Contact us
닫기
Article Search
닫기

Microbiology and Biotechnology Letters

보문(Article)

View PDF

Molecular and Cellular Microbiology / Biomedical Sciences  |  Molecular Genetics, Omics, and Systems Biology

Microbiol. Biotechnol. Lett. 2018; 46(3): 300-312

https://doi.org/10.4014/mbl.1808.08012

Received: August 21, 2018; Accepted: August 28, 2018

Genome Sequencing and Genome-Wide Identification of Carbohydrate-Active Enzymes (CAZymes) in the White Rot Fungus Flammulina fennae

Chang-Soo Lee 1, Won-Sik Kong 2 and Young-Jin Park 1*

1Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea, 2Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Republic of Korea

Abstract

Go to

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

Keywords: Flammulina fennae, genome, carbohydrate active enzyme, white rot fungus

References

Go to
  1. Bas C. 1983. Flammulina in western Europe. Persoonia-Molecular Phylogeny and Evolution of Fungi 12: 51-66.
  2. Ripková S, Hughes K, Adamčík S, Kučera V, Adamčíková K. 2010. The delimitation of Flammulina fennae. Mycol. Prog. 9: 469-484.
    CrossRef
  3. Pérez-Butrón JL, Ferdnández-Vicente J. 2007. Una nuevaespecie de Flammulina P. Karsten, F. cephalariae (Agaricales) encontradaen España. Rev. Catalana. Micol. 29: 81-91.
  4. Eriksson K, Blanchette RA, Ander P. 1990. Morphological aspects of wood degradation by fungi and bacteria. pp. 1-87. In Microbial and enzymatic degradation of wood and wood components. Springer: Berlin, Heidelberg.
    CrossRef
  5. Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. 2014. Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol. Mol. Biol. Rev. 78: 614-649.
    Pubmed KoreaMed CrossRef
  6. Boraston AB, Bolam DN, Gilbert HJ, Davies GJ. 2004. Carbohydratebinding modules: fine-tuning polysaccharide recognition. Biochem. J. 382: 769-781.
    Pubmed KoreaMed CrossRef
  7. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42: D490-D495.
    Pubmed KoreaMed CrossRef
  8. Shoseyov O, Shani Z, Levy I. 2006. Carbohydrate binding modules:biochemical properties and novel applications. Microbiol. Mol. Biol. Rev. 70: 283-295.
    Pubmed KoreaMed CrossRef
  9. Zhao Z, Liu H, Wang C, Xu JR. 2013. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 14: 274.
    Pubmed KoreaMed CrossRef
  10. Park YJ, Baek JH, Lee S, Kim C, Rhee H, Kim H, et al. 2014. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 9: e93560.
    Pubmed KoreaMed CrossRef
  11. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 21142120.
    Pubmed KoreaMed CrossRef
  12. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821-829.
    Pubmed KoreaMed CrossRef
  13. Stanke M, Morgenstern B. 2005. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33: W465-W467.
    Pubmed KoreaMed CrossRef
  14. Buchfink B, Xie C, Huson D. 2015. Fast and sensitive protein alignment using DIAMOND, Nat. Methods 12: 59-60.
    Pubmed CrossRef
  15. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44: D279-D285.
    Pubmed KoreaMed CrossRef
  16. Lowe TM, Eddy SR. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
    Pubmed KoreaMed
  17. Emms D, Kelly S. 2015. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16: 157.
    Pubmed KoreaMed CrossRef
  18. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, et al. 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105-1115.
    Pubmed CrossRef
  19. Staats M, van Kan JA. 2012. Genome update of Botrytis cinerea strains B05. 10 and T4. Eukaryot. Cell 11: 1413-1414.
    Pubmed KoreaMed CrossRef
  20. Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagye LG, et al. 2012. Genome sequence of the button mushroom Agaricusbisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc. Natl. Acad. Sci. USA 109: 17501-17506.
    Pubmed KoreaMed CrossRef
  21. Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, et al. 2010. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc. Natl. Acad. Sci. USA 107: 11889-11894.
    Pubmed KoreaMed CrossRef
  22. Zheng P, Xia Y, Xiao G, Xiong C, Hu X, Zhang S, et al. 2011. Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol. 12:R116.
    Pubmed KoreaMed CrossRef
  23. Janbon G, Ormerod KL, Paulet D, Byrnes III EJ, Yadav V, Chatterjee G, et al. 2014. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 10: e1004261.
    Pubmed KoreaMed CrossRef
  24. Martin F, Aerts A, Ahrén D, Brun A, Danchin EGJ, Duchaussoy F, et al. 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92.
    Pubmed CrossRef
