Genetic Manipulation and Transformation Methods for Aspergillus spp.

References

• Bennett JW. An overview of the genus Aspergillus. In: Machida M, Gomi K, editors. Aspergillus: molecular biology and genomics. Norfolk (UK): Caister Academic Press; 2010. p. 1–17.
   Google Scholar
• Samson RA, Visagie CM, Houbraken J, et al. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol. 2014;78:141–173.
   PubMed Web of Science ®Google Scholar
• de Vries RP, Riley R, Wiebenga A, et al. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol. 2017;18:28.
   PubMed Web of Science ®Google Scholar
• Latge JP. Aspergillus fumigatus and aspergillosis. Clin Microbiol Rev. 1999;12:310–350.
   PubMed Web of Science ®Google Scholar
• Paulussen C, Hallsworth JE, Alvarez-Perez S, et al. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb Biotechnol. 2017;10:296–322.
   PubMed Web of Science ®Google Scholar
• Latge JP, Chamilos G. Aspergillus fumigatus and Aspergillosis in 2019. Clin Microbiol Rev. 2019;33:e00140-18.
   PubMed Web of Science ®Google Scholar
• Bastos RW, Valero C, Silva LP, et al. Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans. mSphere. 2020;5:e00153-20.
   Web of Science ®Google Scholar
• Hedayati MT, Pasqualotto AC, Warn PA, et al. Aspergillus flavus: human pathogen, allergen and mycotoxin producer. Microbiology (Reading). 2007;153:1677–1692.
   PubMed Web of Science ®Google Scholar
• Perrone G, Susca A, Cozzi G, et al. Biodiversity of Aspergillus species in some important agricultural products. Stud Mycol. 2007;59:53–66.
   PubMed Web of Science ®Google Scholar
• Perrone G, Gallo A. Aspergillus species and their associated mycotoxins. Methods Mol Biol. 2017;1542:33–49.
   Google Scholar
• Agriopoulou S, Stamatelopoulou E, Varzakas T. Advances in analysis and detection of major mycotoxins in foods. Foods. 2020;9:518.
   PubMed Web of Science ®Google Scholar
• Kitamoto K. Cell biology of the Koji mold Aspergillus oryzae. Biosci Biotechnol Biochem. 2015;79:863–869.
   PubMed Web of Science ®Google Scholar
• Park HS, Jun SC, Han KH, et al. Diversity, application, and synthetic biology of industrially important Aspergillus fungi. Adv Appl Microbiol. 2017;100:161–202.
   PubMed Web of Science ®Google Scholar
• Cairns TC, Nai C, Meyer V. How a fungus shapes biotechnology: 100 years of Aspergillus niger research. Fungal Biol Biotechnol. 2018;5:13.
   Google Scholar
• Bourdichon F, Casaregola S, Farrokh C, et al. Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol. 2012;154:87–97.
   PubMed Web of Science ®Google Scholar
• Lu H, Cao W, Liu X, et al. Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition. Sci Rep. 2018;8:14404.
   PubMed Web of Science ®Google Scholar
• Ojeda-Lopez M, Chen W, Eagle CE, et al. Evolution of asexual and sexual reproduction in the aspergilli. Stud Mycol. 2018;91:37–59.
   PubMedGoogle Scholar
• Wang S, Chen H, Tang X, et al. Molecular tools for gene manipulation in filamentous fungi. Appl Microbiol Biotechnol. 2017;101:8063–8075.
   PubMed Web of Science ®Google Scholar
• Song R, Zhai Q, Sun L, et al. CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective. Appl Microbiol Biotechnol. 2019;103:6919–6932.
   PubMed Web of Science ®Google Scholar
• Nodvig CS, Nielsen JB, Kogle ME, et al. A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS One. 2015;10:e0133085.
   PubMed Web of Science ®Google Scholar
• Ruiz-Diez B. Strategies for the transformation of filamentous fungi. J Appl Microbiol. 2002;92:189–195.
