메뉴 건너뛰기




Volumn 69, Issue 11, 2015, Pages 2954-2962

Robustness of predictions of extremely thermally stable proteins in ancient organisms

Author keywords

Ancestral sequence reconstruction; Nucleoside diphosphate kinase; Phylogenetic tree; Substitution model; Unfolding temperature

Indexed keywords

AMINO ACID; ANCESTRY; COMPUTER SIMULATION; DATA SET; ENZYME ACTIVITY; EVOLUTIONARY THEORY; PHYLOGENETICS; PROTEIN; RNA; TEMPERATURE; THERMOPHILY;

EID: 84955214204     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12779     Document Type: Article
Times cited : (29)

References (49)
  • 2
    • 0029819318 scopus 로고    scopus 로고
    • The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny
    • Baldauf, S. L., J. D. Palmer, and W. F. Doolittle . 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93:7749-7754.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 7749-7754
    • Baldauf, S.L.1    Palmer, J.D.2    Doolittle, W.F.3
  • 3
    • 47249122561 scopus 로고    scopus 로고
    • A site- and time-heterogeneous model of amino acid replacement
    • Blanquart, S. and N. Lartillot . 2008. A site- and time-heterogeneous model of amino acid replacement. Mol. Biol. Evol. 25:842-858.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2
  • 4
    • 57749185463 scopus 로고    scopus 로고
    • Parallel adaptations to high temperatures in the Archaean eon
    • Boussau, B., S. Blanquart, A. Necsulea, N. Lartillot, and M. Gouy . 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature 456:942-945.
    • (2008) Nature , vol.456 , pp. 942-945
    • Boussau, B.1    Blanquart, S.2    Necsulea, A.3    Lartillot, N.4    Gouy, M.5
  • 5
    • 33645691679 scopus 로고    scopus 로고
    • Evolution of hormone-receptor complexity by molecular exploitation
    • Bridgham, J. T., S. M. Carroll, and J. W. Thornton . 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 312:97-101.
    • (2006) Science , vol.312 , pp. 97-101
    • Bridgham, J.T.1    Carroll, S.M.2    Thornton, J.W.3
  • 6
    • 0037118037 scopus 로고    scopus 로고
    • Phylogeny: a non-hyperthermophilic ancestor for bacteria
    • Brochier, C., and H. Philippe . 2002. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature 417:244.
    • (2002) Nature , vol.417 , pp. 244
    • Brochier, C.1    Philippe, H.2
  • 7
    • 0036792118 scopus 로고    scopus 로고
    • Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code
    • Brooks, D. J., J. R. Fresco, A. M. Lesk, and M. Singh . 2002. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol. Biol. Evol. 19:1645-1655.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1645-1655
    • Brooks, D.J.1    Fresco, J.R.2    Lesk, A.M.3    Singh, M.4
  • 8
    • 5044244494 scopus 로고    scopus 로고
    • A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
    • Brooks, D. J., J. R. Fresco, and M. Singh . 2004. A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics 20:2251-2257.
    • (2004) Bioinformatics , vol.20 , pp. 2251-2257
    • Brooks, D.J.1    Fresco, J.R.2    Singh, M.3
  • 9
    • 0028941917 scopus 로고
    • Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications
    • Brown, J. R., and W. F. Doolittle . 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92:2441-2445.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 2441-2445
    • Brown, J.R.1    Doolittle, W.F.2
  • 10
    • 84896730564 scopus 로고    scopus 로고
    • Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants
    • Butzin, N. C., P. Lapierre, A. G. Green, K. S. Swithers, J. P. Gogarten, and K. M. Noll . 2013. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 8:e84300.
    • (2013) PLoS One , vol.8
    • Butzin, N.C.1    Lapierre, P.2    Green, A.G.3    Swithers, K.S.4    Gogarten, J.P.5    Noll, K.M.6
  • 11
    • 0036155782 scopus 로고    scopus 로고
    • The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification
    • Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int. J. Syst. Evol. Mic robiol. 52:7-76.
    • (2002) Int. J. Syst. Evol. Mic robiol. , vol.52 , pp. 7-76
    • Cavalier-Smith, T.1
  • 12
    • 33745468278 scopus 로고    scopus 로고
    • Cell evolution and Earth history: stasis and revolution
    • Cavalier-Smith, T. 2006. Cell evolution and Earth history: stasis and revolution. Philos. Trans. R Soc. Lond. B Biol. Sci. 361:969-1006.
    • (2006) Philos. Trans. R Soc. Lond. B Biol. Sci. , vol.361 , pp. 969-1006
    • Cavalier-Smith, T.1
  • 13
    • 33846349924 scopus 로고    scopus 로고
    • Rooting the tree of life by transition analyses
    • Cavalier-Smith, T. 2006b. Rooting the tree of life by transition analyses. Biol. Direct. 1:19.
    • (2006) Biol. Direct. , vol.1 , pp. 19
    • Cavalier-Smith, T.1
  • 14
    • 75449103540 scopus 로고    scopus 로고
    • Deep phylogeny, ancestral groups and the four ages of life
    • Cavalier-Smith, T. 2010. Deep phylogeny, ancestral groups and the four ages of life. Philos. Trans. R Soc. Lond. B Biol. Sci. 365:111-132.
    • (2010) Philos. Trans. R Soc. Lond. B Biol. Sci. , vol.365 , pp. 111-132
    • Cavalier-Smith, T.1
  • 15
    • 0034615794 scopus 로고    scopus 로고
    • The universal ancestor lived in a thermophilic or hyperthermophilic environment
    • Di Giulio, M. 2000. The universal ancestor lived in a thermophilic or hyperthermophilic environment. J. Theor. Biol. 203:203-213.
    • (2000) J. Theor. Biol. , vol.203 , pp. 203-213
    • Di Giulio, M.1
  • 16
    • 0346104820 scopus 로고    scopus 로고
    • The universal ancestor and the ancestor of bacteria were hyperthermophiles
    • Di Giulio, M. 2003. The universal ancestor and the ancestor of bacteria were hyperthermophiles. J. Mol. Evol. 57:721-730.
    • (2003) J. Mol. Evol. , vol.57 , pp. 721-730
    • Di Giulio, M.1
  • 17
    • 0037424668 scopus 로고    scopus 로고
    • The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence
    • Di Giulio, M. 2003b. The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence. J. Theor. Biol. 221:425-436.
    • (2003) J. Theor. Biol. , vol.221 , pp. 425-436
    • Di Giulio, M.1
  • 18
    • 84857913153 scopus 로고    scopus 로고
    • Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life
    • Fournier, G. P., C. P. Andam, E. J. Alm, and J. P. Gogarten . 2011. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig. Life Evol. Biosph. 41:621-632.
    • (2011) Orig. Life Evol. Biosph. , vol.41 , pp. 621-632
    • Fournier, G.P.1    Andam, C.P.2    Alm, E.J.3    Gogarten, J.P.4
  • 19
    • 84940003703 scopus 로고    scopus 로고
    • Ancestral reconstruction of a pre-LUCA aminoacyl-tRNA synthetase Ancestor supports the late addition of Trp to the genetic code
    • Fournier, G. P. and E. J. Alm . 2015. Ancestral reconstruction of a pre-LUCA aminoacyl-tRNA synthetase Ancestor supports the late addition of Trp to the genetic code. J. Mol. Evol. 80:171-185.
    • (2015) J. Mol. Evol. , vol.80 , pp. 171-185
    • Fournier, G.P.1    Alm, E.J.2
  • 20
    • 0033534584 scopus 로고    scopus 로고
    • A nonhyperthermophilic common ancestor to extant life forms
    • Galtier, N., N. Tourasse, and M. Gouy . 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283:220-221.
    • (1999) Science , vol.283 , pp. 220-221
    • Galtier, N.1    Tourasse, N.2    Gouy, M.3
  • 21
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher, E. A., J. M. Thomson, M. F. Burgan, and S. A. Benner . 2003. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425:285-288.
    • (2003) Nature , vol.425 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 22
    • 38949093003 scopus 로고    scopus 로고
    • Palaeotemperature trend for Precambrian life inferred from resurrected proteins
    • Gaucher, E. A., S. Govindarajan, and O. K. Ganesh . 2008. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451:704-707.
    • (2008) Nature , vol.451 , pp. 704-707
    • Gaucher, E.A.1    Govindarajan, S.2    Ganesh, O.K.3
  • 24
    • 0024448151 scopus 로고
    • Calculation of protein extinction coefficients from amino acid sequence data
    • Gill, S. C., and P. H. von Hippel . 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326.
    • (1989) Anal. Biochem. , vol.182 , pp. 319-326
    • Gill, S.C.1    von Hippel, P.H.2
  • 26
    • 34247193011 scopus 로고    scopus 로고
    • Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles
    • Greaves, R. B., and J. Warwicker . 2007. Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles. BMC Struct. Biol. 7:18.
    • (2007) BMC Struct. Biol. , vol.7 , pp. 18
    • Greaves, R.B.1    Warwicker, J.2
  • 27
    • 80052160609 scopus 로고    scopus 로고
    • Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea
    • Groussin, M., and M. Gouy . 2011. Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea. Mol. Biol. Evol. 28:2661-2674.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2661-2674
    • Groussin, M.1    Gouy, M.2
  • 28
    • 84947756127 scopus 로고    scopus 로고
    • The molecular signal for the adaptation to cold temperature during early life on Earth
    • Groussin, M., B. Boussau, S. Charles, S. Blanquart, and M. Gouy . 2013. The molecular signal for the adaptation to cold temperature during early life on Earth. Biol. Lett. 9:20130608.
    • (2013) Biol. Lett. , vol.9
    • Groussin, M.1    Boussau, B.2    Charles, S.3    Blanquart, S.4    Gouy, M.5
  • 30
    • 0024358140 scopus 로고
    • Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
    • Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata . 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-9359.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 9355-9359
    • Iwabe, N.1    Kuma, K.2    Hasegawa, M.3    Osawa, S.4    Miyata, T.5
  • 31
    • 13444259388 scopus 로고    scopus 로고
    • TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
    • Jobb, G., A. von Haeseler, and K. Strimmer . 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4:18.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 18
    • Jobb, G.1    von Haeseler, A.2    Strimmer, K.3
  • 35
    • 0015955554 scopus 로고
    • Description of Thermus thermophilus (Yoshida and Oshima) comb. novl, A nonsporulating thermophilic bacterium from a Japanese thermal spa
    • Oshima, T., and K. Imahori . 1974. Description of Thermus thermophilus (Yoshida and Oshima) comb. novl, A nonsporulating thermophilic bacterium from a Japanese thermal spa. Int. J. System. Bacteriol. 24:102-112.
    • (1974) Int. J. System. Bacteriol. , vol.24 , pp. 102-112
    • Oshima, T.1    Imahori, K.2
  • 36
    • 0025901140 scopus 로고
    • Origin of life-facing up to the physical setting
    • Pace, N. R. 1991. Origin of life-facing up to the physical setting. Cell 65:531-533.
    • (1991) Cell , vol.65 , pp. 531-533
    • Pace, N.R.1
  • 37
    • 0028871804 scopus 로고
    • How to measure and predict the molar absorption coefficient of a protein
    • Pace, C. N., F. Vajdos, L. Fee, G. Grimsley, and T. Gray . 1995. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4:2411-2423.
    • (1995) Protein Sci , vol.4 , pp. 2411-2423
    • Pace, C.N.1    Vajdos, F.2    Fee, L.3    Grimsley, G.4    Gray, T.5
  • 38
    • 0027341494 scopus 로고
    • Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life
    • Schopf, J. W. 1993. Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260:640-646.
    • (1993) Science , vol.260 , pp. 640-646
    • Schopf, J.W.1
  • 40
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins . 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 42
    • 1942531303 scopus 로고    scopus 로고
    • Resurrecting ancient genes: experimental analysis of extinct molecules
    • Thornton, J. W. 2004. Resurrecting ancient genes: experimental analysis of extinct molecules. Nat. Rev. Genet. 5:366-375.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 366-375
    • Thornton, J.W.1
  • 43
    • 0034736513 scopus 로고    scopus 로고
    • Consensus temporal order of amino acids and evolution of the triplet code
    • Trifonov, E. N. 2000. Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139-151.
    • (2000) Gene , vol.261 , pp. 139-151
    • Trifonov, E.N.1
  • 44
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M., and J. A. Eisen, 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:R151
    • (2008) Genome Biol , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 45
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 46
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"
    • Woese, C. R., S. Winker, and R. R. Gutell . 1990. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". Proc. Natl. Acad. Sci. USA 87:8467-8471.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Gutell, R.R.3
  • 48
    • 0030683599 scopus 로고    scopus 로고
    • PAML: a program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.