Efficient design strategy for whole-cell and cell-free biosensors based on engineered riboswitches

Analytical Letters

Volumn 42, Issue 1, 2009, Pages 108-122

  Muranaka, Norihito ^a   Sharma, Vandana ^a   Nomura, Yoko ^a   Yokobayashi, Yohei ^a  

^a University of California   (United States)

Author keywords

Cell free biosensor; Dual genetic selection; Riboswitch; Whole cell biosensor

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 60549087743     PISSN: 00032719     EISSN: 1532236X     Source Type: Journal    
DOI: 10.1080/00032710802568556     Document Type: Article

References (37)

1. Belkin, S. 2003. Microbial whole-cell sensing systems of environmental pollutants. Curr. Opin. Microbiol., 6(3): 206-212.
2. Bolivar, F., Rodriguez, R.L., Greene, P.J., Betlach, M.C., Heyneker, H.L., and Boyer, H.W. 1977. Construction and characterization of new cloning vehicles, II: A multipurpose cloning system. Gene., 2(2): 95-113.
3. Courtois, F., Olguin, L.F., Whyte, G., Bratton, D., Huck, W.T., Abell, C., and Hollfelder, F. 2008. An integrated device for monitoring time-dependent in vitro expression from single genes in picolitre droplets. Chembiochem., 9(3): 439-446.
4. Daunert, S., Barrett, G., Feliciano, J.S., Shetty, R.S., Shrestha, S., and Smith-Spencer, W. 2000. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem. Rev., 100(7): 2705-2738.
5. Desai, S.K. and Gallivan, J.P. 2004. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc., 126(41): 13247-13254.
6. Dittrich, P.S., Jahnz, M., and Schwille, P. 2005. A new embedded process for compartmentalized cell-free protein expression and on-line detection in microfluidic devices. Chembiochem., 6(5): 811-814.
7. Ellington, A.D. and Szostak, J.W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature, 346(6287): 818-822.
8. Fowler, C.C., Brown, E.D., and Li, Y. 2008. A FACS-based approach to engineering Artificial Riboswitches. Chembiochem., 9(12): 1906-1911.
9. Galvao, T.C. and de Lorenzo, V. 2006. Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr. Opin. Biotechnol., 17(1): 34-42.
10. Hartig, J.S. 2007. Teaching bacteria new tricks - with RNA switches. Angew. Chem., Int. Ed. Engl., 46(41): 7741-7743.
11. Ishikawa, K., Sato, K., Shima, Y., Urabe, I., and Yomo, T. 2004. Expression of a cascading genetic network within liposomes. FEBS Lett., 576(3): 387-390.
12. Jenison, R.D., Gill, S.C., Pardi, A., and Polisky, B. 1994. High-resolution molecular discrimination by RNA. Science, 263(5152): 1425-1429.
13. Kajihara, D., Abe, R., Iijima, I., Komiyama, C., Sisido, M. and Hohsaka, T. 2006. FRET analysis of protein conformational change through position-specific incorporation of fluorescent amino acids. Nat. Methods., 3(11): 923-929.
14. Lynch, S.A., Desai, S.K., Sajja, H.K., and Gallivan, J.P. 2007. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem. Biol., 14(2): 173-184.
15. Mei, Q., Fredrickson, C.K., Jin, S., and Fan, Z.H. 2005. Toxin detection by a miniaturized in vitro protein expression array. Anal. Chem., 77(17): 5494-5500.
16. Mei, Q., Fredrickson, C. K., Simon, A., Khnouf, R., and Fan, Z.H. 2007. Cell-free protein synthesis in microfluidic array devices. Biotechnol. Prog., 23(6): 1305-1311.
17. Navani, N.K. and Li, Y. 2006. Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol., 10(3): 272-281.
18. Noireaux, V. and Libchaber, A. 2004. A vesicle bioreactor as a step toward an artificial cell assembly. Proc. Natl. Acad. Sci. USA, 101(51): 17669-17674.
19. Nomura, Y. and Yokobayashi, Y. 2007a. Dual selection of a genetic switch by a single selection marker. Biosystems, 90(1): 115-120.
20. Nomura, Y. and Yokobayashi, Y. 2007b. Reengineering a natural riboswitch by dual genetic selection. J. Am. Chem. Soc., 129(45): 13814-13815.
21. Nudler, E. and Mironov, A.S. 2004. The riboswitch control of bacterial metabolism. Trends Biochem. Sci., 29(1): 11-17.
22. Ogawa, A. and Maeda, M. 2007. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg. Med. Chem. Lett., 17(11): 3156-3160.
23. Ogawa, A. and Maeda, M. 2008. An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem., 9(2): 206-209.
24. Pellinen, T., Huovinen, T. and Karp, M. 2004. A cell-free biosensor for the detection of transcriptional inducers using firefly luciferase as a reporter. Anal. Biochem., 330(1): 52-57.
25. Rentmeister, A., Mayer, G., Kuhn, N. and Famulok, M. 2007. Conformational changes in the expression domain of the Escherichia coli thiM riboswitch. Nucleic Acids. Res., 35(11): 3713-3722.
26. Sando, S., Narita, A., Abe, K. and Aoyama, Y. 2005. Doubly catalytic sensing of HIV-1-related CCR5 sequence in prokaryotic cell-free translation system using riboregulator-controlled luciferase activity. J. Am. Chem. Soc., 127(15): 5300-5301.
27. Schwalbe, H., Buck, J., Furtig, B., Noeske, J., and Wohnert, J. 2007. Structures of RNA switches: Insight into molecular recognition and tertiary structure. Angew. Chem., Int. Ed. Engl., 46(8): 1212-1219.
28. Soukup, G. A. and Breaker, R.R. 1999. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA, 96(7): 3584-3589.
29. Suess, B., Fink, B., Berens, C., Stentz, R., and Hillen, W. 2004. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids. Res., 32(4): 1610-1614.
30. Thompson, K.M., Syrett, H.A., Knudsen, S.M., and Ellington, A. D. 2002. Group I aptazymes as genetic regulatory switches. BMC Biotechnol., 2: 21.
31. Tucker, B.J. and Breaker, R.R. 2005. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol., 15(3): 342-348.
32. Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249(4968): 505-510.
33. Welz, R. and Breaker, R.R. 2007. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA, 13(4): 573-582.
34. Winkler, W., Nahvi, A., and Breaker, R.R. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature, 419(6910): 952-956.
35. Yagi, K. 2007. Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl. Microbiol. Biotechnol., 73(6): 1251-1258.
36. Yamamoto, T., Fujii, T., and Nojima, T. 2002. PDMS-glass hybrid microreactor array with embedded temperature control device: Application to cell-free protein synthesis. Lab. Chip., 2(4): 197-202.
37. Yamamoto, T., Hino, M., Kakuhata, R., Nojima, T., Shinohara, Y., Baba, Y., and Fujii, T. 2008. Evaluation of cell-free protein synthesis using PDMS-based microreactor arrays. Anal. Sci., 24(2): 243-246.