Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma

Microbiology

Volumn 158, Issue 1, 2012, Pages 147-154

  Baker, Scott E ^a   Perrone, Giancarlo ^b   Richardson, Nathan M ^c   Gallo, Antonia ^b   Kubicek, Christian P ^d  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b INSTITUTE OF SCIENCES OF FOOD PRODUCTION   (Italy)

^c WASHINGTON STATE UNIVERSITY   (United States)

^d VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

POLYKETIDE SYNTHASE;

ARTICLE; FUNGAL GENE; FUNGAL GENOME; GENE CLUSTER; HYPOCREA VIRENS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS; PRIORITY JOURNAL; TRICHODERMA; TRICHODERMA ATROVIRIDE; TRICHODERMA REESIE;

FUNGAL PROTEINS; GENOME, FUNGAL; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYKETIDE SYNTHASES; TRICHODERMA;

FUNGI; HYPOCREA JECORINA; HYPOCREA VIRENS; TRICHODERMA; TRICHODERMA ATROVIRIDE;

EID: 84855225440     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.053462-0     Document Type: Article

References (40)

1. Baker, S. E. (2008). Aspergillus genomics and DHN-melanin conidial pigmentation. In Aspergillus in the Genomic Era, pp. 73-85. Edited by J. Varga & R. A. Samson. Wageningen, The Netherlands: Wageningen Academic Publishers.
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.
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.
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
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-c-pyrone. Fungal Genet Biol 48, 430-437
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
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
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
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
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
11. Jørgensen, T. R., Park, J., Arentshorst, M., vanWelzen, 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
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
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
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.
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
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
17. Librado, P. & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452
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
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
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 biomassdegrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26, 553-560
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
22. Papadopoulos, J. S. & Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23, 1073-1079
23. Rice, P., Longden, I. & Bleasby, A. (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16, 276-277
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
25. Schuster, A. & Schmoll, M. (2010). Biology and biotechnology of Trichoderma. Appl Microbiol Biotechnol 87, 787-799
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
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
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
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
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
31. Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57, 758-771
32. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595
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
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
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 chainlength shortening of a heptaketide precursor. J Biol Chem 276, 29292-29298
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
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
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
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
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.