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Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z - PLoS Genet. (2013)

Bottom Line: Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA. Schardl@uky.edu

ABSTRACT
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.

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Phylogenies of rpbA from sequenced isolates and other Clavicipitaceae.The phylogenetic tree is based on nucleotide alignment for a portion of the RNA polymerase II largest subunit gene, rpbA. This tree is rooted with Fusarium graminearum as the outgroup. Epichloae are indicated in green, Claviceps species are indicated in blue, Periglandula species are indicated in red, and Aciculosporium take is in black. Species for which genomes were sequenced in this study are shown in bold type, and asterisks indicate plant-associated fungi. Alkaloids listed are the major pathway end-products predicted from the genome sequences, abbreviated as shown in Figure 2, Figure 3, Figure 4. Other abbreviations: (−) = some genes or remnants present, but not predicted to make alkaloids of this class, – = no genes present for this alkaloid class, EA = ergot alkaloids may be produced; IDT = indole-diterpenes may be produced, (ΔR*) = deletion of terminal reductase domain of perA.
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pgen-1003323-g005: Phylogenies of rpbA from sequenced isolates and other Clavicipitaceae.The phylogenetic tree is based on nucleotide alignment for a portion of the RNA polymerase II largest subunit gene, rpbA. This tree is rooted with Fusarium graminearum as the outgroup. Epichloae are indicated in green, Claviceps species are indicated in blue, Periglandula species are indicated in red, and Aciculosporium take is in black. Species for which genomes were sequenced in this study are shown in bold type, and asterisks indicate plant-associated fungi. Alkaloids listed are the major pathway end-products predicted from the genome sequences, abbreviated as shown in Figure 2, Figure 3, Figure 4. Other abbreviations: (−) = some genes or remnants present, but not predicted to make alkaloids of this class, – = no genes present for this alkaloid class, EA = ergot alkaloids may be produced; IDT = indole-diterpenes may be produced, (ΔR*) = deletion of terminal reductase domain of perA.

Mentions: Clusters of genes have been identified for the four alkaloid biosynthesis classes [16], [41]–[43], but in the absence of complete genome sequences it was unknown if the clusters had been fully characterized for any known producers in the Clavicipitaceae. Therefore, we sequenced 15 genomes of diverse species in the family with various alkaloid profiles (Figure 5, Table 1). The genomes were primarily sequenced by shotgun pyrosequencing, but paired-end and mate-pair reads were used to scaffold several assemblies. Notably, adding mate-pair pyrosequencing of C. purpurea DNA resulted in a 186-supercontig (scaffold) assembly of 32.1 Mb, and adding end-sequencing of fosmid clones E. festucae Fl1 DNA resulted in a 170-supercontig assembly of 34.9 Mb. Annotated genome sequences have been posted at www.endophyte.uky.edu, and (for C. purpurea 20.1) at http://www.ebi.ac.uk/ena/data/view/Project:76493, and GenBank and EMBL project numbers are listed in Table S2. Assembled genome sizes among the sequenced strains varied 2-fold from 29.2 to 58.7 Mb, with wide ranges even within the genera Claviceps (31–52.3 Mb) and Epichloë (29.2–49.3 Mb) (Table 1). The majority of genome size variation was due to repeat sequences, which ranged from 4.7–56.9% overall (excluding P. ipomoeae from consideration because contigs that lacked coding sequences may have been filtered from that assembly), and from 13.7–44.9% repeat DNA among the epichloae (Table 2). Also, the average GC contents of repeat sequences varied widely, from 22% in C. fusiformis PRL 1980 to 50% in C. purpurea 20.1 (Table 3). The sums of coding sequence lengths were estimated from ab initio gene predictions with FGENESH, and ranged from 9.4 Mb in A. take MAFF-241224 to 15.9 Mb in P. ipomoeae IasaF13 (Table 2). Most of the epichloae had approximately 11 Mb of coding sequence, with the exception of E. glyceriae E277, which had 14.9 Mb of coding sequence. Gene contents were not correlated with genome size, and although A. take had the largest genome at 58.7 Mb, it had the least coding sequence at 9.4 Mb.


Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z - PLoS Genet. (2013)

Phylogenies of rpbA from sequenced isolates and other Clavicipitaceae.The phylogenetic tree is based on nucleotide alignment for a portion of the RNA polymerase II largest subunit gene, rpbA. This tree is rooted with Fusarium graminearum as the outgroup. Epichloae are indicated in green, Claviceps species are indicated in blue, Periglandula species are indicated in red, and Aciculosporium take is in black. Species for which genomes were sequenced in this study are shown in bold type, and asterisks indicate plant-associated fungi. Alkaloids listed are the major pathway end-products predicted from the genome sequences, abbreviated as shown in Figure 2, Figure 3, Figure 4. Other abbreviations: (−) = some genes or remnants present, but not predicted to make alkaloids of this class, – = no genes present for this alkaloid class, EA = ergot alkaloids may be produced; IDT = indole-diterpenes may be produced, (ΔR*) = deletion of terminal reductase domain of perA.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585121&req=5

pgen-1003323-g005: Phylogenies of rpbA from sequenced isolates and other Clavicipitaceae.The phylogenetic tree is based on nucleotide alignment for a portion of the RNA polymerase II largest subunit gene, rpbA. This tree is rooted with Fusarium graminearum as the outgroup. Epichloae are indicated in green, Claviceps species are indicated in blue, Periglandula species are indicated in red, and Aciculosporium take is in black. Species for which genomes were sequenced in this study are shown in bold type, and asterisks indicate plant-associated fungi. Alkaloids listed are the major pathway end-products predicted from the genome sequences, abbreviated as shown in Figure 2, Figure 3, Figure 4. Other abbreviations: (−) = some genes or remnants present, but not predicted to make alkaloids of this class, – = no genes present for this alkaloid class, EA = ergot alkaloids may be produced; IDT = indole-diterpenes may be produced, (ΔR*) = deletion of terminal reductase domain of perA.
Mentions: Clusters of genes have been identified for the four alkaloid biosynthesis classes [16], [41]–[43], but in the absence of complete genome sequences it was unknown if the clusters had been fully characterized for any known producers in the Clavicipitaceae. Therefore, we sequenced 15 genomes of diverse species in the family with various alkaloid profiles (Figure 5, Table 1). The genomes were primarily sequenced by shotgun pyrosequencing, but paired-end and mate-pair reads were used to scaffold several assemblies. Notably, adding mate-pair pyrosequencing of C. purpurea DNA resulted in a 186-supercontig (scaffold) assembly of 32.1 Mb, and adding end-sequencing of fosmid clones E. festucae Fl1 DNA resulted in a 170-supercontig assembly of 34.9 Mb. Annotated genome sequences have been posted at www.endophyte.uky.edu, and (for C. purpurea 20.1) at http://www.ebi.ac.uk/ena/data/view/Project:76493, and GenBank and EMBL project numbers are listed in Table S2. Assembled genome sizes among the sequenced strains varied 2-fold from 29.2 to 58.7 Mb, with wide ranges even within the genera Claviceps (31–52.3 Mb) and Epichloë (29.2–49.3 Mb) (Table 1). The majority of genome size variation was due to repeat sequences, which ranged from 4.7–56.9% overall (excluding P. ipomoeae from consideration because contigs that lacked coding sequences may have been filtered from that assembly), and from 13.7–44.9% repeat DNA among the epichloae (Table 2). Also, the average GC contents of repeat sequences varied widely, from 22% in C. fusiformis PRL 1980 to 50% in C. purpurea 20.1 (Table 3). The sums of coding sequence lengths were estimated from ab initio gene predictions with FGENESH, and ranged from 9.4 Mb in A. take MAFF-241224 to 15.9 Mb in P. ipomoeae IasaF13 (Table 2). Most of the epichloae had approximately 11 Mb of coding sequence, with the exception of E. glyceriae E277, which had 14.9 Mb of coding sequence. Gene contents were not correlated with genome size, and although A. take had the largest genome at 58.7 Mb, it had the least coding sequence at 9.4 Mb.

Bottom Line: Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA. Schardl@uky.edu

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus