The site of the Media Sphera Publishers contains materials intended solely for healthcare professionals.
By closing this message, you confirm that you are a certified medical professional or a student of a medical educational institution.

Login
EN
+7 (495) 482-4118
+7 (495) 482-0604

  • © 1998-2025
+7 (495) 482-43-29
EN
All journals
Journal
Year
Year
Search result: 0

Vasilev R.A.

Lomonosov Moscow State University;
National Research Center “Kurchatov Institute”

Chernikovich V.Yu.

Dmitry Mendeleev University of Chemical Technology of Russia

Evteeva M.A.

National Research Center “Kurchatov Institute”

Sakharov D.A.

Dmitry Mendeleev University of Chemical Technology of Russia

Patrushev M.V.

Dmitry Mendeleev University of Chemical Technology of Russia;
National Research Center “Kurchatov Institute”

Synthetic biology. Current state and applications

Authors:

Vasilev R.A., Chernikovich V.Yu., Evteeva M.A., Sakharov D.A., Patrushev M.V.

More about the authors

Journal: Molecular Genetics, Microbiology and Virology. 2021;39(1): 18‑30

DOI: 10.17116/molgen20213901118

Views: 1243

Downloaded: 39

Download PDF (RU)
Contact the author
Table of contents

To cite this article:

Vasilev RA, Chernikovich VYu, Evteeva MA, Sakharov DA, Patrushev MV. Synthetic biology. Current state and applications. Molecular Genetics, Microbiology and Virology. 2021;39(1):18‑30. (In Russ.)
https://doi.org/10.17116/molgen20213901118

 
МСФ на ЯМ
Close metadata

This review is devoted to synthetic biology, a field where the methods and techniques of molecular biology are applied to form a determined cell behavior based on theoretically constructed regulatory networks using engineering approaches. One can imagine a cell as a device that performs several types of basic functions: sensory, processing of incoming information, formation of a response. The input signals present as endogenous and exogenous, physical and chemical factors, the impact of which leads to the launch of information processing cascades. These include signaling and metabolic pathways, changes in which, as a rule, lead to a modification of the transcriptional profile. The answer lies in a change in metabolic profile followed by physiological changes. Taking this into account, it is possible to draw a direct analogy between a cell and a computer, which in turn gives every reason to apply the principles of engineering to natural biological systems in general and to genetic networks in particular. In addition to the main directions of synthetic biology, their principles and methods, specific examples of the application of the synthetic-biological approach in medicine and other fields are considered.

Keywords:

synthetic biology
artificial gene circuits
logic gates
orthogonality
expression regulation

Authors:

Vasilev R.A.

Lomonosov Moscow State University;
National Research Center “Kurchatov Institute”

Chernikovich V.Yu.

Dmitry Mendeleev University of Chemical Technology of Russia

Evteeva M.A.

National Research Center “Kurchatov Institute”

Sakharov D.A.

Dmitry Mendeleev University of Chemical Technology of Russia

Patrushev M.V.

Dmitry Mendeleev University of Chemical Technology of Russia;
National Research Center “Kurchatov Institute”

Received:

18.03.2020

Accepted:

18.07.2020

List of references:

