Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans

English version

Autoři: Diana K. Summers ^aff001; Daniela S. Perry ^aff001; Beiduo Rao ^aff001; Hiten D. Madhani ^aff001
Působiště autorů: Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America ^aff001; Chan-Zuckerberg Biohub, San Francisco, CA, United States of America ^aff002
Vyšlo v časopise: Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans. PLoS Genet 16(9): e32767. doi:10.1371/journal.pgen.1008744
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008744

Souhrn

Qsp1 is a secreted quorum sensing peptide required for virulence of the fungal meningitis pathogen Cryptococcus neoformans. Qsp1 functions to control cell wall integrity in vegetatively growing cells and also functions in mating. Rather than acting on a cell surface receptor, Qsp1 is imported to act intracellularly via the predicted oligopeptide transporter Opt1. Here, we identify a transcription factor network as a target of Qsp1. Using whole-genome chromatin immunoprecipitation, we find Qsp1 controls the genomic associations of three transcription factors to genes whose outputs are regulated by Qsp1. One of these transcription factors, Cqs2, is also required for the action of Qsp1 during mating, indicating that it might be a shared proximal target of Qsp1. Consistent with this hypothesis, deletion of CQS2 impacts the binding of other network transcription factors specifically to Qsp1-regulated genes. These genetic and genomic studies illuminate mechanisms by which an imported peptide acts to modulate eukaryotic gene expression.

Klíčová slova:

Cell walls – Cryptococcus neoformans – DNA transcription – Gene expression – Quorum sensing – Transcription factors – Transcriptional control – Virulence factors

Zdroje

1. Armstrong-James D, Meintjes G, Brown GD. A neglected epidemic: fungal infections in HIV/AIDS. Trends Microbiol. 2014 Mar 1;22(3):120–7. doi: 10.1016/j.tim.2014.01.001 24530175

2. Bassler BL, Miller MB. Quorum Sensing. In: Rosenberg E, DeLong EF, S Lory, E Stackebrandt, Thompson F, editors. The Prokaryotes: Prokaryotic Communities and Ecophysiology [Internet]. Berlin, Heidelberg: Springer; 2013 [cited 2020 Feb 29]. p. 495–509. Available from: https://doi.org/10.1007/978-3-642-30123-0_60

3. de Kievit TR, Iglewski BH. Bacterial Quorum Sensing in Pathogenic Relationships. Infect Immun. 2000 Sep;68(9):4839–49. doi: 10.1128/iai.68.9.4839-4849.2000 10948095

4. Homer CM, Summers DK, Goranov AI, Clarke SC, Wiesner D, Diedrich JK, et al. Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe. 2016 Jun 8;19(6):849–64. doi: 10.1016/j.chom.2016.05.001 27212659

5. Lee H, Chang YC, Nardone G, Kwon-Chung KJ. TUP1 disruption in Cryptococcus neoformans uncovers a peptide-mediated density-dependent growth phenomenon that mimics quorum sensing. Mol Microbiol. 2007 May 1;64(3):591–601. doi: 10.1111/j.1365-2958.2007.05666.x 17462010

6. Srikantha T, Borneman AR, Daniels KJ, Pujol C, Wu W, Seringhaus MR, et al. TOS9 Regulates White-Opaque Switching in Candida albicans. Eukaryot Cell. 2006 Oct;5(10):1674–87. doi: 10.1128/EC.00252-06 16950924

7. Alkafeef SS, Yu C, Huang L, Liu H. Wor1 establishes opaque cell fate through inhibition of the general co-repressor Tup1 in Candida albicans. PLOS Genet. 2018 Jan 16;14(1):e1007176. doi: 10.1371/journal.pgen.1007176 29337983

8. Huang G, Wang H, Chou S, Nie X, Chen J, Liu H. Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12813–8. doi: 10.1073/pnas.0605270103 16905649

9. Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD. A Conserved Transcriptional Regulator Governs Fungal Morphology in Widely Diverged Species. Genetics. 2012 Feb;190(2):511–21. doi: 10.1534/genetics.111.134080 22095082

10. Nguyen VQ, Sil A. Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4880–5. doi: 10.1073/pnas.0710448105 18339808

11. Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM. Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell. 2008 Oct 3;135(1):174–88. doi: 10.1016/j.cell.2008.07.046 18854164

12. Tian X, He G-J, Hu P, Chen L, Tao C, Cui Y-L, et al. Cryptococcus neoformans sexual reproduction is controlled by a quorum sensing peptide. Nat Microbiol. 2018 Jun;3(6):698. doi: 10.1038/s41564-018-0160-4 29784977

