In vitro engineering of microbial enzymes with multifarious applications: Prospects and perspectives

Bioresource Technology

Volumn 176, Issue , 2015, Pages 273-283

  Joshi, Swati ^a   Satyanarayana, Tulasi ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

In vitro evolution; Industrial biotechnology; Microbial enzymes; Protein engineering; Site directed mutagenesis

Indexed keywords

BIOCHEMICAL ENGINEERING; BIODEGRADATION; BIOINFORMATICS; BIOTECHNOLOGY;

IN-VITRO; INDUSTRIAL BIOTECHNOLOGY; MICROBIAL ENZYMES; PROTEIN ENGINEERING; SITE DIRECTED MUTAGENESIS;

ENZYMES;

BIOFUEL; DETERGENT; HYDROLASE; INDUSTRIAL ENZYME; MICROBIAL ENZYME; PROTEINASE; BACTERIAL PROTEIN; ENZYME; FUNGAL PROTEIN;

BIOENGINEERING; BIOINFORMATICS; ENZYME ACTIVITY; INDUSTRIAL PRACTICE; MICROBIAL ACTIVITY; PROTEIN;

AMINO ACID SEQUENCE; BIOINFORMATICS; BIOTECHNOLOGY; DATA BASE; FOOD INDUSTRY; IN VITRO STUDY; MUTAGENESIS; NONHUMAN; PROTEIN ENGINEERING; REVIEW; SITE DIRECTED MUTAGENESIS; BIOENGINEERING; CHEMICAL STRUCTURE; CHEMISTRY; PROCEDURES; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; TRENDS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOENGINEERING; ENZYMES; FUNGAL PROTEINS; MODELS, MOLECULAR; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 84913582337     PISSN: 09608524     EISSN: 18732976     Source Type: Journal    
DOI: 10.1016/j.biortech.2014.10.151     Document Type: Review

References (74)

