Skip to main content
SpringerLink
Log in

Synthetic Biology: Diverse Layers of Live

  • Chapter
  • First Online:
Synthetic Biology Analysed

Part of the book series: Ethics of Science and Technology Assessment ((ETHICSSCI,volume 44))

Abstract

Prerequisite for any evaluation of synthetic biology is the precise description of its scientific rationale and its biological objects. Here, we develop a layer model that helps to categorize subfields of synthetic biology along their operative procedures and based on the biological status of the organisms generated by synthetic biology. The layer model classifies synthetic and semisynthetic organisms and cells according to their genetic connectivity and to their potential interaction with natural organisms derived by evolution. We use the model to characterize three distinct approaches within synthetic biology: engineering biology, xenobiology and protocell research. While the latter approach generates organisms that hardly could be termed living, xenobiology aims at orthogonal living systems that are disconnected from nature. Synthetic engineering biology could be considered as extreme form of gene technology since all resulting organisms share the universal genetic code with the natural living beings and are based on the same molecular and biochemical principles. Such biological description can be used to determine both the degree of familiarity and the level of uncertainty associated with synthetic organisms and may thus facilitate to judge potential risks of synthetic biology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 64.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 84.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 84.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Interestingly there exist a few exceptions e.g. in Candida yeasts (Ohama et al. 1993; Santos and Tuite 1995), but these species use a code with some small deviations, i.e. the code is not totally unrelated.

References

  • Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A (2013) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29:273–279

    Article  Google Scholar 

  • An W, Chin JW (2009) Synthesis of orthogonal transcription-translation networks. Proc Natl Acad Sci USA 106:8477–8482

    Article  Google Scholar 

  • Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2. doi:10.1038/msb4100073

  • Attwater J, Holliger P (2014) A synthetic approach to abiogenesis. Nat Meth 11:495–498

    Article  Google Scholar 

  • Benner SA, Sismour AM (2005) Synthetic biology. Nat Rev Genet 6:533–543

    Article  Google Scholar 

  • Benner SA, Chen F, Yang ZY (2011) Synthetic biology, tinkering biology, and artificial biology: a perspective from chemistry. In: Luisi LP, Chiarabelli C (eds) Chemical synthetic biology. Wiley, Chichester, pp 69–106

    Chapter  Google Scholar 

  • Bohannon J (2011) The life hacker. Science 333:1236–1237

    Article  Google Scholar 

  • Budisa N (2014) Xenobiology, new-to-nature synthetic cells and genetic firewall. Curr Org Chem 18:936–943

    Article  Google Scholar 

  • Cameron DE, Bashor CJ, Collins JJ (2014) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390

    Article  Google Scholar 

  • Campos L (2009) That was the synthetic biology that was. In: Schmidt M, Keller A, Ganguli-Mitra A, de Vriend H (eds) Synthetic biology. The technoscience and its social consequences. Springer, Heidelberg, pp 6–22

    Google Scholar 

  • Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26:787–793

    Article  Google Scholar 

  • Carlson R (2009) Biology is technology. The promise, peril, and new business of engineering life. Harvard University Press, Cambridge, MA

    Google Scholar 

  • Chan LY, Kosuri S, Endy D (2005) Refactoring bacteriophage T7. Mol Syst Biol 1(2005):0018. doi:10.1038/msb4100025

    Google Scholar 

  • Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG (2003) An expanded eukaryotic genetic code. Science 301:964–967

    Google Scholar 

  • Church GM, Regis E (2012) REGENESIS: how synthetic biology will reinvent nature and ourselves. Basic Books, New York

    Google Scholar 

  • Cohen SN, Chang AC, Hsu L (1972) Non-chromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. Proc Natl Acad Sci USA 69:2110–2114

    Article  Google Scholar 

  • Cohen SN, Chang ACY, Boyer HW, Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA 70:3240–3244

    Article  Google Scholar 

  • Cowie DB, Cohen GN (1957) Biosynthesis by Escherichia coli of active altered proteins containing selenium instead of sulfur. Biochim Biophys Acta 26:252–261

    Article  Google Scholar 

  • Danchin A (2003) The Delphic boat. What genomes tell us. Harvard University Press, Cambridge

    Google Scholar 

  • Danchin A (2009) Information of the chassis and information of the program in synthetic cells. Syst Synth Biol 3:125–134

    Google Scholar 

  • Deplazes A, Huppenbauer M (2009) Synthetic organisms and living machines. Syst Synth Biol 3:55–63

    Article  Google Scholar 

  • Eigen M, Schuster P (1977) The hypercycle: a principle of natural self-organization. Part A: emergence of the hypercycle. Naturwissenschaften 11:541–565

    Google Scholar 

  • Elowitz M, Lim WA (2010) Building life to understand it. Nature 486:889–890

    Article  Google Scholar 

  • Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Google Scholar 

  • ETC Group (2007) Extreme genetic engineering: an introduction to synthetic biology. ETC Group

    Google Scholar 

  • Forster AC, Church GM (2006) Towards synthesis of a minimal cell. Mol Syst Biol. 2:45

    Article  Google Scholar 

  • Gánti T (1975) Organization of chemical reactions into dividing and metabolizing units: the chemotons. Biosystems 7:15–21

    Google Scholar 

  • Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:39–50

    Article  Google Scholar 

  • Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE (2014) Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat Chem Biol 10:178–180

    Article  Google Scholar 

  • Hirao I, Kimoto M (2012) Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. Proc Jpn Acad Ser B Phys Biol Sci. 88:345–367

    Article  Google Scholar 

  • Hoesl MG, Budisa N (2012) Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol 23:751–757

    Article  Google Scholar 

  • Hunter P (2013) XNA marks the spot. EMBO Rep 14:410–413

    Article  Google Scholar 

  • Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333:348–353

    Article  Google Scholar 

  • Jackson DA, Symons RH, Berg P (1972) Biochemical method for inserting new genetic Information into DNA of simian virus 40: Circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc Natl Acad Sci USA 69:2904–2909

    Article  Google Scholar 

  • Joyce GF (2002) The antiquity of RNA-based evolution. Nature 418:214–221

    Article  Google Scholar 

  • Juhas M, Eberl L, Church GM (2012) Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol 30:601–607

    Article  Google Scholar 

  • Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Knight T (2003) Idempotent vector design for standard assembly of biobricks. http://dspace.mit.edu/handle/1721.1/21168 Accessed 08 Mar 2015

  • Kyrpides N, Overbeek R, Ouzounis C (1999) Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49:413–423

    Article  Google Scholar 

  • Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ (2013) Genomically recoded organisms expand biological functions. Science 342:357–360

    Article  Google Scholar 

  • Lazcano A, Forterre P (1999) The molecular search for the last common ancestor. J Mol Evol 49:411–412

    Article  Google Scholar 

  • Leduc S (1912) La biologie synthétique. In: Poinat A (eds) Études de biophysique. Paris

    Google Scholar 

  • Lemeignan B, Sonigo P, Marlière P (1993) Phenotypic suppression by incorporation of an alien amino acid. J Mol Biol 231:161–166

    Article  Google Scholar 

  • Loakes D, Holliger P (2009) Darwinian chemistry: towards the synthesis of a simple cell. Mol BioSyst 5:686–694

    Article  Google Scholar 

  • Liu CC, Schultz PG (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413–444

    Article  Google Scholar 

  • Luisi PL (1998) About various definitions of life. Orig Life Evol Biosphere 28(613–622):1998

    Google Scholar 

  • Luisi PL (2003) Autopoiesis: a review and a reappraisal. Naturwissenschaften 90:49–59

    Google Scholar 

  • Luisi PL (2006) The emergence of life: from chemical origins to synthetic biology. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Luisi PL (2007) Chemical aspects of synthetic biology. Chem Biodivers 4:603–621

    Article  Google Scholar 

  • Ma Y, Biava H, Contestabile R, Budisa N, di Salvo ML (2014) Coupling bioorthogonal chemistries with artificial metabolism: intracellular biosynthesis of azidohomoalanine and its incorporation into recombinant proteins. Molecules 19:1004–1022

    Article  Google Scholar 

  • Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Correa IR Jr, Romesberg FE (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature 509:385–388

    Article  Google Scholar 

  • Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM (2015) Biocontainment of genetically modified organisms by synthetic protein design. Nature 518:55–60

    Article  Google Scholar 

  • Mansy SS, Szostak JW (2009) Reconstructing the emergence of cellular life through the synthesis of model protocells. Cold Spring Harb Symp Quant Biol 74:47–54

    Article  Google Scholar 

  • Marlière P (2009) The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. Syst Synth Biol 3:77–84

    Article  Google Scholar 

  • Miller SJ (1953) A production of amino acids under possible primitive earth conditions. Science 117:528–529

    Article  Google Scholar 

  • Ohama T, Suzuki T, Mori M, Osawa S, Ueda T, Watanabe K, Nakase T (1993) Non-universal decoding of the leucine codon CUG in several Candida species. Nucleic Acids Res 21:4039–4045

    Article  Google Scholar 

  • Pereto J (2012) Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem Soc Rev 41:5394–5403

    Article  Google Scholar 

  • Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336:341–344

    Article  Google Scholar 

  • Rasmussen S, Bedau MA, Chen L, Deamer D, Krakauer DC, Packard NH, Stadler PF (eds) (2009) Protocells: bridging nonliving and living matter. MIT Press, Cambridge

    Google Scholar 

  • Reardon S (2011) Visions of synthetic biology. Science 333:1242–1243

    Article  Google Scholar 

  • Sagan L (1967) On the origin of mitosing cells. J Theor Biol 14:255–274

    Article  Google Scholar 

  • Santos MA, Tuite MF (1995) The CUG codon is decoded in vivo as serine and not leucine in Candida albicans. Nucleic Acids Res 23:1481–1486

    Article  Google Scholar 

  • Schmidt M (2010) Xenobiology: a new form of life as the ultimate biosafety tool. BioEssays 32:322–331

    Article  Google Scholar 

  • Schmidt M, de Lorenzo V (2012) Synthetic constructs in/for the environment: managing the interplay between natural and engineered biology. FEBS Lett 586:2199–2206

    Article  Google Scholar 

  • Schwille P (2011) Bottom-up synthetic biology: engineering in a tinkerer’s world. Science 333:1252–1254

    Article  Google Scholar 

  • Stano P, Luisi PL (2013) Semi-synthetic minimal cells: origin and recent developments. Curr Opin Biotechnol 24:633–638

    Article  Google Scholar 

  • Szybalski W, Skalka A (1978) Nobel prizes and restriction enzymes. Gene 4:181–182

    Article  Google Scholar 

  • Trafton, A (2011) Rewiring cells: how a handful of MIT electrical engineers pioneered synthetic biology. MIT Technology Review. http://www.technologyreview.com/article/423703/rewiring-cells. Accessed 9 Mar 2015

  • Voigt C (2011) Access through refactoring: Rebuilding complex functions from the ground up. Presentation given at the March 14-15, 2011, public workshop, “Synthetic and Systems Biology,” Forum on Microbial Threats, Institute of Medicine, Washington, DC

    Google Scholar 

  • Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894–898

    Article  Google Scholar 

  • Wang K, Sachdeva A, Cox DJ, Wilf NW, Lang K, Wallace S, Mehl RA, Chin JW (2014) Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 6:393–403

    Article  Google Scholar 

  • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854–6859

    Article  Google Scholar 

  • Yeh BJ, Lim WA (2007) Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 3:521–525

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany

    Michael Bölker

  2. EA European Academy of Technology and Innovation Assessment GmbH, Wilhelmstr. 56, 53474, Bad Neuenahr-Ahrweiler, Germany

    Margret Engelhard

  3. Department of Chemistry, TU Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany

    Nediljko Budisa

Authors
  1. Michael Bölker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Margret Engelhard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nediljko Budisa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael Bölker .

Editor information

Editors and Affiliations

  1. & Innovation Assessment GmbH, EA European Academy of Technology, Bad Neuenahr-Ahrweiler, Rheinland-Pfalz, Germany

    Margret Engelhard

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Bölker, M., Engelhard, M., Budisa, N. (2016). Synthetic Biology: Diverse Layers of Live. In: Engelhard, M. (eds) Synthetic Biology Analysed. Ethics of Science and Technology Assessment, vol 44. Springer, Cham. https://doi.org/10.1007/978-3-319-25145-5_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-25145-5_2

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-25143-1

  • Online ISBN: 978-3-319-25145-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation