Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus

Abstract

The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

Figure 1

Relationships among three transcriptomes of Hericium erinaceus. (a) Pairwise correlation of normalized FPKMs between RNA samples. The Pearson correlation coefficient ranges from no correlation (white) to perfect correlation (dark blue). (b) Venn diagram of 9711 expressed genes in three different tissues of H. erinaceus. Abbreviation: MK, monokaryotic mycelium; DK, dikaryotic mycelium; FB, fruiting body.

Figure 2

The typical bioactive secondary compounds isolated from Hericium erinaceus. (a) Pyrone and alkaloids: erinapyron A–C, herierin III; hericene A. (b) Terpenoid: erinacines A–E; cyatha-3,12-diene. (c) sterol compounds. (d) Volatile aromatic compounds: erinaceolactone A, C. (e) Nonribosomal peptides: fumitremorgin C and methylthiogliotoxin.

Figure 3

KEGG mapping of terpenoid backbone biosynthesis pathway identified in Hericium erinaceus and the putative gene expression level on different tissues. (Right) KEGG map 00900. Red stars indicate the hits of differentially expressed genes in this map. (Upper Left) The expression levels (fpkm values) of mapped genes (EC 1.1.1.34, EC 2.5.1.10, EC 2.5.1.1, EC 2.7.4.2, EC 4.1.1.33, EC 2.5.1.82, EC 2.5.1.83, EC 1.8.3.5) of in different tissues. Abbreviation: MK, monokaryotic mycelium; DK, dikaryotic mycelium; FB, fruiting body.

Figure 4

Unrooted Neighbor-Joining phylogram of sesquiterpene synthase (STS) of Hericium erinaceus were constructed based homologous protein sequences. STS from Coprinopsis cinereus (Cop), Omphalotus olearius (Omp), Fomitopsis pinicola (Fompi1), Stereum hirsutum (Sh) and the single STS described from Armillaria gallica (Armga1) and Boreostereum vibrans (SqtB) are labeled. Detail information of the sequences used in phylogram can be found in Supplement Table S4.

Figure 5

Identification of the four putative gene clusters for terpene and polyketides (PKS) in Hericium erinaceus genome by antiSMASH software. ctg ID (black font) in the map represents coding sequence (cds) place in corresponding scaffold. Genes with Pfam accession number (red color) and functional annotation (blue color) were marked in the map. The detail annotation of genes in each cluster was listed in Supplementary Table S5.

Figure 6

An ideogram showing the putative gene clusters involved in secondary metabolic biosynthesis (terpenoid and polyketides) in 42 basidiomycota fungi. The gene clusters of each fungal species were predicted by antiSMASH software and then the syntenic picture was drew using the SVG tool based on the these gene clusters. The square boxes refer to the entire gene cluster involved in secondary metabolism in each fungal species: terpenoid gene cluster (green color); type I PKS gene cluster (blue color); NRPS-type I PKS gene cluster (purple color); TypeIII PKS (yellow brown color) and type I PKS-terpene gene cluster (pale red color). The shaded regions refer to presumably syntenic or homologous gene clusters between fungal species and the same type of gene clusters were connected by thin lines. The symbol “//” was used to separate the gene cluster in different scarffold. # no gene cluster for secondary metaboites biosynthesis was predicted in the Piriformaspora indica and it is not be shown in the figure.