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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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Phylogenetic groupings and modular organization of ChNPS1 and ChNPS3 showing recombinant structure of these NRPSs. A. Modules 1 and 3 of both ChNPS1 and ChNPS3 group with AM toxin synthetase, a trimodular NRPS that biosynthesizes AM-toxin, an Alternaria alternata host-selective toxin. B. Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3 group with A domains (SimA) of cyclosporin synthetases (CYCLO) in a disparate position in the larger phylogeny compared to modules 1 and 3 (A, above) which group in the EAS subfamily (Fig. 2). C. Recombinant domain organization of ChNPS1 and ChNPS3. Blue boxes correspond to modules 2 and 4, purple boxes to modules 1 and 3. Note that single modules homologous to these domains are found in other euascomycete NRPSs. For example, Enniatin synthetases (Esyn1) and MGG00022.6 are also recombinant like ChNPS1 and ChNPS3 with one or more modules grouping with the cyclosporin subfamily (blue boxes) and others also within the EAS subfamily but in a distinct position from the ChNPS1 and ChNPS3 modules (clear boxes). Cyclosporin synthetases itself appears to have arisen by tandem duplication of SimA modules within T. inflatum.
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Figure 9: Phylogenetic groupings and modular organization of ChNPS1 and ChNPS3 showing recombinant structure of these NRPSs. A. Modules 1 and 3 of both ChNPS1 and ChNPS3 group with AM toxin synthetase, a trimodular NRPS that biosynthesizes AM-toxin, an Alternaria alternata host-selective toxin. B. Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3 group with A domains (SimA) of cyclosporin synthetases (CYCLO) in a disparate position in the larger phylogeny compared to modules 1 and 3 (A, above) which group in the EAS subfamily (Fig. 2). C. Recombinant domain organization of ChNPS1 and ChNPS3. Blue boxes correspond to modules 2 and 4, purple boxes to modules 1 and 3. Note that single modules homologous to these domains are found in other euascomycete NRPSs. For example, Enniatin synthetases (Esyn1) and MGG00022.6 are also recombinant like ChNPS1 and ChNPS3 with one or more modules grouping with the cyclosporin subfamily (blue boxes) and others also within the EAS subfamily but in a distinct position from the ChNPS1 and ChNPS3 modules (clear boxes). Cyclosporin synthetases itself appears to have arisen by tandem duplication of SimA modules within T. inflatum.

Mentions: Two NRPSs found in C. heterostrophus, ChNPS1 and ChNPS3, demonstrate the potential role of recombination and modular rearrangement in the generation of multimodular NRPSs. Modules 1 and 3 of both ChNPS1 and ChNPS3 group within the EAS subfamily with AMT synthetase, a lineage specific NRPS found only in a single strain of related A. alternata [52] (Figs. 2, 7, Additional file 6A-C). Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3, however, group with the CYCLO synthetases among the mono/bi-modular NRPS subfamilies (Fig. 2, Additional file 6). The phylogenetically unlinked locations of ChNPS1 and ChNPS3 modules in the larger phylogeny suggests that a recombination event must have given rise to the extant genes in C. heterostrophus (Fig. 9). A domains of several other euascomycete NRPSs, for example, bimodular Fusarium equiseti Enniatin synthetase (FeESYN1) and trimodular M. oryzae, MGG00022, also show recombinant structures. Module 1 A domains of both proteins group in the EAS clade with the C. heterostrophus pseudogene ChNPS13, but without bootstrap support (Fig. 2), at positions distinct from modules 1 and 3 of ChNPS1 and ChNPS3. The C-terminal A domain of ESYN1 and the A domains of the final two modules of MGG00022 group in the CYCLO clade (Figs. 2, 9), like module 2 of ChNPS1 and modules 2 and 4 of ChNPS3. Thus, homologs of modules of ChNPS1 and ChNPS3 appear in different combinations in other fungi and demonstrate that recombination plays an important role in the evolution of multimodular NRPSs.


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

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

Phylogenetic groupings and modular organization of ChNPS1 and ChNPS3 showing recombinant structure of these NRPSs. A. Modules 1 and 3 of both ChNPS1 and ChNPS3 group with AM toxin synthetase, a trimodular NRPS that biosynthesizes AM-toxin, an Alternaria alternata host-selective toxin. B. Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3 group with A domains (SimA) of cyclosporin synthetases (CYCLO) in a disparate position in the larger phylogeny compared to modules 1 and 3 (A, above) which group in the EAS subfamily (Fig. 2). C. Recombinant domain organization of ChNPS1 and ChNPS3. Blue boxes correspond to modules 2 and 4, purple boxes to modules 1 and 3. Note that single modules homologous to these domains are found in other euascomycete NRPSs. For example, Enniatin synthetases (Esyn1) and MGG00022.6 are also recombinant like ChNPS1 and ChNPS3 with one or more modules grouping with the cyclosporin subfamily (blue boxes) and others also within the EAS subfamily but in a distinct position from the ChNPS1 and ChNPS3 modules (clear boxes). Cyclosporin synthetases itself appears to have arisen by tandem duplication of SimA modules within T. inflatum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 9: Phylogenetic groupings and modular organization of ChNPS1 and ChNPS3 showing recombinant structure of these NRPSs. A. Modules 1 and 3 of both ChNPS1 and ChNPS3 group with AM toxin synthetase, a trimodular NRPS that biosynthesizes AM-toxin, an Alternaria alternata host-selective toxin. B. Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3 group with A domains (SimA) of cyclosporin synthetases (CYCLO) in a disparate position in the larger phylogeny compared to modules 1 and 3 (A, above) which group in the EAS subfamily (Fig. 2). C. Recombinant domain organization of ChNPS1 and ChNPS3. Blue boxes correspond to modules 2 and 4, purple boxes to modules 1 and 3. Note that single modules homologous to these domains are found in other euascomycete NRPSs. For example, Enniatin synthetases (Esyn1) and MGG00022.6 are also recombinant like ChNPS1 and ChNPS3 with one or more modules grouping with the cyclosporin subfamily (blue boxes) and others also within the EAS subfamily but in a distinct position from the ChNPS1 and ChNPS3 modules (clear boxes). Cyclosporin synthetases itself appears to have arisen by tandem duplication of SimA modules within T. inflatum.
Mentions: Two NRPSs found in C. heterostrophus, ChNPS1 and ChNPS3, demonstrate the potential role of recombination and modular rearrangement in the generation of multimodular NRPSs. Modules 1 and 3 of both ChNPS1 and ChNPS3 group within the EAS subfamily with AMT synthetase, a lineage specific NRPS found only in a single strain of related A. alternata [52] (Figs. 2, 7, Additional file 6A-C). Module 2 of ChNPS1 and modules 2 and 4 of ChNPS3, however, group with the CYCLO synthetases among the mono/bi-modular NRPS subfamilies (Fig. 2, Additional file 6). The phylogenetically unlinked locations of ChNPS1 and ChNPS3 modules in the larger phylogeny suggests that a recombination event must have given rise to the extant genes in C. heterostrophus (Fig. 9). A domains of several other euascomycete NRPSs, for example, bimodular Fusarium equiseti Enniatin synthetase (FeESYN1) and trimodular M. oryzae, MGG00022, also show recombinant structures. Module 1 A domains of both proteins group in the EAS clade with the C. heterostrophus pseudogene ChNPS13, but without bootstrap support (Fig. 2), at positions distinct from modules 1 and 3 of ChNPS1 and ChNPS3. The C-terminal A domain of ESYN1 and the A domains of the final two modules of MGG00022 group in the CYCLO clade (Figs. 2, 9), like module 2 of ChNPS1 and modules 2 and 4 of ChNPS3. Thus, homologs of modules of ChNPS1 and ChNPS3 appear in different combinations in other fungi and demonstrate that recombination plays an important role in the evolution of multimodular NRPSs.

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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