#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

ChIP-seq and In Vivo Transcriptome Analyses of the SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence


Despite improvements in diagnostics and antifungal drug treatments, mortality rates from invasive mold infections remain high. Defining the fungal adaptation and growth mechanisms at the infection site microenvironment is one research focus that is expected to improve treatment of established invasive fungal infections. The Aspergillus fumigatus transcription factor SrbA is a major regulator of the fungal response to hypoxia found at sites of invasive fungal growth in vivo. In this study, new insights into how SrbA mediates hypoxia adaptation and virulence were revealed through identification of direct transcriptional targets of SrbA under hypoxic conditions. A major novel finding from these studies is the identification of a critical role in fungal hypoxia adaptation and virulence of an SrbA target gene, srbB, which is also in the SREBP family. SrbB plays a major role in regulation of heme biosynthesis and carbohydrate metabolism early in the response to hypoxia. The discovery of SrbA-dependent regulation of srbB gene expression, and the target genes they regulate opens new avenues to understand how SREBPs and their target genes mediate adaptation to the in vivo infection site microenvironment and responses to current antifungal therapies.


Vyšlo v časopise: ChIP-seq and In Vivo Transcriptome Analyses of the SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence. PLoS Pathog 10(11): e32767. doi:10.1371/journal.ppat.1004487
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004487

Souhrn

Despite improvements in diagnostics and antifungal drug treatments, mortality rates from invasive mold infections remain high. Defining the fungal adaptation and growth mechanisms at the infection site microenvironment is one research focus that is expected to improve treatment of established invasive fungal infections. The Aspergillus fumigatus transcription factor SrbA is a major regulator of the fungal response to hypoxia found at sites of invasive fungal growth in vivo. In this study, new insights into how SrbA mediates hypoxia adaptation and virulence were revealed through identification of direct transcriptional targets of SrbA under hypoxic conditions. A major novel finding from these studies is the identification of a critical role in fungal hypoxia adaptation and virulence of an SrbA target gene, srbB, which is also in the SREBP family. SrbB plays a major role in regulation of heme biosynthesis and carbohydrate metabolism early in the response to hypoxia. The discovery of SrbA-dependent regulation of srbB gene expression, and the target genes they regulate opens new avenues to understand how SREBPs and their target genes mediate adaptation to the in vivo infection site microenvironment and responses to current antifungal therapies.


Zdroje

1. BarronMA, MadingerNE (2008) Opportunistic Fungal Infections, Part 2: Candida and Aspergillus. Infections in Medicine 25: 498–505.

2. BrownGD, DenningDW, GowNA, LevitzSM, NeteaMG, et al. (2012) Hidden killers: human fungal infections. Science translational medicine 4: 165rv113.

3. BrownGD, DenningDW, LevitzSM (2012) Tackling human fungal infections. Science 336: 647.

4. Ben-AmiR, LewisRE, KontoyiannisDP (2010) Enemy of the (immunosuppressed) state: an update on the pathogenesis of Aspergillus fumigatus infection. British Journal of Haematology 150: 406–417.

5. SteinbachWJ (2013) Are We There Yet? Recent Progress in the Molecular Diagnosis and Novel Antifungal Targeting of Aspergillus fumigatus and Invasive Aspergillosis. PLoS Pathogens 9: e1003642.

6. WillgerS, GrahlN, CramerR (2009) Aspergillus fumigatus metabolism: Clues to mechanisms of in vivo fungal growth and virulence. Medical Mycology 47: S72–S79.

7. GrahlN, PuttikamonkulS, MacdonaldJM, GamcsikMP, NgoLY, et al. (2011) In vivo hypoxia and a fungal alcohol dehydrogenase influence the pathogenesis of invasive pulmonary aspergillosis. PLoS Pathogens 7: e1002145.

8. TarrandJJ, HanXY, KontoyiannisDP, MayGS (2005) Aspergillus hyphae in infected tissue: Evidence of physiologic adaptation and effect on culture recovery. Journal of Clinical Microbiology 43: 382–386.

