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Unusual carbon fixation gives rise to diverse polyketide extender units

Nature Chemical Biology volume 8, pages 117–124 (2012)Cite this article

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Abstract

Polyketides are structurally diverse and medically important natural products that have various biological activities. During biosynthesis, chain elongation uses activated dicarboxylic acid building blocks, and their availability therefore limits side chain variation in polyketides. Recently, the crotonyl-CoA carboxylase-reductase (CCR) class of enzymes was identified in primary metabolism and was found to be involved in extender-unit biosynthesis of polyketides. These enzymes are, in theory, capable of forming dicarboxylic acids that show any side chain from the respective unsaturated fatty acid precursor. To our knowledge, we here report the first crystal structure of a CCR, the hexylmalonyl-CoA synthase from Streptomyces sp. JS360, in complex with its substrate. Structural analysis and biochemical characterization of the enzyme, including active site mutations, are reported. Our analysis reveals how primary metabolic CCRs can evolve to produce various dicarboxylic acid building blocks, setting the stage to use CCRs for the production of unique extender units and, consequently, altered polyketides.

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Figure 1: Unusual alkylmalonyl thioester building blocks generated by reductive carboxylation and incorporated into bacterial polyketide metabolites.
Figure 2: Structure of CinF.
Figure 3: Ligand binding by CinF.
Figure 4: Comparison of CinF with other structures.

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References

  1. Hertweck, C. The biosynthetic logic of polyketide diversity. Angew. Chem. Int. Edn Engl. 48, 4688–4716 (2009).

    Article  CAS  Google Scholar 

  2. Newman, D.J. & Cragg, G.M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70, 461–477 (2007).

    Article  CAS  Google Scholar 

  3. Staunton, J. & Weissman, K.J. Polyketide biosynthesis: a millennium review. Nat. Prod. Rep. 18, 380–416 (2001).

    Article  CAS  Google Scholar 

  4. Wenzel, S.C. et al. On the biosynthetic origin of methoxymalonyl-acyl carrier protein, the substrate for incorporation of “glycolate” units into ansamitocin and soraphen A. J. Am. Chem. Soc. 128, 14325–14336 (2006).

    Article  CAS  Google Scholar 

  5. Dorrestein, P.C. et al. The bifunctional glyceryl transferase/phosphatase OzmB belonging to the HAD superfamily that diverts 1,3-bisphosphoglycerate into polyketide biosynthesis. J. Am. Chem. Soc. 128, 10386–10387 (2006).

    Article  CAS  Google Scholar 

  6. Chan, Y.A. et al. Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc. Natl. Acad. Sci. USA 103, 14349–14354 (2006).

    Article  CAS  Google Scholar 

  7. Erb, T.J. et al. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc. Natl. Acad. Sci. USA 104, 10631–10636 (2007).

    Article  CAS  Google Scholar 

  8. Erb, T.J., Brecht, V., Fuchs, G., Muller, M. & Alber, B.E. Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase. Proc. Natl. Acad. Sci. USA 106, 8871–8876 (2009).

    Article  CAS  Google Scholar 

  9. Rachid, S. et al. Mining the cinnabaramide biosynthetic pathway to generate novel proteasome inhibitors. ChemBioChem 12, 922–931 (2011).

    Article  CAS  Google Scholar 

  10. Buntin, K. et al. Biosynthesis of thuggacins in myxobacteria: comparative cluster analysis reveals basis for natural product structural diversity. Chem. Biol. 17, 342–356 (2010).

    Article  CAS  Google Scholar 

  11. Eustáquio, A.S. et al. Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine. Proc. Natl. Acad. Sci. USA 106, 12295–12300 (2009).

    Article  Google Scholar 

  12. Mo, S. et al. Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues. J. Am. Chem. Soc. 133, 976–985 (2011).

    Article  CAS  Google Scholar 

  13. Goranovic, D. et al. Origin of the allyl group in FK506 biosynthesis. J. Biol. Chem. 285, 14292–14300 (2010).

    Article  CAS  Google Scholar 

  14. Qu, X. et al. Cloning, sequencing and characterization of the biosynthetic gene cluster of sanglifehrin A, a potent cyclophilin inhibitor. Mol. Biosyst. 7, 852–861 (2011).

