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Addressing Evolutionary Questions with Synthetic Biology

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Evolutionary Systems Biology

Abstract

Synthetic biology emerged as an engineering discipline to design and construct artificial biological systems. Synthetic biological designs aim to achieve specific biological behavior, which can be exploited for biotechnological, medical, and industrial purposes. In addition, mimicking natural systems using well-characterized biological parts also provides powerful experimental systems to study evolution at the molecular and systems level. A strength of synthetic biology is to go beyond nature’s toolkit, to test alternative versions and to study a particular biological system and its phenotype in isolation and in a quantitative manner. Here, we review recent work that implemented synthetic systems, ranging from simple regulatory circuits, rewired cellular networks to artificial genomes and viruses, to study fundamental evolutionary concepts. In particular, engineering, perturbing or subjecting these synthetic systems to experimental laboratory evolution provides a mechanistic understanding on important evolutionary questions, such as: Why did particular regulatory network topologies evolve and not others? What happens if we rewire regulatory networks? Could an expanded genetic code provide an evolutionary advantage? How important is the structure of genome and number of chromosomes? Although the field of evolutionary synthetic biology is still in its teens, further advances in synthetic biology provide exciting technologies and novel systems that promise to yield fundamental insights into evolutionary principles in the near future.

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References

  • Acar, M., Mettetal, J. T., & van Oudenaarden, A. (2008). Stochastic switching as a survival strategy in fluctuating environments. Nature Genetics, 40(4), 471–475.

    Article  CAS  PubMed  Google Scholar 

  • Ackermann, M. (2015). A functional perspective on phenotypic heterogeneity in microorganisms. Nature Reviews Microbiology, 13(8), 497–508.

    Article  CAS  PubMed  Google Scholar 

  • Agarwal, K. L., et al. (1970). Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. Nature, 227(5253), 27–34.

    Article  CAS  PubMed  Google Scholar 

  • Ajo-Franklin, C. M., et al. (2007). Rational design of memory in eukaryotic cells. Genes & Development, 21(18), 2271–2276.

    Article  CAS  Google Scholar 

  • Anosova, I., et al. (2016). The structural diversity of artificial genetic polymers. Nucleic Acids Research, 44(3), 1007–1021.

    Article  CAS  PubMed  Google Scholar 

  • Arnold, F. H. (2010). How proteins adapt: Lessons from directed evolution. Cold Spring Harbor Symposia on Quantitative Biology, 74(0), 41–46.

    Article  Google Scholar 

  • Arnoldini, M., et al. (2014). Bistable expression of virulence genes in Salmonella leads to the formation of an antibiotic-tolerant subpopulation. PLoS Biology, 12(8), e1001928.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Arranz-Gibert, P., Vanderschuren, K., & Isaacs, F. J. (2018). Next-generation genetic code expansion. Current Opinion in Chemical Biology, 46, 203–211.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bacher, J. M., et al. (2004). Evolving new genetic codes. Trends in Ecology & Evolution, 19(2), 69–75.

    Article  Google Scholar 

  • Bachmann, B. O. (2016). Applied evolutionary theories for engineering of secondary metabolic pathways. Current Opinion in Chemical Biology, 35, 133–141.

    Article  CAS  PubMed  Google Scholar 

  • Barbier, I., Perez-Carrasco, R., & Schaerli, Y. (2020). Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch. Molecular Systems Biology, 16(6), 611.

    Article  CAS  Google Scholar 

  • Bashor, C. J., & Collins, J. J. (2018). Understanding biological regulation through synthetic biology. Annual Review of Biophysics, 47, 399–423.

    Article  CAS  PubMed  Google Scholar 

  • Bashor, C. J., et al. (2010). Rewiring cells: Synthetic biology as a tool to interrogate the organizational principles of living systems. Annual Review of Biophysics, 39, 515–537.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baumstark, R., et al. (2015). The propagation of perturbations in rewired bacterial gene networks. Nature Communications, 6, 10105.

    Article  CAS  PubMed  Google Scholar 

  • Becskei, A., & Serrano, L. (2000). Engineering stability in gene networks by autoregulation. Nature, 405, 590–593.

    Article  CAS  PubMed  Google Scholar 

  • Blain, J. C., & Szostak, J. W. (2014). Progress toward synthetic cells. Annual Review of Biochemistry, 83, 615–640.

    Article  CAS  PubMed  Google Scholar 

  • Blomberg, R., et al. (2013). Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature, 503(7476), 418–421.

    Article  CAS  PubMed  Google Scholar 

  • Blount, B. A., et al. (2018). Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome. Nature Communications, 9(1), 1932.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bódi, Z., et al. (2017). Phenotypic heterogeneity promotes adaptive evolution. PLoS Biology, 15(5), e2000644.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boeke, J. D., et al. (2016). The genome project-write. Science, 353(6295), 126–127.

    Article  CAS  PubMed  Google Scholar 

  • Briscoe, J., & Thérond, P. P. (2013). The mechanisms of Hedgehog signalling and its roles in development and disease. Nature Reviews Molecular Cell Biology, 14(7), 416–429.

    Article  PubMed  CAS  Google Scholar 

  • Buddingh, B. C., & van Hest, J. C. M. (2017). Artificial cells: Synthetic compartments with life-like functionality and adaptivity. Accounts of Chemical Research, 50(4), 769–777.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Butterfield, G. L., et al. (2017). Evolution of a designed protein assembly encapsulating its own RNA genome. Nature, 552(7685), 415–420.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014). A brief history of synthetic biology. Nature Reviews Microbiology, 12(5), 381–390.

    Article  CAS  PubMed  Google Scholar 

  • Cello, J., Paul, A. V., & Wimmer, E. (2002). Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template. Science, 297(5583), 1016–1018.

    Article  CAS  PubMed  Google Scholar 

  • Chari, R., & Church, G. M. (2017). Beyond editing to writing large genomes. Nature Reviews Genetics, 18(12), 749–760.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chau, A. H., et al. (2012). Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell, 151(2), 320–332.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chin, J. W. (2014). Expanding and reprogramming the genetic code of cells and animals. Annual Review of Biochemistry, 83(1), 379–408.

    Article  CAS  PubMed  Google Scholar 

  • Chin, J. W. (2017). Expanding and reprogramming the genetic code. Nature, 550(7674), 53–60.

    Article  CAS  PubMed  Google Scholar 

  • Chin, J. W., et al. (2003). An expanded eukaryotic genetic code. Science, 301(5635), 964–967.

    Article  CAS  PubMed  Google Scholar 

  • Ciliberti, S., Martin, O. C., & Wagner, A. (2007). Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Computational Biology, 3(2), e15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Citorik, R. J., Mimee, M., & Lu, T. K. (2014). Bacteriophage-based synthetic biology for the study of infectious diseases. Current Opinion in Microbiology, 19, 59–69.

    Article  CAS  PubMed  Google Scholar 

  • Cobb, R. E., Si, T., & Zhao, H. (2012). Directed evolution: An evolving and enabling synthetic biology tool. Current Opinion in Chemical Biology, 16(3-4), 285–291.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cobb, R. E., Sun, N., & Zhao, H. (2013). Directed evolution as a powerful synthetic biology tool. Methods, 60(1), 81–90.

    Article  CAS  PubMed  Google Scholar 

  • Cotterell, J., & Sharpe, J. (2010). An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients. Molecular Systems Biology, 6, 1–14.

    Article  CAS  Google Scholar 

  • Crocker, J., & Ilsley, G. R. (2017). Using synthetic biology to study gene regulatory evolution. Current Opinion in Genetics & Development, 47, 91–101.

    Article  CAS  Google Scholar 

  • Dai, J., et al. (2020). Sc3.0: Revamping and minimizing the yeast genome. Genome Biology, 21(1), 205.

    Article  PubMed  PubMed Central  Google Scholar 

  • Davidson, E. A., Windram, O. P. F., & Bayer, T. S. (2012). Building synthetic systems to learn nature’s design principles. Advances in Experimental Medicine and Biology, 751, 411–429.

    Article  CAS  PubMed  Google Scholar 

  • Davies, J. (2017). Using synthetic biology to explore principles of development. Development, 144(7), 1146–1158.

    Article  CAS  PubMed  Google Scholar 

  • de Lorenzo, V. (2018). Evolutionary tinkering vs. rational engineering in the times of synthetic biology. Life Sciences, Society and Policy, 14(1), 18.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dean, A. M., & Thornton, J. W. (2007). Mechanistic approaches to the study of evolution: The functional synthesis. Nature Reviews Genetics, 8(9), 675–688.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duarte, J. M., Barbier, I., & Schaerli, Y. (2017). Bacterial microcolonies in gel beads for high-throughput screening of libraries in synthetic biology. ACS Synthetic Biology, 6(11), 1988–1995.

    Article  CAS  PubMed  Google Scholar 

  • Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767), 335–338.

    Article  CAS  PubMed  Google Scholar 

  • Esvelt, K. M., Carlson, J. C., & Liu, D. R. (2011). A system for the continuous directed evolution of biomolecules. Nature, 472(7344), 499–503.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fischer, E. C., et al. (2020). New codons for efficient production of unnatural proteins in a semisynthetic organism. Nature Chemical Biology, 16, 570–576.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Forster, A. C., & Church, G. M. (2006). Towards synthesis of a minimal cell. Molecular Systems Biology, 2, 45.

    Article  PubMed  PubMed Central  Google Scholar 

  • Fredens, J., et al. (2019). Total synthesis of Escherichia coli with a recoded genome. Nature, 569(7757), 514–518.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Friedland, A. E., et al. (2009). Synthetic gene networks that count. Science, 324(5931), 1199–1202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gach, P. C., et al. (2017). Droplet microfluidics for synthetic biology. Lab on a Chip, 17(20), 3388–3400.

    Article  CAS  PubMed  Google Scholar 

  • Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767), 339–342.

    Article  CAS  PubMed  Google Scholar 

  • Gibson, D. G., et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329(5987), 52–56.

    Article  CAS  PubMed  Google Scholar 

  • Giger, L., et al. (2013). Evolution of a designed retro-aldolase leads to complete active site remodeling. Nature Chemical Biology, 9(8), 494–498.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glass, J. I., et al. (2006). Essential genes of a minimal bacterium. Proceedings of the National Academy of Sciences, 103(2), 425–430.

    Article  CAS  Google Scholar 

  • Göpfrich, K., Platzman, I., & Spatz, J. P. (2018). Mastering complexity: Towards bottom-up construction of multifunctional eukaryotic synthetic cells. Trends in Biotechnology, 36(9), 938–951.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Greig, D. (2009). Reproductive isolation in Saccharomyces. Heredity, 102(1), 39–44.

    Article  CAS  PubMed  Google Scholar 

  • Guet, C. C., et al. (2002). Combinatorial synthesis of genetic networks. Science, 296(5572), 1466–1470.

    Article  CAS  PubMed  Google Scholar 

  • Haimovich, A. D., Muir, P., & Isaacs, F. J. (2015). Genomes by design. Nature Reviews Genetics, 16(9), 501–516.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hammerling, M. J., et al. (2014). Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature Chemical Biology, 10(3), 178–180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haseltine, E. L., & Arnold, F. H. (2007). Synthetic gene circuits: Design with directed evolution. Annual Review of Biophysics and Biomolecular Structure, 36(1), 1–19.

    Article  CAS  PubMed  Google Scholar 

  • Hill, M. S., Zande, P. X. T. V., & Wittkopp, P. J. (2020). Molecular and evolutionary processes generating variation in gene expression. Nature Reviews Genetics, 22, 203–215.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hochrein, L., et al. (2018). L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast. Nature Communications, 9(1), 1931.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Holland, S. L., et al. (2014). Phenotypic heterogeneity is a selected trait in natural yeast populations subject to environmental stress. Environmental Microbiology, 16(6), 1729–1740.

    Article  PubMed  Google Scholar 

  • Hoshika, S., et al. (2019). Hachimoji DNA and RNA: A genetic system with eight building blocks. Science, 363, 884–887.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hutchison, C. A., et al. (2016). Design and synthesis of a minimal bacterial genome. Science, 351(6280), aad6253.

    Article  PubMed  CAS  Google Scholar 

  • Ichihashi, N., et al. (2013). Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nature Communications, 4, 2494.

    Article  PubMed  CAS  Google Scholar 

  • Isaacs, F. J., et al. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333(6040), 348–353.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isalan, M., et al. (2008). Evolvability and hierarchy in rewired bacterial gene networks. Nature, 452(7189), 840–845.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiménez, A., et al. (2015). Dynamics of gene circuits shapes evolvability. Proceedings of the National Academy of Sciences of the United States of America, 112(7), 2103–2108.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Joyce, G. F., & Szostak, J. W. (2018). Protocells and RNA self-replication. Cold Spring Harbor Perspectives in Biology, 10(9), a034801.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kaltenbach, M., & Tokuriki, N. (2014). Dynamics and constraints of enzyme evolution. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 322(7), 468–487.

    Article  CAS  Google Scholar 

  • Kaneko, K. (2007). Evolution of robustness to noise and mutation in gene expression dynamics. PLoS One, 2(5), e434.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kannan, K., & Gibson, D. G. (2017). Yeast genome, by design. Science, 355(6329), 1024–1025.

    Article  CAS  PubMed  Google Scholar 

  • Koonin, E. V., & Novozhilov, A. S. (2017). Origin and evolution of the universal genetic code. Annual Review of Genetics, 51(1), 45–62.

    Article  CAS  PubMed  Google Scholar 

  • Kuwahara, H., & Soyer, O. S. (2012). Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, 8, 564.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lagator, M., et al. (2017). Regulatory network structure determines patterns of intermolecular epistasis. eLife, 6, 1–22.

    Article  Google Scholar 

  • Lajoie, M. J., et al. (2013). Genomically recoded organisms expand biological functions. Science, 342(6156), 357–360.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lavickova, B., Laohakunakorn, N., & Maerkl, S. J. (2020). A partially self-regenerating synthetic cell. Nature Communications, 11, 1–11.

    Article  CAS  Google Scholar 

  • Lee, K. Y., et al. (2018). Photosynthetic artificial organelles sustain and control ATP-dependent reactions in a protocellular system. Nature Biotechnology, 36(6), 530–535.

    Article  CAS  PubMed  Google Scholar 

  • Lehner, B. (2011). Molecular mechanisms of epistasis within and between genes. Trends in Genetics, 27(8), 323–331.

    Article  CAS  PubMed  Google Scholar 

  • Lemire, S., Yehl, K. M., & Lu, T. K. (2018). Phage-based applications in synthetic biology. Annual Review of Virology, 5(1), 453–476.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, P., et al. (2018). Morphogen gradient reconstitution reveals Hedgehog pathway design principles. Science, 360(6388), 543–548.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liti, G. (2018). Yeast chromosome numbers minimized using genome editing. Nature, 560(7718), 317–318.

    Article  CAS  PubMed  Google Scholar 

  • Liu, C. C., & Schultz, P. G. (2010). Adding new chemistries to the genetic code. Annual Review of Biochemistry, 79, 413–444.

    Article  CAS  PubMed  Google Scholar 

  • Liu, C. C., et al. (2018a). Toward an orthogonal central dogma. Nature Chemical Biology, 14(2), 103–106.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu, W., et al. (2018b). Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nature Communications, 9, 1–12.

    CAS  Google Scholar 

  • Luo, J., et al. (2018a). Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature, 560(7718), 392–396.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo, Z., et al. (2018b). Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nature Communications, 9(1), 1930.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Luo, Z., et al. (2021). Compacting a synthetic yeast chromosome arm. Genome Biology, 22, 1–18.

    Article  CAS  Google Scholar 

  • Ma, L., et al. (2019). SCRaMbLE generates evolved yeasts with increased alkali tolerance. Microbial Cell Factories, 18, 1–11.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma, N. J., & Isaacs, F. J. (2016). Genomic recoding broadly obstructs the propagation of horizontally transferred genetic elements. Cell Systems, 3(2), 199–207.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malyshev, D. A., et al. (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature, 509(7500), 385–388.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mangan, S., & Alon, U. (2003). Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences, 100(21), 11980–11985.

    Article  CAS  Google Scholar 

  • Matsumura, S., et al. (2016). Transient compartmentalization of RNA replicators prevents extinction due to parasites. Science, 354(6317), 1293–1296.

