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Causal Variation in Yeast Sporulation Tends to Reside in a Pathway Bottleneck
Distinguishing the small number of genetic variants that impact phenotypes from the huge number of innocuous variants within an individual's genome is a difficult problem. Several hypotheses concerning the location of causal variants have been put forward based on the fact that genes are often organized into signaling cascades where the activation of a gene at the top of a pathway in turn activates large numbers of downstream genes. One hypothesis states that causal variations are more likely to reside in the genes at the top of these pathways because their effects are amplified by the signaling cascade. Here we provide support for this hypothesis by showing that causal genetic variants in yeast sporulation cluster around a gene at the top of the sporulation signaling cascade. Our result suggests a way to focus the search for causal genetic variants, including those that cause disease, on a smaller number of genes that are more likely to harbor important variations.
Vyšlo v časopise: Causal Variation in Yeast Sporulation Tends to Reside in a Pathway Bottleneck. PLoS Genet 10(9): e32767. doi:10.1371/journal.pgen.1004634
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004634Souhrn
Distinguishing the small number of genetic variants that impact phenotypes from the huge number of innocuous variants within an individual's genome is a difficult problem. Several hypotheses concerning the location of causal variants have been put forward based on the fact that genes are often organized into signaling cascades where the activation of a gene at the top of a pathway in turn activates large numbers of downstream genes. One hypothesis states that causal variations are more likely to reside in the genes at the top of these pathways because their effects are amplified by the signaling cascade. Here we provide support for this hypothesis by showing that causal genetic variants in yeast sporulation cluster around a gene at the top of the sporulation signaling cascade. Our result suggests a way to focus the search for causal genetic variants, including those that cause disease, on a smaller number of genes that are more likely to harbor important variations.
Zdroje
1. CarrollSB (2005) Evolution at two levels: on genes and form. PLoS Biol 3: e245 doi:10.1371/journal.pbio.0030245
2. HoekstraHE, CoyneJA (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61 : 995–1016 doi:10.1111/j.1558-5646.2007.00105.x
3. SternDL, OrgogozoV (2008) The loci of evolution: how predictable is genetic evolution? Evolution 62 : 2155–2177 doi:10.1111/j.1558-5646.2008.00450.x
4. SternDL, OrgogozoV (2009) Is genetic evolution predictable? Science 323 : 746–751 doi:10.1126/science.1158997
5. GompelN, Prud'hommeB (2009) The causes of repeated genetic evolution. Dev Biol 332 : 36–47 doi:10.1016/j.ydbio.2009.04.040
6. ConteGL, ArnegardME, PeichelCL, SchluterD (2012) The probability of genetic parallelism and convergence in natural populations. Proc Biol Sci 279 : 5039–5047 doi:10.1098/rspb.2012.2146
7. MartinA, OrgogozoV (2013) The Loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution 67 : 1235–1250 doi:10.1111/evo.12081
8. DavidsonEH, RastJP, OliveriP, RansickA, CalestaniC, et al. (2002) A genomic regulatory network for development. Science 295 : 1669–1678 doi:10.1126/science.1069883
9. MarcelliniS, SimpsonP (2006) Two or four bristles: functional evolution of an enhancer of scute in Drosophilidae. PLoS Biol 4: e386 doi:10.1371/journal.pbio.0040386
10. Chanut-DelalandeH, FerrerP, PayreF, PlazaS (2012) Effectors of tridimensional cell morphogenesis and their evolution. Semin Cell Dev Biol 23 : 341–349 doi:10.1016/j.semcdb.2012.03.002
11. YuH, KimPM, SprecherE, TrifonovV, GersteinM (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3: e59 doi:10.1371/journal.pcbi.0030059
12. HahnMW, KernAD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22 : 803–806 doi:10.1093/molbev/msi072
13. KoppA (2009) Metamodels and phylogenetic replication: a systematic approach to the evolution of developmental pathways. Evolution 63 : 2771–2789 doi:10.1111/j.1558-5646.2009.00761.x
