Advertisement

Systems and Synthetic Biology in Hydrocarbon Microbiology: Tools

  • Víctor de Lorenzo
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Systems and synthetic biology represent the two sides of the recent ambition to understand quantitatively biological systems as full, logically organized objects able to perform functions on the basis of their extant blueprint and therefore amenable to being refactored to generate new-to-nature properties. The systemic approach focuses on the cataloguing of all components of the studied entity, their relational logic and their dynamic interplay for comprehending and predicting its behaviour as a whole. The synthetic counterpart adopts straight engineering principles taken from industrial and electric manufacturing for re-creating biological systems from perfectly defined constituents as well as for constructing functionalities that have not yet emerged through the natural evolutionary course.

Keywords:

Containment DNA assembly Modelling Networks Orthogonality Parts 

Notes

Acknowledgements

The work in Author’s Laboratory is supported by the CAMBIOS Project of the Spanish Ministry of Economy and Competitiveness, the ARISYS, EVOPROG and EMPOWERPUTIDA Contracts of the EU, the ERANET-IB and the PROMT Project of the CAM.

References

  1. 1.
    de Lorenzo V (2008) Systems biology approaches to bioremediation. Curr Opin Biotechnol 19:579–589CrossRefPubMedGoogle Scholar
  2. 2.
    de Lorenzo V, Fraile S, Jiménez J (2010) Emerging systems and synthetic biology approaches to hydrocarbon biotechnology. In: Timmis KN, McGenity TJ, van der Meer JR, de Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, pp 1411–1435Google Scholar
  3. 3.
    Kacser H (1986) On parts and wholes in metabolism. In: Welch GR, Clegg JS (eds) The organization of cell metabolism. Plenum, New York, pp 327–337Google Scholar
  4. 4.
    Alon U (2006) An introduction to systems biology: design principles of biological circuits. Chapman and Hall/CRC, Boca RatonGoogle Scholar
  5. 5.
    Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Nogales J (2016) A practical protocol for genome-scale metabolic reconstruction. Springer Protocols Handbooks. doi: 10.1007/8623_2015_98
  7. 7.
    Hausler S (2016) Phenome-ing microbes. Springer Protocols Handbooks. doi: 10.1007/8623_2015_178
  8. 8.
    Chavarria M (2016) Quantitative physiology approaches to understand and optimize reducing power availability in environmental bacteria. Springer Protocols Handbooks. doi: 10.1007/8623_2015_84
  9. 9.
    O'Brien EJ, Monk JM, Palsson BO (2015) Using genome-scale models to predict biological capabilities. Cell 161:971–987CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Palsson BO (2015) Systems biology. Cambridge University Press, CambridgeGoogle Scholar
  11. 11.
    Campos M, Jacobs-Wagner C (2013) Cellular organization of the transfer of genetic information. Curr Opin Microbiol 16:171–176CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Parry BR, Surovtsev IV, Cabeen MT, O’Hern CS, Dufresne ER, Jacobs-Wagner C (2014) The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156:183–194CrossRefPubMedGoogle Scholar
  13. 13.
    Bouyioukos C, Elati M, Kepes F (2016) Protocols for probing genome architecture of regulatory networks in hydrocarbon and lipid microorganisms. In: McGenity TJ, et al. (eds), Springer Protocols Handbooks. doi: 10.1007/8623_2015_92
  14. 14.
    Chistoserdova L (2016) Systems biology tools for methylotrophs. Springer Protocols Handbooks. doi: 10.1007/8623_2015_69
  15. 15.
    ETC Group (2007) Extreme genetic engineering: an introduction to synthetic biology. http://www.etcgroup.org/content/extreme-genetic-engineering-introduction-synthetic-biology
  16. 16.
    de Lorenzo V (2010) Synthetic biology: something old, something new. Bioessays 32:267–270CrossRefPubMedGoogle Scholar
  17. 17.
    de Lorenzo V, Danchin A (2008) Synthetic biology: discovering new worlds and new words. EMBO Rep 9:822–827CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Nørholm. Uracil-excision for assembly of complex pathways.Google Scholar
  19. 19.
    Porcar M, Danchin A, de Lorenzo V, Dos Santos VA, Krasnogor N, Rasmussen S, Moya A (2011) The ten grand challenges of synthetic life. Syst Synth Biol 5:1–9CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 3:4CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Freemont P (2016) Protocol for the standardisation of transcriptional measurements. Springer Protocols Handbooks. doi: 10.1007/8623_2015_148
  22. 22.
    de Las HA, Carreno CA, Martinez-Garcia E, de Lorenzo V (2010) Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev 34:842–865CrossRefGoogle Scholar
  23. 23.
    de Lorenzo V (2011) Beware of metaphors: chasses and orthogonality in synthetic biology. Bioeng Bugs 2:3–7CrossRefPubMedGoogle Scholar
  24. 24.
    Martinez-Garcia E, Benedetti I, Hueso A, De Lorenzo V (2015) Mining environmental plasmids for synthetic biology parts and devices. Microbiol Spectrum 3:Plas-0033-2014Google Scholar
  25. 25.
    Jaric J, Budisa N (2016) Design of orthogonal pairs for protein translation: selection systems for genetically encoding noncanonical amino acids in E. coli. Springer Protocols Handbooks. doi: 10.1007/8623_2015_105
  26. 26.
    Cases I, de Lorenzo V (2005) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8:213–222PubMedGoogle Scholar
  27. 27.
    Schmidt M (2016) Improving biocontainment with synthetic biology: beyond physical containment. Springer Protocols Handbooks. doi: 10.1007/8623_2015_90

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Systems Biology Program, Centro Nacional de Biotecnología CSICMadridSpain

Personalised recommendations