    Article  CAS  PubMed  Google Scholar 

  • Mizuuchi, R., & Ichihashi, N. (2018). Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system. Nature Ecology & Evolution, 2(10), 1654–1660.

    Article  Google Scholar 

  • Mukai, T., et al. (2017). Rewriting the genetic code. Annual Review of Microbiology, 71, 557–577.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mukherji, S., & van Oudenaarden, A. (2009). Synthetic biology: Understanding biological design from synthetic circuits. Nature Reviews Genetics, 10(12), 859–871.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mushegian, A. R., & Koonin, E. V. (1996). A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proceedings of the National Academy of Sciences, 93(19), 10268–10273.

    Article  CAS  Google Scholar 

  • Neumann, H., et al. (2010). Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature, 464(7287), 441–444.

    Article  CAS  PubMed  Google Scholar 

  • Nghe, P., et al. (2020). Predicting evolution using regulatory architecture. Annual Review of Biophysics, 49(1), 181–197.

    Article  CAS  PubMed  Google Scholar 

  • Nielsen, J., & Keasling, J. D. (2016). Engineering cellular metabolism. Cell, 164(6), 1185–1197.

    Article  CAS  PubMed  Google Scholar 

  • Niu, W., Schultz, P. G., & Guo, J. (2013). An expanded genetic code in mammalian cells with a functional quadruplet codon. ACS Chemical Biology, 8(7), 1640–1645.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nyerges, Á., et al. (2018). Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proceedings of the National Academy of Sciences, 115(25), E5726–E5735.

    Article  CAS  Google Scholar 

  • Paaby, A. B., & Rockman, M. V. (2013). The many faces of pleiotropy. Trends in Genetics, 29(2), 66–73.

    Article  CAS  PubMed  Google Scholar 

  • Packer, M. S., & Liu, D. R. (2015). Methods for the directed evolution of proteins. Nature Reviews Genetics, 16(7), 379–394.

    Article  CAS  PubMed  Google Scholar 

  • Pál, C., Papp, B., & Pósfai, G. (2014). The dawn of evolutionary genome engineering. Nature Reviews Genetics, 15(7), 504–512.

    Article  PubMed  CAS  Google Scholar 

  • Payne, J. L., & Wagner, A. (2019). The causes of evolvability and their evolution. Nature Reviews Genetics, 20(1), 24–38.

    Article  CAS  PubMed  Google Scholar 

  • Peisajovich, S. G. (2012). Evolutionary synthetic biology. ACS Synthetic Biology, 1(6), 199–210.

    Article  CAS  PubMed  Google Scholar 

  • Pinheiro, V. B., & Holliger, P. (2012). The XNA world: Progress towards replication and evolution of synthetic genetic polymers. Current Opinion in Chemical Biology, 16(3-4), 245–252.

    Article  CAS  PubMed  Google Scholar 

  • Pinheiro, V. B., et al. (2012). Synthetic genetic polymers capable of heredity and evolution. Science, 336(6079), 341–344.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Purnick, P. E. M., & Weiss, R. (2009). The second wave of synthetic biology: From modules to systems. Nature Reviews Molecular Cell Biology, 10(6), 410–422.

    Article  CAS  PubMed  Google Scholar 

  • Raman, R., Pinto, C. S., & Sonawane, M. (2018). Polarized organization of the cytoskeleton: Regulation by cell polarity proteins. Journal of Molecular Biology, 430(19), 3565–3584.

    Article  CAS  PubMed  Google Scholar 

  • Richardson, S. M., et al. (2017). Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Science, 355(6329), 1040–1044.

    Article  CAS  PubMed  Google Scholar 

  • Rockman, M. V., & Kruglyak, L. (2006). Genetics of global gene expression. Nature Reviews Genetics, 7(11), 862–872.

    Article  CAS  PubMed  Google Scholar 

  • Ruder, W. C., Lu, T., & Collins, J. J. (2011). Synthetic biology moving into the clinic. Science, 333(6047), 1248–1252.

