메뉴 건너뛰기




Volumn 166, Issue 6, 2016, Pages 1585-1596.e22

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ARTICLE; CLONE; DIPLOIDY; DNA BARCODING; GENETIC PROCEDURES; GENOTYPE; HAPLOIDY; MUTATION; NONHUMAN; NUTRIENT; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SELF DIPLOIDIZATION; SIGNAL TRANSDUCTION; WHOLE GENOME SEQUENCING; FUNGAL GENOME; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MUTAGENESIS; REPRODUCTIVE FITNESS;

EID: 84986301161     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.08.002     Document Type: Article
Times cited : (165)

References (60)
  • 1
    • 0015964603 scopus 로고
    • Population studies in microorganisms. I. Evolution of diploidy in Saccharomyces cerevisiae
    • Adams, J., Hansche, P.E., Population studies in microorganisms. I. Evolution of diploidy in Saccharomyces cerevisiae. Genetics 76 (1974), 327–338.
    • (1974) Genetics , vol.76 , pp. 327-338
    • Adams, J.1    Hansche, P.E.2
  • 2
    • 84922384542 scopus 로고    scopus 로고
    • A systematic survey of an intragenic epistatic landscape
    • Bank, C., Hietpas, R.T., Jensen, J.D., Bolon, D.N.A., A systematic survey of an intragenic epistatic landscape. Mol. Biol. Evol. 32 (2015), 229–238.
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 229-238
    • Bank, C.1    Hietpas, R.T.2    Jensen, J.D.3    Bolon, D.N.A.4
  • 4
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson, G., Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (1999), 573–580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 5
    • 84901435099 scopus 로고    scopus 로고
    • Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness
    • Bozek, K., Wei, Y., Yan, Z., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Pieszek, R., Sherwood, C.C., et al. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol., 12, 2014, e1001871.
    • (2014) PLoS Biol. , vol.12 , pp. e1001871
    • Bozek, K.1    Wei, Y.2    Yan, Z.3    Liu, X.4    Xiong, J.5    Sugimoto, M.6    Tomita, M.7    Pääbo, S.8    Pieszek, R.9    Sherwood, C.C.10
  • 7
    • 73249138317 scopus 로고    scopus 로고
    • An efficient high-throughput flow cytometric method for estimating DNA ploidy level in plants
    • Cousin, A., Heel, K., Cowling, W.A., Nelson, M.N., An efficient high-throughput flow cytometric method for estimating DNA ploidy level in plants. Cytometry A 75 (2009), 1015–1019.
    • (2009) Cytometry A , vol.75 , pp. 1015-1019
    • Cousin, A.1    Heel, K.2    Cowling, W.A.3    Nelson, M.N.4
  • 8
    • 0003809032 scopus 로고
    • The Origin of Species
    • John Murray London
    • Darwin, C., The Origin of Species. 1872, John Murray, London.
    • (1872)
    • Darwin, C.1
  • 9
    • 77957980707 scopus 로고    scopus 로고
    • Origins and evolution of antibiotic resistance
    • Davies, J., Davies, D., Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74 (2010), 417–433.
    • (2010) Microbiol. Mol. Biol. Rev. , vol.74 , pp. 417-433
    • Davies, J.1    Davies, D.2
  • 10
    • 0036067771 scopus 로고    scopus 로고
    • The monopolization hypothesis and the dispersal-gene flow paradox in aquatic organisms
    • De Meester, L., Gomez, A., Okamura, B., Schwenk, K., The monopolization hypothesis and the dispersal-gene flow paradox in aquatic organisms. Acta Oecol. 23 (2002), 121–135.
    • (2002) Acta Oecol. , vol.23 , pp. 121-135
    • De Meester, L.1    Gomez, A.2    Okamura, B.3    Schwenk, K.4
  • 11
    • 33847314378 scopus 로고    scopus 로고
    • Beneficial mutation selection balance and the effect of linkage on positive selection
    • Desai, M.M., Fisher, D.S., Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176 (2007), 1759–1798.
