Lipase improvement: Goals and strategies

Computational and Structural Biotechnology Journal

Volumn 2, Issue 3, 2012, Pages e201209005-

  Bassegoda, Arnau ^a   Cesarini, Silvia ^a   Diaz, Pilar ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84899975470     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201209005     Document Type: Article

References (90)

1. Schmidt RD, Verger R (1998) Lipases: Interfacial enzymes with attractive applications. Angew Chem Int Edit 37: 1608-1633.
2. Villeneuve P, Muderhwa JM, Graille J, Haas MJ (2000) Customizing lipases for biocatalysis: a survey of chemical, physical and molecular biological approaches. Journal of Molecular Catalysis B-Enzymatic 9: 113-148. (Pubitemid 30195728)
3. Patel MT, Nagarajan R, Kilara A (1996) Lipase-catalyzed biochemical reactions in novel media: A review. Chemical Engineering Communications 152-53: 365-404. (Pubitemid 126605431)
4. Patel RN (2001) Biocatalytic synthesis of intermediates for the synthesis of chiral drug substances. Curr Opin Biotechnol 12: 587-604. (Pubitemid 34149708)
5. Gupta R, Gupta N, Rathi P (2004) Bacterial lipases: an overview of production, purification and biochemical properties. Applied Microbiology and Biotechnology 64: 763-781. (Pubitemid 38918139)
6. Reetz MT (2002) Directed evolution as a means to create enantioselective enzymes. Abstracts of Papers American Chemical Society 224: 302.
7. Cambon E, Bourlieu C, Salum TFC, Piombo G, Dubreucq E, et al. (2009) Ability of Vdsconcelled heilbornii lipase to catalyse the synthesis of alkyl esters from vegetable oils. Process Biochemistry 44: 1265-1269.
8. Antranikian G, Bornscheuer UT, Liese A (2010) Highlights in Biocatalysis. ChemCatChem 2: 879-880.
9. Bornscheuer UT, Bessler C, Srinivas R, Krishna SH (2002) Optimizing lipases and related enzymes for efficient application. Trends in Biotechnology 20: 433-437. (Pubitemid 35239936)
10. Bommarius A, Bommarius-Riebel B (2005) Fundamentals of Biocatalysis: Weinheim-Wiley-VCH.
11. Luetz S, Giver L, Lalonde J (2008) Engineered enzymes for chemical production. Biotechnol Bioeng 101: 647-653.
12. Du C, Zhao B, Li C, Wang P, Wang Z, et al. (2009) Improvement of the enantioselectivity and activity of lipase from Pseudomonas sp. via adsorption on a hydrophobic support: kinetic resolution of 2-octanol. Biocatalysis and Biotransformation 27: 340-347.
13. Tian R, Yang CH, Wei XF, Xun EN, Wang R, et al. (2011) Optimization of APE1547-catalyzed Enantioselective Transesterification of (R/S)-2-methyl-l- butanol in an Ionic Liquid. Biotechnology and Bioprocess Engineering 16: 337-342.
14. Henke E, Pleiss J, Bornscheuer UT (2002) Activity of Lipases and esterases towards tertiary alcohols: Insights into structure-function relationships. Angewandte Chemie-International Edition 41: 3211.
15. Arnold G (2003) Methods in Molecular Biology. Methods in Molecular Biology: Humana Press Inc.
16. Kazlauskas RJ (2000) Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. Curr Opin ChemBioU: 81-88. (Pubitemid 30098678)
17. Bornscheuer UT, Pohl M (2001) Improved biocatalysts by directed evolution and rational protein design. Current Opinion in Chemical Biology 5: 137-143. (Pubitemid 32245673)
18. Johannes TW, Zhao HM (2006) Directed evolution of enzymes and biosynthetic pathways. Current Opinion in Microbiology 9: 261-267. (Pubitemid 43817614)
19. Williams GJ, Nelson AS, Berry A (2004) Directed evolution of enzymes for biocatalysis and the life sciences. Cellular and Molecular Life Sciences 61: 3034-3046. (Pubitemid 40104579)
20. Bornscheuer UT, Huisman GW, Kazlauskas RJ, Lutz S, Moore JC, et al. (2012) Engineering the third wave of biocatalysis. Nature 485: 185-194.
