Advertisement

Bioengineering Fungi and Yeast for the Production of Enzymes, Metabolites, and Value-Added Compounds

  • Gretty K. VillenaEmail author
  • Ana A. Kitazono
  • María  Lucila Hernández-Macedo
Chapter
  • 89 Downloads
Part of the Fungal Biology book series (FUNGBIO)

Abstract

Fungi have been used since ancient times in the manufacturing of fermented foods and beverages, and these early applications marked the initial development of biotechnology.

Fungal biotechnology has allowed the commercial production of industrial enzymes, pigments, vitamins, organic acids, lipids, and several antibiotics as well as the development of processes that facilitate the degradation of xenobiotics, the obtention of value-added bioproducts from lignocellulosic biomass, etc.

All these applications and products have been facilitated by the advent of molecular biology, metabolic engineering, omics technologies, and synthetic biology.

From a biotechnological point of view, any improvement in the performance and productivity of a fungal strain requires a minimum level of physiological and genetic manipulations. Recently, gene editing through CRISPR/Cas9 technology has been successfully applied in both yeast and filamentous fungi for several applications.

This chapter summarizes the main molecular strategies for the genetic manipulation of filamentous fungi and yeasts and their latest biotechnological applications.

Keywords

Fungal biotechnology Filamentous fungi Genetic manipulation CRIPSR/Cas9 Yeasts 

References

  1. Adrio JL, Demain AL (2003) Fungal biotechnology. Int Microbiol 6(3):191–199PubMedGoogle Scholar
  2. Amen T, Kaganovich D (2017) Integrative modules for efficient genome engineering in yeast. Microb Cell 4(6):182–190PubMedPubMedCentralGoogle Scholar
  3. Anyaogu DC, Mortensen UH (2015) Heterologous production of fungal secondary metabolites in Aspergilli. Front Microbiol 6:77PubMedPubMedCentralGoogle Scholar
  4. Baker SE (2006) Aspergillus niger genomics: past, present and into the future. Med Mycol 44(Supplement_1):S17–S21PubMedGoogle Scholar
  5. Balan V (2014) Current challenges in commercially producing biofuels from lignocellulosic biomass. ISRN Biotechnol 2014:463074PubMedPubMedCentralGoogle Scholar
  6. Barrios-González J, Miranda RU (2010) Biotechnological production and applications of statins. Appl Microbiol Biotechnol 85(4):869–883PubMedGoogle Scholar
  7. Brandl J, Andersen MR (2015) Current state of genome-scale modeling in filamentous fungi. Biotechnol Lett 37(6):1131–1139PubMedPubMedCentralGoogle Scholar
  8. Brown SH, Bashkirova L, Berka R, Chandler T, Doty T, McCall K, McCulloch M, McFarland S, Thompson S, Yaver D, Berry A (2013) Metabolic engineering of Aspergillus oryzae NRRL 3488 for increased production of L-malic acid. Appl Microbiol Biotechnol 97(20):8903–8912PubMedGoogle Scholar
  9. Cairns TC, Nai C, Meyer V (2018) How a fungus shapes biotechnology: 100 years of Aspergillus niger research. Fungal Biol Biotechnol 5(1):13PubMedPubMedCentralGoogle Scholar
  10. Calzado F, Persinoti GF, Terrasan C, Zubieta M, Rubio M, Contesini F, Squina F, Damasio A (2018) Comparative RNA-seq based transcriptomic analysis of Aspergillus nidulans recombinant strains overproducing heterologous glycoside hydrolases. bioRxiv: 241273Google Scholar
  11. Chelius MK, Wodzinski RJ (1994) Strain improvement of Aspergillus niger for phytase production. Appl Microbiol Biotechnol 41(1):79–83Google Scholar
  12. Chesini M, Wagner E, Baruque DJ, Vita CE, Cavalitto SF, Ghiringhelli PD, Rojas NL (2018) High level production of a recombinant acid stable exoinulinase from Aspergillus kawachii. Protein Expr Purif 147:29–37PubMedGoogle Scholar
  13. da Rosa-Garzon NG, Laure HJ, Rosa JC, Cabral H (2019) Fusarium oxysporum cultured with complex nitrogen sources can degrade agricultural residues: evidence from analysis of secreted enzymes and intracellular proteome. Renew Energy 133:941–950Google Scholar
  14. Daboussi M-J, Capy P (2003) Transposable elements in filamentous fungi. Ann Rev Microbiol 57(1):275–299Google Scholar
  15. Dai Z, Liu Y, Guo J, Huang L, Zhang X (2015) Yeast synthetic biology for high-value metabolites. FEMS Yeast Res 15(1):1–11PubMedGoogle Scholar
  16. De Bhowmick G, Sarmah AK, Sen R (2018) Lignocellulosic biorefinery as a model for sustainable development of biofuels and value added products. Bioresour Technol 247:1144–1154PubMedGoogle Scholar
  17. De Groot MJA, Bundock P, Hooykaas PJJ, Beijersbergen AGM (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 16(9):839PubMedGoogle Scholar
  18. de Paula RG, Antonieto ACC, Ribeiro LFC, Srivastava N, O’Donovan A, Mishra PK, Gupta VK, Silva RN (2019) Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 37(6):107347PubMedGoogle Scholar
  19. Demain AL, Adrio JL (2008) Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. In: Petersen F, Amstutz R (eds) Natural Compounds as Drugs Volume I. Progress in Drug Research, vol 65. Birkhäuser Basel Google Scholar
  20. Den Haan R, Rose SH, Lynd LR, van Zyl WH (2007) Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab Eng 9(1):87–94Google Scholar
  21. Deng H, Gao R, Liao X, Cai Y (2017) CRISPR system in filamentous fungi: current achievements and future directions. Gene 627:212–221PubMedGoogle Scholar
  22. Dilworth MV, Piel MS, Bettaney KE, Ma P, Luo J, Sharples D, Poyner DR, Gross SR, Moncoq K, Henderson PJF (2018) Microbial expression systems for membrane proteins. Methods 147:3–39PubMedGoogle Scholar
  23. Dimarogona M, Topakas E (2016) Regulation and heterologous expression of lignocellulosic enzymes in Aspergillus. In: New and future developments in microbial biotechnology and bioengineering. Elsevier, pp 171–190Google Scholar
  24. Dondelinger E, Aubry N, Ben Chaabane F, Cohen C, Tayeb J, Remond C (2016) Contrasted enzymatic cocktails reveal the importance of cellulases and hemicellulases activity ratios for the hydrolysis of cellulose in presence of xylans. AMB Express 6(1):24PubMedPubMedCentralGoogle Scholar
  25. Donohoue PD, Barrangou R, May AP (2018) Advances in industrial biotechnology using CRISPR-Cas systems. Trends Biotechnol 36(2):134–146PubMedGoogle Scholar
  26. Du J, Shao Z, Zhao H (2011) Engineering microbial factories for synthesis of value-added products. J Ind Microbiol Biotechnol 38(8):873–890PubMedPubMedCentralGoogle Scholar
  27. Dufresne A (2013) Nanocellulose: a new ageless bionanomaterial. Mater Today 16(6):220–227Google Scholar
  28. Duina AA, Miller ME, Keeney JB (2014) Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. Genetics 197:33–48PubMedPubMedCentralGoogle Scholar
  29. El-Imam AA, Du C (2014) Fermentative itaconic acid production. J Biodivers Biopros Dev 1(1):1–8Google Scholar
  30. Ellila S, Fonseca L, Uchima C, Cota J, Goldman GH, Saloheimo M, Sacon V, Siika-Aho M (2017) Development of a low-cost cellulase production process using Trichoderma reesei for Brazilian biorefineries. Biotechnol Biofuels 10(1):30PubMedPubMedCentralGoogle Scholar
  31. Enkler L, Richer D, Marchand AL, Ferrandon D, Jossinet F (2016) Genome engineering in the yeast pathogen Candida glabrata using the CRISPR-Cas9 system. Sci Rep 6:35766PubMedPubMedCentralGoogle Scholar
  32. Fávaro LCL, Araújo WL, Azevedo JL, Paccola-Meirelles LD (2005) The biology and potential for genetic research of transposable elements in filamentous fungi. Genet Mol Biol 28(4):804–813Google Scholar
  33. Fiedler MRM, Barthel L, Kubisch C, Nai C, Meyer V (2018) Construction of an improved Aspergillus niger platform for enhanced glucoamylase secretion. Microb Cell Factories 17(1):95Google Scholar
  34. Fincham JR (1989) Transformation in fungi. Microbiol Mol Biol Rev 53(1):148–170Google Scholar
