DOI: https://doi.org/10.7203/metode.11.15975

When biology became engineering: Adopting standards for living systems


Abstract


For decades, molecular biologists have been removing or inserting genes into all kinds of organisms with biotechnological intent or simply to generate fundamental knowledge. Synthetic biology (SynBio) goes one step further by incorporating conceptual frameworks from computing, electronics, and industrial design. This change makes it possible to conceive the creation of complex biological objects that were previously considered too difficult to assemble. To do this, the stages of any industrial production process must be adopted: design, construction of the components, assembly, and final manufacture. This objective requires standardisation of the physical and functional formats of the components involved, DNA assembly methods, activity measurements, and descriptive languages.


Keywords


synthetic biology; standards; repressilator; repository; orthogonality

References


  • Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology, 2(1), 2006.0028. doi: 10.1038/msb4100073

  • Beal, J., Farny, N. G., Haddock-Angelli, T., Selvarajah, V., Baldwin, G. S., Buckley-Taylor, R., … Workman, C. T. (2019). Robust estimation of bacterial cell count from optical density. bioRxiv, 803239. doi: 10.1101/803239

  • Beal, J., Haddock-Angelli, T., Gershater, M., De Mora, K., Lizarazo, M., Hollenhorst, J., & Rettberg, R. (2016). Reproducibility of fluorescent expression from engineered biological constructs in E. coli. PLoS ONE, 11(3), e0150182. doi: 10.1371/journal.pone.0150182

  • Becskei, A., & Serrano, L. (2000). Engineering stability in gene networks by autoregulation. Nature, 405(6786), 590. doi: 10.1038/35014651

  • Casini, A., Storch, M., Baldwin, G. S., & Ellis, T. (2015). Bricks and blueprints: Methods and standards for DNA assembly. Nature Reviews Molecular Cell Biology, 16(9), 568–576. doi: 10.1038/nrm4014

  • De Lorenzo, V. (2018). Evolutionary tinkering vs. rational engineering in the times of synthetic biology. Life Sciences, Society and Policy, 14(18). doi: 10.1186/s40504-018-0086-x

  • De Lorenzo, V., & Danchin, A. (2008). Synthetic biology: Discovering new worlds and new words. EMBO Reports, 9(9), 822–827. doi: 10.1038/embor.2008.159

  • De Lorenzo, V., & Schmidt, M. (2018). Biological standards for the Knowledge-Based BioEconomy: What is at stake. New Biotechnology, 40, 170–180. doi: 10.1016/j.nbt.2017.05.001

  • De Lorenzo, V., Prather, K. L., Chen, G. Q., O’Day, E., Von Kameke, C., Oyarzun, D. A., ... Lee, S. Y. (2018). The power of synthetic biology for bioproduction, remediation and pollution control: The UN’s Sustainable Development Goals will inevitably require the application of molecular biology and biotechnology on a global scale. EMBO Repors, 19(4), e4658. doi: 10.15252/embr.201745658

  • Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767), 335–338. doi: 10.1038/35002125

  • Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449–453. doi: 10.1038/nature04342

  • Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H. M., & Gennari, J. H. (2011). Standard biological parts knowledgebase. PLoS ONE, 6(2), e17005. doi: 10.1371/journal.pone.0017005

  • Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767), 339–342. doi: 10.1038/35002131

  • Kelly, J. R., Rubin, A. J., Davis, J. H., Ajo-Franklin, C. M., Cumbers, J., Czar, M. J., ... Endy, D. (2009). Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering, 3(1), 4. doi: 10.1186/1754-1611-3-4

  • Kosuri, S., Goodman, D. B., Cambray, G., Mutalik, V. K., Gao, Y., Arkin, A. P., ... Church, G. M. (2013). Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proceedings of the National Academy of Sciences, 110(34), 14024–14029. doi: 10.1073/pnas.1301301110

  • O’Day, E., Hosta-Rigau, L., Oyarzún, D. A., Okano, H., De Lorenzo, V., Von Kameke, C., ... Lee, S. Y. (2019). Are we there yet? How and when specific biotechnologies will improve human health. Biotechnology Journal, 14(1), e1800195. doi: 10.1002/biot.201800195

  • Popp, P. F., Dotzler, M., Radeck, J., Bartels, J., & Mascher, T. (2017). The Bacillus BioBrick Box 2.0: Expanding the genetic toolbox for the standardized work with Bacillus subtilis. Scientific Reports, 7(1), 15058. doi: 10.1038/s41598-017-15107-z

  • Porcar, M., Danchin, A., & De Lorenzo, V. (2014). Confidence, tolerance, and allowance in biological engineering: The nuts and bolts of living things. Bioessays, 37(1), 95, doi: 10.1002/bies.201400091

  • Rao, C. V. (2012). Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. Current Opinion in Biotechnology, 23(5), 689–694. doi: 10.1016/j.copbio.2011.12.015

  • Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009). Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology, 27(10), 946–950. doi: 10.1038/nbt.1568

  • Sendy, B., Lee, D. J., Busby, S. J., & Bryant, J. A. (2016). RNA polymerase supply and flux through the lac operon in Escherichia coli. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1707), 20160080. doi: 10.1098/rstb.2016.0080

  • Wang, K., Neumann, H., Peak-Chew, S. Y., & Chin, J. W. (2007). Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nature Biotechnology, 25(7), 770–777. doi: 10.1038/nbt1314







Creative Commons License
Texts in the journal are –unless otherwise indicated– published under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License

____________________________________________________________________________________________________________________