  25. Chen L, Gong Y, Cai Y, Liu W, Zhou Y, Xiao Y, et al. 2016. Genome sequence of the edible cultivated mushroom Lentinula edodes (Shiitake) reveals insights into lignocellulose degradation. PLoS One 11: e0160336.
    Pubmed KoreaMed CrossRef
  26. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
    Pubmed CrossRef
  27. Martinez D, Larrondo LF, Putnam N, Sollewijn Gelpke MD, Huang K, Chapman J, et al. 2004. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol. 22: 695-700.
    Pubmed CrossRef
  28. Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel‐Tarver L, et al. 2006. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23: 857-865.
    Pubmed KoreaMed CrossRef
  29. Ohm RA, De Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, et al. 2010. Genome sequence of the model mushroom Schizophyllum commune. Nat. Biotechnol. 28: 957-963.
    Pubmed CrossRef
  30. Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. 2017. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol. Biofuels 10: 170.
    Pubmed KoreaMed CrossRef
  31. Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, et al. 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101.
    Pubmed CrossRef
  32. Yin Y, Mao X, Yang JC, Chen X, Mao F, Xu Y. 2012. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40: W445-W451.
    Pubmed KoreaMed CrossRef
  33. Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0:discriminating signal peptides from transmembrane regions. Nat. Methods 8: 785-786.
    Pubmed CrossRef
  34. Breton C, Šnajdrová L, Jeanneau C, Koča J, Imberty A. 2006. Structures and mechanisms of glycosyltransferases. Glycobiology 16:29R-37R.
    Pubmed CrossRef
  35. Lairson LL, Henrissat B, Davies GJ, Withers SG. 2008. Glycosyltransferases:structures, functions, and mechanisms. Annu. Rev. Biochem. 77: 521-555.
    Pubmed CrossRef
  36. Paulson JC, Weinstein J, Ujita EL, Riggs KJ, Lai H. 1987. The membranebinding domain of a rat liver Golgi sialyltransferase. Biochem. Soc. Trans. 15: 618-620.
    Pubmed CrossRef
  37. Wickner WT, Lodish HF. 1985. Multiple mechanisms of protein insertion into and across membranes. Science 230: 400-407.
    Pubmed CrossRef
  38. Chou MM, Kendall DA. 1990. Polymeric sequences reveal a functional interrelationship between hydrophobicity and length of signal peptides. J. Biol. Chem. 265: 2873-2880,
    Pubmed
  39. IngMarie N, Whitley P, von Heijne G. 1994. The COOH-terminal ends of internal signal and signal-anchor sequences are positioned differently in the ER translocase. J. Cell Biol. 126: 11271132.
  40. Coutinho PM, Deleury E, Davies GJ, Henrissat B. 2003. An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 328: 307-317.
    CrossRef
  41. Campbell JA, Davies GJ, Bulone V, Henrissat B. 1997. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem. J. 326: 929-939.
    Pubmed KoreaMed CrossRef
  42. Mukai Y, Hirokawa T, Tomii K, Asai K, Akiyama Y, Suwa M. 2008. Identification of glycosyltransferases focusing on Golgi transmembrane region, Trends Glycosci. Glycotechnol. 19: 41-47.
    CrossRef
  43. Berlemont R, Martiny AC. 2016. Glycoside hydrolases across environmental microbial communities. PLoS Comput. Biol. 12:e1005300.
    Pubmed KoreaMed CrossRef
  44. Henrissat B. 1991. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280: 309-316.
    Pubmed KoreaMed CrossRef
  45. Hahn M, Olsen O, Politz O, Borriss R, Heinemann U. 1995. Crystal structure and site-directed mutagenesis of Bacillus macerans endo-1,3-1,4-beta-glucanase. J. Biol. Chem. 270: 3081-3088.
    Pubmed CrossRef
  46. Masuda S, Endo K, Koizumi N, Hayami T, Fukazawa T, Yatsunami R, et al. 2006. Molecular identification of a novel beta-1,3-glucanase from alkaliphilic Nocardiopsis sp. strain F96. Extremophiles 10: 251-255.
    Pubmed CrossRef
  47. Kotake T, Hirata N, Degi Y, Ishiguro M, Kitazawa K, Takata R, et al. 2011. Endo-β-1,3-galactanase from winter mushroom Flammulina velutipes. J. Biol. Chem. 286: 27848-27854.
    Pubmed KoreaMed CrossRef
  48. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, et al. 2007. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35: W585-W587.
    Pubmed KoreaMed CrossRef
  49. Wilson DB. 2011. Microbial diversity of cellulose hydrolysis. Curr. Opin. Microbiol. 14: 259-263.
    Pubmed CrossRef
  50. Berlemont R. 2017. Distribution and diversity of enzymes for polysaccharide degradation in fungi. Sci. Rep. 7: 222.
    Pubmed KoreaMed CrossRef
  51. Eichlerová I, Homolka L, Žifčáková L, Lisá L, Dobiášová P, Baldrian P. 2015. Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. Fungal Ecol. 13:10-22.
