SM URF: genomic mapping of fungal secondary metabolite pathways

Natalie D. Fedorova 1, Nora Khaldi 2, Fayaz T. Seifuddin 1, Dan Haft1, Geoff Turner3, Kenneth W olfe 2, W illiam C. Nierman 1.

Author address: 

1J. Craig Venter Institute, Rockville, MD, USA. 2Trinity College, Dublin 2, Ireland. 3University of Sheffield, Sheffield S10 2TN, UK

Abstract: 

Filamentous fungi produce an impressive array of secondary metabolites (SM s) including mycotoxins, pigments, antibiotics and pharmaceuticals. The genes responsible for SM biosynthesis, export, and transcriptional regulation are often found in SM gene clusters. To search systematically for such clusters, we developed the web-based software SMURF (Secondary M etabolite Unknown Regions Finder) available at www.jcvi.org/smurf. SMURF's predictions are based on the domain content of genes located close to backbone genes that often encode the first steps in SM pathways. In tests, SMURF accurately recovered all known SM clusters and detected 8 additional potential clusters in Aspergillus fumigatus. W e applied SM URF to catalog putative SM clusters in 25 publicly available fungal genomes. Among these taxa, the Aspergilli appear to have the coding capacity for the largest numbers of these metabolites. The genome of A. niger alone encodes 61 backbone enzymes and 58 clusters. Further comparison reveals that SM pathways are very unevenly distributed among fungal taxa suggesting an evolutionary pattern of rapid pathway gain and loss. It also confirmed the correlation between unicellularity and the absence of SMs, and the prominent role of gene duplication in the creation of new pathways.
2009

abstract No: 

28

Full conference title: 

6th International Aspergillus Meeting
    • Asperfest 6 (2009)