14. MitchellAP (1994) Control of meiotic gene expression in Saccharomyces cerevisiae. Microbiol Rev 58 : 56–70.
15. NeimanAM (2011) Sporulation in the budding yeast Saccharomyces cerevisiae. Genetics 189 : 737–765 doi:10.1534/genetics.111.127126
16. EnyenihiAH, SaundersWS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163 : 47–54.
17. HonigbergSM, PurnapatreK (2003) Signal pathway integration in the switch from the mitotic cell cycle to meiosis in yeast. J Cell Sci 116 : 2137–2147 doi:10.1242/jcs.00460
18. PiccirilloS, WhiteMG, MurphyJC, LawDJ, HonigbergSM (2010) The Rim101p/PacC pathway and alkaline pH regulate pattern formation in yeast colonies. Genetics 184 : 707–716 doi:10.1534/genetics.109.113480
19. JambhekarA, AmonA (2008) Control of meiosis by respiration. Curr Biol 18 : 969–975 doi:10.1016/j.cub.2008.05.047
20. ColominaN, GaríE, GallegoC, HerreroE, AldeaM (1999) G1 cyclins block the Ime1 pathway to make mitosis and meiosis incompatible in budding yeast. EMBO J 18 : 320–329 doi:10.1093/emboj/18.2.320
21. ChuS, DeRisiJ, EisenM, MulhollandJ, BotsteinD, et al. (1998) The transcriptional program of sporulation in budding yeast. Science 282 : 699–705 doi:10.1126/science.282.5389.699
22. GerkeJ, LorenzK, CohenB (2009) Genetic interactions between transcription factors cause natural variation in yeast. Science 323 : 498–501 doi:10.1126/science.1166426
23. DeutschbauerAM, DavisRW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37 : 1333–1340 doi:10.1038/ng1674
24. Ben-AriG, ZenvirthD, ShermanA, DavidL, KlutsteinM, et al. (2006) Four linked genes participate in controlling sporulation efficiency in budding yeast. PLoS Genet 2: e195 doi:10.1371/journal.pgen.0020195
25. BaruffiniE, LodiT, DallabonaC, FouryF (2007) A single nucleotide polymorphism in the DNA polymerase gamma gene of Saccharomyces cerevisiae laboratory strains is responsible for increased mitochondrial DNA mutability. Genetics 177 : 1227–1231 doi:10.1534/genetics.107.079293
26. GaisneM, BécamAM, VerdièreJ, HerbertCJ (1999) A “natural” mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet 36 : 195–200.
27. LiuH, StylesCA, FinkGR (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144 : 967–978.
28. DemoginesA, SmithE, KruglyakL, AlaniE (2008) Identification and dissection of a complex DNA repair sensitivity phenotype in Baker's yeast. PLoS Genet 4: e1000123 doi:10.1371/journal.pgen.1000123
29. SteinmetzLM, SinhaH, RichardsDR, SpiegelmanJI, OefnerPJ, et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416 : 326–330 doi:10.1038/416326a
30. GerkeJP, ChenCTL, CohenBA (2006) Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics 174 : 985–997 doi:10.1534/genetics.106.058453
31. FayJC, BenavidesJA (2005) Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae. PLoS Genet 1 : 1–6 doi:10.1371/journal.pgen.0010005
32. LitiG, CarterDM, MosesAM, WarringerJ, PartsL, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458 : 337–341 doi:10.1038/nature07743
33. LorenzK, CohenBA (2012) Small - and large-effect quantitative trait locus interactions underlie variation in yeast sporulation efficiency. Genetics 192 : 1123–1132 doi:10.1534/genetics.112.143107
34. Marchler-BauerA, BryantSH (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32: W327–31 doi:10.1093/nar/gkh454
35. VidanS, MitchellAP (1997) Stimulation of yeast meiotic gene expression by the glucose-repressible protein kinase Rim15p. Mol Cell Biol 17 : 2688–2697.
