SMURF: Genomic mapping of fungal secondary metabolite clusters

Fungal Genetics and Biology

Volumn 47, Issue 9, 2010, Pages 736-741

  Khaldi, Nora ^a   Seifuddin, Fayaz T ^b   Turner, Geoff ^c   Haft, Daniel ^b   Nierman, William C ^b,d   Wolfe, Kenneth H ^a   Fedorova, Natalie D ^b  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b J CRAIG VENTER INSTITUTE   (United States)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

^d GEORGE WASHINGTON UNIVERSITY SCHOOL OF MEDICINE AND HEALTH SCIENCES   (United States)

Author keywords

Antibiotics; Aspergillus; Filamentous fungi; Genome annotation; NRPS; PKS; Polyketides; Prenyltransferases; Secondary metabolism

Indexed keywords

FUNGAL ENZYME; FUNGAL PROTEIN;

ACCURACY; ARTICLE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME SYNTHESIS; FUNGAL GENETICS; FUNGAL GENOME; GENE CLUSTER; GENE MAPPING; GENE SEQUENCE; GENETIC CORRELATION; GENETIC TRAIT; GENETIC VARIABILITY; INTERNET; NONHUMAN; PRIORITY JOURNAL; SPECIES DIFFERENCE; CHEMISTRY; CHROMOSOME MAP; CLUSTER ANALYSIS; ENZYMOLOGY; EVALUATION STUDY; FUNGUS; GENETICS; GENOMICS; METABOLISM; PROCEDURES; SENSITIVITY AND SPECIFICITY;

ASPERGILLUS; FUNGI;

CHROMOSOME MAPPING; CLUSTER ANALYSIS; FUNGAL PROTEINS; FUNGI; GENOMICS; INTERNET; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 77955274600     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2010.06.003     Document Type: Article

References (51)

1. Bok J.W., et al. Secondary metabolic gene cluster silencing in Aspergillus nidulans. Mol. Microbiol. 2006, 61:1636-1645.
2. Bouhired S., et al. Accurate prediction of the Aspergillus nidulans terrequinone gene cluster boundaries using the transcriptional regulator LaeA. Fungal Genet. Biol. 2007, 44:1134-1145.
3. Brakhage A.A., et al. Evolution of beta-lactam biosynthesis genes and recruitment of trans-acting factors. Phytochemistry 2005, 66:1200-1210.
4. Brakhage A.A., et al. Activation of fungal silent gene clusters: a new avenue to drug discovery. Prog. Drug Res. 2008, 66(1):3-12.
5. Brown D.W., et al. Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc. Natl. Acad. Sci. USA 1996, 93:1418-1422.
6. Chiang Y.M., et al. Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the emericellamide biosynthetic pathway. Chem. Biol. 2008, 15:527-532.
7. Chiang Y.M., et al. A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. J. Am. Chem. Soc. 2009, 131:2965-2970.
8. Coyle C.M., Panaccione D.G. An ergot alkaloid biosynthesis gene and clustered hypothetical genes from Aspergillus fumigatus. Appl. Environ. Microbiol. 2005, 71:3112-3118.
9. Eisendle M., et al. The siderophore system is essential for viability of Aspergillus nidulans: functional analysis of two genes encoding l-ornithine N 5-monooxygenase (sidA) and a non-ribosomal peptide synthetase (sidC). Mol. Microbiol. 2003, 49:359-375.
10. Fedorova N.D., et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008, 4:e1000046.
11. Fitzpatrick D.A., et al. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol.Biol. 2006, 6:99.
12. Frisvad J.C., et al. The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi. Mycol. Res. 2008, 112:231-240.
13. Fujii I., et al. Hydrolytic polyketide shortening by ayg1p, a novel enzyme involved in fungal melanin biosynthesis. J. Biol. Chem. 2004, 279:44613-44620.
14. Galagan J.E., et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868.
15. Gardiner D.M., Howlett B.J. Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol. Lett. 2005, 248:241-248.
16. Grundmann A., et al. FtmPT2, an N-prenyltransferase from Aspergillus fumigatus, catalyses the last step in the biosynthesis of fumitremorgin B. ChemBioChem 2008, 9:2059-2063.
17. Hoffmeister D., Keller N.P. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat. Prod. Rep. 2007, 24:393-416.
18. Kato N., et al. Identification of cytochrome P450s required for fumitremorgin biosynthesis in Aspergillus fumigatus. ChemBioChem 2009, 10:920-928.
19. Keller N.P., Hohn T.M. Metabolic pathway gene clusters in filamentous fungi. Fungal Genet. Biol. 1997, 21:17-29.
20. Keller N.P., et al. Fungal secondary metabolism - from biochemistry to genomics. Nat. Rev. Microbiol. 2005, 3:937-947.
21. Kim Y.T., et al. Two different polyketide synthase genes are required for synthesis of zearalenone in Gibberella zeae. Mol. Microbiol. 2005, 58:1102-1113.
22. Liu Y.J., Hall B.D. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. USA 2004, 101:4507-4512.
23. Magan N., Aldred D. Why do fungi produce mycotoxins?. New Challenges in Food Mycology 2006, 121-133. Taylor & Francis, Boca Raton, FL. J. Dijksterhuis, R.A. Samson (Eds.).
24. Maiya S., et al. The fumitremorgin gene cluster of Aspergillus fumigatus: identification of a gene encoding brevianamide F synthetase. ChemBioChem 2006, 7:1062-1069.
25. Malz S., et al. Identification of a gene cluster responsible for the biosynthesis of aurofusarin in the Fusarium graminearum species complex. Fungal Genet. Biol. 2005, 42:420-433.
26. McDonagh A., et al. Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog. 2008, 4:e1000154.
27. Mistry J., Finn R. Pfam: a domain-centric method for analyzing proteins and proteomes. Methods Mol. Biol. 2007, 396:43-58.
28. Nierman W.C., et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005, 438:1151-1156.
29. Palaez F. Biological activities of fungal metabolites. Handbook of Industrial Microbiology 2005, 49-92. Marcel Dekker, New York. Z. An (Ed.).
30. Perrin R.M., et al. Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PLoS Pathog. 2007, 3:e50.
31. Proctor R.H., et al. Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis. Fungal Genet. Biol. 2003, 38:237-249.
32. Reeves E.P., et al. A nonribosomal peptide synthetase (Pes1) confers protection against oxidative stress in Aspergillus fumigatus. FEBS J. 2006, 273:3038-3053.
33. Reiber K., et al. The expression of selected non-ribosomal peptide synthetases in Aspergillus fumigatus is controlled by the availability of free iron. FEMS Microbiol. Lett. 2005, 248:83-91.
34. Schrettl M., et al. Siderophore biosynthesis but not reductive iron assimilation is essential for Aspergillus fumigatus virulence. J. Exp. Med. 2004, 200:1213-1219.
35. Schwecke T., et al. Nonribosomal peptide synthesis in Schizosaccharomyces pombe and the architectures of ferrichrome-type siderophore synthetases in fungi. ChemBioChem 2006, 7:612-622.
36. Selengut J.D., et al. TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007, 35:D260-D264.
37. Shwab E.K., et al. Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryot. Cell 2007, 6:1656-1664.
38. Smith D.J., et al. Cloning and heterologous expression of the penicillin biosynthetic gene cluster from Penicillum chrysogenum. Biotechnology (N Y). 1990, 8:39-41.
39. Song Z., et al. Fusarin C biosynthesis in Fusarium moniliforme and Fusarium venenatum. ChemBioChem 2004, 5:1196-1203.
40. Sonnhammer E.L., et al. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 1998, 26:320-322.
41. Starcevic A., et al. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res. 2008, 36:6882-6892.
42. Szewczyk E., et al. Identification and characterization of the asperthecin gene cluster of Aspergillus nidulans. Appl. Environ. Microbiol. 2008, 74:7607-7612.
43. Townsend C.A. Structural studies of natural product biosynthetic proteins. Chem. Biol. 1997, 4:721-730.
44. Tsai H.F., et al. A developmentally regulated gene cluster involved in conidial pigment biosynthesis in Aspergillus fumigatus. J. Bacteriol. 1999, 181:6469-6477.
45. Unsold I.A., Li S.M. Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus. Microbiology 2005, 151:1499-1505.
46. Unsold I.A., Li S.M. Reverse prenyltransferase in the biosynthesis of fumigaclavine C in Aspergillus fumigatus: gene expression, purification, and characterization of fumigaclavine C synthase FGAPT1. ChemBioChem 2006, 7:158-164.
47. Weber T., et al. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J. Biotechnol. 2009, 140:13-17.
48. Williams R.B., et al. Epigenetic remodeling of the fungal secondary metabolome. Org. Biomol. Chem. 2008, 6:1895-1897.
49. Yu J., et al. Gene profiling for studying the mechanism of aflatoxin biosynthesis in Aspergillus flavus and A. parasiticus. Food Addit. Contam. 2007, 24:1035-1042.
50. Zaleta-Rivera K., et al. A bidomain nonribosomal peptide synthetase encoded by FUM14 catalyzes the formation of tricarballylic esters in the biosynthesis of fumonisins. Biochemistry 2006, 45:2561-2569.
51. Zhang S., et al. Indole-diterpene gene cluster from Aspergillus flavus. Appl. Environ. Microbiol. 2004, 70:6875-6883.