Abstract
By default synthetic biology refers to construction of synthetic genetic programs. Yet, programs must be expressed within a machine, and the elusive but multipurpose “chassis” is usually taken for granted. The program replicates while the chassis reproduces, showing that maturation, ageing and senescence are core processes which must be taken into account in order to explore realistic outcomes. Functional analysis reveals the essential functions that we need to consider. Some are listed in the present chapter, with emphasis on the role of information recruitment. This is a built-in process of living organisms whose outcome is the production of an ever young progeny as a way to cope with ageing and senescence. Life innovates using Maxwell’s demons-like nanomachines. This is at odds with standard engineering practices, opening up new perspectives for synthetic biology.
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Acevedo-Rocha, C. G., Fang, G., Schmidt, M., Ussery, D. W. & Danchin, A. (2013). From essential to persistent genes: a functional approach to constructing synthetic life. Trends in Genetics, 29(5), 273–279. doi:10.1016/j.tig.2012.11.001
Andersson, S. G., Karlberg, O., Canback, B. & Kurland, C. G. (2003). On the origin of mitochondria: a genomics perspective. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 358(1429), 165–177; discussion 177–169. doi:10.1098/rstb.2002.1193
Arisaka, F. (2005). Assembly and infection process of bacteriophage T4. Chaos, 15(4), 047502. doi:10.1063/1.2142136
Binder, P. M. & Danchin, A. (2011). Life’s demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life? EMBO Reports, 12(6), 495–499. doi:10.1038/embor.2011.83
Bittencourt, D., Oliveira, P. F., Prosdocimi, F. & Rech, E. L. (2012). Protein families, natural history and biotechnological aspects of spider silk. Genetics and Molecular Research, 11(3), 2360–2380. doi:10.4238/2012.August.13.10
Celler, K., Koning, R. I., Koster, A. J. & van Wezel, G. P. (2013). Multidimensional view of the bacterial cytoskeleton. Journal of Bacteriology, 195(8), 1627–1636. doi:10.1128/JB.02194-12
Chan, L. Y., Kosuri, S. & Endy, D. (2005). Refactoring bacteriophage T7. Molecular Systems Biology, 1, 0018. doi:10.1038/msb4100025
Charpa, U. (2012). Synthetic biology and the golem of prague: philosophical reflections on a suggestive metaphor. Perspectives in Biology and Medicine, 55(4), 554–570. doi:10.1353/pbm.2012.0036
Danchin, A. (1988). Complete genome sequencing: future and prospects. In A. Goffeau (Ed.), BAP 1988-1989 (pp. 1–24). Brussels: Commission of the European Communities.
Danchin, A. (2003). The Delphic boat. What genomes tell us. (A. Quayle, Trans.). Cambridge, MA: Harvard University Press.
Danchin, A. (2009a). Bacteria as computers making computers. FEMS Microbiology Reviews, 33(1), 3–26.
Danchin, A. (2009b). Cells need safety valves. BioEssays, 31(7), 769–773. doi:10.1002/bies.200900024
Danchin, A. (2009c). Information of the chassis and information of the program in synthetic cells. Systems and Synthetic Biology, 3(1–4), 125–134. doi:10.1007/s11693-009-9036-5
Danchin, A. (2012). Scaling up synthetic biology: Do not forget the chassis. FEBS Letters, 586(15), 2129–2137. doi:10.1016/j.febslet.2011.12.024
Danchin, A., Binder, P. M., & Noria, S. (2011). Antifragility and tinkering in biology (and in business); flexibility provides an efficient epigenetic way to manage risk. Genes, 2(4), 998–1016.
Daniel, R., Rubens, J. R., Sarpeshkar, R. & Lu, T. K. (2013). Synthetic analog computation in living cells. Nature, 497(7451), 619–623. doi:10.1038/nature12148
Danielli, J. F. (1972). Artificial synthesis of new life forms. Bulletin of the Atomic Scientists, 28(10), 20–24.
Danielli, J. F., & Davson, H. (1935). A contribution to the theory of permeability of thin films. Journal of Cellular and Comparative Physiology, 5(4), 495–508.
de Lorenzo, V. (2011). Beware of metaphors: Chasses and orthogonality in synthetic biology. Bioengineered Bugs, 2(1), 3–7. doi:10.4161/bbug.2.1.13388
Endy, D. (2005). Foundations for Engineering Biology. Nature, 438(7067), 449–453. doi:http://dx.doi.org/10.1038/nature04342
Fang, G., Rocha, E., & Danchin, A. (2005). How essential are nonessential genes? Molecular Biology and Evolution, 22(11), 2147–2156.
Fang, G., Rocha, E. P. & Danchin, A. (2008). Persistence drives gene clustering in bacterial genomes. BMC Genomics, 9(4). doi:10.1186/1471-2164-9-4.
Helmus, R. A., Liermann, L. J., Brantley, S. L. & Tien, M. (2012). Growth advantage in stationary-phase (GASP) phenotype in long-term survival strains of Geobacter sulfurreducens. FEMS Microbiology Ecology, 79(1), 218–228. doi:10.1111/j.1574-6941.2011.01211.x
Hosokawa, N., Hatakeyama, T. S., Kojima, T., Kikuchi, Y., Ito, H. & Iwasaki, H. (2011). Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in Synechococcus. Proceedings of the National Academy of Sciences USA, 108(37), 15396–15401. doi:10.1073/pnas.1019612108
Itaya, M., Tsuge, K., Koizumi, M., & Fujita, K. (2005). Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proceedings of the National Academy of Sciences USA, 102(44), 15971–15976.
Lagesen, K., Ussery, D. W. & Wassenaar, T. M. (2010). Genome update: The 1000th genome—a cautionary tale. Microbiology, 156(3), 603–608. doi:10.1099/mic.0.038257-0
Landauer, R. (1961). Irreversibility and heat generation in the computing process. IBM Journal of Research and Development, 5(3), 183–191.
Larsabal, E. & Danchin, A. (2005). Genomes are covered with ubiquitous 11 bp periodic patterns, the “class A flexible patterns”. BMC Bioinformatics, 6, 206. doi:10.1186/1471-2105-6-206
Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison, C. A., III, et al. (2007). Genome transplantation in bacteria: Changing one species to another. Science, 317(5838), 632–638. doi:10.1126/science.1144622
Leduc, S. (1912). La Biologie Synthétique. Paris: A. Poinat. Available in http://www.peiresc.org/bstitre.htm
Maxwell, J. C. (1871). Theory of Heat. London: Longmans, Reed and Co. Available in http://books.google.fr/books?id=0p8AAAAAMAAJ&printsec=frontcover&hl=fr&source=gbs_ge_summary_r&cad=0#v=onepage
Mechold, U., Fang, G., Ngo, S., Ogryzko, V. & Danchin, A. (2007). YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Research, 35(13), 4552–4561, doi:10.1093/nar/gkm462
Mechold, U., Ogryzko, V., Ngo, S. & Danchin, A. (2006). Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells. Nucleic Acids Research, 34(8), 2364–2373. doi:10.1093/nar/gkl247
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 USA, 93(19), 10268–10273.
