Erratum: EcoFlex: A multifunctional MoClo kit for E. coli synthetic biology (ACS Synthetic Biology (2016) 5:10 (1059-1069) DOI: 10.1021/acssynbio.6b00031);EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology

ACS Synthetic Biology

Volumn 5, Issue 10, 2016, Pages 1059-1069

  Moore, Simon J ^a   Lai, Hung En ^a   Kelwick, Richard J R ^a   Chee, Soo Mei ^a   Bell, David J ^a   Polizzi, Karen Marie ^a   Freemont, Paul S ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

cell free protein synthesis; Escherichia coli; Golden Gate; recombinant protein production; synthetic biology; violacein

Indexed keywords

DNA LIGASE; INDOLE DERIVATIVE; RECOMBINANT PROTEIN; VIOLACEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BINDING SITE; BIOSYNTHESIS; COMPARATIVE STUDY; DNA SEQUENCE; ESCHERICHIA COLI; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; RESTRICTION SITE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SYNTHETIC BIOLOGY; GENE LIBRARY; GENE VECTOR; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES; REPRODUCIBILITY;

ESCHERICHIA COLI; GENE LIBRARY; GENETIC ENGINEERING; GENETIC VECTORS; INDOLES; PROMOTER REGIONS, GENETIC; RECOMBINANT PROTEINS; REPRODUCIBILITY OF RESULTS; SYNTHETIC BIOLOGY;

EID: 84993984044     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.0c00177     Document Type: Erratum

References (39)

1. Ran, N., Zhao, L., Chen, Z., and Tao, J. (2008) Recent applications of biocatalysis in developing green chemistry for chemical synthesis at the industrial scale Green Chem. 10, 361 10.1039/B716045C
2. Casini, A., Storch, M., Baldwin, G. S., and Ellis, T. (2015) Bricks and blueprints: methods and standards for DNA assembly Nat. Rev. Mol. Cell Biol. 9, 1-9
3. Engler, C., Kandzia, R., and Marillonnet, S. (2008) A one pot, one step, precision cloning method with high throughput capability PLoS One 3, e3647 10.1371/journal.pone.0003647
4. Engler, C. and Marillonnet, S. (2011) Generation of families of construct variants using golden gate shuffling Methods Mol. Biol. 729, 167-81 10.1007/978-1-61779-065-2-11
5. Engler, C., Gruetzner, R., Kandzia, R., and Marillonnet, S. (2009) Golden gate shuffling: A one-pot DNA shuffling method based on type IIS restriction enzymes PLoS One 4, e5553 10.1371/journal.pone.0005553
6. Weber, E., Gruetzner, R., Werner, S., Engler, C., and Marillonnet, S. (2011) Assembly of designer TAL effectors by Golden Gate cloning PLoS One 6, e19722 10.1371/journal.pone.0019722
7. Sarrion-Perdigones, A., Falconi, E. E., Zandalinas, S. I., Juárez, P., Fernández-del-Carmen, A., Granell, A., and Orzaez, D. (2011) GoldenBraid: An iterative cloning system for standardized assembly of reusable genetic modules PLoS One 6, e21622 10.1371/journal.pone.0021622
8. Werner, S., Engler, C., Weber, E., Gruetzner, R., and Marillonnet, S. (2012) Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system Bioeng. Bugs 3, 38-43 10.4161/bbug.3.1.18223
9. Weber, E., Engler, C., Gruetzner, R., Werner, S., and Marillonnet, S. (2011) A modular cloning system for standardized assembly of multigene constructs PLoS One 6, e16765 10.1371/journal.pone.0016765
10. Engler, C., Youles, M., Gruetzner, R., Ehnert, T.-M., Werner, S., Jones, J. D. G., Patron, N. J., and Marillonnet, S. (2014) A golden gate modular cloning toolbox for plants ACS Synth. Biol. 3, 839-43 10.1021/sb4001504
11. Sarrion-Perdigones, A., Vazquez-Vilar, M., Palací, J., Castelijns, B., Forment, J., Ziarsolo, P., Blanca, J., Granell, A., and Orzaez, D. (2013) GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology Plant Physiol. 162, 1618-31 10.1104/pp.113.217661
12. Agmon, N., Mitchell, L. A., Cai, Y., Ikushima, S., Chuang, J., Zheng, A., Choi, W.-J., Martin, J. A., Caravelli, K., Stracquadanio, G., and Boeke, J. D. (2015) Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units ACS Synth. Biol. 4, 853-9 10.1021/sb500372z
13. Mitchell, L. a., Chuang, J., Agmon, N., Khunsriraksakul, C., Phillips, N. a., Cai, Y., Truong, D. M., Veerakumar, A., Wang, Y., Mayorga, M., Blomquist, P., Sadda, P., Trueheart, J., and Boeke, J. D. (2015) Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae Nucleic Acids Res. 43, 6620-6630 10.1093/nar/gkv466
14. Kakui, Y., Sunaga, T., Arai, K., Dodgson, J., Carazo-salas, R., Ji, L., Csika, A., and Sato, M. (2015) Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe Open Biol. 5, 150054 10.1098/rsob.150054
15. Iverson, S., Haddock, T. L., Beal, J., and Densmore, D. (2015) CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enables Rapid Combinatorial Design for Synthetic and Traditional Biology ACS Synth. Biol. 5, 99 10.1021/acssynbio.5b00124
16. Chen, Y.-J., Liu, P., Nielsen, A. A. K., Brophy, J. A. N., Clancy, K., Peterson, T., and Voigt, C. A. (2013) Characterization of 582 natural and synthetic terminators and quantification of their design constraints Nat. Methods 10, 659-664 10.1038/nmeth.2515
17. Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., and MacDonald, J. T. (2014) R2oDNA designer: computational design of biologically neutral synthetic DNA sequences ACS Synth. Biol. 3, 525-8 10.1021/sb4001323
18. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q.-A., Tran, A. B., Paull, M., Keasling, J. D., Arkin, A. P., and Endy, D. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements Nat. Methods 10, 354-60 10.1038/nmeth.2404
19. Lou, C., Stanton, B., Chen, Y.-J., Munsky, B., and Voigt, C. A. (2012) Ribozyme-based insulator parts buffer synthetic circuits from genetic context Nat. Biotechnol. 30, 1137-42 10.1038/nbt.2401
20. Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., and Keasling, J. D. (2010) BglBricks: A flexible standard for biological part assembly J. Biol. Eng. 4, 1 10.1186/1754-1611-4-1
21. Beyer, H. M., Gonschorek, P., Samodelov, S. L., Meier, M., Weber, W., and Zurbriggen, M. D. (2015) AQUA Cloning: A Versatile and Simple Enzyme-Free Cloning Approach PLoS One 10, e0137652 10.1371/journal.pone.0137652
22. Storch, M., Casini, A., Mackrow, B., Fleming, T., Trewhitt, H., Ellis, T., and Baldwin, G. S. (2015) BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology ACS Synth. Biol. 4, 781-7 10.1021/sb500356d
23. Torella, J. P., Lienert, F., Boehm, C. R., Chen, J.-H., Way, J. C., and Silver, P. A. (2014) Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications Nat. Protoc. 9, 2075-89 10.1038/nprot.2014.145
24. Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. a, and Smith, H. O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases Nat. Methods 6, 343-345 10.1038/nmeth.1318
25. Li, M. Z. and Elledge, S. J. (2012) SLIC: a method for sequence- and ligation-independent cloning Methods Mol. Biol. 852, 51-9 10.1007/978-1-61779-564-0-5
26. Kelly, J. R., Rubin, A. J., Davis, J. H., Ajo-Franklin, C. M., Cumbers, J., Czar, M. J., de Mora, K., Glieberman, A. L., Monie, D. D., and Endy, D. (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard J. Biol. Eng. 3, 4 10.1186/1754-1611-3-4
27. Chappell, J., Jensen, K., and Freemont, P. S. (2013) Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology Nucleic Acids Res. 41, 3471-3481 10.1093/nar/gkt052
28. Jürgen, B., Breitenstein, A., Urlacher, V., Büttner, K., Lin, H., Hecker, M., Schweder, T., and Neubauer, P. (2010) Quality control of inclusion bodies in Escherichia coli Microb. Cell Fact. 9, 41 10.1186/1475-2859-9-41
29. Ceroni, F., Algar, R., Stan, G.-B., and Ellis, T. (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden Nat. Methods 12, 415-418 10.1038/nmeth.3339
30. Knaggs, A. R. (2003) The biosynthesis of shikimate metabolites Nat. Prod. Rep. 20, 119-36 10.1039/b100399m
31. Balibar, C. J. and Walsh, C. T. (2006) in vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum Biochemistry 45, 15444-15457 10.1021/bi061998z
32. Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., Gibbs, R. a., Csörgo, B., Pósfai, G., Weinstock, G. M., and Blattner, F. R. (2008) The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse J. Bacteriol. 190, 2597-2606 10.1128/JB.01695-07
33. Lee, M. E., DeLoache, W. C., Cervantes, B., and Dueber, J. E. (2015) A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly ACS Synth. Biol. 4, 975-86 10.1021/sb500366v
34. Sleight, S. C., Bartley, B. A., Lieviant, J. A., and Sauro, H. M. (2010) Designing and engineering evolutionary robust genetic circuits J. Biol. Eng. 4, 12 10.1186/1754-1611-4-12
35. Jones, J. A., Vernacchio, V. R., Lachance, D. M., Lebovich, M., Fu, L., Shirke, A. N., Schultz, V. L., Cress, B., Linhardt, R. J., and Koffas, M. a. G. (2015) ePathOptimize: A Combinatorial Approach for Transcriptional Balancing of Metabolic Pathways Sci. Rep. 5, 11301 10.1038/srep11301
36. Jeschek, M., Gerngross, D., and Panke, S. (2016) Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort Nat. Commun. 7, 11163 10.1038/ncomms11163
37. Eisenstein, M. (2016) Living factories of the future Nature 531, 401-403 10.1038/531401a
38. Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., and Noireaux, V. (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology J. Visualized Exp. 50762, e50762 10.3791/50762
39. Durán, N., Justo, G. Z., Ferreira, C. V., Melo, P. S., Cordi, L., and Martins, D. (2007) Violacein: properties and biological activities Biotechnol. Appl. Biochem. 48, 127-33 10.1042/BA20070115