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Volumn 23, Issue 1-2, 2013, Pages 152-177

The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm

Author keywords

Acidocalcisome organelles; Coevolution; Origin of life; P loop hydrolases; Protein structure; Pyrophosphate; Ribonucleoprotein world; RNA world; Translation

Indexed keywords

LIPID; NUCLEIC ACID; PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RIBOSOME RNA; RNA;

EID: 84876783818     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000346551     Document Type: Article
Times cited : (39)

References (187)
  • 1
  • 2
    • 84888282870 scopus 로고    scopus 로고
    • A view of RNASe P
    • Altman S. A view of RNase P. Mol Biosys 2009, 3: 604-607
    • (2009) Mol Biosys , vol.3 , pp. 604-607
    • Altman, S.1
  • 3
    • 0034667684 scopus 로고    scopus 로고
    • Plasticity, evolvability, and modularity in RNA
    • Ancel LW, Fontana W. Plasticity, evolvability, and modularity in RNA. J Exp Zool (Mol Dev Evol) 2000; 288: 242-283
    • (2000) J Exp Zool (Mol Dev Evol , vol.288 , pp. 242-283
    • Ancel, L.W.1    Fontana, W.2
  • 4
    • 80052262050 scopus 로고    scopus 로고
    • Finding the balance between the mathematical and biological optima in multiple sequence alignment
    • Anisimova M, Cannarozzi GM, Liberles DA. Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends Evol Biol 2010; 2: e7
    • (2010) Trends Evol Biol , vol.2 , pp. e7
    • Anisimova, M.1    Cannarozzi, G.M.2    Liberles, D.A.3
  • 7
    • 74249115345 scopus 로고    scopus 로고
    • Topology links RNA secondary structure with global conformation, dynamics, and adaptation
    • Bailor MH, Sun X, Al-Hashimi HM. Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science 2010; 327: 202-206
    • (2010) Science , vol.327 , pp. 202-206
    • Bailor, M.H.1    Sun, X.2    Al-Hashimi, H.M.3
  • 9
    • 78649426085 scopus 로고    scopus 로고
    • Crystal structure of the eukaryotic ribosome
    • Ben-Shem A, Jenner L, Yusupova G, Yusupov M. Crystal structure of the eukaryotic ribosome. Science 2010; 330: 1203-1209
    • (2010) Science , vol.330 , pp. 1203-1209
    • Ben-Shem, A.1    Jenner, L.2    Yusupova, G.3    Yusupov, M.4
  • 10
    • 84868677049 scopus 로고    scopus 로고
    • Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA
    • Benner SA, Kim H-J, Carrigan MA. Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. Acc Chem Res 2012; 45: 2025-2034
    • (2012) Acc Chem Res , vol.45 , pp. 2025-2034
    • Benner, S.A.1    Kim, H.-J.2    Carrigan, M.A.3
  • 11
    • 84868685850 scopus 로고    scopus 로고
    • The RNA world hypo thesis the worst theory of the early evolution of life (except for all others
    • Bernhardt HS. The RNA world hypothesis: the worst theory of the early evolution of life (except for all others). Biol Direct 2012; 7: 23
    • (2012) Biol Direct , vol.7 , pp. 23
    • Bernhardt, H.S.1
  • 12
    • 60549112849 scopus 로고    scopus 로고
    • A hierarchical model for evolution of 23S ribosomal RNA
    • Bokov K, Steinberg SV. A hierarchical model for evolution of 23S ribosomal RNA. Nature 2009; 457: 977-980
    • (2009) Nature , vol.457 , pp. 977-980
    • Bokov, K.1    Steinberg, S.V.2
  • 13
    • 84859505162 scopus 로고    scopus 로고
    • Coordination of tRNA synthetase active sites for chemical fidelity
    • Boniecki MT, Martinis SA. Coordination of tRNA synthetase active sites for chemical fidelity. J Biol Chem 2012; 287: 11285-11289
    • (2012) J Biol Chem , vol.287 , pp. 11285-11289
    • Boniecki, M.T.1    Martinis, S.A.2
  • 14
    • 84861138834 scopus 로고    scopus 로고
    • The emergence and early evolution of biological carbon-fixation
    • Braakman R, Smith E. The emergence and early evolution of biological carbon-fixation. PLoS One 2012; 8: e1002455
    • (2012) PLoS One , vol.8 , pp. e1002455
    • Braakman, R.1    Smith, E.2
  • 15
    • 84855969034 scopus 로고    scopus 로고
    • Sequence coevolution between RNA and protein characterized by mutual information between residue triplets
    • Brandman R, Brandman Y, Pande VS. Sequence coevolution between RNA and protein characterized by mutual information between residue triplets. PLoS One 2012; 7: e30022
    • (2012) PLoS One , vol.7 , pp. e30022
    • Brandman, R.1    Brandman, Y.2    Pande, V.S.3
  • 17
    • 0036606550 scopus 로고    scopus 로고
    • Tracing the evolution of RNA structure in ribosomes
    • Caetano-Anolles G. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res 2002; 30: 2527-2587
    • (2002) Nucleic Acids Res , vol.30 , pp. 2527-2587
    • Caetano-Anolles, G.1
  • 18
    • 0038486929 scopus 로고    scopus 로고
    • An evolutionarily structured universe of protein architecture
    • Caetano-Anolles G, Caetano-Anolles D. An evolutionarily structured universe of protein architecture. Genome Res 2003; 13: 1563-1571
    • (2003) Genome Res , vol.13 , pp. 1563-1571
    • Caetano-Anolles, G.1    Caetano-Anolles, D.2
  • 19
    • 84862687324 scopus 로고    scopus 로고
    • The phylogenomic roots of modern biochemistry: Origins of proteins, cofactors and protein biosynthesis
    • Caetano-Anolles G, Kim KM, Caetano-Anolles, D. The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. J Mol Evol 2012; 74: 1-34
    • (2012) J Mol Evol , vol.74 , pp. 1-34
    • Caetano-Anolles, G.1    Kim, K.M.2    Caetano-Anolles, D.3
  • 20
    • 34547170043 scopus 로고    scopus 로고
    • The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
    • Caetano-Anolles G, Kim HS, Mittenthal JE. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci USA 2007; 104: 9358-9363
