Xu, Deming, Jiang, Bo, Ketela, Troy, Lemieux, Sebastien, Veillette, Karynn, Martel, Nick, Davison, John, Sillaots, Susan, Trosok, Steve, Bachewich, Catherine, Bussey, Howard, Youngman, Phil and Roemer, Terry (2007) Genome-Wide Fitness Test and Mechanism-of-Action Studies of Inhibitory Compounds in Candida albicans. PLoS Pathogens, 3 (6). e92. ISSN 1553-7366
Preview |
Text (application/pdf)
994kBBachewich_PLOS2007.pdf - Published Version |
Official URL: http://dx.doi.org/10.1371/journal.ppat.0030092
Abstract
Candida albicans is a prevalent fungal pathogen amongst the immunocompromised population, causing both superficial and life-threatening infections. Since C. albicans is diploid, classical transmission genetics can not be performed to study specific aspects of its biology and pathogenesis. Here, we exploit the diploid status of C. albicans by constructing a library of 2,868 heterozygous deletion mutants and screening this collection using 35 known or novel compounds to survey chemically induced haploinsufficiency in the pathogen. In this reverse genetic assay termed the fitness test, genes related to the mechanism of action of the probe compounds are clearly identified, supporting their functional roles and genetic interactions. In this report, chemical–genetic relationships are provided for multiple FDA-approved antifungal drugs (fluconazole, voriconazole, caspofungin, 5-fluorocytosine, and amphotericin B) as well as additional compounds targeting ergosterol, fatty acid and sphingolipid biosynthesis, microtubules, actin, secretion, rRNA processing, translation, glycosylation, and protein folding mechanisms. We also demonstrate how chemically induced haploinsufficiency profiles can be used to identify the mechanism of action of novel antifungal agents, thereby illustrating the potential utility of this approach to antifungal drug discovery.
Divisions: | Concordia University > Faculty of Arts and Science > Biology |
---|---|
Item Type: | Article |
Refereed: | Yes |
Authors: | Xu, Deming and Jiang, Bo and Ketela, Troy and Lemieux, Sebastien and Veillette, Karynn and Martel, Nick and Davison, John and Sillaots, Susan and Trosok, Steve and Bachewich, Catherine and Bussey, Howard and Youngman, Phil and Roemer, Terry |
Journal or Publication: | PLoS Pathogens |
Date: | 29 June 2007 |
Digital Object Identifier (DOI): | 10.1371/journal.ppat.0030092 |
ID Code: | 7579 |
Deposited By: | Danielle Dennie |
Deposited On: | 11 May 2011 21:12 |
Last Modified: | 18 Jan 2018 17:31 |
References:
Pappas PG, Rex JH, Lee J, Hamill RJ, Larsen RA, et al. (2003) A prospective observational study of candidemia: Epidemiology, therapy, and influences on mortality in hospitalized adult and pediatric patients. Clin Infect Dis 37: 634–643.Wisplinghoff H, Bischoff T, Tallent SM, Seifert H, Wenzel RP, et al. (2004) Nosocomial bloodstream infections in US hospitals: Analysis of 24,179 cases from a prospective nationwide surveillance study. Clin Infect Dis 39: 309–317.
Braun BR, van het Hoog M, d'Enfert C, Martchenko M, Dungan J, et al. (2005) A human-curated annotation of the Candida albicans genome. PLoS Genet 1: e1.. doi:10.1371/journal.pgen.0010001.
Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, et al. (2004) The diploid genome sequence of Candida albicans. Proc Natl Acad Sci USA 101: 7329–7334.
Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617–624.
Roemer T, Jiang B, Davison J, Ketela T, Veillette K, et al. (2003) Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol 50: 167–181.
Veitia RA (2004) Exploring the etiology of haploinsufficiency. Bioessays 24: 175–184.
Uhl MA, Biery M, Craig N, Johnson AD (2003) Haploinsufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen C. albicans. EMBO J 22: 2668–2678.
Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, et al. (2005) Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169: 1915–1925.
Baetz K, McHardy L, Gable K, Tarling T, Reberioux D, et al. (2004) Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc Natl Acad Sci USA 101: 4525–4530.
Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, et al. (2004) Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci USA 101: 793–798.
Giaever G, Shoemaker DD, Jones TW, Liang H, Winzeler EA, et al. (1999) Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet 21: 278–283.
Lum PY, Armour CD, Stepaniants SB, Cavet G, Wolf MK, et al. (2004) Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116: 121–137.
Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet 14: 450–456.
Odds FC, Brown AJ, Gow NA (2003) Antifungal agents: mechanisms of action. Trends Microbiol 11: 272–279.
Saidane S, Weber S, De Deken X, St-Germain G, Raymond M (2006) PDR16-mediated azole resistance in Candida albicans. Mol Microbiol 60: 1546–1562.
White TC, Holleman S, Dy F, Mirels LF, Stevens DA (2002) Resistance mechanisms in clinical isolates of Candida albicans. Antimicrob Agents Chemother 46: 1704–1713.
Mukhopadhyay K, Kohli A, Prasad R (2002) Drug susceptibilities of yeast cells are affected by membrane lipid composition. Antimicrob Agents Chemother 46: 3695–3705.
van den Hazel HB, Pichler H, do Valle Matta MA, Leitner E, Goffeau A, et al. (1999) PDR16 and PDR17, two homologous genes of Saccharomyces cerevisiae, affect lipid biosynthesis and resistance to multiple drugs. J Biol Chem 274: 1934–1941.
Wenz P, Schwank S, Hoja U, Schuller HJ (2001) A downstream regulatory element located within the coding sequence mediates autoregulated expression of the yeast fatty acid synthase gene FAS2 by the FAS1 gene product. Nucleic Acids Res 29: 4625–4632.
Sanglard D, Ischer F, Monod M, Bille J (1996) Susceptibilities of Candida albicans multidrug transporter mutants to various antifungal agents and other metabolic inhibitors. Antimicrob Agents Chemother 40: 2300–2305.
Richards KL, Anders KR, Nogales E, Schwartz K, Downing KH, et al. (2000) Structure-function relationships in yeast tubulins. Mol Biol Cell 11: 1887–1903.
Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387–391.
Burke D, Gasdaska P, Hartwell L (1989) Dominant effects of tubulin overexpression in Saccharomyces cerevisiae. Mol Cell Biol 9: 1049–1059.
Stearns T, Botstein D (1988) Unlinked noncomplementation: Isolation of new conditional-lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae. Genetics 119: 249–160.
Schatz PJ, Solomon F, Botstein (1986) Genetically essential and nonessential alpha-tubulin genes specify functionally interchangeable proteins. Mol Cell Biol 6: 3722–3733.
Nasmyth K, Peters JM, Uhlmann F (2000) Splitting the chromosome: Cutting the ties that bind sister chromatids. Science 288: 1379–1385.
Roe SM, Prodromou C, O'Brien R, Ladbury JE, Piper PW, et al. (1999) Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin. J Med Chem 42: 260–266.
Chiosis G, Vilenchik M, Kim J, Solit D (2004) Hsp90: The vulnerable chaperone. Drug Discovery Today 20: 881–888.
Bansal PK, Abdulle R, Kitagawa K (2004) Sgt1 associates with Hsp90: An initial step of assembly of the core kinetochore complex. Mol Cell Biol 24: 8069–8079.
Tesic M, Marsh JA, Cullinan SB, Gaber RF (2003) Functional interactions between Hsp90 and the co-chaperones Cns1 and Cpr7 in Saccharomyces cerevisiae. J Biol Chem 278: 32692–32701.
Wang K, Vavassori S, Schweizer LM, Schweizer M (2004) Impaired PRPP-synthesizing capacity compromises cell integrity signaling in Saccharomyces cerevisiae. Microbiol 150: 3327–3339.
Exinger F, Lacroute F (1992) 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet 22: 9–11.
Kressler D, Linder P, de la Cruz J (1999) Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 19: 7897–7912.
Jund R, Lacroute F (1970) Genetic and physiological aspects of resistance to 5-fluoropyrimidines in Saccharomyces cerevisiae. J Bacteriol 102: 607–615.
Dodgson AR, Dodgson KJ, Pujol C, Pfaller MA, Soll DR (2004) Clad-specific flucytosine resistance is due to a single nucleotide change in the FUR1 gene of Candida albicans. Antimicrob Agents Chemother 48: 2223–2227.
Hope WW, Tabernero L, Denning DW, Anderson MJ (2004) Molecular mechanisms of primary resistance to flucytosine in Candida albicans. Antimicrob Agents Chemother 48: 4377–4386.
Pfaller MA, Messer SA, Boyken L, Huynh H, Hollis RJ, Diekema DJ (2002) In vitro activities of 5-fluorocytosine against 8,803 clinical isolates of Candida spp.: Global assessment of primary resistance using National Committee for Clinical Laboratory Standards Susceptibility Test Methods. Antimicrob Agents Chemother 46: 3518–3521.
Huffaker TC, Thomas JH, Botstein D (1988) Diverse effects of beta-tubulin mutations on microtubule formation and function. J Cell Biol 106: 1997–2010.
Jacobs CW, Adams AE, Szaniszlo PJ, Pringle JR (1988) Functions of microtubules in the Saccharomyces cerevisiae cell cycle. J Cell Biol 107: 1409–1426.
Bai C, Ramanna N, Wang YM, Wang Y (2002) Spindle assembly checkpoint component CaMad2p is indispensable for Candida albicans survival and virulence in mice. Mol Microbiol 45: 31–44.
Hoyt MA, Totis L, Roberts BT (1991) S. cerevisiae genes required for cell cycle arrest in response to loss of microtubule function. Cell 66: 507–517.
Hu W, Sillaots S, Lemieux S, Davison J, Kauffman S, et al. (2007) Essential gene identification and drug target prioritization in Aspergillus fumigatus. PLoS Pathog 3: e24.. doi:10.1371/journal.ppat.0030024.
Nierman WC, Pain A, Anderson MJ, Wortman JR, et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151–1156.
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321–1324.
Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105–1115.
Machida M, Asai K, Sano M, Tanaka T, Kumagai T (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 1157–1161.
Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25: 319–326.
Bammert GF, Fostel JM (2000) Genome-wide expression patterns in Saccharomyces cerevisiae: Comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrob Agents Chemother 44: 1255–1265.
de Backer MD, Ilyina T, Ma XJ, Vandoninck S, Luyten WH, et al. (2001) Genomic profiling of the response of Candida albicans to itraconazole treatment using a DNA microarray. Antimicrob Agents Chemother 45: 1660–1670.
Eason RG, Pourmand N, Tongprasit W, Herman ZS, Anthony K, et al. (2004) Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains. Proc Natl Acad Sci U S A 101: 11046–11051.
Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, et al. (2000) Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25: 333–337.
Davis DA, Bruno VM, Loza L, Filler SG, Mitchell AP (2002) Candida albicans Mds3p, a conserved regulator of pH responses and virulence identified through insertional mutagenesis. Genetics 162: 1573–1581.
Henry C, Mouyna I, Latge JP (2007) Testing the efficacy of RNA interference constructs in Aspergillus fumigatus. Curr Genet 51: 277–284.
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71–76.
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.
Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906.
McLachlan GJ, Bean RW, Peel D (2002) A mixture model-based approach to the clustering of microarray expression data. Bioinformatics 18: 413–422.
Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509–519.
Repository Staff Only: item control page