Biotechnology Letters

, Volume 32, Issue 12, pp 1765–1775 | Cite as

Mining metagenomes for novel cellulase genes

Review
First Online:
Received:
Accepted:

Abstract

Cellulases hydrolyze the β-1,4 linkages of cellulose and are widely used in food, brewing and wine, animal feed, textiles and laundry, and pulp and paper industries, especially for hydrolyzing cellulosic materials into sugars, which can be fermented to produce useful products such as ethanol. Metagenomics has become an alternative approach to conventional culture-dependent methods as it allows exhaustive mining of microbial genomes in their natural environments. This review covers the current state of research and challenges in mining novel cellulase genes from the metagenomes of various environments, and discusses the potential biotechnological applications of metagenome-derived cellulases.

Keywords

Biotechnological applications Cellulase Function-based approach Metagenomics Sequencing 
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Notes

Acknowledgments

The research work carried out in the authors’ laboratory was supported by grants from the National Natural Science Foundation of China (30960094, 30960013), the Ministry of Science and Technology of China (2009DFA30700), and a the National Hi-tech Research and Development Program of China (863 Program 2007AA021307).

References

  1. Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, Wesolowski-Louvel M, Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1:632–642CrossRefPubMedGoogle Scholar
  2. Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58:521–554CrossRefPubMedGoogle Scholar
  3. Berger E, Zhang D, Zverlov VV, Schwarz WH (2007) Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett 268:194–201CrossRefPubMedGoogle Scholar
  4. Bhat MK (2000) Cellulases and related enzymes in biotechnology. Biotechnol Adv 18:355–383CrossRefPubMedGoogle Scholar
  5. Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948–1953CrossRefPubMedGoogle Scholar
  6. Duan CJ, Xian L, Zhao GC, Feng Y, Pang H, Bai XL, Tang JL, Ma QS, Feng JX (2009) Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens. J Appl Microbiol 107:245–256CrossRefPubMedGoogle Scholar
  7. Edwards IP, Upchurch RA, Zak DR (2008) Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR. Appl Environ Microbiol 74:3481–3489CrossRefPubMedGoogle Scholar
  8. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138CrossRefPubMedGoogle Scholar
  9. Feng Y, Duan CJ, Pang H, Mo XC, Wu CF, Yu Y, Hu YL, Wei J, Tang JL, Feng JX (2007) Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Appl Microbiol Biotechnol 75:319–328CrossRefPubMedGoogle Scholar
  10. Feng Y, Duan CJ, Liu L, Tang JL, Feng JX (2009) Properties of a metagenome-derived beta-glucosidase from the contents of rabbit cecum. Biosci Biotechnol Biochem 73:1470–1473CrossRefPubMedGoogle Scholar
  11. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN (2005) Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol 7:1996–2010CrossRefPubMedGoogle Scholar
  12. Ferrer M, Golyshina O, Beloqui A, Golyshin PN (2007) Mining enzymes from extreme environments. Curr Opin Microbiol 10:207–214CrossRefPubMedGoogle Scholar
  13. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105:3805–3810CrossRefPubMedGoogle Scholar
  14. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3:e3042CrossRefPubMedGoogle Scholar
  15. Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I (2009) Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. Environ Microbiol 11:111–125CrossRefPubMedGoogle Scholar
  16. Grant S, Sorokin DY, Grant WD, Jones BE, Heaphy S (2004) A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. Extremophiles 8:421–429CrossRefPubMedGoogle Scholar
  17. Grant S, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S (2006) Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. Appl Environ Microbiol 72:135–143CrossRefPubMedGoogle Scholar
  18. Healy FG, Ray RM, Aldrich HC, Wilkie AC, Ingram LO, Shanmugam KT (1995) Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl Microbiol Biotechnol 43:667–674CrossRefPubMedGoogle Scholar
  19. Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarity. Biochem J 280:309–316PubMedGoogle Scholar
  20. Izquierdo JA, Sizova MV, Lynd LR (2010) Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl Environ Microbiol 76:3545–3553CrossRefPubMedGoogle Scholar
  21. Jiang C, Ma G, Li S, Hu T, Che Z, Shen P, Yan B, Wu B (2009) Characterization of a novel beta-glucosidase-like activity from a soil metagenome. J Microbiol 47:542–548CrossRefPubMedGoogle Scholar
  22. Jiang C, Hao ZY, Jin K, Li SX, Che ZQ, Ma GF, Wu B (2010) Identification of a metagenome-derived β-glucosidase from bioreactor contents. J Mol Catal B Enzym 63:11–16CrossRefGoogle Scholar