    Article  CAS  Google Scholar 

  15. Kopp, M. et al. Insights into the complex biosynthesis of the leupyrrins in Sorangium cellulosum So ce690. Mol. Biosyst. 7, 1549–1563 (2011).

    Article  CAS  Google Scholar 

  16. Song, L. et al. Type III polyketide synthase I2-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. J. Am. Chem. Soc. 128, 14754–14755 (2006).

    Article  CAS  Google Scholar 

  17. Xu, Z., Ding, L. & Hertweck, C. A branched extender unit shared between two orthogonal polyketide pathways in an endophyte. Angew. Chem. Int. Edn Engl. 50, 4667–4670 (2011).

    Article  CAS  Google Scholar 

  18. Wilson, M.C. et al. Structure and biosynthesis of the marine Streptomycete ansamycin ansalactam A and its distinctive branched chain polyketide extender unit. J. Am. Chem. Soc. published online, doi:10.1021/ja109226s (19 January 2011).

  19. Yoo, H.G. et al. Characterization of 2-octenoyl-CoA carboxylase/reductase utilizing pteB from Streptomyces avermitilis. Biosci. Biotechnol. Biochem. 75, 1191–1193 (2011).

    Article  CAS  Google Scholar 

  20. Xu, L.H. et al. Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis. J. Biol. Chem. 285, 16844–16853 (2010).

    Article  CAS  Google Scholar 

  21. Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    Article  CAS  Google Scholar 

  22. Verdonk, M.L. et al. Modeling water molecules in protein-ligand docking using GOLD. J. Med. Chem. 48, 6504–6515 (2005).

    Article  CAS  Google Scholar 

  23. Li, X., Jayachandran, S., Nguyen, H.H. & Chan, M.K. Structure of the Nitrosomonas europaea Rh protein. Proc. Natl. Acad. Sci. USA 104, 19279–19284 (2007).

    Article  CAS  Google Scholar 

  24. Esposito, L. et al. Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus. Biochemistry 42, 14397–14407 (2003).

    Article  CAS  Google Scholar 

  25. Porté, S. et al. Three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase PIG3. J. Biol. Chem. 284, 17194–17205 (2009).

    Article  Google Scholar 

  26. Weissman, K.J. & Leadlay, P.F. Combinatorial biosynthesis of reduced polyketides. Nat. Rev. Microbiol. 3, 925–936 (2005).

    Article  CAS  Google Scholar 

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Acknowledgements

D.W.H. acknowledges support from the Fonds der Chemischen Industrie. Research in R.M.'s laboratory was funded by the Deutsche Forschungsgemeinschaft and the Bundesministerium für Bildung und Forschung (BMBF). We thank V. Wray for critically reviewing this manuscript. We also would like to thank T. Hoffmann for technical support, K. Harmrolfs for the NMR measurement and S.C. Wenzel for advice during the course of this project. In addition, we appreciate the work of A. Ullrich and K. Schultz from U. Kazmaier's work group for the syntheses of 2-octenoyl-CoA and 2-octenoyl-SNAC.

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  1. Nick Quade and Liujie Huo: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany

    Nick Quade & Dirk W Heinz

  2. Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany

    Liujie Huo, Shwan Rachid & Rolf Müller

  3. Faculty of Science and Health, University of Koya, Koya, Kurdistan, Iraq

    Shwan Rachid

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  1. Nick Quade
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  4. Dirk W Heinz
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Contributions

N.Q. performed protein crystallization, crystallographic data collection and structure determination. L.H. performed gene cloning, protein heterologous expression and purification experiments as well as in vitro characterization of proteins and generation of corresponding point mutations. S.R. contributed initial advice regarding protein expression. R.M. and D.W.H. designed the study, and R.M. wrote the manuscript together with N.Q., L.H. and D.W.H. All authors discussed the results and commented on the manuscript.

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Correspondence to Dirk W Heinz or Rolf Müller.

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Quade, N., Huo, L., Rachid, S. et al. Unusual carbon fixation gives rise to diverse polyketide extender units. Nat Chem Biol 8, 117–124 (2012). https://doi.org/10.1038/nchembio.734

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