  35. Fleißner A, Dersch P (2010) Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol 87(4):1255–1270PubMedGoogle Scholar
  36. Frandsen RJN (2011) A guide to binary vectors and strategies for targeted genome modification in fungi using Agrobacterium tumefaciens-mediated transformation. J Microbiol Methods 87(3):247–262PubMedGoogle Scholar
  37. García-Granados R, Lerma-Escalera JA, Morones-Ramírez JR (2019) Metabolic engineering and synthetic biology: synergies, future, and challenges. Front Bioeng Biotechnol 7:36PubMedPubMedCentralGoogle Scholar
  38. Generoso WC, Schadeweg V, Oreb M, Boles E (2015) Metabolic engineering of Saccharomyces cerevisiae for production of butanol isomers. Curr Opin Biotechnol 33:1–7PubMedGoogle Scholar
  39. Gnugge R, Rudolf F (2017) Saccharomyces cerevisiae Shuttle vectors. Yeast 34(5):205–221PubMedGoogle Scholar
  40. Gombert AK, Madeira JV Jr, Cerdan ME, Gonzalez-Siso MI (2016) Kluyveromyces marxianus as a host for heterologous protein synthesis. Appl Microbiol Biotechnol 100(14):6193–6208PubMedGoogle Scholar
  41. Gomez S, Fernandez FJ, Vega MC (2016) Heterologous expression of proteins in Aspergillus. In: New and future developments in microbial biotechnology and bioengineering. Elsevier, pp 55–68Google Scholar
  42. Goncalves FA, Colen G, Takahashi JA (2014) Yarrowia lipolytica and its multiple applications in the biotechnological industry. Sci World J 2014(476207):476207Google Scholar
  43. Guldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24(13):2519–2524PubMedPubMedCentralGoogle Scholar
  44. Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T (2016) Fungal enzymes for bio-products from sustainable and waste biomass. Trends Biochem Sci 41(7):633–645PubMedGoogle Scholar
  45. Guzmán-Chávez F, Zwahlen R, Bovenberg R, Driessen A (2018) Engineering of the filamentous fungus Penicillium chrysogenum as cell factory for natural products. Front Microbiol 9:2768PubMedPubMedCentralGoogle Scholar
  46. He L, Feng J, Lu S, Chen Z, Chen C, He Y, Yi X, Xi L (2016) Genetic transformation of fungi. Int J Dev Biol 61(6–7):375–381Google Scholar
  47. Heerd D, Tari C, Fernández-Lahore M (2014) Microbial strain improvement for enhanced polygalacturonase production by Aspergillus sojae. Appl Microbiol Biotechnol 98(17):7471–7481PubMedGoogle Scholar
  48. Hegde K, Prabhu A, Sarma S, Brar S, Dasu VV, Menon V, Rao M (2016) Potential applications of renewable itaconic acid for the synthesis of 3-methyltetrahydrofuran trends in bioconversion of lignocellulose: biofuels, platform chemicals & biorefinery concept. Platform Chem Bioref 38(4):181–200Google Scholar
  49. Hihlal E, Braumann I, van den Berg M, Kempken F (2011) Suitability of Vader for transposon-mediated mutagenesis in Aspergillus niger. Appl Environ Microbiol 77(7):2332–2336PubMedPubMedCentralGoogle Scholar
  50. Hillman ET, Readnour LR, Solomon KV (2017) Exploiting the natural product potential of fungi with integrated-omics and synthetic biology approaches. Curr Opin Syst Biol 5:50–56Google Scholar
  51. Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157(6):1262–1278PubMedPubMedCentralGoogle Scholar
  52. Idnurm A, Bailey AM, Cairns TC, Elliott CE, Foster GD, Ianiri G, Jeon J (2017) A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi. Fungal Biol Biotechnol 4(6):6PubMedPubMedCentralGoogle Scholar
  53. Jiang D, Zhu W, Wang Y, Sun C, Zhang K-Q, Yang J (2013) Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv 31(8):1562–1574PubMedGoogle Scholar
  54. Jiang Y, Guo D, Lu J, Durre P, Dong W, Yan W, Zhang W, Ma J, Jiang M, Xin F (2018) Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5. Biotechnol Biofuels 11:89PubMedPubMedCentralGoogle Scholar
  55. Kang HS, Charlop-Powers Z, Brady SF (2016) Multiplexed CRISPR/Cas9- and TAR-mediated promoter engineering of natural product biosynthetic gene clusters in yeast. ACS Synth Biol 5(9):1002–1010PubMedPubMedCentralGoogle Scholar
  56. Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K, Maruyama J-i (2016) Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett 38(4):637–642PubMedGoogle Scholar
  57. Katayama T, Nakamura H, Zhang Y, Pascal A, Fujii W, Maruyama J-i (2019) Forced recycling of an AMA1-based genome-editing plasmid allows for efficient multiple gene deletion/integration in the industrial filamentous fungus Aspergillus oryzae. Appl Environ Microbiol 85(3):e01896–e01818PubMedPubMedCentralGoogle Scholar
  58. Kavscek M, Strazar M, Curk T, Natter K, Petrovic U (2015) Yeast as a cell factory: current state and perspectives. Microb Cell Factories 14(94):94Google Scholar
  59. Kawaguchi H, Hasunuma T, Ogino C, Kondo A (2016) Bioprocessing of bio-based chemicals produced from lignocellulosic feedstocks. Curr Opin Biotechnol 42:30–39PubMedGoogle Scholar
  60. Khan AA, Bacha N, Ahmad B, Lutfullah G, Farooq U, Cox RJ (2014) Fungi as chemical industries and genetic engineering for the production of biologically active secondary metabolites. Asian Pac J Trop Biomed 4(11):859–870Google Scholar
  61. Kim H, Yoo SJ, Kang HA (2015) Yeast synthetic biology for the production of recombinant therapeutic proteins. FEMS Yeast Res 15(1):1–16PubMedGoogle Scholar
  62. Konning D, Kolmar H (2018) Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Factories 17(1):32Google Scholar
  63. Krappmann S (2007) Gene targeting in filamentous fungi: the benefits of impaired repair. Fungal Biol Rev 21(1):25–29Google Scholar
  64. Kuivanen J, Wang YJ, Richard P (2016) Engineering Aspergillus niger for galactaric acid production: elimination of galactaric acid catabolism by using RNA sequencing and CRISPR/Cas9. Microb Cell Factories 15(1):210Google Scholar
  65. Lee SS, Lee JH, Lee I (2013) Strain improvement by overexpression of the laeA gene in Monascus pilosus for the production of monascus-fermented rice. J Microbiol Biotechnol 23(7):959–965PubMedGoogle Scholar
  66. Leitão AL, Enguita FJ (2014) Fungal extrolites as a new source for therapeutic compounds and as building blocks for applications in synthetic biology. Microbiol Res 169(9–10):652–665PubMedGoogle Scholar
  67. Leynaud-Kieffer LMC, Curran SC, Kim I, Magnuson JK, Gladden JM, Baker SE, Simmons BA (2019) A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. PLoS One 14(1):e0210243PubMedPubMedCentralGoogle Scholar
  68. Li X-H, Yang H-J, Roy B, Park EY, Jiang L-J, Wang D, Miao Y-G (2010) Enhanced cellulase production of the Trichoderma viride mutated by microwave and ultraviolet. Microbiol Res 165(3):190–198PubMedGoogle Scholar
  69. Li C, Zhao X, Wang A, Huber GW, Zhang T (2015) Catalytic transformation of lignin for the production of chemicals and fuels. Chem Rev 115(21):11559–11624PubMedGoogle Scholar
  70. Li D, Tang Y, Lin J, Cai W (2017) Methods for genetic transformation of filamentous fungi. Microb Cell Factories 16(1):168Google Scholar
  71. Lin L, Sun Z, Li J, Chen Y, Liu Q, Sun W, Tian C (2018) Disruption of gul-1 decreased the culture viscosity and improved protein secretion in the filamentous fungus Neurospora crassa. Microb Cell Factories 17(1):96Google Scholar
  72. Liu Q, Gao R, Li J, Lin L, Zhao J, Sun W, Tian C (2017) Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering. Biotechnol Biofuels 10:1PubMedPubMedCentralGoogle Scholar
  73. Lu H, Cao W, Ouyang L, Xia J, Huang M, Chu J, Zhuang Y, Zhang S, Noorman H (2017) Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs. Biotechnol Bioeng 114(3):685–695PubMedGoogle Scholar
  74. Lynd LR, van Zyl WH, McBride JE, Laser M (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16(5):577–583PubMedGoogle Scholar
  75. Mans R, Daran JG, Pronk JT (2018) Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production. Curr Opin Biotechnol 50:47–56PubMedGoogle Scholar
