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Volumn 11, Issue 5, 2014, Pages 521-526

Programming biological operating systems: Genome design, assembly and activation

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

EID: 84899698094     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2894     Document Type: Review
Times cited : (52)

References (49)
  • 1
    • 77953584054 scopus 로고    scopus 로고
    • Creation of a bacterial cell controlled by a chemically synthesized genome
    • Gibson, D.G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56 (2010).
    • (2010) Science , vol.329 , pp. 52-56
    • Gibson, D.G.1
  • 2
    • 84858374402 scopus 로고    scopus 로고
    • Oligonucleotide assembly in yeast to produce synthetic DNA fragments
    • Gibson, D.G. Oligonucleotide assembly in yeast to produce synthetic DNA fragments. Methods Mol. Biol. 852, 11-21 (2012).
    • (2012) Methods Mol. Biol. , vol.852 , pp. 11-21
    • Gibson, D.G.1
  • 3
    • 79957471219 scopus 로고    scopus 로고
    • Enzymatic assembly of overlapping DNA fragments
    • Gibson, D.G. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 498, 349-361 (2011).
    • (2011) Methods Enzymol. , vol.498 , pp. 349-361
    • Gibson, D.G.1
  • 4
    • 84857658214 scopus 로고    scopus 로고
    • Gene and genome construction in yeast
    • Gibson, D.G. Gene and genome construction in yeast. Curr. Protoc. Mol. Biol. 94, 3.22 (2011).
    • (2011) Curr. Protoc. Mol. Biol. , vol.94 , pp. 322
    • Gibson, D.G.1
  • 5
    • 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. 37, 6984-6990 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6984-6990
    • Gibson, D.G.1
  • 6
    • 39449112551 scopus 로고    scopus 로고
    • Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome
    • Gibson, D.G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215-1220 (2008).
    • (2008) Science , vol.319 , pp. 1215-1220
    • Gibson, D.G.1
  • 7
    • 58149510036 scopus 로고    scopus 로고
    • One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome
    • Gibson, D.G. et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. USA 105, 20404-20409 (2008).
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20404-20409
    • Gibson, D.G.1
  • 9
    • 67349270900 scopus 로고    scopus 로고
    • Enzymatic assembly of DNA molecules up to several hundred kilobases
    • Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 343-345
    • Gibson, D.G.1
  • 10
    • 77952529484 scopus 로고    scopus 로고
    • Cloning whole bacterial genomes in yeast
    • Benders, G.A. et al. Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38, 2558-2569 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2558-2569
    • Benders, G.A.1
  • 11
    • 34547755976 scopus 로고    scopus 로고
    • Genome transplantation in bacteria: Changing one species to another
    • Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632-638 (2007).
    • (2007) Science , vol.317 , pp. 632-638
    • Lartigue, C.1
  • 12
    • 70349324305 scopus 로고    scopus 로고
    • Creating bacterial strains from genomes that have been cloned and engineered in yeast
    • Lartigue, C. et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693-1696 (2009).
    • (2009) Science , vol.325 , pp. 1693-1696
    • Lartigue, C.1
  • 14
    • 84865283376 scopus 로고    scopus 로고
    • DNA synthesis, assembly and applications in synthetic biology
    • Ma, S., Tang, N. & Tian, J. DNA synthesis, assembly and applications in synthetic biology. Curr. Opin. Chem. Biol. 16, 260-267 (2012).
    • (2012) Curr. Opin. Chem. Biol. , vol.16 , pp. 260-267
    • Ma, S.1    Tang, N.2    Tian, J.3
  • 15
    • 79951501719 scopus 로고    scopus 로고
    • DNA assembly for synthetic biology: From parts to pathways and beyond
    • Ellis, T., Adie, T. & Baldwin, G.S. DNA assembly for synthetic biology: from parts to pathways and beyond. Integr. Biol. (Camb.) 3, 109-118 (2011).
    • (2011) Integr. Biol. (Camb.) , vol.3 , pp. 109-118
    • Ellis, T.1    Adie, T.2    Baldwin, G.S.3
  • 16
    • 27644564234 scopus 로고    scopus 로고
    • Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome
    • Itaya, M., Tsuge, K., Koizumi, M. & Fujita, K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc. Natl. Acad. Sci. USA 102, 15971-15976 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15971-15976
    • Itaya, M.1    Tsuge, K.2    Koizumi, M.3    Fujita, K.4
  • 17
    • 41349113996 scopus 로고    scopus 로고
    • Constructing large DNA segments by iterative clone recombination
    • Smailus, D.E., Warren, R.L. & Holt, R.A. Constructing large DNA segments by iterative clone recombination. Syst. Synth. Biol. 1, 139-144 (2007).
    • (2007) Syst. Synth. Biol. , vol.1 , pp. 139-144
    • Smailus, D.E.1    Warren, R.L.2    Holt, R.A.3
  • 18
    • 0023615620 scopus 로고
    • Plasmid construction by homologous recombination in yeast
    • Ma, H., Kunes, S., Schatz, P.J. & Botstein, D. Plasmid construction by homologous recombination in yeast. Gene 58, 201-216 (1987).
    • (1987) Gene , vol.58 , pp. 201-216
    • Ma, H.1    Kunes, S.2    Schatz, P.J.3    Botstein, D.4
  • 19
    • 84868275346 scopus 로고    scopus 로고
    • Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
    • Tagwerker, C. et al. Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Nucleic Acids Res. 40, 10375-10383 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10375-10383
    • Tagwerker, C.1
  • 20
    • 84868247020 scopus 로고    scopus 로고
    • Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid
    • Karas, B.J., Tagwerker, C., Yonemoto, I.T., Hutchison, C.A. III. & Smith, H.O. Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synth. Biol. 1, 22-28 (2012).
    • (2012) ACS Synth. Biol. , vol.1 , pp. 22-28
    • Karas, B.J.1    Tagwerker, C.2    Yonemoto, I.T.3    Hutchison III, C.A.4    Smith, H.O.5
  • 21
    • 84877582862 scopus 로고    scopus 로고
    • Direct transfer of whole genomes from bacteria to yeast
    • Karas, B.J. et al. Direct transfer of whole genomes from bacteria to yeast. Nat. Methods 10, 410-412 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 410-412
    • Karas, B.J.1
  • 22
    • 0021153574 scopus 로고
    • Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis
    • Schwartz, D.C. & Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67-75 (1984).
    • (1984) Cell , vol.37 , pp. 67-75
    • Schwartz, D.C.1    Cantor, C.R.2
  • 23
    • 84868238000 scopus 로고    scopus 로고
    • Assembly of large, high G+C bacterial DNA fragments in yeast
    • Noskov, V.N. et al. Assembly of large, high G+C bacterial DNA fragments in yeast. ACS Synth. Biol. 1, 267-273 (2012).
    • (2012) ACS Synth. Biol. , vol.1 , pp. 267-273
    • Noskov, V.N.1
  • 24
    • 40649092126 scopus 로고    scopus 로고
    • Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae
    • Kouprina, N. & Larionov, V. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 3, 371-377 (2008).
    • (2008) Nat. Protoc. , vol.3 , pp. 371-377
    • Kouprina, N.1    Larionov, V.2
  • 25
    • 0033370108 scopus 로고    scopus 로고
    • Eukaryotic transcriptional control
    • Kornberg, R.D. Eukaryotic transcriptional control. Trends Cell Biol. 9, M46-M49 (1999).
    • (1999) Trends Cell Biol. , vol.9
    • Kornberg, R.D.1
  • 26
    • 0033061571 scopus 로고    scopus 로고
    • Initiation of translation in prokaryotes and eukaryotes
    • Kozak, M. Initiation of translation in prokaryotes and eukaryotes. Gene 234, 187-208 (1999).
    • (1999) Gene , vol.234 , pp. 187-208
    • Kozak, M.1
  • 27
    • 0032826310 scopus 로고    scopus 로고
    • Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine
    • Marschall, P., Malik, N. & Larin, Z. Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine. Gene Ther. 6, 1634-1637 (1999).
    • (1999) Gene Ther. , vol.6 , pp. 1634-1637
    • Marschall, P.1    Malik, N.2    Larin, Z.3
  • 28
  • 30
    • 68949161807 scopus 로고    scopus 로고
    • Programming cells by multiplex genome engineering and accelerated evolution
    • Wang, H.H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894-898 (2009).
    • (2009) Nature , vol.460 , pp. 894-898
    • Wang, H.H.1
  • 31
    • 79960502359 scopus 로고    scopus 로고
    • Precise manipulation of chromosomes in vivo enables genome-wide codon replacement
    • Isaacs, F.J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348-353 (2011).
    • (2011) Science , vol.333 , pp. 348-353
    • Isaacs, F.J.1
  • 32
    • 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. USA 98, 6742-6746 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6742-6746
    • Ellis, H.M.1    Yu, D.2    Ditizio, T.3    Court, D.L.4
  • 33
    • 80053132391 scopus 로고    scopus 로고
    • Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
    • Dymond, J.S. et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471-476 (2011).
    • (2011) Nature , vol.477 , pp. 471-476
    • Dymond, J.S.1
  • 34
    • 84879264708 scopus 로고    scopus 로고
    • ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
    • Gaj, T., Gersbach, C.A. & Barbas, C.F. III. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31, 397-405 (2013).
    • (2013) Trends Biotechnol. , vol.31 , pp. 397-405
    • Gaj, T.1    Gersbach, C.A.2    Barbas III, C.F.3
  • 35
    • 0037478841 scopus 로고    scopus 로고
    • The first half-century of nuclear transplantation
    • Gurdon, J.B. & Byrne, J.A. The first half-century of nuclear transplantation. Proc. Natl. Acad. Sci. USA 100, 8048-8052 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 8048-8052
    • Gurdon, J.B.1    Byrne, J.A.2
  • 37
    • 33846108255 scopus 로고    scopus 로고
    • Towards synthesis of a minimal cell
    • Forster, A.C. & Church, G.M. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2, 45 (2006).
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 45
    • Forster, A.C.1    Church, G.M.2
  • 38
    • 33845965687 scopus 로고    scopus 로고
    • Synthetic biology projects in vitro
    • Forster, A.C. & Church, G.M. Synthetic biology projects in vitro. Genome Res. 17, 1-6 (2007).
    • (2007) Genome Res. , vol.17 , pp. 1-6
    • Forster, A.C.1    Church, G.M.2
  • 39
    • 77957345108 scopus 로고    scopus 로고
    • Update on designing and building minimal cells
    • Jewett, M.C. & Forster, A.C. Update on designing and building minimal cells. Curr. Opin. Biotechnol. 21, 697-703 (2010).
    • (2010) Curr. Opin. Biotechnol. , vol.21 , pp. 697-703
    • Jewett, M.C.1    Forster, A.C.2
  • 41
    • 28544433105 scopus 로고    scopus 로고
    • Refactoring bacteriophage T7
    • Chan, L.Y., Kosuri, S. & Endy, D. Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005.0018 (2005).
    • (2005) Mol. Syst. Biol. , vol.1 , Issue.2005 , pp. 0018
    • Chan, L.Y.1    Kosuri, S.2    Endy, D.3
  • 42
    • 84870715721 scopus 로고    scopus 로고
    • A fully decompressed synthetic bacteriophage oX174 genome assembled and archived in yeast
    • Jaschke, P.R., Lieberman, E.K., Rodriguez, J., Sierra, A. & Endy, D. A fully decompressed synthetic bacteriophage oX174 genome assembled and archived in yeast. Virology 434, 278-284 (2012).
    • (2012) Virology , vol.434 , pp. 278-284
    • Jaschke, P.R.1    Lieberman, E.K.2    Rodriguez, J.3    Sierra, A.4    Endy, D.5
  • 43
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser, C.M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403 (1995).
    • (1995) Science , vol.270 , pp. 397-403
    • Fraser, C.M.1
  • 44
    • 84864258618 scopus 로고    scopus 로고
    • A whole-cell computational model predicts phenotype from genotype
    • Karr, J.R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389-401 (2012).
    • (2012) Cell , vol.150 , pp. 389-401
    • Karr, J.R.1
  • 45
    • 84878279327 scopus 로고    scopus 로고
    • Synthetic generation of influenza vaccine viruses for rapid response to pandemics
    • Dormitzer, P.R. et al. Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Sci. Transl. Med. 5, 185ra68 (2013).
    • (2013) Sci. Transl. Med. , vol.5
    • Dormitzer, P.R.1
  • 46
    • 84886824017 scopus 로고    scopus 로고
    • Rapid, modular and reliable construction of complex mammalian gene circuits
    • Guye, P., Li, Y., Wroblewska, L., Duportet, X. & Weiss, R. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res. 41, e156 (2013).
    • (2013) Nucleic Acids Res. , vol.41
    • Guye, P.1    Li, Y.2    Wroblewska, L.3    Duportet, X.4    Weiss, R.5
  • 47
    • 84860803588 scopus 로고    scopus 로고
    • Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
    • Temme, K., Zhao, D. & Voigt, C.A. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc. Natl. Acad. Sci. USA 109, 7085-7090 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 7085-7090
    • Temme, K.1    Zhao, D.2    Voigt, C.A.3
  • 48
    • 84859355242 scopus 로고    scopus 로고
    • An exogenous chloroplast genome for complex sequence manipulation in algae
    • O'Neill, B.M. et al. An exogenous chloroplast genome for complex sequence manipulation in algae. Nucleic Acids Res. 40, 2782-2792 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 2782-2792
    • O'Neill, B.M.1
  • 49
    • 0347364647 scopus 로고    scopus 로고
    • Generating a synthetic genome by whole genome assembly: PhiX174 bacteriophage from synthetic oligonucleotides
    • Smith, H.O., Hutchison, C.A. III., Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 100, 15440-15445 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15440-15445
    • Smith, H.O.1    Hutchison III, C.A.2    Pfannkoch, C.3    Venter, J.C.4


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