How cells respond to DNA damage is key to maintaining genome integrity or facilitating genetic change. In fungi, DNA damage responses have been extensively characterized in the model budding yeast Saccharomyces cerevisiae, which is generally not pathogenic. However, it is not clear how closely these responses resemble those in fungal pathogens, in which genetic change plays an important role in the evolutionary arms race between pathogen and host and the evolution of antifungal drug resistance. A close relative of S. cerevisiae, Candida glabrata, is an opportunistic pathogen that displays high variability in chromosome structure among clinical isolates and rapidly evolves antifungal drug resistance. The mechanisms facilitating such genomic flexibility and evolvability in this organism are unknown. Recently we characterized the DNA damage response of C. glabrata and identified several features that distinguish it from the well characterized DNA damage response of S. cerevisiae. First, we discovered that, in contrast to the established paradigm, C. glabrata effector kinase Rad53 is not hyperphosphorylated upon DNA damage. We also uncovered evidence of an attenuated DNA damage checkpoint response, wherein in the presence of DNA damage C. glabrata cells did not accumulate in S-phase and proceeded with cell division, leading to aberrant mitoses and cell death. Finally, we identified evidence of transcriptional rewiring of the DNA damage response of C. glabrata relative to S. cerevisiae, including an upregulation of genes involved in mating and meiosis—processes that have not been reported in C. glabrata. Together, these results open new possibilities and raise tantalizing questions of how this major fungal pathogen facilitates genetic change.
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The RNAseq data are available at the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155701) and have been previously described (Shor et al. 2020).
The heatmaps were generated using the R studio gplots package, and the code is available upon request.
Alby K, Bennett RJ (2011) Interspecies pheromone signaling promotes biofilm formation and same-sex mating in Candida albicans. Proc Natl Acad Sci USA 108:2510–2515. https://doi.org/10.1073/pnas.1017234108
Amin NS, Holm C (1996) In vivo analysis reveals that the interdomain region of the yeast proliferating cell nuclear antigen is important for DNA replication and DNA repair. Genetics 144:479–493
Ayyagari R, Impellizzeri KJ, Yoder BL, Gary SL, Burgers PM (1995) A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol Cell Biol 15:4420–4429. https://doi.org/10.1128/mcb.15.8.4420
Barber AE, Weber M, Kaerger K, Linde J, Golz H, Duerschmied D, Markert A, Guthke R, Walther G, Kurzai O (2019) Comparative Genomics of Serial Candida glabrata Isolates and the Rapid Acquisition of Echinocandin Resistance during Therapy. Antimicrob Agents Chemother 6310.1128/AAC.01628-18
Bennett RJ, Forche A, Berman J (2014) Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med 410.1101/cshperspect.a019604
Bizerra FC, Jimenez-Ortigosa C, Souza AC, Breda GL, Queiroz-Telles F, Perlin DS, Colombo AL (2014) Breakthrough candidemia due to multidrug-resistant Candida glabrata during prophylaxis with a low dose of micafungin. Antimicrob Agents Chemother 58:2438–2440. https://doi.org/10.1128/AAC.02189-13
Bordallo-Cardona MA, Escribano P, de la Pedrosa EG, Marcos-Zambrano LJ, Canton R, Bouza E, Guinea J (2017) In vitro exposure to increasing micafungin concentrations easily promotes echinocandin resistance in candida glabrata isolates. Antimicrob Agents Chemother 6110.1128/AAC.01542–16
Branzei D, Foiani M (2010) Maintaining genome stability at the replication fork. Nat Rev Mol Cell Biol 11:208–219. https://doi.org/10.1038/nrm2852
Brothers M, Rine J (2019) Mutations in the PCNA DNA polymerase clamp of saccharomyces cerevisiae reveal complexities of the cell cycle and ploidy on heterochromatin assembly. Genetics 213:449–463. https://doi.org/10.1534/genetics.119.302452
Carrete L, Ksiezopolska E, Pegueroles C, Gomez-Molero E, Saus E, Iraola-Guzman S, Loska D, Bader O, Fairhead C, Gabaldon T (2018) Patterns of genomic variation in the opportunistic pathogen candida glabrata suggest the existence of mating and a secondary association with humans. Curr Biol 28(15–27):e17. https://doi.org/10.1016/j.cub.2017.11.027
Chen C, Merrill BJ, Lau PJ, Holm C, Kolodner RD (1999) Saccharomyces cerevisiae pol30 (proliferating cell nuclear antigen) mutations impair replication fidelity and mismatch repair. Mol Cell Biol 19:7801–7815. https://doi.org/10.1128/mcb.19.11.7801
Chen ES, Hoch NC, Wang SC, Pellicioli A, Heierhorst J, Tsai MD (2014) Use of quantitative mass spectrometric analysis to elucidate the mechanisms of phospho-priming and auto-activation of the checkpoint kinase Rad53 in vivo. Mol Cell Proteomics 13:551–565. https://doi.org/10.1074/mcp.M113.034058
Coste A, Selmecki A, Forche A, Diogo D, Bougnoux ME, d’Enfert C, Berman J, Sanglard D (2007) Genotypic evolution of azole resistance mechanisms in sequential Candida albicans isolates. Eukaryot Cell 6:1889–1904. https://doi.org/10.1128/EC.00151-07
Edenberg ER, Vashisht A, Benanti JA, Wohlschlegel J, Toczyski DP (2014) Rad53 downregulates mitotic gene transcription by inhibiting the transcriptional activator Ndd1. Mol Cell Biol 34:725–738. https://doi.org/10.1128/MCB.01056-13
Ene IV, Farrer RA, Hirakawa MP, Agwamba K, Cuomo CA, Bennett RJ (2018) Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proc Natl Acad Sci USA 115:E8688–E8697. https://doi.org/10.1073/pnas.1806002115
Forche A, Cromie G, Gerstein AC, Solis NV, Pisithkul T, Srifa W, Jeffery E, Abbey D, Filler SG, Dudley AM, Berman J (2018) Rapid phenotypic and genotypic diversification after exposure to the oral host niche in. Genetics 209:725–741. https://doi.org/10.1534/genetics.118.301019
Friedel AM, Pike BL, Gasser SM (2009) ATR/Mec1: coordinating fork stability and repair. Curr Opin Cell Biol 21:237–244. https://doi.org/10.1016/j.ceb.2009.01.017
Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell 12:2987–3003. https://doi.org/10.1091/mbc.12.10.2987
Haber JE (2012) Mating-type genes and MAT switching in Saccharomyces cerevisiae. Genetics 191:33–64. https://doi.org/10.1534/genetics.111.134577
Healey KR, Jimenez Ortigosa C, Shor E, Perlin DS (2016) Genetic drivers of multidrug resistance in candida glabrata. Front Microbiol 7: 1995 doi: https://doi.org/10.3389/fmicb.2016.01995
Heitman J, Sun S, James TY (2013) Evolution of fungal sexual reproduction. Mycologia 105:1–27. https://doi.org/10.3852/12-253
Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD (2013) Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep 4:174–188. https://doi.org/10.1016/j.celrep.2013.05.041
Jung KW, Lee Y, Huh EY, Lee SC, Lim S, Bahn YS (2019) Rad53- and Chk1-Dependent DNA damage response pathways cooperatively promote fungal pathogenesis and modulate antifungal drug susceptibility. mBio 1010.1128/mBio.01726–18
Lee SJ, Schwartz MF, Duong JK, Stern DF (2003) Rad53 phosphorylation site clusters are important for Rad53 regulation and signaling. Mol Cell Biol 23:6300–6314. https://doi.org/10.1128/mcb.23.17.6300-6314.2003
Lobrich M, Jeggo PA (2007) The impact of a negligent G2/M checkpoint on genomic instability and cancer induction. Nat Rev Cancer 7:861–869. https://doi.org/10.1038/nrc2248
Lopez-Fuentes E, Gutierrez-Escobedo G, Timmermans B, Van Dijck P, De Las Penas A, Castano I (2018) Candida glabrata's genome plasticity confers a unique pattern of expressed cell wall proteins. J Fungi (Basel) 410.3390/jof4020067
Lott TJ, Frade JP, Lockhart SR (2010) Multilocus sequence type analysis reveals both clonality and recombination in populations of Candida glabrata bloodstream isolates from US surveillance studies. Eukaryot Cell 9:619–625. https://doi.org/10.1128/EC.00002-10
Muller H, Hennequin C, Gallaud J, Dujon B, Fairhead C (2008) The asexual yeast Candida glabrata maintains distinct a and alpha haploid mating types. Eukaryot Cell 7:848–858. https://doi.org/10.1128/EC.00456-07
Muller H, Thierry A, Coppee JY, Gouyette C, Hennequin C, Sismeiro O, Talla E, Dujon B, Fairhead C (2009) Genomic polymorphism in the population of Candida glabrata: gene copy-number variation and chromosomal translocations. Fungal Genet Biol 46:264–276. https://doi.org/10.1016/j.fgb.2008.11.006
Myung K, Chen C, Kolodner RD (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411:1073–1076. https://doi.org/10.1038/35082608
Pellicioli A, Foiani M (2005) Signal transduction: How rad53 kinase is activated. Curr Biol 15:R769-771. https://doi.org/10.1016/j.cub.2005.08.057
Perlin DS, Rautemaa-Richardson R, Alastruey-Izquierdo A (2017) The global problem of antifungal resistance: prevalence, mechanisms, and management. Lancet Infect Dis 17:e383–e392. https://doi.org/10.1016/S1473-3099(17)30316-X
Polakova S, Blume C, Zarate JA, Mentel M, Jorck-Ramberg D, Stenderup J, Piskur J (2009) Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. Proc Natl Acad Sci USA 106:2688–2693. https://doi.org/10.1073/pnas.0809793106
Ram Y, Hadany L (2016) Condition-dependent sex: who does it, when and why? Philos Trans R Soc Lond B Biol Sci 37110.1098/rstb.2015.0539
Sanchez Y, Desany BA, Jones WJ, Liu Q, Wang B, Elledge SJ (1996) Regulation of RAD53 by the ATM-like kinases MEC1 and TEL1 in yeast cell cycle checkpoint pathways. Science 271:357–360. https://doi.org/10.1126/science.271.5247.357
Segurado M, Diffley JF (2008) Separate roles for the DNA damage checkpoint protein kinases in stabilizing DNA replication forks. Genes Dev 22:1816–1827. https://doi.org/10.1101/gad.477208
Selmecki A, Forche A, Berman J (2006) Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Science 313:367–370. https://doi.org/10.1126/science.1128242
Selmecki AM, Dulmage K, Cowen LE, Anderson JB, Berman J (2009) Acquisition of aneuploidy provides increased fitness during the evolution of antifungal drug resistance. PLoS Genet 5:e1000705. https://doi.org/10.1371/journal.pgen.1000705
Serero A, Jubin C, Loeillet S, Legoix-Ne P, Nicolas AG (2014) Mutational landscape of yeast mutator strains. Proc Natl Acad Sci USA 111:1897–1902. https://doi.org/10.1073/pnas.1314423111
Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A (2018) Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175:1533-1545.e1520. https://doi.org/10.1016/j.cell.2018.10.023
Sherwood RK, Scaduto CM, Torres SE, Bennett RJ (2014) Convergent evolution of a fused sexual cycle promotes the haploid lifestyle. Nature 506:387–390. https://doi.org/10.1038/nature12891
Shi QM, Wang YM, Zheng XD, Lee RT, Wang Y (2007) Critical role of DNA checkpoints in mediating genotoxic-stress-induced filamentous growth in Candida albicans. Mol Biol Cell 18:815–826. https://doi.org/10.1091/mbc.e06-05-0442
Shin JH, Chae MJ, Song JW, Jung SI, Cho D, Kee SJ, Kim SH, Shin MG, Suh SP, Ryang DW (2007) Changes in karyotype and azole susceptibility of sequential bloodstream isolates from patients with Candida glabrata candidemia. J Clin Microbiol 45:2385–2391. https://doi.org/10.1128/JCM.00381-07
Shor E, Garcia-Rubio R, DeGregorio L, Perlin DS (2020) A Noncanonical DNA Damage Checkpoint Response in a Major Fungal Pathogen. mBio 1110.1128/mBio.03044-20
Smolka MB, Albuquerque CP, Chen SH, Zhou H (2007) Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci USA 104:10364–10369. https://doi.org/10.1073/pnas.0701622104
Sun LL, Li WJ, Wang HT, Chen J, Deng P, Wang Y, Sang JL (2011) Protein phosphatase Pph3 and its regulatory subunit Psy2 regulate Rad53 dephosphorylation and cell morphogenesis during recovery from DNA damage in Candida albicans. Eukaryot Cell 10:1565–1573. https://doi.org/10.1128/EC.05042-11
Sweeney FD, Yang F, Chi A, Shabanowitz J, Hunt DF, Durocher D (2005) Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation. Curr Biol 15:1364–1375. https://doi.org/10.1016/j.cub.2005.06.063
Wang Y, Dohlman HG (2004) Pheromone signaling mechanisms in yeast: a prototypical sex machine. Science 306:1508–1509. https://doi.org/10.1126/science.1104568
Wang H, Gao J, Li W, Wong AH, Hu K, Chen K, Wang Y, Sang J (2012) Pph3 dephosphorylation of Rad53 is required for cell recovery from MMS-induced DNA damage in Candida albicans. PLoS ONE 7:e37246. https://doi.org/10.1371/journal.pone.0037246
Wong S, Fares MA, Zimmermann W, Butler G, Wolfe KH (2003) Evidence from comparative genomics for a complete sexual cycle in the “asexual” pathogenic yeast Candida glabrata. Genome Biol 4:R10. https://doi.org/10.1186/gb-2003-4-2-r10
This work was supported by NIH 5R01AI109025 to D.S.P.
Conflicts of interest
D.S.P. has received funding from the U.S. National Institutes of Health and contracts with The Centers for Disease Control and Prevention, Amplyx, Astellas, Cidara, and Scynexis. He serves on advisory boards for Amplyx, Astellas, Cidara, Matinas, N8 Medical, and Scynexis.
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Communicated by Michael Polymenis.
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Shor, E., Perlin, D.S. DNA damage response of major fungal pathogen Candida glabrata offers clues to explain its genetic diversity. Curr Genet (2021). https://doi.org/10.1007/s00294-021-01162-7
- Candida glabrata
- Genome stability
- DNA damage response
- DNA damage checkpoint
- HO endonuclease