Molecular approaches for ameliorating microbial xylanases

Bioresource Technology

Volumn 117, Issue , 2012, Pages 360-367

  Verma, Digvijay ^a   Satyanarayana, T ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

Alkali stability; Pre bleaching of paper pulp; Protein engineering; Thermostability; Xylanase

Indexed keywords

ALKALI-STABILITY; PAPER PULP; PROTEIN ENGINEERING; THERMOSTABILITY; XYLANASES;

ALKALINITY; BIOCHEMICAL ENGINEERING; BLEACHING; CATALYSIS; CHLORINE; CLEANING; ENZYMES; GENETIC ENGINEERING; PAPER AND PULP INDUSTRY; PAPER AND PULP MILLS; TEXTILE INDUSTRY;

PULP;

ARGININE; ASPARAGINE; ASPARTIC ACID; CYSTEINE; LEUCINE; LIGNOCELLULOSE; LYSINE; PHENYLALANINE; SERINE; THREONINE; TRYPTOPHAN; VALINE; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ALKALINITY; BLEACHING; CATALYSIS; COST-BENEFIT ANALYSIS; ENZYME ACTIVITY; HIGH TEMPERATURE; MICROBIAL ACTIVITY; MOLECULAR ANALYSIS; PH; PROTEIN; SECONDARY SECTOR INDUSTRY; STABILIZATION; TEMPERATURE EFFECT;

ALKALINITY; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL FOOD; BETA SHEET; BINDING AFFINITY; BIOTRANSFORMATION; CATALYSIS; CRYSTAL STRUCTURE; DISULFIDE BOND; DNA SHUFFLING; ENZYME ACTIVITY; ENZYME STABILITY; FOOD INDUSTRY; HYDROGEN BOND; HYDROPHOBICITY; LIGHT SCATTERING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; MUTAGENESIS; NONHUMAN; PAPER; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; REVIEW; STATIC ELECTRICITY; TEXTILE; THERMOSTABILITY; X RAY CRYSTALLOGRAPHY;

BACTERIA; BIOTECHNOLOGY; ENDO-1,4-BETA XYLANASES; MUTAGENESIS, SITE-DIRECTED; PROTEIN ENGINEERING;

ALKALINITY; BIOTECHNOLOGY; BLEACHING; CATALYSTS; CHLORINE; CLEANING; ENZYMES; GENETIC ENGINEERING; PAPER INDUSTRY; PAPER MILLS; PULP INDUSTRY; PULP MILLS; PULPS; XYLANASE;

EID: 84862173590     PISSN: 09608524     EISSN: 18732976     Source Type: Journal    
DOI: 10.1016/j.biortech.2012.04.034     Document Type: Review

References (75)

1. 2+ independent stable xylanases. J. Biol. Chem. 2004, 279:54369-54379.
2. Bandivadekar K.R., Deshpande V.V. Structure-function relationship of xylanase: fluorimetric analysis of the tryptophan environment. Biochem. J. 1996, 315:583-587.
3. Barnard D., Casanueva A., Tuffin M., Cowan D. Extremophiles in biofuel synthesis. Environ. Technol. 2010, 31:871-888.
4. Bayram I., SadiCetingul A., Akkaya B., Uyarlar C. Effects of bacterial xylanase on egg production in the laying quail (Coturnix coturnix japonica) diets based on corn and soybean meal. Arch. Zootech. 2008, 11:69-74.
5. Bhardwaj A., Leelavathi S., Mazumdar-Leighton S., Ghosh A., Ramakumar S., Reddy V.S. The critical role of N- and C-terminal contact in protein stability and folding of a family10 xylanase under extreme conditions. PLoS ONE. 2010, 5:e11347.
6. Borders C.L., Broadwater J.A., Bekeny P.A., Salmon J.E., Lee A.S., Eldridge A.M., Pett V.B. A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens. Protein Sci. 1994, 3:541-548.
7. Bravman T., Belakhov V., Solomon D., Shoham G., Henrissat B., Baasov T., Shoham Y. Identification of the catalytic residues in family 52 glycoside hydrolase, β-xylosidase from Geobacillus stearothermophilus T-6. J. Biol. Chem. 2003, 29:26742-26749.
8. Clarke J.H., Davidson K., Gilbert H.J., Fontes C.M.G.A., Hazlewood G.P. A modular xylanase from mesophilic Cellulomonas jimi contains the same cellulose-binding and thermostabilizing domains as xylanases from thermophilic bacteria. FEMS Microbiol. Lett. 1996, 139:27-35.
9. Davoodi J., Wakarchuk W.W., Surewicz W.K., Carey P.R. Scan-rate dependence in protein calorimetry: the reversible transitions of Bacillus circulans xylanase and a disulfide-bridge mutant. Protein Sci. 1998, 7:1538-1544.
10. Dumon, C., Alexander Varvak, A., Wall, M.A., Flint, J.E., Lewis, R.J., Lakey, J.H., Morland, C., Luginbuhl, P., Healey, S., Todaro, T., DeSantis, G., Sun, M., Gessert, L.P., Tan, X., Weiner, D.P. Gilbert, H.J., 2008. Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure. J. Biol. Chem. 283, 22557-22564.
11. Esteves F.D.L., Ruelle V., Brasseur J.L., Quuiting B., Frere J.M. Acidophilic adaptation of family 11 endo β 1,4-xylanases: modeling and mutational analysis. Protein Sci. 2004, 13:1209-1218.
12. Fenel F., Leisola M., Janis J., Turunen O. A de-novo designed N-terminal disulphide bridge stabilizes the Trichoderma reesei endo-1,4-β-xylanase II. J. Biotechnol. 2004, 108:137-143.
13. Fenel F., Zitting A.J., Kantelinen A. Increased alkali stability in Trichoderma reesei endo-1,4-β-xylanase II by site directed mutagenesis. J. Biotechnol. 2006, 121:102-107.
14. Fujimoto Z., Kuno A., Kaneko S., Yoshida S., Kobayashi H., Kusakabe I., Mizuno H. Crystal structure of Streptomyces olivaceoviridis E-86, xylanase containing xylan-binding domain. J. Mol. Biol. 2000, 300:575-585.
15. Gruber K., Klintschar G., Hayn M., Schlacher A., Steiner W., Kratky C. Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies. Biochem. 1998, 37:475-13485.
16. Hakulinen N., Turunen O., Janis J., Leisola M., Rouvinen J. Three dimensional structures of thermophilic β-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Europ. J. Biochem. 2003, 270:1399-1412.
17. Janis J., Rouvinen J., Leisola M., Turunen O., Vainiotalo P. Thermostability of endo 1,4-β-xylanase II from Trichoderma reesei studied by electrospray ionization Fourie transform ion cyclotron resonance MS, hydrogen/deuterium-exchange reaction and dynamic light scattering. Biochem. J. 2001, 356:453-460.
18. Jeong M.Y., Kim S., Yun C.W., Choi Y.J., Chob S.G. Engineering a de novo internal disulfide bridge to improve the thermal stability of xylanase from Bacillus stearothermophilus No. 236. J. Biotechnol. 2007, 127:300-309.
19. Joo J.C., Yoo Y.J. Cavity design of Bacillus circulans xylanase to increase the thermostability using computational approach. Abstracts/J. Biotechnol. 2008, 136S:S356-S401.
20. Joo J.C., Pohkrel S., Pack S.P., Yoo Y.J. Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity. J. Biotechnol. 2010, 146:31-39.
21. Joo J.C., Pack S.P., Kim Y.H., Yoo Y.J. Thermostailization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. J. Biotechnol. 2011, 151:56-65.
22. Kaneko S., Ichinose H., Fujimoto Z., Kuno A., Yura K., Go M., Mizuno H., Kusakabe I., Kobayashi H. Structure and function of a family 10 β xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex. J. Biochem. 2004, 279:26619-26626.
23. Keskar S.S., Srinivasan M.C., Deshpande V.V. Chemical modification of a xylanase from a thermotolerant Streptomyces. Evidence for essential tryptophan and cysteines residues at the active site. Biochem. J. 1989, 261:49-55.
24. Kozak M. Synchrotron radiation small angle scattering studies of thermal stability of xylanase XYNII from Trichoderma longibrachiatum. Biopolymers 2006, 83:668-674.
25. Krengel U., Dijkstra B.W. Three dimensional structure of endo-1,4-beta-xylanase I from Aspergillus niger. Molecular basis for its low pH optimum. J. Mol. Biol. 1996, 263:70-78.
26. Kumar P.R., Eswaramoorthy S., Vithayathil P.J., Viswamitra M.A. The tertiary structure at 1.59A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti Bainier. J. Mol. Biol. 2000, 295:581-593.
27. Li P.P., Wang X.J., Yuan X.F., Wang X.F., Cao Y.Z., Cui Z.J. Screening of a composite microbial system and its characteristics of wheat straw degradation. Agric. Sci. China 2011, 10:1586-1594.
28. Li J., Wang L. Why substituting the asparagine at position 35 in Bacillus circulans xylanase with an aspartic acid remarkably improves the enzymatic catalytic activity? A quantum chemistry-based calculation study. Poly. Degrad. Stability 2011, 96:1009-1024.
29. Liu L., Zhang G., Zhang Z., Wang S., Chen H. Terminal amino acids disturb xylanase thermostability and activity. J. Biol. Chem. 2011, 286:44710-44715.
30. Lo Y.C., Lu W.C., Chen C.Y., Chang J.S. Dark fermentative hydrogen production from enzymatic hydrolysate of xylan and pretreated rice straw by Clostridium butyricum CGS5. Biores. Technol. 2010, 101:5885-5891.
31. Mamo G., Delgado O., Martinez A., Mattiasson B., Kaul R.J. Cloning, sequencing analysis and expression of a gene encoding an endoxylanase from Bacillus halodurans S7. Mol. Biotechnol. 2006, 33:149-159.
32. McCarthy A.A., Morris D.D., Bergquist P.L., Baker E.N. Structure of XynB, a highly thermostable β-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8A resolution. Acta Crystallogr. 2000, 56:1367-1375.
33. Miyazaki K., Takenouchi M., Kondo H., Noro N., Suzuki M., Suda S.T. Thermal stabilization of Bacillus subtilis family-11 xylanase by directed evolution. J. Biol. Chem. 2006, 281:10236-10242.
34. Noorbatcha, Ali, I., Hamzah, M.S., 2011. Molecular dynamics approach in designing thermostable Bacillus circulans xylanase. In: International Conference on Biotechnology, Engineering, ICBioE11, 17-19.
35. Palackal N., Brennan Y., Callen W.N., Dupree P., Frey G., Goubet F., Hazlewood G.P., et al. An evolutionary route to xylanase process fitness. Protein Sci. 2004, 13:494-503.
36. Patra A.K., Madhu A. Studies on enzymatic pretreatment of linen. Indian J. Fibre Text. 2010, 35:337-341.
37. Pattraporn J., Kinitglang S., Kyu K.L., Ratanakhanokchai K. Substrate binding site of family 11 xylanase from Bacillus firmus K-1 by molecular docking. Biosci. Biotechnol. Biochem. 2009, 73:833-839.
38. Pell G., Szabo L., Charnock S.J., Xie H., Gloster T.M., Davies G.J., Gilbert H.J. Structural and biochemical analysis of Cellvibrio japonicus xylanase 10 C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J. Biol. Chem. 2004, 279:11777-11788.