  76. Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R (2018) Systems and synthetic biology approaches to engineer fungi for fine chemical production. Front Bioeng Biotechnol 6Google Scholar
  77. Matsu-ura T, Baek M, Kwon J, Hong C (2015) Efficient gene editing in Neurospora crassa with CRISPR technology. Fungal Biol Biotechnol 2:4PubMedPubMedCentralGoogle Scholar
  78. Mattanovich D, Sauer M, Gasser B (2014) Yeast biotechnology: teaching the old dog new tricks. Microb Cell Factories 13(1):34Google Scholar
  79. McKelvey SM, Murphy RA (2011) Biotechnological use of fungal enzymes. Biology and Applications, 179Google Scholar
  80. McLean KJ, Hans M, Meijrink B, van Scheppingen WB, Vollebregt A, Tee KL, van der Laan J-M, Leys D, Munro AW, van den Berg MA (2015) Single-step fermentative production of the cholesterol-lowering drug pravastatin via reprogramming of Penicillium chrysogenum. Proc Natl Acad Sci 112(9):2847–2852PubMedGoogle Scholar
  81. Menon V, Rao M (2012) Trends in bioconversion of lignocellulose: biofuels, platform chemicals & biorefinery concept. Prog Energy Combust Sci 38(4):522–550Google Scholar
  82. Meyer V (2008) Genetic engineering of filamentous fungi—progress, obstacles and future trends. Biotechnol Adv 26(2):177–185PubMedGoogle Scholar
  83. Meyer V, Ram AFJ, Punt PJ (2010) Genetics, genetic manipulation, and approaches to strain improvement of filamentous fungi. In: Manual of industrial microbiology and biotechnology, 3rd edn. American Society of Microbiology, pp 318–329Google Scholar
  84. Mohagheghi A, Linger J, Smith H, Yang S, Dowe N, Pienkos PT (2014) Improving xylose utilization by recombinant Zymomonas mobilis strain 8b through adaptation using 2-deoxyglucose. Biotechnol Biofuels 7(1):19PubMedPubMedCentralGoogle Scholar
  85. Mohanta TK, Bae H (2015) The diversity of fungal genome. Biol Proced Online 17(1):8PubMedPubMedCentralGoogle Scholar
  86. Mojsov KD (2016) Aspergillus enzymes for food industries. In: New and future developments in microbial biotechnology and bioengineering. Elsevier, pp 215–222Google Scholar
  87. Moser JW, Prielhofer R, Gerner SM, Graf AB, Wilson IB, Mattanovich D, Dragosits M (2017) Implications of evolutionary engineering for growth and recombinant protein production in methanol-based growth media in the yeast Pichia pastoris. Microb Cell Factories 16(1):49Google Scholar
  88. Motoda T, Yamaguchi M, Tsuyama T, Kamei I (2019) Down-regulation of pyruvate decarboxylase gene of white-rot fungus Phlebia sp. MG-60 modify the metabolism of sugars and productivity of extracellular peroxidase activity. J Biosci Bioeng 127(1):66–72PubMedGoogle Scholar
  89. Nevalainen KMH (2001) Strain improvement in filamentous fungi-an overview. In: Applied mycology and biotechnology, vol 1. Elsevier, pp 289–304Google Scholar
  90. Nielsen JC, Nielsen J (2017) Development of fungal cell factories for the production of secondary metabolites: linking genomics and metabolism. Synth Syst Biotechnol 2(1):5–12PubMedPubMedCentralGoogle Scholar
  91. Nødvig CS, Nielsen JB, Kogle ME, Mortensen UH (2015) A CRISPR-Cas9 system for genetic engineering of filamentous Fungi. PLoS One 10(7):e0133085PubMedPubMedCentralGoogle Scholar
  92. Nødvig CS, Hoof JB, Kogle ME, Jarczynska ZD, Lehmbeck J, Klitgaard DK, Mortensen UH (2018) Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli. Fungal Genet Biol 115:78–89PubMedGoogle Scholar
  93. Nonklang S, Abdel-Banat BMA, Cha-aim K, Moonjai N, Hoshida H, Limtong S, Yamada M, Akada R (2008) High-temperature ethanol fermentation and transformation with linear DNA in the Thermotolerant yeast Kluyveromyces marxianus DMKU3-1042. Appl Environ Microbiol 74(24):7514–7521PubMedPubMedCentralGoogle Scholar
