Protein engineering by random mutagenesis and structure-guided consensus of Geobacillus stearothermophilus lipase T6 for enhanced stability in methanol

Applied and Environmental Microbiology

Volumn 80, Issue 4, 2014, Pages 1515-1527

  Dror, Adi ^a   Shemesh, Einav ^a   Dayan, Natali ^a   Fishman, Ayelet ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIESEL PRODUCTION; ENHANCED STABILITY; FATTY ACID METHYL ESTER; GEOBACILLUS STEAROTHERMOPHILUS; INDUSTRIAL PROCESSS; METHANOL CONCENTRATION; POLAR ORGANIC SOLVENTS; PROTEIN ENGINEERING;

BIOCHEMICAL ENGINEERING; BIODIESEL; ENZYMES; GENETIC ENGINEERING; HYDROGEN BONDS; MUTAGENESIS; ORGANIC SOLVENTS; STABILITY;

METHANOL;

BACTERIUM; BIOENGINEERING; BIOFUEL; CATALYST; CONCENTRATION (COMPOSITION); ENZYME ACTIVITY; METHANOL; MUTAGENICITY; OIL PRODUCTION; PROTEIN; SOLVENT; STABILIZATION;

ENZYME INHIBITOR; METHANOL; MUTANT PROTEIN; SOLVENT; TRIACYLGLYCEROL LIPASE;

AMINO ACID SUBSTITUTION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; GENETICS; GEOBACILLUS STEAROTHERMOPHILUS; METABOLISM; MOLECULAR DYNAMICS; MUTAGENESIS; PROCEDURES; PROTEIN ENGINEERING;

AMINO ACID SUBSTITUTION; ENZYME INHIBITORS; ENZYME STABILITY; GEOBACILLUS STEAROTHERMOPHILUS; LIPASE; METHANOL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS; MUTANT PROTEINS; PROTEIN ENGINEERING; SOLVENTS;

EID: 84893361831     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03371-13     Document Type: Article

References (71)

1. Gupta R, Gupta N, Rathi P. 2004. Bacterial lipases: an overview of production, purification and biochemical properties. Appl. Microbiol. Biotechnol. 64:763-781. http://dx.doi.org/10.1007/s00253-004-1568-8.
2. Guncheva M, Zhiryakova D. 2011. Catalytic properties and potential applications of Bacillus lipases. J. Mol. Catal. B Enzym. 68:1-21. http://dx.doi.org/10.1016/j.molcatb.2010.09.002.
3. Hasan F, Shah AA, Hameed A. 2006. Industrial applications of microbial lipases. Enzyme Microb. Technol. 39:235-251. http://dx.doi.org/10.1016/j.enzmictec.2005.10.016.
4. Villeneuve P, Muderhwa JM, Graille J, Haas MJ. 2000. Customizing lipases for biocatalysis: a survey of chemical, physical and molecular biological approaches. J. Mol. Catal. B Enzym. 9:113-148. http://dx.doi.org/10.1016/S1381-1177(99)00107-1.
5. Jaeger KE, Dijkstra BW, Reetz MT. 1999. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol. 53:315-351. http://dx.doi.org/10.1146/annurev.micro.53.1.315.
6. Jaeger KE, Ransac S, Dijkstra BW, Colson C, van Heuvel M, Misset O. 1994. Bacterial lipases. FEMS Microbiol. Rev. 15:29-63.
7. Arnold FH. 1990. Engineering enzymes for non-aqueous solvents. Trends Biotechnol. 8:244-249. http://dx.doi.org/10.1016/0167-7799(90)90186-2.
8. Doukyu N, Ogino H. 2010. Organic solvent-tolerant enzymes. Biochem. Eng. J. 48:270-282. http://dx.doi.org/10.1016/j.bej.2009.09.009.
9. Ogino H, Ishikawa H. 2001. Enzymes which are stable in the presence of organic solvents. J. Biosci. Bioeng. 91:109-116. http://dx.doi.org/10.1016/S1389-1723(01).
10. Chakravorty D, Parameswaran S, Dubey V, Patra S. 2012. Unraveling the rationale behind organic solvent stability of lipases. Appl. Biochem. Biotechnol. 167:439-461. http://dx.doi.org/10.1007/s12010-012-9669-9.
11. Schulze B, Klibanov AM. 1991. Inactivation and stabilization of stabilisins in neat organic solvents. Biotechnol. Bioeng. 38:1001-1006. http://dx.doi.org/10.1002/bit.260380907.
12. Bajaj A, Lohan P, Jha PN, Mehrotra R. 2010. Biodiesel production through lipase catalyzed transesterification: an overview. J. Mol. Catal. B Enzym. 62:9-14. http://dx.doi.org/10.1016/j.molcatb.2009.09.018.
13. Du W, Li W, Sun T, Chen X, Liu D. 2008. Perspectives for biotechnological production of biodiesel and impacts. Appl. Microbiol. Biotechnol. 79:331-337. http://dx.doi.org/10.1007/s00253-008-1448-8.
14. Al-Zuhair S. 2007. Production of biodiesel: possibilities and challenges. Biofuels Bioprod. Bioref. 1:57-66. http://dx.doi.org/10.1002/bbb.2.
15. Xiao M, Mathew S, Obbard JP. 2009. Biodiesel fuel production via transesterification of oils using lipase biocatalyst. GCB Bioenergy 1:115-125. http://dx.doi.org/10.1111/j.1757-1707.2009.01009.x.
16. Shimada Y, Watanabe Y, Samukawa T, Sugihara A, Noda H, Fukuda H, Tominaga Y. 1999. Conversion of vegetable oil to biodiesel using immobilized Candida antarctica lipase. J. Am. Oil Chem. Soc. 76:789-793.
17. Kumar S, Ola RP, Pahujani S, Kaushal R, Kanwar SS, Gupta R. 2006. Thermostability and esterification of a polyethylene-immobilized lipase from Bacillus coagulans BTS-3. J. Appl. Polym. Sci. 102:3986-3993. http://dx.doi.org/10.1556/AMicr.53.2006.2.8.
18. Bagi K, Simon LM, Szajáni B. 1997. Immobilization and characterization of porcine pancreas lipase. Enzyme Microb. Technol. 20:531-535.
19. Kawakami K, Oda Y, Takahashi R. 2011. Application of a Burkholderia cepacia lipase-immobilized silica monolith to batch and continuous biodiesel production with a stoichiometric mixture of methanol and crude Jatropha oil. Biotechnol. Biofuels 4:42. http://dx.doi.org/10.1186/1754-6834-4-42.
20. Carvalho CML, Cabral JMS. 2000. Reverse micelles as reaction media for lipases. Biochimie 82:1063-1085. http://dx.doi.org/10.1016/S0300-9084(00)01187-1.
21. Yang C-L, Gulari E. 1994. Enzymic esterification of diols in reverse micellar media. Biotechnol. Prog. 10:269-276.
22. Mine Y, Fukunaga K, Yoshimoto M, Nakao K, Sugimura Y. 2001. Modification of lipases with poly(ethylene glycol) and poly(oxyethylene) detergents and their catalytic activities in organic solvents. J. Biosci. Bioeng. 92:539-543. http://dx.doi.org/10.1016/S1389-1723(01)80312-1.
23. Cabrera Z, Fernandez-Lorente G, Fernandez-Lafuente R, Palomo JM, Guisan JM. 2009. Enhancement of Novozym-435 catalytic properties by physical or chemical modification. Process Biochem. 44:226-231. http://dx.doi.org/10.1016/j.procbio.2008.10.005.
24. Uttatree S, Winayanuwattikun P, Charoenpanich J. 2010. Isolation and characterization of a novel thermophilic-organic solvent stable lipase from Acinetobacter baylyi. Appl. Biochem. Biotechnol. 162:1362-1376. http://dx.doi.org/10.1007/s12010-010-8928-x.
25. Khan M, Jithesh K. 2012. Expression and purification of organic solvent stable lipase from soil metagenomic library. World J. Microbiol. Biotechnol. 28:2417-2424. http://dx.doi.org/10.1007/s1274-012-1051-0.
26. Di Lorenzo M, Hidalgo A, Molina R, Hermoso JA, Pirozzi D, Bornscheuer UT. 2007. Enhancement of the stability of a prolipase from Rhizopus oryzae toward aldehydes by saturation mutagenesis. Appl. Environ. Microbiol. 73:7291-7299. http://dx.doi.org/10.1128/AEM.01176-07.
27. Kawata T, Ogino H. 2009. Enhancement of the organic solvent-stability of the LST-03 lipase by directed evolution. Biotechnol. Prog. 25:1605-1611. http://dx.doi.org/10.1002/btpr.264.
28. Park H, Joo J, Park K, Yoo Y. 2012. Stabilization of Candida antarctica lipase B in hydrophilic organic solvent by rational design of hydrogen bond. Biotechnol. Bioprocess Eng. 17:722-728. http://dx.doi.org/10.1007/s12257-012-0092-4.
29. Takagi H, Hirai K, Maeda Y, Matsuzawa H, Nakamori S. 2000. Engineering subtilisin E for enhanced stability and activity in polar organic solvents. J. Biochem. 127:617-625. http://dx.doi.org/10.1093/oxfordjournals.jbchem.a022649.
30. Badoei-Dalfard A, Khajeh K, Asghari SM, Ranjbar B, Karbalaei-Heidari HR. 2010. Enhanced activity and stability in the presence of organic solvents by increased active site polarity and stabilization of a surface loop in a metalloprotease. J. Biochem. 148:231-238. http://dx.doi.org/10.1093/jb/mvq057.
31. Song JK, Rhee JS. 2001. Enhancement of stability and activity of phospholipase A1 in organic solvents by directed evolution. Biochim. Biophys. Acta 1547:370-378. http://dx.doi.org/10.1016/S0167-4838(01)00204-7.
32. Martinez P, Arnold FH. 1991. Surface charge substitutions increase the stability of-lytic protease in organic solvents. J. Am. Chem. Soc. 113: 6336-6337.
33. Chen K, Robinson AC, Van Dam ME, Martinez P, Economou C, Arnold FH. 1991. Enzyme engineering for nonaqueous solvents. II. Additive effects of mutations on the stability and activity of subtilisin E in polar organic media. Biotechnol. Prog. 7:125-129.
34. Zumárraga M, Bulter T, Shleev S, Polaina J, Martínez-Arias A, Plou FJ, Ballesteros A, Alcalde M. 2007. In vitro evolution of a fungal laccase in high concentrations of organic cosolvents. Chem. Biol. 14:1052-1064. http://dx.doi.org/10.1016/j.chembiol.2007.08.010.
35. Takahashi T, Ng KK-S, Oyama H, Oda K. 2005. Molecular cloning of the gene encoding vibrio metalloproteinase vimelysin and isolation of a mutant with high stability in organic solvents. J. Biochem. 138:701-710. http://dx.doi.org/10.1093/jb/mvi173.
36. Kazlauskas RJ, Bornscheuer UT. 2009. Finding better protein engineering strategies. Nat. Chem. Biol. 5:526-529. http://dx.doi.org/10.1038/nchembio0809-526.
37. Turner NJ. 2009. Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 5:567-573. http://dx.doi.org/10.1038/nchembio.203.
38. Reetz MT, Kahakeaw D, Lohmer R. 2008. Addressing the numbers problem in directed evolution. Chembiochem 9:1797-1804. http://dx.doi.org/10.1002/cbic.200800298.
39. Vázquez-Figueroa E, Chaparro-Riggers J, Bommarius AS. 2007. Development of a thermostable glucose dehydrogenase by a structure-guided consensus concept. Chembiochem 8:2295-2301. http://dx.doi.org/10.1002/cbic.200700500.
40. Vazquez-Figueroa E, Yeh V, Broering JM, Chaparro-Riggers JF, Bommarius AS. 2008. Thermostable variants constructed via the structureguided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media. Protein Eng. Des. Sel. 21:673-680. http://dx.doi.org/10.1093/protein/gzn048.
41. Reetz MT, Soni P, Fernandez L, Gumulya Y, Carballeira JD. 2010. Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. Chem. Commun. (Camb.) 46:8657-8658. http://dx.doi.org/10.1039/c0cc02657c.
42. Polizzi KM, Chaparro-Riggers JF, Vazquez-Figueroa E, Bommarius AS. 2006. Structure-guided consensus approach to create a more thermostable penicillin G acylase. Biotechnol. J. 1:531-536. http://dx.doi.org/10.1002/biot.200600029.
43. Miyazaki J, Nakaya S, Suzuki T, Tamakoshi M, Oshima T, Yamagishi A. 2001. Ancestral residues stabilizing 3-isopropylmalate dehydrogenase of an extreme thermophile: experimental evidence supporting the thermophilic common ancestor hypothesis. J. Biochem. 129:777-782. http://dx.doi.org/10.1093/oxfordjournals.jbchem.a002919.
44. Watanabe K, Ohkuri T, Yokobori S-I, Yamagishi A. 2006. Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree. J. Mol. Biol. 355:664-674. http://dx.doi.org/10.1016/j.jmb.2005.10.011.
45. Lehmann M, Loch C, Middendorf A, Studer D, Lassen SF, Pasamontes L, van Loon APGM, Wyss M. 2002. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15:403-411. http://dx.doi.org/10.1093/protein/15.5.403.
46. Steipe B, Schiller B, Plückthun A, Steinbacher S. 1994. Sequence statistics reliably predict stabilizing mutations in a protein domain. J. Mol. Biol. 240:188-192.
47. Amin N, Liu AD, Ramer S, Aehle W, Meijer D, Metin M, Wong S, Gualfetti P, Schellenberger V. 2004. Construction of stabilized proteins by combinatorial consensus mutagenesis. Protein Eng. Des. Sel. 17:787-793. http://dx.doi.org/10.1093/protein/gzh091.
48. Khersonsky O, Rosenblat M, Toker L, Yacobson S, Hugenmatter A, Silman I, Sussman JL, Aviram M, Tawfik DS. 2009. Directed evolution of serum paraoxonase PON3 by family shuffling and ancestor/consensus mutagenesis, and its biochemical characterization. Biochemistry (Wash.) 48:6644-6654. http://dx.doi.org/10.1021/bi900583y.
49. Meshulam-Simon G. 2001. Isolation and characterization of lipases from thermophilic bacteria for the preparation of optically active compounds. Ph.D. thesis. Technion-Israel Institute of Technology, Haifa, Israel.
50. Kristjansson JK. 1989. Thermophilic organisms as sources of thermostable enzymes. Trends Biotechnol. 7:349-353. http://dx.doi.org/10.1016/0167-7799(89)90035-8.
51. Sambrook J, Russel DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
52. Rashid N, Shimada Y, Ezaki S, Atomi H, Imanaka T. 2001. Lowtemperature lipase from psychrotrophic Pseudomonas sp. strain KB700A. Appl. Environ. Microbiol. 67:4064-4069. http://dx.doi.org/10.1128/AEM.67.9.4064-4069.2001.
53. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. 2010. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38:W529-W533. http://dx.doi.org/10.1093/nar/gkq399.
54. Simossis VA, Heringa J. 2005. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 33:289-294. http://dx.doi.org/10.1093/nar/gki170.
55. Simossis VA, Kleinjung J, Heringa J. 2005. Homology-extended sequence alignment. Nucleic Acids Res. 33:816-824. http://dx.doi.org/10.1093/nar/gki233.
56. Tyndall JDA, Sinchaikul S, Fothergill-Gilmore LA, Taylor P, Walkinshaw MD. 2002. Crystal structure of a thermostable lipase from Bacillus stearothermophilus P1. J. Mol. Biol. 323:859-869. http://dx.doi.org/10.1016/S0022-283.6(02)01004-5.
57. Herman A, Tawfik DS. 2007. Incorporating synthetic oligonucleotides via gene reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng. Des. Sel. 20:219-226. http://dx.doi.org/10.1093/protein/gzm014.
58. Bottcher D, Bornscheuer UT. 2006. High-throughput screening of activity and enantioselectivity of esterases. Nat. Protoc. 1:2340-2343. http://dx.doi.org/10.1038/nprot.2006.391.
59. Ben-Yosef VS, Sendovski M, Fishman A. 2010. Directed evolution of tyrosinase for enhanced monophenolase/diphenolase activity ratio. Enzyme Microb. Technol. 47:372-376. http://dx.doi.org/10.1016/j.enzmictec.2010.08.008.
60. Solano F, Garcia E, Perez D, Sanchez-Amat A. 1997. Isolation and characterization of strain MMB-1 (CECT 4803), a novel melanogenic marine bacterium. Appl. Environ. Microbiol. 63:3499-3506.
61. Bommarius AS, Blum JK, Abrahamson MJ. 2011. Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst. Curr. Opin. Chem. Biol. 15:194-200. http://dx.doi.org/10.1016/j.cbpa.2010.11.011.
62. Fishman A, Levy I, Cogan U, Shoseyov O. 2002. Stabilization of horseradish peroxidase in aqueous-organic media by immobilization onto cellulose using a cellulose-binding-domain. J. Mol. Catal. B Enzym. 18:121-131. http://dx.doi.org/10.1016/S1381-1177(02)00075-9.
63. Sellek GA, Chaudhuri JB. 1999. Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb. Technol. 25:471-482.
64. Yao C, Cao Y, Wu S, Li S, He B. 2013. An organic solvent and thermally stable lipase from Burkholderia ambifaria YCJ01: purification, characteristics and application for chiral resolution of mandelic acid. J. Mol. Catal. B Enzym. 85-86:105-110. http://dx.doi.org/10.1016/j.molcatb.2012.08.016.
65. Gog A, Roman M, Toşa M, Paizs C, Irimie FD. 2012. Biodiesel production using enzymatic transesterification: current state and perspectives. Renewable Energy 39:10-16. http://dx.doi.org/10.1016/j.renene.2011.08.007.
66. Bloom JD, Labthavikul ST, Otey CR, Arnold FH. 2006. Protein stability promotes evolvability. Proc. Natl. Acad. Sci. U. S. A. 103:5869-5874. http://dx.doi.org/10.1073/pnas.0510098103.
67. Cèbe R, Geiser M. 2006. Rapid and easy thermodynamic optimization of the 5-end of mRNA dramatically increases the level of wild type protein expression in Escherichia coli. Protein Expr. Purif. 45:374-380. http://dx.doi.org/10.1016/j.pep.2005.07.007.
68. Degryse E. 1990. Influence of the second and third codon on the expression of recombinant hirudin in E. coli. FEBS Lett. 269:244-246. http://dx.doi.org/10.1016/0014-5793(90)81164-J.
69. Eijsink VGH, Gåseidnes S, Borchert TV, van den Burg B. 2005. Directed evolution of enzyme stability. Biomol. Eng. 22:21-30. http://dx.doi.org/10.1016/j.bioeng.2004.12.003.
70. Ogino H, Uchiho T, Doukyu N, Yasuda M, Ishimi K, Ishikawa H. 2007. Effect of exchange of amino acid residues of the surface region of the PST-01 protease on its organic solvent-stability. Biochem. Biophys. Res. Commun. 358:1028-1033. http://dx.doi.org/10.1016/j.bbrc.2007.05.047.
71. Reetz MT, Soni P, Acevedo JP, Sanchis J. 2009. Creation of an amino acid network of structurally coupled residues in the directed evolution of a thermostable enzyme. Angew. Chem. Int. Ed. Engl. 121:8418-8422. http://dx.doi.org/10.1002/anie.200904209.