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Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs

  • Sawyer, Eric M. (Department of Biology, Davidson College) ;
  • Barta, Cody (Department of Biology, Missouri Western State University) ;
  • Clemente, Romina (Department of Biology, Davidson College) ;
  • Conn, Michel (Department of Biology, Missouri Western State University) ;
  • Davis, Clif (Department of Biology, Missouri Western State University) ;
  • Doyle, Catherine (Department of Biology, Davidson College) ;
  • Gearing, Mary (Department of Biology, Davidson College) ;
  • Ho-Shing, Olivia (Department of Biology, Davidson College) ;
  • Mooney, Alyndria (Department of Biology, Davidson College) ;
  • Morton, Jerrad (Department of Biology, Missouri Western State University) ;
  • Punjabi, Shamita (Department of Biology, Davidson College) ;
  • Schnoor, Ashley (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Sun, Siya (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Suresh, Shashank (Department of Mathematics, Davidson College) ;
  • Szczepanik, Bryce (Department of Biology, Missouri Western State University) ;
  • Taylor, D. Leland (Department of Biology, Davidson College) ;
  • Temmink, Annie (Department of Mathematics, Davidson College) ;
  • Vernon, William (Department of Biology, Missouri Western State University) ;
  • Campbell, A. Malcolm (Department of Biology, Davidson College) ;
  • Heyer, Laurie J. (Department of Mathematics, Davidson College) ;
  • Poet, Jeffrey L. (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Eckdahl, Todd T. (Department of Biology, Missouri Western State University)
  • Received : 2012.09.10
  • Accepted : 2012.09.18
  • Published : 2012.09.30
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Abstract

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

Keywords

References

  1. Crick, F.H. (1966) Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 19, 548-555. https://doi.org/10.1016/S0022-2836(66)80022-0
  2. Vendeix, F.A., Dziergowska, A., Gustilo, E.M., Graham, W.D., Sproat, B., Malkiewicz, A., and Agris, P.F. (2008) Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding. Biochemistry 47, 6117-6129. https://doi.org/10.1021/bi702356j
  3. Kurata, S., Ohtsuki, T., Wada, T., Kirino, Y., Takai, K., Saigo, K., Watanabe, K., and Suzuki, T. (2003) Decoding property of C5 uridine modification at the wobble position of tRNA anticodon. Nucleic Acids Res Suppl, 245-246.
  4. Elias, Y., and Huang, R.H. (2005) Biochemical and structural studies of A-to-I editing by tRNA:A34 deaminases at the wobble position of transfer RNA. Biochemistry 44, 12057-12065. https://doi.org/10.1021/bi050499f
  5. Takai, K., Okumura, S., Hosono, K., Yokoyama, S., and Takaku, H. (1999) A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system. FEBS Lett 447, 1-4. https://doi.org/10.1016/S0014-5793(99)00255-0
  6. Qian, Q., Curran, J.F., and Bjork, G.R. (1998) The methyl group of the N6-methyl-N6-threonylcarbamoyladenosine in tRNA of Escherichia coli modestly improves the efficiency of the tRNA. J Bacteriol 180, 1808-1813.
  7. Capone, J.P., Sharp, P.A., and RajBhandary, U.L. (1985) Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene. EMBO J 4, 213-221.
  8. Basso, J., Tiganos, E., and Herrington, M.B. (1993) Nonsense suppression in thymine-requiring strains of Escherichia coli is a consequence of altered folate metabolism. Mol Gen Genet 238, 218-224.
  9. Riabnikova, N.A., Sopova, Iu V., Polozkov, G.V., Savelova, M.V., and Inge- Vechtomov, S.G. (2004) Frameshift suppression through inactivation of translation termination in yeast Saccharomyces cerevisiae: significance of the local context. Genetika 40, 885-892.
  10. Rodriguez, E.A., Lester, H.A., and Dougherty, D.A. (2006) In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. Proc Natl Acad Sci USA 103, 8650-8655. https://doi.org/10.1073/pnas.0510817103
  11. Zadorskii, S.P., Borkhsenius, A.S., Sopova, Iu V., Startsev, V.A., and Inge-Vechtomov, S.G. (2003) Suppression of nonsense and frameshift mutations obtained by different methods for inactivating the translation termination factor eRF3 in yeast Saccharomyces cerevisiae. Genetika 39, 489-494.
  12. Magliery, T.J., Anderson, J.C., and Schultz, P.G. (2001) Expanding the Genetic Code: Selection of Efficient Suppressors of Four-base Codons and Identification of "Shifty" Four-base Codons with a Library Approach in Escherichia coli. J Mol Biol 307, 755-769. https://doi.org/10.1006/jmbi.2001.4518
  13. Anderson, J.C., Magliery, T.J., and Schultz, P.G. (2002) Exploring the limits of codon and anticodon size. Chem Biol 9, 237-244. https://doi.org/10.1016/S1074-5521(02)00094-7
  14. Li, Z., Rosenbaum, M.A., Venkataraman, A., Tam, T.K., Katz, E., and Angenent, L.T. (2011) Bacteria-based AND logic gate: a decision-making and self-powered biosensor. Chem Commun 47, 3060-3062. https://doi.org/10.1039/c0cc05037g
  15. Dixon, N., Duncan, J.N., Geerlings, T., Dunstan, M.S., McCarthy, J.E., Leys, D., and Micklefield, J. (2009) Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci USA 107, 2830-2835.
  16. Benenson, Y. (2009) RNA-based computation in live cells. Curr Opin Biotechnol 20, 471-478. https://doi.org/10.1016/j.copbio.2009.08.002
  17. Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., et al. (2010) Construction of a genetic AND gate under a new standard for assembly of genetic parts. BMC Genomics 11 Suppl 4, S16. https://doi.org/10.1186/1471-2164-11-S4-S16
  18. Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellen, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., and Sole, R. (2011) Distributed biological computation with multicellular engineered networks. Nature 469, 207-211. https://doi.org/10.1038/nature09679
  19. Wagner, N. and Ashkenasy, G. (2009) Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chemistry 15, 1765-1775. https://doi.org/10.1002/chem.200801850
  20. Ho-Shing, O., Lau, K.H., Vernon, W., Eckdahl, T.T., and Campbell, A.M. (2012) Assembly of Standardized DNA Parts Using BioBrick Ends in E. coli. In: J P, editor. Gene Synthesis: Methods and Protocols. (New York: Humana Press), pp. 61-76.
  21. Registry of Standard Biological Parts. (2003) [cited 2012 August 14]; Available from: http://partsregistry.org/Main_Page.
  22. Gray, K.M., and Garey, J.R. (2001) The evolution of bacterial LuxI and LuxR quorum sensing regulators. Microbiology 147, 2379-2387. https://doi.org/10.1099/00221287-147-8-2379
  23. O'Connor, M. (2003) tRNA hopping: effects of mutant tRNAs. Biochim Biophys Acta 1630, 41-46. https://doi.org/10.1016/j.bbaexp.2003.09.002
  24. O'Connor, M. (1998) tRNA imbalance promotes -1 frameshifting via near-cognate decoding. J Mol Biol 279, 727-736. https://doi.org/10.1006/jmbi.1998.1832
  25. Baumgardner, J., Acker, K, Adefuye, O., Crowley, S.T., DeLoache, W., Dickson, J.O., Heard, L., Marten, A.T., Morton, N., Ritter, M., et al. (2009) Solving a Hamiltonian Path Problem with a bacterial computer. J Biol Eng 3, 11. https://doi.org/10.1186/1754-1611-3-11
  26. Haynes, K.A., Broderick, M.L., Brown, A.D., Butner, T.L., Dickson, J.O., Harden, W.L., Heard, L.H., Jessen, E.L., Malloy, K.J., Ogden, B.J., et al. (2008) Engineering bacteria to solve the Burnt Pancake Problem. J Biol Eng 2, 8. https://doi.org/10.1186/1754-1611-2-8
  27. Olaniran, A.O., Motebejane, R.M., and Pillay, B. (2008) Bacterial biosensors for rapid and effective monitoring of biodegradation of organic pollutants in wastewater effluents. J Environ Monit 10, 889-893. https://doi.org/10.1039/b805055d
  28. Dua, M., Singh, A., Sethunathan, N., and Johri, A.K. (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59, 143-152. https://doi.org/10.1007/s00253-002-1024-6
  29. Zhang, X. (2009) Twenty years development of metabolic engineering- -a review. Sheng Wu Gong Cheng Xue Bao 25, 1285-1295.
  30. Win, M.N., Liang, J.C., and Smolke, C.D. (2009) Frameworks for programming biological function through RNA parts and devices. Chem Biol 16, 298-310. https://doi.org/10.1016/j.chembiol.2009.02.011
  31. Win, M.N., and Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-460. https://doi.org/10.1126/science.1160311
  32. Pearson, B., Lau, K.H., Alen, A., Barron, J., Cool, R., Davis, K., DeLoache, W., Feeney, E., Gordon, A., Igo, J., et al. (2011) Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter. Interdisc Bio Central 3, 1-10.
  33. Penumetcha, P.L.K., Zhu, X., Davis, K., Eckdahl, T.T., and Campbell, A.M. (2010) Improving the Lac System for Synthetic Biology. BIOS 81, 7-15. https://doi.org/10.1893/011.081.0104
  34. Knight, T.F. (2003) Idempotent Vector Design for Standard Assembly of Biobricks. MIT Synthetic Biology Working Group.
  35. Ellington, A. (2005) [cited 2012 August 14]; Available from: https://www. biosci.utexas.edu/images/upload/DirectoryID_1533/123_andy.jpg.
  36. 2010 Cambridge iGEM team. (2010) [cited 2012 August 14]; Available from: http://2010.igem.org/Team:Cambridge/Tools/Lighting.
  37. 2008 Harvard iGEM team. (2008) [cited 2012 August 14]; Available from: http://2008.igem.org/Team:Harvard/Hardware.
  38. E. coli. (2005) [cited 2012 August 14]; Available from: http://en.wikipedia. org/wiki/File:EscherichiaColi_NIAID.jpg.
  39. 2008 Cambridge iGEM team. (2008) [cited 2012 August 14]; Available from: http://openwetware.org/wiki/IGEM:Cambridge/2008/Improved_GFP.
  40. Center for BioMolecular Modeling. (2008) [cited 2012 August 20]; Available from: http://www.rpc.msoe.edu/cbm/.
  41. Genome Consortium for Active Teaching - Synthetic Biology (GCAT-SynBio) (2011) [cited 2012 August 20]; Available from: http://www.bio.davidson.edu/projects/gcat/GCATSynBio.html.

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