Skip to main content
SpringerLink
Log in

Improving Biocontainment with Synthetic Biology: Beyond Physical Containment

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Genetically engineered organisms are per se subject to a biosafety risk assessment to define whether the resulting organism is safe for humans and the environment, either for contained use or environmental release. Contained use currently means physical containment and allows for a less strict assessment compared to environmental release. With developments in synthetic biology, we are currently witnessing the evolution of different forms of nonphysical containment enabled by sophisticated forms of genetic engineering, genome recoding, and xenobiology. Design and implementation of cells that use advanced suicide circuits, different genetic codes, alternative nucleic acids, amino acids, etc., will allow for a semantic or informational containment restricting and possibly eliminating horizontal gene flow with natural species. Here, we describe the scientific advances in this field and map the different approaches to design safe xeno-organisms. Finally, we address the questions that will have to be answered when semantic biocontainment systems become a reality.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

References

  1. Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age. Nat Rev Genet 11(5):367–379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Armstrong R, Schmidt M, Bedau M (2012) Other developments in synthetic biology. In: Schmidt M (ed) Synthetic biology industrial and environmental applications. Wiley, Weinheim

    Google Scholar 

  3. Moe-Behrens GH, Davis R, Haynes KA (2013) Preparing synthetic biology for the world. Front Microbiol 4:5

    Article  PubMed  PubMed Central  Google Scholar 

  4. DFG, acatech and Lepoldina (2009) Synthetic biology: positions. http://www.dfg.de/download/pdf/dfg_im_profil/reden_stellungnahmen/2009/stellungnahme_synthetische_biologie.pdf

  5. EGE (2009) Ethics of synthetic biology. http://ec.europa.eu/bepa/european-group-ethics/docs/opinion25_en.pdf

  6. Gaisser S, Reiss T, Lunkes A, Muller K, Bernauer H (2009) Making the most of synthetic biology. Strategies for synthetic biology development in Europe. EMBO Rep 10(Suppl 1):S5–S8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Schmidt M, Ganguli-Mitra A, Torgersen H, Kelle A, Deplazes A, Biller-Andorno N (2009) A priority paper for the societal and ethical aspects of synthetic biology. Syst Synth Biol 3(1–4):3–7

    Article  PubMed  PubMed Central  Google Scholar 

  8. The Royal Academy of Engineering (2009) Synthetic biology: scope, applications and implications. The Royal Academy of Engineering, London

    Google Scholar 

  9. Bubela T, Hagen G, Einsiedel E (2012) Synthetic biology confronts publics and policy makers: challenges for communication, regulation and commercialization. Trends Biotechnol 30(3):132–137

    Article  CAS  PubMed  Google Scholar 

  10. Torgersen H, Schmidt M (2013) Frames and comparators: how might a debate on synthetic biology evolve? Futures 48(100):44–54

    Article  PubMed  PubMed Central  Google Scholar 

  11. Wright O, Stan GB, Ellis T (2013) Building-in biosafety for synthetic biology. Microbiology 159(Pt 7):1221–1235

    Article  CAS  PubMed  Google Scholar 

  12. Schmidt M, de Lorenzo V (2012) Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett 586(15):2199–2206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wright O, Delmans M, Stan G-B, Ellis T (2014) GeneGuard: a modular plasmid system designed for biosafety. ACS Synth Biol 4:307–316

    Article  PubMed  Google Scholar 

  14. Davison J (1999) Genetic exchange between bacteria in the environment. Plasmid 42(2):73–91

    Article  CAS  PubMed  Google Scholar 

  15. Townsend JP, Bohn T, Nielsen KM (2012) Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front Microbiol 3:27

    Article  PubMed  PubMed Central  Google Scholar 

  16. Marris C, Jefferson C (2013) Workshop on “Synthetic biology: containment and release of engineered micro-organisms” held on 29 April 2013 at King’s College London: Summary of Discussions. https://kclpure.kcl.ac.uk/portal/en/publications/workshop-on-synthetic-biology-containment-and-release-of-engineered-microorganisms-held-on-29-april-2013-at-kings-college-london%28df5f0ce4-61a9-4067-9705-1851926aa2a2%29/export.html

  17. Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA (2014) Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A 111:4838–4843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  19. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342

    Article  CAS  PubMed  Google Scholar 

  20. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338

    Article  CAS  PubMed  Google Scholar 

  21. Campos L (2009) That was the synthetic biology that was. In: Schmidt M, Kelle A, Ganguli-Mitra A, de Vriend H (eds) Synthetic biology: the technoscience and its societal consequences. Springer, Dordrecht, pp 5–21

    Chapter  Google Scholar 

  22. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22(7):841–847

    Article  CAS  PubMed  Google Scholar 

  23. Bayer TS, Smolke CD (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 23(3):337–343

    Article  CAS  PubMed  Google Scholar 

  24. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434(7037):1130–1134

    Article  CAS  PubMed  Google Scholar 

  25. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516–519

    Article  CAS  PubMed  Google Scholar 

  26. Brigulla M, Wackernagel W (2010) Molecular aspects of gene transfer and foreign DNA acquisition in prokaryotes with regard to safety issues. Appl Microbiol Biotechnol 86(4):1027–1041

    Article  CAS  PubMed  Google Scholar 

  27. Yang S, Sleight SC, Sauro HM (2013) Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits. Nucleic Acids Res 41(1):e33

    Article  CAS  PubMed  Google Scholar 

  28. Carroll D (2011) Zinc-finger nucleases: a panoramic view. Curr Gene Ther 11(1):2–10

    Article  CAS  PubMed  Google Scholar 

  29. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29(2):143–148

    Article  CAS  PubMed  Google Scholar 

  30. Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 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(5987):52–56

    Article  CAS  PubMed  Google Scholar 

  33. Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344(6179):55–58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Pennisi E (2014) Building the ultimate yeast genome. Science 343:1426–1429

    Article  PubMed  Google Scholar 

  35. Budisa N, Minks C, Alefelder S, Wenger W, Dong F, Moroder L, Huber R (1999) Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J 13(1):41–51

    CAS  PubMed  Google Scholar 

  36. Hoesl MG, Budisa N (2012) Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol 23(5):751–757

    Article  CAS  PubMed  Google Scholar 

  37. Budisa N (2013) Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs). Curr Opin Biotechnol 24(4):591–598

    Article  CAS  PubMed  Google Scholar 

  38. di Salvo ML, Budisa N, Contestabile R (2013) PLP-dependent Enzymes: a powerful tool for metabolic synthesis of non-canonical amino acids. In: Beilstein Bozen symposium on molecular engineering and control. Beilstein Institute, Prien, pp 27–66

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  40. Neumann H, Wang K, Davis L, Garcia-Alai M, Chin JW (2010) Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464(7287):441–444

    Article  CAS  PubMed  Google Scholar 

  41. 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(1):1004–1022

    Article  PubMed  Google Scholar 

  42. Doering V (2007) Sense codon reassignment as means of synthesizing safe genetically engineered microorganism. SB3.0, Zurich

    Google Scholar 

  43. Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Soll D, Podar M (2013) UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A 110(14):5540–5545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ling J, Daoud R, Lajoie MJ, Church GM, Soll D, Lang BF (2014) Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Res 42(1):499–508

    Article  CAS  PubMed  Google Scholar 

  45. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477(7365):471–476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 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(6040):348–353

    Article  CAS  PubMed  Google Scholar 

  47. Lajoie MJ, Kosuri S, Mosberg JA, Gregg CJ, Zhang D, Church GM (2013) Probing the limits of genetic recoding in essential genes. Science 342(6156):361–363

    Article  CAS  PubMed  Google Scholar 

  48. 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(6156):357–360

    Article  CAS  PubMed  Google Scholar 

  49. 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  CAS  PubMed  PubMed Central  Google Scholar 

  50. Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature 518:89–93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Sc2.0. “Synthetic Yeast 2.0”. http://biostudio.bme.jhu.edu/sc2/?page_id=63

  52. Ravikumar A, Arrieta A, Liu CC (2014) An orthogonal DNA replication system in yeast. Nat Chem Biol 10:175–177

    Article  CAS  PubMed  Google Scholar 

  53. Marliere P, Patrouix J, Doring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R (2011) Chemical evolution of a bacterium’s genome. Angew Chem Int Ed Engl 50(31):7109–7114

    Article  CAS  PubMed  Google Scholar 

  54. Schmidt M (2010) Xenobiology: a new form of life as the ultimate biosafety tool. Bioessays 32(4):322–331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Acevedo-Rocha CG, Budisa N (2011) On the road towards chemically modified organisms endowed with a genetic firewall. Angew Chem Int Ed Engl 50(31):6960–6962

    Article  CAS  PubMed  Google Scholar 

  56. Burns CC, Shaw J, Campagnoli R, Jorba J, Vincent A, Quay J, Kew O (2006) Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. J Virol 80(7):3259–3272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S (2008) Virus attenuation by genome-scale changes in codon pair bias. Science 320(5884):1784–1787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Mueller S, Coleman JR, Papamichail D, Ward CB, Nimnual A, Futcher B, Skiena S, Wimmer E (2010) Live attenuated influenza virus vaccines by computer-aided rational design. Nat Biotechnol 28(7):723–726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Bull JJ, Molineux IJ, Wilke CO (2012) Slow fitness recovery in a codon-modified viral genome. Mol Biol Evol 29(10):2997–3004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243–1247

    Article  CAS  PubMed  Google Scholar 

  61. Eschenmoser A (1999) Chemical etiology of nucleic acid structure. Science 284(5423):2118–2124

    Article  CAS  PubMed  Google Scholar 

  62. Pace NR (2001) The universal nature of biochemistry. Proc Natl Acad Sci U S A 98(3):805–808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Chaput JC, Ichida JK, Szostak JW (2003) DNA polymerase-mediated DNA synthesis on a TNA template. J Am Chem Soc 125(4):856–857

    Article  CAS  PubMed  Google Scholar 

  64. Ichida JK, Horhota A, Zou K, McLaughlin LW, Szostak JW (2005) High fidelity TNA synthesis by Therminator polymerase. Nucleic Acids Res 33(16):5219–5225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kempeneers V, Renders M, Froeyen M, Herdewijn P (2005) Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization. Nucleic Acids Res 33(12):3828–3836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Marliere P (2009) The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. Syst Synth Biol 3(1–4):77–84

    Article  PubMed  PubMed Central  Google Scholar 

  67. Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA (2006) Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 34(21):6095–6101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. 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(6079):341–344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. SCHER, SCENIHR, SCCS (2014) Preliminary opinion on synthetic biology I definition. http://ec.europa.eu/health/scientific_committees/emerging/docs/scenihr_o_044.pdf

Download references

Acknowledgments

Author acknowledges the financial support of the EC-FP7 project METACODE (EC Grant No. 289572), and MS acknowledges the financial support of the EC-FP7 project ST-FLOW (EC Grant No. 289326).

Author information

Authors and Affiliations

  1. Technology Assessment, Biofaction KG, Kundmanngasse 39/12, Vienna, Austria

    Markus Schmidt & Lei Pei

Authors
  1. Markus Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lei Pei
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Markus Schmidt .

Editor information

Editors and Affiliations

  1. University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Schmidt, M., Pei, L. (2015). Improving Biocontainment with Synthetic Biology: Beyond Physical Containment. In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols . Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_90

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_90

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-50430-7

  • Online ISBN: 978-3-662-50432-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation