Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains

Nature Chemistry volume 11, pages 653–661 (2019)Cite this article

Subjects

Abstract

Non-ribosomal peptide synthetases (NRPSs) are giant enzyme machines that activate amino acids in an assembly line fashion. As NRPSs are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would enable microbial production of a diverse range of peptides; however, the structural requirements for reprogramming NRPSs to facilitate the production of new peptides are not clear. Here we describe a new fusion point inside the condensation domains of NRPSs that results in the development of the exchange unit condensation domain (XUC) concept, which enables the efficient production of peptides, even containing non-natural amino acids, in yields up to 280 mg l−1. This allows the generation of more specific NRPSs, reducing the number of unwanted peptide derivatives, but also the generation of peptide libraries. The XUC might therefore be suitable for the future optimization of peptide production and the identification of bioactive peptide derivatives for pharmaceutical and other applications.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Modulation of C domain substrate specificity.
Fig. 2: Design of recombinant NRPS for peptide production.
Fig. 3: Elongation XUCs can be used as starting XUC.
Fig. 4: Creation of functionalized xenotetrapeptide derivatives.
Fig. 5: Targeted randomization of GxpS.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available from the corresponding author upon request.

References

  1. Clardy, J., Fischbach, M. A. & Walsh, C. T. New antibiotics from bacterial natural products. Nat. Biotechnol. 24, 1541–1550 (2006).

    Article  CAS  Google Scholar 

  2. von Nussbaum, F., Brands, M., Hinzen, B., Weigand, S. & Häbich, D. Antibacterial natural products in medicinal chemistry—exodus or revival? Angew. Chem. Int. Ed. 45, 5072–5129 (2006).

    Article  Google Scholar 

  3. Nathan, C. Antibiotics at the crossroads. Nature 431, 899–902 (2004).

    Article  CAS  Google Scholar 

  4. Felnagle, E. A. et al. Nonribosomal peptide synthetases involved in the production of medically relevant natural products. Mol. Pharmaceut. 5, 191–211 (2008).

    Article  CAS  Google Scholar 

  5. 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  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. O’Connell, K. M. G. et al. Combating multidrug-resistant bacteria: current strategies for the discovery of novel antibacterials. Angew. Chem. Int. Ed. 52, 10706–10733 (2013).

    Article  Google Scholar 

  8. Bush, K. Improving known classes of antibiotics: an optimistic approach for the future. Curr. Opin. Pharmacol. 12, 527–534 (2012).

    Article  CAS  Google Scholar 

  9. Kirschning, A. & Hahn, F. Merging chemical synthesis and biosynthesis: a new chapter in the total synthesis of natural products and natural product libraries. Angew. Chem. Int. Ed. 51, 4012–4022 (2012).

    Article  CAS  Google Scholar 

  10. Baltz, R. H. Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways. ACS Synth. Biol. 3, 748–758 (2014).

    Article  CAS  Google Scholar 

  11. Winn, M., Fyans, J. K., Zhuo, Y. & Micklefield, J. Recent advances in engineering nonribosomal peptide assembly lines. Nat. Prod. Rep. 33, 317–347 (2016).

    Article  CAS  Google Scholar 

  12. Caboche, S., Leclere, V., Pupin, M., Kucherov, G. & Jacques, P. Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity. J. Bacteriol. 192, 5143–5150 (2010).

    Article  CAS  Google Scholar 

  13. Grünewald, J. & Marahiel, M. A. Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides. Microbiol. Mol. Biol. Rev. 70, 121–146 (2006).

    Article  Google Scholar 

  14. Cane, D. E., Walsh, C. T. & Khosla, C. Harnessing the biosynthetic code: combinations, permutations and mutations. Science 282, 63–68 (1998).

    Article  CAS  Google Scholar 

  15. Mootz, H. D., Schwarzer, D. & Marahiel, M. A. Ways of assembling complex natural products on modular nonribosomal peptide synthetases. ChemBioChem 3, 490–504 (2002).

    Article  CAS  Google Scholar 

  16. Süssmuth, R. D. & Mainz, A. Nonribosomal peptide synthesis—principles and prospects. Angew. Chem. Int. Ed. 56, 3770–3821 (2017).

