High molecular weight DNA assembly in vivo for synthetic biology applications

References

• Kosuri S, Eroshenko N, Leproust EM, et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol. 2010;28:1295–1299.
   PubMed Web of Science ®Google Scholar
• Matzas M, Stähler PF, Kefer N, et al. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol. 2010;28:1291–1294.
   PubMed Web of Science ®Google Scholar
• Merryman C, Gibson DG. Methods and applications for assembling large DNA constructs. Metab Eng. 2012;14:196–204.
   PubMed Web of Science ®Google Scholar
• Blake WJ, Chapman BA, Zindal A, et al. Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Res. 2010;38:2594–2602.
   PubMed Web of Science ®Google Scholar
• Quan J, Tian J. Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc. 2011;6:242–251.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Werling U, Edelmann W. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 2012;40:e55
   PubMed Web of Science ®Google Scholar
• Storch M, Casini A, Mackrow B,, et al. BASIC: a new biopart assembly standard for idempotent cloning provides accurate, single-tier DNA assembly for synthetic biology. ACS Synth Biol. 2015;4(7):781–7
   PubMed Web of Science ®Google Scholar
• Trubitsyna M, Michlewski G, Cai Y, et al. PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic Acids Res. 2014;42:e154
   PubMed Web of Science ®Google Scholar
• Juhas M, Davenport PW, Brown JR, et al. Meeting report: The Cambridge BioDesign TechEvent – synthetic biology, a new “age of wonder”? Biotechnol J. 2013;8:761–763
   Web of Science ®Google Scholar
• Seo SW, Yang J, Min BE, et al. Synthetic biology: tools to design microbes for the production of chemicals and fuels. Biotechnol Adv. 2013;31(6):811–7
   PubMed Web of Science ®Google Scholar
• Juhas M. On the road to synthetic life: the minimal cell and genome-scale engineering. Crit Rev Biotechnol. 2015;1–8. Epub ahead of print.
   PubMed Web of Science ®Google Scholar
• Gibson D, Young L, Chuang R, et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343–345.
   PubMed Web of Science ®Google Scholar
• Li MZ, Elledge SJ. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods. 2007;4:251–256.
   PubMed Web of Science ®Google Scholar
• Tsuge K, Matsui K, Itaya M. One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid. Nucleic Acids Res. 2003;31:e133.
   PubMed Web of Science ®Google Scholar
• Nishizaki T, Tsuge K, Itaya M, et al. Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis. Appl Environ Microbiol 2007;73:1355–1361.
   PubMed Web of Science ®Google Scholar
• Tsuge K, Matsui K, Itaya M. Production of the non-ribosomal peptide plipastatin in Bacillus subtilis regulated by three relevant gene blocks assembled in a single movable DNA segment. J Biotechnol. 2007;129:592–603.
   PubMed Web of Science ®Google Scholar
• Tsuge K, Sato Y, Kobayashi Y, et al. Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments. Sci Rep. 2015;5:10655.
   PubMed Web of Science ®Google Scholar
• de Kok S, Stanton LH, Slaby T, et al. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth Biol 2014;3(2):97–106
   PubMed Web of Science ®Google Scholar
• Quan J, Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One. 2009;4:e6441.
   PubMed Web of Science ®Google Scholar
• Juhas M, Reuß DR, Zhu B, et al. Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology. 2014;160:2341–2351.
   PubMed Web of Science ®Google Scholar
• Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast. FEBS Lett. 2012;586:2112–2121.
   PubMed Web of Science ®Google Scholar
• Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J. 2013;8:1017–1034.
   PubMed Web of Science ®Google Scholar
• Li M, Borodina I. Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res. 2014. Epub ahead of print.
   Web of Science ®Google Scholar
• Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res. 2014. Epub ahead of print.
   PubMed Web of Science ®Google Scholar
• Dai Z, Liu Y, Guo J,, et al. Yeast synthetic biology for high-value metabolites. FEMS Yeast Res. 2014. Epub ahead of print.
   PubMed Web of Science ®Google Scholar
• Gibson D, Glass J, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010;329:52–56.
   PubMed Web of Science ®Google Scholar
• Gibson D, Benders G, Andrews-Pfannkoch C, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008;319:1215–1220.
   PubMed Web of Science ®Google Scholar
• Itaya M, Fujita K, Kuroki A, et al. Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat Methods. 2008;5:41–43.
   PubMed Web of Science ®Google Scholar
• Perkel JM. Genome engineering: writing a better genome. Biotechniques. 2012;53:21–35.
   Web of Science ®Google Scholar
• Dymond JS, Richardson SM, Coombes CE, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 2011;477:471–476.
   PubMed Web of Science ®Google Scholar
• Nawy T. Yeast 2.0. Nat Methods. 2011;8:895.
   PubMed Web of Science ®Google Scholar
• Enyeart PJ, Ellington AD. Synthetic biology: a yeast for all reasons. Nature. 2011;477:413–414.
   PubMed Web of Science ®Google Scholar
• Jovicevic D, Blount BA, Ellis T. Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast. Bioessays. 2014;36:855–860.
   PubMed Web of Science ®Google Scholar
• Annaluru N, Muller H, Mitchell LA, et al. Total synthesis of a functional designer eukaryotic chromosome. Science. 2014;344:55–58.
   PubMed Web of Science ®Google Scholar
• Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One. 2008;3:e3647.
   PubMed Web of Science ®Google Scholar
• Engler C, Gruetzner R, Kandzia R, et al. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One. 2009;4:e5553.
   PubMed Web of Science ®Google Scholar
• Chen WH, Qin ZJ, Wang J, et al. The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Res. 2013;41:e93.
   PubMed Web of Science ®Google Scholar
• Sarrion-Perdigones A, Falconi EE, Zandalinas SI, et al. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One. 2011;6:e21622.
   PubMed Web of Science ®Google Scholar
• Casini A, MacDonald JT, De Jonghe J, et al. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Nucleic Acids Res. 2014;42:e7.
   PubMed Web of Science ®Google Scholar
• Weber E, Engler C, Gruetzner R, et al. A modular cloning system for standardized assembly of multigene constructs. PLoS One. 2011;6:e16765.
   PubMed Web of Science ®Google Scholar
• Chao R, Yuan Y, Zhao H. Recent advances in DNA assembly technologies. FEMS Yeast Res. 2014. Epub ahead of print.
   PubMed Web of Science ®Google Scholar
• Lisby M, Rothstein R. Cell biology of mitotic recombination. Cold Spring Harb Perspect Biol. 2015;7:a016535
   PubMed Web of Science ®Google Scholar
• Muller H, Annaluru N, Schwerzmann JW, et al. Assembling large DNA segments in yeast. Methods Mol Biol. 2012;852:133–150.
   PubMedGoogle Scholar
• T Jakociunas, AS Rajkumar, J Zhang, et al. CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae. ACS Synth Biol. 2015;4(11):1226–1234
   PubMed Web of Science ®Google Scholar
• Shao Z, Zhao H. Construction and engineering of large biochemical pathways via DNA assembler. Methods Mol Biol. 2013;1073:85–106.
   PubMedGoogle Scholar
• Kuijpers NG, Solis-Escalante D, Bosman L, et al. A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences. Microb Cell Fact. 2013;12:47.
   PubMed Web of Science ®Google Scholar
• Lin Q, Jia B, Mitchell LA, et al. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth Biol. 2015;4:213–220.
   PubMed Web of Science ®Google Scholar
• Kuijpers NG, Chroumpi S, Vos T, et al. One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Res. 2013;13:769–781.
   PubMed Web of Science ®Google Scholar
• Storici F, Lewis LK, Resnick MA. In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol. 2001;19:773–776.
   PubMed Web of Science ®Google Scholar
• Chou CC, Patel MT, Gartenberg MR. A series of conditional shuttle vectors for targeted genomic integration in budding yeast. FEMS Yeast Res. 2015;15.
   PubMed Web of Science ®Google Scholar
• Manabe K, Kageyama Y, Morimoto T, et al. Improved production of secreted heterologous enzyme in Bacillus subtilis strain MGB874 via modification of glutamate metabolism and growth conditions. Microb Cell Fact. 2013;12:18.
   PubMed Web of Science ®Google Scholar
• Hao T, Han B, Ma H, et al. In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol. Mol Biosyst. 2013;9:2034–2044.
   PubMed Web of Science ®Google Scholar
• Commichau FM, Alzinger A, Sande R, et al. Overexpression of a non-native deoxyxylulose-dependent vitamin B6 pathway in Bacillus subtilis for the production of pyridoxine. Metab Eng. 2014;25:38–49.
   PubMed Web of Science ®Google Scholar
• Yadav T, Carrasco B, Serrano E, et al. Roles of Bacillus subtilis DprA and SsbA in RecA-mediated genetic recombination. J Biol Chem. 2014;289:27640–27652.
   PubMed Web of Science ®Google Scholar
• Shi T, Wang G, Wang Z, et al. Establishment of a markerless mutation delivery system in Bacillus subtilis stimulated by a double-strand break in the chromosome. PLoS One. 2013;8:e81370.
   PubMed Web of Science ®Google Scholar
• Ogawa T, Iwata T, Kaneko S, et al. An inducible recA expression Bacillus subtilis genome vector for stable manipulation of large DNA fragments. BMC Genomics. 2015;16:209.
   PubMed Web of Science ®Google Scholar
• Carrasco B, Yadav T, Serrano E, et al. Bacillus subtilis RecO and SsbA are crucial for RecA-mediated recombinational DNA repair. Nucleic Acids Res. 2015;43:5984–5997.
   PubMed Web of Science ®Google Scholar
• Watanabe S, Shiwa Y, Itaya M, et al. 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. 2012;194:7007.
   PubMed Web of Science ®Google Scholar
• Iwata T, Kaneko S, Shiwa Y, et al. Bacillus subtilis genome vector-based complete manipulation and reconstruction of genomic DNA for mouse transgenesis. BMC Genomics. 2013;14:300.
   PubMed Web of Science ®Google Scholar
• Ajikumar PK, Xiao WH, Tyo KE, et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science. 2010;330:70–74.
   PubMed Web of Science ®Google Scholar
• Park SJ, Lee TW, Lim SC, et al. Biosynthesis of polyhydroxyalkanoates containing 2-hydroxybutyrate from unrelated carbon source by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol. 2012;93:273–283.
   PubMed Web of Science ®Google Scholar
• Yim H, Haselbeck R, Niu W, et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol. 2011;7:445–452.
   PubMed Web of Science ®Google Scholar
• Zhou L, Niu DD, Tian KM, et al. Genetically switched D-lactate production in Escherichia coli. Metab Eng. 2012;14:560–568.
   PubMed Web of Science ®Google Scholar
• Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA. 2000;97:6640–6645.
   PubMed Web of Science ®Google Scholar
• Copeland NG, Jenkins NA, Court DL. Recombineering: a powerful new tool for mouse functional genomics. Nat Rev Genet. 2001;2:769–779.
   PubMed Web of Science ®Google Scholar
• Murphy KC. The lambda Gam protein inhibits RecBCD binding to dsDNA ends. J Mol Biol. 2007;371:19–24.
   PubMed Web of Science ®Google Scholar
• Fu J, Bian X, Hu S, et al. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol. 2012;30:440–446.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Buchholz F, Muyrers JP, et al. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet. 1998;20:123–128.
   PubMed Web of Science ®Google Scholar
• Marcellin E, Chen WY, Nielsen LK. Understanding plasmid effect on hyaluronic acid molecular weight produced by Streptococcus equi subsp. zooepidemicus. Metab Eng. 2010;12:62–69.
   PubMed Web of Science ®Google Scholar
• Sabri S, Steen JA, Bongers M, et al. Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb Cell Fact. 2013;12:60.
   PubMed Web of Science ®Google Scholar
• Ublinskaya AA, Samsonov VV, Mashko SV, et al. A PCR-free cloning method for the targeted ϕ80 Int-mediated integration of any long DNA fragment, bracketed with meganuclease recognition sites, into the Escherichia coli chromosome. J Microbiol Methods. 2012;89:167–173.
   PubMed Web of Science ®Google Scholar
• Kuhlman TE, Cox EC. Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res. 2010;38:e92.
   PubMed Web of Science ®Google Scholar
• Yang J, Sun B, Huang H, et al. High-efficiency scarless genetic modification in Escherichia coli by using lambda red recombination and I-SceI cleavage. Appl Environ Microbiol. 2014;80:3826–3834.
   PubMed Web of Science ®Google Scholar
• Juhas M, Evans LD, Frost J, et al. Escherichia coli Flagellar Genes as Target Sites for Integration and Expression of Genetic Circuits. PLoS One. 2014;9:e111451.
   PubMed Web of Science ®Google Scholar
• Juhas M, Ajioka JW. Identification and validation of novel chromosomal integration and expression loci in Escherichia coli flagellar region 1. PLoS One. 2015;10:e0123007.
   PubMed Web of Science ®Google Scholar
• Juhas M, Ajioka JW. Flagellar region 3b supports strong expression of integrated DNA and the highest chromosomal integration efficiency of the Escherichia coli flagellar regions. Microb Biotechnol. 2015;8:726–738.
   PubMed Web of Science ®Google Scholar
• Gibson DG. Programming biological operating systems: genome design, assembly and activation. Nat Methods. 2014;11:521–526.
   PubMed Web of Science ®Google Scholar
• Itaya M. A synthetic DNA transplant. Nat Biotechnol. 2010;28:687–689.
   PubMed Web of Science ®Google Scholar
• Karas BJ, Jablanovic J, Sun L, et al. Direct transfer of whole genomes from bacteria to yeast. Nat Methods. 2013;10(5):410–2
   PubMed Web of Science ®Google Scholar
• Isaacs FJ, Carr PA, Wang HH, et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science. 2011;333:348–353.
   PubMed Web of Science ®Google Scholar
• Mandell DJ, Lajoie MJ, Mee MT, et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature. 2015;518:55–60.
   PubMed Web of Science ®Google Scholar
• Glass JI. Synthetic genomics and the construction of a synthetic bacterial cell. Perspect Biol Med. 2012;55:473–489.
   PubMed Web of Science ®Google Scholar
• Juhas M. Pseudomonas aeruginosa essentials: an update on investigation of essential genes. Microbiology 2015;161:2053–2060
   PubMed Web of Science ®Google Scholar
• Juhas M, Eberl L, Church GM. Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol. 2012;30:601–607.
   PubMed Web of Science ®Google Scholar
• Werneburg M, Zerbe K, Juhas M, et al. Inhibition of lipopolysaccharide transport to the outer membrane in Pseudomonas aeruginosa by peptidomimetic antibiotics. Chembiochem. 2012;13:1767–1775.
   PubMed Web of Science ®Google Scholar
• Glass J, Assad-Garcia N, Alperovich N, et al. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA. 2006;103:425–430.
   PubMed Web of Science ®Google Scholar
• Pósfai G, Plunkett Gr, Fehér T, et al. Emergent properties of reduced-genome Escherichia coli. Science. 2006;312:1044–1046.
   PubMed Web of Science ®Google Scholar
• Langridge GC, Phan MD, Turner DJ, et al. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 2009;19:2308–2316.
   PubMed Web of Science ®Google Scholar
• Moya A, Gil R, Latorre A, et al. Toward minimal bacterial cells: evolution vs. design. FEMS Microbiol Rev. 2009;33:225–235.
   PubMed Web of Science ®Google Scholar
• Juhas M, Stark M, von Mering C, et al. High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS One. 2012;7:e40064
   PubMed Web of Science ®Google Scholar
• Juhas M, Eberl L, Glass JI. Essence of life: essential genes of minimal genomes. Trends Cell Biol. 2011;21:562–568.
   PubMed Web of Science ®Google Scholar
• Lee SA, Gallagher LA, Thongdee M, et al. General and condition-specific essential functions of Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 2015;112(16):5189–94.
   PubMed Web of Science ®Google Scholar
• Turner KH, Wessel AK, Palmer GC, et al. Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proc Natl Acad Sci USA. 2015;112:4110–4115.
   PubMed Web of Science ®Google Scholar
• Yu B, Sung B, Koob M, et al. Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol. 2002;20:1018–1023.
   PubMed Web of Science ®Google Scholar
• Noskov VN, Ma L, Chen S, et al. Recombinase-mediated cassette exchange (RMCE) system for functional genomics studies in Mycoplasma mycoides. Biol Proced Online. 2015;17:6.
   PubMed Web of Science ®Google Scholar
• Suzuki Y, Assad-Garcia N, Kostylev M, et al. Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling. Genome Res. 2015;25:435–444.
   PubMed Web of Science ®Google Scholar
• Quiles-Puchalt N, Carpena N, Alonso JC, et al. Staphylococcal pathogenicity island DNA packaging system involving cos-site packaging and phage-encoded HNH endonucleases. Proc Natl Acad Sci USA. 2014;111:6016–6021.
   PubMed Web of Science ®Google Scholar
• Oliveira L, Tavares P, Alonso JC. Headful DNA packaging: bacteriophage SPP1 as a model system. Virus Res. 2013;173:247–259.
   PubMed Web of Science ®Google Scholar
• Zhang L, Sun Y, Chang L, et al. A novel method to produce armored double-stranded DNA by encapsulation of MS2 viral capsids. Appl Microbiol Biotechnol. 2015;99:7047–7057.
   PubMed Web of Science ®Google Scholar
• Gallagher LA, Shendure J, Manoil C. Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. MBio. 2011;2:e00315–e00310.
   PubMed Web of Science ®Google Scholar
• Skurnik D, Roux D, Aschard H, et al. A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries. PLoS Pathog. 2013;9:e1003582.
   PubMed Web of Science ®Google Scholar