Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus

Fungal Genetics and Biology

Volumn 86, Issue , 2016, Pages 47-57

  Zhang, Chi ^a   Meng, Xiuhua ^a   Wei, Xiaolei ^a   Lu, Ling ^a  

^a NANJING NORMAL UNIVERSITY   (China)

Author keywords

CRISPR mutagenesis; In situ tag insertion; Microhomology; Multi locus genomic mutagenesis

Indexed keywords

FUNGAL DNA; CODON; DNA DIRECTED RNA POLYMERASE III; FUNGAL PROTEIN;

ARTICLE; ASPERGILLUS FUMIGATUS; CAS9 GENE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CNAA GENE; CODON USAGE; DNA FLANKING REGION; DNA REPAIR; GENE; GENE EXPRESSION; GENE INSERTION; GENE INTERACTION; KU80 GENE; LOSS OF FUNCTION MUTATION; MICROHOMOLOGY MEDIATED END JOINING; MUTAGENESIS; PKSP GENE; PRIORITY JOURNAL; AMINO ACID SEQUENCE; CODON; CRISPR CAS SYSTEM; GENE EXPRESSION REGULATION; GENETICS; HUMAN; MOLECULAR GENETICS; PROCEDURES; PROMOTER REGION;

AMINO ACID SEQUENCE; ASPERGILLUS FUMIGATUS; CODON; CRISPR-CAS SYSTEMS; FUNGAL PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PROMOTER REGIONS, GENETIC; RNA POLYMERASE III;

EID: 84950264293     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2015.12.007     Document Type: Article

References (44)

1. Aleksenko A., Clutterbuck A.J. Autonomous plasmid replication in Aspergillus nidulans: AMA1 and MATE elements. Fungal Genet. Biol. 1997, 21:373-387.
2. Cai Z.D., et al. The Gbeta-like protein CpcB is required for hyphal growth, conidiophore morphology and pathogenicity in Aspergillus fumigatus. Fungal Genet. Biol. 2015, 81:120-131.
3. da Silva Ferreira M.E., et al. Functional characterization of the Aspergillus fumigatus calcineurin. Fungal Genet. Biol. 2007, 44:219-230.
4. KU80 mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus. Eukaryot. Cell 2006, 5:207-211.
5. Denning D.W., Bromley M.J. How to bolster the antifungal pipeline. Science 2015, 347:1414-1416.
6. Denning D.W., et al. Global burden of chronic pulmonary aspergillosis as a sequel to pulmonary tuberculosis. Bullet. World Health Organ. 2011, 89:864-872.
7. Denning D.W., et al. Global burden of allergic bronchopulmonary aspergillosis with asthma and its complication chronic pulmonary aspergillosis in adults. Med. Mycol. 2013, 51:361-370.
8. DiCarlo J.E., et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013, 41:4336-4343.
9. Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346:1258096.
10. Dyer P.S., O'Gorman C.M. Sexual development and cryptic sexuality in fungi: insights from Aspergillus species. FEMS Microbiol. Rev. 2012, 36:165-192.
11. Farboud B., Meyer B.J. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design. Genetics 2015, 199:959-971.
12. Fox D.S., Heitman J. Good fungi gone bad: the corruption of calcineurin. Bioessays 2002, 24:894-903.
13. Fu Y., et al. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 2014, 32:279-284.
14. Fuller K.K., et al. Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot. Cell 2015, 10.1128/EC.00107-15.
15. Gravelat F.N., et al. Targeted gene deletion in Aspergillus fumigatus using the hygromycin-resistance split-marker approach. Methods Mol. Biol. 2012, 845:119-130.
16. Hill J.A., et al. Genetic and genomic architecture of the evolution of resistance to antifungal drug combinations. PLoS Genet. 2013, 9:e1003390.
17. Hsu P.D., et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013, 31:827-832.
18. Hu W., et al. Essential gene identification and drug target prioritization in Aspergillus fumigatus. PLoS Pathog. 2007, 3:e24.
19. Jacobs J.Z., et al. Implementation of the CRISPR-Cas9 system in fission yeast. Nat. Commun. 2014, 5:5344.
20. Jiang H., et al. Deletion of the putative stretch-activated ion channel Mid1 is hypervirulent in Aspergillus fumigatus. Fungal Genet. Biol. 2014, 62:62-70.
21. Jinek M., et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
22. Juvvadi P.R., et al. Calcineurin localizes to the hyphal septum in Aspergillus fumigatus: implications for septum formation and conidiophore development. Eukaryot. Cell 2008, 7:1606-1610.
23. Juvvadi P.R., et al. Localization and activity of the calcineurin catalytic and regulatory subunit complex at the septum is essential for hyphal elongation and proper septation in Aspergillus fumigatus. Mol. Microbiol. 2011, 82:1235-1259.
24. Kim H., et al. A Co-CRISPR Strategy for efficient genome editing in Caenorhabditis elegans. Genetics 2014, 197:1069-1080.
25. Krappmann S., et al. Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end-joining-deficient genetic background. Eukaryot. Cell 2006, 5:212-215.
26. Krappmann S., et al. Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end-joining-deficient genetic background. Eukaryot. Cell 2006, 5:212-215.
27. Langfelder K., et al. Identification of a polyketide synthase gene (pksP) of Aspergillus fumigatus involved in conidial pigment biosynthesis and virulence. Med. Microbiol. Immunol. 1998, 187:79-89.
28. Liu F.F., et al. Calcium signaling mediates antifungal activity of triazole drugs in the Aspergilli. Fungal Genet. Biol. 2015, 81:182-190.
29. Liu R., et al. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov. 2015, 1:15007.
30. Nielsen M.L., et al. Efficient PCR-based gene targeting with a recyclable marker for Aspergillus nidulans. Fungal Genet. Biol. 2006, 43:54-64.
31. Nodvig C.S., et al. A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS One 2015, 10:e0133085.
32. O'Gorman C.M., et al. Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature 2009, 457:471-474.
33. Ran F.A., et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 2013, 8:2281-2308.
34. Ryan O.W., et al. Selection of chromosomal DNA libraries using a multiplex CRISPR system. Elife 2014, 3.
35. Schoberle T.J., et al. Plasmids for increased efficiency of vector construction and genetic engineering in filamentous fungi. Fungal Genet. Biol. 2013, 58-59:1-9.
36. Shalem O., et al. High-throughput functional genomics using CRISPR-Cas9. Nat. Rev. Genet. 2015, 16:299-311.
37. Steinbach W.J., et al. Calcineurin controls growth, morphology, and pathogenicity in Aspergillus fumigatus. Eukaryot. Cell 2006, 5:1091-1103.
38. Sugui J.A., et al. Identification and characterization of an Aspergillus fumigatus "supermater" pair. MBio 2011, 2.
39. Szewczyk E., et al. Fusion PCR and gene targeting in Aspergillus nidulans. Nat. Protoc. 2006, 1:3111-3120.
40. Tsai H.F., et al. The developmentally regulated alb1 gene of Aspergillus fumigatus: its role in modulation of conidial morphology and virulence. J. Bacteriol. 1998, 180:3031-3038.
41. Vyas V.K., et al. A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci. Adv. 2015, 1:e1500248.
42. Wei X., et al. The molecular mechanism of azole resistance in Aspergillus fumigatus: from bedside to bench and back. J. Microbiol. 2015, 53:91-99.
43. Wong K.H., et al. Sumoylation in Aspergillus nidulans: sumO inactivation, overexpression and live-cell imaging. Fungal Genet. Biol. 2008, 45:728-737.
44. Xue T., et al. Isogenic auxotrophic mutant strains in the Aspergillus fumigatus genome reference strain Af293. Arch. Microbiol. 2004, 182:346-353.