    Article  Google Scholar 

  17. Balibar, C. J., Vaillancourt, F. H. & Walsh, C. T. Generation of d amino acid residues in assembly of arthrofactin by dual condensation/epimerization domains. Chem. Biol. 12, 1189–1200 (2005).

    Article  CAS  Google Scholar 

  18. Stachelhaus, T., Schneider, A. & Marahiel, M. A. Rational design of peptide antibiotics by targeted replacement of bacterial and fungal domains. Science 269, 69–72 (1995).

    Article  CAS  Google Scholar 

  19. Calcott, M. J., Owen, J. G., Lamont, I. L. & Ackerley, D. F. Biosynthesis of novel pyoverdines by domain substitution in a nonribosomal peptide synthetase of Pseudomonas aeruginosa. Appl. Environ. Microbiol. 80, 5723–5731 (2014).

    Article  Google Scholar 

  20. Thirlway, J. et al. Introduction of a non-natural amino acid into a nonribosomal peptide antibiotic by modification of adenylation domain specificity. Angew. Chem. Int. Ed. 51, 7181–7184 (2012).

    Article  CAS  Google Scholar 

  21. Kries, H. et al. Reprogramming nonribosomal peptide synthetases for ‘clickable’ amino acids. Angew. Chem. Int. Ed. 53, 10105–10108 (2014).

    Article  CAS  Google Scholar 

  22. Nguyen, K. T. et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin. Proc. Natl Acad. Sci. USA 103, 17462–17467 (2006).

    Article  CAS  Google Scholar 

  23. Yakimov, M. M., Giuliano, L., Timmis, K. N. & Golyshin, P. N. Recombinant acylheptapeptide lichenysin: high level of production by Bacillus subtilis cells. J. Mol. Microbiol. Biotechnol. 2, 217–224 (2000).

    CAS  PubMed  Google Scholar 

  24. Beer, R. et al. Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange. Mol. BioSyst. 10, 1709–1710 (2014).

    Article  CAS  Google Scholar 

  25. Calcott, M. J. & Ackerley, D. F. Portability of the thiolation domain in recombinant pyoverdine non-ribosomal peptide synthetases. BMC Microbiol. 15, 1–13 (2015).

    Article  CAS  Google Scholar 

  26. Chiocchini, C., Linne, U. & Stachelhaus, T. In vivo biocombinatorial synthesis of lipopeptides by COM domain-mediated reprogramming of the surfactin biosynthetic complex. Chem. Biol. 13, 899–908 (2006).

    Article  CAS  Google Scholar 

  27. Duerfahrt, T., Doekel, S., Sonke, T., Quaedflieg, P. J. L. M. & Marahiel, M. A. Construction of hybrid peptide synthetases for the production of alpha-l-aspartyl-l-phenylalanine, a precursor for the high-intensity sweetener aspartame. Eur. J. Biochem. 270, 4555–4563 (2003).

    Article  CAS  Google Scholar 

  28. Brown, A. S., Calcott, M. J., Owen, J. G. & Ackerley, D. F. Structural, functional and evolutionary perspectives on effective re-engineering of non-ribosomal peptide synthetase assembly lines. Nat. Prod. Rep. 49, 104–119 (2018).

    Google Scholar 

  29. Kries, H. Biosynthetic engineering of nonribosomal peptide synthetases. J. Pept. Sci. 22, 564–570 (2016).

    Article  CAS  Google Scholar 

  30. Bozhüyük, K. A. J. et al. De novo design and engineering of non-ribosomal peptide synthetases. Nat. Chem. 10, 275–281 (2018).

    Article  Google Scholar 

  31. Linne, U. & Marahiel, M. A. Control of directionality in nonribosomal peptide synthesis: role of the condensation domain in preventing misinitiation and timing of epimerization. Biochemistry 39, 10439–10447 (2000).

    Article  CAS  Google Scholar 

  32. Bode, H. B. et al. Determination of the absolute configuration of peptide natural products by using stable isotope labeling and mass spectrometry. Chem. Eur. J. 18, 2342–2348 (2012).

    Article  CAS  Google Scholar 

  33. Nollmann, F. I. et al. Insect-specific production of new GameXPeptides in Photorhabdus luminescens TTO1, widespread natural products in entomopathogenic bacteria. ChemBioChem 16, 205–208 (2015).

