Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids


Microbial production of chemicals is now an attractive alternative to chemical synthesis. Current efforts focus mainly on constructing pathways to produce different types of molecules1,2,3. However, there are few strategies for engineering regulatory components to improve product titers and conversion yields of heterologous pathways4. Here we developed a dynamic sensor-regulator system (DSRS) to produce fatty acid–based products in Escherichia coli, and demonstrated its use for biodiesel production. The DSRS uses a transcription factor that senses a key intermediate and dynamically regulates the expression of genes involved in biodiesel production. This DSRS substantially improved the stability of biodiesel-producing strains and increased the titer to 1.5 g/l and the yield threefold to 28% of the theoretical maximum. Given the large number of natural sensors available, this DSRS strategy can be extended to many other biosynthetic pathways to balance metabolism, thereby increasing product titers and conversion yields and stabilizing production hosts.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Design of FA/acyl-CoA biosensors.
Figure 2: Hybrid FA/acyl-CoA–regulated promoters.
Figure 3: Regulation of FAEE production by the DSRS.
Figure 4: Metabolite analysis and dynamic behavior of FAEE-producing strains.


  1. Ajikumar, P.K. et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330, 70–74 (2010).

    CAS  Article  Google Scholar 

  2. Atsumi, S., Hanai, T. & Liao, J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86–89 (2008).

    CAS  Article  Google Scholar 

  3. Steen, E.J. et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463, 559–562 (2010).

    CAS  Article  Google Scholar 

  4. Zhang, F. & Keasling, J.D. Biosensors and their applications in metabolic engineering. Trends Microbiol. 19, 323–329 (2011).

    CAS  Article  Google Scholar 

  5. Keasling, J.D. Manufacturing molecules through metabolic engineering. Science 330, 1355–1358 (2010).

    CAS  Article  Google Scholar 

  6. Harcum, S.W. & Bentley, W.E. Heat-shock and stringent responses have overlapping protease activity in Escherichia coli. Implications for heterologous protein yield. Appl. Biochem. Biotechnol. 80, 23–37 (1999).

    CAS  Article  Google Scholar 

  7. De Mey, M., Maertens, J., Lequeux, G.J., Soetaert, W.K. & Vandamme, E.J. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnol. 7, 34 (2007).

    Article  Google Scholar 

  8. Pfleger, B.F., Pitera, D.J., Smolke, C.D. & Keasling, J.D. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 24, 1027–1032 (2006).

    CAS  Article  Google Scholar 

  9. Salis, H.M., Mirsky, E.A. & Voigt, C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946–950 (2009).

    CAS  Article  Google Scholar 

  10. Holtz, W.J. & Keasling, J.D. Engineering static and dynamic control of synthetic pathways. Cell 140, 19–23 (2010).

    CAS  Article  Google Scholar 

  11. Farmer, W.R. & Liao, J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18, 533–537 (2000).

    CAS  Article  Google Scholar 

  12. Zhang, F., Rodriguez, S. & Keasling, J.D. Metabolic engineering of microbial pathways for advanced biofuels production. Curr. Opin. Biotechnol. 775–783 (2011).

  13. Fujita, Y., Matsuoka, H. & Hirooka, K. Regulation of FA metabolism in bacteria. Mol. Microbiol. 66, 829–839 (2007).

    CAS  Article  Google Scholar 

  14. Cronan, J.E. Jr. In vivo evidence that acyl coenzyme A regulates DNA binding by the Escherichia coli FadR global transcription factor. J. Bacteriol. 179, 1819–1823 (1997).

    CAS  Article  Google Scholar 

  15. DiRusso, C.C., Heimert, T.L. & Metzger, A.K. Characterization of FadR, a global transcriptional regulator of FA metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A. J. Biol. Chem. 267, 8685–8691 (1992).

    CAS  PubMed  Google Scholar 

  16. Iram, S.H. & Cronan, J.E. Unexpected functional diversity among FadR FA transcriptional regulatory proteins. J. Biol. Chem. 280, 32148–32156 (2005).

    CAS  Article  Google Scholar 

  17. Henry, M.F. & Cronan, J.E. Jr. A new mechanism of transcriptional regulation: release of an activator triggered by small molecule binding. Cell 70, 671–679 (1992).

    CAS  Article  Google Scholar 

  18. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1–I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).

    CAS  Article  Google Scholar 

  19. van Aalten, D.M., DiRusso, C.C. & Knudsen, J. The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J. 20, 2041–2050 (2001).

    CAS  Article  Google Scholar 

  20. Lanzer, M. & Bujard, H. Promoters largely determine the efficiency of repressor action. Proc. Natl. Acad. Sci. USA 85, 8973–8977 (1988).

    CAS  Article  Google Scholar 

  21. Spencer, A.K., Greenspan, A.D. & Cronan, J.E. Jr. Thioesterases I and II of Escherichia coli. Hydrolysis of native acyl-acyl carrier protein thioesters. J. Biol. Chem. 253, 5922–5926 (1978).

    CAS  PubMed  Google Scholar 

  22. Corchero, J.L. & Villaverde, A. Plasmid maintenance in Escherichia coli recombinant cultures is dramatically, steadily, and specifically influenced by features of the encoded proteins. Biotechnol. Bioeng. 58, 625–632 (1998).

    CAS  Article  Google Scholar 

  23. Friehs, K. Plasmid copy number and plasmid stability. Adv. Biochem. Eng. Biotechnol. 86, 47–82 (2004).

    CAS  PubMed  Google Scholar 

  24. Wilkinson, S.P. & Grove, A. Ligand-responsive transcriptional regulation by members of the MarR family of winged helix proteins. Curr. Issues Mol. Biol. 8, 51–62 (2006).

    PubMed  Google Scholar 

  25. Carothers, J.M., Goler, J.A., Juminaga, D. & Keasling, J.D. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334, 1716–1719 (2012).

    Article  Google Scholar 

  26. Lee, T.S. et al. BglBrick vectors and datasheets: A synthetic biology platform for gene expression. J. Biol. Eng. 5, 12 (2011).

    CAS  Article  Google Scholar 

  27. Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).

    Article  Google Scholar 

  28. Hajimorad, M., Gray, P.R. & Keasling, J.D. A framework and model system to investigate linear system behavior in Escherichia coli. J. Biol. Eng. 5, 3 (2011).

    CAS  Article  Google Scholar 

  29. Ramsey, S., Orrell, D. & Bolouri, H. Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3, 415–436 (2005).

    CAS  Article  Google Scholar 

Download references


The authors would like to thank W. Holtz, E. Steen and N. Hillson for discussion and critical reading of the manuscript. This work was supported in part by the Synthetic Biology Engineering Research Center, which is funded by National Science Foundation award no. 0540879, and by the Joint BioEnergy Institute, which is funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231. F.Z. is supported by the Postdoctoral Fellowships Program of the Natural Sciences and Engineering Research Council of Canada.

Author information

Authors and Affiliations



F.Z. and J.D.K. conceived the project and designed the experiments. F.Z. performed the experiments. J.M.C. designed and performed the DSRS modeling. F.Z., J.M.C. and J.D.K. analyzed the data and wrote the paper.

Corresponding author

Correspondence to Jay D Keasling.

Ethics declarations

Competing interests

J.D.K. has a financial interest in Amyris, LS9 and Lygos.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–5 and Supplementary Figures 1–9 (PDF 860 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zhang, F., Carothers, J. & Keasling, J. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30, 354–359 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing