Dealing with the genetic load in bacterial synthetic biology circuits: Convergences with the Ohm's law

Nucleic Acids Research

Volumn 44, Issue 1, 2016, Pages 496-507

  Carbonell Ballestero, M ^a,b   Garcia Ramallo, E ^a,b   Montanez R ^a,b   Rodriguez Caso, Carlos ^a,b   Macia J ^a,b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DEVICES; ELECTRIC CURRENT; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC DEVICE; GENETIC LOAD; GENETIC TRANSCRIPTION; MATHEMATICAL MODEL; NONHUMAN; OHM LAW; PRIORITY JOURNAL; RNA TRANSLATION; SYNTHETIC BIOLOGY; ALGORITHM; BACTERIUM; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

ALGORITHMS; BACTERIA; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC LOAD; MODELS, BIOLOGICAL; SYNTHETIC BIOLOGY;

EID: 84959319814     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1280     Document Type: Article

References (33)

1. Andrianantoandro,E., Basu,S., Karig,D.K. and Weiss,R. (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol., 2, doi:10.1038/msb410007.
2. Endy,D. (2005) Foundations for engineering biology. Nature, 438, 449-453.
3. Purnick,P.E.M. and Weiss,R. (2009) The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol., 10, 410-422.
4. Brophy,J.A.N. and Voigt,C.A. (2014) Principles of genetic circuit design. Nat. Methods, 11, 508-520.
5. Collins,J.J., Maxon,M., Ellington,A., Fussenegger,M., Weiss,R. and Sauro,H. (2014) Synthetic biology: how best to build a cell. Nature, 509, 155-157.
6. Canton,B., Labno,A. and Endy,D. (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol., 26, 787-793.
7. Carbonell-Ballestero,M., Duran-Nebreda,S, Montañez,R, Macia,J and Rodriguez-Caso,C. (2014) A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology. Nucleic Acids Res., 42, 14060-14069.
8. Cardinale,S. and Arkin,A.P. (2012) Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems. Biotechnol. J., 7, 856-866.
9. Kwok,R. (2010) Five hard truths for synthetic biology. Nature, 463, 288-290.
10. Peretti,S.W. and Bailey,J.E. (1987) Simulations of host-plasmid interactions in Escherichia coli: Copy number, promoter strength, and ribosome binding site strength effects on metabolic activity and plasmid gene expression. Biotechnol. Bioeng., 29, 316-328.
11. de Vos,D., Bruggeman,F.J., Westerhoff,H.V. and Bakker,B.M. (2011) How molecular competition influences fluxes in gene expression networks. PLoS One, 6, e28494.
12. Bentley,W.E. and Kompala,D.S. (1990) Optimal induction of protein synthesis in recombinant bacterial cultures. Ann. N.Y. Acad. Sci., 589, 121-138.
13. Ceroni,F., Algar,R., Stan,G.-B. and Ellis,T. (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat. Methods, 12, 415-418.
14. Glick,B.R. (1995) Metabolic load and heterologous gene expression. Biotechnol. Adv., 13, 247-261.
15. Scott,M., Mateescu,E.M., Zhang,Z. and Hwa,T. (2010) Interdependence of cell growth origins and consequences. Science, 330, 1099-1102.
16. Klumpp,S. (2011) Growth-rate dependence reveals design principles of plasmid copy number control. PLoS One, 6, e20403.
17. Gyorgy,A. and Del Vecchio,D. (2014) Limitations and trade-offs in gene expression due to competition for shared cellular resources. Proc. IEEE Conf. Decis. Control, 5431-5436.
18. Del Vecchio,D. and Murray,R.M. (2014) Biomolecular Feedback Systems. Princeton University Press, New Jersey.
19. Mishra,D., Rivera,P. and Del Vecchio,D. (2014) A load driver device for engineering modularity in biological networks. Nat. Biotechnol., 32, 1268-1275.
20. Gyorgy,A., Jiménez,J.I., Yazbek,J., Huang,H., Chung,H., Weiss,R. and Del Vecchio,D. (2015) Isocost lines describe the cellular economy of genetic circuits. Biophys. J. 109, 639-646.
21. Registry of Standard Biological Parts. (2015) http://parts.igem.org/Main-Page.
22. Shetty,R.P., Endy,D. and Knight,T.F. (2008) Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng., 2, doi:10.1186/1754-1611-2-5.
23. Pasotti,L., Politi,N., Zucca,S., Cusella De Angelis,M.G. and Magni,P. (2012) Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices. PLoS One, 7, e39407.
24. Nilsson,J.W. and Riedel,S.A. (2011) Electric Circuits. 9th edn. Prentice Hall, New Jersey.
25. Bertram,R. and Hillen,W. (2008) The application of Tet repressor in prokaryotic gene regulation and expression. Microb. Biotechnol., 1, 2-16.
26. Akers,A., Gassman,M. and Smith,R. (2006) Hydraulic Power System Analysis. Taylor & Francis, Boca Raton, FL.
27. Guyton,A. and Hall,J. (2006) Textbook of Medical Physiology. 11th edn. Elsevier Inc., Philadelphia, Pennsylvania.
28. Sarpeshkar,R. (2010) Ultra Low Power Bioelectronics. Cambridge University Press, Cambridge.
29. Yallop,C.A. and Svendsen,I. (2001) Recombinant Protein Production with Prokaryotic and Eukaryotic Cells. A Comparative View on Host Physiology. Springer, Netherlands.
30. Yallop,C.A. and Svendsen,I. (2001) The effects of G418 on the growth and metabolism of recombinant mammalian cell lines. Cytotechnology, 35, 101-114.
31. Van Rensburg,E., Den Haan,R., Smith,J., Van Zyl,W.H. and Görgens,J.F. (2012) The metabolic burden of cellulase expression by recombinant Saccharomyces cerevisiae Y294 in aerobic batch culture. Appl. Microbiol. Biotechnol., 96, 197-209.
32. Glisson,T.H. (2011) Introduction to Circuit Analysis and Design. Springer Scicence+Bussines Media B.V. NY.
33. Hughes,E. (1969) Electrical Technology, 7th edn. Longman, London.