidoreductase. Morphological features, ergot alkaloid production, and pathogenicity on five common cereal crops of each species were evaluated and presented in taxonomic descriptions. A synoptic key was also provided for identification.


Claviceps/classification , Claviceps/genetics , Claviceps/pathogenicity , Ergot Alkaloids/biosynthesis , Ergot Alkaloids/genetics , Fruiting Bodies, Fungal/cytology , Plant Diseases , Spores, Fungal/cytology , Canada , Crops, Agricultural/microbiology , Fruiting Bodies, Fungal/classification , Genes, Fungal , Phylogeny , Poaceae/microbiology , Sequence Analysis, DNA , Spores, Fungal/classification
10.
Mycologia ; 112(2): 230-243, 2020.
Article En | MEDLINE | ID: mdl-31910144

Claviceps species affecting Paspalum spp. are a serious problem, as they infect forage grasses such as Paspalum dilatatum and P. plicatulum, producing the ergot disease. The ascomycete C. paspali is known to be the pathogen responsible for this disease in both grasses. This fungus produces alkaloids, including ergot alkaloids and indole-diterpenes, that have potent neurotropic activities in mammals. A total of 32 isolates from Uruguay were obtained from infected P. dilatatum and P. plicatulum. Isolates were phylogenetically identified using partial sequences of the genes coding for the second largest subunit of RNA polymerase subunit II (RPB2), translation elongation factor 1-α (TEF1), ß-tubulin (TUB2), and the nuc rDNA 28S subunit (28S). Isolates were also genotyped by randomly amplified polymorphic DNA (RAPD) and presence of genes within the ergot alkaloid (EAS) and indole-diterpene (IDT) biosynthetic gene clusters. This study represents the first genetic characterization of several isolates of C. paspali. The results from this study provide insight into the genetic and genotypic diversity of Claviceps paspali present in P. dilatatum and suggest that isolates from P. plicatulum could be considered an ecological subspecies or specialized variant of C. paspali. Some of these isolates show hypothetical alkaloid genotypes never reported before.


Claviceps/genetics , Ergot Alkaloids/genetics , Alkaloids/genetics , Claviceps/classification , Claviceps/metabolism , Diterpenes , Genotype , Genotyping Techniques , Host Specificity , Indoles , Multigene Family , Paspalum/microbiology , Phylogeny , Plant Diseases/microbiology , Random Amplified Polymorphic DNA Technique
11.
Fungal Genet Biol ; 125: 71-83, 2019 04.
Article En | MEDLINE | ID: mdl-30731202

Epichloë festucae forms mutualistic symbiotic interactions with grasses of the Lolium and Festuca genera. Protection from insect and mammalian herbivory are the best-documented host benefits of these associations. The two main classes of anti-mammalian alkaloids synthesized by E. festucae are the ergot alkaloids and indole diterpenes, of which ergovaline and lolitrems are the principal terminal products. Synthesis of both metabolites require multiple gene products encoded by clusters of 11 genes located at the subtelomeric regions of chromosomes I and III respectively. These loci are essentially unexpressed in axenic culture but among the most highly expressed genes in planta. We show here that heterochromatin 1 protein (HepA) is an important component of the regulatory machinery that maintains these loci in a silent state in culture. Deletion of this gene led to derepression of eas and ltm gene expression under non-symbiotic culture conditions. Although there was no obvious culture phenotype, RNAseq analysis revealed that around 1000 genes were differentially expressed in the ΔhepA mutant compared to wild type with just one-third upregulated. Inoculation of the ΔhepA mutants into seedlings of Lolium perenne led to a severe host interaction phenotype characterized by a reduction in tiller length but an increase in tiller number. Hyphae within the leaves of these associations were much more abundant in the intercellular spaces of the leaves and aberrantly colonized the vascular bundles. This physiological change was accompanied by a dramatic change in the transcriptome with around 900 genes differentially expressed, with two thirds of these upregulated. This major physiological change was accompanied by a decrease in ltm gene expression and loss of the ability to synthesize lolitrems. These results show that HepA has an important role in controlling the chromatin state of these sub-telomeric secondary metabolite genes, including their symbiosis-specific regulation.


Chromosomal Proteins, Non-Histone/genetics , Epichloe/genetics , Ergot Alkaloids/genetics , Symbiosis/genetics , Chromobox Protein Homolog 5 , Diterpenes/metabolism , Endophytes/genetics , Endophytes/growth & development , Epichloe/growth & development , Epigenesis, Genetic , Ergot Alkaloids/biosynthesis , Fungal Proteins/genetics , Gene Expression Regulation, Fungal/genetics , Heterochromatin/genetics , Hyphae/genetics , Hyphae/growth & development , Lolium/genetics , Lolium/microbiology
12.
Appl Microbiol Biotechnol ; 101(15): 6111-6121, 2017 Aug.
Article En | MEDLINE | ID: mdl-28620689

Penicillium roqueforti produces several prenylated indole alkaloids, including roquefortine C and clavine alkaloids. The first step in the biosynthesis of roquefortine C is the prenylation of tryptophan-derived dipeptides by a dimethylallyltryptophan synthase, specific for roquefortine biosynthesis (roquefortine prenyltransferase). A second dimethylallyltryptophan synthase, DmaW2, different from the roquefortine prenyltransferase, has been studied in this article. Silencing the gene encoding this second dimethylallyltryptophan synthase, dmaW2, proved that inactivation of this gene does not prevent the production of roquefortine C, but suppresses the formation of other indole alkaloids. Mass spectrometry studies have identified these compounds as isofumigaclavine A, the pathway final product and prenylated intermediates. The silencing does not affect the production of mycophenolic acid and andrastin A. A bioinformatic study of the genome of P. roqueforti revealed that DmaW2 (renamed IfgA) is a prenyltransferase involved in isofumigaclavine A biosynthesis encoded by a gene located in a six genes cluster (cluster A). A second three genes cluster (cluster B) encodes the so-called yellow enzyme and enzymes for the late steps for the conversion of festuclavine to isofumigaclavine A. The yellow enzyme contains a tyrosine-181 at its active center, as occurs in Neosartorya fumigata, but in contrast to the Clavicipitaceae fungi. A complete isofumigaclavines A and B biosynthetic pathway is proposed based on the finding of these studies on the biosynthesis of clavine alkaloids.


Alkyl and Aryl Transferases/genetics , Ergot Alkaloids/genetics , Gene Silencing , Multigene Family , Penicillium/genetics , Alkyl and Aryl Transferases/metabolism , Biosynthetic Pathways/genetics , Cheese/microbiology , Genome, Fungal , Heterocyclic Compounds, 4 or More Rings/metabolism , Indole Alkaloids/metabolism , Indoles/metabolism , Mass Spectrometry , Penicillium/enzymology , Piperazines/metabolism , Secondary Metabolism , Tryptophan/metabolism
13.
Phytopathology ; 107(5): 504-518, 2017 May.
Article En | MEDLINE | ID: mdl-28168931

Ergot alkaloids are highly diverse in structure, exhibit diverse effects on animals, and are produced by diverse fungi in the phylum Ascomycota, including pathogens and mutualistic symbionts of plants. These mycotoxins are best known from the fungal family Clavicipitaceae and are named for the ergot fungi that, through millennia, have contaminated grains and caused mass poisonings, with effects ranging from dry gangrene to convulsions and death. However, they are also useful sources of pharmaceuticals for a variety of medical purposes. More than a half-century of research has brought us extensive knowledge of ergot-alkaloid biosynthetic pathways from common early steps to several taxon-specific branches. Furthermore, a recent flurry of genome sequencing has revealed the genomic processes underlying ergot-alkaloid diversification. In this review, we discuss the evolution of ergot-alkaloid biosynthesis genes and gene clusters, including roles of gene recruitment, duplication and neofunctionalization, as well as gene loss, in diversifying structures of clavines, lysergic acid amides, and complex ergopeptines. Also reviewed are prospects for manipulating ergot-alkaloid profiles to enhance suitability of endophytes for forage grasses.


Claviceps/genetics , Ergot Alkaloids/genetics , Evolution, Molecular , Hypocreales/genetics , Plant Diseases/microbiology , Poaceae/microbiology , Biosynthetic Pathways , Claviceps/chemistry , Claviceps/metabolism , Endophytes , Ergot Alkaloids/chemistry , Ergot Alkaloids/metabolism , Genomics , Hypocreales/chemistry , Hypocreales/metabolism , Multigene Family , Mycotoxins/chemistry , Mycotoxins/genetics , Mycotoxins/metabolism , Symbiosis
14.
G3 (Bethesda) ; 6(8): 2601-10, 2016 08 09.
Article En | MEDLINE | ID: mdl-27334939

Molecular genetic techniques to precisely eliminate genes in asexual filamentous fungi require the introduction of a marker gene into the target genome. We developed a novel strategy to eliminate genes or gene clusters located in subterminal regions of chromosomes, and then eliminate the marker gene and vector backbone used in the transformation procedure. Because many toxin gene clusters are subterminal, this method is particularly suited to generating nontoxic fungal strains. We tested this technique on Epichloë coenophiala, a seed-transmissible symbiotic fungus (endophyte) of the important forage grass, tall fescue (Lolium arundinaceum). The endophyte is necessary for maximal productivity and sustainability of this grass but can produce ergot alkaloids such as ergovaline, which are toxic to livestock. The genome sequence of E. coenophiala strain e19 revealed two paralogous ergot alkaloid biosynthesis gene clusters, designated EAS1 and EAS2. EAS1 was apparently subterminal, and the lpsB copy in EAS2 had a frame-shift mutation. We designed a vector with a fungal-active hygromycin phosphotransferase gene (hph), an lpsA1 gene fragment for homologous recombination at the telomere-distal end of EAS1, and a telomere repeat array positioned to drive spontaneous loss of hph and other vector sequences, and to stabilize the new chromosome end. We transformed E. coenophiala with this vector, then selected "knockoff" endophyte strains, confirmed by genome sequencing to lack 162 kb of a chromosome end including most of EAS1, and also to lack vector sequences. These ∆EAS1 knockoff strains produced no detectable ergovaline, whereas complementation with functional lpsB restored ergovaline production.


Alkaloids/metabolism , Chromosomes, Fungal , Endophytes/genetics , Epichloe/genetics , Epichloe/metabolism , Alkaloids/genetics , Animal Feed , Ecotype , Endophytes/metabolism , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Ergotamines/metabolism , Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Genome, Fungal , Microorganisms, Genetically-Modified , Multigene Family , Poaceae/microbiology , Seeds/microbiology , Symbiosis , Telomere/genetics
15.
Fungal Genet Biol ; 86: 71-80, 2016 Jan.
Article En | MEDLINE | ID: mdl-26688468

Clavicipitaceae is a fungal group that comprises species that closely interact with plants as pathogens, parasites or symbionts. A key factor in these interactions is the ability of these fungi to synthesize toxic alkaloid compounds that contribute to the protection of the plant host against herbivores. Some of these compounds such as ergot alkaloids are toxic to humans and have caused important epidemics throughout history. The gene clusters encoding the proteins responsible for the synthesis of ergot alkaloids and lolines in Clavicipitaceae have been elucidated. Notably, homologs to these gene clusters can be found in distantly related species such as Aspergillus fumigatus and Penicillium expansum, which diverged from Clavicipitaceae more than 400 million years ago. We here use a phylogenetic approach to analyze the evolution of these gene clusters. We found that the gene clusters conferring the ability to synthesize ergot alkaloids and loline emerged first in Eurotiomycetes and were then likely transferred horizontally to Clavicipitaceae. Horizontal gene transfer is known to play a role in shaping the distribution of secondary metabolism clusters across distantly related fungal species. We propose that HGT events have played an important role in the capability of Clavicipitaceae to produce two key secondary metabolites that have enhanced the ability of these species to protect their plant hosts, therefore favoring their interactions.


Alkaloids/genetics , Ergot Alkaloids/genetics , Evolution, Molecular , Gene Transfer, Horizontal , Hypocreales/genetics , Alkaloids/biosynthesis , Ergot Alkaloids/biosynthesis , Hypocreales/classification , Hypocreales/metabolism , Multigene Family , Phylogeny
17.
Toxins (Basel) ; 7(4): 1273-302, 2015 Apr 14.
Article En | MEDLINE | ID: mdl-25875294

The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.


Ergot Alkaloids/genetics , Ergot Alkaloids/biosynthesis , Ergot Alkaloids/chemistry , Genetic Loci , Genetic Variation , Genomics , Humans , Phylogeny , Synteny
18.
Arch Microbiol ; 197(5): 701-13, 2015 Jun.
Article En | MEDLINE | ID: mdl-25796201

Ergot alkaloids are important as mycotoxins or as drugs. Naturally occurring ergot alkaloids as well as their semisynthetic derivatives have been used as pharmaceuticals in modern medicine for decades. We identified 196 putative ergot alkaloid biosynthetic genes belonging to at least 31 putative gene clusters in 31 fungal species by genome mining of the 360 available genome sequences of ascomycetous fungi with known proteins. Detailed analysis showed that these fungi belong to the families Aspergillaceae, Clavicipitaceae, Arthrodermataceae, Helotiaceae and Thermoascaceae. Within the identified families, only a small number of taxa are represented. Literature search revealed a large diversity of ergot alkaloid structures in different fungi of the phylum Ascomycota. However, ergot alkaloid accumulation was only observed in 15 of the sequenced species. Therefore, this study provides genetic basis for further study on ergot alkaloid production in the sequenced strains.


Ascomycota/metabolism , Ergot Alkaloids/biosynthesis , Mycotoxins/biosynthesis , Arthrodermataceae/classification , Arthrodermataceae/genetics , Arthrodermataceae/metabolism , Ascomycota/classification , Ascomycota/genetics , Base Sequence , Claviceps/classification , Claviceps/genetics , Claviceps/metabolism , Ergot Alkaloids/genetics , Genes, Fungal , Multigene Family , Phylogeny , Sequence Alignment
19.
Mol Plant Microbe Interact ; 28(3): 218-31, 2015 Mar.
Article En | MEDLINE | ID: mdl-25496592

Beneficial plant-fungal interactions play an important role in the ability of plants to survive changing environmental conditions. In contrast, phytopathogenic fungi fall at the opposite end of the symbiotic spectrum, causing reduced host growth or even death. In order to exploit beneficial interactions and prevent pathogenic ones, it is essential to understand the molecular differences underlying these alternative states. The association between the endophyte Epichloë festucae and Lolium perenne (perennial ryegrass) is an excellent system for studying these molecular patterns due to the existence of several fungal mutants that have an antagonistic rather than a mutualistic interaction with the host plant. By comparing gene expression in a wild-type beneficial association with three mutant antagonistic associations disrupted in key signaling genes, we identified a core set of 182 genes that show common differential expression patterns between these two states. These gene expression changes are indicative of a nutrient-starvation response, as supported by the upregulation of genes encoding degradative enzymes, transporters, and primary metabolism, and downregulation of genes encoding putative small-secreted proteins and secondary metabolism. These results suggest that disruption of a mutualistic symbiotic interaction may lead to an elevated uptake and degradation of host-derived nutrients and cell-wall components, reminiscent of phytopathogenic interactions.


Epichloe/genetics , Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Lolium/microbiology , Symbiosis , Cell Wall/metabolism , Down-Regulation , Endophytes , Epichloe/chemistry , Epichloe/metabolism , Ergot Alkaloids/chemistry , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Gene Deletion , High-Throughput Nucleotide Sequencing , Host-Pathogen Interactions , Hyphae , Indole Alkaloids/chemistry , Indole Alkaloids/metabolism , Multigene Family , Mycotoxins/chemistry , Mycotoxins/genetics , Mycotoxins/metabolism , Plant Leaves/microbiology , Plant Shoots/microbiology , Sequence Analysis, RNA , Signal Transduction , Up-Regulation
20.
PLoS Genet ; 9(2): e1003323, 2013.
Article En | MEDLINE | ID: mdl-23468653

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.


Alkaloids , Claviceps , Epichloe , Ergot Alkaloids , Selection, Genetic , Alkaloids/chemistry , Alkaloids/classification , Alkaloids/genetics , Alkaloids/metabolism , Claviceps/genetics , Claviceps/metabolism , Claviceps/pathogenicity , Epichloe/genetics , Epichloe/metabolism , Epichloe/pathogenicity , Ergot Alkaloids/genetics , Ergot Alkaloids/metabolism , Gene Expression Regulation, Fungal , Hypocreales/genetics , Hypocreales/metabolism , Neotyphodium , Poaceae/genetics , Poaceae/metabolism , Poaceae/parasitology , Symbiosis/genetics
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