Programming cells by multiplex genome engineering and accelerated evolution

Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)

Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554–557 (2005)

Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457–469 (2003)

Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990)

Crameri, A., Raillard, S.-A., Bermudez, E., Stemmer, W. P. & C DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288–291 (1998)

Joo, H., Lin, Z. & Arnold, F. H. Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature 399, 670–673 (1999)

Zhang, Y. X. et al. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415, 644–646 (2002)

Pfleger, B. F., Pitera, D. J., Smolke, C. D. & Keasling, J. D. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nature Biotechnol. 24, 1027–1032 (2006)

Cadwell, R. C. & Joyce, G. F. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2, 28–33 (1992)

Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005)

Zhang, Y., Buchholz, F., Muyrers, J. P. & Stewart, A. F. A new logic for DNA engineering using recombination in Escherichia coli . Nature Genet. 20, 123–128 (1998)

Costantino, N. & Court, D. L. Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants. Proc. Natl Acad. Sci. USA 100, 15748–15753 (2003)

Sharan, S. K., Thomason, L. C., Kuznetsov, S. G. & Court, D. L. Recombineering: a homologous recombination-based method of genetic engineering. Nature Protocols 4, 206–223 (2009)

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)

Markham, N. R. & Zuker, M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33, W577–W581 (2005)

Jin, Y. S. & Stephanopoulos, G. Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli . Metab. Eng. 9, 337–347 (2007)

Kang, M. J. et al. Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method. Biotechnol. Bioeng. 91, 636–642 (2005)

Chen, H., Bjerknes, M., Kumar, R. & Jay, E. Determination of the optimal aligned spacing between the Shine – Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res. 22, 4953–4957 (1994)

Alper, H., Jin, Y. S., Moxley, J. F. & Stephanopoulos, G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli . Metab. Eng. 7, 155–164 (2005)

Alper, H., Miyaoku, K. & Stephanopoulos, G. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nature Biotechnol. 23, 612–616 (2005)

Farmer, W. R. & Liao, J. C. Precursor balancing for metabolic engineering of lycopene production in Escherichia coli . Biotechnol. Prog. 17, 57–61 (2001)

Kim, S. W. & Keasling, J. D. Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. Biotechnol. Bioeng. 72, 408–415 (2001)

Yuan, L. Z., Rouviere, P. E., Larossa, R. A. & Suh, W. Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli . Metab. Eng. 8, 79–90 (2006)

Khosla, C. & Keasling, J. D. Metabolic engineering for drug discovery and development. Nature Rev. Drug Discov. 2, 1019–1025 (2003)

Cropp, T. A. & Schultz, P. G. An expanding genetic code. Trends Genet. 20, 625–630 (2004)

Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2008)

Metzgar, D. et al. Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Res. 32, 5780–5790 (2004)

Nakayama, M. & Ohara, O. Improvement of recombination efficiency by mutation of Red proteins. Biotechniques 38, 917–924 (2005)

Datta, S., Costantino, N., Zhou, X. & Court, D. L. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc. Natl Acad. Sci. USA 105, 1626–1631 (2008)

Tian, J. et al. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432, 1050–1054 (2004)

Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli . Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000)

Cunningham, F. X., Sun, Z., Chamovitz, D., Hirschberg, J. & Gantt, E. Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell 6, 1107–1121 (1994)