   PubMed Web of Science ®Google Scholar
• Balabanova LA, Shkryl YN, Slepchenko LV, et al. Development of host strains and vector system for an efficient genetic transformation of filamentous fungi. Plasmid. 2019;101:1–9.
   Web of Science ®Google Scholar
• van den Hombergh JP, van de Vondervoort PJ, Fraissinet-Tachet L, et al. Aspergillus as a host for heterologous protein production: the problem of proteases. Trends Biotechnol. 1997;15:256–263.
   PubMed Web of Science ®Google Scholar
• Yoon J, Maruyama J, Kitamoto K. Disruption of ten protease genes in the filamentous fungus Aspergillus oryzae highly improves production of heterologous proteins. Appl Microbiol Biotechnol. 2011;89:747–759.
   PubMed Web of Science ®Google Scholar
• Xie H, Ma Q, Wei D, et al. Metabolic engineering of an industrial Aspergillus niger strain for itaconic acid production. 3 Biotech. 2020;10:113.
   Google Scholar
• Jin FJ, Maruyama J, Juvvadi PR, et al. Development of a novel quadruple auxotrophic host transformation system by argB gene disruption using adeA gene and exploiting adenine auxotrophy in Aspergillus oryzae. FEMS Microbiol Lett. 2004;239:79–85.
   PubMed Web of Science ®Google Scholar
• He ZM, Price MS, Obrian GR, et al. Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus. BMC Microbiol. 2007;7:104.
   Web of Science ®Google Scholar
• Niu J, Arentshorst M, Seelinger F, et al. A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger. Arch Microbiol. 2016;198:861–868.
   PubMed Web of Science ®Google Scholar
• Palmer LM, Cove DJ. Pyrimidine biosynthesis in Aspergillus nidulans: isolation and preliminary characterisation of auxotrophic mutants. Mol Gen Genet. 1975;138:243–255.
   Google Scholar
• Xue T, Nguyen CK, Romans A, et al. Isogenic auxotrophic mutant strains in the Aspergillus fumigatus genome reference strain AF293. Arch Microbiol. 2004;182:346–353.
   PubMed Web of Science ®Google Scholar
• Nguyen KT, Ho QN, Pham TH, et al. The construction and use of versatile binary vectors carrying pyrG auxotrophic marker and fluorescent reporter genes for Agrobacterium-mediated transformation of Aspergillus oryzae. World J Microbiol Biotechnol. 2016;32:204.
   Web of Science ®Google Scholar
• da Silva Ferreira ME, Kress MR, Savoldi M, et al. The akuB(KU80) mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus. Eukaryot Cell. 2006;5:207–211.
   PubMed Web of Science ®Google Scholar
• Nayak T, Szewczyk E, Oakley CE, et al. A versatile and efficient gene-targeting system for Aspergillus nidulans. Genetics. 2006;172:1557–1566.
   PubMed Web of Science ®Google Scholar
• Takahashi T, Masuda T, Koyama Y. Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol Genet Genomics. 2006;275:460–470.
   PubMed Web of Science ®Google Scholar
• Meyer V, Arentshorst M, El-Ghezal A, et al. Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol. 2007;128:770–775.
   Web of Science ®Google Scholar
• Chang PK, Scharfenstein LL, Wei Q, et al. Development and refinement of a high-efficiency gene-targeting system for Aspergillus flavus. J Microbiol Methods. 2010;81:240–246.
   PubMed Web of Science ®Google Scholar
• He B, Tu Y, Jiang C, et al. Functional genomics of Aspergillus oryzae: strategies and progress. Microorganisms. 2019;7:103.
   Web of Science ®Google Scholar
• Gravelat FN, Askew DS, Sheppard DC. Targeted gene deletion in Aspergillus fumigatus using the hygromycin-resistance split-marker approach. Methods Mol Biol. 2012;845:119–130.
