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A mass spectrometry–guided genome mining approach for natural product peptidogenomics

Nature Chemical Biology volume 7, pages 794–802 (2011)Cite this article

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Abstract

Peptide natural products show broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce here natural product peptidogenomics (NPP), a new MS–guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo tandem MS (MSn) structures to genomics-based structures following biosynthetic logic. In this study, we show that NPP enabled the rapid characterization of over ten chemically diverse ribosomal and nonribosomal peptide natural products of previously unidentified composition from Streptomycete bacteria as a proof of concept to begin automating the genome-mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which are from well-characterized model Streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms.

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Figure 1
Figure 2: General workflow of natural product peptidogenomics.
Figure 3: Peptidogenomic connection of a RNP chemotype with its biosynthetic genes in the characterization of the class III lantipeptide AmfS from S. griseus IFO 13350.
Figure 4: Peptidogenomic connection of a NRP chemotype with its biosynthetic genes in the characterization of the lipopeptide stendomycin complex from S. hygroscopicus ATCC 53653.

References

  1. Daffre, S. et al. Bioactive natural peptides. in Studies in Natural Products Chemistry, 1st edn., Vol. 35 (ed. Rahman, A.U.) 597–691 (Elsevier, 2008).

  2. Nolan, E.M. & Walsh, C.T. How nature morphs peptide scaffolds into antibiotics. ChemBioChem 10, 34–53 (2009).

    Article  CAS  Google Scholar 

  3. Donadio, S., Monciardini, P. & Sosio, M. Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat. Prod. Rep. 24, 1073–1109 (2007).

    Article  CAS  Google Scholar 

  4. Velásquez, J.E. & van der Donk, W.A. Genome mining for ribosomally synthesized natural products. Curr. Opin. Chem. Biol. 15, 11–21 (2011).

    Article  Google Scholar 

  5. Ganz, T. Defensins and host defense. Science 286, 420–421 (1999).

    Article  CAS  Google Scholar 

  6. Moore, B.S. Extending the biosynthetic repertoire in ribosomal peptide assembly. Angew. Chem. Int. Edn Engl. 47, 9386–9388 (2008).

    Article  CAS  Google Scholar 

  7. Willey, J.M. & van der Donk, W.A. Lantibiotics: peptides of diverse structure and function. Annu. Rev. Microbiol. 61, 477–501 (2007).

    Article  CAS  Google Scholar 

  8. Li, C. & Kelly, W.L. Recent advances in thiopeptide antibiotic biosynthesis. Nat. Prod. Rep. 27, 153–164 (2010).

    Article  CAS  Google Scholar 

  9. Donia, M.S., Ravel, J. & Schmidt, E.W. A global assembly line for cyanobactins. Nat. Chem. Biol. 4, 341–343 (2008).

    Article  CAS  Google Scholar 

  10. Duquesne, S. et al. Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli. Chem. Biol. 14, 793–803 (2007).

    Article  CAS  Google Scholar 

  11. Duquesne, S., Petit, V., Peduzzi, J. & Rebuffat, S. Structural and functional diversity of microcins, gene-encoded antibacterial peptides from enterobacteria. J. Mol. Microbiol. Biotechnol. 13, 200–209 (2007).

    Article  CAS  Google Scholar 

  12. Cotter, P.D., Hill, C. & Ross, R.P. Bacteriocins: developing innate immunity for food. Nat. Rev. Microbiol. 3, 777–788 (2005).

    Article  CAS  Google Scholar 

  13. Oman, T.J. & van der Donk, W.A. Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat. Chem. Biol. 6, 9–18 (2010).

    Article  CAS  Google Scholar 

  14. Challis, G.L., Ravel, J. & Townsend, C.A. Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem. Biol. 7, 211–224 (2000).

    Article  CAS  Google Scholar 

  15. Finn, R.D. et al. The Pfam protein families database. Nucleic Acids Res. 36, D281–D288 (2008).

    Article  CAS  Google Scholar 

  16. Winter, J.M., Behnken, S. & Hertweck, C. Genomics-inspired discovery of natural products. Curr. Opin. Chem. Biol. 15, 22–31 (2011).

    Article  CAS  Google Scholar 

  17. Lautru, S., Deeth, R.J., Bailey, L.M. & Challis, G.L. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat. Chem. Biol. 1, 265–269 (2005).

    Article  CAS  Google Scholar 

  18. Claesen, J. & Bibb, M. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc. Natl. Acad. Sci. USA 107, 16297–16302 (2010).

    Article  CAS  Google Scholar 

  19. Li, B. et al. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proc. Natl. Acad. Sci. USA 107, 10430–10435 (2010).

    Article  CAS  Google Scholar 

  20. Kodani, S. et al. The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. Proc. Natl. Acad. Sci. USA 101, 11448–11453 (2004).

    Article  CAS  Google Scholar 

  21. Gressler, M., Zaehle, C., Scherlach, K., Hertweck, C. & Brock, M. Multifactorial induction of an orphan PKS-NRPS gene cluster in Aspergillus terreus. Chem. Biol. 18, 198–209 (2011).

    Article  CAS  Google Scholar 

  22. Ng, J. et al. Dereplication and de novo sequencing of nonribosomal peptides. Nat. Methods 6, 596–599 (2009).

    Article  CAS  Google Scholar 

  23. Tsur, D., Tanner, S., Zandi, E., Bafna, V. & Pevzner, P.A. Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol. 23, 1562–1567 (2005).

    Article  CAS  Google Scholar 

  24. Duncan, M.W., Aebersold, R. & Caprioli, R.M. The pros and cons of peptide-centric proteomics. Nat. Biotechnol. 28, 659–664 (2010).

    Article  CAS  Google Scholar 

  25. Yang, Y.L., Xu, Y., Straight, P. & Dorrestein, P.C. Translating metabolic exchange with imaging mass spectrometry. Nat. Chem. Biol. 5, 885–887 (2009).

    Article  CAS  Google Scholar 

  26. Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).

    Article  CAS  Google Scholar 

  27. Ueda, K. et al. AmfS, an extracellular peptidic morphogen in Streptomyces griseus. J. Bacteriol. 184, 1488–1492 (2002).

    Article  CAS  Google Scholar 

  28. McIntosh, J.A., Donia, M.S. & Schmidt, E.W. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat. Prod. Rep. 26, 537–559 (2009).

    Article  CAS  Google Scholar 

  29. Ohnishi, Y. et al. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J. Bacteriol. 190, 4050–4060 (2008).

    Article  CAS  Google Scholar 

  30. Willey, J.M., Willems, A., Kodani, S. & Nodwell, J.R. Morphogenetic surfactants and their role in the formation of aerial hyphae in Streptomyces coelicolor. Mol. Microbiol. 59, 731–742 (2006).

    Article  CAS  Google Scholar 

  31. Wilkinson, B. & Micklefield, J. Biosynthesis of nonribosomal peptide precursors. Methods Enzymol. 458, 353–378 (2009).

    Article  CAS  Google Scholar 

  32. Romano, A., Vitullo, D., Di Pietro, A., Lima, G. & Lanzotti, V. Antifungal lipopeptides from Bacillus amyloliquefaciens strain BO7. J. Nat. Prod. 74, 145–151 (2011).

    Article  CAS  Google Scholar 

  33. Li, M.H., Ung, P.M., Zajkowski, J., Garneau-Tsodikova, S. & Sherman, D.H. Automated genome mining for natural products. BMC Bioinformatics 10, 185 (2009).

    Article  Google Scholar 

  34. Medema, M.H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Res. 39, W339–W346 (2011).

    Article  CAS  Google Scholar 

  35. Bodanszky, M., Izdebski, J. & Muramatsu, I. Structure of the peptide antibiotic stendomycin. J. Am. Chem. Soc. 91, 2351–2358 (1969).

    Article  CAS  Google Scholar 

  36. Strieker, M. & Marahiel, M.A. The structural diversity of acidic lipopeptide antibiotics. ChemBioChem 10, 607–616 (2009).

    Article  CAS  Google Scholar 

  37. Roongsawang, N., Washio, K. & Morikawa, M. Diversity of nonribosomal peptide synthetases involved in the biosynthesis of lipopeptide biosurfactants. Int. J. Mol. Sci. 12, 141–172 (2010).

    Article  Google Scholar 

  38. Visca, P., Imperi, F. & Lamont, I.L. Pyoverdine siderophores: from biogenesis to biosignificance. Trends Microbiol. 15, 22–30 (2007).

    Article  CAS  Google Scholar 

  39. Liu, W.T., Kersten, R.D., Yang, Y.L., Moore, B.S. & Dorrestein, P.C. Imaging mass spectrometry and genome mining via short sequence tagging identified the anti-infective agent arylomycin in Streptomyces roseosporus. J. Am. Chem. Soc. (in the press).

  40. 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 

  41. Kawulka, K.E. et al. Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to α-carbon cross-links: formation and reduction of α-thio-α-amino acid derivatives. Biochemistry 43, 3385–3395 (2004).

    Article  CAS  Google Scholar 

  42. Knappe, T.A., Linne, U., Xie, X. & Marahiel, M.A. The glucagon receptor antagonist BI-32169 constitutes a new class of lasso peptides. FEBS Lett. 584, 785–789 (2010).

    Article  CAS  Google Scholar 

  43. Bentley, S.D. et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147 (2002).

    Article  Google Scholar 

  44. Nett, M., Ikeda, H. & Moore, B.S. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep. 26, 1362–1384 (2009).

    Article  CAS  Google Scholar 

  45. Vats, P. & Rothfield, L. Duplication and segregation of the actin (MreB) cytoskeleton during the prokaryotic cell cycle. Proc. Natl. Acad. Sci. USA 104, 17795–17800 (2007).

    Article  CAS  Google Scholar 

  46. Miao, V. et al. Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology 151, 1507–1523 (2005).

    Article  CAS  Google Scholar 

  47. Koal, T. & Deigner, H.P. Challenges in mass spectrometry based targeted metabolomics. Curr. Mol. Med. 10, 216–226 (2010).

    Article  CAS  Google Scholar 

  48. Warren, A.S., Archuleta, J., Feng, W.C. & Setubal, J.C. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics 11, 131 (2010).

    Article  Google Scholar 

  49. Röttig, M. et al. NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39, W362–W367 (2011).

    Article  Google Scholar 

  50. Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank N. Castellana and V. Bafna for providing the algorithm to enable the six-frame translations of supercontigs. We also thank M. Meehan for FTMS training. Financial support was provided by the US National Institutes of Health (GM085770 to B.S.M. and GM086283 to P.C.D.) and the Beckman Foundation.

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Authors and Affiliations

  1. Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA

    Roland D Kersten, Sang-Jip Nam, William Fenical, Bradley S Moore & Pieter C Dorrestein

  2. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA

    Yu-Liang Yang, Yuquan Xu, William Fenical, Bradley S Moore & Pieter C Dorrestein

  3. Department of Bioengineering and Therapeutic Sciences and California Institute of Quantitative Biosciences, University of California, San Francisco, California, USA

    Peter Cimermancic & Michael A Fischbach

  4. Department of Pharmacology and Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA

    Pieter C Dorrestein

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Contributions

R.D.K. designed and carried out experiments, analyzed data and wrote the paper. Y.-L.Y., Y.X. and S.-J.N. carried out experiments and analyzed data. P.C. and M.A.F. carried out the bioinformatic analysis and analyzed data. W.F. analyzed data. B.S.M. and P.C.D. designed experiments, analyzed data and wrote the paper.

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Correspondence to Bradley S Moore or Pieter C Dorrestein.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods, Supplementary Results, Supplementary Tables 1–13 and Supplementary Figures 1–17 (PDF 7941 kb)

Supplementary Table 6

Mass shifts of RNP monomers and modifications and their corresponding precursor amino acids in precursor peptides (XLS 38 kb)

Supplementary Table 7

Mass shifts of NRP monomers (NORINE monomer list excluding lipids) and corresponding NRPS monomers and genome mining accessibility by NRPSpredictor2 (AntiSMASH, * - biosynthetic monomers can be putative due to lack of biosynthetic knowledge) (XLS 75 kb)

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Kersten, R., Yang, YL., Xu, Y. et al. A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 7, 794–802 (2011). https://doi.org/10.1038/nchembio.684

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