Combination of versatile platforms for the development of synthetic biology

Abstract

Background: Synthetic biology has attracted enormous attention in recent years. A key focus of synthetic biology is to utilize modular biological building blocks to assemble the cell-based circuits.

Results: Scientists have programmed the living organisms using these circuits to attain multiple, delicate and well-defined functions. With the integration of tools or technologies from other disciplines, these rewired cells can achieve even more complex tasks.

Conclusions: In this review, we will focus on the recent achievements in new materials and devices assembly, next generation therapeutics development and versatile manufacturing by combining the synthetic gene circuits, various tools and technologies from multiple fields, such as printing technology, material engineering and electronic engineering.

Graphical abstract

Keywords

synthetic biology / material engineering / printing technology / electronic engineering

References

[1] Cameron, D. E., Bashor, C. J. and Collins, J. J. (2014) A brief history of synthetic biology. Nat. Rev. Microbiol., 12, 381–390

[2] Jacob, F. and Monod, J.(1961) On the regulation of gene activity. Cold Spring Harb. Symp. Quant. Biol., 26, 193–211

[3] Gardner, T. S., Cantor, C. R. and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339–342

[4] Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335–338

[5] Teo, J. J. Y., Woo, S. S. and Sarpeshkar, R. (2015) Synthetic biology: A unifying view and review using analog circuits. IEEE Trans. Biomed. Circuits Syst., 9, 453–474

[6] Ye, H. and Fussenegger, M. (2014) Synthetic therapeutic gene circuits in mammalian cells. FEBS Lett., 588, 2537–2544

[7] Gardner, T. S., Cantor, C. R. and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339–342

[8] 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

[9] Ellis, T., Wang, X. and Collins, J. J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol., 27, 465–471

[10] 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

[11] Danino, T., Mondragón-Palomino, O., Tsimring, L. and Hasty, J. (2010) A synchronized quorum of genetic clocks. Nature, 463, 326–330

[12] Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A. and Ellington, A. D. (2009) A synthetic genetic edge detection program. Cell, 137, 1272–1281

[13] Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation. Nature, 434, 1130–1134

[14] Bulter, T., Lee, S. G., Wong, W. W., Fung, E., Connor, M. R. and Liao, J. C. (2004) Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl. Acad. Sci. USA, 101, 2299–2304

[15] Zhao, T. and Zhong, C. (2017) Applications of synthetic biology in materials science. Chinese Journal of Biotechnology, 33, 494–505, in Chinese

[16] MacDonald, I. C. and Deans, T. L. (2016) Tools and applications in synthetic biology. Adv. Drug Deliv. Rev., 105, 20–34

[17] Wagner, H. J., Sprenger, A., Rebmann, B. and Weber, W. (2016) Upgrading biomaterials with synthetic biological modules for advanced medical applications. Adv. Drug Deliv. Rev., 105, 77–95

[18] Schwarz, K. A. and Leonard, J. N. (2016) Engineering cell-based therapies to interface robustly with host physiology. Adv. Drug Deliv. Rev., 105, 55–65

[19] Khalil, A. S. and Collins, J. J. (2010) Synthetic biology: applications come of age. Nat. Rev. Genet., 11, 367–379

[20] Smanski, M. J., Zhou, H., Claesen, J., Shen, B., Fischbach, M. A. and Voigt, C. A. (2016) Synthetic biology to access and expand nature’s chemical diversity. Nat. Rev. Microbiol., 14, 135–149

[21] Looger, L. L., Dwyer, M. A., Smith, J. J. and Hellinga, H. W. (2003) Computational design of receptor and sensor proteins with novel functions. Nature, 423, 185–190

[22] 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

[23] Shepherd, T. R., Du, L., Liljeruhm, J., Samudyata, Wang, J., Sjödin, M. O. D., Wetterhall, M., Yomo, T. and ForsterA. C. (2017) De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Res., 45, 10895–10905

[24] Koepnick, B., Flatten, J., Husain, T., Ford, A., Silva, D. A., Bick, M. J., Bauer, A., Liu, G., Ishida, Y., Boykov, A., (2019) De novo protein design by citizen scientists. Nature, 570, 390–394

[25] Si, T. and Zhao, H. (2016) A brief overview of synthetic biology research programs and roadmap studies in the United States. Synth. Syst. Biotechnol., 1, 258–264

[26] Zhao, H. (2013) Synthetic Biology: Tools And Applications. Amsterdam: Academic Press-Elsevier

[27] Segall-Shapiro, T. H., Sontag, E. D. and Voigt, C. A. (2018) Engineered promoters enable constant gene expression at any copy number in bacteria. Nat. Biotechnol., 36, 352–358

[28] Nandagopal, N. and Elowitz M.B., (2011) Synthetic Biology: Integrated Gene Circuits. Science, 333, 1244–1248

[29] Crocker, J. and Ilsley, G. R. (2017) Using synthetic biology to study gene regulatory evolution. Curr. Opin. Genet. Dev., 47, 91–101

[30] Lienert, F., Lohmueller, J. J., Garg, A. and Silver, P. A. (2014) Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol., 15, 95–107

[31] Bashor, C.J., Helman , N.C., Yan, S., and Lim, W.A. (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science, 319, 1539–1543

[32] Peisajovich, S.G., Garbarino , J.E., Wei, P., Lim, W.A. (2010) Rapid diversification of cell signaling phenotypes by modular domain recombination. Science, 328, 368–372

[33] Johnston, R. J. Jr and Desplan, C. (2010) Preview. A penetrating look at stochasticity in development. Cell, 140, 610–612

[34] Chen, A. Y., Zhong, C. and Lu, T. K. (2015) Engineering living functional materials. ACS Synth. Biol., 4, 8–11

[35] Le Feuvre, R. A. and Scrutton, N. S. (2018) A living foundry for synthetic biological materials: a synthetic biology roadmap to new advanced materials. Synth. Syst. Biotechnol., 3, 105–112

[36] Din, M. O., Danino, T., Prindle, A., Skalak, M., Selimkhanov, J., Allen, K., Julio, E., Atolia, E., Tsimring, L. S., Bhatia, S. N., (2016) Synchronized cycles of bacterial lysis for in vivo delivery. Nature, 536, 81–85

[37] Raje, P. V. and Murmu, N. C. (2014) A review on electrohydrodynamic-inkjet printing technology. IjetaeCom, 4, 174–183

[38] Srimongkon, T., Mandai, S. and Enomae, T. (2015) Application of biomaterials and inkjet printing to develop bacterial culture system. Adv. Mater. Sci. Eng., 2015, 1–9

[39] Merrin, J., Leibler, S. and Chuang, J. S. (2007) Printing multistrain bacterial patterns with a piezoelectric inkjet printer. PLoS One, 2, e663

[40] Cao, Y., Feng, Y., Ryser, M. D., Zhu, K., Herschlag, G., Cao, C., Marusak, K., Zauscher, S. and You, L. (2017) Programmable assembly of pressure sensors using pattern-forming bacteria. Nat. Biotechnol., 35, 1087–1093

[41] Ngo, T. D., Kashani, A., Imbalzano, G., Nguyen, K. T. Q. and Hui, D. (2018) Additive manufacturing (3D printing): A review of materials, methods, applications and challenges. Compos., Part B Eng., 143, 172–196

[42] Wang, X., Xu, S., Zhou, S., Xu, W., Leary, M., Choong, P., Qian, M., Brandt, M. and Xie, Y. M. (2016) Topological design and additive manufacturing of porous metals for bone scaffolds and orthopaedic implants: A review. Biomaterials, 83, 127–141

[43] Labeaga-Martínez, N., Sanjurjo-Rivo, M., Díaz-Álvarez, J. and Martínez-Frías, J. (2017) Additive manufacturing for a Moon village. Procedia. Manuf., 13, 794–801

[44] Goyanes, A., Wang, J., Buanz, A., MartVnez-Pacheco, R., Telford, R., Gaisford, S. and Basit, A. W. (2015) 3D printing of medicines: engineering novel oral devices with unique design and drug release characteristics. Mol. Pharm., 12, 4077–4084