   PubMedGoogle Scholar
• Punt PJ, Oliver RP, Dingemanse MA, et al. Transformation of Aspergillus based on the hygromycin B resistance marker from Escherichia coli. Gene. 1987;56:117–124.
   PubMed Web of Science ®Google Scholar
• Ventura L, Ramon D. Transformation of Aspergillus terreus with the hygromycin B resistance marker from Escherichia coli. FEMS Microbiol Lett. 1991;66:189–193.
   Google Scholar
• Suzuki S, Tada S, Fukuoka M, et al. A novel transformation system using a bleomycin resistance marker with chemosensitizers for Aspergillus oryzae. Biochem Biophys Res Commun. 2009;383:42–47.
   Web of Science ®Google Scholar
• Pronk JT. Auxotrophic yeast strains in fundamental and applied research. Appl Environ Microbiol. 2002;68:2095–2100.
   Web of Science ®Google Scholar
• Nguyen KT, Ho QN, Do L, et al. A new and efficient approach for construction of uridine/uracil auxotrophic mutants in the filamentous fungus Aspergillus oryzae using Agrobacterium tumefaciens-mediated transformation. World J Microbiol Biotechnol. 2017;33:107.
   Web of Science ®Google Scholar
• Oakley BR, Rinehart JE, Mitchell BL, et al. Cloning, mapping and molecular analysis of the pyrG (orotidine-5'-phosphate decarboxylase) gene of Aspergillus nidulans. Gene. 1987;61:385–399.
   PubMed Web of Science ®Google Scholar
• Nielsen ML, Albertsen L, Lettier G, et al. Efficient PCR-based gene targeting with a recyclable marker for Aspergillus nidulans. Fungal Genet Biol. 2006;43:54–64.
   PubMed Web of Science ®Google Scholar
• Maruyama J, Kitamoto K. Multiple gene disruptions by marker recycling with highly efficient gene-targeting background (DeltaligD) in Aspergillus oryzae. Biotechnol Lett. 2008;30:1811–1817.
   PubMed Web of Science ®Google Scholar
• Tani S, Tsuji A, Kunitake E, et al. Reversible impairment of the ku80 gene by a recyclable marker in Aspergillus aculeatus. AMB Express. 2013;3:4.
   Web of Science ®Google Scholar
• Dohn JW Jr, Grubbs AW, Oakley CE, et al. New multi-marker strains and complementing genes for Aspergillus nidulans molecular biology. Fungal Genet Biol. 2018;111:1–6.
   Web of Science ®Google Scholar
• Li D, Tang Y, Lin J, et al. Methods for genetic transformation of filamentous fungi. Microb Cell Fact. 2017;16:168.
   PubMed Web of Science ®Google Scholar
• Herzog RW, Daniell H, Singh NK, et al. A comparative study on the transformation of Aspergillus nidulans by microprojectile bombardment of conidia and a more conventional procedure using protoplasts treated with polyethyleneglycol. Appl Microbiol Biotechnol. 1996;45:333–337.
   Web of Science ®Google Scholar
• Meyer V, Mueller D, Strowig T, et al. Comparison of different transformation methods for Aspergillus giganteus. Curr Genet. 2003;43:371–377.
   Web of Science ®Google Scholar
• Hutchison HT, Hartwell LH. Macromolecule synthesis in yeast spheroplasts. J Bacteriol. 1967;94:1697–1705.
   PubMed Web of Science ®Google Scholar
• Anne J, Eyssen H, Somer PD. Formation and regeneration of Penicillium chrysogenum protoplasts. Arch Microbiol. 1974;98:159–166.
   Web of Science ®Google Scholar
• Tilburn J, Scazzocchio C, Taylor GG, et al. Transformation by integration in Aspergillus nidulans. Gene. 1983;26:205–221.
   PubMed Web of Science ®Google Scholar
• Szewczyk E, Nayak T, Oakley CE, et al. Fusion PCR and gene targeting in Aspergillus nidulans. Nat Protoc. 2006;1:3111–3120.
   PubMed Web of Science ®Google Scholar
• Peberdy JF. 1995. Fungal protoplasts. In: Kück U, editor. Genetics and biotechnology. The mycota (a comprehensive treatise on fungi as experimental systems for basic and applied research). Berlin (Germany): Springer. p. 49–60.
   Google Scholar
• Zhao C, Fraczek MG, Dineen L, et al. High-throughput gene replacement in Aspergillus fumigatus. Curr Protoc Microbiol. 2019;54:e88.
   Google Scholar
• Gelvin SB. Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol Rev. 2003;67:16–37.
   PubMed Web of Science ®Google Scholar
• de Groot MJ, Bundock P, Hooykaas PJ, et al. Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol. 1998;16:839–842.
   PubMed Web of Science ®Google Scholar
• Gouka RJ, Gerk C, Hooykaas PJ, et al. Transformation of Aspergillus awamori by Agrobacterium tumefaciens-mediated homologous recombination. Nat Biotechnol. 1999;17:598–601.
   PubMed Web of Science ®Google Scholar
• Park S-M. Improved transformation of the filamentous fungus Aspergillus niger using Agrobacterium tumefaciens. Mycobiology. 2001;29:132–134.
   Google Scholar
• Sugui JA, Chang YC, Kwon-Chung KJ. Agrobacterium tumefaciens-mediated transformation of Aspergillus fumigatus: an efficient tool for insertional mutagenesis and targeted gene disruption. Appl Environ Microbiol. 2005;71:1798–1802.
   PubMed Web of Science ®Google Scholar
• Michielse CB, Hooykaas PJ, van den Hondel CA, et al. Agrobacterium-mediated transformation of the filamentous fungus Aspergillus awamori. Nat Protoc. 2008;3:1671–1678.
   PubMed Web of Science ®Google Scholar
• Kunitake E, Tani S, Sumitani J, et al. Agrobacterium tumefaciens-mediated transformation of Aspergillus aculeatus for insertional mutagenesis. AMB Express. 2011;1:46.
   PubMed Web of Science ®Google Scholar
• Li M, Zhou L, Liu M, et al. Construction of an engineering strain producing high yields of α-transglucosidase via Agrobacterium tumefaciens-mediated transformation of Asperillus niger. Biosci Biotechnol Biochem. 2013;77:1860–1866.
   PubMed Web of Science ®Google Scholar
• Kalleda N, Naorem A, Manchikatla RV. Targeting fungal genes by diced siRNAs: a rapid tool to decipher gene function in Aspergillus nidulans. PLoS One. 2013;8:e75443.
   PubMed Web of Science ®Google Scholar
• Mora-Lugo R, Zimmermann J, Rizk AM, et al. Development of a transformation system for Aspergillus sojae based on the Agrobacterium tumefaciens-mediated approach. BMC Microbiol. 2014;14:247.
   Web of Science ®Google Scholar
• Wang D, He D, Li G, et al. An efficient tool for random insertional mutagenesis: Agrobacterium tumefaciens-mediated transformation of the filamentous fungus Aspergillus terreus. J Microbiol Methods. 2014;98:114–118.
   Web of Science ®Google Scholar
• Fan Z, Yu H, Guo Q, et al. Identification and characterization of an anti-oxidative stress-associated mutant of Aspergillus fumigatus transformed by Agrobacterium tumefaciens. Mol Med Rep. 2016;13:2367–2376.
   Web of Science ®Google Scholar
• Weyda I, Yang L, Vang J, et al. A comparison of Agrobacterium-mediated transformation and protoplast-mediated transformation with CRISPR-Cas9 and bipartite gene targeting substrates, as effective gene targeting tools for Aspergillus carbonarius. J Microbiol Methods. 2017;135:26–34.