36. PnueliL, EdryI, CohenM, KassirY (2004) Glucose and nitrogen regulate the switch from histone deacetylation to acetylation for expression of early meiosis-specific genes in budding yeast. Mol Cell Biol 24 : 5197–5208 doi:10.1128/MCB.24.12.5197-5208.2004
37. CherryJM, HongEL, AmundsenC, BalakrishnanR, BinkleyG, et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700–5 doi:10.1093/nar/gkr1029
38. HoltLJ, HuttiJE, CantleyLC, MorganDO (2007) Evolution of Ime2 phosphorylation sites on Cdk1 substrates provides a mechanism to limit the effects of the phosphatase Cdc14 in meiosis. Mol Cell 25 : 689–702 doi:10.1016/j.molcel.2007.02.012
39. TevzadzeGG, PierceJV, EspositoRE (2007) Genetic evidence for a SPO1-dependent signaling pathway controlling meiotic progression in yeast. Genetics 175 : 1213–1227 doi:10.1534/genetics.106.069252
40. PiekarskaI, RytkaJ, RempolaB (2010) Regulation of sporulation in the yeast Saccharomyces cerevisiae. Acta Biochim Pol 57 : 241–250.
41. SmithHE, MitchellAP (1989) A transcriptional cascade governs entry into meiosis in Saccharomyces cerevisiae. Mol Cell Biol 9 : 2142–2152 doi:10.1128/MCB.9.5.2142.Updated
42. SuSS, MitchellAP (1993) Molecular characterization of the yeast meiotic regulatory gene RIM1. Nucleic Acids Res 21 : 3789–3797.
43. LambTM, MitchellAP (2003) The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol 23 : 677–686 doi:10.1128/MCB.23.2.677
44. LiW, MitchellAP (1997) Proteolytic activation of Rim1p, a positive regulator of yeast sporulation and invasive growth. Genetics 145 : 63–73.
45. BogengruberE, EichbergerT, BrizaP, DawesIW, BreitenbachM, et al. (1998) Sporulation-specific expression of the yeast DIT1/DIT2 promoter is controlled by a newly identified repressor element and the short form of Rim101p. Eur J Biochem 258 : 430–436.
46. RothfelsK, TannyJC, MolnarE, FriesenH, CommissoC, et al. (2005) Components of the ESCRT pathway, DFG16, and YGR122w are required for Rim101 to act as a corepressor with Nrg1 at the negative regulatory element of the DIT1 gene of Saccharomyces cerevisiae. Mol Cell Biol 25 : 6772–6788 doi:10.1128/MCB.25.15.6772-6788.2005
47. ManolioTA, CollinsFS, CoxNJ, GoldsteinDB, HindorffLA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461 : 747–753 doi:10.1038/nature08494
48. ZukO, HechterE, SunyaevSR, LanderES (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A 109 : 1193–1198 doi:10.1073/pnas.1119675109
49. HemaniG, KnottS, HaleyC (2013) An evolutionary perspective on epistasis and the missing heritability. PLoS Genet 9: e1003295 doi:10.1371/journal.pgen.1003295
50. WachA, BrachatA, PöhlmannR, PhilippsenP (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10 : 1793–1808.
51. GoldsteinAL, McCuskerJH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15 : 1541–1553 doi:;10.1002/(SICI)1097-0061(199910)15 : 14<1541::AID-YEA476>3.0.CO;2-K
52. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25 doi:10.1186/gb-2009-10-3-r25
53. Wang S, Basten CJ, Zeng Z-B (2011) Windows QTL Cartographer 2.5.
54. ThompsonJD, HigginsDG, GibsonTJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673–4680.
55. StoriciF, LewisLK, ResnickMA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19 : 773–776 doi:10.1038/90837
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