9. HallLA, DenningDW (1994) Oxygen Requirements of Aspergillus Species. Journal of Medical Microbiology 41: 311–315.

10. BrockM, JouvionG, Droin-BergereS, DussurgetO, NicolaMA, et al. (2008) Bioluminescent Aspergillus fumigatus, a new tool for drug eficiency testing and in vivo monitoring of invasive aspergillosis. Applied and Environmental Microbiology 74: 7023–7035.

11. BrownJM, WilsonWR (2004) Exploiting tumour hypoxia in cancer treatment. Nature reviews Cancer 4: 437–447.

12. KoeppenM, EckleT, EltzschigHK (2011) The hypoxia-inflammation link and potential drug targets. Current opinion in anaesthesiology 24: 363–369.

13. EltzschigHK, CarmelietP (2011) Hypoxia and inflammation. The New England Journal of Medicine 364: 656–665.

14. MoellerBJ, RichardsonRA, DewhirstMW (2007) Hypoxia and radiotherapy: opportunities for improved outcomes in cancer treatment. Cancer Metastasis Reviews 26: 241–248.

15. GrahlN, CramerRAJr (2010) Regulation of hypoxia adaptation: an overlooked virulence attribute of pathogenic fungi? Medical Mycology: Official Publication of the International Society for Human and Animal Mycology 48: 1–15.

16. ErnstJF, TielkerD (2009) Responses to hypoxia in fungal pathogens. Cellular Microbiology 11: 183–190.

17. HsuJL, KhanMA, SobelRA, JiangX, ClemonsKV, et al. (2013) Aspergillus fumigatus invasion increases with progressive airway ischemia. PloS One 8: e77136.

18. ChunCD, LiuOW, MadhaniHD (2007) A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathogens 3: e22.

19. ChangYC, BienCM, LeeH, EspenshadePJ, Kwon-ChungKJ (2007) Sre1p, a regulator of oxygen sensing and sterol homeostasis, is required for virulence in Cryptococcus neoformans. Molecular microbiology 64: 614–629.

20. GrahlN, ShepardsonKM, ChungD, CramerRA (2012) Hypoxia and fungal pathogenesis: to air or not to air? Eukaryotic cell 11: 560–570.

21. BienCM, EspenshadePJ (2010) Sterol regulatory element binding proteins in fungi: hypoxic transcription factors linked to pathogenesis. Eukaryotic Cell 9: 352–359.

22. HuaX, WuJ, GoldsteinJL, BrownMS, HobbsHH (1995) Structure of the human gene encoding sterol regulatory element binding protein-1 (SREBF1) and localization of SREBF1 and SREBF2 to chromosomes 17p11.2 and 22q13. Genomics 25: 667–673.

23. HortonJD (2002) Sterol regulatory element-binding proteins: transcriptional activators of lipid synthesis. Biochemical Society transactions 30: 1091–1095.

24. SeoYK, ChongHK, InfanteAM, ImSS, XieX, et al. (2009) Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proceedings of the National Academy of Sciences of the United States of America 106: 13765–13769.

25. SeoYK, JeonTI, ChongHK, BiesingerJ, XieX, et al. (2011) Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy. Cell Metabolism 13: 367–375.

26. ReedBD, CharosAE, SzekelyAM, WeissmanSM, SnyderM (2008) Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genetics 4: e1000133.

27. HughesAL, ToddBL, EspenshadePJ (2005) SREBP pathway responds to sterols and functions as an oxygen sensor in fission yeast. Cell 120: 831–842.

28. ToddBL, StewartEV, BurgJS, HughesAL, EspenshadePJ (2006) Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast. Molecular and Cellular Biology 26: 2817–2831.

29. PorterJR, BurgJS, EspenshadePJ, IglesiasPA (2010) Ergosterol regulates sterol regulatory element binding protein (SREBP) cleavage in fission yeast. The Journal of Biological Chemistry 285: 41051–41061.

30. LloydSJ, RaychaudhuriS, EspenshadePJ (2013) Subunit architecture of the Golgi Dsc E3 ligase required for sterol regulatory element-binding protein (SREBP) cleavage in fission yeast. The Journal of Biological Chemistry 288: 21043–21054.

31. CheungR, EspenshadePJ (2013) Structural requirements for sterol regulatory element-binding protein (SREBP) cleavage in fission yeast. The Journal of Biological Chemistry 288: 20351–20360.

32. PorterJR, LeeCY, EspenshadePJ, IglesiasPA (2012) Regulation of SREBP during hypoxia requires Ofd1-mediated control of both DNA binding and degradation. Molecular Biology of the Cell 23: 3764–3774.

33. StewartEV, LloydSJ, BurgJS, NwosuCC, LintnerRE, et al. (2012) Yeast sterol regulatory element-binding protein (SREBP) cleavage requires Cdc48 and Dsc5, a ubiquitin regulatory X domain-containing subunit of the Golgi Dsc E3 ligase. The Journal of Biological Chemistry 287: 672–681.

34. HughesBT, NwosuCC, EspenshadePJ (2009) Degradation of sterol regulatory element-binding protein precursor requires the endoplasmic reticulum-associated degradation components Ubc7 and Hrd1 in fission yeast. The Journal of Biological Chemistry 284: 20512–20521.

35. HughesBT, EspenshadePJ (2008) Oxygen-regulated degradation of fission yeast SREBP by Ofd1, a prolyl hydroxylase family member. The EMBO Journal 27: 1491–1501.

36. WillgerSD, PuttikamonkulS, KimKH, BurrittJB, GrahlN, et al. (2008) A sterol-regulatory element binding protein is required for cell polarity, hypoxia adaptation, azole drug resistance, and virulence in Aspergillus fumigatus. PLoS Pathogens 4: e1000200.

37. WillgerSD, CornishEJ, ChungD, FlemingBA, LehmannMM, et al. (2012) Dsc orthologs are required for hypoxia adaptation, triazole drug responses, and fungal virulence in Aspergillus fumigatus. Eukaryotic Cell 11: 1557–1567.

38. BlatzerM, BarkerBM, WillgerSD, BeckmannN, BlosserSJ, et al. (2011) SREBP coordinates iron and ergosterol homeostasis to mediate triazole drug and hypoxia responses in the human fungal pathogen Aspergillus fumigatus. PLoS Genetics 7: e1002374.

39. ChangYC, IngavaleSS, BienC, EspenshadeP, Kwon-ChungKJ (2009) Conservation of the sterol regulatory element-binding protein pathway and its pathobiological importance in Cryptococcus neoformans. Eukaryotic Cell 8: 1770–1779.

40. BarkerBM, KrollK, VodischM, MazurieA, KniemeyerO, et al. (2012) Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC genomics 13: 62.

41. ButlerG (2013) Hypoxia and gene expression in eukaryotic microbes. Annual Review of Microbiology 67: 291–312.

42. SailsberyJK, AtchleyWR, DeanRA (2012) Phylogenetic analysis and classification of the fungal bHLH domain. Molecular Biology and Evolution 29: 1301–1318.

43. DaviesBS, RineJ (2006) A role for sterol levels in oxygen sensing in Saccharomyces cerevisiae. Genetics 174: 191–201.

44. LosadaL, BarkerBM, PakalaS, JoardarV, ZafarN, et al. (2014) Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA. Mycopathologia [Epub ahead of print].

45. ZhangY, LiuT, MeyerCA, EeckhouteJ, JohnsonDS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137.

46. GrantCE, BaileyTL, NobleWS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017–1018.

47. LindeJ, HortschanskyP, FaziusE, BrakhageAA, GuthkeR, et al. (2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Systems Biology 6: 6.

48. YokoyamaC, WangX, BriggsMR, AdmonA, WuJ, et al. (1993) SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Cell 75: 187–197.

49. KimJB, SpottsGD, HalvorsenYD, ShihHM, EllenbergerT, et al. (1995) Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Molecular and Cellular Biology 15: 2582–2588.

