Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors

Methods in Molecular Biology

Volumn 1073, Issue , 2013, Pages 107-129

  Xu, Peng ^a   Koffas, Mattheos A G ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

Combinatorial pathway library; ePathBrick; Gene assembly; Metabolic engineering; Synthetic biology

Indexed keywords

BIOFUEL; DNA; DNA FRAGMENT; FLAVONOID; GENOMIC DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; BINDING SITE; DENATURATION; DNA LIBRARY; FUNGAL GENOME; GENE; GENE CLUSTER; GENE INSERTION; GENE ORDER; GENE STRUCTURE; HIGH THROUGHPUT SCREENING; HOMOLOGOUS RECOMBINATION; METABOLIC ENGINEERING; METABOLISM; MOLECULAR CLONING; MOLECULAR LIBRARY; MYCOPLASMA GENITALIUM; NONHUMAN; OPERATOR GENE; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; RESTRICTION SITE; RIBOSOME; SEQUENCE HOMOLOGY; SYNECHOCOCCUS ELONGATUS; SYNTHETIC BIOLOGY; YEAST;

ACETYL-COA CARBOXYLASE; DNA SHUFFLING; FLAVONOIDS; GENE LIBRARY; GENETIC VECTORS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; SYNTHETIC BIOLOGY;

EID: 84884187734     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-625-2_10     Document Type: Article

References (23)

1. Cheng AA, Lu TK (2012) Synthetic biology: an emerging engineering discipline. Annu Rev Biomed Eng 14:155-178
2. Ellis T, Adie T, Baldwin GS (2011) DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol (Camb) 3:109-118
3. Xu P, Koffas MAG (2010) Metabolic engineering of Escherichia coli for biofuel production. Biofuels 1:493-504
4. Westfall PJ et al (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci USA 109:E111-E118
5. Ajikumar PK et al (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70-74
6. Xu P, Ranganathan S et al (2011) Genomescale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng 13:578-587
7. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4:251-256
8. Jeong J-Y et al (2012) One-step sequence-and ligation-independent cloning as a rapid and versatile cloning method for functional genomics studies. Appl Environ Microbiol 78:5440-5443
9. Gibson DG et al (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345
10. Schmid-Burgk JL et al (2012) Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Res 40:e92
11. Wang R-Y, Shi Z-Y et al (2012) Cloning large gene clusters from E. coli using in vitro single-strand overlapping annealing. ACS Synth Biol 1:291-295
12. Shao Z, Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:e16
13. Wingler LM, Cornish VW (2011) Reiterative recombination for the in vivo assembly of libraries of multigene pathways. Proc Natl Acad Sci USA 108:15135-15140
14. Gibson DG et al (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52-56
15. Noskov VN et al (2012) Assembly of large, high G + C bacterial DNA fragments in yeast. ACS Synth Biol 1:267-273
16. Quan J, Tian J (2011) Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 6:242-251
17. Hillson NJ, Rosengarten RD, Keasling JD (2011) j5 DNA assembly design automation software. ACS Synth Biol 1:14-21
18. Xu P, Bhan N, Koffas MAG (2013) Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr Opin Biotechnol 24:291-299. doi:10.1016/j.copbio. 2012.08.010
19. Xu P, Vansiri A et al (2012) ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth Biol 1:256-266
20. Vick JE et al (2011) Optimized compatible set of BioBrick™ vectors for metabolic pathway engineering. Appl Microbiol Biotechnol 92:1275-1286
21. Du L, Villarreal S, Forster AC (2012) Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase. Biotechnol Bioeng 109: 1043-1050
22. Norville JE et al (2010) Introduction of customized inserts for s-treamlined assembly and optimization of BioBrick synthetic genetic circuits. J Biol Eng 4:17
23. Leonard E, Lim K et al (2007) Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Appl Environ Microbiol 73:3877-3886