Differential retention of gene functions in a secondary metabolite cluster

Authors: RENOLDS, H - The Ohio State University; SLOT, JASON - The Ohio State University; DIVON, H - Norwegian Veterinary Institute; LYSOE, E - Bioforsk; Proctor, Robert; Brown, Daren

Submitted to: Molecular Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2017
Publication Date: 4/28/2017
Citation: Reynolds, H.T., Slot, J.C., Divon, H.H., Lysoe, E., Proctor, R.H., Brown, D.W. 2017. Differential retention of gene functions in a secondary metabolite cluster. Molecular Biology and Evolution. doi: 10.1093/molbev/msx145.

Interpretive Summary: Some fungi infect crop plants and produce toxic metabolites (mycotoxins) that accumulate in the crops. As a result, mycotoxins pose a health risk to humans and domestic animals. Genes responsible for mycotoxin synthesis are typically located adjacent to one another along fungal chromosomes in biosynthetic gene clusters. Fungi vary markedly in their ability to produce mycotoxins, and this can result from variation in the presence of the corresponding gene clusters. Mechanisms responsible for this variation are of substantial interest, because they could provide information on how to prevent mycotoxin contamination. In this study, we examined 585 fungal species to elucidate the mechanisms that result in variation in the presence and absence of the gene cluster responsible for synthesis of the mycotoxin depudecin. The results indicate that three mechanisms have contributed significantly to the variation. The first mechanism is vertical inheritance; that is, passage of the cluster from parent to offspring. The second mechanism is horizontal transfer; that is, direct transfer of the cluster from one species to another. The third mechanism is loss of one or more depudecin cluster genes. The data indicate that loss of depudecin cluster genes has occurred numerous times among fungi. However, when loss occurs, there is preferential retention of two genes: 1) the gene responsible for export of depudecin from fungal cells; and 2) the gene that controls activity of the depudecin gene cluster. This research provides knowledge of mechanisms responsible for variation in the ability of fungi to cause mycotoxin contamination of crops. This knowledge will be of use to plant pathologists, plant breeders, and other scientists working to develop methods to reduce mycotoxin contamination.

Technical Abstract: In fungi, distribution of secondary metabolite (SM) gene clusters is often associated with host- or environment-specific benefits provided by the SMs. In the plant pathogen Alternaria brassicicola (Dothideomycetes), the DEP cluster confers an ability to synthesize the SM depudecin, a histone deacetylase inhibitor that contributes weakly to virulence. The DEP cluster includes genes encoding enzymes, a transporter, and a transcription regulator. We investigated the distribution and evolution of the DEP cluster in 585 fungal genomes and found a wide but sporadic distribution among Dothideomycetes, Sordariomycetes, and Eurotiomycetes. We confirmed DEP gene expression and depudecin production in one fungus, Fusarium langsethiae. Phylogenetic analyses suggested 6-9 horizontal gene transfers (HGTs) of the cluster, including a transfer that lead to the presence of closely related cluster homologs in Alternaria and Fusarium. The analyses also indicated that HGTs were frequently followed by loss/pseudogenization of one or more DEP genes. Independent cluster inactivation was inferred in at least four fungal classes. Analyses of transitions among functional, pseudogenized, and absent states of DEP genes among Fusarium species suggest enzyme-encoding genes are lost at higher rates than the transporter (DEP3) and regulatory (DEP6) genes. The phenotype of an experimentally-induced DEP3 mutant of Fusarium did not support the hypothesis that selective retention of DEP3 and DEP6 protects fungi from exogenous depudecin. Together, the results suggest that HGT and gene loss have contributed significantly to DEP cluster distribution, and that some DEP genes provide a greater fitness benefit possibly due to a differential tendency to form network connections.