    • (2007) Genetics , vol.176 , pp. 1759-1798
    • Desai, M.M.1    Fisher, D.S.2
  • 12
    • 84860663163 scopus 로고    scopus 로고
    • Evolutionary insight from whole-genome sequencing of experimentally evolved microbes
    • Dettman, J.R., Rodrigue, N., Melnyk, A.H., Wong, A., Bailey, S.F., Kassen, R., Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 21 (2012), 2058–2077.
    • (2012) Mol. Ecol. , vol.21 , pp. 2058-2077
    • Dettman, J.R.1    Rodrigue, N.2    Melnyk, A.H.3    Wong, A.4    Bailey, S.F.5    Kassen, R.6
  • 13
    • 1642491749 scopus 로고    scopus 로고
    • Chronological aging-independent replicative life span regulation by Msn2/Msn4 and Sod2 in Saccharomyces cerevisiae
    • Fabrizio, P., Pletcher, S.D., Minois, N., Vaupel, J.W., Longo, V.D., Chronological aging-independent replicative life span regulation by Msn2/Msn4 and Sod2 in Saccharomyces cerevisiae. FEBS Lett. 557 (2004), 136–142.
    • (2004) FEBS Lett. , vol.557 , pp. 136-142
    • Fabrizio, P.1    Pletcher, S.D.2    Minois, N.3    Vaupel, J.W.4    Longo, V.D.5
  • 14
    • 84905217368 scopus 로고    scopus 로고
    • Deep mutational scanning: a new style of protein science
    • Fowler, D.M., Fields, S., Deep mutational scanning: a new style of protein science. Nat. Methods 11 (2014), 801–807.
    • (2014) Nat. Methods , vol.11 , pp. 801-807
    • Fowler, D.M.1    Fields, S.2
  • 15
    • 33749420389 scopus 로고    scopus 로고
    • Genomic convergence toward diploidy in Saccharomyces cerevisiae
    • Gerstein, A.C., Chun, H.-J.E., Grant, A., Otto, S.P., Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genet., 2, 2006, e145.
    • (2006) PLoS Genet. , vol.2 , pp. e145
    • Gerstein, A.C.1    Chun, H.-J.E.2    Grant, A.3    Otto, S.P.4
  • 17
    • 0036270543 scopus 로고    scopus 로고
    • Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method
    • Gietz, R.D., Woods, R.A., Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350 (2002), 87–96.
    • (2002) Methods Enzymol. , vol.350 , pp. 87-96
    • Gietz, R.D.1    Woods, R.A.2
  • 18
    • 84931572965 scopus 로고    scopus 로고
    • Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution
    • Givnish, T.J., Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution. New Phytol. 207 (2015), 297–303.
    • (2015) New Phytol. , vol.207 , pp. 297-303
    • Givnish, T.J.1
  • 19
    • 84856013431 scopus 로고    scopus 로고
    • Clonal evolution in cancer
    • Greaves, M., Maley, C.C., Clonal evolution in cancer. Nature 481 (2012), 306–313.
    • (2012) Nature , vol.481 , pp. 306-313
    • Greaves, M.1    Maley, C.C.2
  • 21
    • 84874535714 scopus 로고    scopus 로고
    • Parallel evolutionary dynamics of adaptive diversification in Escherichia coli
    • Herron, M.D., Doebeli, M., Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol., 11, 2013, e1001490.
    • (2013) PLoS Biol. , vol.11 , pp. e1001490
    • Herron, M.D.1    Doebeli, M.2
  • 22
    • 84888829471 scopus 로고    scopus 로고
    • Shifting fitness landscapes in response to altered environments
    • Hietpas, R.T., Bank, C., Jensen, J.D., Bolon, D.N.A., Shifting fitness landscapes in response to altered environments. Evolution 67 (2013), 3512–3522.
    • (2013) Evolution , vol.67 , pp. 3512-3522
    • Hietpas, R.T.1    Bank, C.2    Jensen, J.D.3    Bolon, D.N.A.4
  • 23
    • 84893817979 scopus 로고    scopus 로고
    • Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments
    • Hong, J., Gresham, D., Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments. PLoS Genet., 10, 2014, e1004041.
    • (2014) PLoS Genet. , vol.10 , pp. e1004041
    • Hong, J.1    Gresham, D.2
  • 25
    • 56749107039 scopus 로고    scopus 로고
    • Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae
    • Kao, K.C., Sherlock, G., Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat. Genet. 40 (2008), 1499–1504.
