Secondary Metabolite Unique Regions Finder (SMURF)

Secondary Metabolite Unique Regions Finder (SMURF)

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Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics, and pharmaceuticals. Researchers can now get a preview of an organism's secondary metabolome by analyzing its genomic sequence. Combined with other -omics data, this approach may provide a cost-effective alternative to industrial high-throughput screening in drug discovery.

The genes responsible for biosynthesis, export, and transcriptional regulation in SMs are often found in contiguous gene clusters. To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based software Secondary Metabolite Unique Regions Finder (SMURF) to systematically predict clustered SM genes based on their genomic context and domain content.

We applied SMURF to catalog putative clusters in 27 publicly available fungal genomes. Comparison with genetically characterized clusters from six fungal species showed that SMURF accurately recovered all clusters and detected additional potential clusters. Subsequent comparative analysis revealed the striking biosynthetic capacity and variability of the fungal SM pathways and the correlation between unicellularity and the absence of SMs. Further genetics studies are needed to experimentally confirm these clusters.

Publications

Bioinformatics approaches and software for detection of secondary metabolic gene clusters.
Methods in molecular biology (Clifton, N.J.). 2012-01-01; 944.23-45.
PMID: 23065606
SMURF: Genomic mapping of fungal secondary metabolite clusters.
Fungal genetics and biology : FG & B. 2010-09-01; 47.9: 736-41.
PMID: 20554054