21. Geddie ML, Matsumura I (2004) Rapid evolution of |3-glucuronidase specificity by saturation mutagenesis of an active site loop. J Biol Chem 279: 26462-26468. (Pubitemid 38798799)
22. Reetz MT, Carballeira JD (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nature Protocols 2: 891-903. (Pubitemid 46758808)
23. Reetz MT (2011) Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Edit 50: 138-174.
24. Reetz MT, Carballeira JD, Peyralans J, Hobenreich H, Maichele A, et al. (2006) Expanding the substrate scope of enzymes: Combining mutations obtained by CASTing. Chemistry-a European Journal 12: 6031-6038.
25. Schmidt M, Hasenpusch D, Kahler M, Kirchner U, Wiggenhorn K, et al. (2006) Directed evolution of an esterase from Pseudomonas fluorescens yields a mutant with excellent enantioselectivity and activity for the kinetic resolution of a chiral building block. ChemBioChem 7: 805-809. (Pubitemid 43764190)
26. DeSantis G, Wong K, Farwell B, Chatman K, Zhu ZL, et al. (2003) Creation of a productive, highly enantioselective nitrilase through gene site saturation mutagenesis (GSSM). Journal of the American Chemical Society 125: 11476-11477. (Pubitemid 37210080)
27. Gersbach CA, Gaj T, Gordley RM, Barbas CF (2010) Directed evolution of recombinase specificity by split gene reassembly. Nucleic Acids Research 38: 4198-4206.
28. Dalby PA (2007) Engineering Enzymes for Biocatalysis. Recent Patents on Biotechnology 1: 1-9.
29. Reetz MT, Carballeira J, Vogel A (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angewandte Chemie-International Edition 45:7745-7751. (Pubitemid 44871333)
30. Luetz S, Patrick WM (2004) Novel methods for directed evolution of enzymes: quality, not quantity. Curr Opin Biotechnol 15: 291-297. (Pubitemid 39024689)
31. Gumulya Y, Sanchis J, Reetz MT (2012) Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima. Chembiochem 13: 1060-1066.
32. Gumulya Y, Reetz MT (2011) Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways. ChemBioChem 12: 2502-2510.
33. Bornscheuer U, Kazlauskas RJ (2011) Survey of protein engineering strategies. Current protocols in protein science / editorial board, John E Coligan [et al] Chapter 26: Unit26.27.
34. Kazlauskas RJ, Bornscheuer UT (2009) Finding better protein engineering strategies. Nature Chemical Biology 5: 526-529.
35. Fischer M, Pleiss J (2003) The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Research 31: 319-321. (Pubitemid 36150394)
36. Fischer M, Thai QK, Grieb M, Pleiss J (2006) DWARF-a data warehouse system for analyzing protein families. BMC Bioinformatics 7: 10.
37. Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, et al. (2010) The alpha/beta-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering. Chembiochem 11: 1635-1643.
38. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, et al. (2002) GenBank. Nucl Acids Res 30: 17-20. (Pubitemid 34679493)
39. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, et al. (2002) The Protein Data Bank. Acta Crystallographica Section D-Biological Crystallography 58: 899-907. (Pubitemid 34653017)
40. Ruslan R, Abd Rahman RN, Leow TC, Ali MSM, Basri M, et al. (2012) Improvement of Thermal Stability via Outer-Loop Ion Pair Interaction of Mutated Tl Lipase from Geobacillus zalihae Strain Tl. International Journal of Molecular Sciences 13: 943-960.
41. Siddiqui KS, Cavicchioli R (2005) Improved thermal stability and activity in the cold-adapted lipase B from Candida antarctica following chemical modification with oxidized polysaccharides. Extremophiles 9: 471-476. (Pubitemid 41831055)
42. Zhang NY, Suen WC, Windsor W, Xiao L, Madison V, et al. (2003) Improving tolerance of Candida antarctica lipase B towards irreversible thermal inactivation through directed evolution. Protein Engineering 16: 599-605. (Pubitemid 37139710)
43. Han ZL, Han SY, Zheng SP, Lin Y (2009) Enhancing thermostability of a Rhizomucor miehei lipase by engineering a disulfide bond and displaying on the yeast cell surface. Applied Microbiology and Biotechnology 85: 117-126.
44. Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM (2008) Thermostable Bacillus subtilis lipases: In vitro evolution and structural insight. Journal of Molecular Biology 381: 324-340.
45. Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability. Microbiology and Molecular Biology Reviews 65: 1.
46. Suhre K, Claverie JM (2003) Genomic correlates of hyperthermostability, an update. Journal of Biological Chemistry 278: 17198-17202. (Pubitemid 36799600)
47. Nawani N, Kaur J (2007) Studies on lipolytic isoenzymes from a thermophilic Bacillus sp.: Production, purification and biochemical characterization. Enzyme and Microbial Technology 40: 881-887. (Pubitemid 46329084)
48. Sharma PK, Kumar R, Mohammad O, Singh R, Kaur J (2012) Engineering of a metagenome derived lipase toward thermal tolerance: Effect of asparagine to lysine mutation on the protein surface. Gene 491: 264-271.
49. Gatti-Lafranconi P, Caldarazzo SM, Villa A, Alberghina L, Lotti M (2008) Unscrambling thermal stability and temperature adaptation in evolved variants of a cold-active lipase. Febs Letters 582: 2313-2318.
50. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, et al. (2004) Protein flexibility and intrinsic disorder. Protein Science 13: 71-80. (Pubitemid 38021142)
51. Zhang JH, Lin Y, Sun YF, Ye YR, Zheng SP, et al. (2012) High-throughput screening of B factor saturation mutated Rhizomucor miehei lipase thermostability based on synthetic reaction. Enzyme and Microbial Technology 50: 325-330.
52. Cesarini S, Bofill C, Pastor FIJ, Reetz MT, Diaz P (2012) A thermostable variant of P. aeruginosa cold-adapted LipC obtained by rational design and saturation mutagenesis. Process Biochemistry, in press.
53. Augustyniak W, Brzezinska AA, Pijning T, Wienk H, Boelens R, et al. (2012) Biophysical characterization of mutants of Bacillus subtilis lipase evolved for thermostability: Factors contributing to increased activity retention. Protein Science 21: 487-497.
54. Siadat OR, Lougarre A, Lamouroux L, Ladurantie C, Fournier D (2006) The effect of engineered disulfide bonds on the stability of Drosophila melanogaster acetylcholinesterase. BMC Biochemistry 7: 12-18.
55. Le QA, Joo JC, Yoo YJ, Kim YH (2012) Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge. Biotechnology and Bioengineering 109: 867-876.
56. Capriotti E, Fariselli P, Casadio R (2005) Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research 33: 306-310.
57. Illanes A, Cauerhff A, Wilson L, Castro GR (2012) Recent trends in biocatalysis engineering. Bioresource Technology 115: 48-57.
58. Kawata T, Ogino H (2009) Enhancement of the Organic Solvent-Stability of the LST-03 Lipase by Directed Evolution. Biotechnology Progress 25: 1605-1611.
59. Ogino H, Katou Y, Akagi R, Mimitsuka T, Hiroshima S, et al. (2007) Cloning and expression of gene, and activation of an organic solvent-stable lipase from Pseudomonas aeruginosa LST-03. Extremophiles 11: 809-817. (Pubitemid 350045898)
60. Kawata T, Ogino H (2010) Amino acid residues involved in organic solvent-stability of the LST-03 lipase. Biochemical and Biophysical Research Communications 400: 384-388.
61. Reetz MT (2009) Directed Evolution of Enantioselective Enzymes: An Unconventional Approach to Asymmetric Catalysis in Organic Chemistry. Journal of Organic Chemistry 74: 5767-5778.
62. 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. Chemical Communications 46: 8657-8658.
63. Han S-y, Zhang J-h, Han Z-l, Zheng S-p, Lin Y (2011) Combination of site-directed mutagenesis and yeast surface display enhances Rhizomucor miehei lipase esterification activity in organic solvent. Biotechnology Letters 33: 2431-2438.
64. Muralidhar RV, Chirumamilla RR, Marchant R, Ramachandran VN, Ward OP, et al. (2002) Understanding lipase stereoselectivity. World Journal of Microbiology & Biotechnology 18: 81-97. (Pubitemid 34227985)
65. Kovac A, Scheib H, Pleiss J, Schmid RD, Paltauf F (2000) Molecular basis of lipase stereoselectivity. European Journal of Lipid Science and Technology 102: 61-77.
66. Jaeger KE, Dijkstra BW, Reetz MT (1999) Bacterial biocatalysts: Molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annual Review of Microbiology 53: 315-.
67. Pleiss J, Fischer M, Schmid RD (1998) Anatomy of lipase binding sites: the scissile fatty acid binding site. Chemistry and Physics of Lipids 93: 67-80. (Pubitemid 28383206)
68. Ni Z, Zhou P, Jin X, Lin XF (2011) Integrating In Silico and In vitro Approaches to Dissect the Stereoselectivity of Bacillus subtilis Lipase A toward Ketoprofen Vinyl Ester. Chemical Biology & Drug Design 78: 301-308.
69. Brundiek HB, Evitt AS, Kourist R, Bornscheuer UT (2012) Creation of a Lipase Highly Selective for trans Fatty Acids by Protein Engineering. Angewandte Chemie-International Edition 51: 412-414.
70. Ema T, Kamata S, Takeda M, Nakano Y, Sakai T (2010) Rational creation of mutant enzyme showing remarkable enhancement of catalytic activity and enantioselectivity toward poor substrates. Chemical Communications 46: 5440-5442.
71. Engstrom K, Nyhlen J, Sandstrom AG, Backvall JE (2010) Directed Evolution of an Enantioselective Lipase with Broad Substrate Scope for Hydrolysis of alpha-Substituted Esters. Journal of the American Chemical Society 132: 7038-7042.
72. Bordes F, Cambon E, Dossat-Letisse V, Andre I, Croux C, et al. (2009) Improvement of Yarrowia lipolytica Lipase Enantioselectivity by Using Mutagenesis Targeted to the Substrate Binding Site. ChemBioChem 10: 1705-1713.
73. Cambon E, Piamtongkam R, Bordes F, Duquesne S, Andre I, et al. (2010) Rationally Engineered Double Substituted Variants of Yarrowia lipolytica Lipase With Enhanced Activity Coupled With Highly Inverted Enantioselectivity Towards 2-Bromo Phenyl Acetic Acid Esters. Biotechnology and Bioengineering 106: 852-859.
74. Schliessmann A, Hidalgo A, Berenguer J, Bornscheuer UT (2009) Increased Enantioselectivity by Engineering Bottleneck Mutants in an Esterase from Pseudomonas fluorescens, Chembiochem 10: 2920-2923.
75. Sandstrom AG, Wikmark Y, Engstrom K, Nyhlen J, Backvall JE (2012) Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library. Proceedings of the National Academy of Sciences of the United States of America 109: 78-83.
76. Boersma YL, Pijning T, Bosma MS, van der Sloot AM, Godinho LF, et al. (2008) Loop grafting of Bacillus subtilis lipase A: Inversion of enantioselectivity. Chemistry & Biology 15: 782-789.
77. Pleiss J, Fischer M, Peiker M, Thiele C, Schmid RD (2000) Lipase engineering database-Understanding and exploiting sequence-structure-function relationships. Journal of Molecular Catalysis B-Enzymatic 10: 491-508. (Pubitemid 30628635)
78. Henke E, Bornscheuer UT, Schmid RD, Pleiss J (2003) A Molecular Mechanism of Enantiorecognition of Tertiary Alcohols by Carboxylesterases. Chem Eur J of Chem Bio 4: 485-493. (Pubitemid 36749618)
79. Bassegoda A, Nguyen GS, Schmidt M, Kourist R, Diaz P, et al. (2010) Rational Protein Design of Paenibacillus barcinonensis Esterase EstA for Kinetic Resolution of Tertiary Alcohols. ChemCatChem 2: 962-967.
80. Wiggers M, Holt J, Kourist R, Bartsch S, Arends IWCE, et al. (2009) Probing the enantioselectivity of Bacillus subtilis esterase BS2 for tert. alcohols. Journal of Molecular Catalysis B Enzymatic 60: 82-86.
81. Heinze B, Kourist R, Fransson L, Huh K, Bornscheuer UT (2007) Highly enantioselective kinetic resolution of two tertiary alcohols using mutants of an esterase from Bacillus subtilis. Protein Engineering Design & Selection 20: 125-131. (Pubitemid 46536746)
82. Kourist R, Bartsch S, Bornscheuer UT (2007) Highly enantioselective synthesis of arylaliphatic tertiary alcohols using mutants of an esterase from Bacillus subtilis. Advanced Synthesis & Catalysis 349: 1393-1398.
83. Reyes-Duarte D, Polaina J, Lopez-Cortes N, Alcalde M, Plou FJ, et al. (2005) Conversion of a carboxylesterase into a triacylglycerol lipase by a random mutation. Angewandte Chemie-International Edition 44: 7553-7557. (Pubitemid 41713712)
84. Yen CC, Malnis CC, Lee GC, Lee LC, Shaw JF (2010) Site-Specific Saturation Mutagenesis on Residues 132 and 450 of Candida rugosa LIP2 Enhances Catalytic Efficiency and Alters Substrate Specificity in Various Chain Lengths of Triglycerides and Esters. Journal of Agricultural and Food Chemistry 58: 10899-10905.
85. Schmitt J, Brocca S, Schmid RD, Pleiss J (2002) Blocking the tunnel: engineering of Candida rugosa lipase mutants with short chain length specificity. Protein Engineering 15: 595-601. (Pubitemid 34984250)
86. Brundiek H, Padhi SK, Kourist R, Evitt A, Bornscheuer UT (2012) Altering the Scissile Fatty Acid Binding Site of Candida antarctica Lipase A by Protein Engineering for the Selective Hydrolysis of Medium Chain Fatty Acids. European Journal of Lipid Science and technology
87. Juhl PB, Doderer K, Hollmann F, Thum O, Pleiss J (2010) Engineering of Candida antarctica lipase B for hydrolysis of bulky carboxylic acid esters. Journal of Biotechnology 150: 474-480.
88. Madan B, Mishra P (2010) Co-expression of the lipase and foldase of Pseudomonas aeruginosa to a functional lipase in Escherichia coli. Applied Microbiology and Biotechnology 85: 597-604.
89. Kim EK, Jang WH, Ko JH, Kang JS, Noh MJ, et al. (2001) Lipase and its modulator from Pseudomonas sp strain KFCC 10818: Proline-to-glutamine substitution at position 112 induces formation of enzymatically active lipase in the absence of the modulator. Journal of Bacteriology 183: 5937-5941. (Pubitemid 32917413)
90. Bofill C (2010) Comprehensive analysis of Pseudomonas sp. 42A2 LipA and LipC lipases [Experimental Thesis. European Mention]. Barcelona: University of Barcelona. 300 p.