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RESEARCH ARTICLE

Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes

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Pages 104-114 | Received 05 Oct 2019, Accepted 22 Jan 2020, Published online: 21 Feb 2020

References

  • Cho KS, Ryu HW. Biodecolorization and biodegradation of dye by fungi: a review. KSBB J. 2015;30:203–222.
  • Ryu H, Ryu HW, Cho KS. Characterization of dye decolorization in cell-free culture broth of Trametes versicolor CBR43. J Microbiol Biotechnol. 2017;27:155–160.
  • Justo A, Miettinen O, Floudas D, et al. A revised family-level classification of the Polyporales (Basidiomycota). Fungal Biol. 2017;121:798–824.
  • Ferreira DSS, Kato RB, Miranda FM, et al. Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil. Data Brief. 2018;18:1581–1587.
  • Knežević A, Stajić M, Sofrenić I, et al. Antioxidative, antifungal, cytotoxic and antineurodegenerative activity of selected Trametes species from Serbia. PLoS One. 2018;13:e0203064.
  • Yang XQ, Zhao XX, Liu CY, et al. Decolorization of azo, triphenylmethane and anthraquinone dyes by a newly isolated Trametes sp. SQ01 and its laccase. Process Biochem. 2009;44:1185–1189.
  • Levin L, Herrmann C, Papinutti VL. Optimization of lignocellulolytic enzyme production by the white-rot fungus Trametes trogii in solid-state fermentation using response surface methodology. Biochem Eng J. 2008;39:207–214.
  • Neves M, Baseia I, Drechsler-Santos E, et al. Guide to the common fungi of the semiarid region of Brazil. Florianópolis: TECC Editora; 2013.
  • Milton RD, Giroud F, Thumser AE, et al. Hydrogen peroxide produced by glucose oxidase affects the performance of laccase cathodes in glucose/oxygen fuel cells: FAD-dependent glucose dehydrogenase as a replacement. Phys Chem Chem Phys. 2013;15:19371–19379.
  • Salaj-Kosla U, Pöller S, Schuhmann W, et al. Direct electron transfer of Trametes hirsuta laccase adsorbed at unmodified nanoporous gold electrodes. Bioelectrochemistry. 2013;91:15–20.
  • Davies GJ, Williams SJ. Carbohydrate-active enzymes: sequences, shapes, contortions and cells. Biochem Soc Trans. 2016;44:79–87.
  • Sista Kameshwar AK, Qin W. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology. 2018;9:93–105.
  • Zhao Z, Liu H, Wang C, et al. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics. 2013;14:274.
  • Dai W, Chen X, Wang X, et al. The Algicidal Fungus Trametes versicolor F21a eliminating blue algae via genes encoding degradation enzymes and metabolic pathways revealed by transcriptomic analysis. Front Microbiol. 2018;9:826.
  • Newman DJ, Cragg GM. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod. 2012;75:311–335.
  • Blin K, Wolf T, Chevrette MG, et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45:W36–W41.
  • Pusztahelyi T, Holb IJ, Pócsi I. Secondary metabolites in fungus–plant interactions. Front Plant Sci. 2015;6:573.
  • Keller NP. Fungal secondary metabolism: regulation, function and drug discovery. Nat Rev Microbiol. 2018; 17(3):167–180.
  • Collemare J, Billard A, Böhnert HU, et al. Biosynthesis of secondary metabolites in the rice blast fungus Magnaporthe grisea: the role of hybrid PKS-NRPS in pathogenicity. Mycol Res. 2008;112:207–215.
  • Cimermancic P, Medema MH, Claesen J, et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014;158:412–421.
  • Clevenger KD, Bok JW, Ye R, et al. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol. 2017;13:895–901.
  • Nielsen JC, Grijseels S, Prigent S, et al. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nat Microbiol. 2017;2:17044.
  • Hyatt D, Chen GL, Locascio PF, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
  • Aherfi S, Andreani J, Baptiste E, et al. A large open pangenome and a small core genome for giant pandoraviruses. Front Microbiol. 2018;9:1486.
  • Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–2189.
  • Schoch CL, Seifert KA, Huhndorf S, et al.; Fungal Barcoding Consortium. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA. 2012;109:6241–6246.
  • Blaalid R, Kumar S, Nilsson RH, et al. ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol Ecol Resour. 2013;13:218–224.
  • Bengtsson‐Palme J, Ryberg M, Hartmann M, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:914–919.
  • Lesage-Meessen L, Haon M, Uzan E, et al. Phylogeographic relationships in the polypore fungus Pycnoporus inferred from molecular data. FEMS Microbiol Lett. 2011;325:37–48.
  • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797.
  • Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564–577.
  • Retief JD. Phylogenetic analysis using PHYLIP. Methods Mol Biol. 1999;132:243–258.
  • Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–2739.
  • Tatusov RL, Fedorova ND, Jackson JD, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.
  • Huerta-Cepas J, Szklarczyk D, Forslund K, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286–D293.
  • Lombard V, Golaconda Ramulu H, Drula E, et al. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495.
  • Cantarel BL, Coutinho PM, Rancurel C, et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 2009;37:D233–D238.
  • Mäkelä M, DiFalco M, McDonnell E, et al. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Stud Mycol. 2018;91:79–99.
  • Lomascolo A, Cayol JL, Roche M, et al. Molecular clustering of Pycnoporus strains from various geographic origins and isolation of monokaryotic strains for laccase hyperproduction. Mycol Res. 2002;106:1193–1203.
  • Levasseur A, Lomascolo A, Chabrol O, et al. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics. 2014;15:486.
  • Busk PK, Lange M, Pilgaard B, et al. Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature. PLoS One. 2014;9:e114138.
  • Couturier M, Navarro D, Chevret D, et al. Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. Biotechnol Biofuels. 2015;8:216.
  • Pavlov AR, Tyazhelova TV, Moiseenko KV, et al. Draft genome sequence of the fungus Trametes hirsuta 072. Genome Announc. 2015;3:e01287–01215.
  • Cerrón LM, Romero-Suárez D, Vera N, et al. Decolorization of textile reactive dyes and effluents by biofilms of Trametes polyzona LMB-TM5 and Ceriporia sp. LMB-TM1 isolated from the Peruvian Rainforest. Water Air Soil Pollut. 2015;226:235.
  • Granchi Z, Peng M, Chi-A-Woeng T, et al. Genome sequence of the basidiomycete white-rot fungus Trametes pubescens FBCC735. Genome Announc. 2017;5:e0164301616.
  • Wang J, Zhang Y, Xu Y, et al. Genome sequence of a laccase producing fungus Trametes sp. AH28-2. J Biotechnol. 2015;216:167–168.
  • Floudas D, Binder M, Riley R, et al. The Paleozoic origin of enzymatic mechanisms for decay of lignin reconstructed using 31 fungal genomes. Science. 2012;336:1715–1719.
  • de Oliveira Carneiro RT, Lopes MA, Silva MLC, et al. Trametes villosa lignin peroxidase (TvLiP): genetic and molecular characterization. J Microbiol Biotechnol. 2017;27:179–188.
  • Rytioja J, Hildén K, Yuzon J, et al. Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev. 2014;78:614–649.
  • Berrin JG, Navarro D, Couturier M, et al. Exploring the natural fungal biodiversity of tropical and temperate forests toward improvement of biomass conversion. Appl Environ Microbiol. 2012;78:6483–6490.
  • Yin Y, Mao X, Yang J, et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:W445–W451.
  • Murphy C, Powlowski J, Wu M, et al. Curation of characterized glycoside hydrolases of fungal origin. Database (Oxford). 2011;2011:bar020.
  • Viborg AH, Terrapon N, Lombard V, et al. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J Biol Chem. 2019;294:15973–15986.