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Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth


Cellular processes in eukaryotes are brought about through the contributions of large gene sets, and a continuing obstacle in studying these processes lies in the identification of critical constituent genes. The yeast pseudohyphal growth transition is an important example of a complex cellular growth transition. During pseudohyphal growth, yeast cells form connected chains or filaments, constituting a means of foraging for nutrients under conditions of nitrogen and/or glucose limitation. Yeast pseudohyphal growth has been studied for over two decades as a model of signaling systems controlling stress responses, cell shape, and fungal virulence. Hundreds of genes are required for pseudohyphal growth, however, and the critical genes that determine the filamentous phenotype have not been elucidated. Towards this goal, we implemented a genetic approach to identify alleles linked with the pseudohyphal growth phenotype. These studies identified previously unstudied variation in proteins functioning in a complex that controls cell polarity and in a protein of the mitochondrial inner membrane. This work indicates that proteins in complexes and organelles have coevolved within a given genome to yield distinct outputs and phenotype, while highlighting the application of an approach that is useful for the analysis of complex phenotypes in many eukaryotes.


Vyšlo v časopise: Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth. PLoS Genet 10(8): e32767. doi:10.1371/journal.pgen.1004570
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004570

Souhrn

Cellular processes in eukaryotes are brought about through the contributions of large gene sets, and a continuing obstacle in studying these processes lies in the identification of critical constituent genes. The yeast pseudohyphal growth transition is an important example of a complex cellular growth transition. During pseudohyphal growth, yeast cells form connected chains or filaments, constituting a means of foraging for nutrients under conditions of nitrogen and/or glucose limitation. Yeast pseudohyphal growth has been studied for over two decades as a model of signaling systems controlling stress responses, cell shape, and fungal virulence. Hundreds of genes are required for pseudohyphal growth, however, and the critical genes that determine the filamentous phenotype have not been elucidated. Towards this goal, we implemented a genetic approach to identify alleles linked with the pseudohyphal growth phenotype. These studies identified previously unstudied variation in proteins functioning in a complex that controls cell polarity and in a protein of the mitochondrial inner membrane. This work indicates that proteins in complexes and organelles have coevolved within a given genome to yield distinct outputs and phenotype, while highlighting the application of an approach that is useful for the analysis of complex phenotypes in many eukaryotes.


Zdroje

1. GimenoCJ, LjungdahlPO, StylesCA, FinkGR (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68: 1077–1090.

2. CullenPJ, SpragueGF (2000) Glucose depletion causes haploid invasive growth in yeast. Proc Natl Acad Sci U S A 97: 13461–13463.

3. KronSJ, StylesCA, FinkGR (1994) Symmetric cell division in pseudohyphae of the yeast Saccharomyces cerevisiae. Mol Biol Cell 5: 1003–1022.

4. GuoB, StylesCA, FengQ, FinkG (2000) A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating. Proc Natl Acad Sci U S A 97: 12158–12163.

5. LoWS, DranginisAM (1998) The cell surface flocculin Flo11 is required for pseudohyphae formation and invasion by Saccharomyces cerevisiae. Mol Biol Cell 9: 161–171.

6. RuppS, SummersE, LoHJ, MadhaniH, FinkG (1999) MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. Embo J 18: 1257–1269.

7. KarunanithiS, VadaieN, ChavelCA, BirkayaB, JoshiJ, et al. (2010) Shedding of the mucin-like flocculin Flo11p reveals a new aspect of fungal adhesion regulation. Curr Biol 20: 1389–1395.

8. AhnSH, AcurioA, KronSJ (1999) Regulation of G2/M progression by the STE mitogen-activated protein kinase pathway in budding yeast filamentous growth. Mol Biol Cell 10: 3301–3316.

9. MiledC, MannC, FayeG (2001) Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth. Mol Cell Biol 21: 3714–3724.

10. RobertsRL, FinkGR (1994) Elements of a single MAP kinase cascade in Saccharomyces cerevisiae mediate two developmental programs in the same cell type: mating and invasive growth. Genes Dev 8: 2974–2985.

11. TaheriN, KohlerT, BrausGH, MoschHU (2000) Asymmetrically localized Bud8p and Bud9p proteins control yeast cell polarity and development. EMBO J 19: 6686–6696.

12. CullenPJ, SpragueGFJr (2002) The roles of bud-site-selection proteins during haploid invasive growth in yeast. Mol Biol Cell 13: 2990–3004.

13. LoHJ, KohlerJ, DiDomenicoB, LoebenbergD, CacciapuotiA, et al. (1997) Nonfilamentous C. albicans mutants are avirulent. Cell 90: 939–949.

14. LiuH, StylesCA, FinkGR (1993) Elements of the yeast pheromone response pathway required for filamentous growth of diploids. Science 262: 1741–1744.

15. BuehrerBM, ErredeB (1997) Coordination of the mating and cell integrity mitogen-activated protein kinase pathways in Saccharomyces cerevisiae. Mol Cell Biol 17: 6517–6525.

16. MadhaniHD, FinkGR (1997) Combinatorial control required for the specificity of yeast MAPK signaling. Science 275: 1314–1317.

