Engineered riboregulators enable post-transcriptional control of gene expression

Nature Biotechnology

Volumn 22, Issue 7, 2004, Pages 841-847

  Isaacs, Farren J ^a,b   Dwyer, Daniel J ^a,c   Ding, Chunming ^a   Pervouchine, Dmitri D ^a   Cantor, Charles R ^a,b   Collins, James J ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

^c Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CELLS; ESCHERICHIA COLI; RNA;

RIBOSOME BINDING; STEM-LOOP STRUCTURE;

GENES;

MESSENGER RNA;

5' UNTRANSLATED REGION; ARTICLE; BINDING SITE; ENZYME STRUCTURE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE INSERTION; GENE SEQUENCE; GENE TARGETING; GENETIC ENGINEERING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROCESSING; RNA RNA HYBRIDIZATION; RNA STRUCTURE; TRANSCRIPTION REGULATION;

5' UNTRANSLATED REGIONS; ANIMALS; ESCHERICHIA COLI; GENE SILENCING; GENETIC ENGINEERING; GREEN FLUORESCENT PROTEINS; RIBOSOMES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA, UNTRANSLATED; TRANS-ACTIVATION (GENETICS);

ESCHERICHIA COLI; INSERTION SEQUENCES;

EID: 3042741121     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt986     Document Type: Article

References (50)

1. Gesteland, R.F., Cech, T.R. & Atkins, J.F. The RNA World, edn. 2 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1999).
2. Joyce, G.F. The antiquity of RNA-based evolution. Nature 418, 214-221 (2002).
3. Eddy, S.R. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2, 919-929 (2001).
4. Kruger, K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena, Cell 31, 147-157 (1982).
5. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The TNA moiety of ribonuclease P is the catalytic subunit of the enzyme, Cell 35, 849-857 (1983).
6. Doudna, J.A. & Cech, T.R. The chemical repertoire of natural ribozymes. Nature 418, 222-228 (2002).
7. Steward, P., Molin, S. & Nordstrom, K. RNAs involved in copy-number control and incompatibility of plasmid R1. Proc. Natl. Acad. Sci. USA 78, 6008-6012 (1981).
8. Wagner, E.G.H. & Simons, R.W. Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol. 48, 713-742 (1994).
9. Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854 (1993).
10. Gottesman, S. Stealth regulation: biological circuits with small RNA switches. Genes Dev. 16, 2829-2842 (2002).
11. Gelfand, M.S., Mironov, A.A., Jomantas, J., Kozlov, Y.I. & Perumov, D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15, 439-442 (1999).
12. Winkler, W., Nahvi, A. & Breaker, R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952-656 (2002).
13. Johansson, J. et al. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110, 551-561 (2002).
14. Mironov, A. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747-756 (2002).
15. Morita, M.T. et al. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 13, 655-665 (2002).
16. Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C. & Breaker, R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577-586 (2003).
17. Winkler, W., Nahvi, A., Roth, A., Collins, J.A. & Breaker, R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281-286 (2004).
18. Lease, R.A. & Belfort, M. A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl. Acad. Sci. USA 97, 9919-9924 (2000).
19. Majdalani, N., Hernandez, D. & Gottesman, S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46, 813-826 (2002).
20. Opalinska, J.B. & Gewirtz, A.M. Nucleic-acid therapeutics: basic principles and recent applications. Nat. Rev. Drug Discov. 1, 503-514 (2002).
21. Good, L. Translation repression by antisense sequences. Cell. Mol. LifeSci. 60, 854-861 (2003).
22. Ji, Y. et al. Identification of critical Staphylococcal gene using conditional phenotypes generated by antisense RNA. Science 293, 2266-2269 (2001).
23. Dykxhoorn, D., Novina, C.D. & Sharp, P.A. Killing the messenger: Short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol. 4, 457-467 (2003).
24. Wagner, E.G.H. & Flardh, K. Antisense RNAs everywhere? Trends Genet. 18, 223-226 (2002).
25. Engdahl, H.M., Lindell, M. & Wagner, E.G.H. Introduction of an RNA stability element at the 5′-end of an antisense RNA cassette increases the inhibition of target RNA translation. Antisense Nucleic A. 11, 29-40 (2001).
26. Morfeldt, E., Taylor, D., von Gabain, A. & Arvidson, S. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J. 14, 4569-4577 (1995).
27. Franch, T., Petersen, M., Wagner, E.G.H., Jacobsen, J.P. & Gerdes, K. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J. Mol. Biol. 294, 1115-1125 (1999).
28. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003).
29. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/0, the TetR/0 and AraCl1-12 regulatory elements. Nucleic Acids Res. 25, 1203-1210 (1997).
30. Cormack, B.P., Valdivia, R.C. & Falkow, S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173, 33-38 (1996).
31. Hjalt, T.A.H. & Wagner, E.G.H. Bulged-out nucleotides protect an antisense RNA from RNase III cleavage. Nucleic Acids Res. 23, 571-579 (1995).
32. Court, D. RNA processing and degradation by RNase III, Control of Messenger RNA Stability, (eds. Belasco, J. & Brawerman, G.) 71-116. (Academic Press, New York, 1993).
33. Rivas, E., Klein, R.J., Jones, T.A. & Eddy, S.R. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr. Biol. 11, 1369-1373 (2001).
34. Altuvia, S. & Wagner, E.G.H. Switching on and off with RNA. Proc. Natl. Acad. Sci. USA 97, 9824-9826 (2000).
35. Hasty, J., McMillen, D. & Collins, J.J. Engineered gene circuits, Nature 420, 224-230 (2002).
36. Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105 (2003).
37. Bartel, D.P. & Szostak, J.W. Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411-1418 (1993).
38. Wilson, D.S. & Szostak, J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611-647 (1999).
39. Ellington, A.D. & Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822 (1990).
40. Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510 (1990).
41. Joyce, G.F. Amplification, mutation and selection of catalytic RNA. Gene 82, 83-87 (1989).
42. Robertson, M.P. & Ellington, A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol. 17, 62-66 (1999).
43. Faulhammer, D., Cukras, A.R., Lipton, R.J. & Landweber, L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA 97, 1385-1389 (2000).
44. Smith, H.O., Hutchison, C.A. III, Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: φx174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 100, 15440-15445 (2003).
45. Tabor, J.J. & Ellington, A.D. Playing to win at DNA computation. Nat. Biotechnol. 21, 1013-1015 (2003).
46. Stojanovic, M.N. & Stefanovic, D. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21, 1069-1074 (2003).
47. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual edn. 2 (Cold Spring Harbor Laboratory Press, Plainview, New York, 1989).
48. Andersen, J.B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64, 2240-2246 (1998).
49. Ding, C. & Cantor, C.R. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc. Natl. Acad. Sci. USA 100, 3059-3064 (2003).
50. Marky, L.A. & Breslauer, K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26, 1601-1620 (1987).