  1. Monod J, Jacob F. General Conclusions: Teleonomic Mechanisms in Cellular Metabolism, Growth, and Differentiation. Cold Spring Harbor Symposia on Quantitative Biology. 1961;26(0):389-401.  https://doi.org/10.1101/SQB.1961.026.01.048
  2. Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nat Rev Microbiol. 2014;12(5):381-390.  https://doi.org/10.1038/nrmicro3239
  3. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000;403(6767):339-342.  https://doi.org/10.1038/35002131
  4. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000;403(6767):335-338.  https://doi.org/10.1038/35002125
  5. Weiss R, Knight TF. Engineered communications for microbial robotics. In: Condon A, Rozenberg G, eds. DNA Computing. Vol 2054. Lecture Notes in Computer Science. Springer Berlin Heidelberg; 2001;1-16.  https://doi.org/10.1007/3-540-44992-2_1
  6. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicellular system for programmed pattern formation. Nature. 2005;434(7037):1130-1134. https://doi.org/10.1038/nature03461
  7. McAdams H, Shapiro L. Circuit simulation of genetic networks. Science. 1995;269(5224):650-656.  https://doi.org/10.1126/science.7624793
  8. Beal J, Phillips A, Densmore D, Cai Y. High-Level Programming Languages for Biomolecular Systems. In: Koeppl H, Setti G, di Bernardo M, Densmore D, eds. Design and Analysis of Biomolecular Circuits. Springer New York; 2011;225-252.  https://doi.org/10.1007/978-1-4419-6766-4_11
  9. Konur S, Gheorghe M, Dragomir C, Ipate F, Krasnogor N. Conventional Verification for Unconventional Computing: a Genetic XOR Gate Example. Fundamenta Informaticae. 2014;134(1-2):97-110.  https://doi.org/10.3233/FI-2014-1093
  10. Tamsir A, Tabor JJ, Voigt CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires.’ Nature. 2011;469(7329):212-215.  https://doi.org/10.1038/nature09565
  11. Weinberg BH, Pham NTH, Caraballo LD, 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;35(5):453-462.  https://doi.org/10.1038/nbt.3805
  12. Cardinale S, Arkin AP. Contextualizing context for synthetic biology — identifying causes of failure of synthetic biological systems. Biotechnology Journal. 2012;7(7):856-866.  https://doi.org/10.1002/biot.201200085
  13. Daniel R, Rubens JR, Sarpeshkar R, Lu TK. Synthetic analog computation in living cells. Nature. 2013;497(7451):619-623.  https://doi.org/10.1038/nature12148
  14. Wong A, Wang H, Poh CL, Kitney RI. Layering genetic circuits to build a single cell, bacterial half adder. BMC Biol. 2015;13(1):40.  https://doi.org/10.1186/s12915-015-0146-0
  15. 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;411(19):4293-4302. https://doi.org/10.1007/s00216-019-01622-7
  16. Ausländer D, Ausländer S, Pierrat X, Hellmann L, Rachid L, Fussenegger M. Programmable full-adder computations in communicating three-dimensional cell cultures. Nat Methods. 2018;15(1):57-60.  https://doi.org/10.1038/nmeth.4505
  17. Gaj T, Sirk SJ, Barbas CF. Expanding the scope of site-specific recombinases for genetic and metabolic engineering: Expanding the Scope of Site-Specific Recombinases. Biotechnol Bioeng. 2014;111(1):1-15.  https://doi.org/10.1002/bit.25096
  18. Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK. Synthetic recombinase-based state machines in living cells. Science. 2016;353(6297):aad8559-aad8559. https://doi.org/10.1126/science.aad8559
  19. Carroll D. Genome Engineering with Targetable Nucleases. Annu Rev Biochem. 2014;83(1):409-439.  https://doi.org/10.1146/annurev-biochem-060713-035418
  20. Pickar-Oliver A, Gersbach CA. The next generation of CRISPR—Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20(8):490-507.  https://doi.org/10.1038/s41580-019-0131-5
  21. Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol. 2019;37(6):657-666.  https://doi.org/10.1038/s41587-019-0095-1
  22. Brödel AK, Jaramillo A, Isalan M. Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nat Commun. 2016;7(1):13858. https://doi.org/10.1038/ncomms13858
  23. Stripecke R, Oliveira CC, McCarthy JE, Hentze MW. Proteins binding to 5’ untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells. Mol Cell Biol. 1994;14(9):5898-5909. https://doi.org/10.1128/MCB.14.9.5898
  24. Yen L, Svendsen J, Lee JS, Gray JT, Magnier M, Baba T, et al. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature. 2004;431(7007):471-476.  https://doi.org/10.1038/nature02844
  25. Ausländer S, Ketzer P, Hartig JS. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol BioSyst. 2010;6(5):807.  https://doi.org/10.1039/b923076a
