生物技术进展 ›› 2022, Vol. 12 ›› Issue (5): 696-704.DOI: 10.19586/j.2095-2341.2022.0038
收稿日期:
2022-03-17
接受日期:
2022-06-10
出版日期:
2022-09-25
发布日期:
2022-09-30
通讯作者:
余永涛
作者简介:
于鲲 E-mail:yk1018120@163.com;
基金资助:
Kun YU1(), Jiaqi XUE1, Jinkuan WANG2, Yongtao YU1()
Received:
2022-03-17
Accepted:
2022-06-10
Online:
2022-09-25
Published:
2022-09-30
Contact:
Yongtao YU
摘要:
随着对丝状真菌基因水平研究的不断深入,CRISPR/Cas9技术作为先进的基因编辑技术,已被广泛应用于丝状真菌的基因编辑。探究了CRISPR/Cas9系统在不同丝状真菌中的应用情况,主要从sgRNA的构建与表达、Cas9蛋白的改造与表达、不同的DNA双链断裂修复(DNA double-strand break,DSB)方式等方面进行概述,并对编辑效率、脱靶效应进行总结,旨在为今后丝状真菌中CRISPR/Cas9系统的构建及改良提供思路。
中图分类号:
于鲲, 薛佳琪, 王进宽, 余永涛. CRISPR/Cas9基因编辑技术在丝状真菌中的应用[J]. 生物技术进展, 2022, 12(5): 696-704.
Kun YU, Jiaqi XUE, Jinkuan WANG, Yongtao YU. Research Progress on Application of CRISPR/Cas9 Gene Editing Technique in Filamentous Fungi[J]. Current Biotechnology, 2022, 12(5): 696-704.
1 | MAUMELA P, ROSE S, van RENSBURG E, et al.. Bioprocess optimisation for high cell density endoinulinase production from recombinant Aspergillus niger [J]. Appl. Biochem. Biotechnol., 2021, 193(10): 3271-3286. |
2 | DSOUZA G C, SHERIFF R S, ULLANAT V, et al.. Fungal biodegradation of low-density polyethylene using consortium of Aspergillus species under controlled conditions[J/OL]. Heliyon, 2021, 7(5): e7008 [2021-12-06]. . |
3 | HOFFMAN J J, BURTON M J, LECK A. Mycotic keratitis—a global threat from the filamentous fungi[J/OL]. J. Fungi (Basel), 2021, 7(4): 273 [2022-06-25]. . |
4 | LIU X, YANG J, MA W. Primary cutaneous aspergillosis caused by Aspergillus.fumigatus in an immunocompetent patient[J/OL]. Medicine, 2017, 96(48): e8916 [2021-10-18] . |
5 | QUOC N B, CHAU N. The Role of cell wall degrading enzymes in pathogenesis of Magnaporthe oryzae [J]. Curr. Sci, 2017, 18(10): 1019-1034. |
6 | KOZHAR O, PEEVER T L. How does Botrytis cinerea infect red raspberry?[J]. Phytopathology, 2018, 108(11): 1287-1298. |
7 | SALAZAR-CEREZO S, KUN R S, DE VRIES R P, et al.. CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer[J/OL]. Enzyme Microb. Technol., 2020,133: 109463 [2021-10-22]. . |
8 | FEHR A R. Bacterial artificial chromosome-based lambda red recombination with the I-SceI homing endonuclease for genetic alteration of MERS-CoV[J]. Methods Mol. Biol., 2020, 2099: 53-68. |
9 | WANG S, CHEN H, TANG X, et al.. Molecular tools for gene manipulation in filamentous fungi[J]. Appl. Microbiol. Biotechnol., 2017, 101(22): 8063-8075. |
10 | KIM Y G, CHA J, CHANDRASEGARAN S. Hybrid restriction enzymes: Zinc Finger fusions to Fok I cleavage domain[J]. Proc. Natl. Acad. Sci. USA, 1996, 93(3): 1156-1160. |
11 | MOSCOU M J, BOGDANOVE A J. A simple cipher governs DNA recognition by TAL effectors[J/OL]. Science, 2009, 326(5959): 1501[2022-4-22]. . |
12 | ISHINO Y, SHINAGAWA H, MAKINO K, et al.. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. J. Bacteriol., 1987, 169(12): 5429-5433. |
13 | JANSEN R, EMBDEN J D A V, GAASTRA W, et al.. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Mol. Microbiol., 2002, 43(6): 1565-1575. |