    Article  CAS  Google Scholar 

  34. Fuchs, S. W. et al. Neutral loss fragmentation pattern based screening for arginine-rich natural products in Xenorhabdus and Photorhabdus. Anal. Chem. 84, 6948–6955 (2012).

    Article  CAS  Google Scholar 

  35. Samel, S. A., Schoenafinger, G., Knappe, T. A., Marahiel, M. A. & Essen, L.-O. Structural and functional insights into a peptide bond-forming bidomain from a nonribosomal peptide synthetase. Structure 15, 781–792 (2007).

    Article  CAS  Google Scholar 

  36. Keating, T. A., Marshall, C. G., Walsh, C. T. & Keating, A. E. The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains. Nat. Struct. Biol. 9, 522–526 (2002).

    CAS  PubMed  Google Scholar 

  37. Tanovic, A., Samel, S. A., Essen, L.-O. & Marahiel, M. A. Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 321, 659–663 (2008).

    Article  CAS  Google Scholar 

  38. Bloudoff, K., Rodionov, D. & Schmeing, T. M. Crystal structures of the first condensation domain of CDA synthetase suggest conformational changes during the synthetic cycle of nonribosomal peptide synthetases. J. Mol. Biol. 425, 3137–3150 (2013).

    Article  CAS  Google Scholar 

  39. Rausch, C., Hoof, I., Weber, T., Wohlleben, W. & Huson, D. H. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evol. Biol. 7, 78 (2007).

    Article  Google Scholar 

  40. Marahiel, M. A. A structural model for multimodular NRPS assembly lines. Nat. Prod. Rep. 33, 136–140 (2016).

    Article  CAS  Google Scholar 

  41. Konz, D., Klens, A., Schörgendorfer, K. & Marahiel, M. A. The bacitracin biosynthesis operon of Bacillus licheniformis ATCC 10716: molecular characterization of three multi-modular peptide synthetases. Chem. Biol. 4, 927–937 (1997).

    Article  CAS  Google Scholar 

  42. Cosmina, P. et al. Sequence and analysis of the genetic locus responsible for surfactin synthesis in Bacillus subtilis. Mol. Microbiol. 8, 821–831 (1993).

    Article  CAS  Google Scholar 

  43. Krätzschmar, J., Krause, M. & Marahiel, M. A. Gramicidin S biosynthesis operon containing the structural genes grsA and grsB has an open reading frame encoding a protein homologous to fatty acid thioesterases. J. Bacteriol. 171, 5422–5429 (1989).

    Article  Google Scholar 

  44. Mootz, H. D. & Marahiel, M. A. The tyrocidine biosynthesis operon of Bacillus brevis: complete nucleotide sequence and biochemical characterization of functional internal adenylation domains. J. Bacteriol. 179, 6843–6850 (1997).

    Article  CAS  Google Scholar 

  45. Li, R., Oliver, R. A. & Townsend, C. A. Identification and characterization of the sulfazecin monobactam biosynthetic gene cluster. Cell Chem. Biol. 24, 24–34 (2017).

    Article  CAS  Google Scholar 

  46. Meyer, S. et al. Biochemical dissection of the natural diversification of microcystin provides lessons for synthetic biology of NRPS. Cell Chem. Biol. 23, 462–471 (2016).

    Article  CAS  Google Scholar 

  47. Schimming, O., Fleischhacker, F., Nollmann, F. I. & Bode, H. B. Yeast homologous recombination cloning leading to the novel peptides ambactin and xenolindicin. ChemBioChem 15, 1290–1294 (2014).

    Article  CAS  Google Scholar 

  48. Roy, A. D., Grüschow, S., Cairns, N. & Goss, R. J. M. Gene expression enabling synthetic diversification of natural products: chemogenetic generation of pacidamycin analogs. J. Am. Chem. Soc. 132, 12243–12245 (2010).

    Article  CAS  Google Scholar 

  49. Sletten, E. M. & Bertozzi, C. R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Ed. 48, 6974–6998 (2009).

    Article  CAS  Google Scholar 

  50. Kolb, H. C., Finn, M. G. & Sharpless, K. B. Click‐chemie: diverse chemische Funktionalität mit einer Handvoll guter Reaktionen. Angew. Chem. 113, 2056–2075 (2001).

    Article  Google Scholar 

  51. Pérez, A. J., Wesche, F., Adihou, H. & Bode, H. B. Solid-phase enrichment and analysis of azide-labeled natural products: fishing downstream of biochemical pathways. Chem. Eur. J. 22, 639–645 (2016).

