Advertisement

Natural and Designed Enzymes for Cellulose Degradation

  • Eva Cunha
  • Christine L. Hatem
  • Doug Barrick
Chapter

Abstract

Biofuels hold significant promise as an environmentally friendly means to displace a significant amount of fossil fuel from the global liquid transportation fuel mix. Compared with current corn and sugarcane-based feedstocks, which are agriculturally intensive, lignocellulosic feedstocks are abundant, can be produced cheaply, and have a much smaller carbon footprint per unit energy output. However, conversion of cellulosic materials into simple sugars (an intermediate step in biofuel production) is a significant challenge, owing to the rigidity and high resistance of cellulose to degradation. Recent efforts to improve enzymatic breakdown of cellulose have taken advantage of expanding genome sequence databases, advances in structural biology of cellulose degradation enzymes (cellulases), biochemical studies of enzymatic breakdown of cellulose, and protein engineering studies. In this chapter, the structural features of cellulose and cellulose-degrading enzymes will be reviewed, along with methods used to determine cellulase activity. We will focus on models for synergistic effects among enzymes, strategies used by bacteria and fungi to increase reactivity through synergistic enhancement, and approaches by which synergistic enhancement can be engineered into artificial enzymes to be used for large-scale cellulose-based biofuels production.

Keywords

Catalytic Domain Corn Stover Cellulose Chain Cellulose Degradation Cellulosic Substrate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Arai T et al (2007) Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proc Natl Acad Sci U S A 104(5):1456–1460CrossRefGoogle Scholar
  2. 2.
    Barr BK et al (1996) Identification of two functionally different classes of exocellulases. Biochemistry 35(2):586–592CrossRefGoogle Scholar
  3. 3.
    Bayer EA et al (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58:521–554CrossRefGoogle Scholar
  4. 4.
    Beldman G et al (1988) Synergism in cellulose hydrolysis by endoglucanases and exoglucanases purified from Trichoderma viride. Biotechnol Bioeng 31(2):173–178CrossRefGoogle Scholar
  5. 5.
    Boraston AB et al (2004) Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 382(pt 3):769–781Google Scholar
  6. 6.
    Breuil C, Saddler JN (1985) Comparison of the 3,5-dinitrosalicylic acid and Nelson-Somogyi methods of assaying for reducing sugars and determining cellulase activity. Enzyme Microb Technol 7(7):327–332CrossRefGoogle Scholar
  7. 7.
    Cantarel BL et al (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37(database issue):D233–D238CrossRefGoogle Scholar
  8. 8.
    Caspi J et al (2008) Conversion of Thermobifida fusca free exoglucanases into cellulosomal components: comparative impact on cellulose-degrading activity. J Biotechnol 135(4):351–357CrossRefGoogle Scholar
  9. 9.
    Charles D (2009) Biofuels. Corn-based ethanol flunks key test. Science 324(5927):587CrossRefGoogle Scholar
  10. 10.
    Davies GJ et al (1996) Structure determination and refinement of the Humicola insolens endoglucanase V at 1.5 A resolution. Acta Crystallogr D Biol Crystallogr 52(pt 1):7–17CrossRefGoogle Scholar
  11. 11.
    Deguchi S, Tsujii K, Horikoshi K (2006) Cooking cellulose in hot and compressed water. Chem Commun 31:3293–3295CrossRefGoogle Scholar
  12. 12.
    DeLano WL (2003) MacPyMOL: PyMOL enhanced for Mac OS X. DeLano Scientific, Palo AltoGoogle Scholar
  13. 13.
    Enebro J et al (2009) Liquid chromatography combined with mass spectrometry for the investigation of endoglucanase selectivity on carboxymethyl cellulose. Carbohydr Res 344(16):2173–2181CrossRefGoogle Scholar
  14. 14.
    Eriksson KE, Hollmark BH (1969) Kinetic studies of action of cellulase upon sodium carboxymethyl cellulose. Arch Biochem Biophys 133(2):233CrossRefGoogle Scholar
  15. 15.
    Fierobe HP et al (2001) Design and production of active cellulosome chimeras. Selective incorporation of dockerin-containing enzymes into defined functional complexes. J Biol Chem 276(24):21257–21261CrossRefGoogle Scholar