39. Puchkaev A.V., Koo L.S., Ortiz de Montellano P.R. Aromatic stacking as determinant of the thermal stability of CYP119 from Sulfolobus solfataricus. Arch. Biochem. Biophys. 2003, 409:52-58.
40. Purmonen M., Valjakka J., Takkinen K., Laitinen T., Rouvinen J. Molecular dynamics studies on the thermostability of family 11 xylanases. Prot. Eng. Des. Sel. 2007, 20:551-559.
41. Sharma S., Adhikari S., Satyanarayana T. Alkali-thermostable and cellulase-free xylanase production by an extreme thermophile Geobacillus thermoleovorans. World J. Microbiol. Biotechnol. 2007, 23:483-490.
42. Simpson P.J., Xie H.F., Bolam D.N., Gilbert H.J., Williamson M.P. The structural basis for the ligand specificity of family 2 carbohydrate binding modules. J. Biol. Chem. 2000, 275:41137-41142.
43. Sinma K., Khucharoenphaisan K., Kitpreechavanich V., Tokuyama S. Dark fermentative hydrogen production from enzymatic hydrolysate of xylan and pretreated rice straw by Clostridium butyricum CGS5. Biosci. Biotechnol. Biochem. 2011, 75:1957-1963.
44. Soliman M.E.S., Ruggiero R.D., Pernia J.J.R., Greig I.R., Williams I.H. Computational mutagenesis reveals the role of active site tyrosine in stabilizing a boat conformation for the substrate: QM/MM molecular dynamics studies of wild type and mutant xylanases. Org. Biomol. Chem. 2009, 7:460-468.
45. Stephens D.E., Rumbold K., Permaul K., Prior B.A., Singh S. Directed evolution of the thermostable xylanase from Thermomyces lanuginosus. J. Biotechnol. 2007, 127:348-354.
46. Stephens D.E., Singh S., Permaul K. Error-prone PCR of a fungal xylanase for improvementof its alkaline and thermal stability. FEMS Microbiol. Lett. 2009, 293:42-47.
47. Sriprang R., Asano K., Gobsuk J., Tanapongpipat S., Champreda V., Eurwilaichitr L. Improvement of thermostability of fungal xylanase by using site-directed mutagenesis. J. Biotechnol. 2006, 12:454-462.
48. Subramaniyan S., Prema P. Biotechnology of microbial xylanases: enzymology, molecular biology, and application. Crit. Rev. Biotechnol. 2002, 22:33-64.
49. Sun J.Y., Liu M.Q., Xu Y.L., Xu Z.R., Pan L., Gao H. Improvement of the thermostability and catalytic activity of a mesophilic family 11 xylanase by N-terminus replacement. Protein Express. Purif. 2005, 42:122-130.
50. Sunna A., Bergquist P.L. A gene encoding a novel extremely thermostable 1,4-β-xylanase isolated directly from an environmental DNA sample. Extremophiles 2003, 7:63-70.
51. Taibi Z., Saoudi B., Boudelaa M., Trigui H., Belghith H., Gargouri A., Ladjama A. Purification and biochemical characterization of a highly thermostable xylanase from Actinomadura sp. strain Cpt20 isolated from poultry compost. Appl. Biochem. Biotechnol. 2012, 166:663-679.
52. Torronen A., Harkki A., Rouvinen J. Three dimensional structure of endo-1,4-β-xylanase II from Trichoderma reesei: two conformational states in the active site. EMBO J. 1994, 13:2493-2501.
53. Torronen A., Rouvinen J. Structural and functional properties of low molecular weight endo-1,4-beta-xylanases. J. Biotechnol. 1997, 57:137-149.
54. Turunen O., Etuaho K., Fenel F., Vehmaanpera J., Wu X., Rouvinen J., Leisola M. A combination of weakly stabilizing mutations with a disulfide bridge in the alpha-helix region of Trichoderma reesei endo-1,4-beta-xylanase II increases the thermal stability through synergism. J. Biotechnol. 2001, 88:37-46.
55. Turunen O., Vuorio M., Fenel F., Leisola M. Engineering of multiple arginines into the Ser/Thr surface of Trichoderma reesei endo-1,4- beta-xylanase II increases the thermotolerance and shifts the pH optimum towards alkaline pH. Protein Eng. 2002, 15:141-145.
56. Uzuner U., Shi W., Liu L., Liu S., Dai S.Y., Yuan J.S. Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum. BMC Bioinformatics 2011, 11(Suppl 6):S12.
57. Vieira D.S., Degreve L. An insight into the thermostability of a pair of xylanases: the role of hydrogen bonds. Mol. Phys. 2009, 107:59-69.
58. Viikari, L., Ranua, M., Kantelinen, A., Sundquist, J., Linko, M., 1986. Bleaching with enzymes. Proceedings of Third International Conference on Biotechnology. Pulp and Paper Industry, Stockholm, pp. 67-69.
59. Vocadlo D.J., Wicki J., Rupitz K., Withers S.G. A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum β-xylosidase and detailed kinetic analysis of a site-directed mutant. Biochemistry 2002, 41:9736-9746.
60. Wakarchuk W.W., Sung W.L., Campbell R.L., Cunningham A., Watson D.C., Yaguchi M. Thermostabilization of the Bacillus circulans xylanase by the introduction of disulfide bonds. Protein Eng. 1994, 7:1379-1386.
61. Wang T., Liu X., Yu Q., Zhang X., Qu Y., Gao P., Wang T. Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei. Biomol. Eng. 2005, 22:89-94.
62. Wang Q., Xia T. Enhancement of the activity and alkaline pH stability of Thermobifida fusca xylanase A by directed evolution. Biotech. Lett. 2008, 30:937-944.
63. Wang G., Wang Y., Yang P., Luo H., Huang H., Shi P., Meng K., Yao B. Molecular detection and diversity of xylanase genes in alpine tundra soil. Appl. Microbiol. Biotechnol. 2010, 87:1383-1393.
64. Winterhalter C., Liebl W. Two extremely thermostable xylanases of the hyperthermophilic bacterium Thermotoga maritima MSB8. Appl. Environ. Microbiol. 1995, 61:1810-1815.
65. Xia T., Wang Q. Directed evolution of Streptomyces lividans xylanase B toward enhanced thermal and alkaline pH stability. World J. Microbiol. Biotechnol. 2009, 25:93-100.
66. Xie H., Flint J., Vardakou M., Lakey J.H., Lewis R.J., Gilbert H.J., Dumon C. Probing the structural basis for the difference in thermostability displayed by family 10 xylanases. J. Mol. Biol. 2006, 360:157-167.
67. Xie J., Song L., Li X., Yi X., Xu H., Li J., Qiao D., Cao Y. Site-directed mutagenesis and thermostability of xylanase XYNB from Aspergillus niger 400264. Curr. Microbiol. 2011, 62:242-248.
68. Yang H.M., Meng K., Luo H.Y., Wang Y.R., Yuan T.Z., Bai Y.J., Yao B., Fan Y.N. Improvement of the thermostability of xylanase by N-terminus replacement. Chinese J. Biotechnol. 2006, 21:414-419.
69. Yang H.M., Yao B., Meng K., Wang Y.R., Bai Y.G., Wu N.W. Introduction of a disulfide bridge enhances the thermostability of a Streptomyces olivaceoviridis xylanase mutant. J. Ind. Microbiol. Biotechnol. 2007, 34:213-218.
70. Yang J.H., Park J.Y., Kim S.H., Yoo Y.J. Shifting pH optimum of Bacillus circulans xylanase based on molecular modeling. J. Biotechnol. 2008, 133:294-300.
71. Yoon H.S., Han N.S., Kim C.H. Expression of Thermotoga maritima endo-β-1,4-xylanase gene in E. coli and characterization of the recombinant enzyme. Agric. Chem. Biotechnol. 2004, 47:157-160.
72. You C., Yuan H., Huang Q., Lu H. Substrate molecule enhances the thermostability of a mutant of a family 11 xylanase from Neocallimastix patriciarum. African J. Biotechnol. 2010, 9:1288-1294.
73. Zhang M., Jiang Z., Yang S., Hua C., Li L. Cloning and expression of a Paecilomyces thermophila xylanase gene in E. coli and characterization of the recombinant xylanase. Biores. Technol. 2010, 101:688-695.
74. Zhang S., Zhang K., Chen X., Chu X., Sun F., Dong Z. Five mutations in N- terminus confer thermostability on mesophilic xylanase. Biochem. Biophys. Res. Commun. 2010, 395:200-206.
75. Zhang Z.G., Yi Z.L., Pei X.Q., Wu Z.L. Improving the thermostability of Geobacillus stearothermophilus xylanase XT6 by directed evolution and site-directed mutagenesis. Biores. Technol. 2010, 101:9272-9278.