Optimization of Synthetic Operons Using Libraries of Post-Transcriptional Regulatory Elements

Methods in Molecular Biology

Volumn 765, Issue , 2011, Pages 99-111

  Agnew, Daniel E ^a   Pfleger, Brian F ^a  

^a University of Wisconsin Madison   (United States)

Author keywords

Intergenic sequence; Megaprimer PCR; Metabolic engineering; mRNA stability; Operon; Promoter; Ribosome binding site; Synthetic biology; Transcription termination

Indexed keywords

PROKARYOTA;

SYNTHETIC DNA;

ARTICLE; GENE LIBRARY; GENETIC TRANSCRIPTION; GENETICS; OPERON; PROTEIN SYNTHESIS; REGULATORY RNA SEQUENCE; RNA STABILITY;

GENE LIBRARY; GENES, SYNTHETIC; OPERON; PROTEIN BIOSYNTHESIS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA STABILITY; TRANSCRIPTION, GENETIC;

EID: 80052960456     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-197-0_7     Document Type: Chapter

References (47)

1. Khosla C., and Keasling J. D. (2003) Timeline-Metabolic engineering for drug discovery and development. Nature Reviews Drug Discovery 2, 1019–1025.
2. Martin V. J. J., Pitera D. J., Withers S. T., Newman J. D., and Keasling J. D. (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796–802.
3. Baga M., Goransson M., Normark S., and Uhlin B. E. (1988) Processed messenger-RNA with differential stability in the regulation of E. coli pilin gene expression. Cell 52, 197–206.
4. Nishizaki T., Tsuge K., Itaya M., Doi N., and Yanagawa H. (2007) Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis. Appl. Environ. Microbiol. 73, 1355–1361.
5. 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-U112.
6. Kizer L., Pitera D. J., Pfleger B. F., and Keasling J. D. (2008) Application of functional genomics to pathway optimization for increased isoprenoid production. Appl. Environ. Microbiol. 74, 3229–3241.
7. Guzman L. M., Belin D., Carson M. J., and Beckwith J. (1995) Tight Regulation, Modulation, and High-Level Expression by Vectors Containing the Arabinose PBAD Promoter. J. Bacteriol. 177, 4121–4130.
8. Carrier T. A., and Keasling J. D. (1999) Library of synthetic 5‘ secondary structures to manipulate mRNA stability in Escherichia coli. Biotechnol. Prog. 15, 58–64.
9. Smolke C. D., Carrier T. A., and Keasling J. D. (2000) Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures. Appl. Environ. Microbiol. 66, 5399–5405.
10. Jana S., and Deb J. K. (2005) Strategies for efficient production of heterologous proteins in Escherichia coli. Appl. Microbiol. Biotechnol. 67, 289–298.
11. Hammer K., Mijakovic I., and Jensen P. R. (2006) Synthetic promoter libraries-tuning of gene expression. Trends Biotechnol. 24, 53–55.
12. Kozak M. (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361, 13–37.
13. Seo S. W., Yang J., and Jung G. Y. (2009) Quantitative Correlation Between mRNA Secondary Structure Around the Region Downstream of the Initiation Codon and Translational Efficiency in Escherichia coli. Biotechnol. Bioeng. 104, 611–616.
14. Pfleger B. F., Pitera D. J., D Smolke C., and Keasling J. D. (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 24, 1027–1032.
15. Sambrook J., Russell D. W. (2001) Molecular cloning: a laboratory manual Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
16. Studier F. W., Rosenberg A. H., Dunn J. J., and Dubendorff J. W. (1990) Use of T7 RNA-polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60–89.
17. Bartlett J. M. S., and Stirling D., (Eds.) (2003) PCR Protocols, Vol. 226, second ed., Humana Press.
18. Ambion’s Appendix-DNA and RNA Molecular Weights and Conversions, Applied Biosystems. http://www.ambion.com/techlib/append/na_mw_tables.html.
19. Meynial-Salles I., Cervin M. A., and Soucaille P. (2005) New tool for metabolic pathway engineering in Escherichia coli: One-step method to modulate expression of chromosomal genes. Appl. Environ. Microbiol. 71, 2140–2144.
20. Graham J. E. (2004) Sequence-specific Rho-RNA interactions in transcription termination. Nucleic Acids Res. 32, 3093–3100.
21. Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.
22. Desmit M. H., and Vanduin J. (1994) Translational initiation on structured messengers: another role for the Shine-Dalgarno interaction. J. Mol. Biol. 235, 173–184.
