Abstract
This review is devoted to synthetic biology. In this field, molecular biology methods and techniques are applied to develop a predetermined cell behavior based on theoretically constructed regulatory networks using engineering approaches. A cell can be considered the device that performs several types of basic functions. These are sensory, information processing, and response formation functions. Endogenous and exogenous physical or chemical factors that trigger information processing cascades are input signals. These include signaling and metabolic pathways. As a rule, changes in these pathways lead to the modification of the transcriptional profile. The response includes alterations in the metabolic profile followed by physiological changes. Taking this into account, a cell and a computer can be considered analogs. Therefore, the principles of engineering can be applied to natural biological systems in general and genetic circuits in particular. In addition to the main areas of synthetic biology, as well as their principles and methods, specific examples of the application of the synthetic biology approach in medicine and other fields were discussed.
This is a preview of subscription content, access via your institution.



REFERENCES
Monod, J. and Jacob, F., General conclusions: Teleonomic mechanisms in cellular metabolism, growth, and differentiation, Cold Spring Harbor Symp. Quant. Biol., 1961, vol. 26, pp. 389–401. https://doi.org/10.1101/SQB.1961.026.01.048
Cameron, D.E., Bashor, C.J., and Collins, J.J., A brief history of synthetic biology, Nat. Rev. Microbiol., 2014, vol. 12, no. 5, pp. 381–390. https://doi.org/10.1038/nrmicro3239
Gardner, T.S., Cantor, C.R., and Collins, J.J., Construction of a genetic toggle switch in Escherichia coli, Nature, 2000, vol. 403, no. 6767, pp. 339–342. https://doi.org/10.1038/35002131
Elowitz, M.B. and Leibler, S., A synthetic oscillatory network of transcriptional regulators, Nature, 2000, vol. 403, no. 6767, pp. 335–338. https://doi.org/10.1038/35002125
Weiss, R. and Knight, T.F., Engineered communications for microbial robotics, in Lecture Notes in Computer Science, vol. 2054: DNA Computing, Condon, A. and Rozenberg, G., Eds., Berlin, Heidelberg: Springer, 2001, pp. 1–16. https://doi.org/10.1007/3-540-44992-2_1
Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H., and Weiss, R., A synthetic multicellular system for programmed pattern formation, Nature, 2005, vol. 434, no. 7037, pp. 1130–1134. https://doi.org/10.1038/nature03461
McAdams, H. and Shapiro, L., Circuit simulation of genetic networks, Science, 1995, vol. 269, no. 5224, pp. 650–656. https://doi.org/10.1126/science.7624793
Beal, J., Phillips, A., Densmore, D., and Cai, Y., High-level programming languages for biomolecular systems, in Design and Analysis of Biomolecular Circuits, Koeppl, H., Setti, G., di Bernardo, M., and Densmore, D., Eds., New York: Springer, 2011, pp. 225–252. https://doi.org/10.1007/978-1-4419-6766-4_11.
