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Heterochiral coupling in non-ribosomal peptide macrolactamization

Nature Catalysis volume 3, pages 507–515 (2020)Cite this article

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Abstract

Heterochiral coupling is favoured in abiotic peptide bond formation, whereas biotic peptide bond formation is dominated by homochiral coupling. Here, we report that heterochiral coupling is a rather general paradigm in the head-to-tail macrolactamization of non-ribosomal peptide biosynthesis. The canonical cis-acting offloading cyclases, such as type I thioesterase (TE) and terminal condensation-like domains, catalyse head-to-tail macrolactamization between N- and C-terminal residues with d- and l-configurations, respectively. In contrast, the penicillin-binding protein-type TEs, a recently identified family of trans-acting cyclases, couple heterochiral residues with complementary stereoselectivity to the canonical one. Thus, a suite of cis- and trans-TE non-ribosomal peptide synthetases could overcome the stereochemical constraints present in heterochiral head-to-tail macrolactam formation in bacterial non-ribosomal peptide biosynthesis. Furthermore, we provide the structural rationale for the C-terminal stereoselectivity of non-canonical offloading cyclases. Penicillin-binding protein-type TEs with broad substrate specificity are potentially applicable as biocatalysts and genetic tools for synthetic biology.

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Fig. 1: PBP-type TEs for non-ribosomal macrolactam biosynthesis.
Fig. 2: Crystal structure of SurE.
Fig. 3: Engineering surNRPS revealed the plasticity of SurE.

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Data availability

The crystallographic data that support the findings of this study are available from the Protein Data Bank (http://www.rcsb.org). The coordinates and the structure factor amplitudes for the structures of SurE apo and SurE complexed with 4 have been deposited under accession codes 6KSU and 6KSV, respectively. All other data supporting the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.

References

  1. Hill, R. R., Birch, D., Jeff, G. E. & North, M. Enantioselection in peptide bond formation. Org. Biomol. Chem. 1, 965–972 (2003).

    Article  CAS  PubMed  Google Scholar 

  2. Brady, S. F. et al. Practical synthesis of cyclic peptides, with an example of dependence of cyclization yield upon linear sequence. J. Org. Chem. 44, 3101–3105 (1979).

    Article  CAS  Google Scholar 

  3. Rich, D. H., Bhatnagar, P., Mathiaparanam, P., Grant, J. A. & Tam, J. P. Synthesis of tentoxin and related dehydro cyclic tetrapeptides. J. Org. Chem. 43, 296–302 (1978).

    Article  CAS  PubMed  Google Scholar 

  4. Sieber, S. A. & Marahiel, M. A. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem. Rev. 105, 715–738 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Trauger, J. W., Kohli, R. M., Mootz, H. D., Marahiel, M. A. & Walsh, C. T. Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Nature 407, 215–218 (2000).

    Article  CAS  PubMed  Google Scholar 

  6. Gao, X. et al. Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain. Nat. Chem. Biol. 8, 823–830 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Tsomaia, N. Peptide therapeutics: targeting the undruggable space. Eur. J. Med. Chem. 94, 459–470 (2015).

    Article  CAS  PubMed  Google Scholar 

  8. Kuranaga, T. et al. Total synthesis of the nonribosomal peptide surugamide B and identification of a new offloading cyclase family. Angew. Chem. Int. Ed. 57, 9447–9451 (2018).

    Article  CAS  Google Scholar 

  9. Takada, K. et al. Surugamides A–E, cyclic octapeptides with four d-amino acid residues, from a marine Streptomyces sp.: LC-MS-aided inspection of partial hydrolysates for the distinction of d- and l-amino acid residues in the sequence. J. Org. Chem. 78, 6746–6750 (2013).

    Article  CAS  PubMed  Google Scholar 

  10. Mohiman, H. et al. Dereplication of peptidic natural products through database search of mass spectra. Nat. Chem. Biol. 13, 30–37 (2016).

    Article  CAS  Google Scholar 

  11. Xu, F., Nazari, B., Moon, K., Bushin, L. B. & Seyedsayamdost, M. R. Discovery of a cryptic antifungal compound from Streptomyces albus J1074 using high-throughput elicitor screens. J. Am. Chem. Soc. 139, 9203–9212 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ninomiya, A. et al. Biosynthetic gene cluster for surugamide A encompasses an unrelated decapeptide, surugamide F. ChemBioChem 17, 1709–1712 (2016).

    Article  CAS  PubMed  Google Scholar 

  13. Matsuda, K. et al. SurE is a trans-acting thioesterase cyclizing two distinct non-ribosomal peptides. Org. Biomol. Chem. 17, 1058–1061 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Magarvey, N. A., Haltli, B., He, M., Greenstein, M. & Hucul, J. A. Biosynthetic pathway for mannopeptimycins, lipoglycopeptide antibiotics active against drug-resistant gram-positive pathogens. Antimicrob. Agents Chemother. 50, 2167–2177 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Li, Q. et al. Identification of the biosynthetic gene cluster for the anti-infective desotamides and production of a new analogue in a heterologous host. J. Nat. Prod. 78, 944–948 (2015).

    Article  CAS  PubMed  Google Scholar 

  16. Son, S. et al. Genomics-driven discovery of chlorinated cyclic hexapeptides ulleungmycins A and B from a Streptomyces species. J. Nat. Prod. 80, 3025–3031 (2017).

    Article  CAS  PubMed  Google Scholar 

  17. Zhou, Y. et al. Investigation of penicillin binding protein (PBP)-like peptide cyclase and hydrolase in surugamide non-ribosomal peptide biosynthesis. Cell Chem. Biol. 26, 737–744 (2019).

    Article  CAS  PubMed  Google Scholar 

  18. Thankachan, D. et al. A trans-acting cyclase offloading strategy for nonribosomal peptide synthetases. ACS Chem. Biol. 14, 845–849 (2019).

    Article  CAS  PubMed  Google Scholar 

  19. White, C. J. & Yudin, A. K. Contemporary strategies for peptide macrocyclization. Nat. Chem. 3, 509–524 (2011).

    Article  CAS  PubMed  Google Scholar 

  20. Yu, X. & Sun, D. Macrocyclic drugs and synthetic methodologies toward macrocycles. Molecules 18, 6230–6268 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Medema, M. H. et al. Minimum information about a biosynthetic gene cluster. Nat. Chem. Biol. 11, 625–631 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Schultz, A. W. et al. Biosynthesis and structures of cyclomarins and cyclomarazines, prenylated cyclic peptides of marine actinobacterial origin. J. Am. Chem. Soc. 130, 4507–4516 (2008).

    Article  CAS  PubMed  Google Scholar 

  23. Ma, J. et al. Biosynthesis of ilamycins featuring unusual building blocks and engineered production of enhanced anti-tuberculosis agents. Nat. Commun. 8, 391 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lahiri, S. D. et al. Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC β-lactamases. Antimicrob. Agents Chemother. 57, 2496–2505 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Nakano, S. et al. Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline d-peptidase from Bacillus cereus DF4-B. Sci. Rep. 5, 13836–13836 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Delfosse, V. et al. Structure of the archaeal Pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS ONE 4, e4712–e4712 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Calcott, M. J. & Ackerley, D. F. Genetic manipulation of non-ribosomal peptide synthetases to generate novel bioactive peptide products. Biotechnol. Lett. 36, 2407–2416 (2014).

    Article  CAS  PubMed  Google Scholar 

  29. Bozhüyük, K. A. J. et al. De novo design and engineering of non-ribosomal peptide synthetases. Nat. Chem. 10, 275–281 (2017).

