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

Full Text:

PDF

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. http://doi.org/10.1038/msb4100073

Beal, J., Farny, N. G., Haddock-Angelli, T., Selvarajah, V., Baldwin, G. S., Buckley-Taylor, R., Gershater, M., Kiga, D., Marken, J., Sanchania, V., Sison, A., & Workman, C. T. (2019). Robust estimation of bacterial cell count from optical density. BioRxiv, 803239. http://doi.org/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. coliPLOS ONE, 11(3), e0150182. http://doi.org/10.1371/journal.pone.0150182

Becskei, A., & Serrano, L. (2000). Engineering stability in gene networks by autoregulation. Nature, 405(6786), 590. http://doi.org/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. http://doi.org/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). http://doi.org/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. http://doi.org/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. http://doi.org/10.1016/j.nbt.2017.05.001

De Lorenzo, V., Prather, K. L. J., Chen, G.-Q., O’Day, E., Kameke, C., Oyarzún, D. A., Hosta-Rigau, L., Alsafar, H., Cao, C., Ji, W., Okano, H., Roberts, R. J., Ronaghi, M., Yeung, K., Zhang, F., & 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 Reports, 19(4), e4658. http://doi.org/10.15252/embr.201745658

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

Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449–453. http://doi.org/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. http://doi.org/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. http://doi.org/10.1038/35002131

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

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

O’Day, E., Hosta-Rigau, L., Oyarzún, D. A., Okano, H., de Lorenzo, V., von Kameke, C., Alsafar, H., Cao, C., Chen, G.-Q., Ji, W., Roberts, R. J., Ronaghi, M., Yeung, K., Zhang, F., & Lee, S. Y. (2018). Are we there yet? How and when specific biotechnologies will improve human health. Biotechnology Journal, 14(1), e1800195. http://doi.org/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 subtilisScientific Reports, 7(1), 15058. http://doi.org/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. http://doi.org/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. http://doi.org/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. http://doi.org/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 coliPhilosophical Transactions of the Royal Society B: Biological Sciences, 371(1707), 20160080. http://doi.org/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. http://doi.org/10.1038/nbt1314


Refbacks

  • There are currently no refbacks.





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

____________________________________________________________________________________________________________________