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      CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective

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          Abstract

          Filamentous fungi play an important role in human health and industrial/agricultural production. With the increasing number of full genomes available for fungal species, the study of filamentous fungi has brought about a wider range of genetic manipulation opportunities. However, the utilization of traditional methods to study fungi is time consuming and laborious. Recent rapid progress and wide application of a versatile genome editing technology, i.e., the CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 (CRISPR-related nuclease 9) system, has revolutionized biological research and has many innovative applications in a wide range of fields showing great promise in research and application of filamentous fungi. In this review, we introduce the CRISPR/Cas9 genome editing technology focusing on its application in research of filamentous fungi and we discuss the general considerations of genome editing using CRISPR/Cas9 system illustrating vector construction, multiple editing strategies, technical consideration of different sizes of homology arms on genome editing efficiency, off-target effects, and different transformation methodologies. In addition, we discuss the challenges encountered using CRISPR/Cas9 technology and give the perspectives of future applications of CRISPR/Cas9 technology for basic research and practical application of filamentous fungi.

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          Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements.

          Francisco Mojica, César Díez-Villaseñor, Jesús García-Martínez … (2005)
          Prokaryotes contain short DN repeats known as CRISPR, recognizable by the regular spacing existing between the recurring units. They represent the most widely distributed family of repeats among prokaryotic genomes suggesting a biological function. The origin of the intervening sequences, at present unknown, could provide clues about their biological activities. Here we show that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such as bacteriophages and conjugative plasmids. Remarkably, these extrachromosomal elements fail to infect the specific spacer-carrier strain, implying a relationship between CRISPR and immunity against targeted DNA. Bacteriophages and conjugative plasmids are involved in prokaryotic population control, evolution, and pathogenicity. All these biological traits could be influenced by the presence of specific spacers. CRISPR loci can be visualized as mosaics of a repeated unit, separated by sequences at some time present elsewhere in the cell.
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            Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

            Sergey Shmakov, Omar Abudayyeh, Kira Makarova … (2015)
            Microbial CRISPR-Cas systems are divided into Class 1, with multisubunit effector complexes, and Class 2, with single protein effectors. Currently, only two Class 2 effectors, Cas9 and Cpf1, are known. We describe here three distinct Class 2 CRISPR-Cas systems. The effectors of two of the identified systems, C2c1 and C2c3, contain RuvC-like endonuclease domains distantly related to Cpf1. The third system, C2c2, contains an effector with two predicted HEPN RNase domains. Whereas production of mature CRISPR RNA (crRNA) by C2c1 depends on tracrRNA, C2c2 crRNA maturation is tracrRNA independent. We found that C2c1 systems can mediate DNA interference in a 5'-PAM-dependent fashion analogous to Cpf1. However, unlike Cpf1, which is a single-RNA-guided nuclease, C2c1 depends on both crRNA and tracrRNA for DNA cleavage. Finally, comparative analysis indicates that Class 2 CRISPR-Cas systems evolved on multiple occasions through recombination of Class 1 adaptation modules with effector proteins acquired from distinct mobile elements.
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              Regulation of DNA repair throughout the cell cycle.

              Dana Branzei, Marco Foiani (2008)
              The repair of DNA lesions that occur endogenously or in response to diverse genotoxic stresses is indispensable for genome integrity. DNA lesions activate checkpoint pathways that regulate specific DNA-repair mechanisms in the different phases of the cell cycle. Checkpoint-arrested cells resume cell-cycle progression once damage has been repaired, whereas cells with unrepairable DNA lesions undergo permanent cell-cycle arrest or apoptosis. Recent studies have provided insights into the mechanisms that contribute to DNA repair in specific cell-cycle phases and have highlighted the mechanisms that ensure cell-cycle progression or arrest in normal and cancerous cells.
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                Author and article information

                Contributors
                Qingyun Guo: guoqingyunqh@163.com
                Hao Lu: +86-29-87092429 , luhao@nwsuaf.edu.cn
                Journal
                Journal ID (nlm-ta): Appl Microbiol Biotechnol
                Journal ID (iso-abbrev): Appl. Microbiol. Biotechnol
                Title: Applied Microbiology and Biotechnology
                Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )
                ISSN (Print): 0175-7598
                ISSN (Electronic): 1432-0614
                Publication date (Electronic): 22 July 2019
                Publication date PMC-release: 22 July 2019
                Publication date (Print): 2019
                Volume: 103
                Issue: 17
                Pages: 6919-6932
                Affiliations
                [1 ]ISNI 0000 0004 1760 4150, GRID grid.144022.1, College of Veterinary Medicine, , Northwest A&F University, ; Yangling, 712100 Shaanxi China
                [2 ]GRID grid.464485.f, Tibet Academy of Agricultural and Animal Husbandry Sciences, ; Lhasa, 850000 Tibet China
                [3 ]GRID grid.262246.6, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province/State Key Laboratory of Plateau Ecology and Agriculture, , Qinghai University, ; Xining, 810016 Qinghai China
                [4 ]ISNI 0000 0004 4687 2082, GRID grid.264756.4, Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, , Texas A&M University, ; College Station, TX 77843 USA
                Article
                Publisher ID: 10007
                DOI: 10.1007/s00253-019-10007-w
                PMC ID: 6690858
                PubMed ID: 31332488
                SO-VID: bc956402-0fb8-4671-8e98-5fddbed53d01
                Copyright © © The Author(s) 2019
                License:

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                Date received : 24 May 2019
                Date revision received : 28 June 2019
                Date accepted : 1 July 2019
                Funding
                Funded by: National Natural Science Foundation
                Award ID: No. 31201958
                Award Recipient :
                Categories
                Subject: Mini-Review
                Custom metadata
                issue-copyright-statement © Springer-Verlag GmbH Germany, part of Springer Nature 2019

                ScienceOpen disciplines: Biotechnology
                Keywords: filamentous fungi,crispr/cas9,genome editing,off-target
                Data availability:
                ScienceOpen disciplines: Biotechnology
                Keywords: filamentous fungi, crispr/cas9, genome editing, off-target

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