Konur, S., Gheorghe, M., Dragomir, C., Ipate, F., and Krasnogor, N., Conventional verification for unconventional computing: A genetic XOR gate example, Fundam. Inf., 2014, vol. 134, nos. 1–2, pp. 97–110. https://doi.org/10.3233/FI-2014-1093
Tamsir, A., Tabor, J.J., and Voigt, C.A., Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’, Nature, 2011, vol. 469, no. 7329, pp. 212–215. https://doi.org/10.1038/nature09565
Weinberg, B.H., Pham, N.T.H., Caraballo, L.D., Lozanoski, T., Engel, A., Bhatia, S., et al., Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells, Nat. Biotechnol., 2017, vol. 35, no. 5, pp. 453–462. https://doi.org/10.1038/nbt.3805
Cardinale, S. and Arkin, A.P., Contextualizing context for synthetic biology—identifying causes of failure of synthetic biological systems, Biotechnol. J., 2012, vol. 7, no. 7, pp. 856–866. https://doi.org/10.1002/biot.201200085
Daniel, R., Rubens, J.R., Sarpeshkar, R., and Lu, T.K., Synthetic analog computation in living cells, Nature, 2013, vol. 497, no. 7451, pp. 619–623. https://doi.org/10.1038/nature12148
Wong, A., Wang, H., Poh, C.L., and Kitney, R.I., Layering genetic circuits to build a single cell, bacterial half adder, BMC Biol., 2015, vol. 13, no. 1, p. 40. https://doi.org/10.1186/s12915-015-0146-0
Rossetti, M., Del Grosso, E., Ranallo, S., Mariottini, D., Idili, A., Bertucci, A., et al., Programmable RNA-based systems for sensing and diagnostic applications, Anal. Bioanal. Chem., 2019, vol. 411, no. 19, pp. 4293–4302. https://doi.org/10.1007/s00216-019-01622-7
Ausländer, D., Ausländer, S., Pierrat, X., Hellmann, L., Rachid, L., and Fussenegger, M., Programmable full-adder computations in communicating three-dimensional cell cultures, Nat. Methods, 2018, vol. 15, no. 1, pp. 57–60. https://doi.org/10.1038/nmeth.4505
Gaj, T., Sirk, S.J., and Barbas, C.F., Expanding the scope of site-specific recombinases for genetic and metabolic engineering, Biotechnol. Bioeng., 2014, vol. 111, no. 1, pp. 1–15. https://doi.org/10.1002/bit.25096
Roquet, N., Soleimany, A.P., Ferris, A.C., Aaronson, S., and Lu, T.K., Synthetic recombinase-based state machines in living cells, Science, 2016, vol. 353, no. 6297, p. aad8559. https://doi.org/10.1126/science.aad8559
Carroll, D., Genome engineering with targetable nucleases, Annu. Rev. Biochem., 2014, vol. 83, no. 1, pp. 409–439. https://doi.org/10.1146/annurev-biochem-060713-035418
Pickar-Oliver, A. and Gersbach, C.A., The next generation of CRISPR-Cas technologies and applications, Nat. Rev. Mol. Cell Biol., 2019, vol. 20, no. 8, pp. 490–507. https://doi.org/10.1038/s41580-019-0131-5
Kocak, D.D., Josephs, E.A., Bhandarkar, V., Adkar, S.S., Kwon, J.B., and Gersbach, C.A., Increasing the specificity of CRISPR systems with engineered RNA secondary structures, Nat. Biotechnol., 2019, vol. 37, no. 6, pp. 657–666. https://doi.org/10.1038/s41587-019-0095-1
Brödel, A.K., Jaramillo, A., and Isalan, M., Engineering orthogonal dual transcription factors for multi-input synthetic promoters, Nat. Commun., 2016, vol. 7, no. 1, p. 13858. https://doi.org/10.1038/ncomms13858
Stripecke, R., Oliveira, C.C., McCarthy, J.E., and 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, vol. 14, no. 9, pp. 5898–5909. https://doi.org/10.1128/MCB.14.9.5898
Yen, L., Svendsen, J., Lee, J.S., Gray, J.T., Magnier, M., Baba, T., et al., Exogenous control of mammalian gene expression through modulation of RNA self-cleavage, Nature, 2004, vol. 431, no. 7007, pp. 471–476. https://doi.org/10.1038/nature02844
Ausländer, S., Ketzer, P., and Hartig, J.S., A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression, Mol. BioSyst., 2010, vol. 6, no. 5, p. 807. https://doi.org/10.1039/b923076a
Win, M.N. and Smolke, C.D., Higher-order cellular information processing with synthetic RNA devices, Science, 2008, vol. 322, no. 5900, pp. 456–460. https://doi.org/10.1126/science.1160311
Rackham, O. and Chin, J.W., A network of orthogonal ribosome mRNA pairs, Nat. Chem. Biol., 2005, vol. 1, no. 3, pp. 159–166. https://doi.org/10.1038/nchembio719
Chen, Z., Lichtor, P.A., Berliner, A.P., Chen, J.C., and Liu, D.R., Evolution of sequence-defined highly functionalized nucleic acid polymers, Nat. Chem., 2018, vol. 10, no. 4, pp. 420–427. https://doi.org/10.1038/s41557-018-0008-9
Davis, L. and Chin, J.W., Designer proteins: Applications of genetic code expansion in cell biology, Nat. Rev. Mol. Cell Biol., 2012, vol. 13, no. 3, pp. 168–182. https://doi.org/10.1038/nrm3286
Forster, A.C., Tan, Z., Nalam, M.N., Lin, H., Qu, H., Cornish, V.W., et al., Programming peptidomimetic syntheses by translating genetic codes designed de novo, Proc. Natl. Acad. Sci. U. S. A., 2003, vol. 100, no. 11, pp. 6353–6357. https://doi.org/10.1073/pnas.1132122100
O’Donoghue, P., Ling, J., Wang, Y.-S., and Söll, D., Upgrading protein synthesis for synthetic biology, Nat. Chem. Biol., 2013, vol. 9, no. 10, pp. 594–598. https://doi.org/10.1038/nchembio.1339
Farzadfard, F., Gharaei, N., Higashikuni, Y., Jung, G., Cao, J., and Lu, T.K., Single-nucleotide-resolution computing and memory in living cells, Mol. Cell, 2019, vol. 75, no. 4, pp. 769–780. https://doi.org/10.1016/j.molcel.2019.07.011
Amiram, M., Haimovich, A.D., Fan, C., Wang, Y.S., Aerni, H.R., Ntai, I., et al., Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids, Nat. Biotechnol., 2015, vol. 33, no. 12, pp. 1272–1279. https://doi.org/10.1038/nbt.3372
Park, S.-H., Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms, Science, 2003, vol. 299, no. 5609, pp. 1061–1064. https://doi.org/10.1126/science.1076979
Ryu, J. and Park, S.-H., Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells, Sci. Signaling, 2015, vol. 8, no. 383, p. ra66. https://doi.org/10.1126/scisignal.aab3397
Truong, D.J., Kühner, K., Kühn, R., Werfel, S., Engelhardt, S., Wurst, W., et al., Development of an intein-mediated split – Cas9 system for gene therapy, Nucleic Acids Res., 2015, vol. 43, no. 13, pp. 6450–6458. https://doi.org/10.1093/nar/gkv601
Kanno, A., Ozawa, T., and Umezawa, Y., Bioluminescent imaging of MAPK function with intein-mediated reporter gene assay, in Methods in Molecular Biology, vol. 574: Bioluminescence, Rich, P.B. and Douillet, C., Eds., Humana Press, 2009, pp. 185–192. https://doi.org/10.1007/978-1-60327-321-3_15.
Davis, K.M., Pattanayak, V., Thompson, D.B., Zuris, J.A., and Liu, D.R., Small molecule–triggered Cas9 protein with improved genome-editing specificity, Nat. Chem. Biol., 2015, vol. 11, no. 5, pp. 316–318. https://doi.org/10.1038/nchembio.1793
Callahan, B.P., Topilina, N.I., Stanger, M.J., Van Roey, P., and Belfort, M., Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications, Nat. Struct. Mol. Biol., 2011, vol. 18, no. 5, pp. 630–633. https://doi.org/10.1038/nsmb.2041
Lohmueller, J.J., Armel, T.Z., and Silver, P.A., A tunable zinc finger-based framework for Boolean logic computation in mammalian cells, Nucleic Acids Res., 2012, vol. 40, no. 11, pp. 5180–5187. https://doi.org/10.1093/nar/gks142
Lienert, F., Torella, J.P., Chen, J.-H., Norsworthy, M., Richardson, R.R., and Silver, P.A., Two- and three-input TALE-based AND logic computation in embryonic stem cells, Nucleic Acids Res., 2013, vol. 41, no. 21, pp. 9967–9975. https://doi.org/10.1093/nar/gkt758
Schaerli, Y., Gili, M., and Isalan, M., A split intein T7 RNA polymerase for transcriptional AND-logic, Nucleic Acids Res., 2014, vol. 42, vol. 19, pp. 12322–12328. https://doi.org/10.1093/nar/gku884
To, A.C., Chu, D.H., Wang, A.R., Li, F.C., Chiu, A.W., Gao, D.Y., et al., A comprehensive web tool for toehold switch design, Bioinformatics, 2018, vol. 34, no. 16, pp. 2862–2864. https://doi.org/10.1093/bioinformatics/bty216
Hall, R.A. and Macdonald, J., Synthetic biology provides a toehold in the fight against Zika, Cell Host Microbe, 2016, vol. 19, no. 6, pp. 752–754. https://doi.org/10.1016/j.chom.2016.05.020
Takahashi, M.K., Tan, X., Dy, A.J., Braff, D., Akana, R.T., Furuta, Y., et al., A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers, Nat. Commun., 2018, vol. 9, no. 1, p. 3347. https://doi.org/10.1038/s41467-018-05864-4
Steidler, L., Treatment of murine colitis by Lactococcus lactis secreting interleukin-10, Science, 2000, vol. 289, no. 5483, pp. 1352–1355. https://doi.org/10.1126/science.289.5483.1352
Vandenbroucke, K., de Haard, H., Beirnaert, E., Dreier, T., Lauwereys, M., Huyck, L., et al., Orally administered L. lactis secreting an anti-TNF Nanobody demonstrate efficacy in chronic colitis, Mucosal Immunol., 2010, vol. 3, no. 1, pp. 49–56. https://doi.org/10.1038/mi.2009.116
Xiang, S., Fruehauf, J., and Li, C.J., Short hairpin RNA-expressing bacteria elicit RNA interference in mammals, Nat. Biotechnol., 2006, vol. 24, no. 6, pp. 697–702. https://doi.org/10.1038/nbt1211
Piñero-Lambea, C., Bodelón, G., Fernández-Periañez, R., Cuesta, A.M., Álvarez-Vallina, L., and Fernández, L.Á., Programming controlled adhesion of E. coli to target surfaces, cells, and tumors with synthetic adhesins, ACS Synth. Biol., 2015, vol. 4, no. 4, pp. 463–473. https://doi.org/10.1021/sb500252a
Duan, F.F., Liu, J.H., and March, J.C., Engineered commensal bacteria reprogram intestinal cells into glucose-responsive insulin-secreting cells for the treatment of diabetes, Diabetes, 2015, vol. 64, no. 5, pp. 1794–1803. https://doi.org/10.2337/db14-0635
Lagenaur, L.A., Sanders-Beer, B.E., Brichacek, B., Pal, R., Liu, X., Liu, Y., et al., Prevention of vaginal SHIV transmission in macaques by a live recombinant Lactobacillus, Mucosal Immunol., 2011, vol. 4, no. 6, pp. 648–657. https://doi.org/10.1038/mi.2011.30
Lim, W.A. and June, C.H., The principles of engineering immune cells to treat cancer, Cell, 2017, vol. 168, no. 4, pp. 724–740. https://doi.org/10.1016/j.cell.2017.01.016
Roybal, K.T., Williams, J.Z., Morsut, L., Rupp, L.J., Kolinko, I., Choe, J.H., et al., Engineering T cells with customized therapeutic response programs using synthetic notch receptors, Cell, 2016, vol. 167, no. 2, pp. 419–432.e16. https://doi.org/10.1016/j.cell.2016.09.011
Ausländer, D., Ausländer, S., Charpin-El Hamri, G., Sedlmayer, F., Müller, M., Frey, O., et al., A Synthetic multifunctional mammalian pH sensor and CO2 transgene-control device, Mol. Cell, 2014, vol. 55, no. 3, pp. 397–408. https://doi.org/10.1016/j.molcel.2014.06.007
Ye, H., Baba, M.D.-E., Peng, R.-W., and Fussenegger, M., A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice, Science, 2011, vol. 332, no. 6037, pp. 1565–1568. https://doi.org/10.1126/science.1203535
Roössger, K., Charpin-El-Hamri, G., and Fussenegger, M., A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice, Nat. Commun., 2013, vol. 4, no. 1, p. 2825. https://doi.org/10.1038/ncomms3825
Kotas, M.E. and Medzhitov, R., Homeostasis, inflammation, and disease susceptibility, Cell, 2015, vol. 160, no. 5, pp. 816–827. https://doi.org/10.1016/j.cell.2015.02.010
Xie, M., Ye, H., Wang, H., Charpin-El Hamri, G., Lormeau, C., Saxena, P., et al., β-cell-mimetic designer cells provide closed-loop glycemic control, Science, 2016, vol. 354, no. 6317, pp. 1296–1301. https://doi.org/10.1126/science.aaf4006
Mimee, M., Nadeau, P., Hayward, A., Carim, S., Flanagan, S., Jerger, L., et al., An ingestible bacterial-electronic system to monitor gastrointestinal health, Science, 2018, vol. 360, no. 6391, pp. 915–918. https://doi.org/10.1126/science.aas9315
Purcell, O. and Lu, T.K., Synthetic analog and digital circuits for cellular computation and memory, Curr. Opin. Biotechnol., 2014, vol. 29, pp. 146–155. https://doi.org/10.1016/j.copbio.2014.04.009
Hirai, H., Tani, T., and Kikyo, N., Structure and functions of powerful transactivators: VP16, MyoD and FoxA, Int. J. Dev. Biol., 2010, vol. 54, nos. 11–12, pp. 1589–1596. https://doi.org/10.1387/ijdb.103194hh
Saxena, P., Bojar, D., Zulewski, H., and Fussenegger, M., Generation of glucose-sensitive insulin-secreting beta-like cells from human embryonic stem cells by incorporating a synthetic lineage-control network, J. Biotechnol., 2017, vol. 259, pp. 39–45. https://doi.org/10.1016/j.jbiotec.2017.07.018
Prindle, A., Samayoa, P., Razinkov, I., Danino, T., Tsimring, L.S., and Hasty, J., A sensing array of radically coupled genetic ‘biopixels’, Nature, 2012, vol. 481, no. 7379, pp. 39–44. https://doi.org/10.1038/nature10722
Lee, W., Wood, T.K., and Chen, W., Engineering TCE-degrading rhizobacteria for heavy metal accumulation and enhanced TCE degradation, Biotechnol. Bioeng., 2006, vol. 95, no. 3, pp. 399–403. https://doi.org/10.1002/bit.20950
Jagadevan, S., Banerjee, A., Banerjee, C., Guria, C., Tiwari, R., Baweja, M., et al., Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production, Biotechnol. Biofuels, 2018, vol. 11, no. 1, p. 185. https://doi.org/10.1186/s13068-018-1181-1
Balaban, P.M., Vorontsov, D.D., Dyakonova, V.E., Dyakonova, T.L., Zakharov, I.S., Korshunova, T.A., et al., The central pattern generators, Zh. Vyssh. Nervn. Deyat. im. I. P. Pavlova, 2013, vol. 63, no. 5, pp. 520–541. https://doi.org/10.7868/S0044467713050031
Lu, J., Yang, J., Kim, Y.-B., and Ayers, J., Low power, high PVT variation tolerant central pattern generator design for a bio-hybrid micro robot, Proc. 2012 IEEE 55th Int. Midwest Symposium on Circuits and Systems (MWSCAS), Boise, ID, IEEE, 2012, pp. 782–785. https://doi.org/10.1109/MWSCAS.2012.6292137.
Funding
The study was supported by the Russian Foundation for Basic Research (project no. 18-29-07046).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.
Additional information
Translated by A. Panyushkina
ADDITIONAL INFORMATION
Vasilev R.A., https://orcid.org/0000-0002-6839-905X; e-mail: ruavasilev@gmail.com
Chernikovich V.Yu., e-mail: victoria.artistcat@gmail.com
Evteeva M.A., e-mail: evteeva_ma@rrcki.ru
Sakharov D.A., https://orcid.org/0000-0001-9333-586X; e-mail: sakharov@muctr.ru
Patrushev M.V., https://orcid.org/0000-0002-4748-9283; e-mail: maxpatrushev@yandex.ru
About this article
Cite this article
Vasilev, R.A., Chernikovich, V.Y., Evteeva, M.A. et al. Synthetic Biology: Current State and Applications. Mol. Genet. Microbiol. Virol. 36, 15–26 (2021). https://doi.org/10.3103/S0891416821010079
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.3103/S0891416821010079