    • (2008) Nat. Genet. , vol.40 , pp. 1499-1504
    • Kao, K.C.1    Sherlock, G.2
  • 26
    • 84899629319 scopus 로고    scopus 로고
    • Turning ecology and evolution against cancer
    • Korolev, K.S., Xavier, J.B., Gore, J., Turning ecology and evolution against cancer. Nat. Rev. Cancer 14 (2014), 371–380.
    • (2014) Nat. Rev. Cancer , vol.14 , pp. 371-380
    • Korolev, K.S.1    Xavier, J.B.2    Gore, J.3
  • 27
    • 84903291815 scopus 로고    scopus 로고
    • Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity
    • Kryazhimskiy, S., Rice, D.P., Jerison, E.R., Desai, M.M., Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 344 (2014), 1519–1522.
    • (2014) Science , vol.344 , pp. 1519-1522
    • Kryazhimskiy, S.1    Rice, D.P.2    Jerison, E.R.3    Desai, M.M.4
  • 28
    • 79955590028 scopus 로고    scopus 로고
    • Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
    • Kvitek, D.J., Sherlock, G., Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet., 7, 2011, e1002056.
    • (2011) PLoS Genet. , vol.7 , pp. e1002056
    • Kvitek, D.J.1    Sherlock, G.2
  • 29
    • 84888213196 scopus 로고    scopus 로고
    • Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment
    • Kvitek, D.J., Sherlock, G., Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet., 9, 2013, e1003972.
    • (2013) PLoS Genet. , vol.9 , pp. e1003972
    • Kvitek, D.J.1    Sherlock, G.2
  • 32
  • 34
    • 0034703217 scopus 로고    scopus 로고
    • Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae
    • Lin, S.J., Defossez, P.A., Guarente, L., Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae. Science 289 (2000), 2126–2128.
    • (2000) Science , vol.289 , pp. 2126-2128
    • Lin, S.J.1    Defossez, P.A.2    Guarente, L.3
  • 35
    • 0019321628 scopus 로고
    • The pH and temperature dependence of the activity of the high Km cyclic nucleotide phosphodiesterase of bakers’ yeast
    • Londesborough, J., Lukkari, T.M., The pH and temperature dependence of the activity of the high Km cyclic nucleotide phosphodiesterase of bakers’ yeast. J. Biol. Chem. 255 (1980), 9262–9267.
    • (1980) J. Biol. Chem. , vol.255 , pp. 9262-9267
    • Londesborough, J.1    Lukkari, T.M.2
  • 36
    • 84941934046 scopus 로고    scopus 로고
    • Elucidating the molecular architecture of adaptation via evolve and resequence experiments
    • Long, A., Liti, G., Luptak, A., Tenaillon, O., Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat. Rev. Genet. 16 (2015), 567–582.
    • (2015) Nat. Rev. Genet. , vol.16 , pp. 567-582
    • Long, A.1    Liti, G.2    Luptak, A.3    Tenaillon, O.4
  • 37
    • 84940653986 scopus 로고    scopus 로고
    • Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage
    • Marcet-Houben, M., Gabaldón, T., Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage. PLoS Biol., 13, 2015, e1002220.
    • (2015) PLoS Biol. , vol.13 , pp. e1002220
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 39
    • 0017167185 scopus 로고
    • The clonal evolution of tumor cell populations
    • Nowell, P.C., The clonal evolution of tumor cell populations. Science 194 (1976), 23–28.
    • (1976) Science , vol.194 , pp. 23-28
    • Nowell, P.C.1
  • 41
    • 35548954250 scopus 로고    scopus 로고
    • The evolutionary consequences of polyploidy
    • Otto, S.P., The evolutionary consequences of polyploidy. Cell 131 (2007), 452–462.