   Web of Science ®Google Scholar
• Han G, Shao Q, Li C, et al. An efficient Agrobacterium-mediated transformation method for aflatoxin generation fungus Aspergillus flavus. J Microbiol. 2018;56:356–364.
   Web of Science ®Google Scholar
• Min T, Xiong L, Liang Y, et al. Disruption of stcA blocks sterigmatocystin biosynthesis and improves echinocandin B production in Aspergillus delacroxii. World J Microbiol Biotechnol. 2019;35:109.
   Web of Science ®Google Scholar
• Sun Y, Niu Y, He B, et al. A dual selection marker transformation system using Agrobacterium tumefaciens for the industrial Aspergillus oryzae 3.042. J Microbiol Biotechnol. 2019;29:230–234.
   Web of Science ®Google Scholar
• Setoguchi S, Mizutani O, Yamada O, et al. Effect of pepA deletion and overexpression in Aspergillus luchuensis on sweet potato shochu brewing. J Biosci Bioeng. 2019;128:456–462.
   Web of Science ®Google Scholar
• Zhu SY, Xu Y, Yu XW. Improved homologous expression of the acidic lipase from Aspergillus niger. J Microbiol Biotechnol. 2020;30:196–205.
   Web of Science ®Google Scholar
• Chakraborty BN, Kapoor M. Transformation of filamentous fungi by electroporation. Nucleic Acids Res. 1990;18:6737.
   PubMed Web of Science ®Google Scholar
• Richey MG, Marek ET, Schardl CL, et al. Transformation of filamentous fungi with plasmid DNA by electroporation. Phytopathology. 1989;79:844–847.
   Web of Science ®Google Scholar
• Chakraborty BN, Patterson NA, Kapoor M. An electroporation-based system for high-efficiency transformation of germinated conidia of filamentous fungi. Can J Microbiol. 1991;37:858–863.
   PubMed Web of Science ®Google Scholar
• Ozeki K, Kyoya F, Hizume K, et al. Transformation of intact Aspergillus niger by electroporation. Biosci Biotechnol Biochem. 1994;58:2224–2227.
   PubMed Web of Science ®Google Scholar
• Sanchez O, Aguirre J. Efficient transformation of Aspergillus nidulans by electroporation of germinated conidia. Fungal Genet Newsl. 1996;43:48–51.
   Google Scholar
• Brown JS, Aufauvre-Brown A, Holden DW. Insertional mutagenesis of Aspergillus fumigatus. Mol Gen Genet. 1998;259:327–335.
   Google Scholar
• Weidner G, d'Enfert C, Koch A, et al. Development of a homologous transformation system for the human pathogenic fungus Aspergillus fumigatus based on the pyrG gene encoding orotidine 5'-monophosphate decarboxylase. Curr Genet. 1998;33:378–385.
   PubMed Web of Science ®Google Scholar
• Firon A, Beauvais A, Latge JP, et al. Characterization of essential genes by parasexual genetics in the human fungal pathogen Aspergillus fumigatus: impact of genomic rearrangements associated with electroporation of DNA. Genetics. 2002;161:1077–1087.
   PubMed Web of Science ®Google Scholar
• Firon A, Villalba F, Beffa R, et al. Identification of essential genes in the human fungal pathogen Aspergillus fumigatus by transposon mutagenesis. Eukaryot Cell. 2003;2:247–255.
   PubMedGoogle Scholar
• Kuck U, Hoff B. New tools for the genetic manipulation of filamentous fungi. Appl Microbiol Biotechnol. 2010;86:51–62.
   Web of Science ®Google Scholar
• Sheppard DC, Doedt T, Chiang LY, et al. The Aspergillus fumigatus StuA protein governs the up-regulation of a discrete transcriptional program during the acquisition of developmental competence. Mol Biol Cell. 2005;16:5866–5879.
