Synthetic RNA switches as a tool for temporal and spatial control over gene expression

Current Opinion in Biotechnology

Volumn 23, Issue 5, 2012, Pages 679-688

  Chang, Andrew L ^a   Wolf, Joshua J ^b   Smolke, Christina D ^b  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SYSTEM; CHEMICAL SYNTHESIS; CONTROL FUNCTIONS; DYNAMIC MODULATION; ENERGY PRODUCTIONS; ENVIRONMENTAL REMEDIATION; ENVIRONMENTAL SIGNALS; ENVIRONMENTAL SUSTAINABILITY; FUNCTIONAL DIVERSITY; GENETIC CIRCUITS; GENETIC SYSTEMS; RNA INTERFERENCE; SPATIAL CONTROL;

DATA PROCESSING; FUNCTIONAL PROGRAMMING; GENE EXPRESSION; GENETIC PROGRAMMING;

RNA;

APTAMER; ATRAZINE; BIM PROTEIN; DICER; INTERLEUKIN 15; INTERLEUKIN 2; MESSENGER RNA; PROTEIN BCL XL; RIBONUCLEASE; RIBOZYME; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; TETRACYCLINE; THEOPHYLLINE;

ALTERNATIVE RNA SPLICING; APOPTOSIS; BIOREMEDIATION; CYTOKINE PRODUCTION; GENE CONTROL; GENE EXPRESSION REGULATION; HETEROLOGOUS EXPRESSION; HUMAN; IMMUNOTHERAPY; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; REVIEW; RNA DEGRADATION; RNA INTERFERENCE; RNA STABILITY; RNA STRUCTURE; SYNTHETIC BIOLOGY; SYNTHETIC RNA SWITCH; T LYMPHOCYTE; TRANSCRIPTION REGULATION; TRANSLATION REGULATION; UNTRANSLATED REGION;

ENVIRONMENT; ENVIRONMENTAL REMEDIATION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENES, SWITCH; HUMANS; MEDICINE; RNA; RNA INTERFERENCE; RNA SPLICING; RNA STABILITY; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 84867195988     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2012.01.005     Document Type: Review

References (71)

1. Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat Biotechnol 2009, 27:1139-1150.
2. Liang J.C., Bloom R.J., Smolke C.D. Engineering biological systems with synthetic RNA molecules. Mol Cell 2011, 43:915-926.
3. Saito H., Kobayashi T., Hara T., Fujita Y., Hayashi K., Furushima R., Inoue T. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat Chem Biol 2010, 6:71-78.
4. Stoltenburg R., Reinemann C., Strehlitz B. SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007, 24:381-403.
5. Lucks J.B., Qi L., Mutalik V.K., Wang D., Arkin A.P. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A 2011, 108:8617-8622.
6. Culler S.J., Hoff K.G., Smolke C.D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 2010, 330:1251-1255.
7. Win M.N., Smolke C.D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 2007, 104:14283-14288.
8. Chen Y.Y., Jensen M.C., Smolke C.D. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci U S A 2010, 107:8531-8536.
9. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
10. Saito H., Fujita Y., Kashida S., Hayashi K., Inoue T. Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun 2011, 2:160.
11. Rinaudo K., Bleris L., Maddamsetti R., Subramanian S., Weiss R., Benenson Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007, 25:795-801.
12. Narberhaus F., Waldminghaus T., Chowdhury S. RNA thermometers. FEMS Microbiol Rev 2006, 30:3-16.
13. Breaker R.R. Prospects for riboswitch discovery and analysis. Mol Cell 2011, 43:867-879.
14. Neupert J., Karcher D., Bock R. Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli. Nucleic Acids Res 2008, 36:e124.
15. Waldminghaus T., Kortmann J., Gesing S., Narberhaus F. Generation of synthetic RNA-based thermosensors. Biol Chem 2008, 389:1319-1326.
16. Isaacs F.J., Dwyer D.J., Ding C., Pervouchine D.D., Cantor C.R., Collins J.J. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 2004, 22:841-847.
17. Famulok M., Mayer G. Intramers and aptamers: applications in protein-function analyses and potential for drug screening. Chembiochem 2005, 6:19-26.
18. Hunsicker A., Steber M., Mayer G., Meitert J., Klotzsche M., Blind M., Hillen W., Berens C., Suess B. An RNA aptamer that induces transcription. Chem Biol 2009, 16:173-180.
19. Auslander D., Wieland M., Auslander S., Tigges M., Fussenegger M. Rational design of a small molecule-responsive intramer controlling transgene expression in mammalian cells. Nucleic Acids Res 2011, 39:e155.
20. Redmond M.C., Valentine D.L. Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A 2011, 10.1073/pnas.1108756108.
21. Sinha J., Reyes S.J., Gallivan J.P. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol 2010, 6:464-470.
22. Friedland A.E., Lu T.K., Wang X., Shi D., Church G., Collins J.J. Synthetic gene networks that count. Science 2009, 324:1199-1202.
23. Callura J.M., Dwyer D.J., Isaacs F.J., Cantor C.R., Collins J.J. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A 2010, 107:15898-15903.
24. Xie Z., Wroblewska L., Prochazka L., Weiss R., Benenson Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 2011, 333:1307-1311.
25. Sharma V., Yamamura A., Yokobayashi Y. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth Biol 2011, 1:6-13.
26. Storz G., Vogel J., Wassarman K.M. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011, 43:880-891.
27. Karginov F.V., Hannon G.J. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 2010, 37:7-19.
28. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011, 43:904-914.
29. Ogawa A. Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. RNA 2011, 17:478-488.
30. Joyce G.F. Forty years of in vitro evolution. Angew Chem Int Ed Engl 2007, 46:6420-6436.
31. Beisel C.L., Bayer T.S., Hoff K.G., Smolke C.D. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol 2008, 4:224.
32. Beisel C.L., Smolke C.D. Design principles for riboswitch function. PLoS Comput Biol 2009, 5:e1000363.
33. Win M.N., Smolke C.D. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456-460.
34. Muranaka N., Yokobayashi Y. A synthetic riboswitch with chemical band-pass response. Chem Commun 2010, 46:6825-6827.
35. Muranaka N., Yokobayashi Y. Posttranscriptional signal integration of engineered riboswitches yields band-pass output. Angew Chem Int Ed Engl 2010, 49:4653-4655.
36. Sharma V., Nomura Y., Yokobayashi Y. Engineering complex riboswitch regulation by dual genetic selection. J Am Chem Soc 2008, 130:16310-16315.
37. Topp S., Gallivan J.P. Guiding bacteria with small molecules and RNA. J Am Chem Soc 2007, 129:6807-6811.
38. Delebecque C.J., Lindner A.B., Silver P.A., Aldaye F.A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 2011, 333:470-474.
39. Stapleton J.A., Endo K., Fujita Y., Hayashi K., Takinoue M., Saito H., Inoue T. Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol 2011, 10.1021/sb200005w.
40. Buskirk A.R., Landrigan A., Liu D.R. Engineering a ligand-dependent RNA transcriptional activator. Chem Biol 2004, 11:1157-1163.
41. Thompson K.M., Syrett H.A., Knudsen S.M., Ellington A.D. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2002, 2:21.
42. Weigand J.E., Suess B. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res 2007, 35:4179-4185.
43. Yoshimatsu T., Nagawa F. Control of gene expression by artificial introns in Saccharomyces cerevisiae. Science 1989, 244:1346-1348.
44. Kim D.S., Gusti V., Dery K.J., Gaur R.K. Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing. BMC Mol Biol 2008, 9:23.
45. Babiskin A.H., Smolke C.D. Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules. Nucleic Acids Res 2011, 39:5299-5311.
46. Auslander S., Ketzer P., Hartig J.S. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol BioSyst 2010, 6:807-814.
47. Beisel C.L., Chen Y.Y., Culler S.J., Hoff K.G., Smolke C.D. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res 2011, 39:2981-2994.
48. Kumar D., An C.I., Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. J Am Chem Soc 2009, 131:13906-13907.
49. An C.I., Trinh V.B., Yokobayashi Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006, 12:710-716.
50. Tuleuova N., An C.I., Ramanculov E., Revzin A., Yokobayashi Y. Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction. Biochem Biophys Res Commun 2008, 376:169-173.
51. Leisner M., Bleris L., Lohmueller J., Xie Z., Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol 2010, 5:666-670.
52. Lynch S.A., Desai S.K., Sajja H.K., Gallivan J.P. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol 2007, 14:173-184.
53. Lynch S.A., Gallivan J.P. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 2009, 37:184-192.
54. Topp S., Gallivan J.P. Random walks to synthetic riboswitches-a high-throughput selection based on cell motility. Chembiochem 2008, 9:210-213.
55. Topp S., Gallivan J.P. Riboswitches in unexpected places-a synthetic riboswitch in a protein coding region. RNA 2008, 14:2498-2503.
56. Topp S., Reynoso C.M., Seeliger J.C., Goldlust I.S., Desai S.K., Murat D., Shen A., Puri A.W., Komeili A., Bertozzi C.R., et al. Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol 2010, 76:7881-7884.
57. Suess B., Fink B., Berens C., Stentz R., Hillen W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 2004, 32:1610-1614.
58. Verhounig A., Karcher D., Bock R. Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc Natl Acad Sci U S A 2010, 107:6204-6209.
59. Nomura Y., Yokobayashi Y. Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 2007, 129:13814-13815.
60. Muranaka N., Sharma V., Nomura Y., Yokobayashi Y. An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res 2009, 37:e39.
61. Dixon N., Duncan J.N., Geerlings T., Dunstan M.S., McCarthy J.E., Leys D., Micklefield J. Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci U S A 2010, 107:2830-2835.
62. Ogawa A., Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007, 17:3156-3160.
63. Wieland M., Hartig J.S. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 2008, 47:2604-2607.
64. Wieland M., Benz A., Klauser B., Hartig J.S. Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl 2009, 48:2715-2718.
65. Grate D., Wilson C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 2001, 9:2565-2570.
66. Kotter P., Weigand J.E., Meyer B., Entian K.D., Suess B. A fast and efficient translational control system for conditional expression of yeast genes. Nucleic Acids Res 2009, 37:e120.
67. Weigand J.E., Sanchez M., Gunnesch E.B., Zeiher S., Schroeder R., Suess B. Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008, 14:89-97.
68. Stripecke R., Oliveira C.C., McCarthy J.E., Hentze M.W. Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells. Mol Cell Biol 1994, 14:5898-5909.
69. Bayer T.S., Smolke C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 2005, 23:337-343.
70. Harvey I., Garneau P., Pelletier J. Inhibition of translation by RNA-small molecule interactions. RNA 2002, 8:452-463.
71. Werstuck G., Green M.R. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282:296-298.