1887

Abstract

Members of the economically important ascomycete genus are ubiquitously distributed around the world. The mycoparasitic lifestyle and plant defence-inducing interactions of spp. make them ideal biocontrol agents. Of the enzymes that produce secondary metabolites, some of which likely play important roles in biocontrol processes, polyketide synthase (PKSs) have garnered less attention than non-ribosomal peptide synthetases such as those that produce peptaibols. We have taken a phylogenomic approach to study the PKS repertoire encoded in the genomes of , and . Our analysis lays a foundation for future research related to PKSs within the genus and in other filamentous fungi.

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2012-01-01
2024-03-28
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References

  1. Baker S. E. ( 2008). Aspergillus genomics and DHN-melanin conidial pigmentation. Aspergillus in the Genomic Era73–85 Varga J., Samson R. A. Wageningen, The Netherlands: Wageningen Academic Publishers;
    [Google Scholar]
  2. Bushley K. E., Turgeon B. G. ( 2010). Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol Biol 10:26 [View Article][PubMed]
    [Google Scholar]
  3. Bushley K. E., Ripoll D. R., Turgeon B. G. ( 2008). Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. BMC Evol Biol 8:328 [View Article][PubMed]
    [Google Scholar]
  4. Chiang Y. M., Oakley B. R., Keller N. P., Wang C. C. ( 2010). Unraveling polyketide synthesis in members of the genus Aspergillus . Appl Microbiol Biotechnol 86:1719–1736 [View Article][PubMed]
    [Google Scholar]
  5. Chiang Y. M., Meyer K. M., Praseuth M., Baker S. E., Bruno K. S., Wang C. C. ( 2011). Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone. Fungal Genet Biol 48:430–437 [View Article][PubMed]
    [Google Scholar]
  6. Cox R. J. ( 2007). Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem 5:2010–2026 [View Article][PubMed]
    [Google Scholar]
  7. Cramer R. A. Jr, Stajich J. E., Yamanaka Y., Dietrich F. S., Steinbach W. J., Perfect J. R. ( 2006). Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus . Gene 383:24–32 [View Article][PubMed]
    [Google Scholar]
  8. Frandsen R. J., Schütt C., Lund B. W., Staerk D., Nielsen J., Olsson S., Giese H. ( 2011). Two novel classes of enzymes are required for the biosynthesis of aurofusarin in Fusarium graminearum . J Biol Chem 286:10419–10428 [View Article][PubMed]
    [Google Scholar]
  9. Gaffoor I., Brown D. W., Plattner R., Proctor R. H., Qi W., Trail F. ( 2005). Functional analysis of the polyketide synthase genes in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum). Eukaryot Cell 4:1926–1933 [View Article][PubMed]
    [Google Scholar]
  10. Galagan J. E., Calvo S. E., Borkovich K. A., Selker E. U., Read N. D., Jaffe D., FitzHugh W., Ma L. J., Smirnov S. & other authors ( 2003). The genome sequence of the filamentous fungus Neurospora crassa . Nature 422:859–868 [View Article][PubMed]
    [Google Scholar]
  11. Jørgensen T. R., Park J., Arentshorst M., van Welzen A. M., Lamers G., Vankuyk P. A., Damveld R. A., van den Hondel C. A., Nielsen K. F. & other authors ( 2011). The molecular and genetic basis of conidial pigmentation in Aspergillus niger . Fungal Genet Biol 48:544–553 [View Article][PubMed]
    [Google Scholar]
  12. Kim J. E., Han K. H., Jin J., Kim H., Kim J. C., Yun S. H., Lee Y. W. ( 2005). Putative polyketide synthase and laccase genes for biosynthesis of aurofusarin in Gibberella zeae . Appl Environ Microbiol 71:1701–1708 [View Article][PubMed]
    [Google Scholar]
  13. Kroken S., Glass N. L., Taylor J. W., Yoder O. C., Turgeon B. G. ( 2003). Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc Natl Acad Sci U S A 100:15670–15675 [View Article][PubMed]
    [Google Scholar]
  14. Kubicek C. P., Herrera-Estrella A., Seidl-Seiboth V., Martinez D. A., Druzhinina I. S., Thon M., Zeilinger S., Casas-Flores S., Horwitz B. A. & other authors ( 2011). Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma . Genome Biol 12:R40 [View Article][PubMed]
    [Google Scholar]
  15. Langfelder K., Jahn B., Gehringer H., Schmidt A., Wanner G., Brakhage A. A. ( 1998). Identification of a polyketide synthase gene (pksP) of Aspergillus fumigatus involved in conidial pigment biosynthesis and virulence. Med Microbiol Immunol (Berl) 187:79–89 [View Article][PubMed]
    [Google Scholar]
  16. Lee B. N., Kroken S., Chou D. Y., Robbertse B., Yoder O. C., Turgeon B. G. ( 2005). Functional analysis of all nonribosomal peptide synthetases in Cochliobolus heterostrophus reveals a factor, NPS6, involved in virulence and resistance to oxidative stress. Eukaryot Cell 4:545–555 [View Article][PubMed]
    [Google Scholar]
  17. Librado P., Rozas J. ( 2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452 [View Article][PubMed]
    [Google Scholar]
  18. Linnemannstöns P., Schulte J., del Mar Prado M., Proctor R. H., Avalos J., Tudzynski B. ( 2002). The polyketide synthase gene pks4 from Gibberella fujikuroi encodes a key enzyme in the biosynthesis of the red pigment bikaverin. Fungal Genet Biol 37:134–148 [View Article][PubMed]
    [Google Scholar]
  19. Malz S., Grell M. N., Thrane C., Maier F. J., Rosager P., Felk A., Albertsen K. S., Salomon S., Bohn L. & other authors ( 2005). Identification of a gene cluster responsible for the biosynthesis of aurofusarin in the Fusarium graminearum species complex. Fungal Genet Biol 42:420–433 [View Article][PubMed]
    [Google Scholar]
  20. Martinez D., Berka R. M., Henrissat B., Saloheimo M., Arvas M., Baker S. E., Chapman J., Chertkov O., Coutinho P. M. & other authors ( 2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26:553–560 [View Article][PubMed]
    [Google Scholar]
  21. Muggia L., Schmitt I., Grube M. ( 2008). Purifying selection is a prevailing motif in the evolution of ketoacyl synthase domains of polyketide synthases from lichenized fungi. Mycol Res 112:277–288 [View Article][PubMed]
    [Google Scholar]
  22. Papadopoulos J. S., Agarwala R. ( 2007). cobalt: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23:1073–1079 [View Article][PubMed]
    [Google Scholar]
  23. Rice P., Longden I., Bleasby A. ( 2000). emboss: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277 [View Article][PubMed]
    [Google Scholar]
  24. Ridley C. P., Lee H. Y., Khosla C. ( 2008). Evolution of polyketide synthases in bacteria. Proc Natl Acad Sci U S A 105:4595–4600 [View Article][PubMed]
    [Google Scholar]
  25. Schuster A., Schmoll M. ( 2010). Biology and biotechnology of Trichoderma . Appl Microbiol Biotechnol 87:787–799 [View Article][PubMed]
    [Google Scholar]
  26. Seidl V., Huemer B., Seiboth B., Kubicek C. P. ( 2005). A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases. FEBS J 272:5923–5939 [View Article][PubMed]
    [Google Scholar]
  27. Selker E. U., Garrett P. W. ( 1988). DNA sequence duplications trigger gene inactivation in Neurospora crassa . Proc Natl Acad Sci U S A 85:6870–6874 [View Article][PubMed]
    [Google Scholar]
  28. Selker E. U., Jensen B. C., Richardson G. A. ( 1987a). A portable signal causing faithful DNA methylation de novo in Neurospora crassa . Science 238:48–53 [View Article][PubMed]
    [Google Scholar]
  29. Selker E. U., Cambareri E. B., Jensen B. C., Haack K. R. ( 1987b). Rearrangement of duplicated DNA in specialized cells of Neurospora . Cell 51:741–752 [View Article][PubMed]
    [Google Scholar]
  30. Sharp P. M., Li W. H. ( 1987). The codon adaptation index–a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295 [View Article][PubMed]
    [Google Scholar]
  31. Stamatakis A., Hoover P., Rougemont J. ( 2008). A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57:758–771 [View Article][PubMed]
    [Google Scholar]
  32. Tajima F. ( 1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595[PubMed]
    [Google Scholar]
  33. Tamura K., Dudley J., Nei M., Kumar S. ( 2007). mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  34. Tsai H. F., Chang Y. C., Washburn R. G., Wheeler M. H., Kwon-Chung K. J. ( 1998). The developmentally regulated alb1 gene of Aspergillus fumigatus: its role in modulation of conidial morphology and virulence. J Bacteriol 180:3031–3038[PubMed]
    [Google Scholar]
  35. Tsai H. F., Fujii I., Watanabe A., Wheeler M. H., Chang Y. C., Yasuoka Y., Ebizuka Y., Kwon-Chung K. J. ( 2001). Pentaketide melanin biosynthesis in Aspergillus fumigatus requires chain-length shortening of a heptaketide precursor. J Biol Chem 276:29292–29298 [View Article][PubMed]
    [Google Scholar]
  36. Viterbo A., Wiest A., Brotman Y., Chet I., Kenerley C. ( 2007). The 18mer peptaibols from Trichoderma virens elicit plant defence responses. Mol Plant Pathol 8:737–746 [View Article][PubMed]
    [Google Scholar]
  37. Watanabe A., Fujii I., Sankawa U., Mayorga M. E., Timberlake W. E., Ebizuka Y. ( 1999). Re-identification of Aspergillus nidulans wA gene to code for a polyketide synthase of naphthopyrone. Tetrahedron Lett 40:91–94 [View Article]
    [Google Scholar]
  38. Watanabe A., Fujii I., Tsai H., Chang Y. C., Kwon-Chung K. J., Ebizuka Y. ( 2000). Aspergillus fumigatus alb1 encodes naphthopyrone synthase when expressed in Aspergillus oryzae . FEMS Microbiol Lett 192:39–44 [View Article][PubMed]
    [Google Scholar]
  39. Wiemann P., Willmann A., Straeten M., Kleigrewe K., Beyer M., Humpf H. U., Tudzynski B. ( 2009). Biosynthesis of the red pigment bikaverin in Fusarium fujikuroi: genes, their function and regulation. Mol Microbiol 72:931–946 [View Article][PubMed]
    [Google Scholar]
  40. Zucko J., Cullum J., Hranueli D., Long P. F. ( 2011). Evolutionary dynamics of modular polyketide synthases, with implications for protein design and engineering. J Antibiot (Tokyo) 64:89–92 [View Article][PubMed]
    [Google Scholar]
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