Login Register Cart 0
Generic placeholder image

Current Protein & Peptide Science

Editor-in-Chief

ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Review Article

Protein Engineering Strategies for Tailoring the Physical and Catalytic Properties of Enzymes for Defined Industrial Applications

Author(s): Rakesh Kumar, Arbind Kumar and Jagdeep Kaur*

Volume 24, Issue 2, 2023

Published on: 25 January, 2023

Page: [113 - 129] Pages: 17

DOI: 10.2174/1389203724666230110163234

Price: $65

Abstract

Background: Highly evolved biocatalysts that can endure harsh environmental conditions during industrial processes are highly desirable. The availability of suitable biocatalysts with high enzyme activity, substrate selectivity, and stability could lower the production costs in the pharmaceutical, chemical, and food industries, resulting in more economical products.

Objectives: Naturally evolved enzymes could not be exploited in industrial applications because of their compromised properties. Till date, protein engineering strategies have helped us to improve the desired physical and catalytic properties of enzymes to meet their performance needs in industrial and medical applications.

Results: Protein engineering technologies such as directed evolution and rational designing are wellsuited for improving biocatalytic properties. Each approach has its own set of limitations, and the implementation of techniques is contingent on the availability of prerequisite information about the biocatalyst. Protein structure information is essential for rational design, but no prior structural knowledge is required for directed evolution. Furthermore, semi-rational approaches and enzyme designing are also being used. Considering these facts, this study outlines the various molecular techniques used to improve the physical and catalytic properties of enzymes. It also emphasises the magnitude of strategies used to improve the properties of biocatalysts to meet the needs of industrial processes.

Conclusion: Protein engineering frequently employs for improving crucial enzyme characteristics. A semi-rational approach has now emerged as the preferred technology for protein engineering. However, adopting an engineering strategy to achieve the desired characteristic depends on the availability of resources and subject-matter knowledge.

Keywords: Protein engineering, biocatalyst, enzymes, directed evolution, rational design, catalysis.