1. Araujo R., Casal M., Cavaco-Paulo A. Part I - Technologies involved in textile biotechnology. Design and engineering of novel enzymes for textile applications. Advances in Textile Biotechnology 2010, 3-31. Woodhead Publishing Ltd., Cambridge. V. Nierstrasz, A. Cavaco-Paulo (Eds.).
2. Aronson N.N., Halloran B.A., Alexeyev M.F., Zhou X.E., Wang Y., Meehan E.J. Mutation of a conserved tryptophan in the chitin binding cleft of Serratia marcescens chitinase A enhances transglycosylation. Biosci. Biotechnol. Biochem. 2006, 70:243-251.
3. Autore F., Vecchio C.D., Fraternali F., Giardina P., Sannia G., Faraco V. Molecular determinants of peculiar properties of a Pleurotus ostreatus laccase: analysis by site-directed mutagenesis. Enzyme Microb. Technol. 2009, 45:507-513.
4. Bei J., Chen Z., Fua J., Jiang Z., Wang J., Wang X. Structure-based fragment shuffling of two fungal phytases for combination of desirable properties. J. Biotechnol. 2009, 139:86-193.
5. Boer H., Simolin H., Cottaz S., Soderlund H., Koivula A. Heterologous expression and site-directed mutagenesis studies of two Trichoderma harzianum chitinases, Chit33 and Chit42, in Escherichia coli. Protein Expr. Purif. 2007, 51:216-226.
6. Chai W., Sha L., Zhou J., Huang Z., Guan X. Functional analysis of active site residues of Bacillus thuringiensis WB7 chitinase by site-directed mutagenesis. World J. Microbiol. Biotechnol. 2009, 25:2147-2155.
7. Chang Y.S., Ko T.P., Huang J.W., Wu T.H., Lin C.Y., Luo W., Li Q., Ma Y., Huang C.H., Wang A.H., Liu J.R., Guo R.T. Enhanced activity of Thermotoga maritima cellulase 12A by mutating a unique surface loop. Appl. Microbiol. Biotechnol. 2012, 95:661-669.
8. Chen X., Xu S., Zhu M., Cui L., Zhu H., Liang Y., Zhang Z. Site-directed mutagenesis of an Aspergillus niger xylanase B and its expression, purification and enzymatic characterization in Pichia pastoris. Process Biochem. 2010, 45:75-80.
9. Chen Y.C., Chiang Y.C., Hsu F.Y., Tsai L.C., Cheng H.L. Structural modeling and further improvement in pH stability and activity of a highly-active xylanase from an uncultured rumen fungus. Bioresour. Technol. 2012, 123:125-134.
10. Chiang L.W., Kovari I., Howe M.M. Mutagenic oligonucleotide-directed PCR amplification (Mod-PCR): an efficient method for generating random base substitution mutations in a DNA sequence element. PCR Methods Appl. 1993, 2:210-217.
11. Coco W.M., Levinson W.E., Crist M.J., Hektor H.J., Darzins A., Pienkos P.T., Squires C.H., Monticello D.J. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat. Biotechnol. 2001, 19:354-359.
12. Dennig A., Shivange A.V., Marienhagen J., Schwaneberg U. OmniChange: the sequence independent method for simultaneous site-saturation of five codons. PLoS One 2011, 6:e26222.
13. Dror A., Shemesh E., Dayan N., Fishman A. Protein engineering by random mutagenesis and structure guided consensus of Geobacillus stearothermophilus lipase T6 for enhanced stability in methanol. Appl. Environ. Microbiol. 2014, 80:1515-1527.
14. Duan X., Chen J., Wu J. Improving the thermostability and catalytic efficiency of Bacillus deramificans pullulanase by site-directed mutagenesis. Appl. Environ. Microbiol. 2013, 79:4072-4077.
15. 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. 2005, 37:4650-4651.
16. Engstrom K., Nyhlen J., Sandstrom A.G., Backvall J.E. Directed evolution of an enantioselective lipase with broad substrate scope for hydrolysis of r-substituted esters. J. Am. Chem. Soc. 2010, 132:7038-7042.
17. Fa M., Radeghieri A., Henry A., Romesberg F. Expanding the substrate repertoire of a DNA polymerase by directed evolution. J. Am. Chem. Soc. 2004, 126:1748-1754.
18. Farhat-Khemakhem A., Ali M.B., Boukhris I., Khemakhem B., Maguin E., Bejar S., Chouayekh H. Crucial role of Pro 257 in the thermostability of Bacillus phytases: biochemical and structural investigation. Int. J. Biol. Macromol. 2013, 54:9-15.
19. Garrett J.B., Kretz K.A., O'Donoghue E., Kerovuo J., Kim W., Barton N.R., Hazlewood G.P., Short J.M., Robertson D.E., Gray K.A. Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement. Appl. Environ. Microbiol. 2004, 70:3041-3046.
20. Ghadessy F.J., Ramsay N., Boudsocq F., Loakes D., Brown A., Iwai S., Vaisman A., Woodgate R., Holliger P. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat. Biotechnol. 2004, 22:755-759.
21. Gupta N., Farinas E.T. Directed evolution of CotA laccase for increased substrate specificity using Bacillus subtilis spores. Protein Eng. Des. Sel. 2010, 23:679-682.
22. Hahn V.V., Kim K. Improvement of cellulase activity using error-prone rolling circle amplification and site-directed mutagenesis. J. Microbiol. Biotechnol. 2012, 22:607-613.
23. Han M., Wanga X., Yana G., Wang W., Taoa Y., Liua X., Caoa H., Yu X. Modification of recombinant elastase expressed in Pichia pastoris by introduction of N-glycosylation sites. J. Biotechnol. 2014, 171:3-7.
24. Hara M., Sugimoto H., Uemura M., Akagi K.I., Suzuki K., Ikegami T., Watanabe T. Involvement of Gln679, in addition to Trp687, in chitin-binding activity of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12. J. Biochem. 2013, 154:185-193.
25. Hokanson C.A., Cappuccilli G., Odineca T., Bozic M., Behnke C.A., Mendez M., Coleman W.J., Crea R. Engineering highly thermostable xylanase variants using an enhanced combinatorial library method. Protein Eng. Des. Sel. 2011, 24:597-605.
26. Inoue T., Takao K., Yoshida T., Wada K., Daifuku T., Yoneda Y., Fukuyama K., Sako Y. Cysteine 295 indirectly affects Ni coordination of carbon monoxide dehydrogenase-II C-cluster. Biochem. Biophys. Res. Commun. 2013, 441:13-17.
27. Irani M., Tornavall U., Genheden S., Larsen M.W., Kaul R.H., Ryde U. Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics and site directed mutagenesis. Biochemistry 2013, 52:1280-1289.
28. Joo J.C., Pack S.P., Kimc Y.H., Yooa Y.J. Thermostabilization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. J. Biotechnol. 2011, 151:56-65.
29. Joshi S., Satyanarayana T. Biotechnology of cold-active proteases. Biology 2013, 2:755-783.
30. Kachan A.V., Evtushenkov A.N. Thermostable mutant variants of Bacillus sp.406 α-amylase generated by site-directed mutagenesis. Cent. Eur. J. Biol. 2013, 8:346-356.
31. Kegler-Ebo D.M., Docktor C.M., DiMaio D. Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes. Nucleic Acids Res. 1994, 22:1593-1599.
32. Kim T., Mullaney E.J., Porres J.M., Roneker K.R., Crowe S., Rice S., et al. Shifting the pH profile of Aspergillus niger PhyA phytase to match the stomach pH enhances its effectiveness as an animal feed additive. Appl. Environ. Microbiol. 2006, 72:4397-4403.
33. Koschorreck K., Schmid R.D., Urlacher V.B. Improving the functional expression of a Bacillus licheniformis laccase by random and site-directed mutagenesis. BMC Biotechnol. 2009, 9:12.
34. 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, 26:755-761.
35. Kumari A., Gupta R. Phenylalanine to leucine point mutation in oxyanion 1 hole improved catalytic efficiency of Lip12 from Yarrowia lipolytica. Enzyme Microb. Technol. 2013, 53:386-390.
36. Le Q.A., 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, 109:867-876.
37. Mabrouk S.B., Ayadi-Zouari D., Hlima H.B., Bejar S. Changes in the catalytic properties and substrate specificity of Bacillus sp. US149 maltogenic amylase by mutagenesis of residue 46. J. Ind. Microbiol. Biotechnol. 2013, 40:947-953.
38. Mate D., Garcia-Burgos C., Garcia-Ruiz E., Ballesteros A., Camarero S., Alcalde M. Laboratory evolution of high-redox potential laccases. Chem. Biol. 2010, 17:1030-1041.
39. Mehta D., Satyanarayana T. Dimerization mediates thermo-adaptation, substrate affinity and transglycosylation in a highly thermostable maltogenic amylase of Geobacillus thermoleovorans. PLoS One 2013, 8:e73612.
40. Misset O. Developments of new lipases. Enzymes in Detergency 1997, 107-133. Marcel Dekker Inc., New York. J.H. Ee, O. Misset, E.J. Bass (Eds.).
41. Mullaney M., Sethumadhavan K., Boone S., Lei X.G., Ullah A.H.J. Elimination of a disulfide bridge in Aspergillus niger NRRL 3135 phytase (PhyA) enhances heat tolerance and optimizes its temperature versus activity profile. Adv. Biol. Chem. 2012, 2:372-378.
42. 2+ binding to the ExDxD motif regulate the DNA cleavage specificity of a promiscuous endonuclease. Biochemistry 2012, 51:8939-8949.
43. Ni J., Takehara M., Watanabe H. Identification of activity related amino acid mutations of a GH9 termite cellulase. Bioresour. Technol. 2010, 101:6438-6443.
44. Ong J.L., Loakes D., Too S.J.K., Holliger P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J. Mol. Biol. 2006, 361:537-550.
45. Ortiz V.R., Heins R.A., Cheng G., Kim E.Y., Vernon B.C., Elandt R.B., Adams P.D., Sale K.L., Hadi M.Z., Simmons B.A., Kent M.S., Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol. Biofuels 2013, 6:93.
46. Ozturk H., Ece S., Gundeger S., Evran S. Site-directed mutagenesis of methionine residues for improving the oxidative stability of α-amylase from Thermotoga maritima. J. Biosci. Bioeng. 2013, 116:449-451.
47. Paes G., O'Donohue M.J. Engineering increased thermostability in the thermostable GH-11 xylanase from Thermobacillus xylanilyticus. J. Biotechnol. 2006, 125:338-350.
48. Pei X.Q., Yi Z.L., Tang C.G., Wu Z.L. Three amino acid changes contribute markedly to the thermostability β-glucosidase BglC from Thermobifida fusca. Bioresour. Technol. 2011, 102:3337-3342.
49. Rahimzadeh M., Khajeha K., Mirshahia M., Khayatianb M., Schwarzenbacherc R. Probing the role of asparagine mutation in thermostability of Bacillus KR-8104 α-amylase. Int. J. Biol. Macromol. 2012, 50:1175-1182.
50. Rajput R., Tiwary E., Sharma R., Gupta R. Swapping of pro-sequences between keratinases of Bacillus licheniformis and Bacillus pumilus: altered substrate specificity and thermostability. Enzyme Microb. Technol. 2012, 51:131-138.
51. Rha E., Kim S., Choi S.L., Hong S.P., Sung M.H., Song J.J., Lee S.G. Simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol-lyase by directed evolution. FEBS J. 2009, 276:6187-6194.
52. Sharma N., Rathore M., Sharma M. Microbial pectinase: sources, characterization and applications. Rev. Environ. Sci. Biotechnol. 2013, 12:45-60.
53. Sherif M., Waung D., Korbeci B., Mavisakalyan V., Flick R., Brown G., et al. Biochemical studies of the multicopper oxidase (small. laccase) from Streptomyces coelicolor using bioactive phytochemicals and site-directed mutagenesis. Microb. Biotechnol. 2013, 6:588-597.
54. Sipma J., Henstra A.M., Parshina S.N., Lens P.N.L., Lettinga G., Stams A.J.M. Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization. Crit. Rev. Biotechnol. 2006, 26:41-65.
55. Solbak A.I., Richardson T.H., McCann R.T., Kline K.A., Bartnek F., Tomlinson G., Tan X., Parra-Gessert L., Frey G.J., Podar M., Luginbühl P., Gray K.A., Mathur E.J., Robertson D.E., Burk M.J., Hazlewood G.P., Short J.M., Kerovuo J. Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric. J. Biol. Chem. 2005, 280:9431-9438.
56. Song L., Siguier B., Dumon C., Bozonnet S., O'Donohue M.J. Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy. Biotechnol. Biofuels 2012, 5:3.
57. Strausberg S.L., Alexander P.A., Gallagher D.T., Gilliland G.L., Barnett B.L., Bryan P.N. Directed evolution of a subtilisin with calcium-independent stability. Nat. Biotechnol. 1995, 13:669-673.
58. Sun J., Wang H., Lv W., Ma C., Lou Z., Dai Y. Construction and characterization of a fusion β-1,3-1,4-glucanase to improve hydrolytic activity and thermostability. Biotechnol. Lett. 2011, 33:2193-2199.
59. Tian Y.S., Peng R.H., Xu J., Zhao W., Gao F., Fu X.Y., Xiong A.S., Yao Q.H. Mutations in two amino acids in phyI1s from Aspergillus niger 113 improve its phytase activity. Mol. Biol. Rep. 2011, 38:977-982.
60. Vahed M., Motalebi E., Rigi G., Noghabi K.A., Soudi M.R., Sadeghi M., et al. Improving chitinolytic activity of Bacillus pumilus SG2 by random mutagenesis. J. Microbiol. Biotechnol. 2013, 23:1519-1528.
61. Valle R.P.C., Falgout B. Mutagenesis of the NS3 protease of dengue virus type 2. J. Virol. 1998, 72:624-632.
62. Vasu K., Nagamalleswari E., Zahran M., Imhof P., Xu S.Y., Zhu Z., Chan S.H., Nagaraja V. Increasing cleavage specificity and activity of restriction endonuclease KpnI. Nucleic Acids Res. 2013, 41:9812-9824.
63. Vega M.D., Lazaro J.M., Mencia M., Blanco L., Salas M. Improvement of ϕ29 DNA polymerase amplification performance by fusion of DNA binding motifs. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:16506-16511.
64. Verma D., Satyanarayana T. Molecular approaches for ameliorating microbial xylanases. Bioresour. Technol. 2012, 117:360-367.
65. Verma D., Satyanarayana T. Improvement in thermostability of metagenomic GH11 endoxylanase (Mxyl) by site-directed mutagenesis and its applicability in paper pulp bleaching process. J. Ind. Microbiol. Biotechnol. 2013, 40:1373-1381.
66. Voutilainen S.P., Boer H., Alapuranen M., Janis J., Vehmaanpera J., Koivula A. Improving the thermostability and activity of Melanocarpus albomyces cellobiohydrolase Cel7B. Appl. Microbiol. Biotechnol. 2009, 83:261-272.
67. Walsh G. Protein engineering: case studies of commercialized engineered products. Enzyme Microb. Technol. 2006, 39:235-251.
68. Wang C., Huang R., He B., Du Q. Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. BMC Bioinform. 2012, 13:263.
69. Wang Q., Xia T. Enhancement of the thermostability and hydrolytic activity of GH10 xylanase by module shuffling between Cellulomonas fimi Cex and Thermomonospora alba XylA. World J. Microbiol. Biotechnol. 2007, 23:1047-1055.
70. Wang Y., Yuan H., Wang J., Yu Z. Truncation of the cellulose binding domain improved thermal stability of endo-β-1,4-glucanase from Bacillus subtilis JA18. Bioresour. Technol. 2009, 100:345-349.
71. Wunderlich M., Martin A., Staab C.A., Schmid F.X. Evolutionary protein stabilization in comparison with computational design. J. Mol. Biol. 2005, 351:1160-1168.
72. Xiao Z., Bergeron H., Grosse S., Beauchemin M., Garron M.L., Shaya D., Sulea T., Cygler M., Lau P.C. Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment. Appl. Environ. Microbiol. 2008, 74:1183-1189.
73. Zhang J.H., Jiang Y.Y., Lin Y., Sun Y.F., Zheng S.P., Han S.Y. Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids. PLoS One 2013, 8:e67892.
74. Zhang Z.G., Yi Z.L., Pei X.Q., Wua Z.L. Improving the thermostability of Geobacillus stearothermophilus xylanase XT6 by directed evolution and site-directed mutagenesis. Bioresour. Technol. 2010, 101:9272-9278.