Shuttle vectors for facile gap repair cloning and integration into a neutral locus in Candida albicans

Microbiology (United Kingdom)

Volumn 159, Issue PART3, 2013, Pages 565-579

  Gerami Nejad, Maryam ^a   Zacchi, Lucia F ^a,b   McClellan, Mark ^a   Matter, Kathleen ^a   Berman, Judith ^a,c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CANDIDA ALBICANS; CONTROLLED STUDY; GENE EXPRESSION; GENE LOCUS; GENE VECTOR; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SHUTTLE VECTOR; YEAST;

CANDIDA ALBICANS; CLONING, MOLECULAR; GENETIC ENGINEERING; GENETIC VECTORS; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE;

EID: 84874773315     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.064097-0     Document Type: Article

References (68)

1. Adams, A., Gotschling, D., Kaiser, C. & Stearns, T. (1997). Methods in Yeast Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
2. Backen, A. C., Broadbent, I. D., Fetherston, R. W., Rosamond, J. D., Schnell, N. F. & Stark, M. J. (2000). Evaluation of the CaMAL2 promoter for regulated expression of genes in Candida albicans. Yeast 16, 1121-1129.
3. Barelle, C. J., Manson, C. L., MacCallum, D. M., Odds, F. C., Gow, N. A. & Brown, A. J. (2004). GFP as a quantitative reporter of gene regulation in Candida albicans. Yeast 21, 333-340.
4. Basso, L. R., Jr, Bartiss, A., Mao, Y., Gast, C. E., Coelho, P. S., Snyder, M. & Wong, B. (2010). Transformation of Candida albicans with a synthetic hygromycin B resistance gene. Yeast 27, 1039-1048.
5. Beckerman, J., Chibana, H., Turner, J. & Magee, P. T. (2001). Singlecopy IMH3 allele is sufficient to confer resistance to mycophenolic acid in Candida albicans and to mediate transformation of clinical Candida species. Infect Immun 69, 108-114.
6. Brand, A., MacCallum, D. M., Brown, A. J., Gow, N. A. & Odds, F. C. (2004). Ectopic expression of URA3 can influence the virulence phenotypes and proteome of Candida albicans but can be overcome by targeted reintegration of URA3 at the RPS10 locus. Eukaryot Cell 3, 900-909.
7. Care, R. S., Trevethick, J., Binley, K. M. & Sudbery, P. E. (1999). The MET3 promoter: a new tool for Candida albicans molecular genetics. Mol Microbiol 34, 792-798.
8. Cheng, S., Nguyen, M. H., Zhang, Z., Jia, H., Handfield, M. & Clancy, C. J. (2003). Evaluation of the roles of four Candida albicans genes in virulence by using gene disruption strains that express URA3 from the native locus. Infect Immun 71, 6101-6103.
9. Cruz, M. C., Goldstein, A. L., Blankenship, J., Del Poeta, M., Perfect, J. R., McCusker, J. H., Bennani, Y. L., Cardenas, M. E. & Heitman, J. (2001). Rapamycin and less immunosuppressive analogs are toxic to Candida albicans and Cryptococcus neoformans via FKBP12-dependent inhibition of TOR. Antimicrob Agents Chemother 45, 3162-3170.
10. Davis, D. A., Bruno, V. M., Loza, L., Filler, S. G. & Mitchell, A. P. (2002). Candida albicans Mds3p, a conserved regulator of pH responses and virulence identified through insertional mutagenesis. Genetics 162, 1573-1581.
11. Dennison, P. M., Ramsdale, M., Manson, C. L. & Brown, A. J. (2005). Gene disruption in Candida albicans using a synthetic, codonoptimised Cre-loxP system. Fungal Genet Biol 42, 737-748.
12. Doyle, T. C., Nawotka, K. A., Purchio, A. F., Akin, A. R., Francis, K. P. & Contag, P. R. (2006). Expression of firefly luciferase in Candida albicans and its use in the selection of stable transformants. Microb Pathog 40, 69-81.
13. Eckert-Boulet, N., Pedersen, M. L., Krogh, B. O. & Lisby, M. (2012). Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae. Yeast 29, 323-334.
14. Enloe, B., Diamond, A. & Mitchell, A. P. (2000). A singletransformation gene function test in diploid Candida albicans. J Bacteriol 182, 5730-5736.
15. Falagas, M. E., Apostolou, K. E. & Pappas, V. D. (2006). Attributable mortality of candidemia: a systematic review of matched cohort and case-control studies. Eur J Clin Microbiol Infect Dis 25, 419-425.
16. Ferrara, A., Cafferkey, R. & Livi, G. P. (1992). Cloning and sequence analysis of a rapamycin-binding protein-encoding gene (RBP1) from Candida albicans. Gene 113, 125-127.
17. Finkel, J. S., Yudanin, N., Nett, J. E., Andes, D. R. & Mitchell, A. P. (2011). Application of the systematic DAmP approach to create a partially defective C. albicans mutant. Fungal Genet Biol 48, 1056-1061.
18. Fonzi, W. A. & Irwin, M. Y. (1993). Isogenic strain construction and gene mapping in Candida albicans. Genetics 134, 717-728.
19. Ganguly, S. & Mitchell, A. P. (2012). Mini-blaster-mediated targeted gene disruption and marker complementation in Candida albicans. Methods Mol Biol 845, 19-39.
20. Gerami-Nejad, M., Berman, J. & Gale, C. A. (2001). Cassettes for PCR-mediated construction of green, yellow, and cyan fluorescent protein fusions in Candida albicans. Yeast 18, 859-864.
21. Gerami-Nejad, M., Hausauer, D., McClellan, M., Berman, J. & Gale, C. (2004). Cassettes for the PCR-mediated construction of regulatable alleles in Candida albicans. Yeast 21, 429-436.
22. Gerami-Nejad, M., Dulmage, K. & Berman, J. (2009). Additional cassettes for epitope and fluorescent fusion proteins in Candida albicans. Yeast 26, 399-406.
23. Gerami-Nejad, M., Forche, A., McClellan, M. & Berman, J. (2012). Analysis of protein function in clinical C. albicans isolates. Yeast 29, 303-309.
24. Glowczewski, L., Waterborg, J. H. & Berman, J. G. (2004). Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol Cell Biol 24, 10180-10192.
25. Gola, S., Martin, R., Walther, A., Dunkler, A. & Wendland, J. (2003). New modules for PCR-based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region. Yeast 20, 1339-1347.
26. Gudlaugsson, O., Gillespie, S., Lee, K., Vande Berg, J., Hu, J., Messer, S., Herwaldt, L., Pfaller, M. & Diekema, D. (2003). Attributable mortality of nosocomial candidemia, revisited. Clin Infect Dis 37, 1172-1177.
27. Heitman, J., Movva, N. R. & Hall, M. N. (1991). Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253, 905-909.
28. Henikoff, S. (1992). Position effect and related phenomena. Curr Opin Genet Dev 2, 907-912.
29. Huber, D. & Rustchenko, E. (2001). Large circular and linear rDNA plasmids in Candida albicans. Yeast 18, 261-272.
30. Igyártó, B. Z., Haley, K., Ortner, D., Bobr, A., Gerami-Nejad, M., Edelson, B. T., Zurawski, S. M., Malissen, B., Zurawski, G. & other authors (2011). Skin-resident murine dendritic cell subsets promote distinct and opposing antigen-specific T helper cell responses. Immunity 35, 260-272.
31. Iizasa, E. & Nagano, Y. (2006). Highly efficient yeast-based in vivo DNA cloning of multiple DNA fragments and the simultaneous construction of yeast/Escherichia coli shuttle vectors. Biotechniques 40, 79-83.
32. Keppler-Ross, S., Noffz, C. & Dean, N. (2008). A new purple fluorescent color marker for genetic studies in Saccharomyces cerevisiae and Candida albicans. Genetics 179, 705-710.
33. Kurtz, M. B., Cortelyou, M. W. & Kirsch, D. R. (1986). Integrative transformation of Candida albicans, using a cloned Candida ADE2 gene. Mol Cell Biol 6, 142-149.
34. Kurtz, M. B., Cortelyou, M. W., Miller, S. M., Lai, M. & Kirsch, D. R. (1987). Development of autonomously replicating plasmids for Candida albicans. Mol Cell Biol 7, 209-217.
35. Lai, W. C., Tseng, T. L., Jian, T., Lee, T. L., Cheng, C. W. & Shieh, J. C. (2011). Construction of Candida albicans Tet-on tagging vectors with a Ura-blaster cassette. Yeast 28, 253-263.
36. Lay, J., Henry, L. K., Clifford, J., Koltin, Y., Bulawa, C. E. & Becker, J. M. (1998). Altered expression of selectable marker URA3 in genedisrupted Candida albicans strains complicates interpretation of virulence studies. Infect Immun 66, 5301-5306.
37. Lebel, K., MacPherson, S. & Turcotte, B. (2006). New tools for phenotypic analysis in Candida albicans: the WAR1 gene confers resistance to sorbate. Yeast 23, 249-259.
38. Ma, H., Kunes, S., Schatz, P. J. & Botstein, D. (1987). Plasmid construction by homologous recombination in yeast. Gene 58, 201-216.
39. Marykwas, D. L. & Passmore, S. E. (1995). Mapping by multifragment cloning in vivo. Proc Natl Acad Sci U S A 92, 11701-11705.
40. Muhlrad, D., Hunter, R. & Parker, R. (1992). A rapid method for localized mutagenesis of yeast genes. Yeast 8, 79-82.
41. Murad, A. M., Lee, P. R., Broadbent, I. D., Barelle, C. J. & Brown, A. J. (2000). CIp10, an efficient and convenient integrating vector for Candida albicans. Yeast 16, 325-327.
42. Nobile, C. J. & Mitchell, A. P. (2009). Large-scale gene disruption using the UAU1 cassette. Methods Mol Biol 499, 175-194.
43. Nunes, A., Thathy, V., Bruderer, T., Sultan, A. A., Nussenzweig, R. S. & Ménard, R. (1999). Subtle mutagenesis by ends-in recombination in malaria parasites. Mol Cell Biol 19, 2895-2902.
44. Oh, J., Fung, E., Schlecht, U., Davis, R. W., Giaever, G., St Onge, R. P., Deutschbauer, A. & Nislow, C. (2010). Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection. PLoS Pathog 6, e1001140.
45. Park, N. H. & Choi, W. (2002). Vectors designed for efficient molecular manipulation in Candida albicans. Yeast 19, 1057-1066.
46. Pirrotta, V. & Gross, D. S. (2005). Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol Cell 18, 395-398.
47. Reijnst, P., Walther, A. & Wendland, J. (2011). Dual-colour fluorescence microscopy using yEmCherry-/GFP-tagging of eisosome components Pil1 and Lsp1 in Candida albicans. Yeast 28, 331-338.
48. Reuß, O., Vik, A., Kolter, R. & Morschhauser, J. (2004). The SAT1 flipper, an optimized tool for gene disruption in Candida albicans. Gene 341, 119-127.
49. Sánchez-Martínez, C. & Pérez-Martín, J. (2002). Site-specific targeting of exogenous DNA into the genome of Candida albicans using the FLP recombinase. Mol Genet Genomics 268, 418-424.
50. Sasse, C. & Morschhauser, J. (2012). Gene deletion in Candida albicans wild-type strains using the SAT1-flipping strategy. Methods Mol Biol 845, 3-17.
51. Shen, J., Guo, W. & Kohler, J. R. (2005). CaNAT1, a heterologous dominant selectable marker for transformation of Candida albicans and other pathogenic Candida species. Infect Immun 73, 1239-1242.
52. Sikorski, R. S. & Hieter, P. (1989). A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19-27.
53. Spreghini, E., Davis, D. A., Subaran, R., Kim, M. & Mitchell, A. P. (2003). Roles of Candida albicans Dfg5p and Dcw1p cell surface proteins in growth and hypha formation. Eukaryot Cell 2, 746-755.
54. Srikantha, T., Klapach, A., Lorenz, W. W., Tsai, L. K., Laughlin, L. A., Gorman, J. A. & Soll, D. R. (1996). The sea pansy Renilla reniformis luciferase serves as a sensitive bioluminescent reporter for differential gene expression in Candida albicans. J Bacteriol 178, 121-129.
55. Staab, J. F. & Sundstrom, P. (2003). URA3 as a selectable marker for disruption and virulence assessment of Candida albicans genes. Trends Microbiol 11, 69-73.
56. Staab, J. F., Bahn, Y. S. & Sundstrom, P. (2003). Integrative, multifunctional plasmids for hypha-specific or constitutive expression of green fluorescent protein in Candida albicans. Microbiology 149, 2977-2986.
57. Stynen, B., Van Dijck, P. & Tournu, H. (2010). A CUG codon adapted two-hybrid system for the pathogenic fungus Candida albicans. Nucleic Acids Res 38, e184.
58. Tartof, K. D. (1994). Position effect variegation in yeast. Bioessays 16, 713-714.
59. Umeyama, T., Nagai, Y., Niimi, M. & Uehara, Y. (2002). Construction of FLAG tagging vectors for Candida albicans. Yeast 19, 611-618.
60. Vieira, N., Pereira, F., Casal, M., Brown, A. J., Paiva, S. & Johansson, B. (2010). Plasmids for in vivo construction of integrative Candida albicans vectors in Saccharomyces cerevisiae. Yeast 27, 933-939.
61. Vojtek, A. B., Hollenberg, S. M. & Cooper, J. A. (1993). Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 74, 205-214.
62. Wilson, R. B., Davis, D. & Mitchell, A. P. (1999). Rapid hypothesis testing with Candida albicans through gene disruption with short homology regions. J Bacteriol 181, 1868-1874.
63. Wilson, R. B., Davis, D., Enloe, B. M. & Mitchell, A. P. (2000). A recyclable Candida albicans URA3 cassette for PCR product-directed gene disruptions. Yeast 16, 65-70.
64. Wolf, J. M. & Davis, D. A. (2010). Mutational analysis of Candida albicans SNF7 reveals genetically separable Rim101 and ESCRT functions and demonstrates divergence in bro1-domain protein interactions. Genetics 184, 673-694.
65. Wullschleger, S., Loewith, R. & Hall, M. N. (2006). TOR signaling in growth and metabolism. Cell 124, 471-484.
66. Xu, T., Bharucha, N. & Kumar, A. (2011). Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans. Methods Mol Biol 765, 207-224.
67. Zacchi, L. F., Gomez-Raja, J. & Davis, D. A. (2010). Mds3 regulates morphogenesis in Candida albicans through the TOR pathway. Mol Cell Biol 30, 3695-3710.
68. Zaoutis, T. E., Argon, J., Chu, J., Berlin, J. A., Walsh, T. J. & Feudtner, C. (2005). The epidemiology and attributable outcomes of candiedmia in adults and children hospitalized in the United States: a propensity analysis. Clin Infect Dis 41, 1232-1239.