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Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships.

Bushley KE, Turgeon BG - BMC Evol. Biol. (2010)

Bottom Line: We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi.It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs.The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology & Plant-Microbe Biology, 334 Plant Science Bldg, Cornell University, Ithaca, NY, 14853, USA.

ABSTRACT

Background: Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi.

Results: Phylogenomic analysis identified nine major subfamilies of fungal NRPSs which fell into two main groups: one corresponds to NPS genes encoding primarily mono/bi-modular enzymes which grouped with bacterial NRPSs and the other includes genes encoding primarily multimodular and exclusively fungal NRPSs. AARs shared a closer phylogenetic relationship to NRPSs than to other acyl-adenylating enzymes. Phylogenetic analyses and taxonomic distribution suggest that several mono/bi-modular subfamilies arose either prior to, or early in, the evolution of fungi, while two multimodular groups appear restricted to and expanded in fungi. The older mono/bi-modular subfamilies show conserved domain architectures suggestive of functional conservation, while multimodular NRPSs, particularly those unique to euascomycetes, show a diversity of architectures and of genetic mechanisms generating this diversity.

Conclusions: This work is the first to characterize subfamilies of fungal NRPSs. Our analyses suggest that mono/bi-modular NRPSs have more ancient origins and more conserved domain architectures than most multimodular NRPSs. It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs. Several groups of mono/bi-modular NRPS metabolites are predicted to play more pivotal roles in cellular metabolism than products of multimodular NRPSs. In contrast, multimodular subfamilies of NRPSs are of more recent origin, are restricted to fungi, show less stable domain architectures, and biosynthesize metabolites which perform more niche-specific functions than mono/bi-modular NRPS products. The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.

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Modular organization of Peptaibol synthetases and proposed evolution by tandem duplication. A domains from peptaibol synthetases form three distinct, well-supported clades in the EAS subfamily (Fig. 7). A. Modular structure of the H. virens TEX 1 peptaibol synthetase and two peptaibol synthetases in the related species, T. reesii (T.reesii 2_23171 and T.reesii 2_123786. Color coding corresponds to clades identified in phylogenetic analyses (B and C, and Fig. 7). Arrows indicate bootstrap support for module relationships (B, C. and Fig. 7). While T. reesii 2_23171 is clearly a homolog of TEX1, domain duplication of modules 18 to 19 or vice versa and addition of module 2 have occurred since the common ancestor of these species. B. Two of the peptaibol synthetases clades (light green and dark blue, Fig. 7), group together as a monophyletic group but without bootstrap support. A domains shown in stippled boxes indicate modules from T.reesii 2_123786 which do not have a clear counterpart in the other peptaibol synthetases and may represent ancestral domains. C. The third clade (purple, Fig. 7) groups in a distinct position within the EAS subtree.
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Figure 8: Modular organization of Peptaibol synthetases and proposed evolution by tandem duplication. A domains from peptaibol synthetases form three distinct, well-supported clades in the EAS subfamily (Fig. 7). A. Modular structure of the H. virens TEX 1 peptaibol synthetase and two peptaibol synthetases in the related species, T. reesii (T.reesii 2_23171 and T.reesii 2_123786. Color coding corresponds to clades identified in phylogenetic analyses (B and C, and Fig. 7). Arrows indicate bootstrap support for module relationships (B, C. and Fig. 7). While T. reesii 2_23171 is clearly a homolog of TEX1, domain duplication of modules 18 to 19 or vice versa and addition of module 2 have occurred since the common ancestor of these species. B. Two of the peptaibol synthetases clades (light green and dark blue, Fig. 7), group together as a monophyletic group but without bootstrap support. A domains shown in stippled boxes indicate modules from T.reesii 2_123786 which do not have a clear counterpart in the other peptaibol synthetases and may represent ancestral domains. C. The third clade (purple, Fig. 7) groups in a distinct position within the EAS subtree.

Mentions: Peptaibol synthetases illustrate a more complex process of tandem duplication of modules of an NRPS. Peptaibol synthetases are highly lineage specific and found only within the Hypocreales to date. Using H. virens TEX1 as a point of reference, we found that all modules of TEX1 group together in three separate, well-supported clades with modules of two peptaibol synthetases (Trire2_23171 and Trire2_123786) in the related species, Trichoderma reesii (Figs. 2, 7). TEX1 module 13 falls outside of the other two TEX1 clades (Figs. 2, 7, 8), The nearly one-to-one relationship between modules of TEX1 and modules of T. reesii Trire2_23171 suggests that tandem duplication of modules giving rise to these orthologous genes must have occurred prior to divergence of these two species (Fig. 8). However, at least one additional internal duplication has occurred since divergence from an ancestral species (e.g., note the relationship between T. reesii Trire2_23171 modules 18 and 19) (Fig. 8). The relationship of these two peptaibol synthetases with the T. reesii 14 module peptaibol synthetases, Trire2_123786 is less straightforward. However, we note that certain A domains from Trire2_123786 modules 2, 6, and 11 form widowed branches at the base of clades which contain A domains of at least two, and more often, all three peptaibol synthetases (Fig. 8, stippled boxes). We hypothesize that these may be ancestral domains. Previous studies suggest that like T. reesii, T. virens also harbors additional NRPSs involved in peptaibol biosynthesis [92].


Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships.

Bushley KE, Turgeon BG - BMC Evol. Biol. (2010)

Modular organization of Peptaibol synthetases and proposed evolution by tandem duplication. A domains from peptaibol synthetases form three distinct, well-supported clades in the EAS subfamily (Fig. 7). A. Modular structure of the H. virens TEX 1 peptaibol synthetase and two peptaibol synthetases in the related species, T. reesii (T.reesii 2_23171 and T.reesii 2_123786. Color coding corresponds to clades identified in phylogenetic analyses (B and C, and Fig. 7). Arrows indicate bootstrap support for module relationships (B, C. and Fig. 7). While T. reesii 2_23171 is clearly a homolog of TEX1, domain duplication of modules 18 to 19 or vice versa and addition of module 2 have occurred since the common ancestor of these species. B. Two of the peptaibol synthetases clades (light green and dark blue, Fig. 7), group together as a monophyletic group but without bootstrap support. A domains shown in stippled boxes indicate modules from T.reesii 2_123786 which do not have a clear counterpart in the other peptaibol synthetases and may represent ancestral domains. C. The third clade (purple, Fig. 7) groups in a distinct position within the EAS subtree.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 8: Modular organization of Peptaibol synthetases and proposed evolution by tandem duplication. A domains from peptaibol synthetases form three distinct, well-supported clades in the EAS subfamily (Fig. 7). A. Modular structure of the H. virens TEX 1 peptaibol synthetase and two peptaibol synthetases in the related species, T. reesii (T.reesii 2_23171 and T.reesii 2_123786. Color coding corresponds to clades identified in phylogenetic analyses (B and C, and Fig. 7). Arrows indicate bootstrap support for module relationships (B, C. and Fig. 7). While T. reesii 2_23171 is clearly a homolog of TEX1, domain duplication of modules 18 to 19 or vice versa and addition of module 2 have occurred since the common ancestor of these species. B. Two of the peptaibol synthetases clades (light green and dark blue, Fig. 7), group together as a monophyletic group but without bootstrap support. A domains shown in stippled boxes indicate modules from T.reesii 2_123786 which do not have a clear counterpart in the other peptaibol synthetases and may represent ancestral domains. C. The third clade (purple, Fig. 7) groups in a distinct position within the EAS subtree.
Mentions: Peptaibol synthetases illustrate a more complex process of tandem duplication of modules of an NRPS. Peptaibol synthetases are highly lineage specific and found only within the Hypocreales to date. Using H. virens TEX1 as a point of reference, we found that all modules of TEX1 group together in three separate, well-supported clades with modules of two peptaibol synthetases (Trire2_23171 and Trire2_123786) in the related species, Trichoderma reesii (Figs. 2, 7). TEX1 module 13 falls outside of the other two TEX1 clades (Figs. 2, 7, 8), The nearly one-to-one relationship between modules of TEX1 and modules of T. reesii Trire2_23171 suggests that tandem duplication of modules giving rise to these orthologous genes must have occurred prior to divergence of these two species (Fig. 8). However, at least one additional internal duplication has occurred since divergence from an ancestral species (e.g., note the relationship between T. reesii Trire2_23171 modules 18 and 19) (Fig. 8). The relationship of these two peptaibol synthetases with the T. reesii 14 module peptaibol synthetases, Trire2_123786 is less straightforward. However, we note that certain A domains from Trire2_123786 modules 2, 6, and 11 form widowed branches at the base of clades which contain A domains of at least two, and more often, all three peptaibol synthetases (Fig. 8, stippled boxes). We hypothesize that these may be ancestral domains. Previous studies suggest that like T. reesii, T. virens also harbors additional NRPSs involved in peptaibol biosynthesis [92].

Bottom Line: We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi.It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs.The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology & Plant-Microbe Biology, 334 Plant Science Bldg, Cornell University, Ithaca, NY, 14853, USA.

ABSTRACT

Background: Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi.

Results: Phylogenomic analysis identified nine major subfamilies of fungal NRPSs which fell into two main groups: one corresponds to NPS genes encoding primarily mono/bi-modular enzymes which grouped with bacterial NRPSs and the other includes genes encoding primarily multimodular and exclusively fungal NRPSs. AARs shared a closer phylogenetic relationship to NRPSs than to other acyl-adenylating enzymes. Phylogenetic analyses and taxonomic distribution suggest that several mono/bi-modular subfamilies arose either prior to, or early in, the evolution of fungi, while two multimodular groups appear restricted to and expanded in fungi. The older mono/bi-modular subfamilies show conserved domain architectures suggestive of functional conservation, while multimodular NRPSs, particularly those unique to euascomycetes, show a diversity of architectures and of genetic mechanisms generating this diversity.

Conclusions: This work is the first to characterize subfamilies of fungal NRPSs. Our analyses suggest that mono/bi-modular NRPSs have more ancient origins and more conserved domain architectures than most multimodular NRPSs. It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs. Several groups of mono/bi-modular NRPS metabolites are predicted to play more pivotal roles in cellular metabolism than products of multimodular NRPSs. In contrast, multimodular subfamilies of NRPSs are of more recent origin, are restricted to fungi, show less stable domain architectures, and biosynthesize metabolites which perform more niche-specific functions than mono/bi-modular NRPS products. The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.

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