A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans

English version

Autoři: Anaïs Burgain ^aff001; Émilie Pic ^aff001; Laura Markey ^aff003; Faiza Tebbji ^aff001; Carol A. Kumamoto ^aff004; Adnane Sellam ^aff001
Působiště autorů: CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada ^aff001; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada ^aff002; Program in Molecular Microbiology, Tufts University, Boston, Massachusetts, United States of America ^aff003; Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America ^aff004; Big Data Research Centre (BDRC-UL), Université Laval, Faculty of Sciences and Engineering, Quebec City, Quebec, Canada ^aff005
Vyšlo v časopise: A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans. PLoS Pathog 15(12): e32767. doi:10.1371/journal.ppat.1007823
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1007823

Souhrn

Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reversibly reprogram the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway interacted genetically with Snf5. Our study yielded new insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans.

Klíčová slova:

Saccharomyces cerevisiae – Carbohydrate metabolism – Hypoxia – Oxygen – Candida albicans – Transcriptional control – Regulator genes – Oxygen metabolism

Zdroje

1. Wheaton WW, Chandel NS. Hypoxia. 2. Hypoxia regulates cellular metabolism. AJP Cell Physiol. 2011; doi: 10.1152/ajpcell.00485.2010 21123733

2. Solaini G, Baracca A, Lenaz G, Sgarbi G. Hypoxia and mitochondrial oxidative metabolism. Biochimica et Biophysica Acta—Bioenergetics. 2010. doi: 10.1016/j.bbabio.2010.02.011 20153717

3. Eales KL, Hollinshead KER, Tennant DA. Hypoxia and metabolic adaptation of cancer cells. Oncogenesis. 2016; doi: 10.1038/oncsis.2015.50 26807645

4. Ernst JF, Tielker D. Responses to hypoxia in fungal pathogens. Cellular Microbiology. 2009. doi: 10.1111/j.1462-5822.2008.01259.x 19016786

5. Kowalski CH, Beattie SR, Fuller KK, McGurk EA, Tang YW, Hohl TM, et al. Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence. mBio. 2016; doi: 10.1128/mBio.01515-16 27651366

6. Desai PR, van Wijlick L, Kurtz D, Juchimiuk M, Ernst JF. Hypoxia and Temperature Regulated Morphogenesis in Candida albicans. PLoS Genet. 2015; doi: 10.1371/journal.pgen.1005447 26274602

7. Lopes JP, Stylianou M, Backman E, Holmberg S, Jass J, Claesson R, et al. Evasion of Immune Surveillance in Low Oxygen Environments Enhances Candida albicans Virulence. mBio. 2018; doi: 10.1128/mBio.02120-18 30401781

8. Butler G. Hypoxia and Gene Expression in Eukaryotic Microbes. Annu Rev Microbiol. 2013; doi: 10.1146/annurev-micro-092412-155658 23808338

9. Sellam A, Al-Niemi T, McInnerney K, Brumfield S, Nantel A, Suci PA. A Candida albicans early stage biofilm detachment event in rich medium. Bmc Microbiol. 2009;9.

10. Fox EP, Cowley ES, Nobile CJ, Hartooni N, Newman DK, Johnson AD. Anaerobic bacteria grow within candida albicans biofilms and induce biofilm formation in suspension cultures. Curr Biol. 2014; doi: 10.1016/j.cub.2014.08.057 25308076

11. Pradhan A, Avelar GM, Bain JM, Childers DS, Larcombe DE, Netea MG, et al. Hypoxia Promotes Immune Evasion by Triggering β-Glucan Masking on the Candida albicans Cell Surface via Mitochondrial and cAMP-Protein Kinase A Signaling. mBio. 2018; doi: 10.1128/mBio.01318-18 30401773

12. Brown AJ, Brown GD, Netea MG, Gow NA. Metabolism impacts upon Candida immunogenicity and pathogenicity at multiple levels. Trends Microbiol. 2014;22: 614–622. doi: 10.1016/j.tim.2014.07.001 25088819

13. Ene IV, Brunke S, Brown AJ, Hube B. Metabolism in fungal pathogenesis. Cold Spring Harb Perspect Med. 2014;4: a019695. doi: 10.1101/cshperspect.a019695 25190251

