메뉴 건너뛰기




Volumn 411, Issue 4, 2011, Pages 837-853

Directed evolution of sulfotransferases and paraoxonases by ancestral libraries

Author keywords

cytosolic sulfotransferases; directed evolution; protein phylogeny; serum paraoxonase (PON); SULT

Indexed keywords

ARYLDIALKYLPHOSPHATASE; ARYLDIALKYLPHOSPHATASE 1; ARYLDIALKYLPHOSPHATASE 2; SULFOTRANSFERASE; XENOBIOTIC AGENT;

EID: 80051669875     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.06.037     Document Type: Article
Times cited : (55)

References (55)
  • 1
    • 56149121547 scopus 로고    scopus 로고
    • Directed enzyme evolution via small and effective neutral drift libraries
    • Gupta R.D., and Tawfik D.S. Directed enzyme evolution via small and effective neutral drift libraries Nat. Methods 5 2008 939 942
    • (2008) Nat. Methods , vol.5 , pp. 939-942
    • Gupta, R.D.1    Tawfik, D.S.2
  • 2
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • DOI 10.1038/nprot.2007.72, PII NPROT.2007.72
    • Reetz M.T., and Carballeira J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes Nat. Protoc. 2 2007 891 903 (Pubitemid 46758808)
    • (2007) Nature Protocols , vol.2 , Issue.4 , pp. 891-903
    • Reetz, M.T.1    Carballeira, J.D.2
  • 3
    • 77956234144 scopus 로고    scopus 로고
    • Natural diversity to guide focused directed evolution
    • Helge J., and Bornscheuer U.T. Natural diversity to guide focused directed evolution ChemBioChem 11 2010 1861 1866
    • (2010) ChemBioChem , vol.11 , pp. 1861-1866
    • Helge, J.1    Bornscheuer, U.T.2
  • 4
    • 76649090003 scopus 로고    scopus 로고
    • Reconstructed Evolutionary Adaptive Paths give polymerases accepting reversible terminators for sequencing and SNP detection
    • Chen F., Gaucher E.A., Leal N.A., Hutter D., Havemann S.A., and Govindarajan S. Reconstructed Evolutionary Adaptive Paths give polymerases accepting reversible terminators for sequencing and SNP detection Proc. Natl Acad. Sci. USA 107 2010 1948 1953
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 1948-1953
    • Chen, F.1    Gaucher, E.A.2    Leal, N.A.3    Hutter, D.4    Havemann, S.A.5    Govindarajan, S.6
  • 5
    • 78349313517 scopus 로고    scopus 로고
    • Beyond directed evolution-semi-rational protein engineering and design
    • Lutz S. Beyond directed evolution-semi-rational protein engineering and design Curr. Opin. Biotechnol. 21 2010 734 743
    • (2010) Curr. Opin. Biotechnol. , vol.21 , pp. 734-743
    • Lutz, S.1
  • 6
    • 34548858708 scopus 로고    scopus 로고
    • Engineering by homologous recombination: exploring sequence and function within a conserved fold
    • DOI 10.1016/j.sbi.2007.08.005, PII S0959440X07001121
    • Carbone M.N., and Arnold F.H. Engineering by homologous recombination: exploring sequence and function within a conserved fold Curr. Opin. Struct. Biol. 17 2007 454 459 (Pubitemid 47451771)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.4 , pp. 454-459
    • Carbone, M.N.1    Arnold, F.H.2
  • 7
    • 0035025314 scopus 로고    scopus 로고
    • Libraries of hybrid proteins from distantly related sequences
    • DOI 10.1038/88129
    • Sieber V., Martinez C.A., and Arnold F.H. Libraries of hybrid proteins from distantly related sequences Nat. Biotechnol. 19 2001 456 460 (Pubitemid 32428289)
    • (2001) Nature Biotechnology , vol.19 , Issue.5 , pp. 456-460
    • Sieber, V.1    Martinez, C.A.2    Arnold, F.H.3
  • 8
    • 65649133585 scopus 로고    scopus 로고
    • Critical reviews in biochemistry and molecular biology. Introduction
    • Wickens M., and Cox M.M. Critical reviews in biochemistry and molecular biology. Introduction Crit. Rev. Biochem. Mol. Biol. 44 2009 2
    • (2009) Crit. Rev. Biochem. Mol. Biol. , vol.44 , pp. 2
    • Wickens, M.1    Cox, M.M.2
  • 9
    • 54149114377 scopus 로고    scopus 로고
    • Ohno's model revisited: Measuring the frequency of potentially adaptive mutations under various mutational drifts
    • Bershtein S., and Tawfik D.S. Ohno's model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts Mol. Biol. Evol. 25 2008 2311 2318
