Ku70 or Ku80 deficiencies in the fungus Botrytis cinerea facilitate targeting of genes that are hard to knock out in a wild-type context

FEMS Microbiology Letters

Volumn 289, Issue 2, 2008, Pages 225-232

  Choquer, Mathias ^a,b   Robin, Guillaume ^a   Le Pêcheur, Pascal ^a   Giraud, Corinne ^a   Levis, Caroline ^a   Viaud, Muriel ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

Botrytis cinerea; Gene targeting; Homologous recombination; Ku70; Ku80; Nonhomologous end joining

Indexed keywords

KU ANTIGEN; KU80 PROTEIN; PROTEIN DERIVATIVE; SESQUITERPENE; UNCLASSIFIED DRUG;

ARTICLE; BOTRYTIS CINEREA; DNA REPAIR; FUNGAL STRAIN; GENE SEQUENCE; GENE TARGETING; GENETIC POLYMORPHISM; HOMOLOGOUS RECOMBINATION; KNOCKOUT GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEFICIENCY; VIRULENCE; WILD TYPE;

BOTRYOTINIA FUCKELIANA; FUNGI;

EID: 56649089441     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2008.01388.x     Document Type: Article

References (34)

1. Aylon Y Kupiec M (2004) New insights into the mechanism of homologous recombination in yeast. Mutat Res 566 : 231 248.
2. Baudin A, Ozier-Kalogeropoulos O, Denouel A, Lacroute F Cullin C (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res 21 : 3329 3330.
3. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17 : 540 552.
4. Chang PK (2008) A highly efficient gene-targeting system for Aspergillus parasiticus. Lett Appl Microbiol 46 : 587 592.
5. Chevenet F, Brun C, Banuls AL, Jacq B Chisten R (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7 : 439.
6. Choquer M, Dekkers KL, Chen HQ, Cao L, Ueng PP, Daub ME Chung KR (2005) The CTB1 gene encoding a fungal polyketide synthase is required for cercosporin biosynthesis and fungal virulence of Cercospora nicotianae. Mol Plant Microbe In 18 : 468 476.
7. Choquer M, Fournier E, Kunz C, Levis C, Pradier JM, Simon A Viaud M (2007) Botrytis cinerea virulence factors: new insights into a necrotrophic and polyphageous pathogen. FEMS Microbiol Lett 277 : 1 10.
8. da Silva Ferreira ME, Kress MR, Savoldi M, Goldman MH, Härtl A, Heinekamp T, Brakhage AA Goldman GH (2006) The akuB(KU80) mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus. Eukaryot Cell 5 : 207 211.
9. Dellaporta SL, Wood J Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1 : 19 21.
10. Dereeper A, Guignon V, Blanc G et al 2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36 : W465 W469.
11. Dudásová Z, Dudás A Chovanec M (2004) Non-homologous end-joining factors of Saccharomyces cerevisiae. FEMS Microbiol Rev 28 : 581 601.
12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32 : 1792 1797.
13. El-Khoury R, Sellem CH, Coppin E, Boivin A, Maas MF, Debuchy R Sainsard-Chanet A (2008) Gene deletion and allelic replacement in the filamentous fungus Podospora anserina. Curr Genet 53 : 249 258.
14. Fillinger S, Amselem J, Artiguenave F et al 2007) The genome projects of the plant pathogenic fungi Botrytis cinerea and Sclerotinia sclerotiorum. Macromolecules and Secondary Metabolites of Grapevine and Wine (Jeandet P, Clément C Conreux A, eds). Lavoisier, London.
15. Gioti A, Simon A, Le Pêcheur P, Giraud C, Pradier JM, Viaud M Levis C (2006) Expression profiling of Botrytis cinerea genes identifies three patterns of up-regulation in planta and an FKBP12 protein affecting pathogenicity. J Mol Biol 358 : 372 386.
16. Goins CL, Gerik KJ Lodge JK (2006) Improvements to gene deletion in the fungal pathogen Cryptococcus neoformans: absence of Ku proteins increases homologous recombination, and co-transformation of independent DNA molecules allows rapid complementation of deletion phenotypes. Fungal Genet Biol 43 : 531 544.
17. Guindon S Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 : 696 704.
18. Haarmann T, Lorenz N Tudzynski P (2008) Use of a nonhomologous end joining deficient strain (Deltaku70) of the ergot fungus Claviceps purpurea for identification of a nonribosomal peptide synthetase gene involved in ergotamine biosynthesis. Fungal Genet Biol 45 : 35 44.
19. Kooistra R, Hooykaas PJ Steensma HY (2004) Efficient gene targeting in Kluyveromyces lactis. Yeast 21 : 781 792.
20. Krappmann S, Sasse C Braus GH (2006) Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end-joining-deficient genetic background. Eukaryot Cell 5 : 212 215.
21. Lan X, Yao Z, Zhou Y, Shang J, Lin H, Nuss DL Chen B (2008) Deletion of the cpku80 gene in the chestnut blight fungus, Cryphonectria parasitica, enhances gene disruption efficiency. Curr Genet 53 : 59 66.
22. Lehman JA, Hoelz DJ Turchi JJ (2008) DNA-dependent conformational changes in the ku heterodimer. Biochemistry 47 : 4359 4368.
23. Levis C, Fortini D Brygoo Y (1997) Transformation of Botrytis cinerea with the nitrate reductase gene (niaD) shows a high frequency of homologous recombination. Curr Genet 32 : 157 162.
24. Levy M, Erental A Yarden O (2008) Efficient gene replacement and direct hyphal transformation in Sclerotinia sclerotiorum. Mol Plant Pathol 9 : 719 725.
25. Meyer V, Arentshorst M, El-Ghezal A, Drews AC, Kooistra R, van den Hondel CA Ram AF (2007) Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol 128 : 770 775.
26. Nayak T, Szewczyk E, Oakley CE, Osmani A, Ukil L, Murray SL, Hynes MJ, Osmani SA Oakley BR (2006) A versatile and efficient gene-targeting system for Aspergillus nidulans. Genetics 172 : 1557 1566.
27. Ninomiya Y, Suzuki K, Ishii C Inoue H (2004) Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. P Natl Acad Sci USA 101 : 12248 12253.
28. Pöggeler S Kück U (2006) Highly efficient generation of signal transduction knockout mutants using a fungal strain deficient in the mammalian ku70 ortholog. Gene 378 : 1 10.
29. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33 : W116 W120.
30. Quidde T, Osbourn AE Tudzynski P (1998) Detoxification of -tomatine by Botrytis cinerea. Physiol Mol Plant P 52 : 151 165.
31. Siewers V, Viaud M, Jimenez-Teja D, Collado IG, Gronover CS, Pradier JM, Tudzynski B Tudzynski P (2005) Functional analysis of the cytochrome P450 monooxygenase gene bcbot1 of Botrytis cinerea indicates that botrydial is a strain-specific virulence factor. Mol Plant Microbe In 18 : 602 612.
32. Takahashi T, Masuda T Koyama Y (2006) Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol Genet Genomics 275 : 460 470.
33. Viaud M, Brunet-Simon A, Brygoo Y, Pradier JM Levis C (2003) Cyclophilin A and calcineurin functions investigated by gene inactivation, cyclosporin A inhibition and cDNA arrays approaches in the phytopathogenic fungus Botrytis cinerea. Mol Microbiol 50 : 1451 1465.
34. Villalba F, Collemare J, Landraud P, Lambou K, Brozek V, Cirer B, Morin D, Bruel C, Beffa R Lebrun MH (2008) Improved gene targeting in Magnaporthe grisea by inactivation of MgKU80 required for non-homologous end joining. Fungal Genet Biol 45 : 68 75.