Development of a CRISPR/Cpf1 system for multiplex gene editing in Aspergillus oryzae.

Aspergillus oryzae CRISPR/Cpf1 system Filamentous fungi Multiplex gene editing

Journal

Folia microbiologica
ISSN: 1874-9356
Titre abrégé: Folia Microbiol (Praha)
Pays: United States
ID NLM: 0376757

Informations de publication

Date de publication:
25 Jul 2023
Historique:
received: 08 05 2023
accepted: 18 07 2023
medline: 25 7 2023
pubmed: 25 7 2023
entrez: 25 7 2023
Statut: aheadofprint

Résumé

CRISPR/Cas technology is a powerful tool for genome engineering in Aspergillus oryzae as an industrially important filamentous fungus. Previous study has reported the application of the CRISPR/Cpf1 system based on the Cpf1 (LbCpf1) from Lachnospiraceae bacterium in A. oryzae. However, multiplex gene editing have not been investigated using this system. Here, we presented a new CRISPR/Cpf1 multiplex gene editing system in A. oryzae, which contains the Cpf1 nuclease (FnCpf1) from Francisella tularensis subsp. novicida U112 and CRISPR-RNA expression cassette. The crRNA cassette consisted of direct repeats and guide sequences driven by the A. oryzae U6 promoter and U6 terminator. Using the constructed FnCpf1 gene editing system, the wA and pyrG genes were mutated successfully. Furthermore, simultaneous editing of wA and pyrG genes in A. oryzae was performed using two guide sequences targeting these gene loci in a single crRNA array. This promising CRISPR/Cpf1 genome-editing system provides a powerful tool for genetically engineering A. oryzae.

Identifiants

DOI: 10.1007/s12223-023-01081-9 PMID: 37490214
pubmed: 37490214
doi: 10.1007/s12223-023-01081-9
pii: 10.1007/s12223-023-01081-9
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2023. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.

