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Title: Deciphering the cryptic genome: Genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites

item WIEMANN, P - Wilhelms University
item SIEBER, C - German Research Center For Environmental Health
item VON BARGEN, K - Wilhelms University
item STUDT, L - Wilhelms University
item NIEHAUS, E - Wilhelms University
item MICHIELSE, C - Wilhelms University
item ALBERMANN, S - Wilhelms University
item WAGNER, D - Wilhelms University
item Brown, Daren
item Proctor, Robert

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/18/2013
Publication Date: 6/27/2013
Citation: Wiemann, P., Sieber, C.M., Von Bargen, K.W., Studt, L., Niehaus, E.M., Michielse, C., Albermann, S., Wagner, D., Brown, D.W., Proctor, R., et al. 2013. Deciphering the cryptic genome: Genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathogens. 9(6):1-35.

Interpretive Summary: Mycotoxins are fungal metabolites that can contaminate crops and pose serious health risks to humans and other animals. Fungal toxins, antibiotics and pigments are often classified as secondary metabolites because they are not essential for life but can provide an ecological advantage in some environments. In fungi, genes directly involved in the synthesis of secondary metabolites are typically located adjacent to one another in gene clusters. In the current study, 45 secondary metabolite gene clusters were identified in the fungus Fusarium fujikuroi, which causes a destructive rice disease and produces a number of mycotoxins, including the carcinogens fumonisins. Genes in many of the clusters were activated during infection of rice and maize and in response to varying levels and sources of nitrogen. For some clusters, this activation was associated with modifications to histone H3, one of the proteins that together with DNA make up chromosomes. In comparisons with other Fusarium species, two clusters were unique to F. fujikuroi and responsible for synthesis of novel metabolites. These results further elucidate physiological and genetic mechanisms that coordinate production of mycotoxins and other secondary metabolites in fungi. Such information can be used by scientists to develop novel strategies to reduce mycotoxin contamination of crops and thereby ensure food and feed safety.

Technical Abstract: The fungus Fusarium fujikuroi is agriculturally important because it produces the phytohormones gibberellic acids (GAs) and causes bakanae (“foolish seedling”) disease of rice. The fungus also produces multiple other secondary metabolites, including pigments and mycotoxins. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the Gibberella fujikuroi species complex, a lineage of Fusarium that includes F. fujikuroi. We used the genome sequence along with transcriptome, proteome, HPLC-FTMS and ChIP-seq analyses to identify all potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability. The results indicate that expression of genes within most, but not all, of the clusters are regulated in a nitrogen-dependent manner and that expression profiles are correlated with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among all species examined and provided new insights into the divergence of secondary metabolism in Fusarium. Comparisons of homologous clusters indicate that some were likely acquired by horizontal gene transfer while others were present in ancient Fusarium species. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Our results indicate that together comparative genomics and genome-wide experimental analyses are powerful tools for discovering novel secondary metabolites and understanding how their production is regulated at the transcriptional, translational and epigenetic levels.