  94. Olmedo-Monfil V, Cortés-Penagos C, Herrera-Estrella A (2004) Three decades of fungal transformation. In: Balbás P, Lorence A (eds) Recombinant gene expression. Methods in Molecular Biology, vol 267. Humana PressGoogle Scholar
  95. Østergaard LH, Olsen HS (2011) Industrial applications of fungal enzymes. In: Industrial applications. Springer, pp 269–290Google Scholar
  96. Parekh S, Vinci VA, Strobel RJ (2000) Improvement of microbial strains and fermentation processes. Appl Microbiol Biotechnol 54(3):287–301PubMedGoogle Scholar
  97. Park H-S, Jun S-C, Han K-H, Hong S-B, Yu J-H (2017) Diversity, application, and synthetic biology of industrially important Aspergillus fungi. Adv Appl Microbiol (Elsevier) 100:161–202Google Scholar
  98. Paul S, Zhang A, Ludeña Y, Villena GK, Yu F, Sherman DH, Gutiérrez-Correa M (2017) Insights from the genome of a high alkaline cellulase producing Aspergillus fumigatus strain obtained from Peruvian Amazon rainforest. J Biotechnol 251:53–58PubMedGoogle Scholar
  99. Peberdy JF (1986) The biology of Penicillium. Biotechnology Series [Biotechnol. Ser.]. 1986Google Scholar
  100. Peterson R, Nevalainen H (2012) Trichoderma reesei RUT-C30–thirty years of strain improvement. Microbiology 158(Pt 1):58–68PubMedGoogle Scholar
  101. Prielhofer R, Barrero JJ, Steuer S, Gassler T, Zahrl R, Baumann K, Sauer M, Mattanovich D, Gasser B, Marx H (2017) GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris. BMC Syst Biol 11(1):123PubMedPubMedCentralGoogle Scholar
  102. Rantasalo A, Vitikainen M, Paasikallio T, Jäntti J, Landowski CP, Mojzita D (2019) Novel genetic tools that enable highly pure protein production in Trichoderma reesei. Sci Rep 9(1):5032PubMedPubMedCentralGoogle Scholar
  103. Reddy GPK, Sridevi A, Kumar KD, Ramanjaneyulu G, Ramya A, Kumari BS, Reddy BR (2017) Strain improvement of aspergillus niger for the enhanced production of cellulase in solid state fermentation. In Microbial Biotechnology. Apple Academic Press, pp 201–218Google Scholar
  104. Rivera AL, Magana-Ortiz D, Gomez-Lim M, Fernandez F, Loske AM (2014) Physical methods for genetic transformation of fungi and yeast. Phys Life Rev 11(2):184–203PubMedGoogle Scholar
  105. Rodicio R, Heinisch JJ (2013) Yeast on the milky way: genetics, physiology and biotechnology of Kluyveromyces lactis. Yeast 30(5):165–177PubMedGoogle Scholar
  106. Rothstein R (1991) [19] targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Meth Enzymol (Elsevier) 194:281–301. %@ 0076-6879Google Scholar
  107. Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ (2016) The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 95:26–37PubMedGoogle Scholar
  108. Ruiz-Díez B (2002) Strategies for the transformation of filamentous fungi. J Appl Microbiol 92(2):189–195PubMedGoogle Scholar
  109. Ryan OW, Cate JH (2014) Multiplex engineering of industrial yeast genomes using CRISPRm. Methods Enzymol 546:473–489PubMedGoogle Scholar
  110. Sakai K, Kinoshita H, Nihira T (2012) Heterologous expression system in Aspergillus oryzae for fungal biosynthetic gene clusters of secondary metabolites. Appl Microbiol Biotechnol 93(5):2011–2022PubMedGoogle Scholar
  111. Sakamoto T, Sakuradani E, Okuda T, Kikukawa H, Ando A, Kishino S, Izumi Y, Bamba T, Shima J, Ogawa J (2017) Metabolic engineering of oleaginous fungus Mortierella alpina for high production of oleic and linoleic acids. Bioresour Technol 245:1610–1615PubMedGoogle Scholar
  112. Salame TM, Ziv C, Hadar Y, Yarden O (2011) RNAi as a potential tool for biotechnological applications in fungi. Appl Microbiol Biotechnol 89(3):501–512PubMedGoogle Scholar
  113. Schaepe P, Kwon MJ, Baumann B, Gutschmann B, Jung S, Lenz S, Nitsche B, Paege N, Schuetze T, Cairns TC (2018) Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks. Nucleic Acids Res 47(2):559–569Google Scholar
  114. Schuster M, Kahmann R (2019) CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes. Fungal Genet Biol 130:43–53Google Scholar