Références

Abdulrachman D, Champreda V, Eurwilaichitr L, Chantasingh D, Pootanakit K (2022) Efficient multiplex CRISPR/Cpf1 (Cas12a) genome editing system in Aspergillus aculeatus TBRC 277. J Biotechnol 355:53–64. https://doi.org/10.1016/j.jbiotec.2022.06.011
doi: 10.1016/j.jbiotec.2022.06.011 pubmed: 35788357
Abdulrachman D, Eurwilaichitr L, Champreda V, Chantasingh D, Pootanakit K (2021) Development of a CRISPR/Cpf1 system for targeted gene disruption in Aspergillus aculeatus TBRC 277. BMC Biotechnol 21:15. https://doi.org/10.1186/s12896-021-00669-8
doi: 10.1186/s12896-021-00669-8 pubmed: 33573639 pmcid: 7879532
Braglia P, Percudani R, Dieci G (2005) Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 280:19551–19562. https://doi.org/10.1074/jbc.M412238200
doi: 10.1074/jbc.M412238200 pubmed: 15788403
DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336–4343. https://doi.org/10.1093/nar/gkt135
doi: 10.1093/nar/gkt135 pubmed: 23460208 pmcid: 3627607
Donohoue PD, Barrangou R, May AP (2018) Advances in industrial biotechnology using CRISPR-Cas systems. Trends Biotechnol 36:134–146. https://doi.org/10.1016/j.tibtech.2017.07.007
doi: 10.1016/j.tibtech.2017.07.007 pubmed: 28778606
Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532:517–521. https://doi.org/10.1038/nature17945
doi: 10.1038/nature17945 pubmed: 27096362
Ichishima E (2016) Development of enzyme technology for Aspergillus oryzae, A. sojae, and A. luchuensis, the national microorganisms of Japan. Biosci Biotechnol Biochem 80:1681–1692. https://doi.org/10.1080/09168451.2016.1177445
doi: 10.1080/09168451.2016.1177445 pubmed: 27151561
Ishi K, Watanabe T, Juvvadi PR, Maruyama J, Kitamoto K (2005) Development of a modified positive selection medium that allows to isolate Aspergillus oryzae strains cured of the integrated niaD-based plasmid. Biosci Biotechnol Biochem 69:2463–2465. https://doi.org/10.1271/bbb.69.2463
doi: 10.1271/bbb.69.2463 pubmed: 16377911
Jiang F, Doudna JA (2017) CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys 46:505–529. https://doi.org/10.1146/annurev-biophys-062215010822
doi: 10.1146/annurev-biophys-062215010822 pubmed: 28375731
Jiménez A, Hoff B, Revuelta JL (2020) Multiplex genome editing in Ashbya gossypii using CRISPR-Cpf1. N Biotechnol 57:29–33. https://doi.org/10.1016/j.nbt.2020.02.002
doi: 10.1016/j.nbt.2020.02.002 pubmed: 32194155
Jin FJ, Maruyama J, Juvvadi PR, Arioka M, Kitamoto K (2004) 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 239:79–85. https://doi.org/10.1016/j.femsle.2004.08.025
doi: 10.1016/j.femsle.2004.08.025 pubmed: 15451104
Kadooka C, Yamaguchi M, Okutsu K, Yoshizaki Y, Takamine K, Katayama T, Maruyama JI, Tamaki H, Futagami T (2020) A CRISPR/Cas9-mediated gene knockout system in Aspergillus luchuensis mut. kawachii. Biosci Biotechnol Biochem 84:2179–2183. https://doi.org/10.1080/09168451.2020.1792761
doi: 10.1080/09168451.2020.1792761 pubmed: 32657224
Katayama T, Maruyama JI (2022) CRISPR/Cpf1-mediated mutagenesis and gene deletion in industrial filamentous fungi Aspergillus oryzae and Aspergillus sojae. J Biosci Bioeng 133:353–361. https://doi.org/10.1016/j.jbiosc.2021.12.017
doi: 10.1016/j.jbiosc.2021.12.017 pubmed: 35101371
Katayama T, Nakamura H, Zhang Y, Pascal A, Fujii W, Maruyama JI (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:e01896–e1918. https://doi.org/10.1128/AEM.01896-18
doi: 10.1128/AEM.01896-18 pubmed: 30478227 pmcid: 6344613
Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K, Maruyama J (2016) Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett 38:637–642. https://doi.org/10.1007/s10529-015-2015-x
doi: 10.1007/s10529-015-2015-x pubmed: 26687199
Kobayashi T, Abe K, Asai K, Gomi K, Juvvadi PR, Kato M, Kitamoto K, Takeuchi M, Machida M (2007) Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem 71:646–670. https://doi.org/10.1271/bbb.60550
doi: 10.1271/bbb.60550 pubmed: 17341818
Kwon MJ, Schütze T, Spohner S, Haefner S, Meyer V (2019) Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi. Fungal Biol Biotechnol 6:15. https://doi.org/10.1186/s40694-019-0079-4
doi: 10.1186/s40694-019-0079-4 pubmed: 31641526 pmcid: 6796461
Labuhn M, Adams FF, Ng M, Knoess S, Schambach A, Charpentier EM, Schwarzer A, Mateo JL, Klusmann JH, Heckl D (2018) Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications. Nucleic Acids Res 46:1375–1385. https://doi.org/10.1093/nar/gkx1268
doi: 10.1093/nar/gkx1268 pubmed: 29267886
Li YZ, Zhang HX, Chen ZM, Fan JX, Chen TM, Zeng B, Zhang Z (2022) Construction of single, double, or triple mutants within kojic acid synthesis genes kojA, kojR, and kojT by the CRISPR/Cas9 tool in Aspergillus oryzae. Folia Microbiol 67:459–468. https://doi.org/10.1007/s12223-022-00949-6
doi: 10.1007/s12223-022-00949-6
