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Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter

  • Pearson, Brianna (Department of Biology, Davidson College) ;
  • Lau, Kin H. (Department of Biology, Davidson College) ;
  • Allen, Alicia (Department of Biology, Missouri Western State University) ;
  • Barron, James (Department of Biology, Davidson College) ;
  • Cool, Robert (Department of Biology, Missouri Western State University) ;
  • Davis, Kelly (Department of Mathematics, Davidson College) ;
  • DeLoache, Will (Department of Biology, Davidson College) ;
  • Feeney, Erin (Department of Biology, Davidson College) ;
  • Gordon, Andrew (Department of Biology, Missouri Western State University) ;
  • Igo, John (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Lewis, Aaron (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Muscalino, Kristi (Department of Mathematics, Davidson College) ;
  • Parra, Madeline (Department of Mathematics, Davidson College) ;
  • Penumetcha, Pallavi (Department of Biology, Davidson College) ;
  • Rinker, Victoria G. (Department of Biology, Davidson College) ;
  • Roland, Karlesha (Department of Biology, Davidson College) ;
  • Zhu, Xiao (Department of Biology, Missouri Western State University) ;
  • Poet, Jeffrey L. (Department of Computer Science, Math and Physics, Missouri Western State University) ;
  • Eckdahl, Todd T. (Department of Biology, Missouri Western State University) ;
  • Heyer, Laurie J. (Department of Mathematics, Davidson College) ;
  • Campbell, A. Malcolm (Department of Biology, Davidson College)
  • Received : 2011.07.08
  • Accepted : 2011.07.15
  • Published : 2011.09.30
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Abstract

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST's "International Call for Hash Function", we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations. Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ${\ss}$-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the op-position of two promoters. Our results showed that $P_{lux}$ and $P_{OmpC}$ functioned as expected individually, but $P_{lux}$ did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the $P_{lux}$ promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the $P_{lux}$ promoter and induce backwards transcription. Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of $P_{lux}$. In the absence of autoinducer 3OC6, LuxR binds to $P_{lux}$ and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the $P_{lux}$ promoter.

Keywords

References

  1. Schneier, B. (2008). America's next top hash function. [http://www.wired.com/politics/security/commentary/securitymatters/2008/11/securitymatters_1120]. Wired.
  2. Mackenzie, D. (2008). Computer science. Cryptologists cook up some hash for new 'bake-off'. Science 319, 1480-1481. https://doi.org/10.1126/science.319.5869.1480
  3. Barker, E., Bassham, L., Burr, W., Caswell, S., Chang, D., Chang, S.-j., Chen, L., Dang, Q., Dworkin, M., Kelsey, J., et al. (2009). Cryptographic hash algorithm competition. [http://www. nist.gov/itl/csd/ct/hash_competition.cfm]. The National Institute of Standards and Technology.
  4. Tiwari, H., and Asawa, K. (2010). Cryptographic hash function: an elevated view. EJSR 43, 452-465.
  5. Haynes, K.A., Broderick, M.L., Brown, A.D., Butner, T.L., Dick-son, 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
  6. Baumgardner, J., Acker, K., Adefuye, O., Crowley, S.T., De-loache, W., Dickson, J.O., Heard, L., Martens, 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
  7. Goni-Moreno, A., Redondo-Nieto, M., Arroyo, F., and Castella-nos, J. (2010). Biocircuit design through engineering bacterial logic gates. Nat Comput 10, 1007.
  8. de Silva, A.P., and McClenaghan, N.D. (2004). Molecular-scale logic gates. Chemistry 10, 574-586. https://doi.org/10.1002/chem.200305054
  9. Western, D.-M. (2008). Our Models. [http://2008.igem.org/Team: Davidson-Missouri_Western/Our_Models] Accessed 25 May, 2011. iGEM.
  10. Credi, A., Balzani, V., Langford, SJ., and Stoddart, JF. (1997). Logic operations at the molecular level: An XOR gate based on a molecular machine. J. Am. Chem. Soc. 119, 2679-2681. https://doi.org/10.1021/ja963572l
  11. Tamsir, A., Tabor, J.J., and Voigt, C.A. (2011). Robust multicellu-lar computing using genetically encoded NOR gates and chemi-cal 'wires'. Nature 469, 212-215. https://doi.org/10.1038/nature09565
  12. Stojanovic, M.N., Mitchell, T.E., and Stefanovic, D. (2002). Deoxyribozyme-based logic gates. J Am Chem Soc 124, 3555-3561. https://doi.org/10.1021/ja016756v
  13. Kramer, B.P., Fischer, C., and Fussenegger, M. (2004). BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng 87, 478-484. https://doi.org/10.1002/bit.20142
  14. Egland, K.A., and Greenberg, E.P. (2000). Conversion of the Vibrio fischeri transcriptional activator, LuxR, to a repressor. J Bacteriol 182, 805-811. https://doi.org/10.1128/JB.182.3.805-811.2000
  15. Nasser, W., and Reverchon, S. (2007). New insights into the regulatory mechanisms of the LuxR family of quorum sensing regulators. Anal Bioanal Chem 387, 381-390. https://doi.org/10.1007/s00216-006-0702-0
  16. Forst, S., Delgado, J., and Inouye, M. (1989). Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli. Proc Natl Acad Sci U S A 86, 6052-6056. https://doi.org/10.1073/pnas.86.16.6052
  17. Jung, K., Hamann, K., and Revermann, A. (2001). K+ stimulates specifically the autokinase activity of purified and reconstituted EnvZ of Escherichia coli. J Biol Chem 276, 40896-40902. https://doi.org/10.1074/jbc.M107871200
  18. Cai, S.J., and Inouye, M. (2002). EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J Biol Chem 277, 24155-24161. https://doi.org/10.1074/jbc.M110715200
  19. Yoshida, T., Qin, L., Egger, L.A., and Inouye, M. (2006). Tran-scription regulation of ompF and ompC by a single transcription factor, OmpR. J Biol Chem 281, 17114-17123. https://doi.org/10.1074/jbc.M602112200
  20. OpenWetWare (2008). Ampicillin. (http://openwetware.org/wiki/ Ampicillin). Accessed 25 May, 2011. .
  21. Chandrakala, B., Elias, B.C., Mehra, U., Umapathy, N.S., Dwa-rakanath, P., Balganesh, T.S., and deSousa, S.M. (2001). Novel scintillation proximity assay for measuring membrane-associated steps of peptidoglycan biosynthesis in Escherichia coli. Antimicrob Agents Chemother 45, 768-775. https://doi.org/10.1128/AAC.45.3.768-775.2001
  22. Georgiou, G., Shuler, M.L., and Wilson, D.B. (1988). Release of periplasmic enzymes and other physiological effects of beta-lactamase overproduction in Escherichia coli. Biotechnol Bioeng 32, 741-748. https://doi.org/10.1002/bit.260320603
  23. Toama, M.A., Issa, A.A., and Ashour, M.S. (1978). Effect of agar percentage, agar thickness, and medium constituents on anti-biotics assay by disc diffusion method. Die Pharmazie 33, 100-102.
  24. Shadel, G.S., and Baldwin, T.O. (1992). Positive autoregulation of the Vibrio fischeri luxR gene. LuxR and autoinducer activate cAMP-catabolite gene activator protein complex-independent and -dependent luxR transcription. J Biol Chem 267, 7696-7702.
  25. Stevens, A.M., Dolan, K.M., and Greenberg, E.P. (1994). Syner-gistic binding of the Vibrio fischeri LuxR transcriptional activator domain and RNA polymerase to the lux promoter region. Proc Natl Acad Sci U S A 91, 12619-12623. https://doi.org/10.1073/pnas.91.26.12619
  26. Long, T., Tu, K.C., Wang, Y., Mehta, P., Ong, N.P., Bassler, B.L., and Wingreen, N.S. (2009). Quantifying the integration of quo-rum-sensing signals with single-cell resolution. PLoS Biol 7, e68. https://doi.org/10.1371/journal.pbio.1000068
  27. Manuel, S.a.S., N. (2007). XOR-Hash: A hash function based on XOR. WEWoRC 2007.
  28. Anderson, J.C., Clarke, E.J., Arkin, A.P., and Voigt, C.A. (2006). Environmentally controlled invasion of cancer cells by engi-neered bacteria. J Mol Biol 355, 619-627. https://doi.org/10.1016/j.jmb.2005.10.076
  29. Sleight, S.C., Bartley, B.A., Lieviant, J.A., and Sauro, H.M. (2010). Designing and engineering evolutionary robust genetic circuits. J Biol Eng 4, 12. https://doi.org/10.1186/1754-1611-4-12
  30. Hasty, J., McMillen, D., and Collins, J.J. (2002). Engineered gene circuits. Nature 420, 224-230. https://doi.org/10.1038/nature01257
  31. Dunlap, P.V. (1999). Quorum regulation of luminescence in Vi-brio fischeri. J Mol Microbiol Biotechnol 1, 5-12.
  32. Ahmer, B.M. (2004). Cell-to-cell signalling in Escherichia coli and Salmonella enterica. Mol Microbiol 52, 933-945. https://doi.org/10.1111/j.1365-2958.2004.04054.x
  33. Dyszel, J.L., Soares, J.A., Swearingen, M.C., Lindsay, A., Smith, J.N., and Ahmer, B.M. (2010). E. coli K-12 and EHEC genes re-gulated by SdiA. PLoS One 5, e8946. https://doi.org/10.1371/journal.pone.0008946
  34. Ohashi, K., Yamashino, T., and Mizuno, T. (2005). Molecular basis for promoter selectivity of the transcriptional activator OmpR of Escherichia coli: isolation of mutants that can activate the non-cognate kdpABC promoter. J Biochem 137, 51-59. https://doi.org/10.1093/jb/mvi006
  35. Knight, T. (2004). Idempotent Vector Design for Standard Assembly of Biobricks. MIT Articial Intelligence Laboratory, 1-11.
  36. Retberg, R. (2005). MIT Registry of Standard Biological Parts . Accessed 8 May, 2011.
  37. Kennell, D., and Riezman, H. (1977). Transcription and transla-tion initiation frequencies of the Escherichia coli lac operon. J Mol Biol 114, 1-21. https://doi.org/10.1016/0022-2836(77)90279-0
  38. Barron, J., Parra, M, and Win, M. (2008). BioBrick PCR Primer Designer. (http://gcat.davidson.edu/iGEM08/bbprimer.html). Ac-cessed 8 May, 2011..
  39. Urbanowski, M.L., Lostroh, C.P., and Greenberg, E.P. (2004). Reversible acyl-homoserine lactone binding to purified Vibrio fi-scheri LuxR protein. J Bacteriol 186, 631-637. https://doi.org/10.1128/JB.186.3.631-637.2004
  40. Harden, L. (2006). Oligo Cuts Optimization Program . Accessed 8 May, 2011. .
  41. Jacob, F., Monod, J. (1961). On the regulation of gene activity. Cold Spring Harb Symp Quant Biol 26, 193-211. https://doi.org/10.1101/SQB.1961.026.01.024

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