13. Jung K-W, Yang D-H, Maeng S, Lee K-T, So Y-S, Hong J, et al. Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. Nat Commun [Internet]. 2015 Apr 7 [cited 2019 Mar 6];6. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391232/

14. Cramer KL, Gerrald QD, Nichols CB, Price MS, Alspaugh JA. Transcription Factor Nrg1 Mediates Capsule Formation, Stress Response, and Pathogenesis in Cryptococcus neoformans. Eukaryot Cell. 2006 Jul;5(7):1147–56. doi: 10.1128/EC.00145-06 16835458

15. Wyrick JJ, Young RA. Deciphering gene expression regulatory networks. Curr Opin Genet Dev. 2002 Apr 1;12(2):130–6. doi: 10.1016/s0959-437x(02)00277-0 11893484

16. Fukui Y, Miyake S, Satoh M, Yamamoto M. Characterization of the Schizosaccharomyces pombe ral2 gene implicated in activation of the ras1 gene product. Mol Cell Biol. 1989 Dec;9(12):5617–22. doi: 10.1128/mcb.9.12.5617 2586528

17. Imai Y, Miyake S, Hughes DA, Yamamoto M. Identification of a GTPase-activating protein homolog in Schizosaccharomyces pombe. Mol Cell Biol. 1991 Jun;11(6):3088–94. doi: 10.1128/mcb.11.6.3088 2038319

18. Dekker N, Speijer D, Grün CH, van den Berg M, de Haan A, Hochstenbach F. Role of the α-Glucanase Agn1p in Fission-Yeast Cell Separation. Mol Biol Cell. 2004 Aug;15(8):3903–14. doi: 10.1091/mbc.e04-04-0319 15194814

19. Zhang H-B, Wang L-H, Zhang L-H. Genetic control of quorum-sensing signal turnover in Agrobacterium tumefaciens. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4638–43. doi: 10.1073/pnas.022056699 11930013

20. Chatterjee A, Cook LCC, Shu C-C, Chen Y, Manias DA, Ramkrishna D, et al. Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer. Proc Natl Acad Sci. 2013 Apr 23;110(17):7086–90. doi: 10.1073/pnas.1212256110 23569272

21. Schneider KB, Palmer TM, Grossman AD. Characterization of comQ and comX, Two Genes Required for Production of ComX Pheromone in Bacillus subtilis. J Bacteriol. 2002 Jan;184(2):410–9. doi: 10.1128/jb.184.2.410-419.2002 11751817

22. Comella N, Grossman AD. Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis. Mol Microbiol. 2005;57(4):1159–74. doi: 10.1111/j.1365-2958.2005.04749.x 16091051

23. Hogan DA. Talking to Themselves: Autoregulation and Quorum Sensing in Fungi. Eukaryot Cell. 2006 Apr;5(4):613–9. doi: 10.1128/EC.5.4.613-619.2006 16607008

24. Honigberg SM, Purnapatre K. Signal pathway integration in the switch from the mitotic cell cycle to meiosis in yeast. J Cell Sci. 2003 Jun 1;116(11):2137–47.

25. Grossman AD, Losick R. Extracellular control of spore formation in Bacillus subtilis. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4369–73. doi: 10.1073/pnas.85.12.4369 3132711

26. Pottathil M, Lazazzera BA. The extracellular Phr peptide-Rap phosphatase signaling circuit of Bacillus subtilis. Front Biosci J Virtual Libr. 2003 Jan 1;8:d32–45.

27. Perego M. Forty Years in the Making: Understanding the Molecular Mechanism of Peptide Regulation in Bacterial Development. PLoS Biol [Internet]. 2013 Mar 19 [cited 2020 Feb 29];11(3). Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601992/

28. Slamti L, Lereclus D. A cell–cell signaling peptide activates the PlcR virulence regulon in bacteria of the Bacillus cereus group. EMBO J. 2002 Sep 2;21(17):4550–9. doi: 10.1093/emboj/cdf450 12198157

29. Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D, Nessler S. Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR. Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1047–52. doi: 10.1073/pnas.1213770110 23277548

30. Kozlowicz BK, Shi K, Gu Z-Y, Ohlendorf DH, Earhart CA, Dunny GM. Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Mol Microbiol. 2006 Nov;62(4):958–69. doi: 10.1111/j.1365-2958.2006.05434.x 17038121

31. Murad AMA, Leng P, Straffon M, Wishart J, Macaskill S, MacCallum D, et al. NRG1 represses yeast–hypha morphogenesis and hypha-specific gene expression in Candida albicans. EMBO J. 2001 Sep 3;20(17):4742–52. doi: 10.1093/emboj/20.17.4742 11532938