50. PerezJC, KumamotoCA, JohnsonAD (2013) Candida albicans commensalism and pathogenicity are intertwined traits directed by a tightly knit transcriptional regulatory circuit. PLoS Biology 11: e1001510.

51. PriebeS, LindeJ, AlbrechtD, GuthkeR, BrakhageAA (2011) FungiFun: a web-based application for functional categorization of fungal genes and proteins. Fungal Genetics and Biology 48: 353–358.

52. GeissGK, BumgarnerRE, BirdittB, DahlT, DowidarN, et al. (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnology 26: 317–325.

53. MalkovVA, SerikawaKA, BalantacN, WattersJ, GeissG, et al. (2009) Multiplexed measurements of gene signatures in different analytes using the Nanostring nCounter Assay System. BMC Research Notes 2: 80.

54. SchrettlM, KimHS, EisendleM, KraglC, NiermanWC, et al. (2008) SreA-mediated iron regulation in Aspergillus fumigatus. Molecular Microbiology 70: 27–43.

55. ZnaidiS, NesseirA, ChauvelM, RossignolT, d'EnfertC (2013) A comprehensive functional portrait of two heat shock factor-type transcriptional regulators involved in Candida albicans morphogenesis and virulence. PLoS Pathogens 9: e1003519.

56. ZagorecM, BuhlerJM, TreichI, KengT, GuarenteL, et al. (1988) Isolation, sequence, and regulation by oxygen of the yeast HEM13 gene coding for coproporphyrinogen oxidase. The Journal of Biological Chemistry 263: 9718–9724.

57. KengT (1992) HAP1 and ROX1 form a regulatory pathway in the repression of HEM13 transcription in Saccharomyces cerevisiae. Molecular and Cellular Biology 12: 2616–2623.

58. SorianiFM, MalavaziI, FerreiraMED, SavoldiM, KressMRV, et al. (2008) Functional characterization of the Aspergillus fumigatus CRZ1 homologue, CrzA. Molecular Microbiology 67: 1274–1291.

59. BlosserSJ, MerrimanB, GrahlN, ChungD, CramerRA (2014) Two C4-sterol methyl oxidases (Erg25) catalyze ergosterol intermediate demethylation and impact environmental stress adaptation in Aspergillus fumigatus. Microbiology DOI: 10.1099/mic.0.080440-0

60. ZhouS, FushinobuS, KimSW, NakanishiY, MaruyamaJ, et al. (2011) Functional analysis and subcellular location of two flavohemoglobins from Aspergillus oryzae. Fungal Genetics and Biology 48: 200–207.

61. LiH, BarkerBM, GrahlN, PuttikamonkulS, BellJD, et al. (2011) The small GTPase RacA mediates intracellular reactive oxygen species production, polarized growth, and virulence in the human fungal pathogen Aspergillus fumigatus. Eukaryotic Cell 10: 174–186.

62. BornemanAR, GianoulisTA, ZhangZD, YuH, RozowskyJ, et al. (2007) Divergence of transcription factor binding sites across related yeast species. Science 317: 815–819.

63. OdomDT, DowellRD, JacobsenES, GordonW, DanfordTW, et al. (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nature Genetics 39: 730–732.

64. SchmidtD, WilsonMD, BallesterB, SchwaliePC, BrownGD, et al. (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036–1040.

65. TuchBB, GalgoczyDJ, HerndayAD, LiH, JohnsonAD (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biology 6: e38.

66. HughesTR, de BoerCG (2013) Mapping yeast transcriptional networks. Genetics 195: 9–36.

67. ZitomerRS, LowryCV (1992) Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiological Reviews 56: 1–11.

68. HonT, DoddA, DirmeierR, GormanN, SinclairPR, et al. (2003) A mechanism of oxygen sensing in yeast. Multiple oxygen-responsive steps in the heme biosynthetic pathway affect Hap1 activity. The Journal of Biological Chemistry 278: 50771–50780.

69. HickmanMJ, WinstonF (2007) Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor. Molecular and Cellular Biology 27: 7414–7424.

70. ThorsnessM, SchaferW, D'AriL, RineJ (1989) Positive and negative transcriptional control by heme of genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae. Molecular and Cellular Biology 9: 5702–5712.

71. JinFJ, TakahashiT, MatsushimaK, HaraS, ShinoharaY, et al. (2011) SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae. Eukaryotic cell 10: 945–955.

72. RosenbachA, DignardD, PierceJV, WhitewayM, KumamotoCA (2010) Adaptations of Candida albicans for growth in the mammalian intestinal tract. Eukaryotic Cell 9: 1075–1086.

73. NobileCJ, FoxEP, NettJE, SorrellsTR, MitrovichQM, et al. (2012) A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell 148: 126–138.

74. NettJE, LepakAJ, MarchilloK, AndesDR (2009) Time course global gene expression analysis of an in vivo Candida biofilm. The Journal of Infectious Diseases 200: 307–313.

75. LaneS, ZhouS, PanT, DaiQ, LiuH (2001) The basic helix-loop-helix transcription factor Cph2 regulates hyphal development in Candida albicans partly via TEC1. Molecular and Biology 21: 6418–6428.

76. SellamA, van het HoogM, TebbjiF, BeaurepaireC, WhitewayM, et al. (2014) Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans. Eukaryot Cell 13: 675–690.

77. DattaS, OsborneTF (2005) Activation domains from both monomers contribute to transcriptional stimulation by sterol regulatory element-binding protein dimers. The Journal of Biological Chemistry 280: 3338–3345.

78. ZoumiA, DattaS, LiawLH, WuCJ, ManthripragadaG, et al. (2005) Spatial distribution and function of sterol regulatory element-binding protein 1a and 2 homo- and heterodimers by in vivo two-photon imaging and spectroscopy fluorescence resonance energy transfer. Molecular and Cellular Biology 25: 2946–2956.

79. RobinsonKA, LopesJM (2000) SURVEY AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes. Nucleic Acids Research 28: 1499–1505.

80. ShaoW, EspenshadePJ (2012) Expanding roles for SREBP in metabolism. Cell Metabolism 16: 414–419.

81. ShimizuK, KellerNP (2001) Genetic involvement of a cAMP-dependent protein kinase in a g protein signaling pathway regulating morphological and chemical transitions in Aspergillus nidulans. Genetics 157: 591–600.

82. YuJH, HamariZ, HanKH, SeoJA, Reyes-DominguezY, et al. (2004) Double-joint PCR: a PCR-based molecular tool for gene manipulations in filamentous fungi. Fungal genetics and biology 41: 973–981.

83. QuailMA, KozarewaI, SmithF, ScallyA, StephensPJ, et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nature Methods 5: 1005–1010.

84. LohseM, BolgerAM, NagelA, FernieAR, LunnJE, et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research 40: W622–627.

85. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.

86. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings/International Conference on Intelligent Systems for Molecular Biology; ISMB International Conference on Intelligent Systems for Molecular Biology 2: 28–36.

87. CarlsonJM, ChakravartyA, DeZielCE, GrossRH (2007) SCOPE: a web server for practical de novo motif discovery. Nucleic Acids Research 35: W259–264.

88. PavesiG, MereghettiP, MauriG, PesoleG (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research 32: W199–203.

89. RobertsA, TrapnellC, DonagheyJ, RinnJL, PachterL (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology 12: R22.

90. KimD, PerteaG, TrapnellC, PimentelH, KelleyR, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14: R36.

91. RDevelopmentCoreTeam (2011) R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.

92. BonkovskyHL, WoodSG, HowellSK, SinclairPR, LincolnB, et al. (1986) High-performance liquid chromatographic separation and quantitation of tetrapyrroles from biological materials. Anal Biochem 155: 56–64.

Štítky
Hygiena a epidemiológia Infekčné lekárstvo Laboratórium

Článok vyšiel v časopise

PLOS Pathogens


2014 Číslo 11
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#