Advertisement

Innovative Techniques for Improving Microbial Enzyme Production

  • Abhishek ThakurEmail author
  • Chayanika Putatunda
  • Rashmi Sharma
  • Rahul Mehta
  • Preeti Solanki
  • Kavita Bhatia
Chapter
  • 59 Downloads

Abstract

Enzymes are biocatalysts which have a central role in the biochemical, physiological, and metabolic functioning of all the organisms from micro to macro level. These catalytic proteins or metalloproteins have wonderful applications in a number of processes for conversion of substrates to useful products and are used in pharmaceutical, nutraceutical, cosmetic, food and beverage, and other industries. Different sources of these enzymes have been explored for commercial production. The reservoir of microbial world has not been investigated to a greater extent. The microorganisms have proved as an effective source of these industrially important enzymes. The reason for exploring enzymes from microorganisms is their stability at different physiological conditions like high and low temperature, pH, salinity, and others like high catalytic activity and ease of standardization and production. In recent times, the enhancement of production of these microbial enzymes can be achieved using different genetic modulatory methodologies, physiological parameter redesigning, and protein bioengineering. These techniques are the focus of researchers for industrial-friendly hyperproduction of microbial enzymes for generating various formulations.

Keywords

Purification Solid-state fermentation Submerged fermentation Hyperproduction 

References

  1. Adeleye T, Kareem S, Dairo O, Atanda O (2019) Studies on amylase from protoplast fusants of Aspergillus species using response surface methodology. Access Microbiol 1(1A)Google Scholar
  2. Adrio JL, Demain AL (2006) Genetic improvement of process yielding microbial products. FEMS Microbiol 30(2):187–214Google Scholar
  3. Adrio JL, Demain AL (2010) Recombinant organisms for production of industrial products. Bioeng Bug 1(2):116–131Google Scholar
  4. Adrio JL, Demain AL (2014) Microbial enzymes: tools for biotechnological processes. Biomol Ther 4(1):117–139Google Scholar
  5. Agrawal R, Satlewal A, Verma AK (2013) Development of a β-glucosidase hyperproducing mutant by combined chemical and UV mutagenesis. 3 Biotech 3:381PubMedGoogle Scholar
  6. Ahmed N (2009) A flood of microbial genomes—do we need more? PLoS One 4:1–5Google Scholar
  7. Aleem B, Muhammad HR, Zeb N, Saqib A, Ihsan A, Iqbal M, Ali H (2018) Random mutagenesis of super Koji (Aspergillus oryzae): improvement in production and thermal stability of α-amylases for maltose syrup production. J BMC Microbiol 18:1471–2180Google Scholar
  8. Alexandrova AN, Rothlisberger D, Baker D, Jorgensen WL (2008) Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J Am Chem Soc 130:15907–15915PubMedPubMedCentralGoogle Scholar
  9. Ali S, Mahmood S (2019) Mutagenesis of a thermophilic Alkalibacillus flavidus for enhanced production of an extracellular acetyl Xylan esterase in semi-solid culture of linseed meal. Waste Biomass Valoriz.  https://doi.org/10.1007/s12649-019-00665-2
  10. Ameri A, Shakibaie M, Soleimani-Kermani M, Faramarzi MA, Doostmohammadi M, Forootanfar H (2019) Overproduction of thermoalkalophilic lipase secreted by Bacillus atrophaeus FSHM2 using UV-induced mutagenesis and statistical optimization of medium components. Prep Biochem Biotechnol 49:184–191PubMedGoogle Scholar
  11. Anitha A, Rebeeth M (2009) Self-fusion of Streptomyces griseus enhances chitinase production and biocontrol activity against Fusarium oxysporum F. Sp. lycopersici. Biosci Biotechnol Res Asia 6:175–180Google Scholar
  12. Atomi H, Sato T, Kanai T (2011) Application of hyperthermophiles and their enzymes. Curr Opin Biotechnol 22:618–626PubMedGoogle Scholar
  13. Auerbach C (1976) Mutation research: problems, results and perspectives. Chapman and Hall, LondonGoogle Scholar
  14. Azin M, Noroozi E (2001) Random mutagenesis and use of 2-deoxy-D-glucose as an antimetabolite for selection of α-amylase-overproducing mutants of Aspergillus oryzae. World J Microbiol Biotechnol 17:747Google Scholar
  15. Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52(1):109–121PubMedGoogle Scholar
  16. Bakare MK, Adewale IO, Ajayi A, Shonukan OO (2005) Purification and characterization of cellulase from the wild-type and two improved mutants of Pseudomonas fluorescens. Afr J Biotechnol 4:898–904Google Scholar
  17. Baweja M, Nain L, Kawarabayasi Y, Shukla P (2016) Current technological improvements in enzymes toward their biotechnological applications. Front Microbiol 7:965PubMedPubMedCentralGoogle Scholar
  18. Bayer S, Birkemeyer C, Ballschmiter M (2011) A nitrilase from ametagenomic library acts regioselectively on aliphatic dinitriles. Appl Microbiol Biotechnol 89:91–98PubMedGoogle Scholar
  19. Ben Mabrouk S, Aghajari N, Ben Ali M, Ben Messaoud E, Juy M, Haser R, Bejar S (2011) Enhancement of the thermostability of the maltogenic amylase MAUS149 by Gly312Ala and Lys436Arg substitutions. Bioresour Technol 102:1740–1746PubMedGoogle Scholar
  20. Bhatia K, Mal G, Bhar R, Jyoti AC, Seth A (2018) Purification and characterization of thermostable superoxide dismutase from Anoxybacillus gonensis KA 55 MTCC 12684. Int J Biol Macromol 117:1133–1139PubMedGoogle Scholar
  21. Bischof RH, Ramoni J, Seiboth B (2016) Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei. Microb Cell Factories 15:106Google Scholar
  22. Borgi I, Gargouri A (2014) Investigations on a hyper-proteolytic mutant of Beauveria bassiana: broad substrate specificity and high biotechnological potential of a serine protease. FEMS Microbiol Lett 351:23–31PubMedGoogle Scholar
  23. Bustos-Jaimes I, Mora-Lugo R, Calcagno ML, Farres A (2010) Kinetic studies of Gly28:Ser mutant form of Bacillus pumilus lipase: changes in kcat and thermal dependence. BiochimBiophysActa 1804:2222–2227Google Scholar
  24. Cedrone F, Ménez A, Quéméneur E (2000) Tailoring new enzyme functions by rational redesign. Curr Opin Struct Biol 10(4):405–410PubMedGoogle Scholar
  25. Chand P, Aruna A, Maqsood AM, Rao LV (2005) Novel mutation method for increased cellulase production. J App Microbiol 98:318–323Google Scholar
  26. Chung D, Potter SC, Tanomrat AC, Ravikumar KM, Toney MD (2017) Site-directed mutant libraries for isolating minimal mutations yielding functional changes. Protein Eng Des Sel 30:347–357PubMedGoogle Scholar
  27. Contesini FJ, de Melo RR, Sato HH (2018) An overview of Bacillus proteases: from production to application. Crit Rev Biotechnol 38:321–334PubMedGoogle Scholar
  28. Cowan D (1996) Industrial enzyme technology. Trends Biotechnol 14:177–178Google Scholar
  29. de Paiva DP, de Oliveira SS, Mazotto AM et al (2019) Keratinolytic activity of Bacillus subtilis LFB-FIOCRUZ 1266 enhanced by whole-cell mutagenesis. 3 Biotech 9:2PubMedGoogle Scholar
  30. Demain AL, Adrio JL (2008) Contributions of microorganisms to industrial biology. Mol Biotechnol 38:41–45PubMedGoogle Scholar
  31. Demain AL, Vaishnav P (2009) Production of recombinant proteins by microbes and higher organisms. Biotechnol Adv 27:297–306PubMedGoogle Scholar
  32. Dillon AJP, Zorgi C, Camassola M, Henriques JA (2006) Use of 2-deoxyglucose in liquid media for the selection of mutant strains of Penicillium echinulatum production increased cellulase increased cellulase and β-glucosidase activities. Appl Microbiol Biotechnol 70:740–746PubMedGoogle Scholar
  33. Dumon C, Varvak A, Wall MA, Flint JE, Lewis RJ, Lakey JH, Morland C, Luginbuhl P, Healey S, Todaro T et al (2008) Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure. J Biol Chem 283:22557–22564PubMedGoogle Scholar
  34. Dunne C, Moënne-Loccoz Y, de Bruijn F, O’Gara F (2000) Overproduction of an inducible extracellular serine protease improves biological control of Pythium ultimum by Stenotrophomonas maltophilia strain W81. Microbiology 146:2069–2078PubMedGoogle Scholar
  35. Dutta JR, Banerjee R (2006) Isolation and characterization of a newly isolated Pseudomonas mutant for protease production. Braz Arch Biol Technol 49:37–47Google Scholar
  36. Ebert M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013) Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. J Bacteriol 195:4769–4777PubMedPubMedCentralGoogle Scholar
  37. Errol CF, Graham CW, Wolfram S, Richard DW, Roger AS, Tom E (2006) DNA repair and mutagenesis, 2nd edn. ASM Press, SterlingGoogle Scholar
  38. Fang Z, Sha C, Peng Z, Zhang J, Du G (2019) Protein engineering to enhance keratinolytic protease activity and excretion in Escherichia coli and its scale-up fermentation for high extracellular yield. Enzym Microb Technol 121:37–44Google Scholar
  39. Farmer WR, Liao JC (2000) Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol 18:533–537PubMedGoogle Scholar
  40. Fenel F, Zitting AJ, Kantelinen A (2006) Increased alkali stability in Trichoderma reesei endo-1,4-β-xylanase II by site directed mutagenesis. J Biotechnol 121:102–107PubMedGoogle Scholar
  41. Frushicheva MP, Cao J, Chu ZT, Warshel A (2010) Exploring challenges in rational enzyme design by simulating the catalysis in artificial kempeliminase. Proc Natl Acad Sci U S A 107:16869–16874PubMedPubMedCentralGoogle Scholar
  42. Frushicheva MP, Mills MJ, Schopf P, Singh MK, Prasad RB, Warshel A (2014) Computer aided enzyme design and catalytic concepts. Curr Opin Chem Biol 21:56–62PubMedGoogle Scholar
  43. Fujii R, Nakagawa Y, Hiratake J, Sogabe A, Sakata K (2005) Directed evolution of Pseudomonas aeruginosa lipase for improved amide-hydrolyzing activity. Protein Eng Des Sel 18:93–101PubMedGoogle Scholar
  44. Gai Y, Chen J, Zhang S, Zhu B, Zhang D (2018) Property improvement of α-amylase from Bacillus stearothermophilus by deletion of amino acid residues arginine 179 and glycine 180. Food Technol Biotechnol 56:58–64PubMedPubMedCentralGoogle Scholar
  45. Gerlt JA, Babbitt PC (2009) Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 13(1):10–18PubMedPubMedCentralGoogle Scholar
  46. Gomes I, Gomes J, Steiner W (2003) Highly thermostable amylase and pullulanase of the extreme thermophilic eubacterium Rhodothermus marinus: production and partial characterization. Bioresour Technol 90:207–214PubMedGoogle Scholar
  47. Goraya A, Asghar F, Javaid I, Ali S (2017) Microbial strain improvement for overproduction of industrial products. J Biol Sci 3:10–29Google Scholar
  48. Gupta PK (2007) Metabolic engineering for over production of metabolites. Elem Biotechnol:458–470Google Scholar
  49. Haq I, Ali S, Javed MM, Hameed U, Saleem A, Adnan F, Qadeer MA (2010) Production of alpha amylase from a randomly induced mutant strain of Bacillus amyloliquefaciens and its application as a desizer in textile industry. Pak J Bot 42:473–484Google Scholar
  50. Hassan MM (2014) Influence of protoplast fusion between two Trichoderma spp. on extracellular enzymes production and antagonistic activity. Biotechnol Biotechnol Equip 28(6):1014–1023Google Scholar
  51. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463–467Google Scholar
  52. Hirokawa K, Ichiyanagi A, Kajiyama N (2008) Enhancement of thermostability of fungal deglycating enzymes by directed evolution. Appl Microbiol Biotechnol 78:775–781PubMedGoogle Scholar
  53. Hou L (2009) Novel methods of genome shuffling in Saccharomyces cerevisiae. Biotechnol Lett 31(5):671–677PubMedGoogle Scholar
  54. Htway HTP, Yu SS, Latt ZK, Yi KP (2018) Improvement of cellulolytic activity in cellulolytic nitrogen-fixing bacteria by transposon mutagenesis. J Bacteriol Mycol 6:147–153Google Scholar
  55. Hu Y, Coates ARM (2005) Transposon mutagenesis identifies genes which control antimicrobial drug tolerance in stationary-phase Escherichia coli. FEMS Microbiol Lett 243:117–124PubMedGoogle Scholar
  56. Hwang JK, Warshel A (1987) Semiquantitative calculations of catalytic free-energies in genetically modified enzymes. Biochemistry 26:2669–2673PubMedGoogle Scholar
  57. Illing GT, Normansell ID, Peberdy JF (1989) Protoplast isolation and regeneration in Streptomyces clavuli-gerus. J Gen Microbiol 135:2289–2297PubMedGoogle Scholar
  58. James TY, Stenlid J, Olson Å, Johannesson H (2008) Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum. Evolution 62:2279–2296PubMedGoogle Scholar
  59. Jeon JH, Kim JT, Kim YJ, Kim HK, Lee HS, Kang SG, Kim SJ, Lee JH (2009) Cloning and characterization of a new-cold active lipase from a deep-se sediment metagenome. Appl Microbiol Biotechnol 81:865–874PubMedGoogle Scholar
  60. Jiang C, Shen P, Yan B, Wua B (2009) Biochemical characterization of a metagenome-derived decarboxylase. Enzym Microb Technol 45:58–63Google Scholar
  61. Johannes TW, Zhao H (2006) Directed evolution of enzymes and biosynthetic pathways. Curr Opin Microbiol 9:261–267PubMedGoogle Scholar