    Article  PubMed  CAS  Google Scholar 

  30. Niquille, D. L. et al. Nonribosomal biosynthesis of backbone-modified peptides. Nat. Chem. 10, 282–287 (2018).

    Article  CAS  PubMed  Google Scholar 

  31. Bozhüyük, K. A. J. et al. Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat. Chem. 11, 653–661 (2019).

    Article  PubMed  CAS  Google Scholar 

  32. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411–2423 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Rice, L. M., Earnest, T. N. & Brunger, A. T. Single-wavelength anomalous diffraction phasing revisited. Acta Crystallogr. D 56, 1413–1420 (2000).

    Article  CAS  PubMed  Google Scholar 

  34. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistic. Acta Crystallogr. D 67, 282–292 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Skubak, P. & Pannu, N. S. Automatic protein structure solution from weak X-ray data. Nat. Commun. 4, 2777 (2013).

    Article  PubMed  CAS  Google Scholar 

  37. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Terwilliger, T. C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D 64, 61–69 (2007).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  39. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  CAS  PubMed  Google Scholar 

  40. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Schüttelkopf, A. W. & van Aalten, D. M. PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr. D 60, 1355–1363 (2004).

    Article  PubMed  CAS  Google Scholar 

  42. Bachmann, B. O. & Ravel, J. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol. 458, 181–217 (2009).

    Article  CAS  PubMed  Google Scholar 

  43. Kim, J. H., Komatsu, M., Shin-ya, K., Omura, S. & Ikeda, H. Distribution and functional analysis of the phosphopantetheinyl transferase superfamily in Actinomycetales microorganisms. Proc. Natl Acad. Sci. USA 115, 6828–6833 (2018).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  44. Komatsu, M., Uchiyama, T., Omura, S., Cane, D. E. & Ikeda, H. Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc. Natl Acad. Sci. USA 107, 2646–2651 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank H. Ikeda (Kitazato University) for providing vectors and the E. coli strain used for genetic manipulation of S. albidoflavus NBRC12854, and A. Katsuyama (Hokkaido University) for technical assistance in the conformational energy calculation. The synchrotron radiation experiments were performed at beamline BL-1A of the Photon Factory. We also thank the beamline staff of the Photon Factory for their help in collecting X-ray diffraction data. This work was partly supported by the Takeda Science Foundation, the Asahi Glass Foundation, the Naito Foundation, the Uehara Memorial Foundation, the Japan Agency for Medical Research and Development (AMED grant no. JP19ae0101045) and Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (JSPS KAKENHI grant nos. JP16703511, JP16H06443, JP18056499, JP19178402 and JP20H00490).

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Authors and Affiliations

  1. Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan

    Kenichi Matsuda, Masakazu Kobayashi, Ayae Sano & Toshiyuki Wakimoto

  2. Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Rui Zhai, Takahiro Mori & Ikuro Abe

  3. Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Takahiro Mori & Ikuro Abe

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Contributions

K.M., T.M., I.A. and T.W. designed the experiments. R.Z. and T.M. performed the crystallization experiment. K.M., R.Z., T.M. and M.K. performed in vitro analysis. K.M. performed kinetic analysis. M.K. and A.S. synthesized substrate analogues. K.M., M.K. and T.W. performed structure determination of enzyme reaction products. M.K. performed genetic manipulation of Streptomyces. K.M., R.Z., T.M., M.K., A.S., I.A. and T.W. analysed the data. K.M., T.M., I.A. and T.W. wrote the paper.

Corresponding authors

Correspondence to Ikuro Abe or Toshiyuki Wakimoto.

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Supplementary information

Supplementary Information

Supplementary Methods, Tables 1 and 2 and Figs. 1–41.

Reporting Summary

Supplementary Data Dataset 1

Model of N-formyl-d-Leu tethered on Ser63 of SurE apo structure.

Supplementary Data Dataset 2

Model of N-formyl-l-Leu tethered on Ser63 of SurE apo structure.

Supplementary Data Dataset 3

Model of I1P tethered on Ser63 of SurE holo structure.

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Matsuda, K., Zhai, R., Mori, T. et al. Heterochiral coupling in non-ribosomal peptide macrolactamization. Nat Catal 3, 507–515 (2020). https://doi.org/10.1038/s41929-020-0456-7

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