Ma XL, Zhang QY, Zhu QL, Liu W, Chen Y, Qiu R, Wang B, Yang ZF, Li HY, Lin YR, Xie YY, Shen RX, Chen SF, Wang Z, Chen YL, Guo JX, Chen LT, Zhao XC, Dong ZC, Liu YG (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284. https://doi.org/10.1016/j.molp.2015.04.007
doi: 10.1016/j.molp.2015.04.007 pubmed: 25917172
Machida M, Yamada O, Gomi K (2008) Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future. DNA Res 15:173–183. https://doi.org/10.1093/dnares/dsn020
doi: 10.1093/dnares/dsn020 pubmed: 18820080 pmcid: 2575883
Malina A, Cameron CJF, Robert F, Blanchette M, Dostie J, Pelletier J (2015) PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing. Nat Commun 6:10124. https://doi.org/10.1038/ncomms10124
doi: 10.1038/ncomms10124 pubmed: 26644285
Maruyama J, Kitamoto K (2011) Targeted gene disruption in Koji mold Aspergillus oryzae. Methods Mol Biol 765:447–456. https://doi.org/10.1007/978-1-61779-197-0_27
doi: 10.1007/978-1-61779-197-0_27 pubmed: 21815109
Nguyen KT, Ho QN, Pham TH, Phan TN, Tran VT (2016) 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 32:204. https://doi.org/10.1007/s11274-016-2168-3
doi: 10.1007/s11274-016-2168-3 pubmed: 27804102
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 115:78–89. https://doi.org/10.1016/j.fgb.2018.01.004
doi: 10.1016/j.fgb.2018.01.004 pubmed: 29325827
Nødvig CS, Nielsen JB, Kogle ME, Mortensen UH (2015) A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PloS one 10:e0133085. https://doi.org/10.1371/journal.pone.0133085
Shan QW, Wang YP, Li J, Zhang Y, Chen KL, Liang Z, Zhang K, Liu JX, Xi JJ, Qiu JL, Gao CX (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688. https://doi.org/10.1038/nbt.2650
doi: 10.1038/nbt.2650 pubmed: 23929338
Song L, Ouedraogo JP, Kolbusz M, Nguyen TTM, Tsang A (2018) Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger. PloS one 13:e0202868. https://doi.org/10.1371/journal.pone.0202868
Vanegas KG, Jarczynska ZD, Strucko T, Mortensen UH (2019) Cpf1 enables fast and efficient genome editing in Aspergilli. Fungal Biol Biotechnol 6:6. https://doi.org/10.1186/s40694-019-0069-6
doi: 10.1186/s40694-019-0069-6 pubmed: 31061713 pmcid: 6492335
Verwaal R, Buiting-Wiessenhaan N, Dalhuijsen S, Roubos JA (2018) CRISPR/Cpf1 enables fast and simple genome editing of Saccharomyces cerevisiae. Yeast 35:201–211. https://doi.org/10.1002/yea.3278
doi: 10.1002/yea.3278 pubmed: 28886218
Wang MG, Mao YF, Lu YM, Tao XP, Zhu JK (2017) Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol Plant 10:1011–1013. https://doi.org/10.1016/j.molp.2017.03.001
doi: 10.1016/j.molp.2017.03.001 pubmed: 28315752
Wang Q, Coleman JJ (2019) Progress and challenges: development and implementation of CRISPR/Cas9 technology in filamentous fungi. Comput Struct Biotechnol J 17:761–769. https://doi.org/10.1016/j.csbj.2019.06.007
doi: 10.1016/j.csbj.2019.06.007 pubmed: 31312414 pmcid: 6607083
Wu XB, Kriz AJ, Sharp PA (2014) Target specificity of the CRISPR-Cas9 system. Quant Biol 2:59–70. https://doi.org/10.1007/s40484-014-0030-x
doi: 10.1007/s40484-014-0030-x pubmed: 25722925 pmcid: 4338555
Xin QL, Wang B, Pan L (2022) Development and application of a CRISPR-dCpf1 assisted multiplex gene regulation system in Bacillus amyloliquefaciens LB1ba02. Microbiol Res 263:127131. https://doi.org/10.1016/j.micres.2022.127131
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771. https://doi.org/10.1016/j.cell.2015.09.038
doi: 10.1016/j.cell.2015.09.038 pubmed: 26422227 pmcid: 4638220
Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F (2016) Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array. Nat Biotechnol 35:31–34. https://doi.org/10.1038/nbt.3737
doi: 10.1038/nbt.3737 pubmed: 27918548 pmcid: 5225075
Zhang C, Meng X, Wei X, Lu L (2016) Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet Biol 86:47–57. https://doi.org/10.1016/j.fgb.2015.12.007
doi: 10.1016/j.fgb.2015.12.007 pubmed: 26701308
Zheng XM, Zheng P, Zhang K, Cairns TC, Meyer V, Sun JB, Ma YH (2019) 5S rRNA promoter for guide RNA expression enabled highly efficient CRISPR/Cas9 genome editing in Aspergillus niger. ACS Synth Biol 8:1568–1574. https://doi.org/10.1021/acssynbio.7b00456
doi: 10.1021/acssynbio.7b00456 pubmed: 29687998

Auteurs

Tianming Chen (T)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.

Ziming Chen (Z)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.

Huanxin Zhang (H)

Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.

Yuzhen Li (Y)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.

Lihua Yao (L)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.

Bin Zeng (B)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China.

Zhe Zhang (Z)

Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China. zz2007138221@163.com.
ORCID: 0000-0003-0632-7672

Classifications MeSH