   PubMed Web of Science ®Google Scholar
• Nielsen ML, de Jongh WA, Meijer SL, et al. Transient marker system for iterative gene targeting of a prototrophic fungus. Appl Environ Microbiol. 2007;73:7240–7245.
   Web of Science ®Google Scholar
• Nielsen JB, Nielsen ML, Mortensen UH. Transient disruption of non-homologous end-joining facilitates targeted genome manipulations in the filamentous fungus Aspergillus nidulans. Fungal Genet Biol. 2008;45:165–170.
   PubMed Web of Science ®Google Scholar
• Goswami RS. Targeted gene replacement in fungi using a split-marker approach. Methods Mol Biol. 2012;835:255–269.
   Google Scholar
• Yu JH, Hamari Z, Han KH, et al. Double-joint PCR: a PCR-based molecular tool for gene manipulations in filamentous fungi. Fungal Genet Biol. 2004;41:973–981.
   PubMed Web of Science ®Google Scholar
• Gaj T, Sirk SJ, Shui SL, et al. Genome-editing technologies: principles and applications. Cold Spring Harb Perspect Biol. 2016;8:a023754.
   Web of Science ®Google Scholar
• Barrangou R, Marraffini LA. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell. 2014;54:234–244.
   PubMed Web of Science ®Google Scholar
• Rath D, Amlinger L, Rath A, et al. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. 2015;117:119–128.
   PubMed Web of Science ®Google Scholar
• Fuller KK, Chen S, Loros JJ, et al. Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot Cell. 2015;14:1073–1080.
   PubMed Web of Science ®Google Scholar
• Zhang C, Meng X, Wei X, et al. Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet Biol. 2016;86:47–57.
   PubMed Web of Science ®Google Scholar
• Katayama T, Tanaka Y, Okabe T, et al. Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett. 2016;38:637–642.
   PubMed Web of Science ®Google Scholar
• Al Abdallah Q, Ge W, Fortwendel JR. A simple and universal system for gene manipulation in Aspergillus fumigatus: in vitro-assembled Cas9-guide RNA ribonucleoproteins coupled with microhomology repair templates. mSphere. 2017;2:e00446-17.
   Web of Science ®Google Scholar
• Weber J, Valiante V, Nodvig CS, et al. Functional reconstitution of a fungal natural product gene cluster by advanced genome editing. ACS Synth Biol. 2017;6:62–68.
   PubMed Web of Science ®Google Scholar
• Nakamura H, Katayama T, Okabe T, et al. Highly efficient gene targeting in Aspergillus oryzae industrial strains under ligD mutation introduced by genome editing: strain-specific differences in the effects of deleting EcdR, the negative regulator of sclerotia formation. J Gen Appl Microbiol. 2017;63:172–178.
   Web of Science ®Google Scholar
• Nodvig CS, Hoof JB, Kogle ME, et al. Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli. Fungal Genet Biol. 2018;115:78–89.
   PubMed Web of Science ®Google Scholar
• Matsuda Y, Bai T, Phippen CBW, et al. Novofumigatonin biosynthesis involves a non-heme iron-dependent endoperoxide isomerase for orthoester formation. Nat Commun. 2018;9:2587.
   PubMed Web of Science ®Google Scholar
• Zheng X, Zheng P, Zhang K, et al. 5S rRNA promoter for guide RNA expression enabled highly efficient CRISPR/Cas9 genome editing in Aspergillus niger. ACS Synth Biol. 2019;8:1568–1574.
   PubMed Web of Science ®Google Scholar
• Leynaud-Kieffer LMC, Curran SC, Kim I, et al. A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. PLoS One. 2019;14:e0210243.
   Web of Science ®Google Scholar
• Kadooka C, Yamaguchi M, Okutsu K, et al. A CRISPR/Cas9-mediated gene knockout system in Aspergillus luchuensis mut. kawachii. Biosci Biotechnol Biochem. 2020;84:2179–2183.
   PubMed Web of Science ®Google Scholar