14 | 曹巧,史占良,张国丛,等.CRISPR/Cas9技术在小麦育种中的应用进展[J].生物技术进展,2021,11(6):661-667. |
15 | 格日乐其木格,牛振峰,董丹,等.CRISPR-Cas系统在微生物研究中的应用进展[J].生物技术进展,2021,11(3):253-259. |
16 | LIU R, CHEN L, JIANG Y, et al.. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system[J/OL]. Cell Discov., 2015, 1: 15007 [2021-10-12]. . |
17 | GARNEAU J E, DUPUIS M E, VILLION M, et al.. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J]. Nature, 2010,468(7320):67-71. |
18 | ARAZOE T, MIYOSHI K, YAMATO T, et al.. Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus[J]. Biotechnol. Bioeng., 2015, 112(12): 2543-2549. |
19 | LIU Q, GAO R, LI J, et al.. Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering[J/OL]. Biotechnol. Biofuels, 2017, 10 :1 [2021-11-13]. . |
20 | WU C, CHEN Y, QIU Y, et al.. A simple approach to mediate genome editing in the filamentous fungus Trichoderma reesei by CRISPR/Cas9-coupled in vivo gRNA transcription[J]. Biotechnol. Lett., 2020, 42(7): 1203-1210. |
21 | LI Y, ZHANG H, FAN J, et al.. A highly efficient identification of mutants generated by CRISPR/Cas9 using the non‑functional DsRed assisted selection in Aspergillus oryzae [J/OL]. World J. Microbiol. Biotechnol., 2021, 37(8): 132 [2022-02-06]. . |
22 | HUANG L, DONG H, ZHENG J, et al.. Highly efficient single base editing in Aspergillus niger with CRISPR/Cas9 cytidine deaminase fusion[J]. Microbiol. Res., 2019, 223: 44-50. |
23 | SONG L, OUEDRAOGO J, KOLBUSZ M, et al.. Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger [J/OL]. PLoS ONE, 2018, 13(8): e202868. [2021-10-28]. . |
24 | 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 [J]. ACS Synth. Biol., 2019, 8(7): 1568-1574. |
25 | SHI T, GAO J, WANG W, et al.. CRISPR/Cas9-Based Genome editing in the filamentous fungus Fusarium fujikuroi and its application in strain engineering for gibberellic acid production[J]. ACS Synth. Biol, 2019,8(2):445-454. |
26 | WANG Q, ZHAO Q, LIU Q, et al.. CRISPR/Cas9-mediated genome editing in Penicillium oxalicum and Trichoderma reesei using 5S rRNA promoter-driven guide RNAs[J]. Biotechnol. Lett., 2021, 43(2): 495-502. |
27 | NISSIM L, PERLI S D, FRIDKIN A, et al.. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells[J]. Mol. Cell, 2014, 54(4): 698-710. |
28 | GAO Y, ZHAO Y. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing[J]. J. Integr. Plant. Biol., 2014, 56(4): 343-349. |
29 | NØDVIG C S, NIELSEN J B, KOGLE M E, et al.. A CRISPR-Cas9 system for genetic engineering of filamentous fungi[J/OL]. PLoS One, 2015, 10(7): e133085 [2021-10-31]. . |
30 | VIEIRA A A, VIANNA G R, CARRIJO J, et al.. Generation of Trichoderma harzianum with pyr4 auxotrophic marker by using the CRISPR/Cas9 system[J/OL]. Sci. Rep., 2021, 11(1): 1085[2022-01-12].. |
31 | ZOU G, ZHOU Z. CRISPR/Cas9-mediated genome editing of Trichoderma reesei [J]. Methods Mol. Biol., 2021, 2234: 87-98. |
32 | ABDALLAH Q A L, SOUZA A C O, MARTIN-VICENTE A, et al.. Whole-genome sequencing reveals highly specific gene targeting by in vitro assembled Cas9-ribonucleoprotein complexes in Aspergillus fumigatus [J/OL]. Fungal Biol. Biotechnol., 2018, 5: 11 [2021-11-13]. . |