14. Askew C, Sellam A, Epp E, Hogues H, Mullick A, Nantel A, et al. Transcriptional regulation of carbohydrate metabolism in the human pathogen Candida albicans. PLoS Pathog. 2009/10/10. 2009;5: e1000612. doi: 10.1371/journal.ppat.1000612 19816560

15. Perez JC, Kumamoto CA, Johnson AD. Candida albicans commensalism and pathogenicity are intertwined traits directed by a tightly knit transcriptional regulatory circuit. PLoS Biol. 2013;11: e1001510. doi: 10.1371/journal.pbio.1001510 23526879

16. Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. In: eLife [Internet]. 10 Sep 2016 [cited 17 Apr 2019]. doi: 10.7554/eLife.18981 27614020

17. Sandai D, Yin Z, Selway L, Stead D, Walker J, Leach MD, et al. The evolutionary rewiring of ubiquitination targets has reprogrammed the regulation of carbon assimilation in the pathogenic yeast Candida albicans. MBio. 2012;3. doi: 10.1128/mBio.00495-12 23232717

18. Van Ende M, Wijnants S, Van Dijck P. Sugar Sensing and Signaling in Candida albicans and Candida glabrata. Front Microbiol. 2019; doi: 10.3389/fmicb.2019.00099 30761119

19. Lorenz MC. Carbon catabolite control in Candida albicans: new wrinkles in metabolism. mBio. 2013;4: e00034–13. doi: 10.1128/mBio.00034-13 23386434

20. Pasricha S, MacRae JI, Chua HH, Chambers J, Boyce KJ, McConville MJ, et al. Extensive Metabolic Remodeling Differentiates Non-pathogenic and Pathogenic Growth Forms of the Dimorphic Pathogen Talaromyces marneffei. Front Cell Infect Microbiol. 2017; doi: 10.3389/fcimb.2017.00368 28861398

21. Ward PS, Thompson CB. Metabolic reprogramming: a cancer hallmark even warburg did not anticipate. Cancer Cell. 2012/03/24. 2012;21: 297–308. doi: 10.1016/j.ccr.2012.02.014 22439925

22. Murima P, McKinney JD, Pethe K. Targeting bacterial central metabolism for drug development. Chem Biol. 2014/12/03. 2014;21: 1423–1432. doi: 10.1016/j.chembiol.2014.08.020 25442374

23. Lorenz MC, Fink GR. Life and death in a macrophage: role of the glyoxylate cycle in virulence. Eukaryot Cell. 2002/11/29. 2002;1: 657–662. doi: 10.1128/EC.1.5.657-662.2002 12455685

24. Sellam A, van het Hoog M, Tebbji F, Beaurepaire C, Whiteway M, Nantel A. Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans. Eukaryot Cell. 2014;13: 675–690. doi: 10.1128/EC.00292-13 24681685

25. Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G. Regulation of the hypoxic response in Candida albicans. Eukaryot Cell. 2010/09/28. 2011;9: 1734–1746. doi: 10.1128/EC.00159-10 20870877

26. Guida A, Lindstädt C, Maguire SL, Ding C, Higgins DG, Corton NJ, et al. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics. 2011; doi: 10.1186/1471-2164-12-628 22192698

27. Setiadi ER, Doedt T, Cottier F, Noffz C, Ernst JF. Transcriptional response of Candida albicans to hypoxia: linkage of oxygen sensing and Efg1p-regulatory networks. J Mol Biol. 2006/07/21. 2006;361: 399–411. doi: 10.1016/j.jmb.2006.06.040 16854431

28. Chun CD, Liu OW, Madhani HD. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathog. 2007; doi: 10.1371/journal.ppat.0030022 17319742

29. Losada L, Barker BM, Pakala S, Pakala S, Joardar V, Zafar N, et al. Large-Scale Transcriptional Response to Hypoxia in Aspergillus fumigatus Observed Using RNAseq Identifies a Novel Hypoxia Regulated ncRNA. Mycopathologia. 2014; doi: 10.1007/s11046-014-9779-8 24996522

30. Laurian R, Dementhon K, Doumèche B, Soulard A, Noel T, Lemaire M, et al. Hexokinase and Glucokinases Are Essential for Fitness and Virulence in the Pathogenic Yeast Candida albicans. Front Microbiol. 2019;10. doi: 10.3389/fmicb.2019.00327 30858840

31. Bonhomme J, Chauvel M, Goyard S, Roux P, Rossignol T, d’Enfert C. Contribution of the glycolytic flux and hypoxia adaptation to efficient biofilm formation by Candida albicans. Mol Microbiol. 2011;80: 995–1013. doi: 10.1111/j.1365-2958.2011.07626.x 21414038

32. Vandeputte P, Pradervand S, Ischer F, Coste AT, Ferrari S, Harshman K, et al. Identification and functional characterization of Rca1, a transcription factor involved in both antifungal susceptibility and host response in Candida albicans. Eukaryot Cell. 2012/05/15. 2012;11: 916–931. doi: 10.1128/EC.00134-12 22581526

33. Homann OR, Dea J, Noble SM, Johnson AD. A phenotypic profile of the Candida albicans regulatory network. PLoS Genet. 2009/12/31. 2009;5: e1000783. doi: 10.1371/journal.pgen.1000783 20041210

34. Finkel JS, Xu W, Huang D, Hill EM, Desai JV, Woolford CA, et al. Portrait of Candida albicans adherence regulators. PLoS Pathog. 2012;8: e1002525. doi: 10.1371/journal.ppat.1002525 22359502

35. Geber A, Williamson PR, Rex JH, Sweeney EC, Bennett JE. Cloning and characterization of a Candida albicans maltase gene involved in sucrose utilization. J Bacteriol. 1992;174: 6992–6996. doi: 10.1128/jb.174.21.6992-6996.1992 1400249

36. Williamson PR, Huber MA, Bennett JE. Role of maltase in the utilization of sucrose by Candida albicans. Biochem J. 1993;291 (Pt 3): 765–771.

37. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U A. 2005;102: 15545–15550. doi: 10.1073/pnas.0506580102 16199517

38. Pierce JV, Dignard D, Whiteway M, Kumamoto CA. Normal adaptation of Candida albicans to the murine gastrointestinal tract requires Efg1p-dependent regulation of metabolic and host defense genes. Eukaryot Cell. 2013;12: 37–49. doi: 10.1128/EC.00236-12 23125349

39. Spiering MJ, Moran GP, Chauvel M, Maccallum DM, Higgins J, Hokamp K, et al. Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model. Eukaryot Cell. 2009/12/22. 9: 251–265. doi: 10.1128/EC.00291-09 20023067

40. Marcil A, Gadoury C, Ash J, Zhang J, Nantel A, Whiteway M. Analysis of PRA1 and its relationship to Candida albicans-macrophage interactions. Infect Immun. 2008; doi: 10.1128/IAI.00588-07 18625733

41. Tebbji F, Chen Y, Sellam A, Whiteway M. The Genomic Landscape of the Fungus-Specific SWI/SNF Complex Subunit, Snf6, in Candida albicans. mSphere. 2017;2: e00497–17. doi: 10.1128/mSphere.00497-17 29152582

42. Finkel JS, Xu W, Huang D, Hill EM, Desai JV, Woolford CA, et al. Portrait of Candida albicans adherence regulators. PLoS Pathog. 2012;8: e1002525. doi: 10.1371/journal.ppat.1002525 22359502

43. Noble SM, French S, Kohn LA, Chen V, Johnson AD. Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity. Nat Genet. 2010/06/15. 2010;42: 590–598. doi: 10.1038/ng.605 20543849

44. Lorenz MC, Bender JA, Fink GR. Transcriptional response of Candida albicans upon internalization by macrophages. Eukaryot Cell. 2004; doi: 10.1128/EC.3.5.1076-1087.2004

45. Gow NAR, van de Veerdonk FL, Brown AJP, Netea MG. Candida albicans morphogenesis and host defence: discriminating invasion from colonization. Nat Rev Microbiol. 2012;10: 112–122. doi: 10.1038/nrmicro2711 22158429

46. Murante D, Murante T, Hung, Koselny K, Krysan DJ, Wellington M, et al. Systematic Complex Haploinsufficiency-Based Genetic Analysis of Candida albicans Transcription Factors: Tools and Applications to Virulence-Associated Phenotypes. G3amp58 GenesGenomesGenetics. 2018; doi: 10.1534/g3.117.300515 29472308

47. Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling complex genetic interactions in a simple eukaryotic genome: Actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev. 2007; doi: 10.1101/gad.1477507 17167106

48. Coccetti P, Nicastro R, Tripodi F. Conventional and emerging roles of the energy sensor Snf1/AMPK in Saccharomyces cerevisiae. Microb Cell Graz Austria. 2018;5: 482–494. doi: 10.15698/mic2018.11.655 30483520

49. Ramirez-Zavala B, Mottola A, Haubenreisser J, Schneider S, Allert S, Brunke S, et al. The Snf1-activating kinase Sak1 is a key regulator of metabolic adaptation and in vivo fitness of Candida albicans. Mol Microbiol. 2017; doi: 10.1111/mmi.13674 28337802

50. Nicastro R, Tripodi F, Gaggini M, Castoldi A, Reghellin V, Nonnis S, et al. Snf1 phosphorylates adenylate cyclase and negatively regulates protein kinase A-dependent transcription in Saccharomyces cerevisiae. J Biol Chem. 2015; doi: 10.1074/jbc.M115.658005 26309257

51. Hsu H-E, Liu T-N, Yeh C-S, Chang T-H, Lo Y-C, Kao C-F. Feedback Control of Snf1 Protein and Its Phosphorylation Is Necessary for Adaptation to Environmental Stress. J Biol Chem. 2015;290: 16786–16796. doi: 10.1074/jbc.M115.639443 25947383

52. Liu Z, Myers LC. Candida albicans Swi/Snf and Mediator Complexes Differentially Regulate Mrr1-Induced MDR1 Expression and Fluconazole Resistance. Antimicrob Agents Chemother. 2017;61: e01344–17, /aac/61/11/e01344-17.atom. doi: 10.1128/AAC.01344-17 28807921

53. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 2010;8: e1000414. doi: 10.1371/journal.pbio.1000414 20625544

54. Sellam A, Whiteway M. Recent advances on Candida albicans biology and virulence. F1000Res. 2016;5: 2582. doi: 10.12688/f1000research.9617.1 27853524

55. García R, Botet J, Rodríguez-Peña JM, Bermejo C, Ribas JC, Revuelta JL, et al. Genomic profiling of fungal cell wall-interfering compounds: identification of a common gene signature. BMC Genomics. 2015;16: 683. doi: 10.1186/s12864-015-1879-4 26341223

56. Dutta A, Sardiu M, Gogol M, Gilmore J, Zhang D, Florens L, et al. Composition and Function of Mutant Swi/Snf Complexes. Cell Rep. 2017;18: 2124–2134. doi: 10.1016/j.celrep.2017.01.058 28249159

57. Sen P, Luo J, Hada A, Hailu SG, Dechassa ML, Persinger J, et al. Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex. Cell Rep. 2017;18: 2135–2147. doi: 10.1016/j.celrep.2017.02.017 28249160

58. Musladin S, Krietenstein N, Korber P, Barbaric S. The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening. Nucleic Acids Res. 2014;42: 4270–4282. doi: 10.1093/nar/gkt1395 24465003

59. Rawal Y, Chereji RV, Qiu H, Ananthakrishnan S, Govind CK, Clark DJ, et al. SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast. Genes Dev. 2018;32: 695–710. doi: 10.1101/gad.312850.118 29785963

60. Neely KE, Hassan AH, Brown CE, Howe L, Workman JL. Transcription activator interactions with multiple SWI/SNF subunits. Mol Cell Biol. 2002;22: 1615–1625. https://www.ncbi.nlm.nih.gov/pubmed/11865042 doi: 10.1128/MCB.22.6.1615-1625.2002

61. Burns LG, Peterson CL. The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol Cell Biol. 1997;17: 4811–4819. https://www.ncbi.nlm.nih.gov/pubmed/9234737 doi: 10.1128/mcb.17.8.4811

62. Huang G, Huang Q, Wei Y, Wang Y, Du H. Multiple roles and diverse regulation of the Ras/cAMP/protein kinase A pathway in Candida albicans. Molecular Microbiology. 2019. doi: 10.1111/mmi.14148 30299574

63. Klengel T, Liang WJ, Chaloupka J, Ruoff C, Schröppel K, Naglik JR, et al. Fungal adenylyl cyclase integrates CO2 sensing with cAMP signaling and virulence. Curr Biol. 2005; doi: 10.1016/j.cub.2005.10.040 16303561

64. Pentland DR, Piper-Brown E, Mühlschlegel FA, Gourlay CW. Ras signalling in pathogenic yeasts. Microb Cell. 5: 63–73. doi: 10.15698/mic2018.02.612 29417055

65. Rando OJ, Winston F. Chromatin and transcription in yeast. Genetics. 2012;190: 351–387. doi: 10.1534/genetics.111.132266 22345607

66. Usaite R, Jewett MC, Oliveira AP, Yates JR, Olsson L, Nielsen J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Syst Biol. 2009;5: 319. doi: 10.1038/msb.2009.67 19888214

67. Zhang J, Vemuri G, Nielsen J. Systems biology of energy homeostasis in yeast. Curr Opin Microbiol. 2010;13: 382–388. doi: 10.1016/j.mib.2010.04.004 20439164

68. Grahl N, Demers EG, Lindsay AK, Harty CE, Willger SD, Piispanen AE, et al. Mitochondrial Activity and Cyr1 Are Key Regulators of Ras1 Activation of C. albicans Virulence Pathways. PLOS Pathog. 2015;11: e1005133. doi: 10.1371/journal.ppat.1005133 26317337

69. Huang X, Chen X, He Y, Yu X, Li S, Gao N, et al. Mitochondrial complex I bridges a connection between regulation of carbon flexibility and gastrointestinal commensalism in the human fungal pathogen Candida albicans. PLOS Pathog. 2017;13: e1006414. doi: 10.1371/journal.ppat.1006414 28570675

70. Miramon P, Lorenz MC. A feast for Candida: Metabolic plasticity confers an edge for virulence. PLoS Pathog. 2017;13: e1006144. doi: 10.1371/journal.ppat.1006144 28182769

71. Xu W, Solis NV, Ehrlich RL, Woolford CA, Filler SG, Mitchell AP. Activation and Alliance of Regulatory Pathways in C. albicans during Mammalian Infection. PLOS Biol. 2015;13: e1002076. doi: 10.1371/journal.pbio.1002076 25693184

72. National Research Council (US) Committee for the Update of the Guide for the Care and Use of Laboratory Animals. Guide for the Care and Use of Laboratory Animals [Internet]. 8th ed. Washington (DC): National Academies Press (US); 2011. http://www.ncbi.nlm.nih.gov/books/NBK54050/.

73. Liu H, Köhler J, Fink GR. Suppression of hyphal formation in Candida albicans by mutation of a STE12 homolog. Science. 1994; doi: 10.1126/science.7992058 7992058

74. Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P. The ctf13-30/CTF13 Genomic Haploinsufficiency Modifier Screen Identifies the Yeast Chromatin Remodeling Complex RSC, Which Is Required for the Establishment of Sister Chromatid Cohesion. Mol Cell Biol. 2004; doi: 10.1128/MCB.24.3.1232-1244.2003

75. Gola S, Martin R, Walther A, Dunkler A, Wendland J. New modules for PCR-based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region. Yeast. 2003/12/10. 2003;20: 1339–1347. doi: 10.1002/yea.1044 14663826

76. NIH Image to ImageJ: 25 years of image analysis | Nature Methods [Internet]. [cited 16 Sep 2019]. https://www.nature.com/articles/nmeth.2089

77. Sellam A, Tebbji F, Nantel A. Role of Ndt80p in sterol metabolism regulation and azole resistance in Candida albicans. Eukaryot Cell. 2009/06/23. 2009;8: 1174–1183. doi: 10.1128/EC.00074-09 19542309

78. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 2013;41: D991–D995. doi: 10.1093/nar/gks1193 23193258

79. White SJ, Rosenbach A, Lephart P, Nguyen D, Benjamin A, Tzipori S, et al. Self-regulation of Candida albicans population size during GI colonization. PLoS Pathog. 2007; doi: 10.1371/journal.ppat.0030184 18069889