  16. 16.
    Fierobe HP et al (2002) Degradation of cellulose substrates by cellulosome chimeras. Substrate targeting versus proximity of enzyme components. J Biol Chem 277(51):49621–49630CrossRefGoogle Scholar
  17. 17.
    Forse GJ et al (2011) Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein Sci 20(1):168–178CrossRefGoogle Scholar
  18. 18.
    Fujita Y et al (2002) Direct and efficient production of ethanol from cellulosic material with a yeast strain displaying cellulolytic enzymes. Appl Environ Microbiol 68(10):5136–5141CrossRefGoogle Scholar
  19. 19.
    Ghose TK (1987) Measurement of cellulase activities. Int Union Pure Appl Chem 59(2):257–268CrossRefGoogle Scholar
  20. 20.
    Gilad R et al (2003) CelI, a noncellulosomal family 9 enzyme from Clostridium thermocellum, is a processive endoglucanase that degrades crystalline cellulose. J Bacteriol 185(2):391–398CrossRefGoogle Scholar
  21. 21.
    Graça MAS, Bärlocher F, Gessner MO (2005) Methods to study litter decomposition: a practical guide. Springer, Dordrecht, p 329Google Scholar
  22. 22.
    Hall M et al (2010) Cellulose crystallinity–a key predictor of the enzymatic hydrolysis rate. FEBS J 277(6):1571–1582CrossRefGoogle Scholar
  23. 23.
    Heinzelman P et al (2009) SCHEMA recombination of a fungal cellulase uncovers a single mutation that contributes markedly to stability. J Biol Chem 284(39):26229–26233CrossRefGoogle Scholar
  24. 24.
    Heinzelman P et al (2010) Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Eng Des Sel 23(11):871–880CrossRefGoogle Scholar
  25. 25.
    Helbert W et al (2003) Fluorescent cellulose microfibrils as substrate for the detection of cellulase activity. Biomacromolecules 4(3):481–487CrossRefGoogle Scholar
  26. 26.
    Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280(pt 2):309–316Google Scholar
  27. 27.
    Henrissat B, Bairoch A (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 293(pt 3):781–788Google Scholar
  28. 28.
    Henrissat B, Bairoch A (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem J 316(pt 2):695–696Google Scholar
  29. 29.
    Henrissat B, Davies G (1997) Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol 7(5):637–644CrossRefGoogle Scholar
  30. 30.
    Heyman A et al (2007) Multiple display of catalytic modules on a protein scaffold: nano-fabrication of enzyme particles. J Biotechnol 131(4):433–439CrossRefGoogle Scholar
  31. 31.
    Hill J et al (2009) Climate change and health costs of air emissions from biofuels and gasoline. Proc Natl Acad Sci U S A 106(6):2077–2082CrossRefGoogle Scholar
  32. 32.
    Himmel ME (2008) Biomass recalcitrance: deconstructing the plant cell wall for bioenergy. Wiley-Blackwell, West SussexGoogle Scholar
  33. 33.
    Hoffert MI et al (1998) Energy implications of future stabilization of atmospheric CO2 content. Nature 395:881–884CrossRefGoogle Scholar
  34. 34.
    Irwin DC et al (1993) Activity studies of eight purified cellulases: specificity, synergism, and binding domain effects. Biotechnol Bioeng 42(8):1002–1013CrossRefGoogle Scholar
  35. 35.
    Josefsson P, Henriksson G, Wagberg L (2008) The physical action of cellulases revealed by a quartz crystal microbalance study using ultrathin cellulose films and pure cellulases. Biomacromolecules 9(1):249–254CrossRefGoogle Scholar
  36. 36.
    Kaar WE et al (1991) The complete analysis of wood polysaccharides by HPLC. J Wood Chem Technol 11:447–463CrossRefGoogle Scholar
  37. 37.
    Klemm D et al (2005) Cellulose: fascinating biopolymer and sustainable raw material. Angew Chem Int Ed Engl 44(22):3358–3393CrossRefGoogle Scholar
  38. 38.
    Lai TE, Pullammanappallil PC, Clarke WP (2006) Quantification of cellulase activity using cellulose-azure. Talanta 69(1):68–72CrossRefGoogle Scholar
  39. 39.
    Lamed R, Setter E, Bayer EA (1983) Characterization of a cellulose-binding, cellulase-containing complex in Clostridium thermocellum. J Bacteriol 156(2):828–836Google Scholar
  40. 40.
    Lilly M et al (2009) Heterologous expression of a Clostridium minicellulosome in Saccharomyces cerevisiae. FEMS Yeast Res 9(8):1236–1249CrossRefGoogle Scholar
