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Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products.

Throckmorton K, Wiemann P, Keller NP - Toxins (Basel) (2015)

Bottom Line: Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V.We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them.Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706-1580, USA. kthrockmorto@wisc.edu.

ABSTRACT
Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs), with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans). This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

No MeSH data available.


Related in: MedlinePlus

A clade of gsf-, pkg-, PskI-, and SNOG_15820-like clusters. An excerpt of the group V phylogenetic tree made with FastTree [60], Figure S2, containing the PKSs from the griseofulvin-producing cluster, GsfA (ADI24953) [48], three alternariol-producing clusters [54,61,62], and a group of related uncharacterized PKSs, is shown at top left. The bootstrap values are presented next to their corresponding nodes. The yellow boxes indicate PKSs from the same species in which the characterized clusters were originally described. Next to the tree are the gene clusters corresponding to the PKSs that were identifiable through MultiGeneBLAST analysis. Genes are represented as arrows with a color corresponding to the proteins they encode which are detailed in the color key below the tree and cluster diagrams. Asterisks signify potential gene truncation due to misannotation. Genes with no color were not identified as homologous to any group V3 cluster gene. The products of the characterized examples from this clade, griseofulvin and alternariol, are shown at bottom. C6TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR2-like, SDH = Short chain dehydrogenase, TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR1-like, DRT = Drug resistance transporter, EmrB subfamily, FDH = Flavin-dependent halogenase, PKS = Polyketide synthase, OMT = O-methyltransferase, NSD = Nucleoside-diphosphate-sugar dehydratase, P450 = Cytochrome P450, ANK = Ankyrin repeat-containing protein, AHD = YcaC-related amidohydrolase, FDH/OMT = Flavin-dependent halogenase and O-methyltransferase bifunctional protein, MβL = Metallo-β-lactamase-type thioesterase. * Asterisks signify potential gene truncation due to misannotation.
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toxins-07-03572-f007: A clade of gsf-, pkg-, PskI-, and SNOG_15820-like clusters. An excerpt of the group V phylogenetic tree made with FastTree [60], Figure S2, containing the PKSs from the griseofulvin-producing cluster, GsfA (ADI24953) [48], three alternariol-producing clusters [54,61,62], and a group of related uncharacterized PKSs, is shown at top left. The bootstrap values are presented next to their corresponding nodes. The yellow boxes indicate PKSs from the same species in which the characterized clusters were originally described. Next to the tree are the gene clusters corresponding to the PKSs that were identifiable through MultiGeneBLAST analysis. Genes are represented as arrows with a color corresponding to the proteins they encode which are detailed in the color key below the tree and cluster diagrams. Asterisks signify potential gene truncation due to misannotation. Genes with no color were not identified as homologous to any group V3 cluster gene. The products of the characterized examples from this clade, griseofulvin and alternariol, are shown at bottom. C6TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR2-like, SDH = Short chain dehydrogenase, TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR1-like, DRT = Drug resistance transporter, EmrB subfamily, FDH = Flavin-dependent halogenase, PKS = Polyketide synthase, OMT = O-methyltransferase, NSD = Nucleoside-diphosphate-sugar dehydratase, P450 = Cytochrome P450, ANK = Ankyrin repeat-containing protein, AHD = YcaC-related amidohydrolase, FDH/OMT = Flavin-dependent halogenase and O-methyltransferase bifunctional protein, MβL = Metallo-β-lactamase-type thioesterase. * Asterisks signify potential gene truncation due to misannotation.

Mentions: This group V subgroup includes heptaketide synthases catalyzing an unusual C1–C6 or C2–C7 first cyclization followed by a C8–C13 second cyclization. Characterized examples include alternariol and griseofulvin. Alternariol is an important mycotoxin produced by members of Alternaria, Aspergillus, and Phaeosphaeria [54,61,62]. This metabolite is a fairly common crop contaminant with carcinogenic, phytotoxic, and antifungal activity. Despite its importance, genetic studies characterizing the biosynthesis of alternariol were only recently undertaken. To date, three gene clusters have been implicated in the synthesis of alternariol, one in Alternaria alternata, one in A. nidulans, and one in Phaeosphaeria nodorum (syn. Parastagonospora nodorum) (Figure 7). Initially, PksJ (AFN68301) was identified in A. alternata using siRNA and gene deletion approaches as the PKS primarily responsible for alternariol production. However, two other PKSs, PksH (AFN68299) and PksI (AFN68300), were shown to be affected by the knockdown of pksJ expression. Notably, no MβL-TE was identified adjacent to PksJ in this study [61]. In A. nidulans, promoter replacement experiments were used to show that PkgA (CBF79143) and PkgB produce alternariol and coumarins [54]. Most recently, in P. nodorum, SNOG_15829 (EAT76667) was also found to produce alternariol. The cluster associated with this NR-PKS includes a gene encoding an MβL-TE (SNOG_15826), but it bears little similarity to the other MBL-TEs of group V clusters [62], which could be due to poor sequence quality. Interestingly, the NR-PKS EAT76667 is most similar to PksI from A. alternata, suggesting that PksI, and not PksJ or PksH, is the alternariol-producing PKS in A. alternata. These clusters were not characterized further than the identification of a PKS and an MβL-TE; the additional genes analyzed by MGB as part of the PkgA (CBF79143) and SNOG_15829 (EAT76667) clusters were included based only on their reported co-regulation with the PKS- and MβL-TE-encoding genes [62,93]. Because of these limitations in the studies characterizing alternariol-producing gene clusters, our product predictions for group V3 PKSs are based only on the presence or absence of genes encoding a PKS and MβL-TE and the closeness of the relationships of these PKSs with the characterized group V3 PKSs (Table 1).


Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products.