    Article  Google Scholar 

  52. Pérez, A. J. & Bode, H. B. ‘Click chemistry’ for the simple determination of fatty-acid uptake and degradation: revising the role of fatty-acid transporters. ChemBioChem 16, 1588–1591 (2015).

    Article  Google Scholar 

  53. Kronenwerth, M. et al. Characterisation of taxlllaids A-G; natural products from Xenorhabdus indica. Chem. Eur. J. 20, 17478–17487 (2014).

    Article  CAS  Google Scholar 

  54. Phelan, V. V., Du, Y., McLean, J. A. & Bachmann, B. O. Adenylation enzyme characterization using gamma-(18)O(4)-ATP pyrophosphate exchange. Chem. Biol. 16, 473–478 (2009).

    Article  CAS  Google Scholar 

  55. Kegler, C. et al. Rapid determination of the amino acid configuration of xenotetrapeptide. ChemBioChem 15, 826–828 (2014).

    Article  CAS  Google Scholar 

  56. Harvey, A. L., Edrada-Ebel, R. & Quinn, R. J. The re-emergence of natural products for drug discovery in the genomics era. Nat. Rev. Drug Discov. 14, 111–129 (2015).

    Article  CAS  Google Scholar 

  57. Gietz, R. D. & Schiestl, R. H. Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 1–4 (2007).

    Article  CAS  Google Scholar 

  58. Bode, H. B. et al. Structure elucidation and activity of kolossin A, the d-/l-pentadecapeptide product of a giant nonribosomal peptide synthetase. Angew. Chem. Int. Ed. 54, 10352–10355 (2015).

    Article  CAS  Google Scholar 

  59. Fuchs, S. W., Proschak, A., Jaskolla, T. W., Karas, M. & Bode, H. B. Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila. Org. Biomol. Chem. 9, 3130–3132 (2011).

    Article  CAS  Google Scholar 

  60. Horsman, M. E., Hari, T. P. A. & Boddy, C. N. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat. Prod. Rep. 33, 183–202 (2016).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank M. Lindner and C. Zizka for help with the construction of selected plasmids and C. Kegler for helpful discussions. This work was funded in part by the LOEWE programme of the state of Hesse as part of the MegaSyn and TBG research clusters. H.B.B. acknowledges the Deutsche Forschungsgemeinschaft for funding of the Impact II qTof mass spectrometer (INST 161/810-1).

Author information

Author notes

  1. These authors contributed equally: Kenan A. J. Bozhüyük, Annabell Linck, Andreas Tietze, Janik Kranz.

Authors and Affiliations

  1. Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main,, Germany

    Kenan A. J. Bozhüyük, Annabell Linck, Andreas Tietze, Janik Kranz, Frank Wesche, Sarah Nowak, Florian Fleischhacker, Yan-Ni Shi, Peter Grün & Helge B. Bode

  2. Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main,, Germany

    Helge B. Bode

Authors
  1. Kenan A. J. Bozhüyük
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Annabell Linck
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andreas Tietze
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Janik Kranz
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Frank Wesche
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sarah Nowak
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Florian Fleischhacker
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yan-Ni Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Peter Grün
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Helge B. Bode
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.A.J.B. and H.B.B. designed the experiments. K.A.J.B., A.L., A.T., J.K., S.N. and F.F. performed all molecular biology and biochemical experiments. F.W. synthesized all peptide standards that were used for the high-performance liquid chromatography–mass spectrometry-based quantification performed by A.L. and A.T. J.K., Y.-N.S. and P.G. isolated selected peptides and Y.-N.S. performed their NMR analysis. All authors analysed the results and K.A.J.B., A.L., A.T., J.K. and H.B.B. wrote the manuscript. All authors saw and approved the manuscript.

Corresponding author

Correspondence to Helge B. Bode.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Supplementary Information

Supplementary Information includes methods, Supplementary Tables 1–7 (containing mass spectrometry data of the produced peptides, strains, plasmids and oligonucleotides used in this study) and Supplementary Figs. 1–42 (including NMR spectra of new peptides).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bozhüyük, K.A.J., Linck, A., Tietze, A. 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). https://doi.org/10.1038/s41557-019-0276-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41557-019-0276-z

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing