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Chapter 5 : The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era

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The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, Page 1 of 2

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Abstract:

This chapter focuses on pioneering works that have laid the foundation for the conversion from the classical study of fungal pathobiology to the molecular era. The most widely used and important molecular biology-based technologies that are now available and in use for the identification of pathogenic fungi and for study of fungal pathobiology are also discussed. The transition from the classical era to the molecular era necessitated the development of models, techniques, and strategies which would facilitate the definition of the genetic and molecular basis of pathogenicity according to the working hypothesis in the molecular Koch’s postulates formulated by Falkow. The chapter talks about classical versus molecular approaches applied to the identification of fungal pathogens. Nucleic acid-based molecular assays can be divided into two classes: PCR based and non-PCR. The major PCR-based assays for fungal diagnosis consist of three different strategies, each of which has a standard polymerase amplification of template DNA as a central component. The discovery of effective drugs and the development of vaccines based on knowledge of molecular biology will indeed contribute to the prevention of and therapy for these infections and better management of patients. Education in medical mycology must be viewed on par with that of other infectious diseases in order to realize the full benefit of the evolution from the classical to molecular era of studies on pathogenic fungi.

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5

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Figures

Image of Figure 1.
Figure 1.

Mycology milestones. The transition from classical mycology to molecular mycology was made possible through a number of biological and technological milestones that were achieved over the last 25 years.

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
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Image of Figure 2.
Figure 2.

ATMT. Transformation is mediated by selection on hygromycin. The hygromycin B phosphotransferase gene is transferred by to the host cell, where it integrates into the genome. L.B, left border; hygromycin B phosphotransferase gene; R.B., right border, T-DNA, transfer DNA present in Ti plasmid; Vir, virulence proteins that lead to production of the single-stranded T-DNA molecule as well as formation of the channel; C, channel through which T-DNA is exported into host cells (

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
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Image of Figure 3.
Figure 3.

rDNA gene cluster. Ribosomal subunits are shown as a single cluster within brackets. The four subunits are identified (18S, 5.8S, 26S, and 5.8S) as boxes. The intervening regions are ITS1 and ITS2 (internal transcribed spacer) and IGS1 and IGS2 (intergenic region). Primers for amplifying the ITS1-ITS2 region are shown by arrows (ITS1 and ITS4), with the general size of the amplicon being ~700 bp.

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
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Image of Figure 4.
Figure 4.

RFLP. Genomic DNA from five isolates (lanes 1 to 5) of digested with EcoRI is shown. DNA appears as a smear except when the restriction enzyme yields fragments identical in size. These fragments appear as more intensely staining bands on the gel against the background of sheared DNA because they migrate to the same place on the gel. The number and pattern can be used to discriminate strains, depending on the enzyme used for digestion. L, size marker (1-kb ladder).

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
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Image of Figure 5.
Figure 5.

RAPD analysis. Four strains of were analyzed by RAPD analysis. Strains 1 and 2 are clinical isolates, and strains 3 and 4 are unrelated controls. RAPD primers are listed under each panel and are from references and . RAPD patterns suggest that strains 1 and 2 are related.

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
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References

/content/book/10.1128/9781555815776.ch05
1. Abuodeh, R. O.,, M. J. Orbach,, M. A. Mandel,, A. Das, and, J. N. Galgiani. 2000. Genetic transformation of Coccidioides immitis facilitated by Agrobacterium tumefaciens. J. Infect. Dis. 181:21062110.
2. Alani, E., and, N. Kleckner. 1987. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116:541545.
3. Armaleo, D.,, G. N. Ye,, T. M. Klein,, K. B. Shark,, J. C. Sanford, and, S. A. Johnston. 1990. Biolistic nuclear transformation of Saccharomyces cerevisiae and other fungi. Curr. Genet. 17:97103.
4. Ballance, D. J., and, G. Turner. 1985. Development of a high frequency transforming vector for Aspergillus nidulans. Gene 36:321331.
5. Becker, D. M., and, L. Guarente. 1991. High-efficiency transformation of yeast by electroporation. Methods Enzymol. 194:182187.
6. Beckerman, J.,, H. Chibana,, J. Turner, and, P. T. Magee. 2001. Single-copy IMH3 allele is sufficient to confer resistance to mycophenolic acid in Candida albicans and to mediate transformation of clinical Candida species. Infect. Immun. 69:108114.
7. Beggs, J. D. 1978. Transformation of yeast by a replicating hybrid plasmid. Nature 275:104109.
8. Berg, C. M., and, E. D. Garber. 1962. A genetic analysis of color mutants of Aspergillus fumigatus. Genetics 47:11391146.
9. Borneman, A. R.,, M. J. Hynes, and, A. Andrianopoulos. 2001. A STE12 homolog from the asexual, dimorphic fungus Penicillium marneffei complements the defect in sexual development of an Aspergillus nidulans steA mutant. Genetics 157:10031014.
10. Brand, A.,, D. M. MacCallum,, A. J. Brown,, N. A. Gow, and, F. C. Odds. 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 3:900909.
11. Brandhorst, T. T.,, M. Wuthrich,, T. Warner, and, B. Klein. 1999. Targeted gene disruption reveals an adhesin indispensable for pathogenicity of Blastomyces dermatitidis. J. Exp. Med. 189:12071216.
12. Bundock, P., and, P. J. J. Hooykaas. 1996. Integration of Agrobacterium tumefaciens T-DNA in the Saccharomyces cerevisiae genome by illegitimate recombination. Proc. Natl. Acad. Sci. 93:1527215275.
13. Buxton, F. P.,, D. I. Gwynne, and, R. W. Davies. 1985. Transformation of Aspergillus niger using the argB gene of Aspergillus nidulans. Gene 37:207214.
14. Case, M. E.,, M. Schweizer,, S. R. Kushner, and, N. H. Giles. 1980. Efficient transformation of Neurospora crassa utilizing hybrid plasmid DNA. Proc. Natl. Acad. Sci. USA 77:52595263.
15. Chang, Y. C., and, K. J. Kwon-Chung. 1994. Complementation of a capsule-deficient mutation of Cryptococcus neoformans restores its virulence. Mol. Cell. Biol. 14:49124918.
16. Chang, Y. C.,, L. A. Penoyer, and, K. J. Kwon-Chung. 1996. The second capsule gene of Cryptococcus neoformans, CAP64, is essential for virulence. Infect. Immun. 64:19771983.
17. Collier, L.,, A. Balows, and, M. Sussman (ed.). 1998. Microbiology and Microbial Infections, 9th ed, vol. 4. Arnold, London, United Kingdom.
18. Cormack, B. P.,, G. Bertram,, M. Egerton,, N. A. Gow,, S. Falkow, and, A. J. Brown. 1997. Yeast-enhanced green fluorescent protein (yEGFP) a reporter of gene expression in Candida albicans. Microbiology 143:303311.
19. Cormack, B. P.,, N. Ghori, and, S. Falkow. 1999. An adhesin of the yeast pathogen Candida glabrata mediating adherence to human epithelial cells. Science 285:578582.
20. Cox, G. M.,, D. L. Toffaletti, and, J. R. Perfect. 1996. Dominant selection system for use in Cryptococcus neoformans. J. Med. Vet. Mycol. 34:385391.
21. Crowhurst, R. N.,, J. Rees-George,, E. H. Rikkerink, and, M. D. Templeton. 1992. High efficiency transformation of Fusarium solani f. sp. cucurbitae race 2 (mating population V). Curr. Genet. 21:463469.
22. Davidson, R. C.,, M. C. Cruz,, R. A. L. Sia,, B. Allen,, J. A. Alspaugh, and, J. Heitman. 2000. Gene disruption by biolistic transformation in serotype D strains of Cryptococcus neoformans. Fungal Genet. Biol. 29:3848.
23. De Groot, M. J. A.,, P. Bundock,, P. J. J. Hooykaas, and, A. G. M. Beijersbergen. 1998. Agrobacterium tumefaciens- mediated transformation of filamentous fungi. Nat. Biotechnol. 16:839842.
24. d’Enfert, C.,, G. Weidner,, P. C. Mol, and, A. A. Brakhage. 1999. Transformation systems of Aspergillus fumigatus. New tools to investigate fungal virulence. Contrib. Microbiol. 2:149166.
25. de Repentigny, L. 1992. Serodiagnosis of candidiasis, aspergillosis, and cryptococcosis. Clin. Infect. Dis. 14:S11S22.
