RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression

Nature Protocols

Volumn 11, Issue 7, 2016, Pages 1175-1190

  Wang, Hailong ^a   Li, Zhen ^a   Jia, Ruonan ^a   Hou, Yu ^a   Yin, Jia ^a   Bian, Xiaoying ^a   Li, Aiying ^a   Müller, Rolf ^a,b   Stewart, A Francis ^c   Fu, Jun ^a,c   Zhang, Youming ^a  

^a SHANDONG UNIVERSITY   (China)

^b SAARLAND UNIVERSITY   (Germany)

^c DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; VIRAL PROTEIN;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BIOSYNTHESIS; CLONING VECTOR; CONJUGATION; DNA TRANSPOSITION; ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE CLUSTER; GENETIC ENGINEERING; HETEROLOGOUS EXPRESSION; HOMOLOGOUS RECOMBINATION; HORIZONTAL GENE TRANSFER; MOLECULAR CLONING; OPERON; PRIORITY JOURNAL; RECOMBINEERING; REPLICON; TRANSGENE; GENE VECTOR; GENETIC RECOMBINATION; GENETICS; MICROBIOLOGY; MULTIGENE FAMILY; PLASMID; PROCEDURES; PROPHAGE;

BACTERIOPHAGE LAMBDA; BIOSYNTHETIC PATHWAYS; CLONING, MOLECULAR; ESCHERICHIA COLI; GENETIC ENGINEERING; GENETIC VECTORS; HOMOLOGOUS RECOMBINATION; INDUSTRIAL MICROBIOLOGY; MULTIGENE FAMILY; OPERON; PLASMIDS; PROPHAGES; RECOMBINATION, GENETIC; TRANSGENES; VIRAL PROTEINS;

EID: 84975885993     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2016.054     Document Type: Article

References (46)

1. Van Lanen, S.G. & Shen, B. Microbial genomics for the improvement of natural product discovery. Curr. Opin. Microbiol. 9, 252-260 (2006).
2. Nett, M., Ikeda, H. & Moore, B.S. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep. 26, 1362-1384 (2009).
3. Lautru, S., Deeth, R.J., Bailey, L.M. & Challis, G.L. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat. Chem. Biol. 1, 265-269 (2005).
4. Bergmann, S. et al. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat. Chem. Biol. 3, 213-217 (2007).
5. Wenzel, S.C. & Möller, R. The impact of genomics on the exploitation of the myxobacterial secondary metabolome. Nat. Prod. Rep. 26, 1385-1407 (2009).
6. Charlop-Powers, Z., Milshteyn, A. & Brady, S.F. Metagenomic small molecule discovery methods. Curr. Opin. Microbiol. 19, 70-75 (2014).
7. Fu, J. et al. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat. Biotechnol. 30, 440-446 (2012).
8. Yamanaka, K. et al. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc. Natl. Acad. Sci. USA 111, 1957-1962 (2014).
9. Tang, Y. et al. Heterologous expression of an orphan NRPS gene cluster from Paenibacillus larvae in Escherichia coli revealed production of sevadicin. J. Biotechnol. 194, 112-114 (2015).
10. Yin, W.B. et al. Discovery of cryptic polyketide metabolites from dermatophytes using heterologous expression in Aspergillus nidulans. ACS Synth. Biol. 2, 629-634 (2013).
11. Wolpert, M., Heide, L., Kammerer, B. & Gust, B. Assembly and heterologous expression of the coumermycin A1 gene cluster and production of new derivatives by genetic engineering. Chembiochem 9, 603-612 (2008).
12. Chai, Y. et al. Heterologous expression and genetic engineering of the tubulysin biosynthetic gene cluster using Red/ET recombineering and inactivation mutagenesis. Chem. Biol. 19, 361-371 (2012).
13. Fu, J. et al. Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition. Nucleic Acids Res. 36, e113 (2008).
14. Perlova, O. et al. Reconstitution of the myxothiazol biosynthetic gene cluster by Red/ET recombination and heterologous expression in Myxococcus xanthus. Appl. Environ. Microbiol. 72, 7485-7494 (2006).
15. Wenzel, S.C. et al. Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via red/ET recombineering. Chem. Biol. 12, 349-356 (2005).
16. Wang, H. et al. Improved seamless mutagenesis by recombineering using ccdB for counterselection. Nucleic Acids Res. 42, e37 (2014).
17. Zhang, Y., Buchholz, F., Muyrers, J.P. & Stewart, A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20, 123-128 (1998).
18. Zhang, Y., Muyrers, J.P., Testa, G. & Stewart, A.F. DNA cloning by homologous recombination in Escherichia coli. Nat. Biotechnol. 18, 1314-1317 (2000).
19. Bian, X. et al. Direct cloning, genetic engineering, and heterologous expression of the syringolin biosynthetic gene cluster in E. coli through Red/ET recombineering. Chembiochem 13, 1946-1952 (2012).
20. Bian, X. et al. Heterologous production of glidobactins/luminmycins in Escherichia coli Nissle containing the glidobactin biosynthetic gene cluster from Burkholderia DSM7029. Chembiochem 15, 2221-2224 (2014).
21. Bian, X. et al. In vivo evidence for a prodrug activation mechanism during colibactin maturation. Chembiochem 14, 1194-1197 (2013).
22. Kouprina, N. & Larionov, V. Selective isolation of genomic loci from complex genomes by transformation-Associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 3, 371-377 (2008).
23. Shao, Z. & Zhao, H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 37, e16 (2009).
24. Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
25. Muyrers, J.P., Zhang, Y., Testa, G. & Stewart, A.F. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 27, 1555-1557 (1999).
26. Muyrers, J.P. et al. Point mutation of bacterial artificial chromosomes by ET recombination. EMBO Rep. 1, 239-243 (2000).
27. Eustaquio, A.S. et al. Heterologous expression of novobiocin and clorobiocin biosynthetic gene clusters. Appl. Environ. Microbiol. 71, 2452-2459 (2005).
28. Binz, T.M., Wenzel, S.C., Schnell, H.J., Bechthold, A. & Möller, R. Heterologous expression and genetic engineering of the phenalinolactone biosynthetic gene cluster by using red/ET recombineering. Chembiochem 9, 447-454 (2008).
29. Ongley, S.E. et al. High-Titer heterologous production in E. coli of lyngbyatoxin, a protein kinase C activator from an uncultured marine cyanobacterium. ACS Chem. Biol. 8, 1888-1893 (2013).
30. Tang, L. et al. Elucidating the mechanism of cis double bond formation in epothilone biosynthesis. J. Am. Chem. Soc. 126, 46-47 (2004).
31. Bian, X., Plaza, A., Yan, F., Zhang, Y. & Möller, R. Rational and efficient site-directed mutagenesis of adenylation domain alters relative yields of luminmide derivatives in vivo. Biotechnol. Bioeng. 112, 1343-1353 (2015).
32. Nguyen, K.T. et al. Genetically engineered lipopeptide antibiotics related to A54145 and daptomycin with improved properties. Antimicrob. Agents Chemother. 54, 1404-1413 (2010).
33. Nguyen, K.T. et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin. Proc. Natl. Acad. Sci. USA 103, 17462-17467 (2006).
34. Alexander, D.C. et al. Development of a genetic system for combinatorial biosynthesis of lipopeptides in Streptomyces fradiae and heterologous expression of the A54145 biosynthesis gene cluster. Appl. Environ. Microbiol. 76, 6877-6887 (2010).
35. Yin, J. et al. Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2). Sci. Rep. 5, 15081 (2015).
36. Wang, J. et al. An improved recombineering approach by adding RecA to lambda Red recombination. Mol. Biotechnol. 32, 43-53 (2006).
37. Sarov, M. et al. A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat. Methods 3, 839-844 (2006).
38. Filutowicz, M., McEachern, M.J. & Helinski, D.R. Positive and negative roles of an initiator protein at an origin of replication. Proc. Natl. Acad. Sci. USA 83, 9645-9649 (1986).
39. Sorensen, H.P. & Mortensen, K.K. Advanced genetic strategies for recombinant protein expression in Escherichia coli. J. Biotechnol. 115, 113-128 (2005).
40. Li, Y. et al. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Sci. Rep. 5, 9383 (2015).
41. Frengen, E. et al. A modular, positive selection bacterial artificial chromosome vector with multiple cloning sites. Genomics 58, 250-253 (1999).
42. Mei, J., Benashski, S. & Firshein, W. Interactions of the origin of replication (oriV) and initiation proteins (TrfA) of plasmid RK2 with submembrane domains of Escherichia coli. J. Bacteriol. 177, 6766-6772 (1995).
43. Nedelkova, M. et al. Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting. Nucleic Acids Res. 39, e137 (2011).
44. Lynch, M.D. & Gill, R.T. Broad host range vectors for stable genomic library construction. Biotechnol. Bioeng. 94, 151-158 (2006).
45. Antoine, R. & Locht, C. Isolation and molecular characterization of a novel broad-host-range plasmid from Bordetella bronchiseptica with sequence similarities to plasmids from gram-positive organisms. Mol. Microbiol. 6, 1785-1799 (1992).
46. Bi, C. et al. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb. Cell Fact. 12, 107 (2013).