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Biosynthetic compartments

Biological systems are able to create very complex molecules using a cascade of enzymatic reactions. Those molecules have very important industrial applications, as we can use them to prepare drugs, dyes, aromas, materials etc. The advantage of enzymatic reactions is that they are very efficient, usually leading to high metabolite yields, occur under mild reaction conditions and they can be stereoselective. Beyond reactions normally occurring in nature cells can, in principle, be used to foster the assembly of metabolic pipelines using enzymes or their mutants from different organisms to create new chemical compounds normally not found in nature. Efficiency of such enzymatic reactions can be increased by new approaches in synthetic biology, such as scaffolding, which mimics properties of some natural enzymatic complexes to cluster the enzymes participating in the reaction cascade. The latest advancements within the field include protein, RNA and DNA synthetic scaffolding systems (Dueber, 2009; Delebecque, 2011; Conrado, 2011). Another promising strategy for enhancing metabolite production in vivo is to compartmentalize biosynthetic enzymes so as to confine them to a small volume which decreases the potential deleterious effects of biosynthetic intermediates on the endogenous cell machinery. The natural solutions to this problem are bacterial microcompartments which some bacteria use to increase the yield of carbon dioxide fixation in carboxysomes.

Partnership between DNA origami and proteins can be used to mimic or enhance this process by the arrangement of biosynthetic enzymes at the surface of DNA origami, based on the sequential order of biosynthetic reactions for the preparation of desired chemicals. Furthermore, creation of a DNA origami-based nanocompartments has already been demonstrated (Andersen, 2009). Site-specific tethering of biosynthetic enzymes into the box or another designed compartment (e.g. with entry and exit for the reagents and reaction products) can create the designed biosynthetic compartment which should increase the rate of reaction as well as decrease the concentration of potentially toxic intermediates.

Figure 39: Organelle-like biosynthetic nanocompartment using DNA origami add-ons approach. Cylindrically shaped DNA origami with ZFP binding staples protruding into interior of the compartment to anchor enzyme-ZFP chimeras in place threreby promoting metabolite chanelling.

  • Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459: 73-76
  • Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, DeLisa MP (2011) DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. in press
  • Delebecque CJ, Lindner AB, Silver PA, Aldaye FA (2011) Organization of intracellular reactions with rationally designed RNA assemblies. Science 333: 470-4.
  • Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nature Biotechnol. 28: 753-9.

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