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2311-2318
    • Bershtein, S.1    Tawfik, D.S.2
  • 10
    • 77954743785 scopus 로고    scopus 로고
    • Mutational effects and the evolution of new protein functions
    • Soskine M., and Tawfik D.S. Mutational effects and the evolution of new protein functions Nat. Rev. Genet. 11 2010 572 582
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 572-582
    • Soskine, M.1    Tawfik, D.S.2
  • 12
    • 36749042777 scopus 로고    scopus 로고
    • Latent evolutionary potentials under the neutral mutational drift of an enzyme
    • Amitai G., Gupta R.D., and Tawfik D.S. Latent evolutionary potentials under the neutral mutational drift of an enzyme HFSP J. 1 2007 67 78
    • (2007) HFSP J. , vol.1 , pp. 67-78
    • Amitai, G.1    Gupta, R.D.2    Tawfik, D.S.3
  • 13
    • 34447559360 scopus 로고    scopus 로고
    • Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution
    • Bloom J.D., Romero P.A., Lu Z., and Arnold F.H. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution Biol. Direct 2 2007 17
    • (2007) Biol. Direct , vol.2 , pp. 17
    • Bloom, J.D.1    Romero, P.A.2    Lu, Z.3    Arnold, F.H.4
  • 14
    • 78649277331 scopus 로고    scopus 로고
    • Thermostabilization of an esterase by alignment-guided focussed directed evolution
    • Jochens H., Aerts D., and Bornscheuer U.T. Thermostabilization of an esterase by alignment-guided focussed directed evolution Protein Eng. Des. Sel. 23 2010 903 909
    • (2010) Protein Eng. Des. Sel. , vol.23 , pp. 903-909
    • Jochens, H.1    Aerts, D.2    Bornscheuer, U.T.3
  • 15
    • 23944434781 scopus 로고    scopus 로고
    • A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase
    • DOI 10.1093/protein/gzi043
    • Flores H., and Ellington A.D. A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase Protein Eng. Des. Sel. 18 2005 369 377 (Pubitemid 41187253)
    • (2005) Protein Engineering, Design and Selection , vol.18 , Issue.8 , pp. 369-377
    • Flores, H.1    Ellington, A.D.2
  • 16
    • 1942531303 scopus 로고    scopus 로고
    • Resurrecting ancient genes: Experimental analysis of extinct molecules
    • DOI 10.1038/nrg1324
    • Thornton J.W. Resurrecting ancient genes: experimental analysis of extinct molecules Nat. Rev. Genet. 5 2004 366 375 (Pubitemid 38529408)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.5 , pp. 366-375
    • Thornton, J.W.1
  • 17
    • 34548014497 scopus 로고    scopus 로고
    • Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A versatile tool for generating targeted libraries
    • DOI 10.1093/protein/gzm014
    • Herman A., and Tawfik D.S. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries Protein Eng. Des. Sel. 20 2007 219 226 (Pubitemid 351321303)
    • (2007) Protein Engineering, Design and Selection , vol.20 , Issue.5 , pp. 219-226
    • Herman, A.1    Tawfik, D.S.2
  • 18
    • 28844466075 scopus 로고    scopus 로고
    • High-throughput screening of enzyme libraries: Thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments
    • DOI 10.1016/j.chembiol.2005.09.012, PII S1074552105003042
    • Aharoni A., Amitai G., Bernath K., Magdassi S., and Tawfik D.S. High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments Chem. Biol. 12 2005 1281 1289 (Pubitemid 41779468)
    • (2005) Chemistry and Biology , vol.12 , Issue.12 , pp. 1281-1289
    • Aharoni, A.1    Amitai, G.2    Bernath, K.3    Magdassi, S.4    Tawfik, D.S.5
  • 19
  • 22
    • 17644367506 scopus 로고    scopus 로고
    • Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase
    • DOI 10.1021/bi047440d
    • Khersonsky O., and Tawfik D.S. Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase Biochemistry 44 2005 6371 6382 (Pubitemid 40570731)
    • (2005) Biochemistry , vol.44 , Issue.16 , pp. 6371-6382
    • Khersonsky, O.1    Tawfik, D.S.2
  • 23
    • 21244491480 scopus 로고    scopus 로고
    • Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities
    • DOI 10.1194/jlr.M400511-JLR200
    • Draganov D.I., Teiber J.F., Speelman A., Osawa Y., Sunahara R., and La Du B.N. Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities J. Lipid Res. 46 2005 1239 1247 (Pubitemid 43109838)
    • (2005) Journal of Lipid Research , vol.46 , Issue.6 , pp. 1239-1247
    • Draganov, D.I.1    Teiber, J.F.2    Speelman, A.3    Osawa, Y.4    Sunahara, R.5    La Du, B.N.6
  • 24
    • 79952197625 scopus 로고    scopus 로고
    • High-performance liquid chromatography analysis of N-acyl homoserine lactone hydrolysis by paraoxonases
    • Teiber J.F., and Draganov D.I. High-performance liquid chromatography analysis of N-acyl homoserine lactone hydrolysis by paraoxonases Methods Mol. Biol. 692 2011 291 298
    • (2011) Methods Mol. Biol. , vol.692 , pp. 291-298
    • Teiber, J.F.1    Draganov, D.I.2
  • 27
    • 30444432098 scopus 로고    scopus 로고
    • Chromogenic and fluorogenic assays for the lactonase activity of serum paraoxonases
    • DOI 10.1002/cbic.200500334
    • Khersonsky O., and Tawfik D.S. Chromogenic and fluorogenic assays for the lactonase activity of serum paraoxonases ChemBioChem 7 2006 49 53 (Pubitemid 43076285)
    • (2006) ChemBioChem , vol.7 , Issue.1 , pp. 49-53
    • Khersonsky, O.1    Tawfik, D.S.2
  • 30
    • 44349161622 scopus 로고    scopus 로고
    • Intense neutral drifts yield robust and evolvable consensus proteins
    • Bershtein S., Goldin K., and Tawfik D.S. Intense neutral drifts yield robust and evolvable consensus proteins J. Mol. Biol. 379 2008 1029 1044
    • (2008) J. Mol. Biol. , vol.379 , pp. 1029-1044
    • Bershtein, S.1    Goldin, K.2    Tawfik, D.S.3
  • 31
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • DOI 10.1038/nature01977
    • Gaucher E.A., Thomson J.M., Burgan M.F., and Benner S.A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins Nature 425 2003 285 288 (Pubitemid 37158402)
    • (2003) Nature , vol.425 , Issue.6955 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 36
    • 0035424955 scopus 로고    scopus 로고
    • Engineering proteins for thermostability: The use of sequence alignments versus rational design and directed evolution
    • DOI 10.1016/S0958-1669(00)00229-9
    • Lehmann M., and Wyss M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution Curr. Opin. Biotechnol. 12 2001 371 375 (Pubitemid 32718790)
    • (2001) Current Opinion in Biotechnology , vol.12 , Issue.4 , pp. 371-375
    • Lehmann, M.1    Wyss, M.2
  • 37
    • 0034607796 scopus 로고    scopus 로고
    • Mutational analysis of the substrate binding/catalytic domains of human M form and P form phenol sulfotransferases
    • DOI 10.1074/jbc.275.18.13460
    • Liu M.C., Suiko M., and Sakakibara Y. Mutational analysis of the substrate binding/catalytic domains of human M form and P form phenol sulfotransferases J. Biol. Chem. 275 2000 13460 13464 (Pubitemid 30257410)
    • (2000) Journal of Biological Chemistry , vol.275 , Issue.18 , pp. 13460-13464
    • Liu, M.-C.1    Suiko, M.2    Sakakibara, Y.3
  • 39
    • 0004242371 scopus 로고    scopus 로고
    • 2nd edit. Wiley New York, NY
    • Copeland R.A. Enzymes 2nd edit. 2000 Wiley New York, NY
    • (2000) Enzymes
    • Copeland, R.A.1
  • 40
    • 33845864966 scopus 로고    scopus 로고
    • Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
    • DOI 10.1038/nature05385, PII NATURE05385
    • Bershtein S., Segal M., Bekerman R., Tokuriki N., and Tawfik D.S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein Nature 444 2006 929 932 (Pubitemid 46025005)
    • (2006) Nature , vol.444 , Issue.7121 , pp. 929-932
    • Bershtein, S.1    Segal, M.2    Bekerman, R.3    Tokuriki, N.4    Tawfik, D.S.5
  • 41
    • 0033963277 scopus 로고    scopus 로고
    • From DNA sequence to improved functionality: Using protein sequence comparisons to rapidly design a thermostable consensus phytase
    • Lehmann M., Kostrewa D., Wyss M., Brugger R., D'Arcy A., Pasamontes L., and van Loon A.P. From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase Protein Eng. 13 2000 49 57 (Pubitemid 30105578)
    • (2000) Protein Engineering , vol.13 , Issue.1 , pp. 49-57
    • Lehmann, M.1    Kostrewa, D.2    Wyss, M.3    Brugger, R.4    D'Arcy, A.5    Pasamontes, L.6    Van Loon, A.P.G.M.7
  • 42
    • 67650507983 scopus 로고    scopus 로고
    • Directed evolution of serum paraoxonase PON3 by family shuffling and ancestor/consensus mutagenesis, and its biochemical characterization
    • Khersonsky O., Rosenblat M., Toker L., Yacobson S., Hugenmatter A., and Silman I. Directed evolution of serum paraoxonase PON3 by family shuffling and ancestor/consensus mutagenesis, and its biochemical characterization Biochemistry 48 2009 6644 6654
    • (2009) Biochemistry , vol.48 , pp. 6644-6654
    • Khersonsky, O.1    Rosenblat, M.2    Toker, L.3    Yacobson, S.4    Hugenmatter, A.5    Silman, I.6
  • 44
    • 0038716425 scopus 로고    scopus 로고
    • Interpretive proteomics - Finding biological meaning in genome and proteome databases
    • DOI 10.1016/S0065-2571(02)00024-9
    • Benner S.A. Interpretive proteomics-finding biological meaning in genome and proteome databases Adv. Enzyme Regul. 43 2003 271 359 (Pubitemid 36872836)
    • (2003) Advances in Enzyme Regulation , vol.43 , pp. 271-359
    • Benner, S.A.1
  • 45
    • 79953326533 scopus 로고    scopus 로고
    • Exploiting models of molecular evolution to efficiently direct protein engineering
    • Cole M.F., and Gaucher E.A. Exploiting models of molecular evolution to efficiently direct protein engineering J. Mol. Evol. 72 2010 193 203
    • (2010) J. Mol. Evol. , vol.72 , pp. 193-203
    • Cole, M.F.1    Gaucher, E.A.2
  • 48
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • DOI 10.1093/bioinformatics/btl158
    • Li W., and Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 2006 1658 1659 (Pubitemid 43985301)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 49
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • DOI 10.1126/science.1158395
    • Loytynoja A., and Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis Science 320 2008 1632 1635 (Pubitemid 351931252)
    • (2008) Science , vol.320 , Issue.5883 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 50
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • DOI 10.1093/molbev/msn067
    • Le S.Q., and Gascuel O. An improved general amino acid replacement matrix Mol. Biol. Evol. 25 2008 1307 1320 (Pubitemid 351882003)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.7 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 51
    • 0242578620 scopus 로고    scopus 로고
    • A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
    • DOI 10.1080/10635150390235520
    • Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 52 2003 696 704 (Pubitemid 37365050)
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 52
    • 0034117082 scopus 로고    scopus 로고
    • A fast algorithm for joint reconstruction of ancestral amino acid sequences
    • Pupko T., Pe'er I., Shamir R., and Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences Mol. Biol. Evol. 17 2000 890 896 (Pubitemid 30346548)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.6 , pp. 890-896
    • Pupko, T.1    Pe'er, I.2    Shamir, R.3    Graur, D.4
  • 53
    • 33747829924 scopus 로고    scopus 로고
    • Expresso: Automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
    • Armougom F., Moretti S., Poirot O., Audic S., Dumas P., and Schaeli B. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee Nucleic Acids Res. 34 2006 W604 W608
    • (2006) Nucleic Acids Res. , vol.34
    • Armougom, F.1    Moretti, S.2    Poirot, O.3    Audic, S.4    Dumas, P.5    Schaeli, B.6
  • 54
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry land cell constants
    • Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry land cell constants J. Appl. Crystallogr. 26 1993 795 800
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 55
    • 0028103275 scopus 로고
    • The CCP4 Suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project Number 4 The CCP4 Suite: programs for protein crystallography Acta Crystallogr., Sect. D.: Biol. Crystallogr. 50 1994 760 763
    • (1994) Acta Crystallogr., Sect. D.: Biol. Crystallogr. , vol.50 , pp. 760-763


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.