메뉴 건너뛰기




Volumn 22, Issue 4, 2011, Pages 576-583

Engineering genomes in multiplex

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX TRAITS; FUNCTIONAL CHANGES; GENOME ENGINEERING; IN-VIVO; METABOLIC ENGINEERING; RECOMBINEERING;

EID: 79960935587     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.04.019     Document Type: Review
Times cited : (23)

References (74)
  • 3
  • 4
    • 0035793858 scopus 로고    scopus 로고
    • Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli
    • Pfeifer B.A., Admiraal S.J., Gramajo H., Cane D.E., Khosla C. Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 2001, 291:1790-1792.
    • (2001) Science , vol.291 , pp. 1790-1792
    • Pfeifer, B.A.1    Admiraal, S.J.2    Gramajo, H.3    Cane, D.E.4    Khosla, C.5
  • 8
    • 71849086611 scopus 로고    scopus 로고
    • Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde
    • Atsumi S., Higashide W., Liao J.C. Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 2009, 27:U1142-U1177.
    • (2009) Nat Biotechnol , vol.27
    • Atsumi, S.1    Higashide, W.2    Liao, J.C.3
  • 9
    • 33845442201 scopus 로고    scopus 로고
    • Engineering yeast transcription machinery for improved ethanol tolerance and production
    • Alper H., Moxley J., Nevoigt E., Fink G.R., Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 2006, 314:1565-1568.
    • (2006) Science , vol.314 , pp. 1565-1568
    • Alper, H.1    Moxley, J.2    Nevoigt, E.3    Fink, G.R.4    Stephanopoulos, G.5
  • 10
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:U13-U86.
    • (2008) Nature , vol.451
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 13
    • 38949178112 scopus 로고    scopus 로고
    • Engineering complex phenotypes in industrial strains
    • Patnaik R. Engineering complex phenotypes in industrial strains. Biotechnol Prog 2008, 24:38-47.
    • (2008) Biotechnol Prog , vol.24 , pp. 38-47
    • Patnaik, R.1
  • 14
    • 68049106179 scopus 로고    scopus 로고
    • Directed evolution drives the next generation of biocatalysts
    • Turner N.J. Directed evolution drives the next generation of biocatalysts. Nat Chem Biol 2009, 5:568-574.
    • (2009) Nat Chem Biol , vol.5 , pp. 568-574
    • Turner, N.J.1
  • 17
    • 73349139923 scopus 로고    scopus 로고
    • Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
    • Gibson D.G. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res 2009, 37:6984-6990.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6984-6990
    • Gibson, D.G.1
  • 19
    • 0031664853 scopus 로고    scopus 로고
    • A new logic for DNA engineering using recombination in Escherichia coli
    • Zhang Y.M., Buchholz F., Muyrers J.P.P., Stewart A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 1998, 20:123-128.
    • (1998) Nat Genet , vol.20 , pp. 123-128
    • Zhang, Y.M.1    Buchholz, F.2    Muyrers, J.P.P.3    Stewart, A.F.4
  • 20
    • 0031924072 scopus 로고    scopus 로고
    • Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli
    • Murphy K.C. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J Bacteriol 1998, 180:2063-2071.
    • (1998) J Bacteriol , vol.180 , pp. 2063-2071
    • Murphy, K.C.1
  • 22
    • 0035810938 scopus 로고    scopus 로고
    • High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
    • Ellis H.M., Yu D.G., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 2001, 98:6742-6746.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 6742-6746
    • Ellis, H.M.1    Yu, D.G.2    DiTizio, T.3    Court, D.L.4
  • 23
    • 40349101854 scopus 로고    scopus 로고
    • Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages
    • Datta S., Costantino N., Zhou X.M., Court D.L. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci U S A 2008, 105:1626-1631.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 1626-1631
    • Datta, S.1    Costantino, N.2    Zhou, X.M.3    Court, D.L.4
  • 24
    • 39149125127 scopus 로고    scopus 로고
    • Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space
    • Fox R.J., Huisman G.W. Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol 2008, 26:132-138.