    • (2007) Cell , vol.131 , pp. 452-462
    • Otto, S.P.1
  • 42
    • 84875212396 scopus 로고    scopus 로고
    • Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance
    • Palmer, A.C., Kishony, R., Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nat. Rev. Genet. 14 (2013), 243–248.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 243-248
    • Palmer, A.C.1    Kishony, R.2
  • 44
    • 84864068244 scopus 로고    scopus 로고
    • Standing genetic variation and the evolution of drug resistance in HIV
    • Pennings, P.S., Standing genetic variation and the evolution of drug resistance in HIV. PLoS Comput. Biol., 8, 2012, e1002527.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002527
    • Pennings, P.S.1
  • 45
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan, A.R., Hall, I.M., BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 (2010), 841–842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 47
    • 0021269292 scopus 로고
    • Construction and genetic characterization of temperature-sensitive mutant alleles of the yeast actin gene
    • Shortle, D., Novick, P., Botstein, D., Construction and genetic characterization of temperature-sensitive mutant alleles of the yeast actin gene. Proc. Natl. Acad. Sci. USA 81 (1984), 4889–4893.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 4889-4893
    • Shortle, D.1    Novick, P.2    Botstein, D.3
  • 48
    • 29144454212 scopus 로고    scopus 로고
    • Loss of dispensable genes is not adaptive in yeast
    • Sliwa, P., Korona, R., Loss of dispensable genes is not adaptive in yeast. Proc. Natl. Acad. Sci. USA 102 (2005), 17670–17674.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 17670-17674
    • Sliwa, P.1    Korona, R.2
  • 50
    • 38549103015 scopus 로고    scopus 로고
    • Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits
    • Stinchcombe, J.R., Hoekstra, H.E., Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100 (2008), 158–170.
    • (2008) Heredity , vol.100 , pp. 158-170
    • Stinchcombe, J.R.1    Hoekstra, H.E.2
  • 52
    • 84555171441 scopus 로고    scopus 로고
    • Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
    • Toprak, E., Veres, A., Michel, J.-B., Chait, R., Hartl, D.L., Kishony, R., Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 44 (2011), 101–105.
    • (2011) Nat. Genet. , vol.44 , pp. 101-105
    • Toprak, E.1    Veres, A.2    Michel, J.-B.3    Chait, R.4    Hartl, D.L.5    Kishony, R.6
  • 53
    • 0017376884 scopus 로고
    • The Use of Benlate for Distinguishing Between Haploid and Diploid Strains of Aspergillus nidulans and Aspergillus terreus
    • Upshall, A., Giddings, B., Mortimore, I.D., The Use of Benlate for Distinguishing Between Haploid and Diploid Strains of Aspergillus nidulans and Aspergillus terreus. J. Gen. Microbiol. 100 (1977), 413–418.
    • (1977) J. Gen. Microbiol. , vol.100 , pp. 413-418
    • Upshall, A.1    Giddings, B.2    Mortimore, I.D.3
  • 55
    • 84937211391 scopus 로고    scopus 로고
    • Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation
    • Voordeckers, K., Verstrepen, K.J., Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation. Curr. Opin. Microbiol. 28 (2015), 1–9.
    • (2015) Curr. Opin. Microbiol. , vol.28 , pp. 1-9
    • Voordeckers, K.1    Verstrepen, K.J.2
  • 57
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • Weinreich, D.M., Delaney, N.F., Depristo, M.A., Hartl, D.L., Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312 (2006), 111–114.
    • (2006) Science , vol.312 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    Depristo, M.A.3    Hartl, D.L.4
  • 58
    • 80052324811 scopus 로고    scopus 로고
    • Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency
    • Wenger, J.W., Piotrowski, J., Nagarajan, S., Chiotti, K., Sherlock, G., Rosenzweig, F., Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. PLoS Genet., 7, 2011, e1002202.
    • (2011) PLoS Genet. , vol.7 , pp. e1002202
    • Wenger, J.W.1    Piotrowski, J.2    Nagarajan, S.3    Chiotti, K.4    Sherlock, G.5    Rosenzweig, F.6
  • 59
    • 0037462494 scopus 로고    scopus 로고
    • An evolutionary advantage of haploidy in large yeast populations
    • Zeyl, C., Vanderford, T., Carter, M., An evolutionary advantage of haploidy in large yeast populations. Science 299 (2003), 555–558.
    • (2003) Science , vol.299 , pp. 555-558
    • Zeyl, C.1    Vanderford, T.2    Carter, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.