The Working Mechanism of CRISPR/Cas9 Genome Editing in Filamentous Fungi and its Industrial Applications


  • Muhammad Furqan Arshad D-1/10 East park, Wah cantt.


CRISPR, filamentous fungi, regulation of gene, aspergillus oryzae, aspergillus niger, aspergillus nidulans


Understanding of regulation of gene and its functions sequence which is coding the gene and genome manipulation are very crucial. For this understanding conventional methods in many filamentous fungi are either non-functional or ineffective. Filamentous fungi plays major role in agriculture, industrial production and in medical field. A broad applications and fast development of system of CRISPR/Cas9 method has given the basic outline to comply this technology of editing of gene for many filamentous fungi. In this review, by focusing the applications of CRISPR/Cas9 in research as well as in industries we give the brief introduction of the CRISPR/Cas9 system. We also give the brief description of overall review of editing of genome, describe the construction of vector, off targeted effects and different methods of transformation of the plasmid


. Osiewacz, H.D. Mitochondria and aging in filamentous fungi. Ageing: Res. 1(3), 425-442. (2002).

. Lander, E.S. The heroes of CRISPR. Cell. 164(1-2), 18-28. (2016).

. Sternberg, S.H., Redding, S., Jinek, M. & Green, E.C. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 507(7490), 62-67. (2014).

. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A. & Charpentier, E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 37(6094), 816-21. (2012).

. Bétermier, M., Bertrand, P., & Lopez, B. S. Is non-homologous end-joining really an inherently error-prone process?. PLoS genetics, 10(1), e1004086. (2014)

. Liu, R., Chen, L., Jiang, Y., Zhou, Z. & Zou, G. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov. 1(15007). (2015).

. Sarkari, P., Marx, H., Blumhoff, M.L., Mattanovich, D., Sauer, M. & Steiger, M.G. An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger. Bioresour Technol. 245(ptB), 1327–1333. (2017).

. Deng, H., Gao, R., Liao, X. & Cai, Y. Characterization of a major facilitator superfamily transporter in Shiraia bambusicola. Res. Microbiol. 168(7), 664–672 (2017).

. Gao, Y. & Zhao, Y. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J Integr Plant Biol. 56(4), 343–349. (2014).

. Liang, Y., Han, Y., Wang, C., Jiang, C. & Xu, J.R. Targeted deletion of the USTA and UvSLT2 genes efficiently in Ustilaginoidea virens with the CRISPR-Cas9 system. Front Plant Sci. 9(89), 699(2018).

. Zheng, X., Zheng, P., Zhang, K., Cairns, T. C., Meyer, V., Sun, J., & Ma, Y. 5S rRNA promoter for guide RNA expression enabled highly efficient CRISPR/Cas9 genome editing in Aspergillus niger. ACS Synth Biol. 7(67), 667-687. . (2018)

. Miao, J., Li, X., Lin, D., Liu, X. & Tyler, B.M. Oxysterol-binding protein related protein 2 is not essential for Phytophthora sojae based on CRISPR/Cas9 deletions. Environ Microbiol Rep. 10(84), 293–298. (2018).

. Branzei, D. & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nat Rev Mol Cell Biol. 9(87), 297–308. (2008).

. Zhao, Y., Zhang, C., Liu, W., Gao, W., Liu, C., Song, G., Li, W.X., Mao, L.,Chen, B., Xu, Y., Li, X. & Xie, C.. An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci Rep. 6(44), 23890. (2016)

. Nagy, G., Vaz, A.G., Szebenyi, C., Takó, M., Tóth, E.J., Csernetics, A., Bencsik, O., Szekeres, A., Homa, M., Ayaydin, F., Galgóczy, L., Vágvölgyi, C. & Papp, T. CRISPR-Cas9-mediated disruption of the HMGCoA reductase genes of Mucorcircinelloides and subcellular localization of the encoded enzymes. Fungal Genet Biol. 129(56), 30–39. (2019).

. Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 32(88), 677–683. (2014).

. Tsai, S.Q., Zheng, Z., Nguyen, N.T., Liebers, M., Topkar, V.V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A.J., Le, L.P., Aryee, M.J., Joung, J.K. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 33(45), 187–197. (2015).

. Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H.R., Hwang, J., Kim, J.I. & Kim, J.S. Digenome-seq:genome-wideprofilingofCRISPR-Cas9offtarget effects in human cells. Nat Methods. 12(237-243), 1–243. (2015).

. Katayama, T., Tanaka, Y., Okabe, T., Nakamura, H., Fujii, W., Kitamoto, K., & Maruyama, J. I. Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnology letters, 38(4), 637-642. (2016).




How to Cite

Arshad, M. F. (2022). The Working Mechanism of CRISPR/Cas9 Genome Editing in Filamentous Fungi and its Industrial Applications. American Scientific Research Journal for Engineering, Technology, and Sciences, 85(1), 313–318. Retrieved from