32. Lu Y, Su C, Unoje O, Liu H. Quorum sensing controls hyphal initiation in Candida albicans through Ubr1-mediated protein degradation. Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1975–80. doi: 10.1073/pnas.1318690111 24449897

33. Gómez-Gil E, Franco A, Madrid M, Vázquez-Marín B, Gacto M, Fernández-Breis J, et al. Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus. PLoS Genet [Internet]. 2019 May 31 [cited 2020 Jan 3];15(5). Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561576/

34. Berkey CD, Vyas VK, Carlson M. Nrg1 and Nrg2 Transcriptional Repressors Are Differently Regulated in Response to Carbon Source. Eukaryot Cell. 2004 Apr;3(2):311–7. doi: 10.1128/ec.3.2.311-317.2004 15075261

35. Kim TS, Lee SB, Kang HS. Glucose Repression of STA1 Expression Is Mediated by the Nrg1 and Sfl1 Repressors and the Srb8-11 Complex. Mol Cell Biol. 2004 Sep;24(17):7695–706. doi: 10.1128/MCB.24.17.7695-7706.2004 15314176

36. Lee SB, Kang HS, Kim T. Nrg1 functions as a global transcriptional repressor of glucose-repressed genes through its direct binding to the specific promoter regions. Biochem Biophys Res Commun. 2013 Oct 4;439(4):501–5. doi: 10.1016/j.bbrc.2013.09.015 24025681

37. Kinnaer C, Dudin O, Martin SG. Yeast-to-hypha transition of Schizosaccharomyces japonicus in response to environmental stimuli. Mol Biol Cell. 2019 01;30(8):975–91. doi: 10.1091/mbc.E18-12-0774 30726171

38. Lazazzera BA. Quorum sensing and starvation: signals for entry into stationary phase. Curr Opin Microbiol. 2000 Apr 1;3(2):177–82. doi: 10.1016/s1369-5274(00)00072-2 10744996

39. Chen H, Fink GR. Feedback control of morphogenesis in fungi by aromatic alcohols. Genes Dev. 2006 May 1;20(9):1150–61. doi: 10.1101/gad.1411806 16618799

40. Herman PK. Stationary phase in yeast. Curr Opin Microbiol. 2002 Dec 1;5(6):602–7. doi: 10.1016/s1369-5274(02)00377-6 12457705

41. Chun CD, Madhani HD. Ctr2 Links Copper Homeostasis to Polysaccharide Capsule Formation and Phagocytosis Inhibition in the Human Fungal Pathogen Cryptococcus neoformans. PLoS ONE. 2010 Sep 2;5(9):e12503.

42. Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, et al. Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense. Cell. 2013 Feb 28;152(5):957–68. doi: 10.1016/j.cell.2013.01.046 23415457

43. Burke JE, Longhurst AD, Natarajan P, Rao B, Liu J, Sales-Lee J, et al. A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans. G3 GenesGenomesGenetics. 2019 May 15;9(7):2235–44.

44. Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012 Dec 28;3 : 9. doi: 10.1186/1758-907X-3-9 23273270

45. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan;29(1):15–21. doi: 10.1093/bioinformatics/bts635 23104886

46. Aligning Short Sequencing Reads with Bowtie—Langmead—2010—Current Protocols in Bioinformatics—Wiley Online Library [Internet]. [cited 2020 Feb 23]. Available from: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi1107s32

47. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943

48. Quinlan AR. BEDTools: the Swiss-army tool for genome feature analysis. Curr Protoc Bioinforma Ed Board Andreas Baxevanis Al. 2014 Sep 8;47 : 11.12.1–11.12.34.

49. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841–2. doi: 10.1093/bioinformatics/btq033 20110278

50. Garcia-Santamarina S, Festa RA, Smith AD, Yu C-H, Probst C, Ding C, et al. Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans. Mol Microbiol. 2018 Jun;108(5):473–94. doi: 10.1111/mmi.13960 29608794

Článek Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock

Článek PIG-1 MELK-dependent phosphorylation of nonmuscle myosin II promotes apoptosis through CES-1 Snail partitioning

Článek Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity

Článek A mega-analysis of expression quantitative trait loci in retinal tissue

Článek Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome

Článek Trichoderma reesei XYR1 activates cellulase gene expression via interaction with the Mediator subunit TrGAL11 to recruit RNA polymerase II

Článek The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

Článek A Novel Recessive Mutation in SPEG Causes Early Onset Dilated Cardiomyopathy

Článek Excess crossovers impede faithful meiotic chromosome segregation in C. elegans

Článek Male-biased aganglionic megacolon in the TashT mouse model of Hirschsprung disease involves upregulation of p53 protein activity and Ddx3y gene expression

Článek Candidate variants in TUB are associated with familial tremor

Článek Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts