On the road to synthetic life: the minimal cell and genome-scale engineering

References

• Annaluru N, Muller H, Mitchell LA, et al. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science, 344, 55–8
   PubMed Web of Science ®Google Scholar
• Baba T, Ara T, Hasegawa M, et al. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol, 2, 2006–8
   PubMed Web of Science ®Google Scholar
• Benders GA, Noskov VN, Denisova EA, et al. (2010). Cloning whole bacterial genomes in yeast. Nucleic Acids Res, 38, 2558–69
   PubMed Web of Science ®Google Scholar
• Benkovic S, Baker S, Alley M, et al. (2005). Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH. J Med Chem, 48, 7468–76
   PubMed Web of Science ®Google Scholar
• Blake WJ, Chapman BA, Zindal A, et al. (2010). Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Res, 38, 2594–602
   PubMed Web of Science ®Google Scholar
• Bohannon J. (2011). The life hacker. Science, 333, 1236–7
   PubMed Web of Science ®Google Scholar
• Boyle NR, Reynolds TS, Evans R, et al. (2013). Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing. Biotechnol J, 8, 515–22
   PubMed Web of Science ®Google Scholar
• Bution ML, Molina G, Abrahão MR, Pastore GM. (2014). Genetic and metabolic engineering of microorganisms for the development of new flavor compounds from terpenic substrates. Crit Rev Biotechnol. [Epub ahead of print]
   Web of Science ®Google Scholar
• Carr PA, Wang HH, Sterling B, et al. (2012). Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res, 40, e132
   PubMedGoogle Scholar
• Chopra I. (2007). Bacterial RNA polymerase: a promising target for the discovery of new antimicrobial agents. Curr Opin Investig Drugs, 8, 600–7
   PubMedGoogle Scholar
• Chung H, Yao Z, Goehring N, et al. (2009). Rapid beta-lactam-induced lysis requires successful assembly of the cell division machinery. Proc Natl Acad Sci USA, 106, 21872–7
   PubMed Web of Science ®Google Scholar
• Cong L, Ran FA, Cox D, et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819–23
   PubMed Web of Science ®Google Scholar
• Copeland MF, Politz MC, Pfleger BF. (2014). Application of TALEs, CRISPR/Cas and sRNAs as trans-acting regulators in prokaryotes. Curr Opin Biotechnol, 29C, 46–54
   Google Scholar
• De Berardinis V, Vallenet D, Castelli V, et al. (2008). A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol, 4, Article number: 174
   Google Scholar
• Delaye L, González-Domenech CM, Garcillán-Barcia MP, et al. (2011). Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942. BMC Genomics, 12, 25
   PubMedGoogle Scholar
• DiCarlo JE, Conley AJ, Penttilä M, et al. (2013a). Yeast oligo-mediated genome engineering (YOGE). ACS Synth Biol, 2, 741–9
   PubMed Web of Science ®Google Scholar
• DiCarlo JE, Norville JE, Mali P, et al. (2013b). Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res, 41, 4336–43
   PubMed Web of Science ®Google Scholar
• Dolt KS, Lawrence ML, Miller-Hodges E, et al. (2013). A universal vector for high-efficiency multi-fragment recombineering of BACs and knock-in constructs. PLoS One, 8, e62054
   PubMedGoogle Scholar
• Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. (2013). TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol, 23, 390–8
   PubMed Web of Science ®Google Scholar
• Dymond JS, Richardson SM, Coombes CE, et al. (2011). Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 477, 471–6
   PubMed Web of Science ®Google Scholar
• Enyeart PJ, Ellington AD. (2011). Synthetic biology: a yeast for all reasons. Nature, 477, 413–14
   PubMed Web of Science ®Google Scholar
• Fehér T, Burland V, Pósfai G. (2012a). In the fast lane: large-scale bacterial genome engineering. J Biotechnol, 160, 72–9
   PubMed Web of Science ®Google Scholar
• Fehér T, Karcagi I, Blattner FR, Pósfai G. (2012b). Bacteriophage recombineering in the lytic state using the lambda red recombinases. Microb Biotechnol, 5, 466–76
   PubMed Web of Science ®Google Scholar
• Fehér T, Papp B, Pal C, Pósfai G. (2007). Systematic genome reductions: theoretical and experimental approaches. Chem Rev, 107, 3498–513
   PubMed Web of Science ®Google Scholar
• Fineran PC, Dy RL. (2014). Gene regulation by engineered CRISPR-Cas systems. Curr Opin Microbiol, 18C, 83–9
   Google Scholar
• Fischbach M, Walsh C. (2009). Antibiotics for emerging pathogens. Science, 325, 1089–93
   PubMed Web of Science ®Google Scholar
• Forster AC, Church GM. (2006). Towards synthesis of a minimal cell. Mol Syst Biol, 2, Article number: 45
   Google Scholar
• French CT, Lao P, Loraine AE, et al. (2008). Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol, 69, 67–76
   PubMed Web of Science ®Google Scholar
• Gaj T, Gersbach CA, Barbas CF. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31, 397–405
   PubMed Web of Science ®Google Scholar
• Ghosal A, Nielsen PE. (2012). Potent antibacterial antisense peptide-peptide nucleic acid conjugates against Pseudomonas aeruginosa. Nucleic Acid Ther, 22, 323–34
   PubMed Web of Science ®Google Scholar
• Gibson D, Benders G, Andrews-Pfannkoch C, et al. (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science, 319, 1215–20
   PubMed Web of Science ®Google Scholar
• Gibson D, Glass J, Lartigue C, et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52–6
   PubMed Web of Science ®Google Scholar
• Gibson D, Young L, Chuang R, et al. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods, 6, 343–5
   PubMed Web of Science ®Google Scholar
• Glass J, Assad-Garcia N, Alperovich N, et al. (2006). Essential genes of a minimal bacterium. Proc Natl Acad Sci USA, 103, 425–30
   PubMed Web of Science ®Google Scholar
• Glass JI. (2012). Synthetic genomics and the construction of a synthetic bacterial cell. Perspect Biol Med, 55, 473–89
   PubMed Web of Science ®Google Scholar
• Hirokawa Y, Kawano H, Tanaka-Masuda K, et al. (2013). Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli. J Biosci Bioeng, 116, 52–8
   PubMed Web of Science ®Google Scholar
• Hwang WY, Fu Y, Reyon D, et al. (2013). Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol, 31, 227–9
   PubMed Web of Science ®Google Scholar
• Isaacs FJ, Carr PA, Wang HH, et al. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333, 348–53
   PubMed Web of Science ®Google Scholar
• Itaya M. (2010). A synthetic DNA transplant. Nat Biotechnol, 28, 687–9
   PubMed Web of Science ®Google Scholar
• Itaya M, Fujita K, Kuroki A, Tsuge K. (2008). Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat Methods, 5, 41–3
   PubMed Web of Science ®Google Scholar
• Itaya M, Kaneko S. (2010). Integration of stable extracellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method. Nucleic Acids Res, 38, 2551–7
   PubMed Web of Science ®Google Scholar
• Jewett MC, Forster AC. (2010). Update on designing and building minimal cells. Curr Opin Biotechnol, 21, 697–703
   PubMed Web of Science ®Google Scholar
• Juhas M, Davenport PW, Brown JR, et al. (2013). Meeting report: the Cambridge BioDesign TechEvent – synthetic biology, a new “Age of Wonder”? Biotechnol J, 8, 761–3
   Web of Science ®Google Scholar
• Juhas M, Eberl L, Church GM. (2012a). Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol, 30, 601–7
   PubMed Web of Science ®Google Scholar
• Juhas M, Eberl L, Glass JI. (2011). Essence of life: essential genes of minimal genomes. Trends Cell Biol, 21, 562–8
   PubMed Web of Science ®Google Scholar
• Juhas M, Stark M, Von Mering C, et al. (2012b). High confidence prediction of essential genes in burkholderia cenocepacia. PLoS One, 7, e40064
   PubMed Web of Science ®Google Scholar
• Juhas M, van der Meer JR, Gaillard M, et al. (2009). Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev, 33, 376–93
   PubMed Web of Science ®Google Scholar
• Kaneko S, Itaya M. (2010). Designed horizontal transfer of stable giant DNA released from Escherichia coli. J Biochem, 147, 819–22
   PubMed Web of Science ®Google Scholar
• Karas BJ, Jablanovic J, Irvine E, et al. (2014). Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing. Nat Protoc, 9, 743–50
   PubMed Web of Science ®Google Scholar
• Karas BJ, Jablanovic J, Sun L, et al. (2013a). Direct transfer of whole genomes from bacteria to yeast. Nat Methods, 10, 410–12
   PubMed Web of Science ®Google Scholar
• Karas BJ, Molparia B, Jablanovic J, et al. (2013b). Assembly of eukaryotic algal chromosomes in yeast. J Biol Eng, 7, 30
   PubMed Web of Science ®Google Scholar
• Karas BJ, Tagwerker C, Yonemoto IT, et al. (2012). Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synth Biol, 1, 22–8
   PubMed Web of Science ®Google Scholar
• Kato J, Hashimoto M. (2007). Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol, 3, Article number: 132
   Google Scholar
• Kosuri S, Eroshenko N, Leproust EM, et al. (2010). Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol, 28, 1295–9
   PubMed Web of Science ®Google Scholar
• Kumar A, Singh S. (2012). Directed evolution: tailoring biocatalysts for industrial applications. Crit Rev Biotechnol, 33, 365–78
   PubMed Web of Science ®Google Scholar
• Lajoie MJ, Gregg CJ, Mosberg JA, et al. (2012). Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering. Nucleic Acids Res, 40, e170
   PubMedGoogle Scholar
• Lajoie MJ, Kosuri S, Mosberg JA, et al. (2013a). Probing the limits of genetic recoding in essential genes. Science, 342, 361–3
   PubMed Web of Science ®Google Scholar
• Lajoie MJ, Rovner AJ, Goodman DB, et al. (2013b). Genomically recoded organisms expand biological functions. Science, 342, 357–60
   PubMed Web of Science ®Google Scholar
• Langridge GC, Phan MD, Turner DJ, et al. (2009). Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res, 19, 2308–16
   PubMed Web of Science ®Google Scholar
• Lartigue C, Glass J, Alperovich N, et al. (2007). Genome transplantation in bacteria: changing one species to another. Science, 317, 632–8
   PubMed Web of Science ®Google Scholar
• Lartigue C, Vashee S, Algire M, et al. (2009). Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science, 325, 1693–6
   PubMed Web of Science ®Google Scholar
• Li L, Blankenstein T. (2013). Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion. Nat Protoc, 8, 1567–82
   PubMed Web of Science ®Google Scholar
• Li MZ, Elledge SJ. (2007). Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods, 4, 251–6
   PubMed Web of Science ®Google Scholar
• Liberati N, Urbach J, Miyata S, et al. (2006). An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci USA, 103, 2833–8
   PubMed Web of Science ®Google Scholar
• Mali P, Yang L, Esvelt KM, et al. (2013). RNA-guided human genome engineering via Cas9. Science, 339, 823–6
   PubMed Web of Science ®Google Scholar
• Manabe K, Kageyama Y, Morimoto T, et al. (2011). Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874. Appl Environ Microbiol, 77, 8370–81
   PubMed Web of Science ®Google Scholar
• Marcusson L, Frimodt-Møller N, Hughes D. (2009). Interplay in the selection of fluoroquinolone resistance and bacterial fitness. PLoS Pathog, 5, e1000541
   PubMed Web of Science ®Google Scholar
• Matzas M, Stähler PF, Kefer N, et al. (2010). High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol, 28, 1291–4
   PubMed Web of Science ®Google Scholar
• McCutcheon J. (2010). The bacterial essence of tiny symbiont genomes. Curr Opin Microbiol, 13, 73–8
   PubMed Web of Science ®Google Scholar
• McCutcheon J, Mcdonald B, Moran N. (2009). Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet, 5, e1000565
   PubMed Web of Science ®Google Scholar
• McCutcheon JP, Moran NA. (2010). Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol Evol, 2, 708–18
   PubMed Web of Science ®Google Scholar
• McCutcheon JP, Moran NA. (2012). Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol, 10, 13–26
   Web of Science ®Google Scholar
• Merryman C, Gibson DG. (2012). Methods and applications for assembling large DNA constructs. Metab Eng, 14, 196–204
   PubMed Web of Science ®Google Scholar
• Morimoto T, Kadoya R, Endo K, et al. (2008). Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res, 15, 73–81
   PubMed Web of Science ®Google Scholar
• Moya A, Gil R, Latorre A, et al. (2009). Toward minimal bacterial cells: evolution vs. design. FEMS Microbiol Rev, 33, 225–35
   PubMed Web of Science ®Google Scholar
• Nandagopal N, Elowitz MB. (2011). Synthetic biology: integrated gene circuits. Science, 333, 1244–8
   PubMed Web of Science ®Google Scholar
• Nawy T. (2011). Yeast 2.0. Nat Methods, 8, 895
   PubMed Web of Science ®Google Scholar
• Noskov VN, Karas BJ, Young L, et al. (2012). Assembly of large, high G + C bacterial DNA fragments in yeast. ACS Synth Biol, 1, 267–73
   PubMed Web of Science ®Google Scholar
• Perkel JM. (2012). Genome engineering: writing a better genome. Biotechniques, 53, 213, 215, 217
   PubMed Web of Science ®Google Scholar
• Pósfai G, Plunkett GR, Fehér T, et al. (2006). Emergent properties of reduced-genome Escherichia coli. Science, 312, 1044–6
   PubMed Web of Science ®Google Scholar
• Quan J, Tian J. (2009). Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One, 4, e6441
   PubMed Web of Science ®Google Scholar
• Quan J, Tian J. (2011). Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc, 6, 242–51
   PubMed Web of Science ®Google Scholar
• Rock FL, Mao W, Yaremchuk A, et al. (2007). An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science, 316, 1759–61
   PubMed Web of Science ®Google Scholar
• Ruder WC, Lu T, Collins JJ. (2011). Synthetic biology moving into the clinic. Science, 333, 1248–52
   PubMed Web of Science ®Google Scholar
• Sampson TR, Weiss DS. (2014). Exploiting CRISPR/Cas systems for biotechnology. Bioessays, 36, 34–8
   PubMed Web of Science ®Google Scholar
• Shoji S, Dambacher CM, Shajani Z, et al. (2011). Systematic chromosomal deletion of bacterial ribosomal protein genes. J Mol Biol, 413, 751–61
   PubMed Web of Science ®Google Scholar
• Sleator RD. (2010). The story of Mycoplasma mycoides JCVI-syn1.0: the forty million dollar microbe. Bioeng Bugs, 1, 229–30
   PubMedGoogle Scholar
• Tagwerker C, Dupont CL, Karas BJ, et al. (2012). Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Nucleic Acids Res, 40, 10375–83
   PubMed Web of Science ®Google Scholar
• Tanaka K, Henry CS, Zinner JF, et al. (2013). Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res, 41, 687–99
   PubMed Web of Science ®Google Scholar
• Val ME, Skovgaard O, Ducos-Galand M, et al. (2012). Genome engineering in Vibrio cholerae: a feasible approach to address biological issues. PLoS Genet, 8, e1002472
   PubMedGoogle Scholar
• van Leuven JT, McCutcheon JP. (2012). An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. Genome Biol Evol, 4, 24–7
   PubMed Web of Science ®Google Scholar
• Wang HH, Church GM. (2011). Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol, 498, 409–26
   PubMed Web of Science ®Google Scholar
• Wang HH, Huang PY, Xu G, et al. (2012a). Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol, 1, 43–52
   PubMed Web of Science ®Google Scholar
• Wang HH, Isaacs FJ, Carr PA, et al. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460, 894–8
   PubMed Web of Science ®Google Scholar
• Wang HH, Kim H, Cong L, et al. (2012b). Genome-scale promoter engineering by coselection MAGE. Nat Methods, 9, 591–3
   PubMed Web of Science ®Google Scholar
• Warner JR, Reeder PJ, Karimpour-Fard A, et al. (2010). Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol, 28, 856–62
   PubMed Web of Science ®Google Scholar
• Watanabe S, Shiwa Y, Itaya M, Yoshikawa H. (2012). Complete sequence of the first chimera genome constructed by cloning the whole genome of Synechocystis strain PCC6803 into the Bacillus subtilis 168 genome. J Bacteriol, 194, 7007
   PubMed Web of Science ®Google Scholar
• Werneburg M, Zerbe K, Juhas M, et al. (2012). Inhibition of lipopolysaccharide transport to the outer membrane in Pseudomonas aeruginosa by peptidomimetic antibiotics. Chembiochem, 13, 1767–75
   PubMed Web of Science ®Google Scholar
• Yu B, Kang K, Lee J, et al. (2008a). Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res, 36, e84
   PubMed Web of Science ®Google Scholar
• Yu B, Sung B, Koob M, et al. (2002). Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol, 20, 1018–23
   PubMed Web of Science ®Google Scholar
• Yu BJ, Kang KH, Lee JH, et al. (2008b). Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res, 36, e84
   PubMed Web of Science ®Google Scholar
• Zhang Y, Werling U, Edelmann W. (2012). SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res, 40, e55
   PubMed Web of Science ®Google Scholar