ARS | Publication request: Retention of genes in a secondary metabolite gene cluster that has degenerated in multiple lineages of the Ascomycota

Submitted to: Fungal Genetics Conference/Asilomar
Publication Type: Abstract Only
Publication Acceptance Date: March 17, 2012
Publication Date: N/A

Technical Abstract: Fungal secondary metabolite (SM) gene clusters encode proteins involved in SM biosynthesis, protection against SMs, and regulation of cluster gene transcription. RNA-Seq analysis of Fusarium langsethiae (class Sordariomycetes) revealed a cluster of six genes that were highly expressed during growth in oat-grain medium, but not in complete medium. All six genes share significant homology and synteny with genes in the Alternaria brassicicola (class Dothideomycete) cluster responsible for production of the SM depudecin. HPLC analysis confirmed the presence of depudecin in oat-grain medium and absence from complete medium cultures. A survey of publically available genome sequences identified eight complete and 14 partial depudecin biosynthetic gene (DEP) cluster homologs in fungi across distantly related classes of Ascomycota. Most of the partial clusters included pseudogenes due to single nucleotide changes and/or multiple nucleotide deletions, indicating that the partial clusters are derived by degeneration of complete clusters. Most of the partial clusters also included apparently functional homologs of the major facilitator superfamily (MFS) transporter (DEP3) and transcription factor (DEP6) genes. Retention of these two genes may provide a defense mechanism against depudecin produced by other fungi. Alternatively, DEP3 and DEP6 in the partial clusters may have been repurposed to provide a selective advantage different from the advantage conferred by depudecin. The shared synteny of putative functional DEP3 and DEP6, as well as phylogenetic analysis of these genes, suggest that the DEP cluster has been transferred horizontally between fungi multiple times.