  62. Johnson EA (2013) Biotechnology of non-Saccharomyces yeasts- the ascomycetes. Appl Microbiol Biotechnol 97:503–517PubMedGoogle Scholar
  63. Kamalambigeswari R, Alagar S, Sivvaswamy N (2018) Strain improvement through mutation to enhance pectinase yield from Aspergillus niger and molecular characterization of Polygalacturonase gene. J Pharm Sci Res 10(2018):989–994Google Scholar
  64. Karn N, Karn SK (2014) Evaluation and characterization of protease production by Bacillus sp. induced by UV mutagenesis. Enzym Eng 3:119Google Scholar
  65. Kaul P, Asano Y (2012) Strategies for discovery and improvement of enzyme function: state of the art and opportunities. Microbiol Biotechnol 5:18–33Google Scholar
  66. Keasling JD (2012) Synthetic biology and the development of tools for metabolic engineering. Metab Eng 14:189–195PubMedGoogle Scholar
  67. Kennedy J, Marchesi JR, Dobson AD (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Factories 7:27–37Google Scholar
  68. Kenyon CJ (1983) The bacterial response to DNA damage. Trend Biochem Sci 2:84–87Google Scholar
  69. Khattab AA, Bazaraa WA (2005) Screening, mutagenesis and protoplast fusion of Aspergillus niger for the enhancement of extracellular glucose oxidase production. J Ind Microbiol Biotechnol 32:289PubMedGoogle Scholar
  70. Khedr MA, Ewais EA, Khalil KMA (2017) Improvement of thermophilic α-amylase productivity through UV mutagenesis and AmyE gene amplification and sequencing. J Innov Pharm Biol Sci 4:58–67Google Scholar
  71. Khersonsky O, Kiss G, Rothlisberger D, Dym O, Albeck S, Houk KN, Baker D, Tawfik DS (2012) Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci U S A 109:10358–10363PubMedPubMedCentralGoogle Scholar
  72. Kiss G, Rothlisberger D, Baker D, Houk KN (2010) Evaluation and ranking of enzyme designs. Protein Sci 19:1760–1773PubMedPubMedCentralGoogle Scholar
  73. Korman TP, Sahachartsiri B, David MC, Grace HL, Beauregard M, Bowie JU (2013) Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution. J Biotechnol Biofuel 6:1754–6834Google Scholar
  74. Kostyleva EV, Sereda AS, Velikoretskaya IA (2017) Development of schemes of induced mutagenesis for improving the productivity of Aspergillus strains producing amylolytic enzymes. Microbiology 86:493Google Scholar
  75. Kostyleva EV, Tsurikova NV, Sereda AS, Velikoretskaya IA, Veselkina TN, Lobanov NS, Shashkov IA, Sinitsyn AP (2018) Enhancement of activity of carbohydrases with endo-depolymerase action in Trichoderma reesei using mutagenesis. Microbiology 87:652–661Google Scholar
  76. Kumar A, Singh S (2013) Directed evolution: tailoring biocatalysis for industrial application. Crit Rev Biotechnol 33:365–378PubMedGoogle Scholar
  77. Kumar L, Awasthi G, Singh B (2011) Extremophiles: a novel source of industrially important enzymes. Biotechnology 10:1–15Google Scholar
  78. Kumar A, Dutt S, Bagler G, Ahuja PS, Kumar S (2012) Engineering a thermo-stable superoxide dismutase functional at sub-zero to >50 °C, which also tolerates autoclaving. Sci Rep 2:387:1–387:8Google Scholar
  79. Laroussi M, Leipold F (2004) Evaluation of the roles of reactive species, heat, and UV radiation in the inactivation of bacterial cells by air plasmas at atmospheric pressure. Int J Mass Spectrom 233:81–86Google Scholar
  80. Lee SH, Kim YW, Lee S, Auh JH, Yoo SS, Kim TJ, Kim JW, Kim ST, Rho HJ, Choi JH (2002) Modulation of cyclizing activity and thermostability of cyclodextrin glucanotransferase and its application as an antistaling enzyme. J Agric Food Chem 50:1411–1415PubMedGoogle Scholar
  81. Lee S, Lee DG, Jang MK, Jeon MJ, Jang HJ, Lee SH (2011) Improvement in the catalytic activity of β-agarase AgaA from Zobellia galactanivorans by site-directed mutagenesis. J Microbiol Biotechnol 21:1116–1122PubMedGoogle Scholar
  82. Lee HL, Chang CK, Jeng WY, Wang AH, Liang PH (2012) Mutations in the substrate entrance region of β-glucosidase from Trichoderma reesei improve enzyme activity and thermostability. Protein Eng Des Sel 25:733–740PubMedGoogle Scholar
  83. Lessard P (1996) Metabolic engineering, the concept coalesces. Nat Biotechnol 14:1654–1655PubMedGoogle Scholar
  84. Li S, Yang X, Yang S, Zhu M, Wang X (2012) Technology prospecting on enzymes: application, marketing and engineering. Comput Struct Biotechnol J 2:1–11Google Scholar
  85. Li S, Wang N, Du ZJ, Chen GJ (2018) Intergeneric hybridization between Streptomyces albulus and Bacillus subtilis facilitates production of ε-Poly-L-lysine from corn starch residues. Biotechnol Bioprocess Eng 23:580–587Google Scholar
  86. Liu L, Yang H, Shin HD, Chen RR, Li J, Du G (2013) How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioengineered 4:212–223PubMedPubMedCentralGoogle Scholar
  87. Liu Z-Q, Zhang X-H, Xue Y-P, Xu M, Zheng Y-G (2014) Improvement of Alcaligenes faecalis Nitrilase by gene site saturation mutagenesis and its application in stereospecific biosynthesis of (R)-(−)-mandelic acid. J Agric Food Chem 62:4685–4694PubMedGoogle Scholar
  88. Luo XJ, Yu HL, Xu JH (2012) Genomic data mining: an efficient way to find new and better enzymes. Enzym Eng 1:104–108Google Scholar
  89. Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A et al (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367–373PubMedPubMedCentralGoogle Scholar
  90. Ma Y, Shen W, Chen X (2016) Significantly enhancing recombinant alkaline amylase production in Bacillus subtilis by integration of a novel mutagenesis-screening strategy with systems-level fermentation optimization. J Biol Eng 10:13PubMedPubMedCentralGoogle Scholar
  91. Maloy SR, Cronan JE, Freifelder D (1994) Microbial genetics, 2nd edn. Jones and Bartlett Publishers, BurlingtonGoogle Scholar
  92. Marek SM, Wu J, Glass NL, Gilchrist DG, Bostock RM (2003) Nuclear DNA degradation during heterokaryon incompatibility in Neurospora crassa. Fungal Genet Biol 40:126–137PubMedGoogle Scholar
  93. May O, Nguyen PT, Arnold FH (2000) Inverting enantioselectivity by directed evolution of hydantoinase for improved production of l-methionine. Nat Biotechnol 18:317–320PubMedGoogle Scholar
  94. Meers JL, Lambert PW (1983) The production of industrial enzymes. Philos Trans R Soc Lond:263–282Google Scholar
  95. Mehtani P, Sharma C, Bhatnagar P (2017) Strain improvement of halotolerant Actinomycete for protease production by sequential mutagenesis. Int J Chem Sci 15:109Google Scholar
  96. Mukhtar H, Haq I (2013) Comparative evaluation of Agroindustrial byproducts for the production of alkaline protease by wild and mutant strains of Bacillus subtilis in submerged and solid state fermentation. Sci World J, Article ID 538067:1–6Google Scholar
  97. Mulholland AJ (2008) Computational enzymology: modelling the mechanisms of biological catalysts. Biochem Soc Trans 36:22–26PubMedGoogle Scholar
  98. Muñoz-López M, García-Pérez JL (2010) DNA transposons: nature and applications in genomics. Curr Genomics 11(2):115–128PubMedPubMedCentralGoogle Scholar
  99. Nadeem M, Qazi JI, Baig S (2010) Enhanced production of alkaline protease by a mutant of Bacillus licheniformis N-2 for dehairing. Braz Arch Bio Technol 53:1015–1025Google Scholar
  100. Ness JE, Del Cardayré SB, Minshull J, Stemmer WP (2000) Molecular breeding: the natural approach to protein design. Adv Protein Chem 55:261–292PubMedGoogle Scholar
  101. Nielsen J (2001) Metabolic engineering. Appl Microbiol Biotechnol 55(3):263–283PubMedGoogle Scholar
  102. Nishioka T, Yasutake Y, Nishiya Y, Tamura T (2012) Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV. FEBS J 279:3264–3275PubMedGoogle Scholar
  103. Ohnishi J, Mitsuhashi S, Hayashi M, Ando S, Yokoi H, Ochiai K, Ikeda M (2002) A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant. Appl Microbiol Biotechnol 58(2):217–223PubMedGoogle Scholar
  104. Okanishi M, Suzuki K, Umezawa H (1974) Formation and reversion of streptomycetes protoplasts: culture? Conditions and morphological study. J Gen Microbiol 80:389–400PubMedGoogle Scholar
  105. Pontecorvo G (1956) The parasexual cycle in fungi. Annu Rev Microbiol 10:393–400PubMedGoogle Scholar
  106. Porter JL, Rusli RA, Ollis DL (2016) Directed evolution of enzymes for industrial biocatalysis. Chembiochem 17(3):197–203PubMedGoogle Scholar
  107. Power JB, Davey MR (1990) Protoplasts of higher and lower plants: isolation, culture, and fusion. Methods Mol Biol 6:237–259PubMedGoogle Scholar
  108. Prabavathy VR, Mathivanan N, Sagadevan E, Murugesan K, Lalithakumari D (2006) Self-fusion of protoplasts enhances chitinase production and biocontrol activity in Trichoderma harzianum. Bioresour Technol 97:2330–2334PubMedGoogle Scholar
  109. Rao SN, Singh UC, Bash PA, Kollman PA (1987) Free-energy perturbation calculations on binding and catalysis after mutating Asn-155 in subtilisin. Nature 328:551–554PubMedGoogle Scholar
  110. Rao MB, Tanksale AM, Ghatge MS, Deshpande VV (1998) Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62:597–635PubMedPubMedCentralGoogle Scholar
  111. Raper JR (1966) Genetics of sexuality in higher fungi. Ronald Press Company, New YorkGoogle Scholar
  112. Read ND, Fleibner A, Roca MG, Glass NL (2010) Hyphal fusion. In: Borkovich KA, Ebbole DJ (eds) Cellular and molecular biology of filamentous fungi. ASM Press, Washington, DC, pp 260–273Google Scholar
  113. Rha E, Kim S, Choi SL, Hong SP, Sung MH, Song JJ, Lee SG (2009) Simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol-lyase by directed evolution. FEBS J 276:6187–6194PubMedGoogle Scholar
  114. Rondon MR, Goodman RM, Handelsman J (1999) The Earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17:403–409PubMedGoogle Scholar
  115. Rondon MR, August PR, Betterman AD, Brady SF, Grossman TH, Liles MR (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547PubMedPubMedCentralGoogle Scholar
  116. Roper M, Simonin A, Hickey PC, Leeder A, Glass NL (2013) Nuclear dynamics in a fungal chimera. Proc Natl Acad Sci U S A 110:12875–12880PubMedPubMedCentralGoogle Scholar
  117. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190–U194PubMedGoogle Scholar
  118. Rowlands RT (1984a) Industrial strain improvement: mutagenesis and random screening procedures. Enzym Microb Technol 6:3–10Google Scholar
  119. Rowlands RT (1984b) Industrial strain improvement: rational screens and genetic recombination techniques. Enzym Microb Technol 6:290–300Google Scholar
  120. Ryu DD, Kim KS, Cho NY, Pai HS (1983) Genetic recombination in Micromonospora rosaria by protoplast fusion. Appl Environ Microbiol 45(6):1854–1858PubMedPubMedCentralGoogle Scholar
  121. Sadhu S, Ghosh PK, Aditya G, Maiti TK (2014) Optimization and strain improvement by mutation for enhanced cellulase production by Bacillus sp. (MTCC10046) isolated from cow dung. J King Saud Univ Sci 26:323–332Google Scholar
  122. Santos CSS, Stephanopoulos G (2008) Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 12:168–176PubMedGoogle Scholar
  123. Schiraldini C, De Rosa M (2002) The production of biocatalysts and biomolecules from extremophiles. Trends Biotechnol 20:515–521Google Scholar
  124. Shih TW, Pan TM (2011) Substitution of Asp189 residue alters the activity and thermostability of Geobacillus sp. NTU 03 lipase. Biotechnol Lett 33:1841–1846PubMedGoogle Scholar
  125. Shin CS, Lee JP, Lee JS, Park SC (2000) Enzyme production of Trichoderma reesei Rut C-30 on various lignocellulosic substrates. Appl Biochem Biotechnol 84–86:237–245PubMedGoogle Scholar
  126. Shoji JY, Charlton ND, Yi M, Young CA, Craven KD (2015) Vegetative hyphal fusion and subsequent nuclear behavior in Epichloë grass endophytes. PLoS One 10:1–21Google Scholar
  127. Shortle D, DiMaio D, Nathans D (1981) Directed mutagenesis. Annu Rev Genet 15:265–294PubMedGoogle Scholar
  128. Sivakumar U, Kalaichelvan G, Ramasamy K (2004) Protoplast fusion in Streptomyces sp. for increased production of laccase and associated ligninolytic enzymes. World J Microbiol Biotechnol 20:563–568Google Scholar
  129. Solís S, Loeza J, Segura G, Tello J, Reyes N, Lappe P et al (2009) Hydrolysis of orange peel by a pectin lyase-overproducing hybrid obtained by protoplast fusion between mutant pectinolytic Aspergillus flavipes and Aspergillus niveus CH-Y-1043. Enzym Microb Technol 44:123–128Google Scholar
  130. Srikrishnan S, Randall A, Baldi P, Da Silva NA (2012) Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates. Biotechnol Bioeng 109:1595–1599PubMedGoogle Scholar
  131. Sriprang R, Asano K, Gobsuk J, Tanapongpipat S, Champreda V, Eurwilaichitr L (2006) Improvement of thermostability of fungal xylanase by using site-directed mutagenesis. J Biotechnol 126:454–462PubMedGoogle Scholar
  132. Sriprapundh D, Vieille C, Zeikus JG (2003) Directed evolution of Thermotoganea politana xylose isomerase: high activity on glucose at low temperature and low pH. Protein Eng 16:683–690PubMedGoogle Scholar
  133. Stanbury PF, Whittaker A, Hall SJ (2016) Principles of fermentation technology, 3rd edn. Butterworth-Heinemann, OxfordGoogle Scholar
  134. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–562PubMedGoogle Scholar
  135. Stephanopoulos G (1999) Metabolic fluxes and metabolic engineering. Metab Eng 1:1–11PubMedGoogle Scholar
  136. Stephanopoulos GN, Aristidou AA, Nielsen J (1998) Metabolic engineering: principles and methodologies. Academic, San DiegoGoogle Scholar
  137. Strom NB, Bushley KE (2016) Two genomes are better than one: history, genetics, and biotechnological applications of fungal heterokaryons. Fungal Biol Biotechnol 3:4PubMedPubMedCentralGoogle Scholar
  138. Sun Y, Yang H, Wang W (2011) Improvement of the thermostability and enzymatic activity of cholesterol oxidase by site-directed mutagenesis. Biotechnol Lett 33:2049–2055PubMedGoogle Scholar
  139. Sunitha K, Park YS, Oh TK, Lee JK (1999) Synthesis of alkaline protease by catabolite repression-resistant Thermoactinomyces sp. E79 mutant. Biotechnol Lett 21:155–158Google Scholar
  140. Suribabu K, Lalitha Govardhan T, Hemalatha KPJ (2014) Strain improvement of Brevibacillus borstelensis R1 for optimization of α-amylase production by mutagens. J Microb Biochem Technol 6:123–127Google Scholar
  141. Thakur A, Kumar P, Lata J, Devi N, Chand D (2018) Thermostable Fe/Mn superoxide dismutase from Bacillus licheniformis SPB-13 from thermal springs of Himalayan region: purification, characterization and antioxidative potential. Int J Biol Macromol 115:1026–1032PubMedGoogle Scholar
  142. Theriot CM, Semcer RL, Shah SS, Grunden AM (2011) Improving the catalytic activity of hyperthermophilic Pyrococcus horikoshii prolidase for detoxification of organophosphorus nerve agents over a broad range of temperatures. Archaea 2011:565127PubMedPubMedCentralGoogle Scholar
  143. Tobe S, Shimogaki H, Ohdera M, Asai Y, Oba K, Iwama M, Irie M (2006) Expression of Bacillus protease (Protease BYA) from Bacillus sp. Y in Bacillus subtilis and enhancement of its specific activity by site-directed mutagenesis-improvement in productivity of detergent enzyme. Biol Pharm Bull 29:26–33PubMedGoogle Scholar
  144. Tracewell CA, Arnold FH (2009) Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr Opin Chem Biol 13(1):3–9PubMedPubMedCentralGoogle Scholar
  145. Uchiyama T, Miyazaki K (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20:616–622PubMedGoogle Scholar
  146. Underkofler LA, Barton RR, Rennert SS (1957) Production of microbial enzymes and their applications. Appl Microbiol 6(3):212–221Google Scholar
  147. Ushijima S, Nakadai T (1987) Breeding by protoplast fusion of koji mold, Aspergillus sojae. Agric Biol Chem 51:1051–1057Google Scholar
  148. Van den Burg B (2003) Extremophiles as a source for novel enzymes. Curr Opin Microbiol 6:213–218PubMedGoogle Scholar
  149. Van der Veen BA, Potocki-Veronese G, Albenne C, Joucla G, Monsan P, Remaud-Simeon M (2004) Combinatorial engineering to enhance amylosucrase performance: construction, selection, and screening of variant libraries for increased activity. FEBS Lett 560:91–97PubMedGoogle Scholar
  150. Varavallo MA, de Queiroz MV, Lana TG, de Brito ATR, Gonçalves DB, de Araújo EF (2007) Isolation of recombinant strains with enhanced pectinase production by protoplast fusion between Penicillium expansum and Penicillium griseoroseum. Braz J Microbiol 38:52–57Google Scholar
  151. Verma R, Schwaneberg U, Roccatanoa D (2012) Computer-aided protein directed evolution: a review of web servers, databases and other computational tools for protein engineering. Comput Struct Biotechnol J 2:e201209008PubMedPubMedCentralGoogle Scholar
  152. Wang XC, Zhao HY, Liu G, Cheng XJ, Feng H (2016) Improving production of extracellular proteases by random mutagenesis and biochemical characterization of a serine protease in Bacillus subtilis S1-4. Genet Mol Res 15Google Scholar
  153. Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley, New YorkGoogle Scholar
  154. Weichert M, Fleibner A (2015) Anastomosis and heterokaryon formation. In: van den Berg MA, Maruthachalam K (eds) Genetic transformation systems in fungi. Springer, Cham, pp 3–21Google Scholar
  155. Weng M, Deng X, Bao W, Zhu L, Wu J, Cai Y, Jia Y, Zheng Z, Zou G (2015) Improving the activity of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation. Biochem Biophys Res Commun 465:580–586PubMedGoogle Scholar
  156. Wong TS, Roccatano D, Schwaneberg U (2007) Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries. Environ Microbiol 9(11):2645–2659PubMedGoogle Scholar
  157. Xu JZ, Zhang WG (2016) Strategies used for genetically modifying bacterial genome: site-directed mutagenesis, gene inactivation, and gene over-expression. J Zhejiang Univ Sci B 17:83–99PubMedPubMedCentralGoogle Scholar
  158. Xu F, Wang J, Chen S, Qin W, Yu Z, Zhao H, Xing X, Li H (2011) Strain improvement for enhanced production of cellulase in Trichoderma viride. Appl Biochem Microbiol 47:53–58Google Scholar
  159. Yang YT, Bennet GN, San KY (1998) Genetic and metabolic engineering. Electron J Biotechnol 1(3):134–141Google Scholar
  160. Yang H, Liu L, Wang M, Li J, Wang NS, Du G, Chen J (2012) Structure-based engineering of methionine residues in the catalytic cores of alkaline amylase from Alkalimonas amylolytica for improved oxidative stability. Appl Environ Microbiol 78:7519–7526PubMedPubMedCentralGoogle Scholar
  161. Yazdani SS, Gonzalez R (2008) Engineering Escherichia Coli for the efficient conversion of glycerol to ethanol and coproducts. Metab Eng 10:340–351Google Scholar
  162. Yi ZL, Pei XQ, Wu ZL (2011) Introduction of glycine and proline residues onto protein surface increases the thermostability of endoglucanase CelA from Clostridium thermocellum. Bioresour Technol 102:3636–3638PubMedGoogle Scholar
  163. Yoneda Y (1980) Increased production of extracellular enzymes by the synergistic effect of genes introduced into Bacillus subtilis by stepwise transformation. Appl Environ Microbiol 39(1):274–276PubMedPubMedCentralGoogle Scholar
  164. Yoneda Y, Maruo B (1975) Mutation of Bacillus subtilis causing hyper-production of α-amylase and protease, and its synergistic effect. J Bac 124:48–54Google Scholar
  165. Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayré SB (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415(6872):644–646PubMedGoogle Scholar
  166. Zhang Y, Adams IP, Ratledge C (2007) Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation. Microbiology 153:2013–2025PubMedGoogle Scholar
  167. Zhang ZG, Yi ZL, Pei XQ, Wu ZL (2010) Improving the thermostability of Geobacillus stearothermophilus xylanase XT6 by directed evolution and site-directed mutagenesis. Bioresour Technol 101:9272–9278PubMedGoogle Scholar
  168. Zhang X, Zhang X-F, Li H-P, Wang L-Y, Zhang C, Xing X-H, Bao C-Y (2014) Atmospheric and room temperature plasma (ARTP) as a new powerful mutagenesis tool. Appl Microbiol Biotechnol 98:5387–5396PubMedPubMedCentralGoogle Scholar
  169. Zhang J, Shi H, Xu L, Zhu X, Li X (2015) Site-directed mutagenesis of a hyperthermophilic endoglucanase Cel12B from Thermotoga maritima based on rational design. PLoS One 10(7):e0133824PubMedPubMedCentralGoogle Scholar
  170. Zhao H, Arnold FH (1997) Optimization of DNA shuffling for high fidelity recombination. Nucleic Acids Res 25(6):1307–1308PubMedPubMedCentralGoogle Scholar
  171. Zheng R-C, Ruan L-T, Ma H-Y, Tang X-L, Zheng Y-G (2016) Enhanced activity of Thermomyces lanuginosus lipase by site-saturation mutagenesis for efficient biosynthesis of chiral intermediate of pregabalin. Biochem Eng J 113:12–18Google Scholar
  172. Zhong CQ, Song S, Fang N, Liang X, Zhu H, Tang XF, Tang B (2009) Improvement of low-temperature caseinolytic activity of a thermophilic subtilase by directed evolution and site-directed mutagenesis. Biotechnol Bioeng 104:862–870PubMedGoogle Scholar
  173. Zou Z, Zhao Y, Zhang T, Xu J, He A, Deng Y (2018) Efficient isolation and characterization of a cellulase hyperproducing mutant strain of Trichoderma reesei. J Microbiol Biotechnol 28:1473–1481PubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Abhishek Thakur
    • 1
    Email author
  • Chayanika Putatunda
    • 1
  • Rashmi Sharma
    • 1
  • Rahul Mehta
    • 1
  • Preeti Solanki
    • 2
  • Kavita Bhatia
    • 3
  1. 1.Department of MicrobiologyDAV UniversityJalandharIndia
  2. 2.Department of BiotechnologyDAV UniversityJalandharIndia
  3. 3.Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanIndia

Personalised recommendations