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Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Abstract

Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.

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Figure 1: Genome organization of M. thermophila and T. terrestris.
Figure 2: Analysis of transcription profiles.
Figure 3: Release of reducing sugars from alfalfa straw by crude extracellular enzymes from thermophilic and nonthermophilic fungi.

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Accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

References

  1. Margaritis, A. & Merchant, R.F.J. Thermostable cellulases from thermophilic microorganisms. Crit. Rev. Biotechnol. 4, 327–367 (1986).

    Article  CAS  Google Scholar 

  2. Margaritis, A. & Merchant, R. Production and thermal stability characteristics of cellulase and xylanase enzymes from Thielavia terrestris. Biotechnol. Bioeng. Symp. 13, 426–428 (1983).

    Google Scholar 

  3. Tansey, M.R. Agar-diffusion assay of cellulolytic ability of thermophilic fungi. Arch. Mikrobiol. 77, 1–11 (1971).

    Article  CAS  Google Scholar 

  4. Wojtczak, G., Breuil, C., Yamada, J. & Saddler, J.N. A comparison of the thermostability of cellulases from various thermophilic fungi. Appl. Microbiol. Biotechnol. 17, 82–87 (1987).

    Google Scholar 

  5. Jensen, E.B. & Boominathan, K.C. Thermophilic fungal expression system. US Patent 5,695,985 (1997).

  6. Jensen, E.B. & Karuppan, C.B. Thermophilic fungal expression system. US Patent 5,602,004 (1997).

  7. Chaetomium globosum Genome Database (Broad Institute, 2005). <http://www.broadinstitute.org/annotation/genome/chaetomium_globosum>.

  8. Henrissat, B. & Davies, G. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 7, 637–644 (1997).

    Article  CAS  Google Scholar 

  9. Karlsson, J. et al. Homologous expression and characterization of Cel61A (EG IV) of Trichoderma reesei. Eur. J. Biochem. 268, 6498–6507 (2001).

    Article  CAS  Google Scholar 

  10. Harris, P.V. et al. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. Biochemistry 49, 3305–3316 (2010).

    Article  CAS  Google Scholar 

  11. Pahkala, K. et al. Production of bioethanol from barley straw and reed canary grass: a raw material study. 15th European Biomass Conference and Exhibition. Berlin, Germany, May 7–11, 2007 (ETA, Florence, Italy and WIP, Munich, 2007).

  12. Dien, B.S. et al. Chemical composition and response to dilute-acid pretreatment and enzymatic saccharification of alfalfa, reed canarygrass, and switchgrass. Biomass Bioenergy 30, 880–891 (2006).

    Article  CAS  Google Scholar 

  13. Kaur, G., Kumar, S. & Satyanarayana, T. Production, characterization and application of a thermostable polygalacturonase of a thermophilic mould Sporotrichum thermophile Apinis. Bioresour. Technol. 94, 239–243 (2004).

    Article  CAS  Google Scholar 

  14. Vafiadi, C., Topakas, E., Biely, P. & Christakopoulos, P. Purification, characterization and mass spectrometric sequencing of a thermophilic glucuronoyl esterase from Sporotrichum thermophile. FEMS Microbiol. Lett. 296, 178–184 (2009).

    Article  CAS  Google Scholar 

  15. Roy, S.K., Dey, S.K., Raha, S.K. & Chakrabarty, S.L. Purification and properties of an extracellular endoglucanase from Myceliophthora thermophila D-14 (ATCC 48104). J. Gen. Microbiol. 136, 1967–1971 (1990).

    Article  CAS  Google Scholar 

  16. van den Brink, J., Samson, R.A., Hagen, F., Boekhout, T. & de Vries, R.P. Phylogeny of the industrial relevant, thermophilic genera Myceliophthora and Corynascus. Fungal Divers. published online, doi:10.1007/s13225–13011–10107-z (28 May 2011).

  17. von Klopotek, A. Thielavia heterothallica spec. nov., die perfekte Form von Chrysosporium thermophilum. Arch. Microbiol. 107, 223–224 (1976).

    Article  CAS  Google Scholar 

  18. Galtier, N. & Lobry, J.R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44, 632–636 (1997).

    Article  CAS  Google Scholar 

  19. Zeldovich, K.B., Berezovsky, I.N. & Shakhnovich, E.I. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput. Biol. 3, e5 (2007).

    Article  Google Scholar 

  20. Glyakina, A.V., Garbuzynskiy, S.O., Lobanov, M.Y. & Galzitskaya, O.V. Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 23, 2231–2238 (2007).

    Article  CAS  Google Scholar 

  21. Wang, G.-Z. & Lercher, M.J. Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes. BMC Evol. Biol. 10, 263 (2010).

    Article  Google Scholar 

  22. Nishio, Y. et al. Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res. 13, 1572–1579 (2003).

    Article  CAS  Google Scholar 

  23. Mouchacca, J. Heat-tolerant fungi and applied research work: a synopsis of name changes and synomomies. World J. Microbiol. Biotechnol. 16, 881–888 (2000).

    Article  Google Scholar 

  24. Berka, R.M., Rey, M.W., Brown, K.M., Byun, T. & Klotz, A.V. Molecular characterization and expression of a phytase gene from the thermophilic fungus Thermomyces lanuginosus. Appl. Environ. Microbiol. 64, 4423–4427 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Murray, P. et al. Expression in and characterisation of a thermostable family 3 β-glucosidase from the moderately thermophilic fungus Talaromyces emersonii. Protein Expr. Purif. 38, 248–257 (2004).

    Article  CAS  Google Scholar 

  26. Voutilainen, S.P., Murray, P.G., Tuohy, M.G. & Koivula, A. Expression of Talaromyces emersonii cellobiohydrolase Cel7A in Saccharomyces cerevisiae and rational mutagenesis to improve its thermostability and activity. Protein Eng. Des. Sel. 23, 69–79 (2010).

    Article  CAS  Google Scholar 

  27. Visser, H. et al. Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1. Ind. Biotechnol. 7, 214–223 (2011).

    Article  CAS  Google Scholar 

  28. Jaffe, D.B. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91–96 (2003).

    Article  CAS  Google Scholar 

  29. Detter, J.C. et al. Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 80, 691–698 (2002).

    Article  CAS  Google Scholar 

  30. Smit, A.F.A., Hubley, R. & Green, P. RepeatMasker Open–3.0. 1996–2010. <http://www.repeatmasker.org/> (2010).

  31. Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).

    Article  CAS  Google Scholar 

  32. Salamov, A.A. Ab initio gene finding in Drosophila Genomic DNA. Genome Res. 10, 516–522 (2000).

    Article  CAS  Google Scholar 

  33. Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O. & Borodovsky, M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18, 1979–1990 (2008).

    Article  CAS  Google Scholar 

  34. Birney, E. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10, 547–548 (2000).

    Article  CAS  Google Scholar 

  35. Kent, W.J. BLAT—The BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

    Article  CAS  Google Scholar 

  36. Lowe, T.M. & Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).

    Article  CAS  Google Scholar 

  37. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst. 8, 581–599 (1997).

    Article  CAS  Google Scholar 

  38. Melén, K., Krogh, A. & von Heijne, G. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327, 735–744 (2003).

    Article  Google Scholar 

  39. Zdobnov, E.M. & Apweiler, R. InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001).

    Article  CAS  Google Scholar 

  40. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

  41. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004).

    Article  CAS  Google Scholar 

  42. Koonin, E.V. et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7 (2004).

    Article  Google Scholar 

  43. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258–D261 (2004).

  44. Enright, A.J., Van Dongen, S. & Ouzounis, C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575–1584 (2002).

    Article  CAS  Google Scholar 

  45. Roy, B.P. & Archibald, F. Effects of kraft pulp and lignin on Trametes versicolor carbon metabolism. Appl. Environ. Microbiol. 59, 1855–1863 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Semova, N. et al. Generation, annotation, and analysis of an extensive Aspergillus niger EST collection. BMC Microbiol. 6, 7 (2006).

    Article  Google Scholar 

  47. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  48. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  Google Scholar 

  49. Hardcastle, T.J. & Kelly, K.A. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422 (2010).

    Article  Google Scholar 

  50. Tsang, A., Butler, G., Powlowski, J., Panisko, E. & Baker, S. Analytical and computational approaches to define the Aspergillus niger secretome. Fungal Genet. Biol. 46, S153–S160 (2009).

    Article  CAS  Google Scholar 

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Acknowledgements

The genome sequencing and analysis were conducted by the US Department of Energy Joint Genome Institute and supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The work on transcriptomes, enzyme characterization and the Myceliophthora exo-proteome was supported by the Cellulosic Biofuel Network of the Agriculture Bioproducts Innovation Program of Agriculture and Agri-Food Canada, Genome Canada and Genome Québec.

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Contributions

The final text of the manuscript was written by R.M.B. and A.T., and reviewed by I.V.G.; who together also coordinated the overall analysis. I.V.G. coordinated both genome projects at the Joint Genome Institute. R.M.B. prepared the genomic DNA of T. terrestris and T.J. the DNA of M. thermophila. A.T. coordinated the transcriptome and exo-proteome work, and analyzed the transcriptomes. S.L. and E.L. led genome and cDNA sequencing. J.G. and J.S. finished and assembled both genomes. R.O. and A.S. annotated and analyzed the genomes, synteny and GC content. I.R. processed the RNA-Seq data and analyzed the cell wall proteins. N.I. coordinated the sample preparation for transcriptome analysis and analyzed the lignocellulolytic proteins. B.H., P.M.C. and V.L. performed the comparative analysis of the carbohydrate-active proteins. C.D. conducted the enzymatic hydrolysis of straws and M.-C.M. prepared the samples for transcriptome and exo-proteome analysis. D.O.N. analyzed the mating types and phylogeny of thermophilic fungi. E.L. coordinated the cDNA synthesis and EST analysis. A.B. coordinated the cloning and expression of xylanase genes. D.T. characterized the biochemical properties of the xylanases. R.P. de V., I.E.A, and J. van den B. examined the growth on different substrates. P.H. analyzed the GH61 proteins and J.P. membrane biogenesis. G.B. analyzed the secretomes. S.U. and R.S. analyzed the chromatin structure and dynamics. A.J.P. examined melanin pigment biogenesis. I.T.P. and L.D.H.E. analyzed transporters. S.E.B. analyzed secondary metabolism. J.M. examined oxidative stress. M.W. reviewed proteases and peptidases. S.L. examined the exo-proteomes. A.J.C. looked for repeat-induced polymorphisms. D.M. contributed computational tools for viewing T. terrestris transcriptome data. A.L.de L. and M.W.R. examined oxidoreductases and chitinases, respectively.

Corresponding author

Correspondence to Adrian Tsang.

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The authors declare no competing financial interests.

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Berka, R., Grigoriev, I., Otillar, R. et al. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol 29, 922–927 (2011). https://doi.org/10.1038/nbt.1976

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