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 9358-9363
    • Caetano-Anolles, G.1    Kim, H.S.2    Mittenthal, J.E.3
  • 21
    • 77954830498 scopus 로고    scopus 로고
    • Exploring the interplay of stability and function in protein evolution
    • Caetano-Anolles G, Mittenthal JE. Exploring the interplay of stability and function in protein evolution. Bioessays 2010; 32: 655-658
    • (2010) Bioessays , vol.32 , pp. 655-658
    • Caetano-Anolles, G.1    Mittenthal, J.E.2
  • 22
    • 84874917944 scopus 로고    scopus 로고
    • Benefits of using molecular structure and abundance in phylogenomic analysis
    • Caetano-Anolles G, Nasir A. Benefits of using molecular structure and abundance in phylogenomic analysis. Front Gene 2012; 3: 172
    • (2012) Front Gene , vol.3 , pp. 172
    • Caetano-Anolles, G.1    Nasir, A.2
  • 24
    • 38949185776 scopus 로고    scopus 로고
    • Evolution of the protein world
    • Caetano-Anolles G, Wang M. Evolution of the protein world. Biochemist 2008; 30: 4-8
    • (2008) Biochemist , vol.30 , pp. 4-8
    • Caetano-Anolles, G.1    Wang, M.2
  • 27
    • 84874833757 scopus 로고    scopus 로고
    • Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism
    • Caetano-Anolles K, Caetano-Anolles G. Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PLoS One 2012; 8: e59300
    • (2012) PLoS One , vol.8 , pp. e59300
    • Caetano-Anolles, K.1    Caetano-Anolles, G.2
  • 28
    • 0037427963 scopus 로고    scopus 로고
    • The general protein secretory pathway: Phylogenetic analyses leading to evolutionary conclusions
    • Cao TB, Saier MH Jr. The general protein secretory pathway: phylogenetic analyses leading to evolutionary conclusions. Biochim Biophys Acta 2003; 1609: 115-125
    • (2003) Biochim Biophys Acta , vol.1609 , pp. 115-125
    • Cao, T.B.1    Saier, M.H.2
  • 31
    • 4444281964 scopus 로고    scopus 로고
    • The emergence of competition between model protocells
    • Chen IA, Roberts RW, Szostak JW. The emergence of competition between model protocells. Science 2004; 305: 1474-1476
    • (2004) Science , vol.305 , pp. 1474-1476
    • Chen, I.A.1    Roberts, R.W.2    Szostak, J.W.3
  • 32
    • 84865762571 scopus 로고    scopus 로고
    • Proteins from an unevolved library of de novo designed sequences bind a range of small molecules
    • Cherny I, Korolev M, Koehler AN, Hecht MH. Proteins from an unevolved library of de novo designed sequences bind a range of small molecules. ACS Synth Biol 2012; 1: 130-138
    • (2012) ACS Synth Biol , vol.1 , pp. 130-138
    • Cherny, I.1    Korolev, M.2    Koehler, A.N.3    Hecht, M.H.4
  • 33
    • 34248396432 scopus 로고    scopus 로고
    • Global extent of horizontal gene transfer
    • Choi I-G, Kim S-H: Global extent of horizontal gene transfer. Proc Natl Acad Sci USA 2007; 104: 4489-4494
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 4489-4494
    • Choi, I.-G.1    Kim, S.-H.2
  • 34
    • 62749097935 scopus 로고    scopus 로고
    • Genomic and structural aspects of protein evolution
    • Chothia C, Gough J. Genomic and structural aspects of protein evolution. Biochem J 2009; 419: 15-28
    • (2009) Biochem J , vol.419 , pp. 15-28
    • Chothia, C.1    Gough, J.2
  • 36
    • 0034601917 scopus 로고    scopus 로고
    • Homology among (βa) 8 barrels: Implications for the evolution of metabolic pathways
    • Copley RR, Bork P. Homology among (βa) 8 barrels: implications for the evolution of metabolic pathways. J Mol Biol 2000; 303: 627-641
    • (2000) J Mol Biol , vol.303 , pp. 627-641
    • Copley, R.R.1    Bork, P.2
  • 37
    • 41049083552 scopus 로고    scopus 로고
    • Why should we care about molecular coevolution
    • Cordoner FM, Fares MA. Why should we care about molecular coevolution? Evol Bioinformatics 2008; 4: 29-38
    • (2008) Evol Bioinformatics , vol.4 , pp. 29-38
    • Cordoner, F.M.1    Fares, M.A.2
  • 38
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FH. The origin of the genetic code. J Mol Biol 1968; 38: 367-379
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.1
  • 40
    • 84865281896 scopus 로고    scopus 로고
    • Kuhlbrandt: Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae
    • Davies KM, Anselmi C, Wittig I, Feralso-Gomez JD, Kuhlbrandt: Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci USA 2012; 109: 13602-13607
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 13602-13607
    • Davies, K.M.1    Anselmi, C.2    Wittig, I.3    Feralso-Gomez, J.D.4
  • 42
    • 0030741176 scopus 로고    scopus 로고
    • The first living systems: A bioenergetic perspective
    • Deamer DW. The first living systems: a bioenergetic perspective. Microbiol Mol Biol Rev 1997; 61: 239-261
    • (1997) Microbiol Mol Biol Rev , vol.61 , pp. 239-261
    • Deamer, D.W.1
  • 43
    • 0000799714 scopus 로고
    • The beginnings of life on earth
    • De Duve C. The beginnings of life on earth. Am Sci 1995; 83: 428-437
    • (1995) Am Sci , vol.83 , pp. 428-437
    • De Duve, C.1
  • 44
    • 48249134102 scopus 로고    scopus 로고
    • Mediation, modulation and consequences of membrane-cytoskeleton interactions
    • Doherty GJ, McMahon HT. Mediation, modulation and consequences of membrane-cytoskeleton interactions. Annu Rev Biophys 2008; 37: 65-95
    • (2008) Annu Rev Biophys , vol.37 , pp. 65-95
    • Doherty, G.J.1    McMahon, H.T.2
  • 45
    • 20444500847 scopus 로고    scopus 로고
    • Evolutionary aspects of whole-genome biology
    • Doolittle RF. Evolutionary aspects of whole-genome biology. Curr Op Struct Biol 2005; 15: 248-253
    • (2005) Curr Op Struct Biol , vol.15 , pp. 248-253
    • Doolittle, R.F.1
  • 46
    • 28644441059 scopus 로고    scopus 로고
    • Rational genomics I antisense open reading frames and codon bias in short oxidoreductase enzymes and the evolution of the genetic code
    • Duax WL, Huether R, Pletnev V, Langs D, Addlagatta A, Connare S, Habegger L, Gill J. Rational genomics I. antisense open reading frames and codon bias in short oxidoreductase enzymes and the evolution of the genetic code. Proteins 2005; 61: 900-906
    • (2005) Proteins , vol.61 , pp. 900-906
    • Duax, W.L.1    Huether, R.2    Pletnev, V.3    Langs, D.4    Addlagatta, A.5    Connare, S.6    Habegger, L.7    Gill, J.8
  • 47
    • 67649182966 scopus 로고    scopus 로고
    • Divergent evolution of a Rossmann fold and identification of its oldest surviving ancestor
    • Duax WL, Huether R, Pletnev V, Umland TC, Weeks CM. Divergent evolution of a Rossmann fold and identification of its oldest surviving ancestor. Int J Bioinform Res Appl 2009; 5: 280-294
    • (2009) Int J Bioinform Res Appl , vol.5 , pp. 280-294
    • Duax, W.L.1    Huether, R.2    Pletnev, V.3    Umland, T.C.4    Weeks, C.M.5
  • 48
    • 0020323998 scopus 로고
    • A model for the origin of life
    • Dyson FJ. A model for the origin of life. J Mol Evol 1982; 18: 344-350
    • (1982) J Mol Evol , vol.18 , pp. 344-350
    • Dyson, F.J.1
  • 49
    • 0004190112 scopus 로고    scopus 로고
    • Cambridge, Cambridge University Press
    • Dyson FJ. Origin of Life. Cambridge, Cambridge University Press, 1999
    • (1999) Origin of Life
    • Dyson, F.J.1
  • 50
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14: 755-763
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 51
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009; 23: 205-211
    • (2009) Genome Inform , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 52
    • 70349556093 scopus 로고    scopus 로고
    • Peptide-dominated membranes preceding the genetic takeover by RNA: Latest thinking on a classic controversy
    • Egel R. Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy. Bioessays 2009; 31: 1100-1109
    • (2009) Bioessays , vol.31 , pp. 1100-1109
    • Egel, R.1
  • 53
    • 0032590020 scopus 로고    scopus 로고
    • Mg2+-dependent folding of a large ribozyme without kinetic traps
    • Fang XW, Pan T, Sosnick TR. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol 1999; 6: 1091-1095
    • (1999) Nat Struct Biol , vol.6 , pp. 1091-1095
    • Fang, X.W.1    Pan, T.2    Sosnick, T.R.3
  • 54
    • 0036903361 scopus 로고    scopus 로고
    • Modelling 'evo-devo' with RNA
    • Fontana W. Modelling 'evo-devo' with RNA. Bioessays 2002; 24: 1164-1177
    • (2002) Bioessays , vol.24 , pp. 1164-1177
    • Fontana, W.1
  • 56
    • 84857913153 scopus 로고    scopus 로고
    • Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life
    • Fournier GP, Andam CP, Alm EJ, Gogarten JP. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig Life Evol Biosph 2011; 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
  • 57
    • 78149403030 scopus 로고    scopus 로고
    • Origin and evolution of the ribosome
    • Fox GE. Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol 2010; 2: a003483
    • (2010) Cold Spring Harb Perspect Biol , vol.2 , pp. a003483
    • Fox, G.E.1
  • 58
    • 71549148346 scopus 로고    scopus 로고
    • TRNA as active chemical scaffold for diverse chemical transformations
    • Francklyn CS, Minajigi A. tRNA as active chemical scaffold for diverse chemical transformations. FEBS Lett 2010; 584: 366-375
    • (2010) FEBS Lett , vol.584 , pp. 366-375
    • Francklyn, C.S.1    Minajigi, A.2
  • 60
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher EA, Thomson JM, Burgan MF, Benner SA. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 2003; 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
  • 63
    • 84901848680 scopus 로고
    • The RNA world
    • Gilbert W. The RNA world. Nature 1986; 31: 618
    • (1986) Nature , vol.31 , pp. 618
    • Gilbert, W.1
  • 64
    • 33846551381 scopus 로고    scopus 로고
    • Biology's next revolution
    • Goldenfeldt N, Woese C. Biology's next revolution. Nature 2007; 445: 369
    • (2007) Nature , vol.445 , pp. 369
    • Goldenfeldt, N.1    Woese, C.2
  • 66
    • 17544367678 scopus 로고    scopus 로고
    • Convergent evolution of domain architectures (is rare
    • Gough J. Convergent evolution of domain architectures (is rare). Bioinformatics 2005; 21: 1464-1471
    • (2005) Bioinformatics , vol.21 , pp. 1464-1471
    • Gough, J.1
  • 67
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001; 31: 903-919
    • (2001) J Mol Biol , vol.31 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 68
    • 84861141850 scopus 로고    scopus 로고
    • PRORP proteins support RNase P activity in both organelles and the nucleous of Arabidopsis
    • Gutmann B, Gobert A, Giege P. PRORP proteins support RNase P activity in both organelles and the nucleous of Arabidopsis. Genes Develop 2012; 26: 1022-1027
    • (2012) Genes Develop , vol.26 , pp. 1022-1027
    • Gutmann, B.1    Gobert, A.2    Giege, P.3
  • 69
    • 0142147270 scopus 로고    scopus 로고
    • Experimental models of primitive cellular compartments: Encapsulation, growth, and division
    • Hanczyc MM, Fujikawa SM, Szostak JW. Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 2003; 302: 618-622
    • (2003) Science , vol.302 , pp. 618-622
    • Hanczyc, M.M.1    Fujikawa, S.M.2    Szostak, J.W.3
  • 70
    • 84858040413 scopus 로고    scopus 로고
    • Ribosomal history reveals origins of modern protein synthesis
