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Revolutionizing agriculture with synthetic biology

Abstract

Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that chance—notwithstanding the shifts in mindset, training and infrastructure investment this demands. Here, we assess opportunities for agricultural synthetic biology and ways to remove barriers to their realization.

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Fig. 1: Plant evolution has explored very little of the possible metabolic design space.
Fig. 2: Plant evolution is far slower than directed evolution.
Fig. 3: The current status of plant SynBio and its constraints.

References

  1. 1.

    Beddington, J. Food, energy, water and the climate: a perfect storm of global events? (UK Government, 2009).

  2. 2.

    Goold, H. D., Wright, P. & Hailstones, D. Emerging opportunities for synthetic biology in agriculture. Genes 9, 341 (2018).

    Article  Google Scholar 

  3. 3.

    Dorit, R. The biology of what is not there. Am. Sci. 99, 20 (2011).

    Article  Google Scholar 

  4. 4.

    Way, J. C., Collins, J. J., Keasling, J. D. & Silver, P. A. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157, 151–161 (2014).

    CAS  Article  Google Scholar 

  5. 5.

    Revolutionizing Agriculture with Synthetic Biology (The Banbury Center, Cold Spring Harbor Laboratory, 2018); https://www.cshl.edu/wp-content/uploads/2018/12/PLANT18_Program.pdf

  6. 6.

    Simon, A. J., d’Oelsnitz, S. & Ellington, A. D. Synthetic evolution. Nat. Biotechnol. 37, 730–743 (2019).

    CAS  Article  Google Scholar 

  7. 7.

    Engqvist, M. K. M. & Rabe, K. S. Applications of protein engineering and directed evolution in plant research. Plant Physiol. 179, 907–917 (2019).

    CAS  Article  Google Scholar 

  8. 8.

    Bar-Even, A. Daring metabolic designs for enhanced plant carbon fixation. Plant Sci. 273, 71–83 (2018).

    CAS  Article  Google Scholar 

  9. 9.

    Tokuriki, N. et al. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat. Commun. 3, 1257 (2012).

    Article  Google Scholar 

  10. 10.

    Davidi, D., Longo, L. M., Jabłońska, J., Milo, R. & Tawfik, D. S. A bird’s-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations. Chem. Rev. 118, 8786–8797 (2018).

    CAS  Article  Google Scholar 

  11. 11.

    Erb, T. J., Jones, P. R. & Bar-Even, A. Synthetic metabolism: metabolic engineering meets enzyme design. Curr. Opin. Chem. Biol. 37, 56–62 (2017).

    CAS  Article  Google Scholar 

  12. 12.

    de Lorenzo, V. et al. The power of synthetic biology for bioproduction, remediation and pollution control. EMBO Rep. 19, e45658 (2018).

    Article  Google Scholar 

  13. 13.

    South, P. F., Cavanagh, A. P., Liu, H. W. & Ort, D. R. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science 363, eaat9077 (2019).

    CAS  Article  Google Scholar 

  14. 14.

    Kubis, A. & Bar-Even, A. Synthetic biology approaches for improving photosynthesis. J. Exp. Bot. 70, 1425–1433 (2019).

    Article  Google Scholar 

  15. 15.

    Amthor, J. et al. Engineering strategies to boost crop productivity by cutting respiratory carbon loss. Plant Cell 31, 297–314 (2019).

    CAS  Article  Google Scholar 

  16. 16.

    Wright, R. C. & Nemhauser, J. Plant synthetic biology: quantifying the “known unknowns” and discovering the “unknown unknowns”. Plant Physiol. 179, 885–893 (2019).

    CAS  Article  Google Scholar 

  17. 17.

    Park, S. Y. et al. Agrochemical control of plant water use using engineered abscisic acid receptors. Nature 520, 545–548 (2015).

    Article  Google Scholar 

  18. 18.

    Liu, W. & Stewart, C. N. Jr. Plant synthetic biology. Trends Plant Sci. 20, 309–317 (2015).

    CAS  Article  Google Scholar 

  19. 19.

    Galanie, S., Thodey, K., Trenchard, I. J., Filsinger Interrante, M. & Smolke, C. D. Complete biosynthesis of opioids in yeast. Science 349, 1095–1100 (2015).

    CAS  Article  Google Scholar 

  20. 20.

    Wang, C., Zheng, P. & Chen, P. Construction of synthetic pathways for raspberry ketone production in engineered Escherichia coli. Appl. Microbiol. Biotechnol. 103, 3715–3725 (2019).

    CAS  Article  Google Scholar 

  21. 21.

    Liu, W. C., Gong, T. & Zhu, P. Advances in exploring alternative Taxol sources. RSC Adv. 6, 48800–48809 (2016).

    CAS  Article  Google Scholar 

  22. 22.

    Cazimoglu, I. et al. Developing a graduate training program in Synthetic Biology: SynBioCDT. Synth. Biol. 4, ysz006 (2019).

    Article  Google Scholar 

  23. 23.

    Delebecque, C. & Philp, J. Training for synthetic biology jobs in the new bioeconomy. Science https://www.sciencemag.org/careers/2015/06/training-synthetic-biology-jobs-new-bioeconomy (2015).

  24. 24.

    Niehaus, T. D., Thamm, A. M., de Crécy-Lagard, V. & Hanson, A. D. Proteins of unknown biochemical function: a persistent problem and a roadmap to help overcome it. Plant Physiol. 169, 1436–1442 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Richard Feynman Wikiquote https://en.wikiquote.org/wiki/Richard_Feynman (2019).

  26. 26.

    Zhao, Y. et al. Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane. Plant Mol. Biol. 100, 247–263 (2019).

    CAS  Article  Google Scholar 

  27. 27.

    Hillson, N. et al. Building a global alliance of biofoundries. Nat. Commun. 10, 2040 (2019).

    Article  Google Scholar 

  28. 28.

    Vazquez-Vilar, M., Orzaez, D. & Patron, N. DNA assembly standards: setting the low-level programming code for plant biotechnology. Plant Sci. 273, 33–41 (2018).

    CAS  Article  Google Scholar 

  29. 29.

    Growing the Future (UK Plant Sciences Federation, 2019); https://www.rsb.org.uk/policy/groups-and-committees/ukpsf/about-ukpsf/growing-the-future-report

  30. 30.

    Agapakis, C. M. Designing synthetic biology. ACS Synth. Biol. 3, 121–128 (2014).

    CAS  Article  Google Scholar 

  31. 31.

    Agapakis, C. Reviving the smell of extinct plants Ginko Bioworks https://www.ginkgobioworks.com/2019/05/03/reviving-the-smell-of-extinct-plants/ (2019).

  32. 32.

    de Lorenzo, V. & Schmidt, M. The do-it-yourself movement as a source of innovation in biotechnology – and much more. Microb. Biotechnol. 10, 517–519 (2017).

    Article  Google Scholar 

  33. 33.

    Bassham, J. A., Benson, A. A. & Calvin, M. The path of carbon in photosynthesis. J. Biol. Chem. 185, 781–787 (1950).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Raven, J. A., Cockell, C. S. & De La Rocha, C. S. The evolution of inorganic carbon concentrating mechanisms in photosynthesis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 2641–2650 (2008).

    CAS  Article  Google Scholar 

  35. 35.

    Berg, I. A., Kockelkorn, D., Buckel, W. & Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318, 1782–1786 (2007).

    CAS  Article  Google Scholar 

  36. 36.

    Zarzycki, J., Brecht, V., Muller, M. & Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl Acad Sci. USA 106, 21317–21322 (2009).

    CAS  Article  Google Scholar 

  37. 37.

    Figueroa, I. A. et al. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. Proc. Natl Acad. Sci. USA 115, E92–E101 (2018).

    CAS  Article  Google Scholar 

  38. 38.

    Ragsdale, S. W. & Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873–1898 (2008).

    CAS  Article  Google Scholar 

  39. 39.

    Evans, M. C. W., Buchanan, B. B. & Arnon, D. I. A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc. Natl Acad. Sci. USA 55, 928–934 (1966).

    CAS  Article  Google Scholar 

  40. 40.

    Huber, H. et al. A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc. Natl Acad. Sci. USA 105, 7851–7856 (2008).

    CAS  Article  Google Scholar 

  41. 41.

    Trudeau, D. L. et al. Design and in vitro realization of carbon-conserving photorespiration. Proc. Natl Acad. Sci. USA 115, E11455–E11464 (2018).

    CAS  Article  Google Scholar 

  42. 42.

    Bar-Even, A., Noor, E., Lewis, N. E. & Milo, R. Design and analysis of synthetic carbon fixation pathways. Proc. Natl Acad. Sci. USA 107, 8889–8894 (2010).

    CAS  Article  Google Scholar 

  43. 43.

    Schwander, T. et al. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354, 900–904 (2016).

    CAS  Article  Google Scholar 

  44. 44.

    Durall, C., Rukminasaria, N. & Lindblad, P. Enhanced growth at low light intensity in the cyanobacterium Synechocystis PCC 6803 by overexpressing phosphoenolpyruvate carboxylase. Algal Res. 16, 275–281 (2016).

    Article  Google Scholar 

Download references

Acknowledgements

This paper was inspired by discussions at the Banbury think-tank meeting, ‘Revolutionizing Agriculture with Synthetic Biology’, held at the Banbury Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2–5 December, 2018. We thank the Cold Spring Harbor Laboratory Banbury Center for hosting the meeting and the Cold Spring Harbor Laboratory Corporate Sponsor Program for funding the meeting. We thank the following meeting presenters for their contributions to the thought-provoking discussions: G. Barbier, D. Bhaya, R. Bock, H. J. Bouwmeester, N. Boyle, M. Cooper, T. J. Erb, S. L. Evans, J. Gershenzon, A. D. Hanson, J. Haseloff, P. J. Hines, A. J. Kinney, S. P. Long, J. L. Matos, J. I. Medford, A. H. Millar, B. L. Møller, T. Muranaka, J. L. Nemhauser, L. Nielsen, P. I. Nikel, D. Orzáez, A. Osbourn, N. J. Patron, P. Rabinowicz, E. S. Sattely, J. Shanklin, C. Vickers and E. T. Wurtzel. Corresponding author A.D.H. acknowledges support from the US National Science Foundation (grant no. MCB-1611711).

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A.D.H., E.T.W., and C.E.V. led the writing of the paper, to which A.H.M., P.I.N., T.J.E., M.C. and K.P.V.-F. contributed; in addition, T.J.E. conceived of and composed Fig. 1, and M.C. and K.P.V.-F. performed evolutionary modelling.

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Correspondence to Eleanore T. Wurtzel or Claudia E. Vickers or Andrew D. Hanson.

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Peer review information Nature Plants thanks Jenny Mortimer, Neal Stewart and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1

Key to abbreviations in Fig. 1. For pathway descriptions, see refs. 33,34,35,36,37,38,39,40,41,42,43,44.

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Wurtzel, E.T., Vickers, C.E., Hanson, A.D. et al. Revolutionizing agriculture with synthetic biology. Nat. Plants 5, 1207–1210 (2019). https://doi.org/10.1038/s41477-019-0539-0

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