    • (2008) Trends Biotechnol , vol.26 , pp. 132-138
    • Fox, R.J.1    Huisman, G.W.2
  • 25
    • 70450242805 scopus 로고    scopus 로고
    • Exploring protein fitness landscapes by directed evolution
    • Romero P.A., Arnold F.H. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 2009, 10:866-876.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 866-876
    • Romero, P.A.1    Arnold, F.H.2
  • 27
    • 3042681604 scopus 로고    scopus 로고
    • Protein tolerance to random amino acid change
    • Guo H.H., Choe J., Loeb L.A. Protein tolerance to random amino acid change. Proc Natl Acad Sci U S A 2004, 101:9205-9210.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 9205-9210
    • Guo, H.H.1    Choe, J.2    Loeb, L.A.3
  • 30
    • 65249177164 scopus 로고    scopus 로고
    • Directed enzyme evolution: climbing fitness peaks one amino acid at a time
    • Tracewell C.A., Arnold F.H. Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr Opin Chem Biol 2009, 13:3-9.
    • (2009) Curr Opin Chem Biol , vol.13 , pp. 3-9
    • Tracewell, C.A.1    Arnold, F.H.2
  • 31
    • 77953022686 scopus 로고    scopus 로고
    • Quantitative analysis and engineering of fatty acid biosynthesis in E. coli
    • Liu T.G., Vora H., Khosla C. Quantitative analysis and engineering of fatty acid biosynthesis in E. coli. Metab Eng 2010, 12:378-386.
    • (2010) Metab Eng , vol.12 , pp. 378-386
    • Liu, T.G.1    Vora, H.2    Khosla, C.3
  • 32
    • 0035957360 scopus 로고    scopus 로고
    • Computational method to reduce the search space for directed protein evolution
    • Voigt C.A., Mayo S.L., Arnold F.H., Wang Z.G. Computational method to reduce the search space for directed protein evolution. Proc Natl Acad Sci U S A 2001, 98:3778-3783.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 3778-3783
    • Voigt, C.A.1    Mayo, S.L.2    Arnold, F.H.3    Wang, Z.G.4
  • 33
    • 0026774225 scopus 로고
    • An algorithm for protein engineering-simulations of recursive ensemble mutagenesis
    • Arkin A.P., Youvan D.C. An algorithm for protein engineering-simulations of recursive ensemble mutagenesis. Proc Natl Acad Sci U S A 1992, 89:7811-7815.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 7811-7815
    • Arkin, A.P.1    Youvan, D.C.2
  • 34
    • 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 2010, 21:734-743.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 734-743
    • Lutz, S.1
  • 35
    • 33845948161 scopus 로고    scopus 로고
    • SCALEs: multiscale analysis of library enrichment
    • Lynch M.D., Warnecke T., Gill R.T. SCALEs: multiscale analysis of library enrichment. Nat Methods 2007, 4:87-93.
    • (2007) Nat Methods , vol.4 , pp. 87-93
    • Lynch, M.D.1    Warnecke, T.2    Gill, R.T.3
  • 37
    • 67650685558 scopus 로고    scopus 로고
    • An integrated network approach identifies the isobutanol response network of Escherichia coli
    • Brynildsen M.P., Liao J.C. An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol 2009, 5.
    • (2009) Mol Syst Biol , vol.5
    • Brynildsen, M.P.1    Liao, J.C.2
  • 38
  • 39
    • 34248196414 scopus 로고    scopus 로고
    • Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostfidium acetobutylicum
    • Borden J.R., Papoutsakis E.T. Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostfidium acetobutylicum. Appl Environ Microbiol 2007, 73:3061-3068.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 3061-3068
    • Borden, J.R.1    Papoutsakis, E.T.2
  • 43
    • 33646568438 scopus 로고    scopus 로고
    • Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research
    • Kitagawa M., Ara T., Arifuzzaman M., Ioka-Nakamichi T., Inamoto E., Toyonaga H., Mori H. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 2005, 12:291-299.
    • (2005) DNA Res , vol.12 , pp. 291-299
    • Kitagawa, M.1    Ara, T.2    Arifuzzaman, M.3    Ioka-Nakamichi, T.4    Inamoto, E.5    Toyonaga, H.6    Mori, H.7
  • 45
    • 66749161542 scopus 로고    scopus 로고
    • Genomics enabled approaches in strain engineering
    • Warner J.R., Patnaik R., Gill R.T. Genomics enabled approaches in strain engineering. Curr Opin Microbiol 2009, 12:223-230.
    • (2009) Curr Opin Microbiol , vol.12 , pp. 223-230
    • Warner, J.R.1    Patnaik, R.2    Gill, R.T.3
  • 46
    • 43049136820 scopus 로고    scopus 로고
    • Combinatorial engineering of microbes for optimizing cellular phenotype
    • Santos C.N.S., Stephanopoulos G. Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 2008, 12:168-176.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 168-176
    • Santos, C.N.S.1    Stephanopoulos, G.2
  • 48
    • 77952530236 scopus 로고    scopus 로고
    • Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process
    • LeProust E.M., Peck B.J., Spirin K., McCuen H.B., Moore B., Namsaraev E., Caruthers M.H. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 2010, 38:2522-2540.
    • (2010) Nucleic Acids Res , vol.38 , pp. 2522-2540
    • LeProust, E.M.1    Peck, B.J.2    Spirin, K.3    McCuen, H.B.4    Moore, B.5    Namsaraev, E.6    Caruthers, M.H.7
  • 49
    • 79952002951 scopus 로고    scopus 로고
    • Probing cellular processes with oligo-mediated recombination; using knowledge gained to optimize recombineering
    • Sawitzke J.A., Costantino N., Li X.T., Thomason L.C., Bubunenko M., Court C., Court D.L. Probing cellular processes with oligo-mediated recombination; using knowledge gained to optimize recombineering. J Mol Biol 2011, 407:45-59.
    • (2011) J Mol Biol , vol.407 , pp. 45-59
    • Sawitzke, J.A.1    Costantino, N.2    Li, X.T.3    Thomason, L.C.4    Bubunenko, M.5    Court, C.6    Court, D.L.7
  • 50
    • 0035810938 scopus 로고    scopus 로고
    • High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
    • Ellis H.M., Yu D., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 2001, 98:6742-6746.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 6742-6746
    • Ellis, H.M.1    Yu, D.2    DiTizio, T.3    Court, D.L.4
  • 51
    • 78951480559 scopus 로고    scopus 로고
    • Lambda Red recombineering in Escherichia coli occurs through a fully single-stranded intermediate
    • Mosberg J.A., Lajoie M.J., Church G.M. Lambda Red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 2010, 186:U759-U791.
    • (2010) Genetics , vol.186
    • Mosberg, J.A.1    Lajoie, M.J.2    Church, G.M.3
  • 57
    • 63249121217 scopus 로고    scopus 로고
    • Application of 'next-generation' sequencing technologies to microbial genetics
    • MacLean D., Jones J.D.G., Studholme D.J. Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 2009, 7:287-296.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 287-296
    • MacLean, D.1    Jones, J.D.G.2    Studholme, D.J.3
  • 58
    • 77951925139 scopus 로고    scopus 로고
    • Synthetic biology: tools to design, build, and optimize cellular processes
    • Young E., Alper H. Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010, 130-781.
    • (2010) J Biomed Biotechnol , pp. 130-781
    • Young, E.1    Alper, H.2
  • 59
    • 33847083318 scopus 로고    scopus 로고
    • Global transcription machinery engineering: a new approach for improving cellular phenotype
    • Alper H., Stephanopoulos G. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 2007, 9:258-267.
    • (2007) Metab Eng , vol.9 , pp. 258-267
    • Alper, H.1    Stephanopoulos, G.2
  • 60
    • 65549147541 scopus 로고    scopus 로고
    • Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes
    • Klein-Marcuschamer D., Santos C.N.S., Yu H.M., Stephanopoulos G. Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microbiol 2009, 75:2705-2711.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 2705-2711
    • Klein-Marcuschamer, D.1    Santos, C.N.S.2    Yu, H.M.3    Stephanopoulos, G.4
  • 61
    • 40649093316 scopus 로고    scopus 로고
    • Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains
    • Klein-Marcuschamer D., Stephanopoulos G. Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci U S A 2008, 105:2319-2324.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 2319-2324
    • Klein-Marcuschamer, D.1    Stephanopoulos, G.2
  • 62
    • 77955955069 scopus 로고    scopus 로고
    • Method for designing and optimizing random-search libraries for strain improvement
    • Klein-Marcuschamer D., Stephanopoulos G. Method for designing and optimizing random-search libraries for strain improvement. Appl Environ Microbiol 2010, 76:5541-5546.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 5541-5546
    • Klein-Marcuschamer, D.1    Stephanopoulos, G.2
  • 63
    • 79251567415 scopus 로고    scopus 로고
    • Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli
    • Chen T., Wang J., Yang R., Li J., Lin M., Lin Z. Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. Plos ONE 2011, 6:e16228.
    • (2011) Plos ONE , vol.6
    • Chen, T.1    Wang, J.2    Yang, R.3    Li, J.4    Lin, M.5    Lin, Z.6
  • 65
    • 79960959790 scopus 로고    scopus 로고
    • Modified enzymes and methods for making same. 1988:United States patent US 4,760,025.
    • Estell DA, Wells JA: Modified enzymes and methods for making same. 1988:United States patent US 4,760,025.
    • Estell, D.A.1    Wells, J.A.2
  • 66
    • 57049153236 scopus 로고    scopus 로고
    • Parallel mapping of genotypes to phenotypes contributing to overall biological fitness
    • Gall S., Lynch M.D., Sandoval N.R., Gill R.T. Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metab Eng 2008, 10:382-393.
    • (2008) Metab Eng , vol.10 , pp. 382-393
    • Gall, S.1    Lynch, M.D.2    Sandoval, N.R.3    Gill, R.T.4
  • 67
    • 55549116661 scopus 로고    scopus 로고
    • Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene
    • Anthony J.R., Anthony L.C., Nowroozi F., Kwon G., Newman J.D., Keasling J.D. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab Eng 2009, 11:13-19.
    • (2009) Metab Eng , vol.11 , pp. 13-19
    • Anthony, J.R.1    Anthony, L.C.2    Nowroozi, F.3    Kwon, G.4    Newman, J.D.5    Keasling, J.D.6
  • 69
    • 33747078696 scopus 로고    scopus 로고
    • Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
    • Pfleger B.F., Pitera D.J., D Smolke C., Keasling J.D. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 2006, 24:1027-1032.
    • (2006) Nat Biotechnol , vol.24 , pp. 1027-1032
    • Pfleger, B.F.1    Pitera, D.J.2    D Smolke, C.3    Keasling, J.D.4
  • 70
    • 70349952276 scopus 로고    scopus 로고
    • Genome shuffling: progress and applications for phenotype improvement
    • Gong J.X., Zheng H.J., Wu Z.J., Chen T., Zhao X.M. Genome shuffling: progress and applications for phenotype improvement. Biotechnol Adv 2009, 27:996-1005.
    • (2009) Biotechnol Adv , vol.27 , pp. 996-1005
    • Gong, J.X.1    Zheng, H.J.2    Wu, Z.J.3    Chen, T.4    Zhao, X.M.5
  • 71
    • 33748953866 scopus 로고    scopus 로고
    • Genetic parts to program bacteria
    • Voigt C.A. Genetic parts to program bacteria. Curr Opin Biotechnol 2006, 17:548-557.
    • (2006) Curr Opin Biotechnol , vol.17 , pp. 548-557
    • Voigt, C.A.1
  • 73
    • 71849110893 scopus 로고    scopus 로고
    • Next-generation synthetic gene networks
    • Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat Biotechnol 2009, 27:1139-1150.
    • (2009) Nat Biotechnol , vol.27 , pp. 1139-1150
    • Lu, T.K.1    Khalil, A.S.2    Collins, J.J.3
  • 74
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding, and selection in evolution
    • Wright S. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proc Sixth Intl Congr of Genet 1932, 1:356-366.
    • (1932) Proc Sixth Intl Congr of Genet , vol.1 , pp. 356-366
    • Wright, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.