  41. 41.
    Liska AJ et al (2008) Improvements in life cycle energy efficiency and greenhouse gas emissions of corn-ethanol. J Ind Ecol 13(1):58–74CrossRefGoogle Scholar
  42. 42.
    Majewicz TG, Podlas TJ (2000) Cellulose ethers. Kirk-Othmer encyclopedia of chemical technology. Wiley, New YorkGoogle Scholar
  43. 43.
    Malet C et al (1996) A specific chromophoric substrate for activity assays of 1,3-1,4-beta-D-glucan 4-glucanohydrolases. J Biotechnol 48(3):209–219CrossRefGoogle Scholar
  44. 44.
    Mandelman D et al (2003) X-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides. J Bacteriol 185(14):4127–4135CrossRefGoogle Scholar
  45. 45.
    Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31(3):426–428CrossRefGoogle Scholar
  46. 46.
    Mingardon F et al (2005) Heterologous production, assembly, and secretion of a minicellulosome by Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 71(3):1215–1222CrossRefGoogle Scholar
  47. 47.
    Mingardon F et al (2007) Incorporation of fungal cellulases in bacterial minicellulosomes yields viable, synergistically acting cellulolytic complexes. Appl Environ Microbiol 73(12):3822–3832CrossRefGoogle Scholar
  48. 48.
    Mingardon F et al (2007) Exploration of new geometries in cellulosome-like chimeras. Appl Environ Microbiol 73(22):7138–7149CrossRefGoogle Scholar
  49. 49.
    Mitsuzawa S et al (2009) The rosettazyme: a synthetic cellulosome. J Biotechnol 143(2):139–144CrossRefGoogle Scholar
  50. 50.
    Morais S et al (2010) Enhanced cellulose degradation by nano-complexed enzymes: synergism between a scaffold-linked exoglucanase and a free endoglucanase. J Biotechnol 147:205–211CrossRefGoogle Scholar
  51. 51.
    Murphy L et al (2010) A calorimetric assay for enzymatic saccharification of biomass. Enzyme Microb Technol 46(2):141–146CrossRefGoogle Scholar
  52. 52.
    Nidetzky B et al (1994) Cellulose hydrolysis by the cellulases from Trichoderma reesei: a new model for synergistic interaction. Biochem J 298(pt 3):705–710Google Scholar
  53. 53.
    Nishiyama Y et al (2003) Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 125(47):14300–14306CrossRefGoogle Scholar
  54. 54.
    Olsen SN et al (2011) Kinetics of enzymatic high-solid hydrolysis of lignocellulosic biomass studied by calorimetry. Appl Biochem Biotechnol 163:626–635CrossRefGoogle Scholar
  55. 55.
    Park S et al (2009) Measuring the crystallinity index of cellulose by solid state C-13 nuclear magnetic resonance. Cellulose 16(4):641–647CrossRefGoogle Scholar
  56. 56.
    Plevin RJ (2009) Modeling corn ethanol and climate. a critical comparison of the BESS and GREET models. J Ind Ecol 13:495–507CrossRefGoogle Scholar
  57. 57.
    Pozzo T et al (2010) Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3. J Mol Biol 397(3):724–739CrossRefGoogle Scholar
  58. 58.
    Rabinovich ML, Melnick MS, Bolobova AV (2002) The structure and mechanism of action of cellulolytic enzymes. Biochemistry (Mosc) 67(8):850–871CrossRefGoogle Scholar
  59. 59.
    Robyt JF, Whelan WJ (1972) Reducing value methods for maltodextrins. 1. Chain-length dependence of alkaline 3,5-dinitrosalicylate and chain-length independence of alkaline copper. Anal Biochem 45(2):510–516CrossRefGoogle Scholar
  60. 60.
    Ruijssenaars HJ, Hartmans S (2001) Plate screening methods for the detection of polysaccharase-producing microorganisms. Appl Microbiol Biotechnol 55(2):143–149CrossRefGoogle Scholar
  61. 61.
    Ryu DD, Kim C, Mandels M (1984) Competitive adsorption of cellulase components and its significance in a synergistic mechanism. Biotechnol Bioeng 26(5):488–496CrossRefGoogle Scholar
  62. 62.
    Sabathe F, Soucaille P (2003) Characterization of the CipA scaffolding protein and in vivo production of a minicellulosome in Clostridium acetobutylicum. J Bacteriol 185(3):1092–1096CrossRefGoogle Scholar
  63. 63.
    Sandgren M, Stahlberg J, Mitchinson C (2005) Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes. Prog Biophys Mol Biol 89(3):246–291CrossRefGoogle Scholar
  64. 64.
    Schmer MR et al (2008) Net energy of cellulosic ethanol from switchgrass. Proc Natl Acad Sci U S A 105(2):464–469CrossRefGoogle Scholar
  65. 65.
    Schulein M (2000) Protein engineering of cellulases. Biochim Biophys Acta 1543(2):239–252CrossRefGoogle Scholar
  66. 66.
    Somogyi M (1952) Notes on sugar determination. J Biol Chem 195(1):19–23Google Scholar
  67. 67.
    Stalbrand H et al (1998) Analysis of molecular size distributions of cellulose molecules during hydrolysis of cellulose by recombinant Cellulomonas fimi beta-1,4-glucanases. Appl Environ Microbiol 64(7):2374–2379Google Scholar
  68. 68.
    Teeri TT (1997) Crystalline cellulose degradation: new insight into the function of cellobiohydrolases. Trends Biotechnol 15(5):160–167CrossRefGoogle Scholar
  69. 69.
    Terashima N et al (2009) Nanostructural assembly of cellulose, hemicellulose, and lignin in the middle layer of secondary wall of ginkgo tracheid. J Wood Sci 55:409–416CrossRefGoogle Scholar
  70. 70.
    Tomme P, Heriban V, Claeyssens M (1990) Adsorption of two cellobiohydrolases from Trichoderma reesei to Avicel: evidence for “exo-exo” synergism and possible “loose complex” formation. Biotechnol Lett 12:525–530CrossRefGoogle Scholar
  71. 71.
    Tomme P et al (1996) Characterization of CenC, an enzyme from Cellulomonas fimi with both endo- and exoglucanase activities. J Bacteriol 178(14):4216–4223Google Scholar
  72. 72.
    Tsai SL, Goyal G, Chen W (2010) Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl Environ Microbiol 76(22):7514–7520CrossRefGoogle Scholar
  73. 73.
    Ubhayasekera W et al (2005) Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors. FEBS J 272(8):1952–1964CrossRefGoogle Scholar
  74. 74.
    Valjamae P et al (1999) Acid hydrolysis of bacterial cellulose reveals different modes of synergistic action between cellobiohydrolase I and endoglucanase I. Eur J Biochem 266(2):327–334CrossRefGoogle Scholar
  75. 75.
    Wilson DB (2004) Studies of Thermobifida fusca plant cell wall degrading enzymes. Chem Rec 4(2):72–82CrossRefGoogle Scholar
  76. 76.
    Wilson DB (2008) Aerobic microbial cellulase systems. In: Himmel ME (ed) Biomass recalcitrance: deconstructing the plant cell wall for bioenergy. Blackwell, West Sussex, pp 374–392Google Scholar
  77. 77.
    Wood TM (1988) Methods for measuring cellulase activities. Methods Enzymol 160:87–112CrossRefGoogle Scholar
  78. 78.
    Wood TM (1988) Preparation of crystalline, amorphous, and dyed cellulase substrates. Methods Enzymol 160:19–25CrossRefGoogle Scholar
  79. 79.
    Wood TM, McCrae SI, Bhat KM (1989) The mechanism of fungal cellulase action. Synergism between enzyme components of Penicillium pinophilum cellulase in solubilizing hydrogen bond-ordered cellulose. Biochem J 260(1):37–43Google Scholar
  80. 80.
    Woodward J, Lima M, Lee NE (1988) The role of cellulase concentration in determining the degree of synergism in the hydrolysis of microcrystalline cellulose. Biochem J 255(3):895–899Google Scholar
  81. 81.
    Zhang Y-HP, Himmel ME, Mielenz JR (2006) Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 24(5):452–481CrossRefGoogle Scholar
  82. 82.
    Zhang YH et al (2006) A transition from cellulose swelling to cellulose dissolution by o-phosphoric acid: evidence from enzymatic hydrolysis and supramolecular structure. Biomacromolecules 7(2):644–648CrossRefGoogle Scholar
  83. 83.
    Zhang YH, Lynd LR (2004) Kinetics and relative importance of phosphorolytic and hydrolytic cleavage of cellodextrins and cellobiose in cell extracts of Clostridium thermocellum. Appl Environ Microbiol 70(3):1563–1569CrossRefGoogle Scholar
  84. 84.
    Zhang YH, Lynd LR (2004) Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems. Biotechnol Bioeng 88(7):797–824CrossRefGoogle Scholar
  85. 85.
    Zhang YH, Lynd LR (2005) Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation. Proc Natl Acad Sci U S A 102(20):7321–7325CrossRefGoogle Scholar
  86. 86.
    Zhou J et al (2009) Optimization of cellulase mixture for efficient hydrolysis of steam-exploded corn stover by statistically designed experiments. Bioresour Technol 100(2):819–825CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreUSA

Personalised recommendations