17. PanX, HeitmanJ (1999) Cyclic AMP-dependent protein kinase regulates pseudohyphal differentiation in Saccharomyces cerevisiae. Mol Cell Biol 19: 4874–4887.

18. ErdmanS, SnyderM (2001) A filamentous growth response mediated by the yeast mating pathway. Genetics 159: 919–928.

19. KuchinS, VyasVK, CarlsonM (2002) Snf1 protein kinase and the repressors Nrg1 and Nrg2 regulate FLO11, haploid invasive growth, and diploid pseudohyphal differentiation. Mol Cell Biol 22: 3994–4000.

20. ChavelCA, DionneHM, BirkayaB, JoshiJ, CullenPJ (2010) Multiple signals converge on a differentiation MAPK pathway. PLoS Genet 6: e1000883.

21. MoschHU, RobertsRL, FinkGR (1996) Ras2 signals via the Cdc42/Ste20/mitogen-activated protein kinase module to induce filamentous growth in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 93: 5352–5356.

22. CookJG, BardwellL, KronSJ, ThornerJ (1996) Two novel targets of the MAP kinase Kss1 are negative regulators of invasive growth in the yeast Saccharomyces cerevisiae. Genes Dev 10: 2831–2848.

23. CookJG, BardwellL, ThornerJ (1997) Inhibitory and activating functions forMAPK Kss1 in the S. cerevisiae filamentous growth signalling pathway. Nature 390: 85–88.

24. RobertsonLS, FinkGR (1998) The three yeast A kinases have specific signaling functions in pseudohyphal growth. Proc Natl Acad Sci U S A 95: 13783–13787.

25. PanX, HeitmanJ (2002) Protein kinase A operates a molecular switch that governs yeast pseudohyphal differentiation. Mol Cell Biol 22: 3981–3993.

26. BornemanAR, Leigh-BellJA, YuH, BertoneP, GersteinM, et al. (2006) Target hub proteins serve as master regulators of development in yeast. Genes Dev 20: 435–448.

27. VyasVK, KuchinS, BerkeyCD, CarlsonM (2003) Snf1 kinases with different beta-subunit isoforms play distinct roles in regulating haploid invasive growth. Mol Cell Biol 23: 1341–1348.

28. JinR, DobryCJ, McCownPJ, KumarA (2008) Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression. Mol Biol Cell 19: 284–296.

29. BharuchaN, MaJ, DobryCJ, LawsonSK, YangZ, et al. (2008) Analysis of the Yeast Kinome Reveals a Network of Regulated Protein Localization During Filamentous Growth. Mol Biol Cell 19: 2708–2717.

30. XuT, ShivelyCA, JinR, EckwahlMJ, DobryCJ, et al. (2010) A profile of differentially abundant proteins at the yeast cell periphery during pseudohyphal growth. J Biol Chem 285: 15476–15488.

31. ShivelyCA, EckwahlMJ, DobryCJ, MellacheruvuD, NesvizhskiiA, et al. (2013) Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression. Genetics 193: 1297–1310.

32. RyanO, ShapiroRS, KuratCF, MayhewD, BaryshnikovaA, et al. (2012) Global gene deletion analysis exploring yeast filamentous growth. Science 337: 1353–1356.

33. LiW, MitchellAP (1997) Proteolytic activation of Rim1p, a positive regulator of yeast sporulation and invasive growth. Genetics 145: 63–73.

34. GrensonM (1966) Multiplicity of the amino acid permeases in Saccharomyces cerevisiae. II. Evidence for a specific lysine-transporting system. Biochim Biophys Acta 127: 339–346.

35. MortimerRK, JohnstonJR (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics 113: 35–43.

36. LiuH, StylesCA, FinkG (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144: 967–978.

37. FidalgoM, BarralesRR, IbeasJI, JimenezJ (2006) Adaptive evolution by mutations in the FLO11 gene. Proc of the Nat Acad of Sci USA 103: 11228–11233.

38. VerstrepenKJ, JansenA, LewitterF, FinkGR (2005) Intragenic tandem repeats generate functional variability. Nat Genet 37: 986–990.

39. VerstrepenKJ, FinkGR (2009) Genetic and epigenetic mechanisms underlying cell-surface variability in protozoa and fungi. Annu Rev Genet 43: 1–24.

40. ValtzN, HerskowitzI (1996) Pea2 protein of yeast is localized to sites of polarized growth and is required for efficient mating and bipolar budding. J Cell Biol 135: 725–739.

41. SheuYJ, SantosB, FortinN, CostiganC, SnyderM (1998) Spa2p interacts with cell polarity proteins and signaling components involved in yeast cell morphogenesis. Mol Cell Biol 18: 4053–4069.

42. ChenevertJ, ValtzN, HerskowitzI (1994) Identification of genes required for normal pheromone-induced cell polarization in Saccharomyces cerevisiae. Genetics 136: 1287–1296.

43. FujiwaraT, TanakaK, MinoA, KikyoM, TakahashiK, et al. (1998) Rho1p-Bni1p-Spa2p interactions: implication in localization of Bni1p at the bud site and regulation of the actin cytoskeleton in Saccharomyces cerevisiae. Mol Biol Cell 9: 1221–1233.

44. ChantJ, PringleJR (1995) Patterns of bud-site selection in the yeast Saccharomyces cerevisiae. J Cell Biol 129: 751–765.

45. NiL, SnyderM (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12: 2147–2170.

46. SnyderM (1989) The SPA2 protein of yeast localizes to sites of cell growth. J Cell Biol 108: 1419–1429.

47. SchachererJ, RuderferDM, GreshamD, DolinskiK, BotsteinD, et al. (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PloS One 2: e322.

48. FujitaA, KikuchiY, KuharaS, MisumiY, MatsumotoS, et al. (1989) Domains of the SFL1 protein of yeasts are homologous to Myc oncoproteins or yeast heat-shock transcription factor. Gene 85: 321–328.

49. SongW, CarlsonM (1998) Srb/mediator proteins interact functionally and physically with transcriptional repressor Sfl1. EMBO J 17: 5757–5765.

50. ConlanRS, TzamariasD (2001) Sfl1 functions via the co-repressor Ssn6-Tup1 and the cAMP-dependent protein kinase Tpk2. J Mol Biol 309: 1007–1015.

51. TorbensenR, MollerHD, GreshamD, AlizadehS, OchmannD, et al. (2012) Amino acid transporter genes are essential for FLO11-dependent and FLO11-independent biofilm formation and invasive growth in Saccharomyces cerevisiae. PloS one 7: e41272.

52. DimmerKS, JakobsS, VogelF, AltmannK, WestermannB (2005) Mdm31 and Mdm32 are inner membrane proteins required for maintenance of mitochondrial shape and stability of mitochondrial DNA nucleoids in yeast. J Cell Biol 168: 103–115.

53. KangCM, JiangYW (2005) Genome-wide survey of non-essential genes required for slowed DNA synthesis-induced filamentous growth in yeast. Yeast 22: 79–90.

54. AunA, TammT, SedmanJ (2013) Dysfunctional mitochondria modulate cAMP-PKA signaling and filamentous and invasive growth of Saccharomyces cerevisiae. Genetics 193: 467–481.

55. RuderferDM, PrattSC, SeidelHS, KruglyakL (2006) Population genomic analysis of outcrossing and recombination in yeast. Nat Genet 38: 1077–1081.

56. BremRB, YvertG, ClintonR, KruglyakL (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755.

57. FossEJ, RadulovicD, ShafferSA, RuderferDM, BedalovA, et al. (2007) Genetic basis of proteome variation in yeast. Nat Genet 39: 1369–1375.

58. PerlsteinEO, RuderferDM, RobertsDC, SchreiberSL, KruglyakL (2007) Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat Genet 39: 496–502.

59. RonaldJ, AkeyJM (2007) The evolution of gene expression QTL in Saccharomyces cerevisiae. PLoS One 2: e678.

60. ClarkNL, AlaniE, AquadroCF (2012) Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res 22: 714–720.

61. ClarkNL, AlaniE, AquadroCF (2013) Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals. Genetics 193: 529–538.

62. LongtineMS, McKenzieAIII, DemariniDJ, ShahNG, WachA, et al. (1998) Additional Modules for Versatile and Economical PCR-based Gene Deletion and Modification in Saccharomyces cerevisiae. Yeast 14: 953–961.

63. GueldenerU, HeinischJ, KoehlerGJ, VossD, HegemannJH (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Research 30: e23.

64. Guthrie C, Fink G (1991) Guide to Yeast Genetics and Molecular Biology. San Diego, CA: Academic Press.

65. BirkelandSR, JinN, OzdemirAC, LyonsRHJr, WeismanLS, et al. (2010) Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing. Genetics 186: 1127–1137.

66. MaJ, JinR, DobryCJ, LawsonSK, KumarA (2007) Overexpression of autophagy-related genes inhibits yeast filamentous growth. Autophagy 3: 604–609.

67. MaJ, JinR, JiaX, DobryCJ, WangL, et al. (2007) An interrelationship between autophagy and filamentous growth in budding yeast. Genetics 177: 205–214.

68. AlbertiS, GitlerAD, LindquistS (2007) A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24: 913–919.

69. MaJ, DobryCJ, KrysanDJ, KumarA (2008) Unconventional genomic architecture in the budding yeast saccharomyces cerevisiae masks the nested antisense gene NAG1. Eukaryot Cell 7: 1289–1298.

70. KumarA, VidanS, SnyderM (2002) Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast. Methods Enzymol 350: 219–229.

71. JohnsonC, KweonHK, SheidyD, ShivelyCA, MellacheruvuD, et al. (2014) The yeast sks1p kinase signaling network regulates pseudohyphal growth and glucose response. PLoS Genet 10: e1004183.

72. ShibataT, TakahashiT, YamadaE, KimuraA, NishikawaH, et al. (2012) T-2307 causes collapse of mitochondrial membrane potential in yeast. Antimicrob Agents Chemo 56: 5892–5897.

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