Navarro Llorens, J. M., Tormo, A. & Martinez-Garcia, E. (2010). Stationary phase in gram-negative bacteria. FEMS Microbiological Reviews, 34(4), 476–495. doi:10.1111/j.1574-6976.2010.00213.x
Pearson, B., Snell, S., Bye-Nagel, K., Tonidandel, S., Heyer, L. J. & Campbell, A. M. (2011). Word selection affects perceptions of synthetic biology. Journal of Biological Engineering, 5(1), 9. doi:10.1186/1754-1611-5-9
Peisajovich, S. G. (2012). Evolutionary synthetic biology. ACS Synthetic Biology, 1(6), 199–210. doi:10.1021/sb300012g
Porcar, M., Danchin, A., de Lorenzo, V., Dos Santos, V. A., Krasnogor, N., Rasmussen, S., et al. (2011). The ten grand challenges of synthetic life. Systems and Synthetic Biology, 5(1–2), 1–9. doi:10.1007/s11693-011-9084-5
Postic, G., Danchin, A. & Mechold, U. (2012). Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA, 18(1), 155–165. doi:10.1261/rna.029132.111
Robinson, N. & Robinson, A. (2004). Molecular clocks deamidation of asparaginyl and glutaminyl residues in peptides and proteins. Cave Junction, OR: Althouse Press. Available in http://www.deamidation.org
Rocha, E. P., & Danchin, A. (2003). Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Research, 31(22), 6570–6577.
Rocha, E. P., Guerdoux-Jamet, P., Moszer, I., Viari, A., & Danchin, A. (2000a). Implication of gene distribution in the bacterial chromosome for the bacterial cell factory. Journal of Biotechnology, 78(3), 209–219.
Rocha, E. P., Sekowska, A., & Danchin, A. (2000b). Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture? FEBS Letters, 476(1–2), 8–11.
Schmidt, M. (2010). Xenobiology: A new form of life as the ultimate biosafety tool. BioEssays, 32(4), 322–331. doi:http://dx.doi.org/10.1002/bies.200900147
Smoluchowski, M. (1914). Gültigkeitsgressen des zweiten Hauptsatzes der Wärmtheorie. In Vorträge über die kinetische Theorie der Materie und der Elektrizität gehalten in Göttingen auf Einladung der Kommission der Wolfskehlstiftung (Wolfskehlstiftung ed., Vol. 6, pp. 87–122, Mathematische Vorlesungen and der Universität Göttingen). Leipzig: Teubner. Available in http://www.bookprep.com/read/mdp.39015030967098
Springman, R., Molineux, I. J., Duong, C., Bull, R. J. & Bull, J. J. (2012). Evolutionary stability of a refactored phage genome. ACS Synthetic Biology, 1(9), 425–430. doi:10.1021/sb300040v
Stadler, P. F., Prohaska, S. J., Forst, C. V. & Krakauer, D. C. (2009). Defining genes: a computational framework. Theory in Biosciences, 128(3), 165–170. doi:10.1007/s12064-009-0067-y
Tamames, J., Gonzalez-Moreno, M., Mingorance, J., Valencia, A., & Vicente, M. (2001). Bringing gene order into bacterial shape. Trends in Genetics, 17(3), 124–126.
van den Belt, H. (2009). Playing God in Frankenstein’s footsteps: synthetic biology and the meaning of life. Nanoethics, 3(3), 257–268. doi:10.1007/s11569-009-0079-6
von Neumann, J. (1966). Theory of self-reproducing automata. Urbana: University of Illinois Press.
Yoon, S. H., Hur, C. G., Kang, H. Y., Kim, Y. H., Oh, T. K. & Kim, J. F. (2005). A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics, 6, 184. doi:10.1186/1471-2105-6-184
Younis, S. & Knight, T. (1993). Practical implementation of charge recovering asymptotically zero power CMOS. In G. Borriello, & C. Ebeling (Eds.), 1993 symposium on research on integrated systems Seattle (pp. 234–250). Washington: MIT Press.
Acknowledgments
This work, which summarises a lecture held at the University of Bremen, on October 24th, 2012, benefited from ongoing discussions of the Stanislas Noria Network. It has been supported by the FP7 European Union programme Microme KBBE–2007–3-2-08-222886-2 grant.
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Danchin, A. (2015). The Cellular Chassis as the Basis for New Functionalities: Shortcomings and Requirements. In: Giese, B., Pade, C., Wigger, H., von Gleich, A. (eds) Synthetic Biology. Risk Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-02783-8_8
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