Posts Tagged ‘endophyte’

Genomics of Fungal Drug Producers

March 2nd, 2013

In a breakthrough paper, Schardl’s group and collaborators have published 15 genomes of diverse species of Clavicipitaceae plant endophytes and parasites in the last issue of PloS Genetics. The Clavicipitaceae (PezizomycotinaSordariomycetes, Hypocreales) includes “ergot” fungi that parasitize ears of cereals and produce  the toxic ergoline derivatives; ergot fungi have historically caused epidemics of gangrenous poisonings, the ergotism, also known as the Saint Anthony’s Fire. The ascomycetous family also includes plant endophytic symbionts 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. They synthesize alkaloids with chemical similarities to biogenic amines that deter insects, livestock, and wildlife from feeding on the fungus or plant. Thanks to this chemical warfare, Epichloae protect their hosts from cattle grazing. The lysergic acid diethylamide (LSD), a semisynthetic ergot alkaloid originally developed as an antidepressant, is the most potent known hallucinogen.

In this study, they sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and the bamboo witch’s broom pathogen (Aciculosporium take), profiled the alkaloids in these species and compared the gene clusters for four classes of alkaloids. The genomes were primarily sequenced by shotgun 454 pyrosequencing, but paired-end and mate-pair reads were used to scaffold several assemblies. Size of the assembled genome 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). This genome size variation is mainly resulting from the abundance of repeated elements, which ranged from 4.7 to 56.9%. Annotated genome sequences have been posted at www.endophyte.uky.edu.

In the epichloae, the clusters of genes coding for enzymes of alkaloid biosynthesis contain very large blocks of repetitive elements which promote gene losses, mutations, and even the evolution of new genes. Two striking features emerged from the detailed analysis of alkaloid biosynthesis gene clusters. Firstly, in most alkaloid loci in most species, the periphery of each cluster was enriched in genes that by virtue of their presence, absence, or sequence variations determined the diversity of alkaloids within the respective chemical class. Second, alkaloid gene loci of the epichloae had extraordinarily large and pervasive blocks of AT- rich repeats derived from retroelements, DNA transposons, and MITEs. This finding suggests that these plant-interacting fungi are under selection for alkaloid diversification.

In their conclusions, the authors suggest that this selection of chemotypes is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the ecologically diverse cool-season grasses.

Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, et al. (2013) Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genet 9(2): e1003323. doi:10.1371/journal.pgen.1003323

Image: Claviceps purpurea -Franz Eugen Köhler, Köhler’s Medizinal-Pflanzen (Wikimedia Commons).

Friend or foe? … a Sweet Story

August 16th, 2010

Sans titreThe sky is overcast with clouds and the rain is ceaseless‘ in Gitanjali by Rabindranath Tagore.

Mid-Summer: Across Lorraine, this is generally the hottest month of the year, and when most everyone is headed to a beach or the mountains to look for a little respite. No scorching mid-Summer heat this year. Over the week-end, the sky was pouring with rain and the sun never shone from dawn to dusk. It poured with rain the entire night.

Well, I take this opportunity to get back to outstanding papers. The study of GH32 invertases in fungi from Jerri Parent, together with Tim James and Andy Taylor, was worth re-reading. In this BMC Evolutionary Biology paper, they tested for occurrence of the glycosyl hydrolase family 32 (GH32) genes in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. This GH32 family, containing mostly invertases, is crucial for plant-interacting fungi. Sucrose is the primary metabolite used by most plants to translocate carbon throughout their tissues, and its abundance within plants makes it a valuable carbon source for the many fungi that are obligate plant associates. To acquire the host sucrose, colonizing fungi must possess the necessary enzymes, such as extracellular invertase(s), to split sucrose into its constituent monosaccharides, glucose and fructose.

Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode (saprobic, endophytic, mutualist, pathogenic). Expansion of gene families was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy (e.g. Puccinia graminis), with the notable exception of mycorrhizal taxa (e.g. Laccaria bicolor). Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota.

We noticed in our Nature paper the lack of invertase in the ectomycorrhizal L. bicolor suggesting that this symbiont depends on its host plant to provide glucose in exchange for nitrogen. I have checked the presence of the extracellular invertase in our draft genome sequences of L. amethystina and Glomus intraradices, and the 454 transcripts of Lactarius quietus and Pisolithus microcarpus. None of these ECM fungi have a gene coding for this enzyme, whereas the poplar rust, Melampsora larici-populina has two sequences similar to the wheat rust Puccinia graminis GH32s. Intriguingly, the genome of the ectomycorrhizal ascomycete, Tuber melanosporum — the Black Truffe of Perigord — contains a gene encoding a GH32 enzyme, suggesting that the truffle may act as a scavenger instead of being a true mutualist. However, the corresponding transcript is lowly expressed in free-living mycelium, fruiting body and ectomycorrhiza according to our NimbleGen oligoarray and RNA-Seq transcript profilings.

As stressed by Parent et al. “Reliance on plant GH32 enzyme activity for C acquisition in these [ECM] symbionts supports earlier predictions of a general absence of invertase in mycorrhizal fungi, and a highly evolved mutualistic relationship between plants and mycorrhizal fungi, a remarkable scenario in light of the high degree of phylogenetic diversity spanned by mycorrhizal fungal taxa. Whether the plant host is able to detect fungal invertase activity and use such a signal to differentiate antagonistic from mutualistic biotrophic symbionts is a completely speculative, though plausible hypothesis.”

Parrent et al. (2009) Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evolutionary Biology 9:148 doi:10.1186/1471-2148-9-148.

Photo: Lorraine Big Sky © F Martin

A Virus in a Fungus in a Plant

August 8th, 2010

YNPFor those interested by plant endophytes (see previous post on poplar endophytes), get back to Márquez’s paper published in Science in 2007. The authors showed that mutualistic association between the fungal endophyte Curvularia protuberata and its host plant, the tropical panic grass from geothermal soils Dichanthelium lanuginosum allows both organisms to grow at high soil temperatures (65°C) in Yellowstone National Park. This stress tolerance requires the presence of a dsRNA  virus colonizing the fungal endophyte. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.

Recently, complex tripartite symbioses have also been found among arthropods, bacteria, and mutualistic bacteriophages.

Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ (2007) A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance. Science 315, 513 – 515.

Photo: © http://www.travlang.com/