Next »
Graphical Abstract

[1]
Rigoldi, F.; Donini, S.; Redaelli, A.; Parisini, E.; Gautieri, A. Review: Engineering of thermostable enzymes for industrial applications. APL Bioeng., 2018, 2(1), 011501.
[http://dx.doi.org/10.1063/1.4997367] [PMID: 31069285]
[2]
Sijbesma, F. White biotechnology: Gateway to a more sustainable future; EuropaBio: Brussels, Belgium, 2003.
[3]
Packer, M.S.; Liu, D.R. Methods for the directed evolution of proteins. Nat. Rev. Genet., 2015, 16(7), 379-394.
[http://dx.doi.org/10.1038/nrg3927] [PMID: 26055155]
[4]
Poluri, K.M.; Gulati, K. Protein Engineering Techniques. SpringerBriefs Appl Sci Technol; Springer Singapore, 2017.
[http://dx.doi.org/10.1007/978-981-10-2732-1]
[5]
Coluzza, I. Computational protein design: a review. J. Phys. Condens. Matter, 2017, 29(14), 143001.
[http://dx.doi.org/10.1088/1361-648X/aa5c76] [PMID: 28140371]
[6]
Huang, P.S.; Boyken, S.E.; Baker, D. The coming of age of de novo protein design. Nature, 2016, 537(7620), 320-327.
[http://dx.doi.org/10.1038/nature19946] [PMID: 27629638]
[7]
Fox, R.J.; Davis, S.C.; Mundorff, E.C.; Newman, L.M.; Gavrilovic, V.; Ma, S.K.; Chung, L.M.; Ching, C.; Tam, S.; Muley, S.; Grate, J.; Gruber, J.; Whitman, J.C.; Sheldon, R.A.; Huisman, G.W. Improving catalytic function by ProSAR-driven enzyme evolution. Nat. Biotechnol., 2007, 25(3), 338-344.
[http://dx.doi.org/10.1038/nbt1286] [PMID: 17322872]
[8]
Karplus, M.; McCammon, J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol., 2002, 9(9), 646-652.
[http://dx.doi.org/10.1038/nsb0902-646] [PMID: 12198485]
[9]
Romero, P.A.; Arnold, F.H. Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol., 2009, 10(12), 866-876.
[http://dx.doi.org/10.1038/nrm2805] [PMID: 19935669]
[10]
Rohl, C.A.; Strauss, C.E.M.; Misura, K.M.S.; Baker, D. Protein structure prediction using Rosetta. Methods Enzymol., 2004, 383, 66-93.
[http://dx.doi.org/10.1016/S0076-6879(04)83004-0] [PMID: 15063647]
[11]
Rocklin, G.J.; Chidyausiku, T.M.; Goreshnik, I.; Ford, A.; Houliston, S.; Lemak, A.; Carter, L.; Ravichandran, R.; Mulligan, V.K.; Chevalier, A.; Arrowsmith, C.H.; Baker, D. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science, 2017, 357(6347), 168-175.
[http://dx.doi.org/10.1126/science.aan0693]
[12]
Leung, D.W.; Chen, E.; Goeddel, D.V. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique., 1989, 1, 11-15.
[13]
Kumar, R.; Singh, R.; Kaur, J. Characterization and molecular modelling of an engineered organic solvent tolerant, thermostable lipase with enhanced enzyme activity. J. Mol. Catal., B Enzym., 2013, 97, 243-251.
[http://dx.doi.org/10.1016/j.molcatb.2013.09.001]
[14]
Fujii, R.; Kitaoka, M.; Hayashi, K. One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res., 2004, 32(19), e145-e145.
[http://dx.doi.org/10.1093/nar/gnh147] [PMID: 15507684]
[15]
Ding, X.; Snyder, A.K.; Shaw, R.; Farmerie, W.G.; Song, W.Y. Direct retransformation of yeast with plasmid DNA isolated from single yeast colonies using rolling circle amplification. Biotechniques, 2003, 35(4), 774-779, 778-779.
[http://dx.doi.org/10.2144/03354st08] [PMID: 14579743]
[16]
Greener, A.; Callahan, M.; Jerpseth, B. An efficient random mutagenesis technique using an E. coli mutator strain. Mol. Biotechnol., 1997, 7(2), 189-195.
[http://dx.doi.org/10.1007/BF02761755] [PMID: 9219234]
[17]
Selifonova, O.; Valle, F.; Schellenberger, V. Rapid evolution of novel traits in microorganisms. Appl. Environ. Microbiol., 2001, 67(8), 3645-3649.
[http://dx.doi.org/10.1128/AEM.67.8.3645-3649.2001] [PMID: 11472942]
[18]
Brockman, H.E.; de Serres, F.J.; Ong, T.M.; Huang, C.Y. Two N-hydroxylaminopurines are highly mutagenic in the ad-3 forward-mutation test in growing cultures of heterokaryon 12 of Neutospora crassa. Mutat. Res., 1987, 177(1), 61-75.
[http://dx.doi.org/10.1016/0027-5107(87)90022-4] [PMID: 2950320]
[19]
Crameri, A.; Raillard, S.A.; Bermudez, E.; Stemmer, W.P.C. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature, 1998, 391(6664), 288-291.
[http://dx.doi.org/10.1038/34663] [PMID: 9440693]
[20]
Lutz, S.; Ostermeier, M.; Moore, G.L.; Maranas, C.D.; Benkovic, S.J. Creating multiple-crossover DNA libraries independent of sequence identity. Proc. Natl. Acad. Sci. USA, 2001, 98(20), 11248-11253.
[http://dx.doi.org/10.1073/pnas.201413698] [PMID: 11562494]
[21]
Ostermeier, M.; Shim, J.H.; Benkovic, S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol., 1999, 17(12), 1205-1209.
[http://dx.doi.org/10.1038/70754] [PMID: 10585719]
[22]
Sieber, V.; Martinez, C.A.; Arnold, F.H. Libraries of hybrid proteins from distantly related sequences. Nat. Biotechnol., 2001, 19(5), 456-460.
[http://dx.doi.org/10.1038/88129] [PMID: 11329016]
[23]
Stemmer, W.P. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA, 1994, 91(22), 10747-10751.
[http://dx.doi.org/10.1073/pnas.91.22.10747] [PMID: 7938023]
[24]
Zhao, H.; Giver, L.; Shao, Z.; Affholter, J.A.; Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol., 1998, 16(3), 258-261.
[http://dx.doi.org/10.1038/nbt0398-258] [PMID: 9528005]
[25]
Ikehata, H.; Ono, T. The mechanisms of UV mutagenesis. J. Radiat. Res. (Tokyo), 2011, 52(2), 115-125.
[http://dx.doi.org/10.1269/jrr.10175] [PMID: 21436607]
[26]
Balashov, S.; Zafri Humayun, M. Specificity of spontaneous mutations induced in mutA mutator cells. Mutat. Res., 2004, 548(1-2), 9-18.
