Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins'

Evrim Özkale

EN

Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins'

Abstract

Several strains of filamentous fungi have been used to produce wide spectrum of natural products including organic acids, antibiotics, other useful proteins for centuries. Besides of these innate features, due to having versatile abilities, many filamentous fungi can be used int he field of bioproduction as host microorganisms. Despite the relevant importance and dense use of filamentous fungi in biotechnology, detailed knowledge about the molecular biology of the metabolism is not available most of them except a few model fungi. Targeting biosytnhetic genes to edit can be achieved existing tools, however, these genetic tools are inefficient and difficult to employ in wide array of filamentous fungi by the reasons such as the low editing efficiency and the therefore large amount of labor time. Recently, CRISPR/Cas9 has become growing gene-editing technology due to significant advantages over existing editing tools such as high efficiency, easy operation, the possibility of multigene editing This technology has been started to introduce to various species of filamentous fungi since 2015. The loss or gain of function of such mutant alleles is the major application of CRIPSR-Cas mediated genome engineering. In this review, state-on-art applications of the CRISPR/Cas9 technology in several filamentous fungi were summarized and the further prospects of this technology briefly discussed.

Keywords

filamentous fungi,genome editing,CRISPR/Cas9 technology,, strain improvement

References

1. Shanmugam K, Ramalingam S, Ventakatamaran G, Hariharan GN. The CRISPR/Cas9 system for targeted genome engineering in free-living fungi: advances and oppurtunities for lichenized fungi. Front in Microbiol 2019; doi: 10.3389/fmicb.2019.00062.
2. Xu X, Liu Y, Du G, Ledesma-Amaro R, Liu L. Microbial chassis development for natural bioproduct synthesis. TIBTEC 2020; https://doi.org/10.1016/j.tibtech.2020.01.002.
3. Katayama T, Tanaka Y, Okabe T, Nakamura H, Fuji W, Kitamoto K, Maruyama J. Development of a genome editing technique using the CRISPR/Cas system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett 2016; 38: 637–642.
4. Jiang D., Zhu W., Wang Y., Sun C., Zhang K.Q., Yang J. Molecular tools for functional genomics in filamnetous fungi: recent advances and new strategies. Biotechnol Adv 2013; 31: 1562-1574.
5. Liu R, Chen L, Jiang YP, Zhou ZH, Zou G. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov 2015; 1:15007.
6. Mei Y-Z, Zhu Y-L, Huang P-W, Yang Q, Dai C-C. Strategies for gene disruption and expression in filamentous fungi. Appl Microbiol Biotechnol 2019; 103: 6041-6059.
7. Nødvig CS, Nielsen JB, Kogle ME, Mortensen UH. A CRISPR/ Cas9 system for genetic engineering of filamentous fungi. PLoS One 2015; 10:e0133085.
8. Pohl C, Kiel JAKW, Driessen AJM, Bovenberg RAL, Nygard Y. CRISPR/Cas9 based genome editing of Penicillium chrysogenum. ACS Synthetic Biol 2016; 5 (7): 754-764.
9. Sander JD and Joung JK. CRIPSR-Cas systems for editing, regulating ad targeting genomes. Nat. Biotechnol 2014; 32(4): 347-355.
10. Kück U, Hoff B. New tools for genetic manipulation of filamentous fungi. Appl Microbiol Biotechnol 2010; 86: 51-62.

11. Krappmann S. CRIPSR-Cas 9, the new kid on the block of fungal molecular biology. Med Mycol 2017; 55: 16-23.
12. Shi T-Q, Liu G-N, Ji R-Y, Shi K, Song P, Ren L-J et al. CRISPR/Cas9 based genome editing of the filamentous fungi: state of the art. Appl Microbiol Biotechnol 2017; 101(20): 7435-7443.
13. Kopke K, Hoff B, Kück U Applications of Saccharomyces cerevisiae FLP/FRT recombination system in filamentous fungi for marker recycling and construction of knockout strains devoid of heterologous genes. Appl Environ Microbiol 2010; 76(14):4664-4674.
14. Wang Q, Coleman . Progress and challenges: Development and implementation of CRISPR/Cas9 technology in filamentous fungi. Comp and Struc Biotechnol 2019; J 17: 761-769.
15. Hsu PD, Lander ES, Zhang F. Development and applicatons of CRISPR-Cas9 for genome engineering. Cell 2014; June5: 157(6): 1262-1278.
16. Zhang C, Meng X, Wei , Lu L. Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet Biol 2015; 86: 47–57.
17. Liu Q, Gao R, Li J, Lin L, Zhao J, Sun W et al. Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering. Biotechnol. Biofuels 2017; 10:1. https://doi.org/ 10.1186/s13068-016-0693-9.
18. Yin CM, Fan XZ, Shi DF, Gao H. CRISPR/Cas genome editing technology and its application in fungi. Biotechnol Bull 2017; 33: 58–65.
19. Song L, Ouedraogo J.-P, Kolbusz M, Nguyen TTM, Tsang A. Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger. PLoSOne 2018; 13(8): e0202868. https://doi.org/10.1371/journal. pone.0202868.
20. Song R, Zhai Q, Sun L, Huang E, Zhang Y, Zhu T et al. CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective. Appl Microbiol Biotechnol 2019; 103: 6919-6932.
21. Zheng X, Zheng P, Zhang K, Cairns TC, Meyer V, Sun J et al. 5srRNA promoter for guide RNA expression enabled highly efficient CRISPR/Cas9 genome editing in Aspergillus niger. ACS in Biol 2019; 8(7): 1568-1574.
22. Zhang Y, Luan X, Zhang H, Garre V, Song Y, Ratledge C. Improved γ-linolenic acid production in Mucor circinelloides by homologous overexpressing of delta-12 and delta-6 desaturases. Microb Cell Factories 2017; 16:113. https://doi.org/10.1186/s12934-017-0723-8.
23. Fang, Y. and Tyler, B.M. The Oomycete Phytophthora sojae uses non‐canonical nuclear localization signals to direct proteins into the nucleus. Fung Genet Rep 61 2015; ( Suppl.), Abstract #165.
24. Shi T-Q, Liu G-N, Ji R-Y, Shi K, Song P, Ren L-J, et al. CRISPR/Cas-9 based genome editing of the filamentous fungi: the state of the art. Appl Microbiol Biotechnol 2017; DOI 10.1007/s00253-017-8497-9.
25. Weber J, Valiante V, Nodvig CS, Mattern DJ, Slotkowski RA, Mortensen UH et al. Functional reconstitution of a fungal natural product gene cluster by advanced genome editing. ACS Synt Biol 2017; 6(1): 62-68.
26. Nielsen ML, Isbrandt T, Rasmussen KB, Thrane U, Hoof JB, Larsen TO et al. Genes linked to production of secondary metabolites in Talaromyces atroroseus revealed using CRISPR/ Cas9. PLoS One 2017; 12:e0169712.
27. Sarkari P, Marx H, Blumhoff ML, Mattanovich D, Sauer M, Steiger MG. An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger. Bioresour Technol 2017; 245 (PtB): 1327-1333.
28. Katayama T, Nakamura H, Zhang Y, Pascal A, Fujii W, Maruyama J-I. Forced recycling of an AMA-1 genome editing plasmid allows for efficient multiple gene deletion/integration in the industrial filamentous fungus Aspergillus oryzae. Appl Environ Microbiol 2019; 85(3): 01896-18.
29. Larson MH, Gilbert LA, Wang X, Lim WA, Weismann JS, Qi LS. CRISPR interference (CRISPRi) for sequence specific control of gene expression. Nat Protoc 2013; 8(11): 2180- 2196.
30. Lau V, Davie JR. The discovery and development of the CRISPR system in applications in genome manipulation. Biochem and Cell Biol 2017; 95(2):

Details

Primary Language

English

Subjects

Structural Biology

Journal Section

Review

Authors

Evrim Özkale ^*
Türkiye

Publication Date

April 22, 2020

Submission Date

April 2, 2020

Acceptance Date

April 13, 2020

Published in Issue

Year 2020 Volume: 1 Number: 2

IZ

https://izlik.org/JA67EW29LK

APA

Özkale, E. (2020). Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’. Zeugma Biological Science, 1(2), 1-8. https://izlik.org/JA67EW29LK

AMA

1.Özkale E. Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’. zbs. 2020;1(2):1-8. https://izlik.org/JA67EW29LK

Chicago

Özkale, Evrim. 2020. “Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’”. Zeugma Biological Science 1 (2): 1-8. https://izlik.org/JA67EW29LK.

EndNote

Özkale E (April 1, 2020) Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’. Zeugma Biological Science 1 2 1–8.

IEEE

[1]E. Özkale, “Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’”, zbs, vol. 1, no. 2, pp. 1–8, Apr. 2020, [Online]. Available: https://izlik.org/JA67EW29LK

ISNAD

Özkale, Evrim. “Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’”. Zeugma Biological Science 1/2 (April 1, 2020): 1-8. https://izlik.org/JA67EW29LK.

JAMA

1.Özkale E. Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’. zbs. 2020;1:1–8.

MLA

Özkale, Evrim. “Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’”. Zeugma Biological Science, vol. 1, no. 2, Apr. 2020, pp. 1-8, https://izlik.org/JA67EW29LK.

Vancouver

1.Evrim Özkale. Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins’. zbs [Internet]. 2020 Apr. 1;1(2):1-8. Available from: https://izlik.org/JA67EW29LK

Abstract

Biotechnologically Relevant Filamentous Fungi Obtained by the System ‘Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins'

Abstract

Keywords

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

IZ

Cite