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Cyclodipeptide synthases are a family of tRNA-dependent peptide bond–forming enzymes

Nature Chemical Biology volume 5, pages 414–420 (2009)Cite this article

Abstract

Cyclodipeptides and their derivatives belong to the diketopiperazine (DKP) family, which is comprised of a broad array of natural products that exhibit useful biological properties. In the few known DKP biosynthetic pathways, nonribosomal peptide synthetases (NRPSs) are involved in the synthesis of cyclodipeptides that constitute the DKP scaffold, except in the albonoursin (1) pathway. Albonoursin, or cyclo(α,β-dehydroPhe-α,β-dehydroLeu), is an antibacterial DKP produced by Streptomyces noursei. In this pathway, the formation of the cyclo(Phe-Leu) (2) intermediate is catalyzed by AlbC, a small protein unrelated to NRPSs. We demonstrated that AlbC uses aminoacyl-tRNAs as substrates to catalyze the formation of the DKP peptide bonds. Moreover, several other bacterial proteins, presenting moderate similarity to AlbC, also use aminoacyl-tRNAs to synthesize various cyclodipeptides. Therefore, AlbC and these related proteins belong to a newly defined family of enzymes that we have named cyclodipeptide synthases (CDPSs).

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Figure 1
Figure 2: In vitro reconstitution of AlbC activity.
Figure 3: Protein sequence alignments of proteins similar to AlbC.
Figure 4: AlbC-related proteins are CDPSs synthesizing various cyclodipeptides.

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Acknowledgements

We thank C. Olaizola and M. Bahut for technical assistance, S. Zinn-Justin and J. Baillon for helpful discussion, and M. Moutiez for the critical reading of the manuscript. We are indebted to M. Springer (Institut de Biologie Physico-Chimique) for the plasmid pBI and to F. Doucet-Populaire (Université Paris Descartes), T. Msadek (Pasteur Institute), A. Bolotin (Institut National de la Recherche Agronomique), T. Baba (Juntendo University) and E. Krin (Pasteur Institute) for the gifts of bacterial strains and bacterial genomic DNAs. This study was supported by Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud 11, Pôle de Recherche et d'Enseignement Supérieur UniverSud Paris and Kyowa Hakko Bio Co. Ltd. L.S. is a recipient of a doctoral fellowship from Commissariat à l'Energie Atomique.

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Author notes

  1. Ludovic Sauguet, Rachel Amouroux, Karine Tuphile, Sandrine Braud, Shin-ichi Hashimoto & Roger Genet

    Present address: Present addresses: Department of Biochemistry, Cambridge University, Cambridge, UK (L.S.); Commissariat à l'Energie Atomique, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation Recombinaison, Fontenay-aux-Roses, France (R.A.); Université Paris-Sud 11, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8619, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Orsay, France (K.T.); ObeTherapy Biotechnology, Evry, France (S.B.); Technology Development & Research Department, Kyowa Hakko Bio Co. Ltd., Chiyoda-ku, Tokyo, Japan (S.-i.H.); Cemagref, Antony Cedex, France (R.G.).,

  2. Muriel Gondry and Ludovic Sauguet: These authors contributed equally to this work.

Authors and Affiliations

  1. Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France

    Muriel Gondry, Ludovic Sauguet, Pascal Belin, Robert Thai, Rachel Amouroux, Carine Tellier, Mickaël Jacquet, Sandrine Braud, Marie Courçon, Cédric Masson, Steven Dubois, Alain Lecoq & Roger Genet

  2. Université Paris-Sud 11, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8621, Institut de Génétique et Microbiologie, Orsay, France

    Rachel Amouroux, Carine Tellier, Karine Tuphile, Sandrine Braud, Sylvie Lautru & Jean-Luc Pernodet

  3. Technical Research Laboratories, Kyowa Hakko Bio Co. Ltd., Hofu-city, Yamaguchi, Japan

    Shin-ichi Hashimoto

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Correspondence to Muriel Gondry or Jean-Luc Pernodet.

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Competing interests

M.G., L.S., P.B., R.T., S.-i.H., R.G. and J.-L.P. are inventors in patent applications related to the use of CDPSs for dipeptide synthesis. The research performed was supported in part by Kyowa Hakko Bio Co. Ltd, a company that is a co-owner of the patent applications. S.-i.H. is an employee of Kyowa Hakko Bio Co. Ltd.

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Gondry, M., Sauguet, L., Belin, P. et al. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond–forming enzymes. Nat Chem Biol 5, 414–420 (2009). https://doi.org/10.1038/nchembio.175

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