[http://dx.doi.org/10.1016/j.mrfmmm.2003.12.005] [PMID: 15063131]
[27]
Sharma, P.K.; Kumar, R.; Kumar, R.; Mohammad, O.; Singh, R.; Kaur, J. Engineering of a metagenome derived lipase toward thermal tolerance: Effect of asparagine to lysine mutation on the protein surface. Gene, 2012, 491(2), 264-271.
[http://dx.doi.org/10.1016/j.gene.2011.09.028] [PMID: 22001407]
[28]
Tan, C.; Zhang, X.; Zhu, Z.; Xu, M.; Yang, T.; Osire, T.; Yang, S.; Rao, Z. Asp305Gly mutation improved the activity and stability of the styrene monooxygenase for efficient epoxide production in Pseudomonas putida KT2440. Microb. Cell Fact., 2019, 18(1), 12.
[http://dx.doi.org/10.1186/s12934-019-1065-5] [PMID: 30678678]
[29]
Ben Mabrouk, S.; Zouari Ayadi, D.; Ben Hlima, H.; Bejar, S. Thermostability improvement of maltogenic amylase MAUS149 by error prone PCR. J. Biotechnol., 2013, 168(4), 601-606.
[http://dx.doi.org/10.1016/j.jbiotec.2013.08.026] [PMID: 23994264]
[30]
Li, G.; Maria-Solano, M.A.; Romero-Rivera, A.; Osuna, S.; Reetz, M.T. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem. Commun. (Camb.), 2017, 53(68), 9454-9457.
[http://dx.doi.org/10.1039/C7CC05377K] [PMID: 28795696]
[31]
Huang, R.; Chen, H.; Zhou, W.; Ma, C.; Zhang, Y.H.P. Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro. Appl. Microbiol. Biotechnol., 2018, 102(7), 3203-3215.
[http://dx.doi.org/10.1007/s00253-018-8798-7] [PMID: 29480380]
[32]
Xu, B.L.; Dai, M.; Chen, Y.; Meng, D.; Wang, Y.; Fang, N.; Tang, X.F.; Tang, B. Improving the thermostability and activity of a thermophilic subtilase by incorporating structural elements of its psychrophilic counterpart. Appl. Environ. Microbiol., 2015, 81(18), 6302-6313.
[http://dx.doi.org/10.1128/AEM.01478-15] [PMID: 26150464]
[33]
Wintrode, P.L.; Miyazaki, K.; Arnold, F.H. Cold adaptation of a mesophilic subtilisin-like protease by laboratory evolution. J. Biol. Chem., 2000, 275(41), 31635-31640.
[http://dx.doi.org/10.1074/jbc.M004503200] [PMID: 10906329]
[34]
Liao, H.; McKenzie, T.; Hageman, R. Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc. Natl. Acad. Sci. USA, 1986, 83(3), 576-580.
[http://dx.doi.org/10.1073/pnas.83.3.576] [PMID: 3003740]
[35]
Nishiya, Y.; Harada, N.; Teshima, S.I.; Yamashita, M.; Fujii, I.; Hirayama, N.; Murooka, Y. Improvement of thermal stability of Streptomyces cholesterol oxidase by random mutagenesis and a structural interpretation. Protein Eng. Des. Sel., 1997, 10(3), 231-235.
[http://dx.doi.org/10.1093/protein/10.3.231] [PMID: 9153088]
[36]
Kusumoto, M.; Kishimoto, T.; Nishiya, Y. Improvement of thermal stability of Leuconostoc pseudomesenteroides glucose6-phosphate dehydrogenase. J Anal Bio Sci, 2010, 33(4), 397-400.
[37]
Ohta, Y.; Hatada, Y.; Hidaka, Y.; Shimane, Y.; Usui, K.; Ito, T.; Fujita, K.; Yokoi, G.; Mori, M.; Sato, S.; Miyazaki, T.; Nishikawa, A.; Tonozuka, T. Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 β-fructofuranosidase. Appl. Microbiol. Biotechnol., 2014, 98(15), 6667-6677.
[http://dx.doi.org/10.1007/s00253-014-5645-3] [PMID: 24633372]
[38]
Chokhawala, H.A.; Roche, C.M.; Kim, T.W.; Atreya, M.E.; Vegesna, N.; Dana, C.M.; Blanch, H.W.; Clark, D.S. Mutagenesis of Trichoderma reesei endoglucanase I: impact of expression host on activity and stability at elevated temperatures. BMC Biotechnol., 2015, 15(1), 11.
[http://dx.doi.org/10.1186/s12896-015-0118-z] [PMID: 25879765]
[39]
Hirokawa, K.; Ichiyanagi, A.; Kajiyama, N. Enhancement of thermostability of fungal deglycating enzymes by directed evolution. Appl. Microbiol. Biotechnol., 2008, 78(5), 775-781.
[http://dx.doi.org/10.1007/s00253-008-1363-z] [PMID: 18246344]
[40]
Pratush, A.; Seth, A.; Bhalla, T. Generation of mutant of Rhodococcus rhodochrous PA-34 through chemical mutagenesis for hyperproduction of nitrile hydratase. Acta Microbiol. Immunol. Hung., 2010, 57(2), 135-146.
[http://dx.doi.org/10.1556/AMicr.57.2010.2.6] [PMID: 20587386]
[41]
Miyazaki, K.; Wintrode, P.L.; Grayling, R.A.; Rubingh, D.N.; Arnold, F.H. Directed evolution study of temperature adaptation in a psychrophilic enzyme. J. Mol. Biol., 2000, 297(4), 1015-1026.
[http://dx.doi.org/10.1006/jmbi.2000.3612] [PMID: 10736234]
[42]
Suen, W.C.; Zhang, N.; Xiao, L.; Madison, V.; Zaks, A. Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. Protein Eng. Des. Sel., 2004, 17(2), 133-140.
[http://dx.doi.org/10.1093/protein/gzh017] [PMID: 15047909]
[43]
Giver, L.; Gershenson, A.; Freskgard, P.O.; Arnold, F.H. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA, 1998, 95(22), 12809-12813.
[http://dx.doi.org/10.1073/pnas.95.22.12809] [PMID: 9788996]
[44]
Tang, S.Y.; Le, Q.T.; Shim, J.H.; Yang, S.J.; Auh, J.H.; Park, C.; Park, K.H. Enhancing thermostability of maltogenic amylase from Bacillus thermoalkalophilus ET2 by DNA shuffling. FEBS J., 2006, 273(14), 3335-3345.
[http://dx.doi.org/10.1111/j.1742-4658.2006.05337.x] [PMID: 16857016]
[45]
Zhao, H.; Arnold, F.H. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng. Des. Sel., 1999, 12(1), 47-53.
[http://dx.doi.org/10.1093/protein/12.1.47] [PMID: 10065710]
[46]
Özgün, G.P.; Ordu, E.B.; Tütüncü, H.E. Yelboğa, E.; Sessions, R.B.; Gül Karagüler, N. Site saturation mutagenesis applications on Candida methylica formate dehydrogenase. Scientifica (Cairo), 2016, 2016, 1-7.
