Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes

Nature Biotechnology

Volumn 24, Issue 8, 2006, Pages 1027-1032

  Pfleger, Brian F ^a   Pitera, Douglas J ^a   Smolke, Christina D ^a,d   Keasling, Jay D ^a,b,c  

^a University of California   (United States)

^b University of California at Berkeley   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; BIOTECHNOLOGY; GENES;

COMBINATORIAL ENGINEERING; OPERONS; SYNTHETIC BIOLOGY; TUNABLE INTERGENIC REGIONS (TIGR);

GENETIC ENGINEERING;

MEVALONIC ACID; SPACER DNA;

ARTICLE; BIOSYNTHESIS; CONTROLLED STUDY; EUKARYOTE; GENE EXPRESSION; GENE LIBRARY; GENETIC TRANSCRIPTION; NONHUMAN; OPERON; PRIORITY JOURNAL; PROKARYOTE; REPORTER GENE;

ALGORITHMS; DNA, INTERGENIC; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE TRANSFER TECHNIQUES; GENETIC ENGINEERING; OPERON;

EUKARYOTA; PROKARYOTA;

EID: 33747078696     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1226     Document Type: Article

References (29)

1. Khosla, C. & Keasling, J.D. Metabolic engineering for drug discovery and development. Nat. Rev. Drug Discov. 2, 1019-1025 (2003).
2. Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D. & Keasling, J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796-802 (2003).
3. White, M.M. Pretty subunits all in a row: using concatenated subunit constructs to force the expression of receptors with defined stoichiometry and spatial arrangement. Mol. Pharmacol. 69, 407-410 (2006).
4. Endy, D. Foundations for engineering biology. Nature 438, 449-453 (2005).
5. Baga, M., Goransson, M., Normark, S. & Uhlin, B.E. Processed mRNA with differential stability in the regulation of E. coli pilin gene expression. Cell 52, 197-206 (1988).
6. Komar, A.A. & Hatzoglou, M. Internal ribosome entry sites in cellular mRNAs: mystery of their existence. J. Biol. Chem. 280, 23425-23428 (2005).
7. Martin, P., Albagli, O., Poggi, M.C., Boulukos, K.E. & Pognonec, P. Development of a new bicistronic retroviral vector with strong IRES activity. BMC Biotechnol. 6, 4 (2006).
8. Chappell, S.A. & Mauro, V.P. The internal ribosome entry site (IRES) contained within the RNA-binding motif protein 3 (Rbm3) mRNA is composed of functionally distinct elements. J. Biol. Chem. 278, 33793-33800 (2003).
9. Fernandez-Miragall, O., Ramos, R., Ramajo, J. & Martinez-Salas, E. Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA 12, 223-234 (2006).
10. Nudler, E. & Gottesman, M.E. Transcription termination and anti-termination in E. coli. Genes Cells 7, 755-768 (2002).
11. Mandal, M. & Breaker, R.R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5, 451-463 (2004).
12. Arraiano, C.M. & Maquat, L.E. Post-transcriptional control of gene expression: effectors of mRNA decay. Mol. Microbiol. 49, 267-276 (2003).
13. Kushner, S.R. mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life 56, 585-594 (2004).
14. de Smit, M.H. & van Duin, J. Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J. Mol. Biol. 244, 144-150 (1994).
15. Isaacs, F.J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841-847 (2004).
16. Majdalani, N., Vanderpool, C.K. & Gottesman, S. Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol. 40, 93-113 (2005).
17. Smolke, C.D., Carrier, T.A. & Keasling, J.D. Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures. Appl. Environ. Microbiol. 66, 5399-5405 (2000).
18. Smolke, C.D. & Keasling, J.D. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotechnol. Bioeng. 80, 762-776 (2002).
19. Deana, A. & Belasco, J.G. Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev. 19, 2526-2533 (2005).
20. Matz, M.V. et al. Fluorescent proteins from nonbioluminescent Anthozoa species. Nat. Biotechnol. 17, 969-973 (1999).
21. Pfleger, B.F., Fawzi, N.J. & Keasling, J.D. Optimization of DsRed production in Escherichia coli: effect of ribosome binding site sequestration on translation efficiency. Biotechnol. Bioeng. 92, 553-558 (2005).
22. Naureckiene, S. & Uhlin, B.E. In vitro analysis of mRNA processing by RNase E in the pap operon of Escherichia coli. Mol. Microbiol. 21, 55-68 (1996).
23. Kaberdin, V.R. Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assay. Nucleic Acids Res. 31, 4710-4716 (2003).
24. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003).
25. Spickler, C. & Mackie, G.A. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol. 182, 2422-2427 (2000).
26. Gottesman, S. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58, 303-328 (2004).
27. Burke, E. & Barik, S. Megaprimer PCR: application in mutagenesis and gene fusion. Methods Mol. Biol. 226, 525-532 (2003).
28. Sambrook, J., Fritsch, E.F. & Maniatis, T.. Molecular Cloning A Laboratory Manual. (Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989).
29. Rodwell, V.W. et al. 3-Hydroxy-3-methylglutaryl-CoA reductase. Methods Enzymol. 324, 259-280 (2000).