Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus

Gene

Volumn 383, Issue , 2006, Pages 24-32

  Cramer Jr , Robert A ^a   Stajich, Jason E ^a   Yamanaka, Yvonne ^a   Dietrich, Fred S ^a   Steinbach, William J ^a   Perfect, John R ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Adenylation domain; Fungal secondary metabolites; Invasive aspergillosis

Indexed keywords

MESSENGER RNA; NONRIBOSOMAL PEPTIDE SYNTHETASE; SYNTHETASE; UNCLASSIFIED DRUG;

ADENYLATION; ARTICLE; ASPERGILLUS; ASPERGILLUS FLAVUS; ASPERGILLUS FUMIGATUS; ASPERGILLUS NIDULANS; ASPERGILLUS ORYZAE; ASPERGILLUS TERREUS; CONTROLLED STUDY; ENZYME ANALYSIS; FUNGAL STRAIN; FUNGAL VIRULENCE; GENEALOGY; GENOME ANALYSIS; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHESIS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ASPERGILLUS; GENES, FUNGAL; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDE SYNTHASES; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RNA, FUNGAL; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID;

ASPERGILLUS; ASPERGILLUS FLAVUS; ASPERGILLUS FUMIGATUS; ASPERGILLUS ORYZAE; ASPERGILLUS TERREUS; FUNGI;

EID: 33750083918     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.07.008     Document Type: Article

References (36)

1. Ansari M.Z., Yadav G., Gokhale R.S., and Mohanty D. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res. 32 (2004) W405-W413
2. Bennett J.W. Mycotoxin research: 1989. Mycopathologia 107 (1989) 65-66
3. Bok J.W., et al. LaeA, a regulator of morphogenetic fungal virulence factors. Eukaryot. Cell 4 (2005) 1574-1582
4. Cramer Jr. R.A., et al. Disruption of a nonribosomal peptide synthetase in Aspergillus fumigatus eliminates gliotoxin production. Eukaryot. Cell 5 (2006) 972-980
5. Eddy S.R. Hidden Markov models. Curr. Opin. Struck. Biol. 6 (1996) 361-365
6. Finn R.D., et al. Pfam: clans, web tools and services. Nucleic Acids Res. 34 (2006) D247-D251
7. Gardiner D.M., Cozijnsen A.J., Wilson L.M., Pedras M.S., and Howlett B.J. The sirodesmin biosynthetic gene cluster of the plant pathogenic fungus Leptosphaeria maculans. Mol. Microbiol. 53 (2004) 1307-1318
8. Hissen A.H., Chow J.M., Pinto L.J., and Moore M.M. Survival of Aspergillus fumigatus in serum involves removal of iron from transferrin: the role of siderophores. Infect. Immun. 72 (2004) 1402-1408
9. Hissen A.H., Wan A.N., Warwas M.L., Pinto L.J., and Moore M.M. The Aspergillus fumigatus siderophore biosynthetic gene sidA, encoding L-ornithine N5-oxygenase, is required for virulence. Infect. Immun. 73 (2005) 5493-5503
10. Johnson J.M., Mason K., Moallemi C., Xi H., Somaroo S., and Huang E.S. Protein family annotation in a multiple alignment viewer. Bioinformatics 19 (2003) 544-545
11. Keller N.P., Turner G., and Bennett J.W. Fungal secondary metabolism - from biochemistry to genomics. Nat. Rev., Microbiol. 3 (2005) 937-947
12. Korf I. Gene finding in novel genomes. BMC Bioinformatics 5 (2004) 59
13. Kroken S., Glass N.L., Taylor J.W., Yoder O.C., and Turgeon B.G. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15670-15675
14. Latge J.P. Aspergillus fumigatus and aspergillosis. Clin. Microbiol. Rev. 12 (1999) 310-350
15. Lee B.N., Kroken S., Chou D.Y., Robbertse B., Yoder O.C., and Turgeon B.G. Functional analysis of all nonribosomal peptide synthetases in Cochliobolus heterostrophus reveals a factor, NPS6, involved in virulence and resistance to oxidative stress. Eukaryot. Cell 4 (2005) 545-555
16. Levitz S.M., Selsted M.E., Ganz T., Lehrer R.I., and Diamond R.D. In vitro killing of spores and hyphae of Aspergillus fumigatus and Rhizopus oryzae by rabbit neutrophil cationic peptides and bronchoalveolar macrophages. J. Infect. Dis. 154 (1986) 483-489
17. Majoros W.H., Pertea M., and Salzberg S.L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20 (2004) 2878-2879
18. Marahiel M.A. Multidomain enzymes involved in peptide synthesis. FEBS Lett. 307 (1992) 40-43
19. Marr K.A., Koudadoust M., Black M., and Balajee S.A. Early events in macrophage killing of Aspergillus fumigatus conidia: new flow cytometric viability assay. Clin. Diagn. Lab. Immunol. 8 (2001) 1240-1247
20. Nessa K., Palmberg L., Johard U., Malmberg P., Jarstrand C., and Camner P. Reaction of human alveolar macrophages to exposure to Aspergillus fumigatus and inert particles. Environ. Res. 75 (1997) 141-148
21. Nierman W.C., et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438 (2005) 1151-1156
22. Osbourn A.E. Tox-boxes, fungal secondary metabolites, and plant disease. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 14187-14188
23. Panaccione D.G., Scott-Craig J.S., Pocard J.A., and Walton J.D. A cyclic peptide synthetase gene required for pathogenicity of the fungus Cochliobolus carbonum on maize. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 6590-6594
24. Perfect J.R., et al. The impact of culture isolation of Aspergillus species: a hospital-based survey of aspergillosis. Clin. Infect. Dis. 33 (2001) 1824-1833
25. 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. 248 (2005) 83-91
26. Silakowski B., Kunze B., and Muller R. Multiple hybrid polyketide synthase/non-ribosomal peptide synthetase gene clusters in the myxobacterium Stigmatella aurantiaca. Gene 275 (2001) 233-240
27. Slater G.S., and Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6 (2005) 31
28. Stajich J.E., et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12 (2002) 1611-1618
29. Stanke M., and Waack S. Gene prediction with a hidden Marcov model and a new intron submodel. Bioinformatics 19 Suppl 2 (2003) II215-II225
30. Szekeres A., et al. Peptaibols and related peptaibiotics of Trichoderma. A review. Acta Microbiol. Immunol. Hung. 52 (2005) 137-168
31. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
32. Waldorf A.R. Pulmonary defense mechanisms against opportunistic fungal pathogens. Immunol. Ser. 47 (1989) 243-271
33. Walton J.D. Two enzymes involved in biosynthesis of the host-selective phytotoxin HC-toxin. Proc. Natl. Acad. Sci. U. S. A. 84 (1987) 8444-8447
34. Walton J.D. Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: an hypothesis. Fungal Genet. Biol. 30 (2000) 167-171
35. Weber T., and Marahiel M.A. Exploring the domain structure of modular nonribosomal peptide synthetases. Structure (Camb) 9 (2001) R3-R9
36. Yuan W.M., Gentil G.D., Budde A.D., and Leong S.A. Characterization of the Ustilago maydis sid2 gene, encoding a multidomain peptide synthetase in the ferrichrome biosynthetic gene cluster. J. Bacteriol. 183 (2001) 4040-4051