[http://dx.doi.org/10.1155/2016/4902450] [PMID: 27847673]
[47]
Andreadeli, A.; Platis, D.; Tishkov, V.; Popov, V.; Labrou, N.E. Structure-guided alteration of coenzyme specificity of formate dehydrogenase by saturation mutagenesis to enable efficient utilization of NADP+. FEBS J., 2008, 275(15), 3859-3869.
[http://dx.doi.org/10.1111/j.1742-4658.2008.06533.x] [PMID: 18616465]
[48]
Takita, T.; Nakatani, K.; Katano, Y.; Suzuki, M.; Kojima, K.; Saka, N.; Mikami, B.; Yatsunami, R.; Nakamura, S.; Yasukawa, K. Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis. Enzyme Microb. Technol., 2019, 130, 109363.
[http://dx.doi.org/10.1016/j.enzmictec.2019.109363] [PMID: 31421720]
[49]
Pan, S.; Yao, T.; Du, L.; Wei, Y. Site-saturation mutagenesis at amino acid 329 of Klebsiella pneumoniae halophilic α-amylase affects enzymatic properties. J. Biosci. Bioeng., 2020, 129(2), 155-159.
[http://dx.doi.org/10.1016/j.jbiosc.2019.09.002] [PMID: 31575478]
[50]
Baba, Y.; Sumitani, J.; Tanaka, K.; Tani, S.; Kawaguchi, T. Site-saturation mutagenesis for β-glucosidase 1 from Aspergillus aculeatus to accelerate the saccharification of alkaline-pretreated bagasse. Appl. Microbiol. Biotechnol., 2016, 100(24), 10495-10507.
[http://dx.doi.org/10.1007/s00253-016-7726-y] [PMID: 27444432]
[51]
Kumar, R.; Sharma, M.; Singh, R.; Kaur, J. Characterization and evolution of a metagenome-derived lipase towards enhanced enzyme activity and thermostability. Mol. Cell. Biochem., 2013, 373(1-2), 149-159.
[http://dx.doi.org/10.1007/s11010-012-1483-8] [PMID: 23104399]
[52]
Akbulut, N. Tuzlakoğlu Öztürk, M.; Pijning, T.; İşsever Öztürk, S.; Gümüşel, F. Improved activity and thermostability of Bacillus pumilus lipase by directed evolution. J. Biotechnol., 2013, 164(1), 123-129.
[http://dx.doi.org/10.1016/j.jbiotec.2012.12.016] [PMID: 23313890]
[53]
Vieille, C.; Zeikus, G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev., 2001, 65(1), 1-43.
[http://dx.doi.org/10.1128/MMBR.65.1.1-43.2001] [PMID: 11238984]
[54]
Kumar, S.; Tsai, C.J.; Nussinov, R. Factors enhancing protein thermostability. Protein Eng. Des. Sel., 2000, 13(3), 179-191.
[http://dx.doi.org/10.1093/protein/13.3.179] [PMID: 10775659]
[55]
Nawani, N.; Kaur, J. Studies on lipolytic isoenzymes from a thermophilic Bacillus sp.: Production, purification and biochemical characterization. Enzyme Microb. Technol., 2007, 40(4), 881-887.
[http://dx.doi.org/10.1016/j.enzmictec.2006.07.006]
[56]
Koyama, Y.; Hidaka, M.; Nishimoto, M.; Kitaoka, M. Directed evolution to enhance thermostability of galacto-N-biose/lacto-N-biose I phosphorylase. Protein Eng. Des. Sel., 2013, 26(11), 755-761.
[http://dx.doi.org/10.1093/protein/gzt049] [PMID: 24065834]
[57]
Kim, Y.W.; Choi, J.H.; Kim, J.W.; Park, C.; Kim, J.W.; Cha, H.; Lee, S.B.; Oh, B.H.; Moon, T.W.; Park, K.H. Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance. Appl. Environ. Microbiol., 2003, 69(8), 4866-4874.
[http://dx.doi.org/10.1128/AEM.69.8.4866-4874.2003] [PMID: 12902281]
[58]
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(3), 348-354.
[http://dx.doi.org/10.1016/j.jbiotec.2006.06.015] [PMID: 16893583]
[59]
Ahmad, S.; Kamal, M.Z.; Sankaranarayanan, R.; Rao, N.M. Thermostable Bacillus subtilis lipases: In vitro evolution and structural insight. J. Mol. Biol., 2008, 381(2), 324-340.
[http://dx.doi.org/10.1016/j.jmb.2008.05.063] [PMID: 18599073]
[60]
Gatti-Lafranconi, P.; Caldarazzo, S.M.; Villa, A.; Alberghina, L.; Lotti, M. Unscrambling thermal stability and temperature adaptation in evolved variants of a cold-active lipase. FEBS Lett., 2008, 582(15), 2313-2318.
[http://dx.doi.org/10.1016/j.febslet.2008.05.037] [PMID: 18534193]
[61]
Zhang, N.; Suen, W.C.; Windsor, W.; Xiao, L.; Madison, V.; Zaks, A. Improving tolerance of Candida antarctica lipase B towards irreversible thermal inactivation through directed evolution. Protein Eng. Des. Sel., 2003, 16(8), 599-605.
[http://dx.doi.org/10.1093/protein/gzg074] [PMID: 12968077]
[62]
Cesarini, S.; Bofill, C.; Pastor, F.I.J.; Reetz, M.T.; Diaz, P. A thermostable variant of P. aeruginosa cold-adapted LipC obtained by rational design and saturation mutagenesis. Process Biochem., 2012, 47(12), 2064-2071.
[http://dx.doi.org/10.1016/j.procbio.2012.07.023]
[63]
Zhang, J.; Lin, Y.; Sun, Y.; Ye, Y.; Zheng, S.; Han, S. High-throughput screening of B factor saturation mutated Rhizomucor miehei lipase thermostability based on synthetic reaction. Enzyme Microb. Technol., 2012, 50(6-7), 325-330.
[http://dx.doi.org/10.1016/j.enzmictec.2012.03.002] [PMID: 22500900]
[64]
Reetz, M.T.; Carballeira, J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc., 2007, 2(4), 891-903.
[http://dx.doi.org/10.1038/nprot.2007.72] [PMID: 17446890]
[65]
Zeymer, C.; Zschoche, R.; Hilvert, D. Optimization of enzyme mechanism along the evolutionary trajectory of a computation-nally designed (retro-)aldolase. J. Am. Chem. Soc., 2017, 139(36), 12541-12549.
[http://dx.doi.org/10.1021/jacs.7b05796] [PMID: 28783336]
[66]
Sharma, M.; Kumar, R.; Singh, R.; Kaur, J. Thirty-degree shift in optimum temperature of a thermophilic lipase by a single-point mutation: effect of serine to threonine mutation on structural flexibility. Mol. Cell. Biochem., 2017, 430(1-2), 21-30.
[http://dx.doi.org/10.1007/s11010-017-2950-z] [PMID: 28190170]