23. Canton B., Labno A., and Endy D. (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 26, 787–793.
24. Aslanidis C., and Dejong P. J. (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069–6074.
25. Datsenko K. A., and Wanner B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U.S.A. 97, 6640–6645.
26. Stols L., Gu M. Y., Dieckman L., Raffen R., Collart F. R., and Donnelly M. I. (2002) A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expression Purif. 25, 8–15.
27. Benders G. A., Noskov V. N., Denisova E. A., Lartigue C., Gibson D. G., Assad-Garcia N., Chuang R. Y., Carrera W., Moodie M., Algire M. A., Phan Q., Alperovich N., Vashee S., Merryman C., Venter J. C., Smith H. O., Glass J. I., and Hutchison C. A. (2010) Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38, 2558–2569.
28. 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-U341.
29. DeWitt W., and Helinski D. R. (1965) Characterization of colicinogenic factor E1 from a non-induced and a mitomycin C-induced Proteus strain. J. Mol. Biol. 13, 692–703.
30. Altingmees M. A., and Short J. M. (1989) pBlueScript II: gene mapping vectors. Nucleic Acids Res. 17, 9494–9494.
31. Short J. M., Fernandez J. M., Sorge J. A., and Huse W. D. (1988) Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res. 16, 7583–7600.
32. Betlach M., Hershfield V., Chow L., Brown W., Goodman H. M., and Boyer H. W. (1976) Restriction endonuclease analysis of bacterial plasmid controlling EcoRI restriction and modification of DNA. Fed Proc 35, 2037–2043.
33. Yanischperron C., Vieira J., and Messing J. (1985) Improved M13 phage cloning vectors and host strains-nucleotide-sequences of the M13mp18 and pUC19 vectors. Gene 33, 103–119.
34. Vieira J., and Messing J. (1982) The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19, 259–268.
35. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., and Falkow S. (1977) Construction and characterization of new cloning vehicles. II. Multipurpose cloning system. Gene 2, 95–113.
36. Antoine R., and Locht C. (1992) Isolation and molecular characterization of a novel broad-host-range plasmid from Bordetella bron-chiseptica with sequence similarities to plasmids from gram-positive organisms. Mol. Microbiol. 6, 1785–1799.
37. Kovach M. E., Phillips R. W., Elzer P. H., Roop R. M., and Peterson K. M. (1994) pBBR1MCS: a broad-host-range cloning vector. BioTechniques 16, 800-&.
38. Cozzarelli N.R, Kelly R. B., and Kornberg A. (1968) A minute circular DNA from Escherichia coli 15. Proc Natl Acad Sci U.S.A. 60, 992–999.
39. Chang A. C. Y., and Cohen S. N. (1978) Construction and characterization of amplifi-able multicopy DNA cloning vehicles derived from p15A cryptic miniplasmid. J. Bacteriol. 134, 1141–1156.
40. Cohen S. N., and Chang A. C. Y. (1973) Recircularization and autonomous replication of a sheared R-factor DNA segment in Escherichia coli transformants: (plasmid/trans-formation/antibiotic resistance/DNA). Proc Natl Acad Sci U.S.A. 70, 1293–1297.
41. Tabor S., and Richardson C. C. (1985) A bacteriophage T7 RNA polymerase promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U.S.A. 82, 1074–1078.
42. Giordano T. J., Deuschle U., Bujard H., and McAllister W. T. (1989) Regulation of coliphage T3 and coliphage T7 RNA poly-merases by the lac repressor-operator system. Gene 84, 209–219.
43. Deboer H. A., Comstock L. J., and Vasser M. (1983) The tac promoter-a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci U.S.A. 80, 21–25.
44. Brosius J., Erfle M., and Storella J. (1985) Spacing of the −10 and −35 regions in the tac promoter: effect on its in vivo activity. J. Biol. Chem. 260, 3539–3541.
45. Elvin C. M., Thompson P. R., Argall M. E., Hendry P., Stamford N. P. J., Lilley P. E., and Dixon N. E. (1990) Modified bacteriophage lambda promoter vectors for overproduction of proteins in Escherichia coli. Gene 87, 123–126.
46. Skerra A. (1994) Use of the tetracycline promoter for the tightly regulated production of a murine antibody fragment in Escherichia coli. Gene 151, 131–135.
47. Lee S. K., and Keasling J. D. (2005) A propi-onate-inducible expression system for enteric bacteria. Appl. Environ. Microbiol. 71, 6856–6862.