33 | WANG Q, COBINE P A, COLEMAN J J. Efficient genome editing in Fusarium oxysporum based on CRISPR/Cas9 ribonucleoprotein complexes[J]. Fungal Genet. Biol., 2018, 117: 21-29. |
34 | NAGY G, SZEBENYI C, CSERNETICS Á, et al.. Development of a plasmid free CRISPR-Cas9 system for the genetic modification of Mucor circinelloides [J/OL]. Sci. Rep., 2017, 7: 16800 [2021-11-10]. . |
35 | FANG Y, TYLER B M. Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9[J]. Mol. Plant Pathol., 2016,17(1): 127-139. |
36 | LEYNAUD-KIEFFER L M C, CURRAN S C, KIM I, et al.. A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable[J/OL]. PLoS ONE, 2019, 14(1): e210243 [2021-10-23]. . |
37 | 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 [J]. Biotechnol. Lett., 2016, 38(4): 637-642. |
38 | HUCK S, BOCK J, GIRARDELLO J, et al.. Marker-free genome editing in Ustilago trichophora with the CRISPR-Cas9 technology[J]. RNA Biol., 2019, 16(4): 397-403. |
39 | LIU R, CHEN L, JIANG Y, et al.. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system[J/OL]. Cell Discov., 2015, 1: 15007[2021-10-20]. . |
40 | VAN RHIJN N, FURUKAWA T, ZHAO C, et al.. Development of a marker-free mutagenesis system using CRISPR-Cas9 in the pathogenic mould Aspergillus fumigatus [J/OL]. Fungal Genet. Biol., 2020, 145: 103479 [2021-12-17]. . |
41 | YANG L, HENRIKSEN M M, HANSEN R S, et al.. Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass[J/OL]. Biotechnol. Biofuels, 2020, 13(1): 206 [2021-12-10]. . |
42 | ZOU G, XIAO M, CHAI S, et al.. Efficient genome editing in filamentous fungi via an improved CRISPR‐Cas9 ribonucleoprotein method facilitated by chemical reagents[J]. Microb. Biotechnol., 2021, 14(6): 2343-2355. |
43 | WEI T, WU Y, XIE Q, et al.. CRISPR/Cas9-based genome editing in the filamentous fungus Glarea lozoyensis and its application in Manipulating glof [J]. ACS Synth. Biol., 2020, 9(8): 1968-1977. |
44 | GABRIEL R, PRINZ J, JECMENICA M, et al.. Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus [J/OL]. Biotechnol. Biofuels, 2020,13(1): 167 [2022-01-05]. . |
45 | BRUNI G O, ZHONG K, LEE S C, et al.. CRISPR-Cas9 induces point mutation in the mucormycosis fungus Rhizopus delemar [J]. Fungal Genet. Biol., 2019, 124: 1-7. |
46 | ZHAO B, ROTHENBERG E, RAMSDEN D A, et al.. The molecular basis and disease relevance of non-homologous DNA end joining[J]. Nat. Rev. Mol. Cell Biol., 2020, 21(12): 765-781. |
47 | BRITTON S, COATES J, JACKSON S P. A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair[J]. J. Cell Biol., 2013, 202(3): 579-595. |
48 | DEANS A J, WEST S C. DNA interstrand crosslink repair and cancer[J]. Nat. Rev. Cancer, 2011, 11(7): 467-480. |
49 | YAO X, WANG X, HU X, et al.. Homology-mediated end joining-based targeted integration using CRISPR/Cas9[J]. Cell Res., 2017, 27(6): 801-814. |
50 | SEEKLES S J, TEUNISSE P P P, PUNT M, et al.. Preservation stress resistance of melanin deficient conidia from Paecilomyces variotii and Penicillium roqueforti mutants generated via CRISPR/Cas9 genome editing[J/OL]. Fungal Biol. Biotechnol., 2021, 8(1): 4[2022-01-25]. . |
51 | KRÁLOVÁ M, BERGOUGNOUX V, FRÉBORT I. CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea [J]. J. Biotechnol., 2021, 325: 341-354. |
52 | KUIVANEN J, KORJA V, HOLMSTRÖM S, et al.. Development of microtiter plate scale CRISPR/Cas9 transformation method for Aspergillus niger based on in vitro assembled ribonucleoprotein complexes[J/OL]. Fungal Biol. Biotechnol., 2019,6: 3 [2021-12-28]. . |
53 | DA S F M, KRESS M R, SAVOLDI M, et al.. The akuB(KU80) mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus [J]. Eukaryot. Cell, 2006, 5(1): 207-211. |
54 | GANDÍA M, XU S, FONT C, et al.. Disruption of ku70 involved in non-homologous end-joining facilitates homologous recombination but increases temperature sensitivity in the phytopathogenic fungus Penicillium digitatum [J]. Fungal Biol., 2016, 120(3): 317-323. |
55 | PATTANAYAK V, LIN S, GUILINGER J P, et al.. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity[J]. Nat. Biotechnol., 2013, 31(9): 839-843. |
56 | FU Y, FODEN J A, KHAYTER C, et al.. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells[J]. Nat. Biotechnol., 2013, 31(9): 822-826. |
57 | CRADICK T J, FINE E J, ANTICO C J, et al.. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity[J]. Nucl. Acids Res., 2013, 41(20): 9584-9592. |
58 | TSAI S Q, ZHENG Z, NGUYEN N T, et al.. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases[J]. Nat. Biotechnol., 2015, 33(2): 187-197. |
59 | KIM D, BAE S, PARK J, et al.. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells[J]. Nat. Methods, 2015, 12(3): 237-243. |
60 | BISCHOF R H, RAMONI J, SEIBOTH B. Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei[J/OL]. Microb. Cell Fact., 2016, 15(1): 106 [2022-04-20]. . |
61 | FONSECA L M, PARREIRAS L S, MURAKAMI M T. Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production[J/OL]. Biotechnol. Biofuels, 2020, 13: 93 [2022-04-20] . |
62 | LIU R, CHEN L, JIANG Y, et al.. A novel transcription factor specifically regulates GH11 xylanase genes in Trichoderma reesei [J/OL]. Biotechnol. Biofuels, 2017, 10: 194 [2022-04-20]. . |
63 | RANTASALO A, VITIKAINEN M, PAASIKALLIO T, et al.. Novel genetic tools that enable highly pure protein production in Trichoderma reesei [J/OL]. Sci. Rep., 2019, 9(1): 5032 [2022-04-27]. . |
64 | ROJAS-SANCHEZ U, LOPEZ-CALLEJA A C, MILLAN-CHIU B E, et al.. Enhancing the yield of human erythropoietin in Aspergillus niger by introns and CRISPR-Cas9[J/OL]. Protein Expr. Purif., 2020, 168: 105570 [2022-04-27]. . |
65 | YANG L, HENRIKSEN M M, HANSEN R S, et al.. Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass[J/OL]. Biotechnol. Biofuels, 2020, 13(1): 206 [2022-05-02]. . |
66 | YIN J, LIU M, LIU Y, et al.. Optimizing genome editing strategy by primer-extension-mediated sequencing[J/OL]. Cell Discov., 2019, 5: 18 [2022-04-27]. . |
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