  26. Win MN, Smolke CD. Higher-Order Cellular Information Processing with Synthetic RNA Devices. Science. 2008;322(5900):456-460.  https://doi.org/10.1126/science.1160311
  27. Rackham O, Chin JW. A network of orthogonal ribosome·mRNA pairs. Nat Chem Biol. 2005;1(3):159-166.  https://doi.org/10.1038/nchembio719
  28. Chen Z, Lichtor PA, Berliner AP, Chen JC, Liu DR. Evolution of sequence-defined highly functionalized nucleic acid polymers. Nature Chem. 2018;10(4):420-427.  https://doi.org/10.1038/s41557-018-0008-9
  29. Davis L, Chin JW. Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol. 2012;13(3):168-182.  https://doi.org/10.1038/nrm3286
  30. Forster AC, Tan Z, Nalam MN, Lin H, Qu H, Cornish VW, et al. Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proceedings of the National Academy of Sciences. 2003;100(11):6353-6357. https://doi.org/10.1073/pnas.1132122100
  31. O’Donoghue P, Ling J, Wang Y-S, Söll D. Upgrading protein synthesis for synthetic biology. Nat Chem Biol. 2013;9(10):594-598.  https://doi.org/10.1038/nchembio.1339
  32. Farzadfard F, Gharaei N, Higashikuni Y, Jung G, Cao J, Lu TK. Single-Nucleotide-Resolution Computing and Memory in Living Cells. Synthetic Biology; 2018. https://doi.org/10.1101/263657
  33. Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, et al. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol. 2015;33(12):1272-1279. https://doi.org/10.1038/nbt.3372
  34. Park S-H. Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms. Science. 2003;299(5609):1061-1064. https://doi.org/10.1126/science.1076979
  35. Ryu J, Park S-H. Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells. Sci Signal. 2015;8(383):ra66-ra66. https://doi.org/10.1126/scisignal.aab3397
  36. Truong DJ, 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;43(13):6450-6458. https://doi.org/10.1093/nar/gkv601
  37. Kanno A, Ozawa T, Umezawa Y. Bioluminescent Imaging of MAPK Function with Intein-Mediated Reporter Gene Assay. In: Rich PB, Douillet C, eds. Bioluminescence. Vol 574. Methods in Molecular Biology. Humana Press; 2009:185-192.  https://doi.org/10.1007/978-1-60327-321-3_15
  38. Davis KM, Pattanayak V, Thompson DB, Zuris JA, Liu DR. Small molecule — triggered Cas9 protein with improved genome-editing specificity. Nat Chem Biol. 2015;11(5):316-318.  https://doi.org/10.1038/nchembio.1793
  39. Callahan BP, Topilina NI, Stanger MJ, Van Roey P, Belfort M. Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications. Nat Struct Mol Biol. 2011;18(5):630-633.  https://doi.org/10.1038/nsmb.2041
  40. Lohmueller JJ, Armel TZ, Silver PA. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Research. 2012;40(11):5180-5187. https://doi.org/10.1093/nar/gks142
  41. Lienert F, Torella JP, Chen J-H, Norsworthy M, Richardson RR, Silver PA. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Research. 2013;41(21):9967-9975. https://doi.org/10.1093/nar/gkt758
  42. Schaerli Y, Gili M, Isalan M. A split intein T7 RNA polymerase for transcriptional AND-logic. Nucleic Acids Research. 2014;42(19):12322-12328. https://doi.org/10.1093/nar/gku884
  43. To AC, Chu DH, Wang AR, Li FC, Chiu AW, Gao DY, et al. A comprehensive web tool for toehold switch design. Wren J, ed. Bioinformatics. 2018;34(16):2862-2864. https://doi.org/10.1093/bioinformatics/bty216
  44. Hall RA, Macdonald J. Synthetic Biology Provides a Toehold in the Fight against Zika. Cell Host & Microbe. 2016;19(6):752-754.  https://doi.org/10.1016/j.chom.2016.05.020
  45. Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, et al. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat Commun. 2018;9(1):3347. https://doi.org/10.1038/s41467-018-05864-4
  46. Steidler L. Treatment of Murine Colitis by Lactococcus lactis Secreting Interleukin-10. Science. 2000;289(5483):1352-1355. https://doi.org/10.1126/science.289.5483.1352
  47. 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;3(1):49-56.  https://doi.org/10.1038/mi.2009.116
  48. Xiang S, Fruehauf J, Li CJ. Short hairpin RNA—expressing bacteria elicit RNA interference in mammals. Nat Biotechnol. 2006;24(6):697-702.  https://doi.org/10.1038/nbt1211
  49. Piñero-Lambea C, Bodelón G, Fernández-Periáñez R, Cuesta AM, Álvarez-Vallina L, Fernández LÁ. Programming Controlled Adhesion of E. coli to Target Surfaces, Cells, and Tumors with Synthetic Adhesins. ACS Synth Biol. 2015;4(4):463-473.  https://doi.org/10.1021/sb500252a
