Modeling information exchange between living and artificial cells

Abstract

Background: The tools of synthetic biology have enabled researchers to explore multiple scientific phenomena by directly engineering signaling pathways within living cells and artificial protocells. Here, we explored the potential for engineered living cells themselves to assemble signaling pathways for non-living protocells. This analysis serves as a preliminary investigation into a potential origin of processes that may be utilized by complex living systems. Specifically, we suggest that if living cells can be engineered to direct the assembly of genetic signaling pathways from genetic biomaterials in their environment, then insight can be gained into how naturally occurring living systems might behave similarly.

Methods: To this end, we have modeled and simulated a system consisting of engineered cells that control the assembly of DNA monomers on microparticle scaffolds. These DNA monomers encode genetic circuits, and therefore, these microparticles can then be encapsulated with minimal transcription and translation systems to direct protocell phenotype. The modeled system relies on multiple previously established synthetic systems and then links these together to demonstrate system feasibility.

Results: In this specific model, engineered cells are induced to synthesize biotin, which competes with biotinylated, circuit-encoding DNA monomers for an avidinized-microparticle scaffold. We demonstrate that multiple synthetic motifs can be controlled in this way and can be tuned by manipulating parameters such as inducer and DNA concentrations.

Conclusions: We expect that this system will provide insight into the origin of living systems as well as serve as a tool for engineering living cells that assemble complex biomaterials in their environment.

Graphical abstract

Keywords

synthetic biology / artificial cells / biotin / microparticles

References

[1] Ricardo, A. and Szostak, J. W. (2009) Origin of life on earth. Sci. Am., 301, 54–61

[2] Szostak, J. W. (2009) Origins of life: systems chemistry on early Earth. Nature, 459, 171–172

[3] Szostak, J. W., Bartel, D. P. and Luisi, P. L. (2001) Synthesizing life. Nature, 409, 387–390

[4] Adamala, K. P., Engelhart, A. E. and Szostak, J. W. (2016) Collaboration between primitive cell membranes and soluble catalysts. Nat. Commun., 7, 11041

[5] Engelhart, A. E., Adamala, K. P. and Szostak, J. W. (2016) A simple physical mechanism enables homeostasis in primitive cells. Nat. Chem., 8, 448–453

[6] 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

[7] Hutchison, C. A. III, Chuang, R. Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., Gill, J., Kannan, K., Karas, B. J., Ma, L., (2016) Design and synthesis of a minimal bacterial genome. Science, 351, aad6253

[8] Glass, J. I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M. R., Maruf, M., Hutchison C. A. III , Smith, H. O. and Venter, J. C. (2006) Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. USA, 103, 425–430

[9] Zhang, R., Heyde, K. C., Scott, F. Y., Paek, S.-H.and Ruder, W. C. (2016) Programming surface chemistry with engineered cells. ACS Synth. Biol., 5, 936–941

[10] Chen, A. Y., Deng, Z., Billings, A. N., Seker, U. O. S., 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

[11] Botyanszki, Z., Tay, P. K. R., Nguyen, P. Q., Nussbaumer, M. G. and Joshi, N. S. (2015) Engineered catalytic biofilms: site-specific enzyme immobilization onto E. coli curli nanofibers. Biotechnol. Bioeng., 112, 2016–2024

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

[13] Ridgley, D. M., Freedman, B. G., Lee, P. W. and Barone, J. R. (2014) Genetically encoded self-assembly of large amyloid fibers. Biomater. Sci., 2, 560–566

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

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

[16] 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

[17] Anderson, J. C., Voigt, C. A. and Arkin, A. P. (2007) Environmental signal integration by a modular AND gate. Mol. Syst. Biol., 3, 133

[18] 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

[19] Levskaya, A., Chevalier, A. A., Tabor, J. J., Simpson, Z. B., Lavery, L. A., Levy, M., Davidson, E. A., Scouras, A., Ellington, A. D., Marcotte, E. M., (2005) Synthetic biology: engineering Escherichia coli to see light. Nature, 438, 441–442

[20] 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

[21] Kramer, B. P., Viretta, A. U., Baba, M. D. -E., Aubel, D., Weber, W. and Fussenegger, M. (2004) An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol., 22, 867–870

[22] Blake, W. J., Balázsi, G., Kohanski, M. A., Isaacs, F. J., Murphy, K. F., Kuang, Y., Cantor, C. R., Walt, D. R. and Collins, J. J. (2006) Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell, 24, 853–865

[23] Eldar, A. and Elowitz, M. B. (2010) Functional roles for noise in genetic circuits. Nature, 467, 167–173

[24] Guet, C. C., Elowitz, M. B., Hsing, W. and Leibler, S. (2002) Combinatorial synthesis of genetic networks. Science, 296, 1466–1470

[25] Kærn, M., Elston, T. C., Blake, W. J. and Collins, J. J. (2005) Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet., 6, 451–464

[26] 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

[27] Balázsi, G., van Oudenaarden, A. and Collins, J. J. (2011) Cellular decision making and biological noise: from microbes to mammals. Cell, 144, 910–925

[28] Elowitz, M. B., Levine, A. J., Siggia, E. D. and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183–1186

[29] Karzbrun, E., Tayar, A. M., Noireaux, V. and Bar-Ziv, R. H. (2014) Programmable on-chip DNA compartments as artificial cells. Science, 345, 829–832

[30] Noireaux, V., Maeda, Y. T. and Libchaber, A. (2011) Development of an artificial cell, from self-organization to computation and self-reproduction. Proc. Natl. Acad. Sci. USA, 108, 3473–3480

[31] Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. and Ueda, T. (2001) Cell-free translation reconstituted with purified components. Nat. Biotechnol., 19, 751–755

[32] Tan, C., Saurabh, S., Bruchez, M. P., Schwartz, R. and Leduc, P. (2013) Molecular crowding shapes gene expression in synthetic cellular nanosystems. Nat. Nanotechnol., 8, 602–608

[33] Weber, P. C., Ohlendorf, D. H., Wendoloski, J. J. and Salemme, F. R. (1989) Structural origins of high-affinity biotin binding to streptavidin. Science, 243, 85–88

[34] Green, N. M. (1963) Avidin. 3. The nature of the biotin-binding site. Biochem. J., 89, 599–609

[35] Huang, S. -C., Stump, M. D., Weiss, R. and Caldwell, K. D. (1996) Binding of biotinylated DNA to streptavidin-coated polystyrene latex: effects of chain length and particle size. Anal. Biochem., 237, 115–122

[36] Noireaux, V., Bar-Ziv, R. and Libchaber, A. (2003) Principles of cell-free genetic circuit assembly. Proc. Natl. Acad. Sci. USA, 100, 12672–12677

[37] Daube, S. S. and Bar-Ziv, R. H. (2013) Protein nanomachines assembly modes: cell-free expression and biochip perspectives. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 5, 613–628

[38] Groisman, A., Lobo, C., Cho, H., Campbell, J. K., Dufour, Y. S., Stevens, A. M. and Levchenko, A. (2005) A microfluidic chemostat for experiments with bacterial and yeast cells. Nat. Methods, 2, 685–689

[39] Hol, F. J. H. and Dekker, C. (2014) Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science, 346, 1251821

[40] Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M. and Noireaux, V. (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. J. Vis. Exp., doi: 10.3791/50762

[41] Lutz, R. and Bujard, H. (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res., 25, 1203–1210

[42] Sanyal, I., Cohen, G. and Flint, D. H. (1994) Biotin synthase: purification, characterization as a [2Fe-2S]cluster protein, and in vitro activity of the Escherichia coli bioB gene product. Biochemistry, 33, 3625–3631

[43] Brophy, J. A. N. and Voigt, C. A. (2014) Principles of genetic circuit design. Nat. Methods, 11, 508–520

[44] Garcia-Ojalvo, J., Elowitz, M. B. and Strogatz, S. H. (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. USA, 101, 10955–10960

[45] Heyde, K. C. and Ruder, W. C. (2015) Exploring host-microbiome interactions using an in silico model of biomimetic robots and engineered living cells. Sci. Rep., 5, 11988

[46] Anderson, J. C., Voigt, C. A. and Arkin, A. P. (2007) Environmental signal integration by a modular AND gate. Mol. Syst. Biol., 3, 133

[47] Cameron, D. E. and Collins, J. J. (2014) Tunable protein degradation in bacteria. Nat. Biotechnol., 32, 1276–1281

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

[49] Johnson, K. A. and Goody, R. S. (2011) The original Michaelis constant: translation of the 1913 Michaelis-Menten paper. Biochemistry, 50, 8264–8269

[50] González, M., Bagatolli, L. A., Echabe, I., Arrondo, J. L. R., Argaraña, C. E., Cantor, C. R. and Fidelio, G. D. (1997) Interaction of biotin with streptavidin. Thermostability and conformational changes upon binding. J. Biol. Chem., 272, 11288–11294

[51] Schwarz-Schilling, M., Aufinger, L., Mückl, A. and Simmel, F. C. (2016) Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets. Integr. Biol., 8, 564–570

[52] Stögbauer, T., Windhager, L., Zimmer, R. and Rädler, J. O. (2012) Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr. Biol., 4, 494–501

[53] Brenner, K., You, L. and Arnold, F. H. (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol., 26, 483–489

[54] Hays, S. G., Patrick, W. G., Ziesack, M., Oxman, N.and Silver, P. A. (2015) Better together: engineering and application of microbial symbioses. Curr. Opin. Biotechnol., 36, 40–49

[55] Wintermute, E. H. and Silver, P. A. (2010) Dynamics in the mixed microbial concourse. Genes Dev., 24, 2603–2614

[56] Balagaddé F. K., Song, H., Ozaki, J., Collins, C. H., Barnet, M. , Arnold, F. H., Quake, S. R.and You, L. (2008) A synthetic Escherichia coli predator-prey ecosystem. Mol. Syst. Biol., 4, 187

[57] Heyde, K. C., Gallagher, P. W. and Ruder, W. C. (2016) Bioinspired decision architectures containing host and microbiome processing units. Bioinspir. Biomim., 11, 056017

[58] Tran, H., Oliveira, S. M. D., Goncalves, N. and Ribeiro, A. S. (2015) Kinetics of the cellular intake of a gene expression inducer at high concentrations. Mol. Biosyst., 11, 2579–2587

[59] Xu, H., Moraitis, M., Reedstrom, R. J. and Matthews, K. S. (1998) Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA. J. Biol. Chem., 273, 8958–8964

[60] Politi, N., Pasotti, L., Zucca, S., Casanova, M., Micoli, G., Cusella De Angelis, M. G. and Magni, P. (2014) Half-life measurements of chemical inducers for recombinant gene expression. J. Biol. Eng., 8, 5

RIGHTS & PERMISSIONS

Higher Education Press and Springer-Verlag Berlin Heidelberg