Multiplex iterative plasmid engineering for combinatorial optimization of metabolic pathways and diversification of protein coding sequences

ACS Synthetic Biology

Volumn 2, Issue 11, 2013, Pages 651-661

  Li, Yifan ^a   Gu, Qun ^a   Lin, Zhenquan ^a   Wang, Zhiwen ^a   Chen, Tao ^a   Zhao, Xueming ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

combinatorial optimization; metabolic engineering; plasmid library; protein directed evolution; ssDNA recombineering; synthetic biology

Indexed keywords

RIBOFLAVIN;

ARTICLE; BIOENGINEERING; BIOSYNTHESIS; CODON; CONTROLLED STUDY; GENE EXPRESSION; METABOLIC ENGINEERING; MOLECULAR CLONING; MULTIPLEX ITERATIVE PLASMID ENGINEERING; NONHUMAN; PLASMID; POINT MUTATION; PRIORITY JOURNAL; RESTRICTION SITE; SEQUENCE ANALYSIS;

BACTERIAL PROTEINS; BIOSYNTHETIC PATHWAYS; DNA PRIMERS; DNA, BACTERIAL; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION; HEAT-SHOCK PROTEINS; INTRAMOLECULAR TRANSFERASES; METABOLIC ENGINEERING; NUCLEOTIDYLTRANSFERASES; OPEN READING FRAMES; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PLASMIDS; PROMOTER REGIONS, GENETIC; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84887959445     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400051t     Document Type: Article

References (43)

1. Santos, C. N. and Stephanopoulos, G. (2008) Combinatorial engineering of microbes for optimizing cellular phenotype Curr. Opin. Chem. Biol. 12, 168-176
2. Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., and Church, G. M. (2009) Programming cells by multiplex genome engineering and accelerated evolution Nature 460, 894-898
3. Yokobayashi, Y., Weiss, R., and Arnold, F. H. (2002) Directed evolution of a genetic circuit Proc. Natl. Acad. Sci. U.S.A. 99, 16587-16591
4. Du, J., Yuan, Y., Si, T., Lian, J., and Zhao, H. (2012) Customized optimization of metabolic pathways by combinatorial transcriptional engineering Nucleic Acids Res. 40, e142
5. Wingler, L. M. and Cornish, V. W. (2011) Reiterative recombination for the in vivo assembly of libraries of multigene pathways Proc. Natl. Acad. Sci. U.S.A. 108, 15135-15140
6. Ellis, T., Wang, X., and Collins, J. J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions Nat. Biotechnol. 27, 465-471
7. Ajikumar, P. K., Xiao, W. H., Tyo, K. E., Wang, Y., Simeon, F., Leonard, E., Mucha, O., Phon, T. H., Pfeifer, B., and Stephanopoulos, G. (2010) Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli Science 330, 70-74
8. Leonard, E., Ajikumar, P. K., Thayer, K., Xiao, W. H., Mo, J. D., Tidor, B., Stephanopoulos, G., and Prather, K. L. (2010) Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control Proc. Natl. Acad. Sci. U.S.A. 107, 13654-13659
9. Alper, H., Fischer, C., Nevoigt, E., and Stephanopoulos, G. (2005) Tuning genetic control through promoter engineering Proc. Natl. Acad. Sci. U.S.A. 102, 12678-12683
10. Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009) Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27, 946-950
11. Pfleger, B. F., Pitera, D. J., Smolke, C. D., and Keasling, J. D. (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes Nat. Biotechnol. 24, 1027-1032
12. Alper, H. and Stephanopoulos, G. (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype Metab. Eng. 9, 258-267
13. Li, M. Z. and Elledge, S. J. (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC Nat. Methods 4, 251-256
14. Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A., 3rd, and Smith, H. O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases Nat. Methods 6, 343-345
15. Shao, Z. and Zhao, H. (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Nucleic Acids Res. 37, e16
16. Quan, J. and Tian, J. (2009) Circular polymerase extension cloning of complex gene libraries and pathways PLoS One 4, e6441
17. Ramon, A. and Smith, H. O. (2011) Single-step linker-based combinatorial assembly of promoter and gene cassettes for pathway engineering Biotechnol. Lett. 33, 549-555
18. Sharan, S. K., Thomason, L. C., Kuznetsov, S. G., and Court, D. L. (2009) Recombineering: A homologous recombination-based method of genetic engineering Nat. Protoc. 4, 206-223
19. Costantino, N. and Court, D. L. (2003) Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants Proc. Natl. Acad. Sci. U.S.A. 100, 15748-15753
20. Carr, P. A., Wang, H. H., Sterling, B., Isaacs, F. J., Lajoie, M. J., Xu, G., Church, G. M., and Jacobson, J. M. (2012) Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection Nucleic Acids Res. 40, e132
21. Thomason, L. C., Costantino, N., Shaw, D. V., and Court, D. L. (2007) Multicopy plasmid modification with phage λ Red recombineering Plasmid 58, 148-158
22. Sawitzke, J. A., Costantino, N., Li, X. T., Thomason, L. C., Bubunenko, M., Court, C., and Court, D. L. (2011) Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering J. Mol. Biol. 407, 45-59
23. Yu, D., Ellis, H. M., Lee, E. C., Jenkins, N. A., Copeland, N. G., and Court, D. L. (2000) An efficient recombination system for chromosome engineering in Escherichia coli Proc. Natl. Acad. Sci. U.S.A. 97, 5978-5983
24. Shi, S., Chen, T., Zhang, Z., Chen, X., and Zhao, X. (2009) Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production Metab. Eng. 11, 243-252
25. Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., Emig, C. J., Bang, D., Hwang, S. J., Jewett, M. C., Jacobson, J. M., and Church, G. M. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement Science 333, 348-353
26. Bloom, J. D. and Arnold, F. H. (2009) In the light of directed evolution: Pathways of adaptive protein evolution Proc. Natl. Acad. Sci. U.S.A. 106 (Suppl 1) 9995-10000
27. Ho, S. N., Hunt, H. D., Horton, R. M., Pullen, J. K., and Pease, L. R. (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction Gene 77, 51-59
28. Miyazaki, K. and Arnold, F. H. (1999) Exploring nonnatural evolutionary pathways by saturation mutagenesis: Rapid improvement of protein function J. Mol. Evol. 49, 716-720
29. Hogrefe, H. H., Cline, J., Youngblood, G. L., and Allen, R. M. (2002) Creating randomized amino acid libraries with the QuikChange Multi Site-Directed Mutagenesis Kit Biotechniques 33, 1158-1160, 1162, 1164-1165
30. Mitchell, L. A., Cai, Y., Taylor, M., Noronha, A. M., Chuang, J., Dai, L., and Boeke, J. D. (2013) Multichange isothermal mutagenesis: A new strategy for multiple site-directed mutations in plasmid DNA ACS Synth Biol. 2, 473-477
31. Shaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N., Palmer, A. E., and Tsien, R. Y. (2004) Improved monomeric red, orange, and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Nat. Biotechnol. 22, 1567-1572
32. Heim, R., Prasher, D. C., and Tsien, R. Y. (1994) Wavelength mutations and posttranslational autoxidation of green fluorescent protein Proc. Natl. Acad. Sci. U.S.A. 91, 12501-12504
33. Wang, H. H., Xu, G., Vonner, A. J., and Church, G. (2011) Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion Nucleic Acids Res. 39, 7336-7347
34. Lajoie, M. J., Gregg, C. J., Mosberg, J. A., Washington, G. C., and Church, G. M. (2012) Manipulating replisome dynamics to enhance λ Red-mediated multiplex genome engineering Nucleic Acids Res. 40, e170
35. Mosberg, J. A., Gregg, C. J., Lajoie, M. J., Wang, H. H., and Church, G. M. (2012) Improving λ Red genome engineering in Escherichia coli via rational removal of endogenous nucleases PLoS One 7, e44638
36. Wang, H. H., Kim, H., Cong, L., Jeong, J., Bang, D., and Church, G. M. (2012) Genome-scale promoter engineering by coselection MAGE Nat. Methods 9, 591-593
37. Wang, H. H., Huang, P. Y., Xu, G., Haas, W., Marblestone, A., Li, J., Gygi, S., Forster, A. C., Jewett, M. C., and Church, G. M. (2012) Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis ACS Synth. Biol. 1, 43-52
38. Egbert, R. G. and Klavins, E. (2012) Fine-tuning gene networks using simple sequence repeats Proc. Natl. Acad. Sci. U.S.A. 109, 16817-16822
39. Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006) RNA synthetic biology Nat. Biotechnol. 24, 545-554
40. Peralta-Yahya, P., Carter, B. T., Lin, H., Tao, H., and Cornish, V. W. (2008) High-throughput selection for cellulase catalysts using chemical complementation J. Am. Chem. Soc. 130, 17446-17452
41. Liang, J. C., Chang, A. L., Kennedy, A. B., and Smolke, C. D. (2012) A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity Nucleic Acids Res. 40, e154
42. Sharma, V., Yamamura, A., and Yokobayashi, Y. (2011) Engineering artificial small RNAs for conditional gene silencing in Escherichia coli ACS Synth. Biol. 1, 6-13
43. Hillson, N. J., Rosengarten, R. D., and Keasling, J. D. (2011) j5 DNA assembly design automation software ACS Synth. Biol. 1, 14-21