Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus

Biotechnology and Bioengineering

Volumn 112, Issue 12, 2015, Pages 2543-2549

  Arazoe, Takayuki ^a   Miyoshi, Kennosuke ^a   Yamato, Tohru ^a   Ogawa, Tetsuo ^a   Ohsato, Shuichi ^a   Arie, Tsutomu ^b   Kuwata, Shigeru ^a  

^a MEIJI UNIVERSITY   (Japan)

^b TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

CRISPR Cas system; Engineered nuclease; Filamentous fungi; Gene targeting; Genome editing; Rice blast fungus

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; DNA HELICASE; RNA POLYMERASE II;

ARTICLE; CODON; CRISPR CAS SYSTEM; DNA DETERMINATION; DNA SEQUENCE; ENZYME ACTIVITY; FILAMENTOUS FUNGUS; FUNGAL STRAIN; FUNGUS; FUNGUS GROWTH; GENE CASSETTE; GENE LOCUS; GENE TARGETING; MAGNAPORTHE ORYZAE; PHENOTYPE; POLYMERASE CHAIN REACTION; PROMOTER REGION; PROTEIN EXPRESSION; PROTOPLAST; RICE BLAST; SACCHAROMYCES CEREVISIAE; SWEET ORANGE; ENZYMOLOGY; GENETICS; HOMOLOGOUS RECOMBINATION; MAGNAPORTHE; MICROBIAL GENETICS; MICROBIOLOGY; ORYZA; PROCEDURES;

CRISPR-CAS SYSTEMS; FUNGI; GENE TARGETING; GENETICS, MICROBIAL; HOMOLOGOUS RECOMBINATION; MAGNAPORTHE; ORYZA;

EID: 84945571205     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.25662     Document Type: Article

References (33)

1. Arazoe T, Ohsato S, Arie T, Yoneyama K, Kuwata S. 2013. Construction of a system for exploring mitotic homologous recombination in the genome of Pyricularia oryzae. J Gen Plant Pathol 79(6):422-430.
2. Arazoe T, Younomaru T, Ohsato S, Kimura M, Arie T, Kuwata S. 2014a. Site-specific DNA double-strand break generated by I-SceI endonuclease enhances ectopic homologous recombination in Pyricularia oryzae. FEMS Microbiol Lett 352(2):221-229.
3. Arazoe T, Kuwata S, Arie T, Ohsato S. 2014b. Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae. J Gen Plant Pathol 80(2):153-157.
4. Arazoe T, Ogawa T, Miyoshi K, Yamato T, Ohsato S, Sakuma T, Yamamoto T, Arie T, Kuwata S. 2015. Tailor-made TALEN system for highly efficient targeted gene replacement in the rice blast fungus. Biotechnol Bioeng DOI: 10.1002/bit.25559
5. Brow DA, Guthrie C. 1988. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature 334(6179):213-218.
6. Carroll D. 2014. Genome engineering with targetable nucleases. Annu Rev Biochem 83:409-439.
7. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39(12):e82.
8. Chuma I, Isobe C, Hotta Y, Ibaragi K, Futamata N, Kusaba M, Yoshida K, Terauchi R, Fujita Y, Nakayashiki H, Valent B, Tosa Y. 2011. Multiple translocation of the Avr-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species. PLoS Pathog 7(7):e1002147.
9. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jang W, Marranffini LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819-823.
10. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun M-H, Bohnert H, Coughlan S, Butler J, Calvo S, Ma LJ, Nicol R, Purcel S, Nusbaum C, Galagan JE, Birren BW. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434(7036):980-986.
11. Gao Y, Zhao Y. 2014. 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.
12. Guilinger JP, Thompson DB, Liu DR. 2014. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotech 32(6):577-582.
13. Jia H, Wang N. 2014. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 9(4):e93806.
14. Jiang DW, Zhu W, Wang YC, Sun C, Zhang KQ, Yang JK. 2013. Molecular tools for functional genomics in filamentous fungi: Recent advances and new strategies. Biotechnol Adv 31(8):1562-1574.
15. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-Guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816-821.
16. Joung JK, Sander JD. 2013. TALENs: A widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14(1):49-55.
17. Kunkel GR, Pederson T. 1988. Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used. Genes Dev 2(2):196-204.
18. Kück U, Hoff B. 2010. New tools for the genetic manipulation of filamentous fungi. Appl Microbiol Biotechnol 86(1):51-62.
19. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. 2013. RNA-guided human genome engineering via Cas9. Science 339(6121):823-826.
20. Miki S, Matsui K, Kito H, Otsuka K, Ashizawa T, Yasuda N, Fukiya S, Sato J, Hirayae K, Fujita Y, Nakajima T, Sone T. 2009. Molecular cloning and characterization of the Avr-Pia locus from a Japanese field isolate of Magnaporthe oryzae. Mol Plant Pathol 10(3):361-374.
21. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. 2014. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 54(4):698-710.
22. O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516(7530):263-266.
23. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173-1183.
24. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. 2013. Genome engineering using the CRISPR-Cas9 system. Nature Protocols 8(11):2281-2308.
25. Rusk N. 2014. CRISPRs and epigenome editing. Nat Methods 11:28.
26. Sakuma T, Ochiai H, Kaneko T, Mashimo T, Tokumatsu D, Sakane Y, Suzuki K, Miyamoto T, Sakamoto N, Matsuura S, Yamamoto T. 2013a. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci Rep 3:3379.
27. Sakuma T, Hosoi S, Woltjen K, Suzuki K, Kashiwagi K, Wada H, Ochiai H, Miyamoto T, Kawai N, Sasakura Y, Matsuura S, Okada Y, Kawahara A, Hayashi S, Yamamoto T. 2013b. Efficient TALEN construction and evaluation methods for human cell and animal applications. Genes Cells 18(4):315-326.
28. Sakuma T, Nishikawa A, Kume S, Chayama K, Yamamoto T. 2014. Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system. Sci Rep 4:5400.
29. Sone T, Takeuchi S, Miki S, Satoh Y, Ohtsuka K, Abe A, Asano K. 2013. Homologous recombination causes the spontaneous deletion of AVR-Pia in Magnaporthe oryzae. FEMS Microbiol Lett 339(2):102-109.
30. Sun N, Zhao H. 2013. Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing. Biotechnol Bioeng 110(7):1811-1821.
31. Upadhyay SK, Kumar J, Alok A, Tuli R. 2013. RNA-guided genome editing for target gene mutations in wheat. G3-Genes Genom Genet 3(12):2233-2238.
32. Yoshida K, Saitoh H, Fujisawa S, Kanzaki H, Matsumura H, Yoshida K, Tosa Y, Chuma I, Takano Y, Win J, Kamoun S, Terauchi R. 2009. Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell 21(5):1573-1591.
33. Zhang S, Xu JR. 2014. Effectors and effector delivery in Magnaporthe oryzae. PLoS Pathog 10(1):e1003826.