  115. Schwartz C, Wheeldon I (2018) CRISPR-Cas9-mediated genome editing and transcriptional control in Yarrowia lipolytica. Methods Mol Biol 1772:327–345PubMedGoogle Scholar
  116. Sewalt V, Shanahan D, Gregg L, La Marta J, Carrillo R (2016) The Generally Recognized as Safe (GRAS) process for industrial microbial enzymes. Ind Biotechnol 12(5):295–302Google Scholar
  117. Sherman F (2002) Getting started with yeast. Meth Enzymol (Elsevier) 350:3–41. %@ 0076-6879Google Scholar
  118. Shi T-Q, Liu G-N, Ji R-Y, Shi K, Song P, Ren L-J, Huang H, Ji X-J (2017) CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art. Appl Microbiol Biotechnol 101(20):7435–7443PubMedGoogle Scholar
  119. Shida Y, Furukawa T, Ogasawara W (2016) Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 80(9):1712–1729PubMedGoogle Scholar
  120. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122(1):19–27. %@ 0016-6731PubMedPubMedCentralGoogle Scholar
  121. Soukup AA, Keller NP, Wiemann P (2016) Enhancing nonribosomal peptide biosynthesis in filamentous fungi. In: Nonribosomal peptide and polyketide biosynthesis. Springer, pp 149–160Google Scholar
  122. Stovicek V, Holkenbrink C, Borodina I (2017) CRISPR/Cas system for yeast genome engineering: advances and applications. FEMS Yeast Res 17(5)Google Scholar
  123. Su X, Schmitz G, Zhang M, Mackie RI, Cann IKO (2012) Heterologous gene expression in filamentous fungi. Adv Appl Microbiol (Elsevier) 81:1–61Google Scholar
  124. Tabañag IDF, Chu I-M, Wei Y-H, Tsai S-L (2018) Ethanol production from hemicellulose by a consortium of different genetically-modified sacharomyces cerevisiae. J Taiwan Inst Chem Eng 89:15–25Google Scholar
  125. Tanaka T, Kondo A (2015) Cell-surface display of enzymes by the yeast Saccharomyces cerevisiae for synthetic biology. FEMS Yeast Res 15(1):1–9PubMedGoogle Scholar
  126. Teotia P, Kumar M, Varma A, Kumar V (2016) Molecular tools for strain improvement in Aspergillus. In: New and future developments in microbial biotechnology and bioengineering. Elsevier, pp 119–124Google Scholar
  127. Tong Z, Zheng X, Tong Y, Shi Y-C, Sun J (2019) Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era. Microb Cell Factories 18(1):28Google Scholar
  128. Turgeon BG, Condon B, Liu J, Zhang N (2010) Protoplast transformation of filamentous fungi. In: Molecular and cell biology methods for fungi. Humana Press, pp 3–19Google Scholar
  129. van Dijck PWM, Selten GCM, Hempenius RA (2003) On the safety of a new generation of DSM Aspergillus niger enzyme production strains. Regul Toxicol Pharmacol 38(1):27–35PubMedGoogle Scholar
  130. Vicente Muñoz I, Sarrocco S, Malfatti L, Baroncelli R, Vannacci G (2019) CRISPR-Cas for fungal genome editing: a new tool for the management of plant diseases. Front Plant Sci 10:135Google Scholar
  131. Vickers CE, Williams TC, Peng B, Cherry J (2017) Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 40:47–56PubMedGoogle Scholar
  132. Vieira Gomes AM, Souza Carmo T, Silva Carvalho L, Mendonca Bahia F, Parachin NS (2018) Comparison of yeasts as hosts for recombinant protein production. Microorganisms 6(2):pii: E38Google Scholar
  133. Vos AM, Lugones LG, Wösten HAB (2015) REMI in Molecular Fungal Biology. In Genetic Transformation Systems in Fungi, vol 1. Springer, Cham, pp 273–287Google Scholar
  134. Vu VH, Pham TA, Kim K (2010) Improvement of a fungal strain by repeated and sequential mutagenesis and optimization of solid-state fermentation for the hyper-production of raw-starch-digesting enzyme. J Microbiol Biotechnol 20(4):718–726Google Scholar
  135. Wakai S, Yoshie T, Asai-Nakashima N, Yamada R, Ogino C, Tsutsumi H, Hata Y, Kondo A (2014) L-lactic acid production from starch by simultaneous saccharification and fermentation in a genetically engineered Aspergillus oryzae pure culture. Bioresour Technol 173:376–383PubMedGoogle Scholar
  136. Wakai S, Arazoe T, Ogino C, Kondo A (2017) Future insights in fungal metabolic engineering. Bioresour Technol 245:1314–1326PubMedGoogle Scholar
  137. Walker GM (1998) Yeast physiology and biotechnology. John Wiley 10 & Sons, ChichesterGoogle Scholar
  138. Walter JM, Chandran SS, Horwitz AA (2016) CRISPR-Cas-Assisted Multiplexing (CAM): simple same-day multi-locus engineering in yeast. J Cell Physiol 231(12):2563–2569PubMedGoogle Scholar
  139. Wang G, Huang M, Nielsen J (2017a) Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr Opin Biotechnol 48:77–84PubMedGoogle Scholar
  140. Wang S, Chen H, Tang X, Zhang H, Chen W, Chen YQ (2017b) Molecular tools for gene manipulation in filamentous fungi. Appl Microbiol Biotechnol 101(22):8063–8075PubMedGoogle Scholar
  141. Weber J, Valiante V, Nodvig CS, Mattern DJ, Slotkowski RA, Mortensen UH, Brakhage AA (2017) Functional reconstitution of a fungal natural product gene cluster by advanced genome editing. ACS Synth Biol 6(1):62–68PubMedGoogle Scholar
  142. Weld RJ, Plummer KM, Carpenter MA, Ridgway HJ (2006) Approaches to functional genomics in filamentous fungi. Cell Res 16(1):31–44PubMedGoogle Scholar
  143. Wen F, Sun J, Zhao H (2010) Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol 76(4):1251–1260PubMedGoogle Scholar
  144. Weninger A, Hatzl AM, Schmid C, Vogl T, Glieder A (2016) Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris. J Biotechnol 235:139–149PubMedGoogle Scholar
  145. Xiao H, Zhong J-J (2016) Production of useful terpenoids by higher-fungus cell factory and synthetic biology approaches. Trends Biotechnol 34(3):242–255PubMedGoogle Scholar
  146. Yadav D, Tanveer A, Malviya N, Yadav S (2018) Overview and principles of bioengineering: the drivers of omics technologies. In: Omics technologies and bio-engineering. Academic Press, pp 3–23Google Scholar
  147. Yang L, Lübeck M, Ahring BK, Lübeck PS (2016) Enhanced succinic acid production in Aspergillus saccharolyticus by heterologous expression of fumarate reductase from Trypanosoma brucei. Appl Microbiol Biotechnol 100(4):1799–1809PubMedGoogle Scholar
  148. Yang L, Lübeck M, Lübeck PS (2017) Aspergillus as a versatile cell factory for organic acid production. Fungal Biol Rev 31(1):33–49Google Scholar
  149. Zhang F, Zhao X, Bai F (2018a) Improvement of cellulase production in Trichoderma reesei Rut-C30 by overexpression of a novel regulatory gene Trvib-1. Bioresour Technol 247:676–683PubMedGoogle Scholar
  150. Zhang J, Zhang G, Wang W, Wei D (2018b) Enhanced cellulase production in Trichoderma reesei RUT C30 via constitution of minimal transcriptional activators. Microb Cell Factories 17(1):75Google Scholar
  151. Zhang Y, Ouyang L, Nan Y, Chu J (2019) Efficient gene deletion and replacement in Aspergillus niger by modified in vivo CRISPR/Cas9 systems. Bioresour Bioprocess 6(1):4Google Scholar
  152. Zhao C, Chen S, Fang H (2018) Consolidated bioprocessing of lignocellulosic biomass to itaconic acid by metabolically engineering Neurospora crassa. Appl Microbiol Biotechnol 102(22):9577–9584PubMedGoogle Scholar
  153. Ziemons S, Koutsantas K, Becker K, Dahlmann T, Kück U (2017) Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes. BMC Biotechnol 17(1):16PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Gretty K. Villena
    • 1
    Email author
  • Ana A. Kitazono
    • 2
  • María  Lucila Hernández-Macedo
    • 3
  1. 1.Laboratory of Mycology and Biotechnology, La Molina National Agrarian UniversityLimaPeru
  2. 2.Laboratory of Biological Chemistry and Bioanalysis, La Molina National Agrarian UniversityLimaPeru
  3. 3.Postgraduate Program in Industrial Biotechnology. Institute of Technology and Research, Laboratory of Molecular Biology, UniversityAracajuBrazil

Personalised recommendations