26. Diaz, M. R., and, J. W. Fell. 2004. High-throughput detection of pathogenic yeasts of the genus Trichosporon. J. Clin. Microbiol. 42:36963706.
27. Dib, C.,, S. Faure,, C. Fizames,, D. Samson,, N. Drouot,, A. Vignal,, P. Millasseau,, S. Marc,, J. Hazan,, E. Seboun,, M. Lathrop,, G. Gyapay,, J. Morissette, and, J. Weissenbach. 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152154.
28. DiSalvo, A. F.,, A. S. Sekhon,, G. A. Land, and, W. H. Fleming. 1980. Evaluation of the exoantigen test for identification of Histoplasma species and Coccidioides immitis cultures. J. Clin. Microbiol. 11:238241.
29. Dixon, D. 2001. US-Japan workshops in medical mycology: past, present and future. Jpn. J. Med. Mycol. 42:7580.
30. Dromer, F.,, A. Varma,, O. Ronin,, S. Mathoulin, and, B. Dupont. 1994. Molecular typing of Cryptococcus neoformans serotype D clinical isolates. J. Clin. Microbiol. 32:23642371.
31. Edman, J. C. 1992. Isolation of telomerelike sequences from Cryptococcus neoformans and their use in high-efficiency transformation. Mol. Cell. Biol. 12:27772783.
32. Edman, J. C.,, J. A. Kovacs,, H. Masur,, D. V. Santi,, H. J. Elwood, and, M. L. Sogin. 1988. Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature 334:519522.
33. Edman, J. C., and, K. J. Kwon-Chung. 1990. Isolation of the URA5 gene from Cryptococcus neoformans var. neoformans and its use as a selective marker for transformation. Mol. Cell. Biol. 10:45384544.
34. Ellis, M. 2002. Invasive fungal infections: evolving challenges for diagnosis and therapeutics. Mol. Immunol. 38:947957.
35. Erickson, T.,, L. Liu,, A. Gueyikian,, X. Zhu,, J. Gibbons, and, P. R. Williamson. 2001. Multiple virulence factors of Cryptococcus neoformans are dependent on VPH1. Mol. Microbiol. 42:11211131.
36. Erjavec, Z., and, P. E. Verweij. 2002. Recent progress in the diagnosis of fungal infections in the immunocompromised host. Drug. Resist. Update 5:310.
37. Falkow, S. 2004. Molecular Koch’s postulates applied to bacterial pathogenicity—a personal recollection 15 years later. Nat. Rev. Microbiol. 2:6772.
38. Falkow, S. 1988. Molecular Koch’s postulates applied to microbial pathogenicity. Rev. Infect. Dis. 10 (Suppl. 2) :S274S276.
39. Feil, E. J., and, M. C. Enright. 2004. Analyses of clonality and the evolution of bacterial pathogens. Curr. Opin. Microbiol. 7:308313.
40. Feil, E. J.,, B. C. Li,, D. M. Aanensen,, W. P. Hanage, and, B. G. Spratt. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186:15181530.
41. Fell, J. W.,, T. Boekhout,, A. Fonseca,, G. Scorzetti, and, A. Statzell-Tallman. 2000. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int. J. Syst. Evol. Microbiol. 50:13511371.
42. Fire, A.,, S. Xu,, M. K. Montgomery,, S. A. Kostas,, S. E. Driver, and, C. C. Mello. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806811.
43. Fisher, M. C.,, G. L. Koenig,, T. J. White, and, J. T. Taylor. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non California population of Coccidioides immitis. Mycologia 94:7384.
44. Fonzi, W. A., and, M. Y. Irwin. 1993. Isogenic strain construction and gene mapping in Candida albicans. Genetics 134:717728.
45. Freydiere, A. M.,, R. Guinet, and, P. Boiron. 2001. Yeast identification in the clinical microbiology laboratory: phenotypical methods. Med. Mycol. 39:933.
46. Garcia-Hermoso, D.,, F. Dromer,, S. Mathoulin-Pelissier, and, G. Janbon. 2001. Are two Cryptococcus neoformans strains epidemiologically linked? J. Clin. Microbiol. 39:14021406.
47. Gardes, M., and, T. D. Bruns. 1993. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol. Ecol. 2:113118.
48. Girardin, H.,, J. P. Latge,, T. Srikantha,, B. Morrow, and, D. R. Soll. 1993. Development of DNA probes for fingerprinting Aspergillus fumigatus. J. Clin. Microbiol. 31:15471554.
49. Glumoff, V.,, O. Kappeli,, A. Fiechter, and, J. Reiser. 1989. Genetic transformation of the filamentous yeast, Trichosporon cutaneum, using dominant selection marker. Gene 84:311318.
50. Gonzalez, R.,, S. Ferrer,, J. Buesa, and, D. Ramon. 1989. Transformation of the dermatophyte Trichophyton mentagrophytes to hygromycin B resistance. Infect. Immun. 57:29232925.
51. Gorman, J. A.,, W. Chan, and, J. W. Gorman. 1991. Repeated use of GAL1 for gene disruption in Candida albicans. Genetics 129:1924.
52. Gruby, D. 1841. Sur les mycodermes que constituent la teigne faveus. C. R. Acad. Sci. (Paris) 13:309312.
53. Haas, L. O.,, J. M. Cregg, and, M. A. Gleeson. 1990. Development of an integrative DNA transformation system for the yeast Candida tropicalis. J. Bacteriol. 172:45714577.
54. Hall, G. S.,, K. Pratt-Rippin, and, J. A. Washington. 1992. Evaluation of a chemiluminescent probe assay for identification of Histoplasma capsulatum isolates. J. Clin. Microbiol. 30:30033004.
55. Hammond, S. M.,, A. A. Caudy, and, G. J. Hannon. 2001. Post-transcriptional gene silencing by double-stranded RNA. Nat. Rev. Genet. 2:110119.
56. Hinnen, A. J.,, B. Hickes, and, G. R. Fink. 1978. Transformation of yeast. Proc. Natl. Acad. Sci. USA 75:19291933.
57. Hogan, L. H., and, B. S. Klein. 1997. Transforming DNA integrates at multiple sites in the dimorphic fungal pathogen Blastomyces dermatitidis. Gene 186:219226.
58. Hube, B.,, D. Sanglard,, F. C. Odds,, D. Hess,, M. Monod,, W. Schafer,, A. J. Brown, and, N. A. Gow. 1997. Disruption of each of the secreted aspartyl proteinase genes SAP1 ,SAP2 , and SAP3 of Candida albicans attenuates virulence. Infect. Immun. 65:35293538.
59. Huffnagle, K. E., and, R. M. Gander. 1993. Evaluation of Gen-Probe’s Histoplasma capsulatum and Cryptococcus neoformans AccuProbes. J. Clin. Microbiol. 31:419421.
60. Idnurm, A.,, J. L. Reedy,, J. C. Nussbaum, and, J. Heitman. 2004. Cryptococcus neoformans virulence gene discovery through insertional mutagenesis. Eukaryot. Cell 3:420429.
61. Iwen, P. C.,, S. H. Hinrichs, and, M. E. Rupp. 2002. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med. Mycol. 40:87109.
62. Jacobson, E. S.,, D. J. Ayers,, A. C. Harrell, and, C. C. Nicholas. 1982. Genetic and phenotypic characterization of capsule mutants of Cryptococcus neoformans. J. Bacteriol. 156:460462.
63. Jahn, B.,, A. Koch,, A. W. Schmidt,, G. H. Gehringer,, S. Bhakdi, and, A. A. Brakhage. 1997. Isolation and characterization of a pigment-conidium mutant of Aspergillus fumigatus with altered conidial surface and reduced virulence. Infect. Immun. 65:51105117.
64. Johnstone, I. L.,, S. G. Hughes, and, A. J. Clutterbuck. 1985. Cloning an Aspergillus nidulans developmental gene by transformation. EMBO J. 4:13071311.
65. Keeling, P. J., and, N. M. Fast. 2002. Microsporidia : biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol. 56:93116.
66. Kelly, R.,, S. M. Miller,, M. B. Kurtz, and, D. R. Kirsh. 1987. Direct mutagenesis in Candida albicans: one-step gene disruption to isolate ura3 mutants. Mol. Cell. Biol. 7:199207.
67. Kersulyte, D.,, J. P. Woods,, E. J. Keath,, W. E. Goldman, and, D. E. Berg. 1992. Diversity among clinical isolates of Histoplasma capsulatum detected by polymerase chain reaction with arbitrary primers. J. Bacteriol. 174:70757079.
68. Kiehn, T. E.,, E. M. Bernard,, J. W. Gold, and, D. Armstrong. 1979. Candidiasis: detection by gas-liquid chromatography of D-arabinitol, a fungal metabolite, in human serum. Science 206:577580.
69. King, D.,, J. Rhine-Chalberg,, M. A. Pfaller,, S. A. Moser, and, W. G. Merz. 1995. Comparison of four DNA-based methods for strain delineation of Candida lusitaniae. J. Clin. Microbiol. 33:14671470.
70. Kistler, H., and, U. Benny. 1988. Genetic transformation of the fungal plant wilt pathogen, Fusarium oxysporum. Curr. Genet. 13:145149.
71. Klein, B. S.,, S. Chaturvedi,, L. H. Hogan,, J. M. Jones, and, S. L. Newman. 1994. Altered expression of surface protein WI-1 in genetically related strains of Blastomyces dermatitidis that differ in virulence regulates recognition of yeasts by human macrophages. Infect. Immun. 62:35363542.
72. Kunze, G.,, C. Petzoldt,, R. Bode,, I. Samsonova,, M. Hecker, and, D. Birnbaum. 1985. Transformation of Candida maltosa and Pichia guilliermondii by a plasmid containing Saccharomyces cerevisiae ARG4 DNA. Curr. Genet. 9:205209.
73. Kurtz, M. B.,, M. W. Cortelyou, and, D. R. Kirsch. 1986. Integrative transformation of Candida albicans, using a cloned Candida ADE2 gene. Mol. Cell. Biol. 6:142149.
74. Kurtz, M. B.,, M. W. Cortelyou,, S. M. Miller,, M. Lai, and, D. R. Kirsch. 1987. Development of autonomously replicating plasmids for Candida albicans. Mol. Cell. Biol. 7:209217.
75. Kwon-Chung, K. 1998. Gene disruption to evaluate the role of fungal candidate virulence genes. Curr. Opin. Microbiol. 1:381389.
76. Kwon-Chung, K. J. 1972. Emmonsiella capsulata : perfect state of Histoplasma capsulatum. Science 177:368369.
77. Kwon-Chung, K. J. 1971. Genetic analysis on the incompatibility system of Ajellomyces dermatitidis. Sabouraudia 9:231238.
78. Kwon-Chung, K. J. 1975. A new genus, Filobasidiella, the perfect state of Cryptococcus neoformans. Mycologia 67:11971200.
79. Kwon-Chung, K. J. 1976. A new species of Filobasidiella, the sexual state of Cryptococcus neoformans B and C serotypes. Mycologia 68:943946.
80. Kwon-Chung, K. J. 1973. Studies on Emmonsiella capsulata. I. Heterothallism and development of the asco-carp. Mycologia 65:109121.
81. Kwon-Chung, K. J., and, J. E. Bennett. 1992. Medical Mycology. Lea & Febiger, Philadelphia, Pa.
82. Kwon-Chung, K. J., and, W. B. Hill. 1970. Studies on the pink adenine-deficient strains of Candida albicans. I. Cultural and morphological characteristics. Sabouraudia 8:4859.
83. Kwon-Chung, K. J.,, D. Lehman,, C. Good, and, P. T. Magee. 1985. Genetic evidence for role of extracellular proteinase in virulence. Infect. Immun. 49:571575.
84. Kwon-Chung, K. J.,, I. Polacheck, and, T. J. Popkin. 1982. Melanin-lacking mutants of Cryptococcus neoformans and their virulence for mice. J. Bacteriol. 150:14141421.
85. Kwon-Chung, K. J., and, J. C. Rhodes. 1986. Encapsulation and melanin formation as indicators of virulence in Cryptococcus neoformans. Infect Immun. 51:218223.
86. Lasker, B. A.,, L. S. Page,, T. J. Lott,, G. S. Kobayashi, and, G. Medoff. 1991. Characterization of CARE-1: Candida albicans repetitive element-1. Gene 102:4550.
87. Lay, J.,, L. K. Henry,, J. Clifford,, Y. Koltin,, C. E. Bulawa, and, J. M. Becker. 1998. Altered expression of selectable marker URA3 in gene-disruptred Candida albicans strains complicates interpretation of virulence studies. Infect. Immun. 66:53015306.
88. Leal, C. V.,, B. A. Montes,, A. C. Mesa,, A. L. Rus,, M. Corredor,, A. Restrepo, and, J. G. McEwen. 2004. Agrobacterium tumefaciens-mediated transformation of Paracoccidioides brasiliensis. Med. Mycol. 42:391395.
89. Lehmann, P. F.,, D. Lin, and, B. A. Lasker. 1992. Genotypic identification and characterization of species and strains within the genus Candida by using random amplified polymorphic DNA. J. Clin. Microbiol. 30:32493254.
90. Litt, M., and, J. A. Luty. 1989. A hypervariable microsatellite revealed by in vitro amplification of a di-nucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44:397401.
91. Litvintseva, A. P.,, R. E. Marra,, K. Nielsen,, J. Heitman,, R. Vilgalys, and, T. G. Mitchell. 2003. Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa. Eukaryot. Cell 2:11621168.
92. Liu, H.,, T. R. Cottrell,, L. M. Pierini,, W. E. Goldman, and, T. L. Doering. 2002. RNA interference in the pathogenic fungus Cryptococcus neoformans. Genetics 160:463470.
93. Lockhart, S. R.,, C. Pujol,, S. Joly, and, D. R. Soll. 2001. Development and use of complex probes for DNA fingerprinting the infectious fungi. Med. Mycol. 39:18.
94. Macdonald, F., and, F. C. Odds. 1983. Virulence for mice of a proteinase-secreting strain of Candida albicans and proteinase-deficient mutant. J. Gen. Microbiol. 129:431438.
95. Magee, B. B.,, T. M. D’Souza, and, P. T. Magee. 1987. Strain and species identification by restriction fragment length polymorphisms in the ribosomal DNA repeat of Candida species. J. Bacteriol. 169:16391643.
96. Maiden, M. C. 1998. Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria. Clin. Infect. Dis. 27 (Suppl. 1):S12S20.
97. Maiden, M. C.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman, and, B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:31403145.
98. Martino, P., and, C. Girmenia. 2000. Making the diagnosis of fungal infection: when to start treatment. Int. J. Antimicrob. Agents 16:323329.
99. McClelland, C. M.,, Y. C. Chang, and, K. J. Kwon-Chung. 2005. High frequency transformation of Cryptococcus neoformans and Cryptococcus gattii by Agrobacterium tumefaciens. Fungal Genet. Biol. 42:904913.
100. Mcdade, H. C., and, G. M. Cox. 2001. A new dominant selectable marker for use in Cryptococcus neoformans. Med. Mycol. 39:151154.
101. McDonough, E. S., and, A. L. Lewis. 1968. The ascigerous stage of Blastomyces dermatitidis. Mycologia 60:7683.
102. Mehra, R. K.,, J. L. Thorvaldsen,, I. G. Macreadie, and, D. R. Winge. 1992. Cloning system for Candida glabrata using elements from the metallothionein-IIa-encoding gene that confer autonomous replication. Gene 113:119124.
103. Merz, W. G. 1990. Candida albicans strain delineation. Clin. Microbiol. Rev. 3:321334.
104. Meyer, W.,, T. G. Mitchell,, E. Z. Freedman, and, R. Vilgalys. 1993. Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J. Clin. Microbiol. 31:22742280.
105. Miller, R. E., Jr., and, L. P. Lu. 1976. Evaluation of a multitest microtechnique for yeast identification. Am. J. Med. Technol. 42:238242.
106. Mouyna, I.,, C. Henry,, T. L. Doering, and, J. P. Latge. 2004. Gene silencing with RNA interference in the human pathogenic fungus Aspergillus fumigatus. FEMS Microbiol. Lett. 237:317324.
107. Mullins, E. D.,, X. Chen,, P. Romaine,, R. Raina,, D. M. Geiser, and, S. Kang. 2001. Agrobacterium -mediated transformation of Fusarium oxysporum: an efficient tool for insertional mutagenesis and gene transfer. Phytopathology 91:173180.
108. Nelson, R. T.,, J. Hua,, B. Pryor, and, J. K. Lodge. 2001. Identification of virulence mutants of the fungal pathogen Cryptococcus neoformans using signature-tagged mutagenesis. Genetics 157:935947.
109. Neumann, E.,, M. Schaefer-Ridder,, Y. Wang, and, P. H. Hofscheider. 1982. Gene transfer into mouse lyoma cells by electroporation in high electric fields. EMBO J. 1:841845.
110. Neuveglise, C.,, J. Sarfati,, J. P. Latge, and, S. Paris. 1996. Afut1, a retrotransposon-like element from Aspergillus fumigatus. Nucleic Acids Res. 24:14281434.
111. Nosek, J.,, L. Adamikova,, J. Zemanova,, L. Tomaska,, R. Zufferey, and, C. B. Mamoun. 2002. Genetic manipulation of the pathogenic yeast Candida parapsilosis. Curr. Genet. 42:2735.
112. Odds, F. C. 1987. Candida infections: an overview. Crit. Rev. Microbiol. 15:15.
113. Padhye, A. A.,, G. Smith,, D. McLaughlin,, P. G. Standard, and, L. Kaufman. 1992. Comparative evaluation of a chemiluminescent DNA probe and an exoantigen test for rapid identification of Histoplasma capsulatum. J. Clin. Microbiol. 30:31083111.
114. Peng, M.,, C. R. Cooper, Jr., and, P. J. Szaniszlo. 1995. Genetic transformation of the pathogenic fungus Wangiella dermatitidis. Appl. Microbiol. Biotechnol. 44:444450.
115. Perfect, J. R.,, D. L. Toffaletti, and, T. H. Rude. 1993. The gene encoding phosphoribosylaminoimidazole carboxylase (ADE2) is essential for growth of Cryptococcus neoformans in cerebrospinal fluid. Infect. Immun. 61:44464451.
116. Poulter, R. T. M.,, V. Hanrahan,, K. Jeffery,, D. Markie,, M. G. Shepherd, and, P. A. Sullivan. 1982. Recombination analysis of naturally diploid Candida albicans. J. Bacteriol. 152:969975.
117. Punt, P. J.,, R. P. Oliver,, M. A. Dingemanse,, P. H. Pouwels, and, C. A. van den Hondel. 1987. Transformation of Aspergillus based on the hygromycin B resistance marker from Escherichia coli. Gene 56:117124.
118. Reichard, U.,, C.-Y. Hung,, P. W. Thomas, and, G. T. Cole. 2000. Disruption of the gene which encodes a serodiagnostic antigen and chitinase of the human fungal pathogen Coccidioides immitis. Infect. Immun. 68:58305838.
119. Reuss, O.,, A. Vik,, R. Kolter, and, J. Morschhauser. 2004. The SAT1 flipper, an optimized tool for gene disruption in Candida albicans. Gene 341:119127.
120. Rhodes, J. C.,, I. Polacheck, and, K. J. Kwon-Chung. 1982. Phenoloxidase activity and virulence in isogenic strains of Cryptococcus neoformans. Infect. Immun. 36:11751184.
121. Roboz, J.,, R. Suzuki, and, J. F. Holland. 1980. Quantification of arabinitol in serum by selected ion monitoring as a diagnostic technique in invasive candidiasis. J. Clin. Microbiol. 12:594601.
122. Rothstein, R. S. 1983. One-step gene disruption in yeast. Methods Enzymol. C 101:202211.
123. Salas, S. D.,, J. E. Bennett,, K. J. Kwon-Chung,, J. R. Perfect, and, P. R. Williamson. 1996. Effect of the laccase gene CNLAC1 , on virulence of Cryptococcus neoformans. J. Exp. Med. 184:377386.
124. Sanglard, D.,, B. Hube,, M. Monod,, F. C. Odds, and, N. A. Gow. 1997. A triple deletion of the secreted aspartyl proteinase genes SAP4,SAP5 , and SAP6 of Candida albicans causes attenuated virulence. Infect. Immun. 65:35393546.
125. Saracheck, A., and, D. A. Weber. 1984. Temperature-dependent internuclear transfer of genetic material in heterokaryons of Candida albicans. Curr. Genet. 8:181187.
126. Scherer, S., and, D. A. Stevens. 1988. A Candida albicans dispersed, repeated gene family and its epidemiologic applications. Proc. Natl. Acad. Sci. USA 85:14521456.
127. Schlotterer, C. 2000. Evolutionary dynamics of microsatellite DNA. Chromosoma 109:365371.
128. Schmid, J.,, M. Rotman,, B. Reed,, C. L. Pierson, and, D. R. Soll. 1993. Genetic similarity of Candida albicans strains from vaginitis patients and their partners. J. Clin. Microbiol. 31:3946.
129. Sebghati, T. S.,, J. T. Engle, and, W. E. Goldman. 2000. Intracellular parasitism by Histoplasma capsulatum: fungal virulence and calcium dependence. Science 290:13681372.
130. Sendid, B.,, M. Tabouret,, J. L. Poirot,, D. Mathieu,, J. Fruit, and, D. Poulain. 1999. New enzyme immunoassays for sensitive detection of circulating Candida albicans mannan and antimannan antibodies: useful combined test for diagnosis of systemic candidiasis. J. Clin. Microbiol. 37:15101517.
131. Skory, C. D. 2002. Homologous recombination and double-strand break repair in the transformation of Rhizopus oryzae. Mol. Genet. Genomics 268:397406.
132. Soll, D. R. 2000. The ins and outs of DNA fingerprinting the infectious fungi. Clin. Microbiol. Rev. 13:332370.
133. Soll, D. R.,, M. Staebell,, C. Langtimm,, M. Pfaller,, J. Hicks, and, T. V. Rao. 1988. Multiple Candida strains in the course of a single systemic infection. J. Clin. Microbiol. 26:14481459.
134. Spitzer, S. G., and, E. D. Spitzer. 1994. Characterization of the CNRE-1 family of repetitive DNA elements in Cryptococcus neoformans. Gene 144:103106.
135. Standard, P. G., and, L. Kaufman. 1976. Specific immuno-logical test for the rapid identification of members of the genus Histoplasma. J. Clin. Microbiol. 3:191199.
136. Stynen, D.,, A. Goris,, J. Sarfati, and, J. P. Latge. 1995. A new sensitive sandwich enzyme-linked immunosorbent assay to detect galactofuran in patients with invasive aspergillosis. J. Clin. Microbiol. 33:497500.
137. Sugui, J.,, Y. C. Chang, and, K. J. Kwon-Chung. 2005. Agrobacterium tumefaciens-mediated transformation of Aspergillus fumigatus: efficient tool for insertional muta-genesis and targeted gene disruption. Appl. Environ. Microbiol. 71:17981802.
138. Sullivan, T. D.,, P. J. Rooney, and, B. S. Klein. 2002. Agrobacterium tumefaciens integrates transfer DNA into single chromosomal sites of dimorphic fungi and yields homokaryotic progeny from multinucleate yeast. Eukaryot. Cell 1:895905.
139. Sundstrom, P.,, J. E. Cutler, and, J. F. Staab. 2002. Reevaluation of the role of HWP1 in systemic candidiasis by use of Candida albicans strains with selectable marker URA3 targeted to the ENO1 locus. Infect. Immun. 70:32813283.
140. Takashima, M.,, T. Sugita,, T. Shinoda, and, T. Nakase. 2003. Three new combinations from the Cryptococcus laurentii complex:Cryptococcus aureus ,Cryptococcus carnescens and Cryptococcus peneaus. Int. J. Syst. Evol. Microbiol. 53:11871194.
141. Tang, C. M.,, J. Cohen, and, D. W. Holden. 1992. An Aspergillus fumigatus alkaline protease mutant constructed by gene disruption is deficient in extracellular elastase activity. Mol. Microbiol. 6:16631671.
142. Thompson, J. R.,, E. Register,, J. Curotto,, M. B. Kurtz, and, R. Kelly. 1998. An improved protocol for the preparation of yeast cells for transformation by electroporation. Yeast 14:565571.
143. Tijsterman, M.,, R. F. Ketting, and, R. H. Plasterk. 2002. The genetics of RNA silencing. Annu. Rev. Genet. 36:489519.
144. Toffaletti, D. L.,, T. H. Rude,, S. A. Johnston,, D. T. Durack, and, J. R. Perfect. 1993. Gene transfer in Cryptococcus neoformans by use of biolistic delivery of DNA. J. Bacteriol. 175:14051411.
145. Tsai, H. F.,, Y. C. Chang,, R. G. Washburn,, M. H. Wheeler, and, K. J. Kwon-Chung. 1998. The developmentally regulated alb1 gene of Aspergillus fumigatus: its role in modulation of conidial morphology and virulence. J. Bacteriol. 180:30313038.
146. Uhl, M. A.,, M. Biery,, N. Craig, and, A. D. Johnson. 2003. Haplosufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen Candida albicans. EMBO J. 22:26682678.
147. Varma, A., and, K. J. Kwon-Chung. 1999. Characterization of the glyceraldehyde-3-phosphate dehydrogenase gene [correction of glyceraldehyde-3-phosphate gene] and the use of its promoter for heterologous expression in Cryptococcus neoformans, a human pathogen. Gene 232:155163.
148. Wada, M.,, T. Beppu, and, S. Horinouchi. 1996. Integrative transformation of the zygomycete Rhizomucor pusillus by homologous recombination. Appl. Microbiol. Biotechnol. 45:652657.
149. Walden, R.,, B. Reiss,, C. Koncz, and, J. Schell. 1997. The impact of Ti-plasmid-derived gene vectors on the study of the mechanism of action of phytohormones. Annu. Rev. Phytopathol. 35:4566.
150. Walther, A. W. J. 2003. An improved transformation protocol for the human fungal pathogen Candida albi-cans. Curr. Genet. 42:339343.
151. Welsh, J.,, N. Rampino,, M. McClelland, and, M. Perucho. 1995. Nucleic acid fingerprinting by PCR-based methods: applications to problems in aging and mutagenesis. Mutat. Res. 338:215229.
152. Whelan, W. L.,, R. M. Partridge, and, P. T. Magee. 1980. Heterozygosity and segregation in Candida albicans. Genetics 180:107113.
153. White, T. J.,, T. D. Bruns,, S. B. Lee, and, J. W. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315–322. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR Protocols. A Guide to Methods and Applications. Academic Press, Inc., San Diego, Calif.
154. Williams, J. G.,, A. R. Kubelik,, K. J. Livak,, J. A. Rafalski, and, S. V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:65316535.
155. Woloshuk, C. P.,, E. R. Seip,, G. A. Payne, and, C. R. Adkins. 1989. Genetic transformation system for the aflatoxin-producing fungus Aspergillus flavus. Appl. Environ. Microbiol. 55:8690.
156. Wong, B.,, E. M. Bernard,, J. W. Gold,, D. Fong,, A. Silber, and, D. Armstrong. 1982. Increased arabinitol levels in experimental candidiasis in rats: arabinitol appearance rates, arabinitol/creatinine ratios, and severity of infection. J. Infect. Dis. 146:346352.
157. Wong, B.,, K. L. Brauer,, R. R. Tsai, and, K. Jayasimhulu. 1989. Increased amounts of the Aspergillus metabolite D-mannitol in tissue and serum of rats with experimental aspergillosis. J. Infect. Dis. 160:95103.
158. Wong, B.,, J. R. Perfect,, S. Beggs, and, K. A. Wright. 1990. Production of the hexitol D-mannitol by Cryptococcus neoformans in vitro and in rabbits with experimental meningitis. Infect. Immun. 58:16641670.
159. Woods, J. P., and, W. E. Goldman. 1992. In vivo generation of linear plasmids with addition of telomeric sequences by Histoplasma capsulatum. Mol. Microbiol. 6:36033610.
160. Woods, J. P.,, E. L. Heinecke, and, W. E. Goldman. 1998. Electrotransformation and expression of bacterial genes encoding hygromycin phosphotransferase and β-galactosidase in the pathogenic fungus Histoplasma capsulatum. Infect. Immun. 66:16971707.
161. Woods, J. P.,, D. M. Retallack,, E. L. Heinecke, and, W. E. Goldman. 1998. Rare homologous gene targeting in Histoplasma capsulatum: disruption of the URA5Hc gene by allelic replacement. J. Bacteriol. 180:51355143.
162. Worsham, P. L., and, W. E. Goldman. 1990. Development of a genetic transformation system for Histoplasma capsulatum: complementation of uracil auxotrophy. Mol. Gen. Genet. 221:358362.
163. Worsham, P. L., and, W. E. Goldman. 1988. Selection and characterization of ura5 mutants of Histoplasma capsulatum. Mol. Gen. Genet. 214:348352.
164. Xu, J.,, C. M. Boyd,, E. Livingston,, W. Meyer,, J. F. Madden, and, T. G. Mitchell. 1999. Species and genotypic diversities and similarities of pathogenic yeasts colonizing women. J. Clin. Microbiol. 37:38353843.
165. Yeo, S. F., and, B. Wong. 2002. Current status of nonculture methods for diagnosis of invasive fungal infections. Clin. Microbiol. Rev. 15:465484.
166. Young, L. Y.,, M. C. Lorenz, and, J. Heitman. 2000. A STE12 homolog is required for mating but dispensable for filamentation in Candida lusitaniae. Genetics 155:1729.
167. Yu, J. J., and, G. T. Cole. 1998. Biolistic transformation of the human pathogenic fungus Coccidioides immitis. J. Microbiol. Methods 33:129141.

Tables

Generic image for table
Table 1.

Pioneering transformation protocols used in different pathogenic fungi

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5
Generic image for table
Table 2.

Genome sequence status of human fungal pathogens

Citation: Kwon-Chung K, Wickes B. 2006. The Conversion from Classical Studies in Fungal Pathogenesis to the Molecular Era, p 49-70. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch5

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