[67]
Bentahir, M.; Feller, G.; Aittaleb, M.; Lamotte-Brasseur, J.; Himri, T.; Chessa, J.P.; Gerday, C. Structural, kinetic, and calorimetric characterization of the cold-active phosphoglycerate kinase from the antarctic Pseudomonas sp. TACII18. J. Biol. Chem., 2000, 275(15), 11147-11153.
[http://dx.doi.org/10.1074/jbc.275.15.11147] [PMID: 10753921]
[68]
Goomber, S.; Kumar, A.; Kaur, J. Disruption of N terminus long range non covalent interactions shifted temp.opt 25°C to cold: Evolution of point mutant Bacillus lipase by error prone PCR. Gene, 2016, 576(1), 237-243.
[http://dx.doi.org/10.1016/j.gene.2015.10.006] [PMID: 26456196]
[69]
Arnold, F.H. Engineering proteins for nonnatural environments. FASEB J., 1993, 7(9), 744-749.
[http://dx.doi.org/10.1096/fasebj.7.9.8330682] [PMID: 8330682]
[70]
Chen, K.; Arnold, F.H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. USA, 1993, 90(12), 5618-5622.
[http://dx.doi.org/10.1073/pnas.90.12.5618] [PMID: 8516309]
[71]
Moore, J.C.; Arnold, F.H. Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nat. Biotechnol., 1996, 14(4), 458-467.
[http://dx.doi.org/10.1038/nbt0496-458] [PMID: 9630920]
[72]
Ren, C.; Wen, X.; Mencius, J.; Quan, S. Selection and screening strategies in directed evolution to improve protein stability. Bioresour. Bioprocess., 2019, 6(1), 53.
[http://dx.doi.org/10.1186/s40643-019-0288-y]
[73]
Fisher, A.C.; Kim, W.; DeLisa, M.P. Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway. Protein Sci., 2006, 15(3), 449-458.
[http://dx.doi.org/10.1110/ps.051902606] [PMID: 16452624]
[74]
Fisher, A.C.; DeLisa, M.P. Efficient isolation of soluble intracellular single-chain antibodies using the twin-arginine translocation machinery. J. Mol. Biol., 2009, 385(1), 299-311.
[http://dx.doi.org/10.1016/j.jmb.2008.10.051] [PMID: 18992254]
[75]
Waraho-Zhmayev, D.; Meksiriporn, B.; Portnoff, A.D.; DeLisa, M.P. Optimizing recombinant antibodies for intracellular function using hitchhiker-mediated survival selection. Protein Eng. Des. Sel., 2014, 27(10), 351-358.
[http://dx.doi.org/10.1093/protein/gzu038] [PMID: 25225416]
[76]
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(1-3), 89-94.
[http://dx.doi.org/10.1016/j.bioeng.2004.10.003] [PMID: 15857788]
[77]
Yin, Q.; Zhou, G.; Peng, C.; Zhang, Y.; Kües, U.; Liu, J.; Xiao, Y.; Fang, Z. The first fungal laccase with an alkaline pH optimum obtained by directed evolution and its application in indigo dye decolorization. AMB Express, 2019, 9(1), 151.
[http://dx.doi.org/10.1186/s13568-019-0878-2] [PMID: 31535295]
[78]
Graber, M.; Irague, R.; Rosenfeld, E.; Lamare, S.; Franson, L.; Hult, K. Solvent as a competitive inhibitor for Candida antarctica lipase B. Biochim. Biophys. Acta. Proteins Proteomics, 2007, 1774(8), 1052-1057.
[http://dx.doi.org/10.1016/j.bbapap.2007.05.013] [PMID: 17602903]
[79]
Kawata, T.; Ogino, H. Enhancement of the organic solvent-stability of the LST-03 lipase by directed evolution. Biotechnol. Prog., 2009, 25(6), NA.
[http://dx.doi.org/10.1002/btpr.264] [PMID: 19731302]
[80]
Dougherty, M.J.; Arnold, F.H. Directed evolution: new parts and optimized function. Curr. Opin. Biotechnol., 2009, 20(4), 486-491.
[http://dx.doi.org/10.1016/j.copbio.2009.08.005] [PMID: 19720520]
[81]
Williams, G.J.; Goff, R.D.; Zhang, C.; Thorson, J.S. Optimizing glycosyltransferase specificity via “hot spot” saturation mutagenesis presents a catalyst for novobiocin glycorandomization. Chem. Biol., 2008, 15(4), 393-401.
[http://dx.doi.org/10.1016/j.chembiol.2008.02.017] [PMID: 18420146]
[82]
Atsumi, S.; Cann, A.F.; Connor, M.R.; Shen, C.R.; Smith, K.M.; Brynildsen, M.P.; Chou, K.J.Y.; Hanai, T.; Liao, J.C. Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng., 2008, 10(6), 305-311.
[http://dx.doi.org/10.1016/j.ymben.2007.08.003] [PMID: 17942358]
[83]
Horton, R.M.; Hunt, H.D.; Ho, S.N.; Pullen, J.K.; Pease, L.R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene, 1989, 77(1), 61-68.
[http://dx.doi.org/10.1016/0378-1119(89)90359-4] [PMID: 2744488]
[84]
Heckman, K.L.; Pease, L.R. Gene splicing and mutagenesis by PCR-driven overlap extension. Nat. Protoc., 2007, 2(4), 924-932.
[http://dx.doi.org/10.1038/nprot.2007.132] [PMID: 17446874]
[85]
Bryksin, A.V.; Matsumura, I. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. Biotechniques, 2010, 48(6), 463-465.
[http://dx.doi.org/10.2144/000113418] [PMID: 20569222]
[86]
Guo, W.; Xie, B.; Jiang, M.; Zhu, X.J.; Qiu, M.; Dai, Z.M. An improved overlap extension PCR for simultaneous multiple sites large fragments insertion, deletion and substitution. Sci. Rep., 2019, 9(1), 15637.
[http://dx.doi.org/10.1038/s41598-019-52122-8]
[87]
Wells, J.A.; Vasser, M.; Powers, D.B. Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites. Gene, 1985, 34(2-3), 315-323.
[http://dx.doi.org/10.1016/0378-1119(85)90140-4] [PMID: 3891521]
[88]
Irfan, M.; Gonzalez, C.F.; Raza, S.; Rafiq, M.; Hasan, F.; Khan, S.; Shah, A.A. Improvement in thermostability of xylanase from Geobacillus thermodenitrificans C5 by site directed mutagenesis. Enzyme Microb. Technol., 2018, 111, 38-47.
[http://dx.doi.org/10.1016/j.enzmictec.2018.01.004] [PMID: 29421035]
[89]
Han, C.; Li, W.; Hua, C.; Sun, F.; Bi, P.; Wang, Q. Enhancement of catalytic activity and thermostability of a thermostable cellobiohydrolase from Chaetomium thermophilum by site-directed mutagenesis. Int. J. Biol. Macromol., 2018, 116, 691-697.
[http://dx.doi.org/10.1016/j.ijbiomac.2018.05.088] [PMID: 29775713]
[90]
Emruzi, Z.; Aminzadeh, S.; Karkhane, A.A.; Alikhajeh, J.; Haghbeen, K.; Gholami, D. Improving the thermostability of Serratia marcescens B4A chitinase via G191V site-directed mutagenesis. Int. J. Biol. Macromol., 2018, 116, 64-70.
[http://dx.doi.org/10.1016/j.ijbiomac.2018.05.014] [PMID: 29733926]
[91]
Chopra, N.; Kumar, A.; Kaur, J. Structural and functional insights into thermostable and organic solvent stable variant Pro247-Ser of Bacillus lipase. Int. J. Biol. Macromol., 2018, 108, 845-852.
[http://dx.doi.org/10.1016/j.ijbiomac.2017.10.176] [PMID: 29101046]
[92]
Zuo, W.; Nie, L.; Baskaran, R.; Kumar, A.; Liu, Z. Characterization and improved properties of Glutamine synthetase from Providencia vermicola by site-directed mutagenesis. Sci. Rep., 2018, 8(1), 15640.
[http://dx.doi.org/10.1038/s41598-018-34022-5] [PMID: 30353099]
[93]
Zhong, C.Q.; Song, S.; Fang, N.; Liang, X.; Zhu, H.; Tang, X.F.; Tang, B. Improvement of low-temperature caseinolytic activity of a thermophilic subtilase by directed evolution and site-directed mutagenesis. Biotechnol. Bioeng., 2009, 104(5), 862-870.
[http://dx.doi.org/10.1002/bit.22473] [PMID: 19609954]
[94]
Gao, H.; Li, C.; Bandikari, R.; Liu, Z.; Hu, N.; Yong, Q. A novel cold-adapted esterase from Enterobacter cloacae: Characterization and improvement of its activity and thermostability via the site of Tyr193Cys. Microb. Cell Fact., 2018, 17(1), 45.
[http://dx.doi.org/10.1186/s12934-018-0885-z]
[95]
Takagi, H.; Morinaga, Y.; Ikemura, H.; Inouye, M. Mutant subtilisin E with enhanced protease activity obtained by site-directed mutagenesis. J. Biol. Chem., 1988, 263(36), 19592-19596.
[http://dx.doi.org/10.1016/S0021-9258(19)77677-7] [PMID: 3143728]
[96]
Sriprapundh, D.; Vieille, C.; Zeikus, J.G. Molecular determinants of xylose isomerase thermal stability and activity: analysis of thermozymes by site-directed mutagenesis. Protein Eng. Des. Sel., 2000, 13(4), 259-265.
[http://dx.doi.org/10.1093/protein/13.4.259] [PMID: 10810157]
[97]
Toyama, M.; Yamashita, M.; Yoneda, M.; Zaborowski, A.; Nagato, M.; Ono, H.; Hirayama, N.; Murooka, Y. Alteration of substrate specificity of cholesterol oxidase from Streptomyces sp. by site-directed mutagenesis. Protein Eng. Des. Sel., 2002, 15(6), 477-483.
[http://dx.doi.org/10.1093/protein/15.6.477] [PMID: 12082166]
[98]
Chow, J.Y.; Xue, B.; Lee, K.H.; Tung, A.; Wu, L.; Robinson, R.C.; Yew, W.S. Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily. J. Biol. Chem., 2010, 285(52), 40911-40920.
[http://dx.doi.org/10.1074/jbc.M110.177139] [PMID: 20980257]
[99]
Pazmiño, D.E.T.; Snajdrova, R.; Rial, D.V.; Mihovilovic, M.D.; Fraaije, M.W. Altering the substrate specificity and enantioselectivity of phenylacetone monooxygenase by structure-inspired enzyme redesign. Adv. Synth. Catal., 2007, 349(8-9), 1361-1368.
[http://dx.doi.org/10.1002/adsc.200700045]
[100]
Gao, B.; Xu, T.; Lin, J.; Zhang, L.; Su, E.; Jiang, Z.; Wei, D. Improving the catalytic activity of lipase LipK107 from Proteus sp. by site-directed mutagenesis in the lid domain based on computer simulation. J. Mol. Catal., B Enzym., 2011, 68(3-4), 286-291.
[http://dx.doi.org/10.1016/j.molcatb.2010.12.001]
[101]
Godinho, L.F.; Reis, C.R.; Rozeboom, H.J.; Dekker, F.J.; Dijkstra, B.W.; Poelarends, G.J.; Quax, W.J. Enhancement of the enantioselectivity of carboxylesterase A by structure-based mutagenesis. J. Biotechnol., 2012, 158(1-2), 36-43.
[http://dx.doi.org/10.1016/j.jbiotec.2011.12.026] [PMID: 22248594]
[102]
Kumar, R.; Singh, R.; Kaur, J. Combinatorial reshaping of a lipase structure for thermostability: Additive role of surface stabilizing single point mutations. Biochem. Biophys. Res. Commun., 2014, 447(4), 626-632. a
[http://dx.doi.org/10.1016/j.bbrc.2014.04.051] [PMID: 24751523]
[103]
Wang, Y.; Fu, Z.; Huang, H.; Zhang, H.; Yao, B.; Xiong, H.; Turunen, O. Improved thermal performance of Thermomyces lanuginosus GH11 xylanase by engineering of an N-terminal disulfide bridge. Bioresour. Technol., 2012, 112, 275-279. b
[http://dx.doi.org/10.1016/j.biortech.2012.02.092] [PMID: 22425398]
[104]
Ding, H.; Gao, F.; Liu, D.; Li, Z.; Xu, X.; Wu, M.; Zhao, Y. Significant improvement of thermal stability of glucose 1-dehydrogenase by introducing disulfide bonds at the tetramer interface. Enzyme Microb. Technol., 2013, 53(6-7), 365-372.
[http://dx.doi.org/10.1016/j.enzmictec.2013.08.001] [PMID: 24315638]
[105]
Le, Q.A.T.; Joo, J.C.; Yoo, Y.J.; Kim, Y.H. Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge. Biotechnol. Bioeng., 2012, 109(4), 867-876.
[http://dx.doi.org/10.1002/bit.24371] [PMID: 22095554]
[106]
Zhang, L.; Tang, X.; Cui, D.; Yao, Z.; Gao, B.; Jiang, S.; Yin, B.; Yuan, Y.A.; Wei, D. A method to rationally increase protein stability based on the charge-charge interaction, with application to lipase LipK107. Protein Sci., 2014, 23(1), 110-116.
[http://dx.doi.org/10.1002/pro.2388] [PMID: 24353171]
[107]
Gribenko, A.V.; Patel, M.M.; Liu, J.; McCallum, S.A.; Wang, C.; Makhatadze, G.I. Rational stabilization of enzymes by computational redesign of surface charge–charge interactions. Proc. Natl. Acad. Sci. USA, 2009, 106(8), 2601-2606.
[http://dx.doi.org/10.1073/pnas.0808220106] [PMID: 19196981]
[108]
Yang, G.; Yao, H.; Mozzicafreddo, M.; Ballarini, P.; Pucciarelli, S.; Miceli, C. Rational engineering of a cold-adapted α-amylase from the antarctic ciliate Euplotes focardii for simultaneous improvement of thermostability and catalytic activity. Appl. Environ. Microbiol., 2017, 83(13), e00449-e17.
[http://dx.doi.org/10.1128/AEM.00449-17] [PMID: 28455329]
[109]
Goomber, S.; Kumar, A.; Singh, R.; Kaur, J. Point mutation Ile137-Met near surface conferred psychrophilic behaviour and improved catalytic efficiency to Bacillus lipase of 1.4 subfamily. Appl. Biochem. Biotechnol., 2016, 178(4), 753-765.
[http://dx.doi.org/10.1007/s12010-015-1907-5] [PMID: 26520838]
[110]
Kumar, V.; Yedavalli, P.; Gupta, V.; Rao, N.M. Engineering lipase A from mesophilic Bacillus subtilis for activity at low temperatures. Protein Eng. Des. Sel., 2014, 27(3), 73-82. b
[http://dx.doi.org/10.1093/protein/gzt064] [PMID: 24402332]
[111]
Schmitt, J.; Brocca, S.; Schmid, R.D.; Pleiss, J. Blocking the tunnel: Engineering of Candida rugosa lipase mutants with short chain length specificity. Protein Eng. Des. Sel., 2002, 15(7), 595-601.
[http://dx.doi.org/10.1093/protein/15.7.595] [PMID: 12200542]
[112]
Wang, Y.B.; Yu, P.; Zhou, Z.P.; Zhang, J.; Wang, J.J.; Luo, S-H.; Gu, Q-S.; Houk, K.N.; Tan, B. Rational design, enantioselective synthesis and catalytic applications of axially chiral EBINOLs. Nat. Catal., 2019, 2(6), 504-513.
[http://dx.doi.org/10.1038/s41929-019-0278-7]
[113]
Rotticci, D.; Rotticci-Mulder, J.C.; Denman, S.; Norin, T.; Hult, K. Improved enantioselectivity of a lipase by rational protein engineering. ChemBioChem, 2001, 2(10), 766-770.
[http://dx.doi.org/10.1002/1439-7633(20011001)2:10<766:AID-CBIC766>3.0.CO;2-K] [PMID: 11948859]
[114]
Ema, T.; Fujii, T.; Ozaki, M.; Korenaga, T.; Sakai, T. Rational control of enantioselectivity of lipase by site-directed mutagenesis based on the mechanism. Chem. Commun. (Camb.), 2005, 7(37), 4650-4651.
[http://dx.doi.org/10.1039/b508244g] [PMID: 16175280]
[115]
Santoro, S.W.; Schultz, P.G. Directed evolution of the site specificity of Cre recombinase. Proc. Natl. Acad. Sci. USA, 2002, 99(7), 4185-4190.
[http://dx.doi.org/10.1073/pnas.022039799] [PMID: 11904359]
[116]
Rui, L.; Cao, L.; Chen, W.; Reardon, K.F.; Wood, T.K. Protein engineering of epoxide hydrolase from Agrobacterium radiobacter AD1 for enhanced activity and enantioselective production of (R)-1-phenylethane-1,2-diol. Appl. Environ. Microbiol., 2005, 71(7), 3995-4003.
[http://dx.doi.org/10.1128/AEM.71.7.3995-4003.2005] [PMID: 16000814]
[117]
Mayer, C.; Dulson, C.; Reddem, E.; Thunnissen, A.W.H.; Roelfes, G. Directed evolution of a designer enzyme featuring an unnatural catalytic amino acid. Angew. Chem. Int. Ed. Engl., 2019, 58(7), 2083-2087.
[http://dx.doi.org/10.1002/anie.201813499]
[118]
Giger, L.; Caner, S.; Obexer, R.; Kast, P.; Baker, D.; Ban, N.; Hilvert, D. Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat. Chem. Biol., 2013, 9(8), 494-498.
[http://dx.doi.org/10.1038/nchembio.1276] [PMID: 23748672]
[119]
Drienovská, I.; Mayer, C.; Dulson, C.; Roelfes, G. A designer enzyme for hydrazone and oxime formation featuring an unnatural catalytic aniline residue. Nat. Chem., 2018, 10(9), 946-952.
[http://dx.doi.org/10.1038/s41557-018-0082-z] [PMID: 29967395]
[120]
Hooks, D.O.; Rehm, B.H.A. Surface display of highly-stable Desulfovibrio vulgaris carbonic anhydrase on polyester beads for CO2 capture. Biotechnol. Lett., 2015, 37(7), 1415-1420.
[http://dx.doi.org/10.1007/s10529-015-1803-7] [PMID: 25773195]
[121]
Ruslan, R.; Rahman, R.N.Z.R.A.; Leow, T.C.; Ali, M.S.M.; Basri, M.; Salleh, A.B. Improvement of thermal stability via outer-loop ion pair interaction of mutated T1 lipase from Geobacillus zalihae strain T1. Int. J. Mol. Sci., 2012, 13(1), 943-960.
[http://dx.doi.org/10.3390/ijms13010943] [PMID: 22312296]
[122]
Alvizo, O.; Nguyen, L.J.; Savile, C.K.; Bresson, J.A.; Lakhapatri, S.L.; Solis, E.O.P.; Fox, R.J.; Broering, J.M.; Benoit, M.R.; Zimmerman, S.A.; Novick, S.J.; Liang, J.; Lalonde, J.J. Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas. Proc. Natl. Acad. Sci. USA, 2014, 111(46), 16436-16441.
[http://dx.doi.org/10.1073/pnas.1411461111] [PMID: 25368146]
[123]
Crean, R.M.; Gardner, J.M.; Kamerlin, S.C.L. Harnessing conformational plasticity to generate designer enzymes. J. Am. Chem. Soc., 2020, 142(26), 11324-11342.
[http://dx.doi.org/10.1021/jacs.0c04924] [PMID: 32496764]
[124]
Althoff, E.A.; Wang, L.; Jiang, L.; Giger, L.; Lassila, J.K.; Wang, Z.; Smith, M.; Hari, S.; Kast, P.; Herschlag, D.; Hilvert, D.; Baker, D. Robust design and optimization of retroaldol enzymes. Protein Sci., 2012, 21(5), 717-726.
[http://dx.doi.org/10.1002/pro.2059] [PMID: 22407837]
[125]
Garrabou, X.; Beck, T.; Hilvert, D. A promiscuous de novo retro-aldolase catalyzes asymmetric michael additions via schiff base intermediates. Angew. Chem. Int. Ed., 2015, 54(19), 5609-5612.
[http://dx.doi.org/10.1002/anie.201500217] [PMID: 25777153]
[126]
Garrabou, X.; Wicky, B.I.M.; Hilvert, D. Fast knoevenagel condensations catalyzed by an artificial schiff-base-forming enzyme. J. Am. Chem. Soc., 2016, 138(22), 6972-6974.
[http://dx.doi.org/10.1021/jacs.6b00816] [PMID: 27196438]
[127]
Romero-Rivera, A.; Garcia-Borràs, M.; Osuna, S. Role of conformational dynamics in the evolution of retro-aldolase activity. ACS Catal., 2017, 7(12), 8524-8532.
[http://dx.doi.org/10.1021/acscatal.7b02954] [PMID: 29226011]
[128]
Davey, J.A.; Chica, R.A. Multistate approaches in computational protein design. Protein Sci., 2012, 21(9), 1241-1252.
[http://dx.doi.org/10.1002/pro.2128] [PMID: 22811394]
[129]
Hilvert, D. Design of protein catalysts. Annu. Rev. Biochem., 2013, 82(1), 447-470.
[http://dx.doi.org/10.1146/annurev-biochem-072611-101825] [PMID: 23746259]
[130]
Khare, S.D.; Fleishman, S.J. Emerging themes in the computational design of novel enzymes and protein-protein interfaces. FEBS Lett., 2013, 587(8), 1147-1154.
[http://dx.doi.org/10.1016/j.febslet.2012.12.009] [PMID: 23262222]
[131]
Allinger, N.L.; Miller, M.A.; Chow, L.W.; Ford, R.A.; Graham, J.C. The calculated electronic spectra and structures of some cyclic conjugated hydrocarbons. J. Am. Chem. Soc., 1965, 87(15), 3430-3435.
[http://dx.doi.org/10.1021/ja01093a025]
[132]
Allinger, N.L.; Miller, M.A.; Van Catledge, F.A.; Hirsch, J.A. Conformational analysis. LVII. The calculation of the conformational structures of hydrocarbons by the Westheimer-Hendrickson-Wiberg method. J. Am. Chem. Soc., 1967, 89(17), 4345-4357.
[http://dx.doi.org/10.1021/ja00993a017]
[133]
Bixon, M.; Lifson, S. Potential functions and conformations in cycloalkanes. Tetrahedron, 1967, 23(2), 769-784.
[http://dx.doi.org/10.1016/0040-4020(67)85023-3]
[134]
Levitt, M.; Warshel, A. Computer simulation of protein folding. Nature, 1975, 253(5494), 694-698.
[http://dx.doi.org/10.1038/253694a0] [PMID: 1167625]
[135]
Lifson, S.; Warshel, A. Consistent force field for calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n ‐alkane molecules. J. Chem. Phys., 1968, 49(11), 5116-5129.
[http://dx.doi.org/10.1063/1.1670007]
[136]
Schafer, J.W.; Zoi, I.; Antoniou, D.; Schwartz, S.D. Optimization of the turnover in artificial enzymes via directed evolution results in the coupling of protein dynamics to chemistry. J. Am. Chem. Soc., 2019, 141(26), 10431-10439.
[http://dx.doi.org/10.1021/jacs.9b04515] [PMID: 31199129]
[137]
Obexer, R.; Godina, A.; Garrabou, X.; Mittl, P.R.E.; Baker, D.; Griffiths, A.D.; Hilvert, D. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat. Chem., 2017, 9(1), 50-56.
[http://dx.doi.org/10.1038/nchem.2596] [PMID: 27995916]
[138]
Chen, M.; Chen, L.; Zeng, A.P. CRISPR/Cas9-facilitated engineering with growth-coupled and sensor-guided in vivo screening of enzyme variants for a more efficient chorismate pathway in E. coli. Metab. Eng. Commun., 2019, 9, e00094.
[http://dx.doi.org/10.1016/j.mec.2019.e00094] [PMID: 31193188]
[139]
Cho, S.; Shin, J.; Cho, B.K. Applications of CRISPR/Cas System to Bacterial Metabolic Engineering. Int. J. Mol. Sci., 2018, 19(4), 1089.
[http://dx.doi.org/10.3390/ijms19041089] [PMID: 29621180]
[140]
Zhang, J.; Zong, W.; Hong, W.; Zhang, Z.T.; Wang, Y. Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production. Metab. Eng., 2018, 47, 49-59. a
[http://dx.doi.org/10.1016/j.ymben.2018.03.007] [PMID: 29530750]
[141]
Guo, X.; Chavez, A.; Tung, A.; Chan, Y.; Kaas, C.; Yin, Y.; Cecchi, R.; Garnier, S.L.; Kelsic, E.D.; Schubert, M.; DiCarlo, J.E.; Collins, J.J.; Church, G.M. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast. Nat. Biotechnol., 2018, 36(6), 540-546.
[http://dx.doi.org/10.1038/nbt.4147] [PMID: 29786095]
[142]
Börner, R.A.; Kandasamy, V.; Axelsen, A.M.; Nielsen, A.T.; Bosma, E.F. Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech. FEMS Microbiol. Lett., 2019, 366(1), fny291.
[http://dx.doi.org/10.1093/femsle/fny291] [PMID: 30561594]
[143]
Zhang, K.; Duan, X.; Wu, J. Multigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/Cas9 system. Sci. Rep., 2016, 6(1), 27943.
[http://dx.doi.org/10.1038/srep27943] [PMID: 27305971]
[144]
Zhang, K.; Su, L.; Wu, J. Enhanced extracellular pullulanase production in Bacillus subtilis using protease-deficient strains and optimal feeding. Appl. Microbiol. Biotechnol., 2018, 102(12), 5089-5103.
[http://dx.doi.org/10.1007/s00253-018-8965-x] [PMID: 29675805]
[145]
Salazar-Cerezo, S.; Kun, R.S.; de Vries, R.P.; Garrigues, S. CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer. Enzyme Microb. Technol., 2020, 133, 109463.
[http://dx.doi.org/10.1016/j.enzmictec.2019.109463] [PMID: 31874686]
[146]
Li, H.; Shen, C.R.; Huang, C.H.; Sung, L.Y.; Wu, M.Y.; Hu, Y.C. CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production. Metab. Eng., 2016, 38, 293-302.
[http://dx.doi.org/10.1016/j.ymben.2016.09.006] [PMID: 27693320]
[147]
Wasels, F.; Jean-Marie, J.; Collas, F.; López-Contreras, A.M.; Lopes Ferreira, N. A two-plasmid inducible CRISPR/Cas9 genome editing tool for Clostridium acetobutylicum. J. Microbiol. Methods, 2017, 140, 5-11.
[http://dx.doi.org/10.1016/j.mimet.2017.06.010] [PMID: 28610973]
[148]
Westbrook, A.W.; Moo-Young, M.; Chou, C.P. Development of a CRISPR-Cas9 Tool Kit for comprehensive engineering of Bacillus subtilis. Appl. Environ. Microbiol., 2016, 82(16), 4876-4895.
[http://dx.doi.org/10.1128/AEM.01159-16] [PMID: 27260361]

Rights & Permissions Print Cite
Article Metrics
45
3
© 2024 Bentham Science Publishers | Privacy Policy