Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

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

Ergot alkaloids and summary of biosynthesis pathway.

<p>(A) Ergoline alkaloid biosynthesis pathways in the Clavicipitaceae. Arrows indicate one or more steps catalyzed by products of genes indicated. Arrows and genes in blue indicate steps in synthesis of the first fully cyclized intermediate (skeleton). Variation in the <i>easA</i> gene (underlined) determines whether the ergoline skeleton is festuclavine or agroclavine. Arrows and genes in red indicate steps in decoration of the skeleton to give the variety of ergolines in the Clavicipitaceae. Asterisks indicate genes newly discovered in the genome sequences of <i>C. paspali</i>, <i>N. gansuense</i> var. <i>inebrians</i> and <i>P. ipomoeae</i>. (B) Ergopeptines produced by strains in this study.</p

Peramine biosynthesis loci (<i>PER</i>) in epichloae and the homologous loci in other Clavicipitaceae.

<p>On each map <i>perA</i> is color-coded blue for a complete gene and as an open box for <i>perA-</i>ΔR*. Domains of <i>perA</i> are indicated as A (adenylation), T (thiolation), C (condensation), M (<i>N</i>-methylation) and R* (reduction). Subscripts indicate postulated specificity of adenylation domains for 1-pyrroline-5-carboxylate (A_P) and arginine (A_R) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen.1003323-Tanaka1" target="_blank">[16]</a>. Other features are indicated as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g007" target="_blank">Figure 7</a>.</p

GC proportions in genic and repeat DNA of sequenced genomes.^a

a<p>Abbreviations: CDS = coding sequence, GC = proportion of sequence that is G or C, non-Rpt-IG = nonrepetitive intergenic DNA, Rpt = repetitive DNA.</p>b<p>Statistics for <i>P. ipomoeae</i> are tentative because the assembly was filtered by selecting only contigs containing tBLASTx matches to genome sequences from the other Clavicipitaceae.</p

Symbiosis of meadow fescue with <i>Epichloë festucae</i>, a heritable symbiont.

<p>Single optical slice confocal micrographs of <i>E. festucae</i> expressing enhanced cyan-fluorescent protein were overlain with DIC bright field images of (A) ovules (bar = 100 µm), (B) embryos (bar = 200 µm), and (C) shoot apical meristem and surrounding new leaves (bar = 200 µm). (D) Asymptomatic (left) and “choked” (right) inflorescences simultaneously produced on a single grass plant infected with a single <i>E. festucae</i> genotype. Vertical (seed) transmission of the symbiont occurs via the asymptomatic inflorescence, whereas the choked inflorescence bears the <i>E. festucae</i> fruiting structure (stroma), which produces sexually derived spores (ascospores) that mediate horizontal transmission.</p

Genic and repeat DNA contents of sequenced genomes.^a

a<p>Abbreviations: CDS = coding sequence, MT = mating type, non-Rpt-IG = nonrepetitive intergenic DNA, Rpt = repetitive DNA.</p>b<p>Based on total of contigs ≥500 bp. These sizes differ slightly from total scaffold lengths given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-t001" target="_blank">Table 1</a> for <i>C. purpurea</i> 20.1, <i>E. festucae</i> E2368, and <i>E. festucae</i> Fl1.</p>c<p><i>C. fusiformis</i> PRL 1980 mating type genes include <i>mtBA</i> and <i>mtAC</i>. <i>P. ipomoeae</i> IasaF13 mating type genes <i>mtAA</i> and <i>mtAC</i> appear to have premature stop codons.</p>d<p>Statistics for <i>P. ipomoeae</i> are tentative because the assembly was filtered by selecting only contigs containing tBLASTx matches to genome sequences from the other Clavicipitaceae.</p

Structures of the indole-diterpene biosynthesis loci (<i>IDT/LTM</i>) in sequenced genomes.

<p><i>IDT/LTM</i> genes are indicated by single letters, whereby <i>Q = idtQ</i> or <i>ltmQ</i> (in <i>E. festucae</i>), and so forth. Tracks from top to bottom of each map represent the following: genes, repeats, MITEs, and graphs of AT (red) and GC (blue) contents. Each gene is represented by a filled arrow indicating its direction of transcription. Closed circles indicate telomeres, and distances from the telomere on the <i>E. festucae</i> map are indicated in kilobasepairs (kb). Cyan bars representing repeat sequences are labeled with names or numbers to indicate relationships between repeats in the different species. Vertical bars beneath the repeat maps indicate MITEs. Genes for the first fully cyclized intermediate, paspaline, are indicated in blue, those for subsequent chemical decorations are shown in red, and <i>idt/ltmS</i>, with undetermined function, is in purple. Identifiable genes flanking the clusters are indicated in gray, and unfilled arrows indicate pseudogenes. The major pathway end-product for each strain is listed at the right of its map, abbreviated as indicated in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g003" target="_blank">Figure 3</a>, and in bold for those confirmed in this study.</p