    Article  CAS  PubMed  Google Scholar 

  • Salathé, M., Van Cleve, J., & Feldman, M. W. (2009). Evolution of stochastic switching rates in asymmetric fitness landscapes. Genetics, 182(4), 1159–1164.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sánchez-Romero, M. A., & Casadesús, J. (2013). Contribution of phenotypic heterogeneity to adaptive antibiotic resistance. Proceedings of the National Academy of Sciences of the United States of America, 111(1), 355–360.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Santos-Moreno, J., & Schaerli, Y. (2018). Using synthetic biology to engineer spatial patterns. Advanced Biosystems, 12, 1800280.

    Google Scholar 

  • Santos-Moreno, J., & Schaerli, Y. (2020a). Changing the biological Rosetta stone: The (commercial) potential of recoded microbes. Microbial Biotechnology, 13(1), 11–13.

    Article  PubMed  Google Scholar 

  • Santos-Moreno, J., & Schaerli, Y. (2020b). CRISPR-based gene expression control for synthetic gene circuits. Biochemical Society Transactions, 48(5), 1979–1993.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santos-Moreno, J., et al. (2020). Multistable and dynamic CRISPRi-based synthetic circuits. Nature Communications, 11, 1–8.

    Article  CAS  Google Scholar 

  • Sato, K., et al. (2003). On the relation between fluctuation and response in biological systems. Proceedings of the National Academy of Sciences, 100(24), 14086–14090.

    Article  CAS  Google Scholar 

  • Schaerli, Y., & Isalan, M. (2013). Building synthetic gene circuits from combinatorial libraries: Screening and selection strategies. Molecular BioSystems, 9(7), 1559–1567.

    Article  CAS  PubMed  Google Scholar 

  • Schaerli, Y., et al. (2014). A unified design space of synthetic stripe-forming networks. Nature Communications, 5, 4905.

    Article  CAS  PubMed  Google Scholar 

  • Schaerli, Y., et al. (2018). Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution. Molecular Systems Biology, 14(9), e8102.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shao, Y., et al. (2019). Creating a functional single-chromosome yeast. Nature, 560(7718), 331–335.

    Article  CAS  Google Scholar 

  • Simon, A. J., d’Oelsnitz, S., & Ellington, A. D. (2019). Synthetic evolution. Nature Biotechnology, 37(7), 730–743.

    Article  CAS  PubMed  Google Scholar 

  • Smith, H. O., et al. (2003). Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences, 100(26), 15440–15445.

    Article  CAS  Google Scholar 

  • Smith, J. M. (1992). Evolutionary biology - Byte-sized evolution. Nature, 355(6363), 772–773.

    Article  CAS  PubMed  Google Scholar 

  • Sun, S. B., Schultz, P. G., & Kim, C. H. (2014). Therapeutic applications of an expanded genetic code. ChemBioChem, 15(12), 1721–1729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Szymanski, E., & Calvert, J. (2018). Designing with living systems in the synthetic yeast project. Nature Communications, 9(1), 2950.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tabor, J. J., et al. (2009). A synthetic genetic edge detection program. Cell, 137(7), 1272–1281.

    Article  PubMed  PubMed Central  Google Scholar 

  • Tang, T.-C., et al. (2020). Materials design by synthetic biology. Nature Reviews Materials, 1–19.

    Google Scholar 

  • Terasaka, N., Azuma, Y., & Hilvert, D. (2018). Laboratory evolution of virus-like nucleocapsids from nonviral protein cages. Proceedings of the National Academy of Sciences of the United States of America, 115(21), 5432–5437.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thao, T., et al. (2020). Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature, 582, 561–565.

    Article  CAS  Google Scholar 

  • Tumpey, T. M., et al. (2005). Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science, 310(5745), 77–80.

    Article  CAS  PubMed  Google Scholar 

  • van Nies, P., et al. (2018). Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nature Communications, 9(1), 1583.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vogele, K., et al. (2018). Towards synthetic cells using peptide-based reaction compartments. Nature Communications, 9(1), 3862.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang, H., La Russa, M., & Qi, L. S. (2016). CRISPR/Cas9 in genome editing and beyond. Annual Review of Biochemistry, 85, 227–264.

    Article  CAS  PubMed  Google Scholar 

  • Wang, H. H., et al. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257), 894–898.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, K., Schmied, W. H., & Chin, J. W. (2012). Reprogramming the genetic code: From triplet to quadruplet codes. Angewandte Chemie International Edition in English, 51(10), 2288–2297.

    Article  CAS  Google Scholar 

  • Wang, L., et al. (2001). Expanding the genetic code of Escherichia coli. Science, 292, 498–500.

    Article  CAS  PubMed  Google Scholar 

  • Wang, Y.-H., Wei, K. Y., & Smolke, C. D. (2013). Synthetic biology: Advancing the design of diverse genetic systems. Annual Review of Chemical and Biomolecular Engineering, 4(1), 69–102.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wannier, T. M., et al. (2018). Adaptive evolution of genomically recoded Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 115(12), 3090–3095.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wannier, T. M., et al. (2020). Improved bacterial recombineering by parallelized protein discovery. Proceedings of the National Academy of Sciences of the United States of America, 117(24), 13689–13698.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber, W., & Fussenegger, M. (2011). Emerging biomedical applications of synthetic biology. Nature Reviews Genetics, 13(1), 21–35.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wightman, E. L. I., et al. (2020). Rapid optimisation of cellulolytic enzymes ratios in Saccharomyces cerevisiae using in vitro SCRaMbLE. Biotechnology for Biofuels, 13, 1–10.

    Article  CAS  Google Scholar 

  • Wimmer, E., & Paul, A. V. (2011). Synthetic poliovirus and other designer viruses: What have we learned from them? Annual Review of Microbiology, 65(1), 583–609.

    Article  CAS  PubMed  Google Scholar 

  • Wolpert, L. (1969). Positional information and the spatial pattern of cellular differentiation. Journal of Theoretical Biology, 25(1), 1–47.

    Article  CAS  PubMed  Google Scholar 

  • Wong, B. G., et al. (2018). Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Nature Biotechnology, 36(7), 614–623.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu, Y., et al. (2018). In vitro DNA SCRaMbLE. Nature Communications, 9(1), 1935.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xie, M., & Fussenegger, M. (2018). Designing cell function: Assembly of synthetic gene circuits for cell biology applications. Nature Reviews Molecular Cell Biology, 19, 507–525.

    Article  CAS  PubMed  Google Scholar 

  • Yokobayashi, Y., Weiss, R., & Arnold, F. H. (2002). Directed evolution of a genetic circuit. Proceedings of the National Academy of Sciences, 99(26), 16587–16591.

    Article  CAS  Google Scholar 

  • Zeymer, C., & Hilvert, D. (2018). Directed evolution of protein catalysts. Annual Review of Biochemistry, 87, 131–157.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, W., Mitchell, L. A., Bader, J. S., & Boeke, J. D. (2020). Synthetic genomes. Annual Review of Biochemistry, 89(1), 77–101.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, W. H., Otting, G., & Jackson, C. J. (2013). Protein engineering with unnatural amino acids. Current Opinion in Structural Biology, 23(4), 581–587.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, Y., & Romesberg, F. E. (2018). Semisynthetic organisms with expanded genetic codes. Biochemistry, 57(15), 2177–2178.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, Y., et al. (2017a). A semisynthetic organism engineered for the stable expansion of the genetic alphabet. Proceedings of the National Academy of Sciences of the United States of America, 114(6), 1317–1322.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, Y., et al. (2017b). A semi-synthetic organism that stores and retrieves increased genetic information. Nature, 551(7682), 644–647.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

We thank Sara Mitri, Nienke Jager, and members of the Schaerli group for critical reading and valuable feedback. We acknowledge support by the Swiss National Science Foundation grant 31003A_175608.

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  1. Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland

    Florian Baier & Yolanda Schaerli

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  1. Florian Baier
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Correspondence to Yolanda Schaerli .

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  1. Inria Lyon Antenne La Doua, Villeurbanne, France

    Anton Crombach

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Baier, F., Schaerli, Y. (2021). Addressing Evolutionary Questions with Synthetic Biology. In: Crombach, A. (eds) Evolutionary Systems Biology. Springer, Cham. https://doi.org/10.1007/978-3-030-71737-7_7

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