  50. Duan FF, Liu JH, March JC. Engineered Commensal Bacteria Reprogram Intestinal Cells Into Glucose-Responsive Insulin-Secreting Cells for the Treatment of Diabetes. Diabetes. 2015;64(5):1794-1803. https://doi.org/10.2337/db14-0635
  51. Lagenaur LA, Sanders-Beer BE, 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;4(6):648-657  https://doi.org/10.1038/mi.2011.30
  52. Lim WA, June CH. The Principles of Engineering Immune Cells to Treat Cancer. Cell. 2017;168(4):724-740.  https://doi.org/10.1016/j.cell.2017.01.016
  53. Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, et al. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell. 2016;167(2):419-432.e16.  https://doi.org/10.1016/j.cell.2016.09.011
  54. 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. Molecular Cell. 2014;55(3):397-408.  https://doi.org/10.1016/j.molcel.2014.06.007
  55. Ye H, Baba MD-E, Peng R-W, Fussenegger M. A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice. Science. 2011;332(6037):1565-1568. https://doi.org/10.1126/science.1203535
  56. Rössger K, Charpin-El-Hamri G, Fussenegger M. A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun. 2013;4(1):2825. https://doi.org/10.1038/ncomms3825
  57. Kotas ME, Medzhitov R. Homeostasis, Inflammation, and Disease Susceptibility. Cell. 2015;160(5):816-827.  https://doi.org/10.1016/j.cell.2015.02.010
  58. 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;354(6317):1296-1301. https://doi.org/10.1126/science.aaf4006
  59. 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;360(6391):915-918.  https://doi.org/10.1126/science.aas9315
  60. Purcell O, Lu TK. Synthetic analog and digital circuits for cellular computation and memory. Current Opinion in Biotechnology. 2014;29:146-155.  https://doi.org/10.1016/j.copbio.2014.04.009
  61. Hirai H, Tani T, Kikyo N. Structure and functions of powerful transactivators: VP16, MyoD and FoxA. Int J Dev Biol. 2010;54(11-12):1589-1596. https://doi.org/10.1387/ijdb.103194hh
  62. Saxena P, Bojar D, Zulewski H, Fussenegger M. Generation of glucose-sensitive insulin-secreting beta-like cells from human embryonic stem cells by incorporating a synthetic lineage-control network. Journal of Biotechnology. 2017;259:39-45.  https://doi.org/10.1016/j.jbiotec.2017.07.018
  63. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. A sensing array of radically coupled genetic ‘biopixels.’ Nature. 2012;481(7379):39-44.  https://doi.org/10.1038/nature10722
  64. Lee W, Wood TK, Chen W. Engineering TCE-degrading rhizobacteria for heavy metal accumulation and enhanced TCE degradation. Biotechnol Bioeng. 2006;95(3):399-403.  https://doi.org/10.1002/bit.20950
  65. 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;11(1):185.  https://doi.org/10.1186/s13068-018-1181-1
  66. Balaban PM, Vorontsov DD, Dyakonova VE, Dyakonova TL, Zakharov IS, Korshunova TA, et al. The Central Pattern Generators. 2013;63(5):520-541.  https://doi.org/10.7868/S0044467713050031
  67. Lu J, Yang J, Kim Y-B, Ayers J. Low power, high PVT variation tolerant central pattern generator design for a bio-hybrid micro robot. In: 2012 IEEE 55th International Midwest Symposium on Circuits and Systems (MWSCAS). IEEE; 2012;782-785.  https://doi.org/10.1109/MWSCAS.2012.6292137

Close metadata

Contact the author
Email
Message
The publishing house "Media Sphere" does not provide treatment services, does not give recommendations on contacting medical institutions and specific specialists, on the prescription of medicines and dietary supplements.

Email Confirmation

An email was sent to test@gmail.com with a confirmation link. Follow the link from the letter to complete the registration on the site.

Email Confirmation

Contact us
If you have any questions, complaints or suggestions, please use this feedback form.
Email
Message
The publishing house "Media Sphere" does not provide treatment services, does not give recommendations on contacting medical institutions and specific specialists, on the prescription of medicines and dietary supplements.
Submit Application

You can become an author of one of our magazines, send a request and we will consider it in during the day.

Name
Phone
E-mail
Message
Login
Registration
E-mail
Password
Forgot Password?

Log in to the site using your account in one of the services

Password recovery
E-mail
Login
Register

We use cооkies to improve the performance of the site. By staying on our site, you agree to the terms of use of cооkies. To view our Privacy and Cookie Policy, please. click here.