Throckmorton K, Wiemann P, Keller NP - Toxins (Basel) (2015)

A clade of gsf-, pkg-, PskI-, and SNOG_15820-like clusters. An excerpt of the group V phylogenetic tree made with FastTree [60], Figure S2, containing the PKSs from the griseofulvin-producing cluster, GsfA (ADI24953) [48], three alternariol-producing clusters [54,61,62], and a group of related uncharacterized PKSs, is shown at top left. The bootstrap values are presented next to their corresponding nodes. The yellow boxes indicate PKSs from the same species in which the characterized clusters were originally described. Next to the tree are the gene clusters corresponding to the PKSs that were identifiable through MultiGeneBLAST analysis. Genes are represented as arrows with a color corresponding to the proteins they encode which are detailed in the color key below the tree and cluster diagrams. Asterisks signify potential gene truncation due to misannotation. Genes with no color were not identified as homologous to any group V3 cluster gene. The products of the characterized examples from this clade, griseofulvin and alternariol, are shown at bottom. C6TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR2-like, SDH = Short chain dehydrogenase, TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR1-like, DRT = Drug resistance transporter, EmrB subfamily, FDH = Flavin-dependent halogenase, PKS = Polyketide synthase, OMT = O-methyltransferase, NSD = Nucleoside-diphosphate-sugar dehydratase, P450 = Cytochrome P450, ANK = Ankyrin repeat-containing protein, AHD = YcaC-related amidohydrolase, FDH/OMT = Flavin-dependent halogenase and O-methyltransferase bifunctional protein, MβL = Metallo-β-lactamase-type thioesterase. * Asterisks signify potential gene truncation due to misannotation.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4591646&req=5

toxins-07-03572-f007: A clade of gsf-, pkg-, PskI-, and SNOG_15820-like clusters. An excerpt of the group V phylogenetic tree made with FastTree [60], Figure S2, containing the PKSs from the griseofulvin-producing cluster, GsfA (ADI24953) [48], three alternariol-producing clusters [54,61,62], and a group of related uncharacterized PKSs, is shown at top left. The bootstrap values are presented next to their corresponding nodes. The yellow boxes indicate PKSs from the same species in which the characterized clusters were originally described. Next to the tree are the gene clusters corresponding to the PKSs that were identifiable through MultiGeneBLAST analysis. Genes are represented as arrows with a color corresponding to the proteins they encode which are detailed in the color key below the tree and cluster diagrams. Asterisks signify potential gene truncation due to misannotation. Genes with no color were not identified as homologous to any group V3 cluster gene. The products of the characterized examples from this clade, griseofulvin and alternariol, are shown at bottom. C6TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR2-like, SDH = Short chain dehydrogenase, TF = GAL4-like Zn(II)2Cys6-domain and fungal-specific transcription factor domain-containing protein, GsfR1-like, DRT = Drug resistance transporter, EmrB subfamily, FDH = Flavin-dependent halogenase, PKS = Polyketide synthase, OMT = O-methyltransferase, NSD = Nucleoside-diphosphate-sugar dehydratase, P450 = Cytochrome P450, ANK = Ankyrin repeat-containing protein, AHD = YcaC-related amidohydrolase, FDH/OMT = Flavin-dependent halogenase and O-methyltransferase bifunctional protein, MβL = Metallo-β-lactamase-type thioesterase. * Asterisks signify potential gene truncation due to misannotation.
Mentions: This group V subgroup includes heptaketide synthases catalyzing an unusual C1–C6 or C2–C7 first cyclization followed by a C8–C13 second cyclization. Characterized examples include alternariol and griseofulvin. Alternariol is an important mycotoxin produced by members of Alternaria, Aspergillus, and Phaeosphaeria [54,61,62]. This metabolite is a fairly common crop contaminant with carcinogenic, phytotoxic, and antifungal activity. Despite its importance, genetic studies characterizing the biosynthesis of alternariol were only recently undertaken. To date, three gene clusters have been implicated in the synthesis of alternariol, one in Alternaria alternata, one in A. nidulans, and one in Phaeosphaeria nodorum (syn. Parastagonospora nodorum) (Figure 7). Initially, PksJ (AFN68301) was identified in A. alternata using siRNA and gene deletion approaches as the PKS primarily responsible for alternariol production. However, two other PKSs, PksH (AFN68299) and PksI (AFN68300), were shown to be affected by the knockdown of pksJ expression. Notably, no MβL-TE was identified adjacent to PksJ in this study [61]. In A. nidulans, promoter replacement experiments were used to show that PkgA (CBF79143) and PkgB produce alternariol and coumarins [54]. Most recently, in P. nodorum, SNOG_15829 (EAT76667) was also found to produce alternariol. The cluster associated with this NR-PKS includes a gene encoding an MβL-TE (SNOG_15826), but it bears little similarity to the other MBL-TEs of group V clusters [62], which could be due to poor sequence quality. Interestingly, the NR-PKS EAT76667 is most similar to PksI from A. alternata, suggesting that PksI, and not PksJ or PksH, is the alternariol-producing PKS in A. alternata. These clusters were not characterized further than the identification of a PKS and an MβL-TE; the additional genes analyzed by MGB as part of the PkgA (CBF79143) and SNOG_15829 (EAT76667) clusters were included based only on their reported co-regulation with the PKS- and MβL-TE-encoding genes [62,93]. Because of these limitations in the studies characterizing alternariol-producing gene clusters, our product predictions for group V3 PKSs are based only on the presence or absence of genes encoding a PKS and MβL-TE and the closeness of the relationships of these PKSs with the characterized group V3 PKSs (Table 1).

Bottom Line: Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V.We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them.Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706-1580, USA. kthrockmorto@wisc.edu.

ABSTRACT
Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs), with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans). This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

No MeSH data available.


Related in: MedlinePlus