  23. Kim SJ, Lee CM, Kim MY, Yeo YS, Yoon SH, Kang HC, Koo BS (2007) Screening and characterization of an enzyme with beta-glucosidase activity from environmental DNA. J Microbiol Biotechnol 17:905–912PubMedGoogle Scholar
  24. Kim SJ, Lee CM, Han BR, Kim MY, Yeo YS, Yoon SH, Koo BS, Jun HK (2008) Characterization of a gene encoding cellulase from uncultured soil bacteria. FEMS Microbiol Lett 282:44–51CrossRefPubMedGoogle Scholar
  25. Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS (2003) Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 27:663–693CrossRefPubMedGoogle Scholar
  26. Liu L, Feng Y, Duan CJ, Pang H, Tang JL, Feng JX (2009) Isolation of a gene encoding endoglucanase activity from uncultured microorganisms in buffalo rumen. World J Microbiol Biotechnol 25:1035–1042CrossRefGoogle Scholar
  27. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577CrossRefPubMedGoogle Scholar
  28. Ohtoko K, Ohkuma M, Moriya S, Inoue T, Usami R, Kudo T (2000) Diverse genes of cellulase homologues of glycosyl hydrolase family 45 from the symbiotic protists in the hindgut of the termite Reticulitermes speratus. Extremophiles 4:343–349CrossRefPubMedGoogle Scholar
  29. Palackal N, Lyon CS, Zaidi S, Luginbuhl P, Dupree P, Goubet F, Macomber JL, Short JM, Hazlewood GP, Robertson DE, Steer BA (2007) A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut. Appl Microbiol Biotechnol 74:113–124CrossRefPubMedGoogle Scholar
  30. Pang H, Zhang P, Duan CJ, Mo XC, Tang JL, Feng JX (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol 58:404–408CrossRefPubMedGoogle Scholar
  31. Pottkämper J, Barthen P, Ilmberger N, Schwaneberg U, Schenk A, Schulte M, Ignatiev N, Streit WR (2009) Applying metagenomics for the identification of bacterial cellulases that are stable in ionic liquids. Green Chem 11:957–965CrossRefGoogle Scholar
  32. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394CrossRefPubMedGoogle Scholar
  33. Rees HC, Grant S, Jones B, Grant WD, Heaphy S (2003) Detecting cellulase and esterase enzyme activities encoded by novel genes present in environmental DNA libraries. Extremophiles 7:415–421CrossRefPubMedGoogle Scholar
  34. Shedova EN, Berezina OV, Lunina NA, Zverlov VV, Schwarz WH, Velikodvorskaya GA (2009) Cloning and characterization of a large metagenomic DNA fragment containing glycosyl-hydrolase genes. Mol Gen Microbiol Virol 24:12–16CrossRefGoogle Scholar
  35. Simon C, Daniel R (2009) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85:265–276CrossRefPubMedGoogle Scholar
  36. Taylor LE 2nd, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, Weiner RM (2006) Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. J Bacteriol 188:3849–3861CrossRefPubMedGoogle Scholar
  37. Todaka N, Moriya S, Saita K, Hondo T, Kiuchi I, Takasu H, Ohkuma M, Piero C, Hayashizaki Y, Kudo T (2007) Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus. FEMS Microbiol Ecol 59:592–599CrossRefPubMedGoogle Scholar
  38. Toyoda A, Iio W, Mitsumori M, Minato H (2009) Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl Environ Microbiol 75:1667–1673CrossRefPubMedGoogle Scholar
  39. Uchiyama T, Miyazaki K (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20:616–622CrossRefPubMedGoogle Scholar
  40. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242CrossRefPubMedGoogle Scholar
  41. Voget S, Steele HL, Streit WR (2006) Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol 126:26–36CrossRefPubMedGoogle Scholar
  42. Wang F, Li F, Chen G, Liu W (2009) Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches. Microbiol Res 164:650–657CrossRefPubMedGoogle Scholar
  43. Warnecke F, Luginbuhl P, Ivanova N et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565CrossRefPubMedGoogle Scholar
  44. Wilson DB (2008) Three microbial strategies for plant cell wall degradation. Ann NY Acad Sci 1125:289–297CrossRefPubMedGoogle Scholar
  45. Wilson DB (2009) Evidence for a novel mechanism of microbial cellulose degradation. Cellulose 16:723–727CrossRefGoogle Scholar
  46. Xie G, Bruce DC, Challacombe JF et al (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl Environ Microbiol 73:3536–3546CrossRefPubMedGoogle Scholar
  47. Yu R, Wang L, Duan X, Gao P (2007) Isolation of cellulolytic enzymes from moldy silage by new culture-independent strategy. Biotechnol Lett 29:1037–1043CrossRefPubMedGoogle Scholar
  48. Zhang YHP, Himmel ME, Mielenz JR (2006) Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 24:452–481CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and TechnologyGuangxi UniversityNanningPeople’s Republic of China
  2. 2.Cellulose Processing Laboratory, National Engineering Research Center for Non-food BiorefineryGuangxi Academy of SciencesNanningPeople’s Republic of China

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