    • Harish A, Caetano-Anolles G. Ribosomal history reveals origins of modern protein synthesis. PLoS One 2012; 7: e32776
    • (2012) PLoS One , vol.7 , pp. e32776
    • Harish, A.1    Caetano-Anolles, G.2
  • 72
    • 0031864850 scopus 로고    scopus 로고
    • The prokaryote-To-eukaryote transition reflected in the evolution of the V/F/A-ATPase catalytic and proteolipid subunits
    • Hilario E, Gogarten JP. The prokaryote-To-eukaryote transition reflected in the evolution of the V/F/A-ATPase catalytic and proteolipid subunits. J Mol Evol 1998; 46: 703-715
    • (1998) J Mol Evol , vol.46 , pp. 703-715
    • Hilario, E.1    Gogarten, J.P.2
  • 73
    • 84870448969 scopus 로고    scopus 로고
    • Comparative analysis of RNA families reveals distinct repertoires for each domain of life
    • Hoeppner MP, Gardner PP, Poole AM. Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol 2012; 8: e1002752
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002752
    • Hoeppner, M.P.1    Gardner, P.P.2    Poole, A.M.3
  • 74
    • 54549088876 scopus 로고    scopus 로고
    • RNase P without RNA: Identification and functional reconstitution of the human mitochondrial tRNA processing enzyme
    • Holzmann J, Frank P, Loffler E, Bennett KL, Gerner C, Rossmanith W. RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 2008; 135: 462-474
    • (2008) Cell , vol.135 , pp. 462-474
    • Holzmann, J.1    Frank, P.2    Loffler, E.3    Bennett, K.L.4    Gerner, C.5    Rossmanith, W.6
  • 75
    • 73349114907 scopus 로고    scopus 로고
    • Peeling the onion: Ribosomes are ancient molecular fossils
    • Hsiao C, Mohan S, Kalahar BK, Williams LD. Peeling the onion: ribosomes are ancient molecular fossils. Mol Biol Evol 2009; 26: 2415-2425
    • (2009) Mol Biol Evol , vol.26 , pp. 2415-2425
    • Hsiao, C.1    Mohan, S.2    Kalahar, B.K.3    Williams, L.D.4
  • 76
    • 21044454225 scopus 로고    scopus 로고
    • Possible steps to the emergence of life: The [GADV]-protein world hypothesis
    • Ikehara K. Possible steps to the emergence of life: The [GADV]-protein world hypothesis. Chem Rec 2005; 5: 107-118
    • (2005) Chem Rec , vol.5 , pp. 107-118
    • Ikehara, K.1
  • 77
    • 70349318376 scopus 로고    scopus 로고
    • Structure is three to ten times more conserved than sequence-A study of structural response in protein cores
    • Illegard K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence-A study of structural response in protein cores. Proteins 2009; 77: 499-508
    • (2009) Proteins , vol.77 , pp. 499-508
    • Illegard, K.1    Ardell, D.H.2    Elofsson, A.3
  • 78
    • 0034539308 scopus 로고    scopus 로고
    • The origin of cellular life
    • Ingber DE. The origin of cellular life. BioEssays 2000; 22: 1160-1170
    • (2000) BioEssays , vol.22 , pp. 1160-1170
    • Ingber, D.E.1
  • 79
    • 84864193567 scopus 로고    scopus 로고
    • Evolution from simple inorganic compounds to chiral peptides
    • Jakschitz T, Rode BM. Evolution from simple inorganic compounds to chiral peptides. Chem Soc Rev 2012; 41: 5484-5489
    • (2012) Chem Soc Rev , vol.41 , pp. 5484-5489
    • Jakschitz, T.1    Rode, B.M.2
  • 80
    • 56949099187 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution
    • James LC, Tawfik DS. Conformational diversity and protein evolution. Trends Biochem Sci 2003; 30: 622-629
    • (2003) Trends Biochem Sci , vol.30 , pp. 622-629
    • James, L.C.1    Tawfik, D.S.2
  • 82
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new functions
    • Jensen RA. Enzyme recruitment in evolution of new functions. Annu Rev Microbiol 1976; 30: 409-425
    • (1976) Annu Rev Microbiol , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 83
    • 0028895702 scopus 로고
    • Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
    • Jermann TM, Opitz JG, Stackhouse J, Benner SA. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 1995; 374: 57-59
    • (1995) Nature , vol.374 , pp. 57-59
    • Jermann, T.M.1    Opitz, J.G.2    Stackhouse, J.3    Benner, S.A.4
  • 84
    • 0021277007 scopus 로고
    • On the origin of enzyme species by means of natural selection
    • Kacser H, Beeby R. On the origin of enzyme species by means of natural selection. J Mol Evol 1984; 20: 38-51
    • (1984) J Mol Evol , vol.20 , pp. 38-51
    • Kacser, H.1    Beeby, R.2
  • 85
    • 0022619420 scopus 로고
    • Autocatalytic sets of proteins
    • Kauffman SA. Autocatalytic sets of proteins. J Theor Biol 1986; 119: 1-24
    • (1986) J Theor Biol , vol.119 , pp. 1-24
    • Kauffman, S.A.1
  • 87
    • 84869444907 scopus 로고    scopus 로고
    • Approaches to the origin of life on Earth
    • Kauffman SA. Approaches to the origin of life on Earth. Life 2011; 1: 34-48
    • (2011) Life , vol.1 , pp. 34-48
    • Kauffman, S.A.1
  • 88
    • 33748313110 scopus 로고    scopus 로고
    • MANET: Tracing evolution of protein architecture in metabolic networks
    • Kim H-S, Mittenthal J, Caetano-Anolles G. MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics 2006; 7: 351
    • (2006) BMC Bioinformatics , vol.7 , pp. 351
    • Kim, H.-S.1    Mittenthal, J.2    Caetano-Anolles, G.3
  • 89
    • 77953753370 scopus 로고    scopus 로고
    • Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data
    • Kim KM, Caetano-Anolles G. Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol Biol Evol 2010; 27: 1710-1733
    • (2010) Mol Biol Evol , vol.27 , pp. 1710-1733
    • Kim, K.M.1    Caetano-Anolles, G.2
  • 90
    • 80053304045 scopus 로고    scopus 로고
    • The proteomic complexity and rise of the primordial ancestor of diversified life
    • Kim KM, Caetano-Anolles G. The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol 2011; 11: 140
