SMURF: genomic mapping of fungal secondary metabolite clusters

By N. Khaldi, F. Seifuddin, G. Turner, Daniel H. Haft, W. Nierman, Kenneth H. Wolfe, N. Fedorova. Fungal Genetics and Biology, 2010

729 citations recorded by the source corpus.

Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics and pharmaceuticals. The genes responsible for their biosynthesis, export, and transcriptional regulation are often found in contiguous gene clusters. To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based software SMURF (www.jcvi.org/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.

Subfields: Molecular Biology, Pharmacology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6110ea345600138bcd7b8230487f0db05bd5df89

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Citations in the corpus

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences (2011, methodology): “For fungal genomes, the SMURF tool (7) has recently become available, which is capable of generating a somewhat more comprehensive list of secondary metabolite biosynthesis gene clusters, but this tool offers little further detailed analysis.”
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014, methodology): “1Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA 2Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Gron”
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers (2013, methodology): “For example, ClustScan (9), CLUSEAN (10), SBSPKS (11) and SMURF (12) are tools for the identiﬁcation and/or analysis of the enzymatic domains in multi-modular polyketide synthases and/or non-ribosomal peptide synthetases, which are the key enzymes for the synthesis of the largest classes of clinical”
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters (2015, background): “While most tools primarily focus on prokaryotic pathways, SMURF (6) also addresses fungal secondary metabolite producers.”