[45] Chohan, J. S., Singh, R., Boparai, K. S., Penna, R. and Fraternali, F. (2017) Dimensional accuracy analysis of coupled fused deposition modeling and vapour smoothing operations for biomedical applications. Compos., Part B Eng., 117, 138–149

[46] Zhang, C., Huang, J., Zhang, J., Liu, S., Cui, M., An, B., Wang, X., Pu, J., Zhao, T., Fan, C., (2019) Engineered Bacillus subtilis biofilms as living glues. Mater. Today, 28, 40–48

[47] Huang, J., Liu, S., Zhang, C., Wang, X., Pu, J., Ba, F., Xue, S., Ye, H., Zhao, T., Li, K., (2019) Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nat. Chem. Biol., 15, 34–41

[48] Kyle, S. (2018) 3D printing of bacteria: the next frontier in biofabrication. Trends Biotechnol., 36, 340–341

[49] Schaffner, M, Rühs , P.A., Coulter, F., Kilcher, S., and Studart, A.R. (2017) 3D printing of bacteria into functional complex materials. Sci. Adv. 3, eaao6804

[50] Lehner, B. A. E., Schmieden, D. T. and Meyer, A. S. (2017) A straightforward approach for 3D bacterial printing. ACS Synth. Biol., 6, 1124–1130

[51] González, L. M., Mukhitov, N. and Voigt, C. A. (2019) Resilient living materials built by printing bacterial spores. Nat. Chem. Biol.

[52] Nguyen, M. K. and Lee, D. S. (2010) Injectable biodegradable hydrogels. Macromol. Biosci., 10, 563–579

[53] Naderi, H., Matin, M. M. and Bahrami, A. R. (2011) Review paper: critical issues in tissue engineering: biomaterials, cell sources, angiogenesis, and drug delivery systems. J. Biomater. Appl., 26, 383–417

[54] Smeets, N. M. B. and Hoare, T. (2013) Designing responsive microgels for drug delivery applications. J. Polymer Sci. Chem, 51, 3027–3043

[55] Suo, H., Zhang, D., Yin, J., Qian, J., Wu, Z. L. and Fu, J. (2018) Interpenetrating polymer network hydrogels composed of chitosan and photocrosslinkable gelatin with enhanced mechanical properties for tissue engineering. Mater. Sci. Eng. C, 92, 612–620

[56] Dai, Z. and Huang, S. (2018) Functional dynamics inside nano- or microscale bio-hybrid systems. Front Chem., 6, 621

[57] Gorelikov, I., Field, L. M. and Kumacheva, E. (2004) Hybrid microgels photoresponsive in the near-infrared spectral range. J. Am. Chem. Soc., 126, 15938–15939

[58] Gu, Z., Dang, T. T., Ma, M., Tang, B. C., Cheng, H., Jiang, S., Dong, Y., Zhang, Y. and Anderson, D. G. (2013) Glucose-responsive microgels integrated with enzyme nanocapsules for closed-loop insulin delivery. ACS Nano, 7, 6758–6766

[59] Trongsatitkul, T. and Budhlall, B. (2013) Microgels or microcapsules? Role of morphology on the release kinetics of thermoresponsive PNIPAm-co-PEGMa hydrogels. Polym. Chem., 4, 1502–1516

[60] English, M.A., Soenksen , L.R., Gayet, R. V., de Puig, H., Angenent-Mari, N.M., Mao, A.S., Nguyen, P. Q. and Collins, J. J. (2019) Programmable CRISPR-responsive smart materials. Science, 365,780–785

[61] Bulter, T., Lee, S. G., Wong, W. W., Fung, E., Connor, M. R. and Liao, J. C. (2004) Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl. Acad. Sci. USA, 101, 2299–2304

[62] Higashikuni, Y., Chen, W. C. and Lu, T. K. (2017) Advancing therapeutic applications of synthetic gene circuits. Curr. Opin. Biotechnol., 47, 133–141

[63] Xue, S., Yin, J., Shao, J., Yu, Y., Yang, L., Wang, Y., Xie, M., Fussenegger, M. and Ye, H. (2017) A synthetic-biology-inspired therapeutic strategy for targeting and treating hepatogenous diabetes. Mol. Ther., 25, 443–455

[64] Mount, N. M., Ward, S. J., Kefalas, P. and Hyllner, J. (2015) Cell-based therapy technology classifications and translational challenges. Philos. Trans. R. Soc. Lond. B Biol. Sci., 370, 20150017

[65] Ye, H., Xie, M., Xue, S., Charpin-El Hamri, G., Yin, J., Zulewski, H. and Fussenegger, M. (2017) Self-adjusting synthetic gene circuit for correcting insulin resistance. Nat. Biomed. Eng., 1, 0005

[66] Abraham, T., Mao, M. and Tan, C. (2018) Engineering approaches of smart, bio-inspired vesicles for biomedical applications. Phys. Biol., 15, 061001

[67] Ding, Y., Contreras-Llano, L. E., Morris, E., Mao, M. and Tan, C. (2018) Minimizing context dependency of gene networks using artificial cells. ACS Appl. Mater. Interfaces, 10, 30137–30146

[68] Dai, Z., Lee, A. J., Roberts, S., Sysoeva, T. A., Huang, S., Dzuricky, M., Yang, X., Zhang, X., Liu, Z., Chilkoti, A., (2019) Versatile biomanufacturing through stimulus-responsive cell-material feedback. Nat. Chem. Biol., 15, 1017–1024

[69] Barnhart, M. M. and Chapman, M. R. (2006) Curli biogenesis and function. Annu. Rev. Microbiol., 60, 131–147

[70] Bian, Z. and Normark, S. (1997) Nucleator function of CsgB for the assembly of adhesive surface organelles in Escherichia coli. EMBO J., 16, 5827–5836

[71] Chapman, M. R., Robinson, L. S., Pinkner, J. S., Roth, R., Heuser, J., Hammar, M., Normark, S. and Hultgren, S. J. (2002) Role of Escherichia coli curli operons in directing amyloid fiber formation. Science, 295, 851–855

[72] Chen, A. Y., Deng, Z., Billings, A. N., Seker, U. O., Lu, M. Y., Citorik, R. J., Zakeri, B. and Lu, T. K. (2014) Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater., 13, 515–523

[73] Wang, X., Pu, J., An, B., Li, Y., Shang, Y., Ning, Z., Liu, Y., Ba, F., Zhang, J. and Zhong, C. (2018) Programming cells for dynamic assembly of inorganic nano-objects with spatiotemporal control. Adv. Mater., 30, e1705968

[74] Wang, X., Pu, J., Liu, Y., Ba, F., Cui, M., Li, K., Xie, Y., Nie, Y., Mi, Q., Li, T., (2019) Immobilization of functional nano-objects in living engineered bacterial biofilms for catalytic applications. Natl. Sci. Rev., 6, 929–943

[75] Shao, J., Xue, S., Yu, G., Yu, Y., Yang, X., Bai, Y., Zhu, S., Yang, L., Yin, J., Wang, Y., (2017) Smartphone-controlled optogenetically engineered cells enable semiautomatic glucose homeostasis in diabetic mice. Sci. Transl. Med., 9, 1–14

[76] Justus, K.B., Hellebrekers , T., Lewis, D.D., Wood, A., Ingham, C., Majidi, C., LeDuc, P.R., and Tan, C. (2019) A biosensing soft robot: Autonomous parsing of chemical signals through integrated organic and inorganic interfaces. Sci Robot., 4, eaax0765

[77] Mimee, M., Nadeau, P., Hayward, A., Carim, S., Flanagan, S., Jerger, L., Collins, J., McDonnell, S., Swartwout, R., Citorik, R.J. (2018) An ingestible bacterial-electronic system to monitor gastrointestinal health. Science, 360, 915–918

ACKNOWLEDGEMENTS

We thank Lingchong You for insightful comments and suggestions. This study was partially supported by the National Key Research and Development Program of China (No. 2018YFA0903000), Guangdong Provincial Key Laboratory of Synthetic Genomics (2019B030301006), Shenzhen Key Laboratory of Synthetic Genomics (ZDSYS201802061806209) and Shenzhen Science and Technology Program (No. KQTD20180413181837372).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Baizhu Chen and Zhuojun Dai declare that they have no conflict of interests.

This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2020 Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature