Synthetic circuits, devices and modules

Hong Zhang, Taijiao Jiang()

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Protein Cell ›› 2010, Vol. 1 ›› Issue (11) : 974-978. DOI: 10.1007/s13238-010-0133-8
MINI-REVIEW
MINI-REVIEW

Synthetic circuits, devices and modules

  • Hong Zhang, Taijiao Jiang()
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Abstract

The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.

Keywords

synthetic biology / genetic circuit / synthetic device / module

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Hong Zhang, Taijiao Jiang. Synthetic circuits, devices and modules. Prot Cell, 2010, 1(11): 974‒978 https://doi.org/10.1007/s13238-010-0133-8

References

[1] Andrianantoandro, E., Basu, S., Karig, D.K., and Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2, 2006.0028.16738572
[2] Atsumi, S., Higashide, W., and Liao, J.C. (2009). Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 27, 1177–1180 10.1038/nbt.158619915552
[3] Beisel, C.L., Bayer, T.S., Hoff, K.G., and Smolke, C.D. (2008). Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol 4, 224–237 .10.1038/msb.2008.6218956013
[4] Buchler, N.E., and Cross, F.R. (2009). Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol 5, 272–278 .10.1038/msb.2009.3019455136
[5] Cello, J., Paul, A.V., and Wimmer, E. (2002). Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297, 1016–1018 10.1126/science.107226612114528
[6] Chan, L.Y., Kosuri, S., and Endy, D. (2005). Refactoring bacteriophage T7. Mol Syst Biol 1, 2005 0018.
[7] Danino, T., Mondragón-Palomino, O., Tsimring, L., and Hasty, J. (2010). A synchronized quorum of genetic clocks. Nature 463, 326–330 10.1038/nature0875320090747
[8] 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, 13247–13254 10.1021/ja048634j15479078
[9] Dhanasekaran, M., Negi, S., and Sugiura, Y. (2006). Designer zinc finger proteins: tools for creating artificial DNA-binding functional proteins. Acc Chem Res 39, 45–52 10.1021/ar050158u16411739
[10] Dickins, R.A., Hemann, M.T., Zilfou, J.T., Simpson, D.R., Ibarra, I., Hannon, G.J., and Lowe, S.W. (2005). Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 37, 1289–1295 .16200064
[11] Dixon, N., Duncan, J.N., Geerlings, T., Dunstan, M.S., McCarthy, J.E., Leys, D., and Micklefield, J. (2010). Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci USA 107, 2830–2835 10.1073/pnas.091120910720133756
[12] Elowitz, M.B., and Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 10.1038/3500212510659856
[13] Friedland, A.E., Lu, T.K., Wang, X., Shi, D., Church, G., and Collins, J.J. (2009). Synthetic gene networks that count. Science 324, 1199–1202 10.1126/science.117200519478183
[14] Fung, E., Wong, W.W., Suen, J.K., Bulter, T., Lee, S.G., and Liao, J.C. (2005). A synthetic gene-metabolic oscillator. Nature 435, 118–122 10.1038/nature0350815875027
[15] Gardner, T.S., Cantor, C.R., and Collins, J.J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 10.1038/3500213110659857
[16] Georgiou, G. (2002). How to flip the (redox) switch. Cell 111, 607–610 10.1016/S0092-8674(02)01165-012464172
[17] Gertz, J., and Cohen, B.A. (2009). Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol 5, 244–252 .10.1038/msb.2009.119225457
[18] Gertz, J., Siggia, E.D., and Cohen, B.A. (2009). Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215–218 10.1038/nature0752119029883
[19] Ghim, C.M., and Almaas, E. (2009). Two-component genetic switch as a synthetic module with tunable stability. Phys Rev Lett 103, 02810110.1103/PhysRevLett.103.02810119659247
[20] Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 10.1126/science.115172118218864
[21] Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., Algire, M.A., Benders, G.A., Montague, M.G., Ma, L., Moodie, M.M., (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 10.1126/science.119071920488990
[22] Hooshangi, S., Thiberge, S., and Weiss, R. (2005). Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci U S A 102, 3581–3586 10.1073/pnas.040850710215738412
[23] Huang, J., Koide, A., Makabe, K., and Koide, S. (2008). Design of protein function leaps by directed domain interface evolution. Proc Natl Acad Sci U S A 105, 6578–6583 10.1073/pnas.080109710518445649
[24] Kemmer, C., Gitzinger, M., Daoud-El Baba, M., Djonov, V., Stelling, J., and Fussenegger, M. (2010). Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol 28, 355–360 10.1038/nbt.161720351688
[25] Kim, D.H., Behlke, M.A., Rose, S.D., Chang, M.S., Choi, S., and Rossi, J.J. (2005). Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23, 222–226 10.1038/nbt105115619617
[26] Kim, J., White, K.S., and Winfree, E. (2006). Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2, 68–79 .10.1038/msb410009917170763
[27] Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T.S., Cantor, C.R., and Collins, J.J. (2004). Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A 101, 8414–8419 10.1073/pnas.040294010115159530
[28] Levskaya, A., Weiner, O.D., Lim, W.A., and Voigt, C.A. (2009). Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997–1001 10.1038/nature0844619749742
[29] Lou, C., Liu, X., Ni, M., Huang, Y., Huang, Q., Huang, L., Jiang, L., Lu, D., Wang, M., Liu, C., (2010). Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol Syst Biol 6, 350–360 .10.1038/msb.2010.220212522
[30] Lundblad, E.W., Xiao, G., Ko, J.H., and Altman, S. (2008). Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences. Proc Natl Acad Sci U S A 105, 2354–2357 10.1073/pnas.071197710518263737
[31] Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D., and Keasling, J.D. (2003). Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21, 796–802 10.1038/nbt83312778056
[32] Mogno, I., Vallania, F., Mitra, R.D., and Cohen, B.A. (2010). TATA is a modular component of synthetic promoters. Genome Res 20, 1391–1397 10.1101/gr.106732.11020627890
[33] Mulhbacher, J., St-Pierre, P., and Lafontaine, D.A. (2010). Therapeutic applications of ribozymes and riboswitches. Curr Opin Pharmacol 10, 551–556 10.1016/j.coph.2010.07.00220685165
[34] Murphy, K.F., Adams, R.M., Wang, X., Balázsi, G., and Collins, J.J. (2010). Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 38, 2712–2726 10.1093/nar/gkq09120211838
[35] Negi, S., Imanishi, M., Matsumoto, M., and Sugiura, Y. (2008). New redesigned zinc-finger proteins: design strategy and its application. Chemistry 14, 3236–3249 10.1002/chem.20070132018236477
[36] Nomura, W., and Sugiura, Y. (2007). Design and synthesis of artificial zinc finger proteins. Methods Mol Biol 352, 83–93 .17041260
[37] Park, S.H., Zarrinpar, A., and Lim, W.A. (2003). Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299, 1061–1064 10.1126/science.107697912511654
[38] Paulsen, C.E., and Carroll, K.S. (2009). Chemical dissection of an essential redox switch in yeast. Chem Biol 16, 217–225 10.1016/j.chembiol.2009.01.00319230722
[39] Peisajovich, S.G., Garbarino, J.E., Wei, P., and Lim, W.A. (2010). Rapid diversification of cell signaling phenotypes by modular domain recombination. Science 328, 368–372 10.1126/science.118237620395511
[40] Pomposiello, P.J., and Demple, B. (2001). Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 19, 109–114 10.1016/S0167-7799(00)01542-011179804
[41] Pósfai, G., Plunkett, G. 3rd, Fehér, T., Frisch, D., Keil, G.M., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S.S., de Arruda, M., (2006). Emergent properties of reduced-genome Escherichia coli. Science 312, 1044–1046 10.1126/science.112643916645050
[42] Radhika, V., Proikas-Cezanne, T., Jayaraman, M., Onesime, D., Ha, J.H., and Dhanasekaran, D.N. (2007). Chemical sensing of DNT by engineered olfactory yeast strain. Nat Chem Biol 3, 325–330 10.1038/nchembio88217486045
[43] Ro, D.K., Paradise, E.M., Ouellet, M., Fisher, K.J., Newman, K.L., Ndungu, J.M., Ho, K.A., Eachus, R.A., Ham, T.S., Kirby, J., (2006). Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940–943 10.1038/nature0464016612385
[44] Saito, H., Kobayashi, T., Hara, T., Fujita, Y., Hayashi, K., Furushima, R., and Inoue, T. (2010). Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat Chem Biol 6, 71–78 10.1038/nchembio.27320016495
[45] Sera, T. (2010). Generation of cell-permeable artificial zinc finger protein variants. Methods Mol Biol 649, 91–96 10.1007/978-1-60761-753-2_520680829
[46] Shen, N., Ko, J.H., Xiao, G., Wesolowski, D., Shan, G., Geller, B., Izadjoo, M., and Altman, S. (2009). Inactivation of expression of several genes in a variety of bacterial species by EGS technology. Proc Natl Acad Sci U S A 106, 8163–8168 10.1073/pnas.090349110619416872
[47] Silverman, J., Liu, Q., Lu, Q., Bakker, A., To, W., Duguay, A., Alba, B.M., Smith, R., Rivas, A., Li, P., (2005). Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol 23, 1556–1561 10.1038/nbt116616299519
[48] Siolas, D., Lerner, C., Burchard, J., Ge, W., Linsley, P.S., Paddison, P.J., Hannon, G.J., and Cleary, M.A. (2005). Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 23, 227–231 10.1038/nbt105215619616
[49] Smith, H.O., Hutchison, C.A. 3rd, Pfannkoch, C., and Venter, J.C. (2003). Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A 100, 15440–15445 10.1073/pnas.223712610014657399
[50] Sprengel, R., and Hasan, M.T. (2007). Tetracycline-controlled genetic switches. Handb Exp Pharmacol , 49–72 .
[51] Steen, E.J., Kang, Y., Bokinsky, G., Hu, Z., Schirmer, A., McClure, A., Del Cardayre, S.B., and Keasling, J.D. (2010). Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463, 559–562 10.1038/nature0872120111002
[52] Stricker, J., Cookson, S., Bennett, M.R., Mather, W.H., Tsimring, L.S., and Hasty, J. (2008). A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 10.1038/nature0738918971928
[53] 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, 1610–1614 10.1093/nar/gkh32115004248
[54] Suryawanshi, H., Scaria, V., and Maiti, S. (2010). Modulation of microRNA function by synthetic ribozymes. Mol Biosyst 6, 1807–1809 10.1039/c0mb00010h20697623
[55] Tietze, L.F., Düfert, A., Lotz, F., S?lter, L., Oum, K., Lenzer, T., Beck, T., and Herbst-Irmer, R. (2009). Synthesis of chiroptical molecular switches by pd-catalyzed domino reactions. J Am Chem Soc 131, 17879–17884 10.1021/ja906260x19911798
[56] Tigges, M., Marquez-Lago, T.T., Stelling, J., and Fussenegger, M. (2009). A tunable synthetic mammalian oscillator. Nature 457, 309–312 10.1038/nature0761619148099
[57] Winkler, W.C. (2005). Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 9, 594–602 10.1016/j.cbpa.2005.09.01616226486
[58] Yen, L., Svendsen, J., Lee, J.S., Gray, J.T., Magnier, M., Baba, T., D’Amato, R.J., and Mulligan, R.C. (2004). Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431, 471–476 10.1038/nature0284415386015
[59] Zhang, K., Sawaya, M.R., Eisenberg, D.S., and Liao, J.C. (2008). Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci U S A 105, 20653–20658 10.1073/pnas.080715710619064911
[60] Zhang, X., Schaffitzel, C., Ban, N., and Shan, S.O. (2009). Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proc Natl Acad Sci U S A 106, 1754–1759 10.1073/pnas.080857310619174514
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