    CrossRef
  52. Treseder KK, Lennon JT. 2015. Fungal traits that drive ecosystem dynamics on land. Microbiol. Mol. Biol. Rev. 79: 243-262.
    Pubmed KoreaMed CrossRef
  53. Sutherland IW. 1995. Polysaccharide lyases. FEMS Microbiol. Rev. 16: 323-347.
    Pubmed CrossRef
  54. Yip VL, Withers SG. 2006. Breakdown of oligosaccharides by the process of elimination. Curr. Opin. Chem. Biol. 10: 147-155.
    Pubmed CrossRef
  55. Garron ML, Cygler M. 2010. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 20: 1547-1573.
    Pubmed CrossRef
  56. van den Brink J, de Vries RP. 2011. Fungal enzyme sets for plant polysaccharide degradation. Appl. Microbiol. Biotechnol. 91:1477-1492.
    Pubmed KoreaMed CrossRef
  57. Xavier-Santos S, Carvalho CC, Bonfá M, Silva R, Capelari M, Gomes E. 2004. Screening for pectinolytic activity of wood-rotting basidiomycetes and characterization of the enzymes. Folia Microbiol. (Praha) 49: 46-52.
    CrossRef
  58. The CAZypedia Consortium. 2018. Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes. Glycobiology 28: 3-8.
    Pubmed CrossRef
  59. Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, et al. 2012. Comparative genomics of Ceriporiopsissubvermispora and Phanerochaetechrysosporium provide insight into selective ligninolysis. Proc. Natl. Acad. Sci. USA 109: 54585463.
    Pubmed KoreaMed CrossRef
  60. Várnai A, Mäkelä MR, Djajadi DT, Rahikainen J, Hatakka A, Viikari L. 2014. Carbohydrate-binding modules of fungal cellulases:occurrence in nature, function, and relevance in industrial biomass conversion. Adv. Appl. Microbiol. 88: 103-165.
    Pubmed CrossRef
  61. Bornscheuer UT. 2002. Microbial carboxyl esterases: Classification, properties and application in biocatalysis. FEMS Microbiol. Rev. 26: 73-81.
    Pubmed CrossRef
  62. Jaeger KE, Eggert T. 2002. Lipases for biotechnology. Curr. Opin. Biotechnol. 13: 390-397.
    CrossRef
  63. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-D238.
    Pubmed KoreaMed CrossRef
  64. Biely P. 2012. Microbial carbohydrate esterases deacetylating plant polysaccharides. Biotechnol. Adv. 30: 1575-1588.
    Pubmed CrossRef
  65. Adesioye FA, Makhalanyane TP, Biely P, Cowan DA. 2016. Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylanesterases. Enzyme Microb. Technol. 93: 79-91.
    Pubmed CrossRef
  66. Christov LP, Prior BA. 1993. Esterases of xylan-degrading microorganisms:Production, properties, and significance. Enzyme Microb. Technol. 15: 460-475.
    CrossRef
  67. Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. 2013. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels 6: 41.
    Pubmed KoreaMed CrossRef
  68. Reiss R, Ihssen J, Richter M, Eichhorn E, Schilling B, Thöny-Meyer L. 2013. Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PLoS One 8: e65633.
    Pubmed KoreaMed CrossRef
  69. Fernandez IS, Ruiz-Duenas FJ, Santillana E, Ferreira P, Martinez MJ, Martinez AT, et al. 2009. Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase. Acta Crystallogr. D65: 1196-1205.
    Pubmed CrossRef
  70. Varela E, Martinet MJ, Martinez AT. 2000. Arylalcohol oxidase protein sequence: a comparison with glucose oxidase and other FAD oxidoreductases. Biochem. Biophys. Acta Protein Struct. Mol. Enzymol. 1481: 202-208.
    CrossRef
  71. Wierenga RK, Drenth J, Schulz GE. 1983. Comparison of the 3dimensional protein and nucleotide structure of the FAD-binding domain of parahydroxybenzoate hydroxylase with the FADbinding as well as NADPH-binding domains of glutathionereductase. J. Mol. Biol. 167: 725-739.
    CrossRef
  72. Ruiz-Dueñas FJ, Martínez AT. 2009. Microbial degradation of lignin:how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this. Microb. Biotechnol. 2: 164-177.
    Pubmed KoreaMed CrossRef
  73. Martínez AT, Ruiz-Dueñas FJ, Martínez MJ, Del Río JC, Gutiérrez A. 2009. Enzymatic delignification of plant cell wall: from nature to mill. Curr. Opin. Biotechnol. 20: 348-357.
    Pubmed CrossRef
  74. Guillén F, Martínez MJ, Gutiérrez A, Del Rio JC. 2005. Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int. Microbiol. 8: 195-204.
    Pubmed
  75. Leonowicz A, Matuszewska A, Luterek J, Ziegenhagen D, WojtasWasilewska M, Cho, NS, et al. 1999. Biodegradation of lignin by white rot fungi. Fungal Genet. Biol. 27: 175-185.
    Pubmed CrossRef

Article Tools

Starts of Metrics

Share this article on :

Related articles in MBL

Most Searched Keywords ?

What is Most Searched Keywords?

  • It is most registrated keyword in articles at this journal during for 2 years.