    • (2011) BMC Evol Biol , vol.11 , pp. 140
    • Kim, K.M.1    Caetano-Anolles, G.2
  • 91
    • 84862830777 scopus 로고    scopus 로고
    • The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
    • Kim KM, Caetano-Anolles G. The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evol Biol 2012; 12: 13
    • (2012) BMC Evol Biol , vol.12 , pp. 13
    • Kim, K.M.1    Caetano-Anolles, G.2
  • 93
    • 77957193832 scopus 로고    scopus 로고
    • The RNA dreamtime
    • Kurland CG. The RNA dreamtime. Bioessays 2010; 32: 866-871
    • (2010) Bioessays , vol.32 , pp. 866-871
    • Kurland, C.G.1
  • 95
    • 79952267368 scopus 로고    scopus 로고
    • An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification
    • Lam BJ, Joyce GF. An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification. J Am Chem Soc 2011; 133: 3191-3197
    • (2011) J Am Chem Soc , vol.133 , pp. 3191-3197
    • Lam, B.J.1    Joyce, G.F.2
  • 96
    • 66749191451 scopus 로고    scopus 로고
    • Emergence of a code in the polymerization of amino acids along RNA templates
    • Lehmann J, Cibils M, Libchaber A. Emergence of a code in the polymerization of amino acids along RNA templates. PLoS One 2009; 4: e5773
    • (2009) PLoS One , vol.4 , pp. e5773
    • Lehmann, J.1    Cibils, M.2    Libchaber, A.3
  • 97
    • 67650497792 scopus 로고    scopus 로고
    • Nature of the protein universe
    • Levitt M. Nature of the protein universe. Proc Natl Acad Sci USA 2009; 106: 11079-11084
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 11079-11084
    • Levitt, M.1
  • 99
    • 61349193830 scopus 로고    scopus 로고
    • Self-sustained replication of an RNA enzyme
    • Lincoln TA, Joyce GF. Self-sustained replication of an RNA enzyme. Science 2009; 323: 1229-1232
    • (2009) Science , vol.323 , pp. 1229-1232
    • Lincoln, T.A.1    Joyce, G.F.2
  • 100
    • 38549144166 scopus 로고    scopus 로고
    • The genome on line database (GOLD) in 2007status of genomic and metagenomic projects and their associated metadata
    • Liolios K, Mavrommatis K, Tavernarakis N, Kyrpides NC. The genome on line database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2007; 36: D475-D479
    • (2007) Nucleic Acids Res , vol.36 , pp. D475-D479
    • Liolios, K.1    Mavrommatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 101
    • 0015209453 scopus 로고
    • Attempts to map a process evolution of peptide biosynthesis
    • Lipmann F. Attempts to map a process evolution of peptide biosynthesis. Science 1971; 173: 875-884
    • (1971) Science , vol.173 , pp. 875-884
    • Lipmann, F.1
  • 102
    • 79960559641 scopus 로고    scopus 로고
    • Resurecction of an ancestral 5S rRNA
    • Lu Q, Fox GE. Resurecction of an ancestral 5S rRNA. BMC Evol Biol 2011; 11: 218
    • (2011) BMC Evol Biol , vol.11 , pp. 218
    • Lu, Q.1    Fox, G.E.2
  • 103
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389: 251-260
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 105
    • 0029125284 scopus 로고
    • No soup for starters? Autotrophy and the origins of metabolism
    • Maden BEH. No soup for starters? Autotrophy and the origins of metabolism. Trends Biochem Sci 1995; 20: 337-341
    • (1995) Trends Biochem Sci , vol.20 , pp. 337-341
    • Maden, B.E.H.1
  • 106
    • 27644598282 scopus 로고    scopus 로고
    • A protein component at the heart of an RNA machine: The importance of protein L27 for the function of the bacterial ribosome
    • Maguire BA, Beniaminov AD, Ramu H, Mankin AS, Zimmermann RA. A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Mol Cell 2005; 20: 427-435
    • (2005) Mol Cell , vol.20 , pp. 427-435
    • Maguire, B.A.1    Beniaminov, A.D.2    Ramu, H.3    Mankin, A.S.4    Zimmermann, R.A.5
  • 107
    • 73349085562 scopus 로고    scopus 로고
    • Working outside the protein-synthesis rules: Insights into non-ribosomal peptide synthesis
    • Marahiel MA. Working outside the protein-synthesis rules: insights into non-ribosomal peptide synthesis. J Pept Sci 2009; 15: 799-807
    • (2009) J Pept Sci , vol.15 , pp. 799-807
    • Marahiel, M.A.1
  • 108
    • 85047688021 scopus 로고    scopus 로고
    • Excess mutual catalysis is required for effective evolvability
    • Markovitch O, Lancet D. Excess mutual catalysis is required for effective evolvability. Artificial Life 2012; 18: 243-266
    • (2012) Artificial Life , vol.18 , pp. 243-266
    • Markovitch, O.1    Lancet, D.2
  • 110
    • 84860393302 scopus 로고    scopus 로고
    • RNase P at last, the key finds its lock
    • Masquida B, Westhof E. RNase P. at last, the key finds its lock. RNA 2011; 17: 1615-1618
    • (2011) RNA , vol.17 , pp. 1615-1618
    • Masquida, B.1    Westhof, E.2
  • 111
    • 33746358181 scopus 로고    scopus 로고
    • Dynamic filaments of the bacterial cytoskeleton
    • Michie KA, Lowe J. Dynamic filaments of the bacterial cytoskeleton. Annu Rev Biochem 2006; 75: 467-492
    • (2006) Annu Rev Biochem , vol.75 , pp. 467-492
    • Michie, K.A.1    Lowe, J.2
  • 112
    • 37049243502 scopus 로고
    • A production of amino acids under possible primitive earth conditions
    • Miller SL. A production of amino acids under possible primitive earth conditions. Science 1953; 117: 528-529
    • (1953) Science , vol.117 , pp. 528-529
    • Miller, S.L.1
  • 114
    • 77957079227 scopus 로고    scopus 로고
    • Homologs of aminoacyl-TRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
    • Mocibob M, Ivic N, Bilokapic S, Maier T, Luic M, Ban N, Weygand-Durasevic I. Homologs of aminoacyl-TRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis. Proc Natl Acad Sci USA 2010; 107: 14585-14590
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 14585-14590
    • Mocibob, M.1    Ivic, N.2    Bilokapic, S.3    Maier, T.4    Luic, M.5    Ban, N.6    Weygand-Durasevic, I.7
  • 115
  • 116
    • 76649085598 scopus 로고    scopus 로고
    • A theory of biochemical organization, metabolic pathways, and evolution
    • Morowitz HJ. A theory of biochemical organization, metabolic pathways, and evolution. Complexity 1999; 4: 39-53
    • (1999) Complexity , vol.4 , pp. 39-53
    • Morowitz, H.J.1
  • 117
    • 0036828867 scopus 로고    scopus 로고
    • How did cells get their size
    • Morris CE. How did cells get their size? Anat Rec 2002; 268: 239-251
    • (2002) Anat Rec , vol.268 , pp. 239-251
    • Morris, C.E.1
  • 118
    • 0242523720 scopus 로고    scopus 로고
    • On the impossibility of reconstructing ancestral data and phylogenies
    • Mossell E. On the impossibility of reconstructing ancestral data and phylogenies. J Comp Biol 2003; 10: 669-678
    • (2003) J Comp Biol , vol.10 , pp. 669-678
    • Mossell, E.1
  • 121
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins for the investigation of sequences and structures
    • Murzin A, Brenner SE, Hubbard T, Clothia C. SCOP: a structural classification of proteins for the investigation of sequences and structures. J Mol Biol 1995; 247: 536-540
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.E.2    Hubbard, T.3    Clothia, C.4
  • 122
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: The evolutionary relationship between TIM barrel families based on their sequences, structures and functions
    • Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationship between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002; 321: 741-765
    • (2002) J Mol Biol , vol.321 , pp. 741-765
    • Nagano, N.1    Orengo, C.A.2    Thornton, J.M.3
  • 123
    • 80052416603 scopus 로고    scopus 로고
    • Quantification of peptide bond types in human proteome indicates how DNA codons were assembled at prebiotic conditions
    • Nahalka J. Quantification of peptide bond types in human proteome indicates how DNA codons were assembled at prebiotic conditions. J Proteom Bioinfo 2011; 4: 8
    • (2011) J Proteom Bioinfo , vol.4 , pp. 8
    • Nahalka, J.1
  • 124
    • 84865305042 scopus 로고    scopus 로고
    • Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea Bacteria and Eukarya
    • Nasir A, Kim KM, Caetano-Anolles G. Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evol Biol 2012; 12: 156
    • (2012) BMC Evol Biol , vol.12 , pp. 156
    • Nasir, A.1    Kim, K.M.2    Caetano-Anolles, G.3
  • 126
    • 0014369024 scopus 로고
    • Evolution of the genetic apparatus
    • Orgel LE. Evolution of the genetic apparatus. J Mol Biol 1968; 38: 381-393
    • (1968) J Mol Biol , vol.38 , pp. 381-393
    • Orgel, L.E.1
  • 127
    • 0026634324 scopus 로고
    • Molecular replication
    • Orgel LE. Molecular replication. Nature 1992; 358: 203-209
    • (1992) Nature , vol.358 , pp. 203-209
    • Orgel, L.E.1
  • 128
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by comformational epistasis
    • Ortlund EA, Brindgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: evolution by comformational epistasis. Science 2007; 317: 1544-1548
    • (2007) Science , vol.317 , pp. 1544-1548
    • Ortlund, E.A.1    Brindgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 129
    • 80053617478 scopus 로고    scopus 로고
    • Evolutionary genomics leads the way
    • Caetano-Anolles G (ed. Hoboken, John Wiley & Sons
    • Penny D, Collins LJ. Evolutionary genomics leads the way; in Caetano-Anolles G (ed): Evolutionary Bioinformatics and Systems Biology. Hoboken, John Wiley & Sons, 2010, pp 3-16
    • (2010) Evolutionary Bioinformatics and Systems Biology , pp. 3-16
    • Penny, D.1    Collins, L.J.2
  • 130
    • 0038354758 scopus 로고    scopus 로고
    • Testing fundamental evolutionary hypotheses
    • Penny D, Hendy MD, Poole AM. Testing fundamental evolutionary hypotheses. J Theor Biol 2003; 223: 377-385
    • (2003) J Theor Biol , vol.223 , pp. 377-385
    • Penny, D.1    Hendy, M.D.2    Poole, A.M.3
  • 133
  • 137
    • 0003075565 scopus 로고
    • On the problems of evolution and biochemical information transfer
    • n Kasha M, Pullman B (eds. New York Academic Press
    • Rich A. On the problems of evolution and biochemical information transfer; in Kasha M, Pullman B (eds): Horizons in Biochemistry. New York, Academic Press, 1962, pp 103-126
    • (1962) Horizons in Biochemistry , pp. 103-126
    • Rich, A.1
  • 139
    • 38049048820 scopus 로고    scopus 로고
    • The first steps of chemical evolution towards the origin of life
    • Rode BM, Fitz D, Jakschitz T. The first steps of chemical evolution towards the origin of life. Chem Biodivers 2007; 4: 2674-2702
    • (2007) Chem Biodivers , vol.4 , pp. 2674-2702
    • Rode, B.M.1    Fitz, D.2    Jakschitz, T.3
  • 140
    • 0033383044 scopus 로고    scopus 로고
    • Are prions a relic of an early stage of peptide evolution
    • Rode BM, Flader W, Sotriffer C, Righi A. Are prions a relic of an early stage of peptide evolution? Peptides 1999; 20: 1513-1516
    • (1999) Peptides , vol.20 , pp. 1513-1516
    • Rode, B.M.1    Flader, W.2    Sotriffer, C.3    Righi, A.4
  • 141
    • 41149161126 scopus 로고    scopus 로고
    • On the origin of the genetic code: Signatures of its primordial complementarity in tRNAs and aminoacyl-TRNA synthetases
    • Rodin SN, Rodin AS. On the origin of the genetic code: Signatures of its primordial complementarity in tRNAs and aminoacyl-TRNA synthetases. Heredity 2008; 100: 341-355
    • (2008) Heredity , vol.100 , pp. 341-355
    • Rodin, S.N.1    Rodin, A.S.2
  • 145
    • 70350654363 scopus 로고    scopus 로고
    • What recent ribosome structures have revealed about the mechanism of translation
    • Schmeing TM, Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature 2009; 461: 1234-1242
    • (2009) Nature , vol.461 , pp. 1234-1242
    • Schmeing, T.M.1    Ramakrishnan, V.2
  • 146
    • 84903527955 scopus 로고    scopus 로고
    • No molecule is an island: Molecular evolution and the study of sequence space
    • in Condon A, Harel D, Joj JN, Salomaa A, Winfree E (eds. New York Springer
    • Schultes EA, Hraber PT, LaBean TH. No molecule is an island: Molecular evolution and the study of sequence space; in Condon A, Harel D, Joj JN, Salomaa A, Winfree E (eds): Algorithmic Bioprocesses, Natural Computing Series. New York, Springer, 2010, pp 675-704
    • (2010) Algorithmic Bioprocesses, Natural Computing Series , pp. 675-704
    • Schultes, E.A.1    Hraber, P.T.2    Labean, T.H.3
  • 147
  • 148
    • 77952278563 scopus 로고    scopus 로고
    • Genotypes and phenotypes in the evolution of molecules
    • in Caetano-Anolles G (ed. Hoboken, John Wiley & Sons
    • Schuster P. Genotypes and phenotypes in the evolution of molecules; in Caetano-Anolles G (ed): Evolutionary Bioinformatics and Systems Biology. Hoboken, John Wiley & Sons, 2010, pp 123-152
    • (2010) Evolutionary Bioinformatics and Systems Biology , pp. 123-152
    • Schuster, P.1
  • 150
    • 79960062888 scopus 로고    scopus 로고
    • MRNA display for the selection and evolution of enzymes from in vitro-Translated protein libraries
    • Seelig B. mRNA display for the selection and evolution of enzymes from in vitro-Translated protein libraries. Nature Protocols 2011; 6: 540-552
    • (2011) Nature Protocols , vol.6 , pp. 540-552
    • Seelig, B.1
  • 152
    • 0034636047 scopus 로고    scopus 로고
    • Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies
    • Segre D, Ben-Eli D, Lancet D. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc Natl Acad Sci USA 2000; 97: 4112-4117
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 4112-4117
    • Segre, D.1    Ben-Eli, D.2    Lancet, D.3
  • 153
    • 0035824758 scopus 로고    scopus 로고
    • The molecular roots of compositional inheritance
    • Segre D, Shenhav B, Kafri R, Lancet D. The molecular roots of compositional inheritance. J Theor Biol 2001b; 213: 481-491
    • (2001) J Theor Biol , vol.213 , pp. 481-491
    • Segre, D.1    Shenhav, B.2    Kafri, R.3    Lancet, D.4
  • 156
    • 80053496265 scopus 로고    scopus 로고
    • Evolution of vacuolar proton pyrophosphatase domains and volutin granules: Clues into the early evolutionary origin of the acidocalcisome
    • Seufferheld MJ, Kim KM, Whitfield J, Valerio A, Caetano-Anolles G. Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. Biology Direct 2011; 6: 50
    • (2011) Biology Direct , vol.6 , pp. 50
    • Seufferheld, M.J.1    Kim, K.M.2    Whitfield, J.3    Valerio, A.4    Caetano-Anolles, G.5
  • 157
    • 34250678485 scopus 로고    scopus 로고
    • A simpler origin for life
    • Shapiro R. A simpler origin for life. Sci Amer 2007; 296: 46-53
    • (2007) Sci Amer , vol.296 , pp. 46-53
    • Shapiro, R.1
  • 159
    • 0036416151 scopus 로고    scopus 로고
    • Testing the hypothesis of common ancestry
    • Sober E, Steel M. Testing the hypothesis of common ancestry. J Theor Biol 2002; 218: 395-408
    • (2002) J Theor Biol , vol.218 , pp. 395-408
    • Sober, E.1    Steel, M.2
  • 160
    • 38649093627 scopus 로고    scopus 로고
    • The origin and evolution of tRNA inferred from phylogenetic analysis of structure
    • Sun F-J, Caetano-Anolles G. The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol 2008; 66: 21-35
    • (2008) J Mol Evol , vol.66 , pp. 21-35
    • Sun, F.-J.1    Caetano-Anolles, G.2
  • 161
    • 72449132771 scopus 로고    scopus 로고
    • The evolutionary history of the structure of 5S ribosomal RNA
    • Sun F-J, Caetano-Anolles G. The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol 2009; 69: 430-443
    • (2009) J Mol Evol , vol.69 , pp. 430-443
    • Sun, F.-J.1    Caetano-Anolles, G.2
  • 162
    • 77952276437 scopus 로고    scopus 로고
    • The ancient history of the structure of ribonuclease P and the early origins of Archaea
    • Sun F-J, Caetano-Anolles G. The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 2010; 11: 153
    • (2010) BMC Bioinformatics , vol.11 , pp. 153
    • Sun, F.-J.1    Caetano-Anolles, G.2
  • 164
    • 84885535303 scopus 로고    scopus 로고
    • Phylogenetic utility of RNA structure: Evolution's arrow and emergence of modern biochemistry and diversified life
    • in Caetano-Anolles G (ed. Hoboken, John Wiley & Sons
    • Sun F-J, Harish A, Caetano-Anolles G. Phylogenetic utility of RNA structure: evolution's arrow and emergence of modern biochemistry and diversified life; in Caetano-Anolles G (ed): Evolutionary Bioinformatics and Systems Biology. Hoboken, John Wiley & Sons, 2010, pp 329-360
    • (2010) Evolutionary Bioinformatics and Systems Biology , pp. 329-360
    • Sun, F.-J.1    Harish, A.2    Caetano-Anolles, G.3
  • 165
    • 77956925998 scopus 로고    scopus 로고
    • Messy biology and the origins of evolutionary innovations
    • Tawfik DS. Messy biology and the origins of evolutionary innovations. Nature Chem Biol 2010; 6: 692-696
    • (2010) Nature Chem Biol , vol.6 , pp. 692-696
    • Tawfik, D.S.1
  • 166
    • 34347383961 scopus 로고    scopus 로고
    • Evolutionary transitions in protein fold space
    • Taylor WR. Evolutionary transitions in protein fold space. Curr Opin Struct Biol 2007; 17: 354-361
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 354-361
    • Taylor, W.R.1
  • 168
    • 0035943351 scopus 로고    scopus 로고
    • The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
    • Teichmann SA, Rison SCG, Thornton JM, Riley M, Gough J, Chothia C. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 2001b; 311: 693-708
    • (2001) J Mol Biol , vol.311 , pp. 693-708
    • Teichmann, S.A.1    Rison, S.C.G.2    Thornton, J.M.3    Riley, M.4    Gough, J.5    Chothia, C.6
  • 169
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • Thirumalai D, Hyeon C. RNA and protein folding: common themes and variations. Biochemistry 2005; 44: 4957-4970
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 170
    • 79960601166 scopus 로고    scopus 로고
    • Slow protein evolutionary rates are dictated by surface-core association
    • Toth-Petroczy A, Tawfik DS. Slow protein evolutionary rates are dictated by surface-core association. Proc Natl Acad Sci USA 2011; 108: 11151-11156
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 11151-11156
    • Toth-Petroczy, A.1    Tawfik, D.S.2
  • 172
    • 9244224677 scopus 로고    scopus 로고
    • Chance and necessity do not explain the origin of life
    • Trevors JT, Abel DL. Chance and necessity do not explain the origin of life. Cell Biol Intl 2004; 28: 729-739
    • (2004) Cell Biol Intl , vol.28 , pp. 729-739
    • Trevors, J.T.1    Abel, D.L.2
  • 173
    • 76549090462 scopus 로고    scopus 로고
    • Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life
    • Vasas V, Szathary, Santos M. Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life. Proc Natl Acad Sci USA 2010; 107: 1470-1475
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 1470-1475
    • Vasas, V.1    Szathary Santos, M.2
  • 174
    • 66149157000 scopus 로고    scopus 로고
    • Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
    • Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 2009; 16: 528-533
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 528-533
    • Voorhees, R.M.1    Weixlbaumer, A.2    Loakes, D.3    Kelley, A.C.4    Ramakrishnan, V.5
  • 175
    • 51149203927 scopus 로고
    • Canalization of development and the inheritance of acquired characters
    • Waddington CH. Canalization of development and the inheritance of acquired characters. Nature 1942; 150: 563-565
    • (1942) Nature , vol.150 , pp. 563-565
    • Waddington, C.H.1
  • 176
    • 36348992094 scopus 로고    scopus 로고
    • Robustness and evolvability: A paradox resolved
    • Wagner A. Robustness and evolvability: a paradox resolved. Proc Biol Sci 2008; 275: 91-100
    • (2008) Proc Biol Sci , vol.275 , pp. 91-100
    • Wagner, A.1
  • 177
    • 58149196295 scopus 로고    scopus 로고
    • The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
    • Wang M, Caetano-Anolles G. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 2009; 17: 66-78
    • (2009) Structure , vol.17 , pp. 66-78
    • Wang, M.1    Caetano-Anolles, G.2
  • 178
    • 78650476811 scopus 로고    scopus 로고
    • A molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
    • Wang M, Jiang Y-Y, Kim KM, Qu G, Ji H-F, Zhang H-Y, Caetano-Anolles G. A molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol Biol Evol 2011; 28: 567-582
    • (2011) Mol Biol Evol , vol.28 , pp. 567-582
    • Wang, M.1    Jiang, Y.-Y.2    Kim, K.M.3    Qu, G.4    Ji, H.-F.5    Zhang, H.-Y.6    Caetano-Anolles, G.7
  • 179
    • 35948990789 scopus 로고    scopus 로고
    • Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
    • Wang M, Yafremava LS, Caetano-Anolles D, Mittenthal JE, Caetano-Anolles G. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res 2007; 17: 1572-1585
    • (2007) Genome Res , vol.17 , pp. 1572-1585
    • Wang, M.1    Yafremava, L.S.2    Caetano-Anolles, D.3    Mittenthal, J.E.4    Caetano-Anolles, G.5
  • 181
    • 34347347191 scopus 로고    scopus 로고
    • On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
    • Wolf YI, Koonin EV. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2007; 2: 14
    • (2007) Biol Direct , vol.2 , pp. 14
    • Wolf, Y.I.1    Koonin, E.V.2
  • 182
    • 84855892823 scopus 로고    scopus 로고
    • Quality control in aminoacyl-TRNA syn thesis Its role in translational fidelity
    • Yadavalli SS, Ibba M. Quality control in aminoacyl-TRNA synthesis: Its role in translational fidelity. Adv Protein Chem Struct Biol 2012; 86: 1-43
    • (2012) Adv Protein Chem Struct Biol , vol.86 , pp. 1-43
    • Yadavalli, S.S.1    Ibba, M.2
  • 183
    • 77949513721 scopus 로고    scopus 로고
    • The evolutionary history of proteins domains viewed by species phylogeny
    • Yang S, Bourne PE. The evolutionary history of proteins domains viewed by species phylogeny. PLoS One 2009; 4: e8378
    • (2009) PLoS One , vol.4 , pp. e8378
    • Yang, S.1    Bourne, P.E.2
  • 185
    • 36949019322 scopus 로고    scopus 로고
    • Detecting coevolution in and among protein domains
    • Yeang CH, Haussler D. Detecting coevolution in and among protein domains. PLoS Comp Biol 2007; 3: e211
    • (2007) PLoS Comp Biol , vol.3 , pp. e211
    • Yeang, C.H.1    Haussler, D.2
  • 187
    • 78751662374 scopus 로고    scopus 로고
    • RNA folding of living cells
    • Zemora G, Waldsich C. RNA folding of living cells. RNA Biol 2010; 7: 634-641
    • (2010) RNA Biol , vol.7 , pp. 634-641
    • Zemora, G.1    Waldsich, C.2


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