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:

Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance

Nature Microbiology volume 4, pages 1862–1871 (2019)Cite this article

Subjects

Abstract

Glycopeptide antibiotics are produced by Actinobacteria through biosynthetic gene clusters that include genes supporting their regulation, synthesis, export and resistance. The chemical and biosynthetic diversities of glycopeptides are the product of an intricate evolutionary history. Extracting this history from genome sequences is difficult as conservation of the individual components of these gene clusters is variable and each component can have a different trajectory. We show that glycopeptide biosynthesis and resistance in Actinobacteria maps to approximately 150–400 million years ago. Phylogenetic reconciliation reveals that the precursors of glycopeptide biosynthesis are far older than other components, implying that these clusters arose from a pre-existing pool of genes. We find that resistance appeared contemporaneously with biosynthetic genes, raising the possibility that the mechanism of action of glycopeptides was a driver of diversification in these gene clusters. Our results put antibiotic biosynthesis and resistance into an evolutionary context and can guide the future discovery of compounds possessing new mechanisms of action, which are especially needed as the usefulness of the antibiotics available at present is imperilled by human activity.

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: GPAs, BGC evolution and precursor biosynthesis.
Fig. 2: Species phylogeny and reconciliation.
Fig. 3: Reconciliation dates of GPA precursor biosynthesis.
Fig. 4: Phylogeny and reconciliation of the dates of the GPA scaffold A-domain.
Fig. 5: Reconciliation dates of GPA tailoring, resistance and regulation.
Fig. 6: Summary of the major events in the evolution of GPA BGCs inferred from reconciliation.

Similar content being viewed by others

Data availability

All genome sequences produced for this study (22 organisms) have been deposited to GenBank under the BioProject accession number PRJNA472056. The source of every BGC is listed in Supplementary Table 1. The dates for all nodes in all of the dated trees are provided in Supplementary Table 2. The input BGC sequences, 16S rRNA sequences, 16S rRNA alignment, 16S rRNA tree, concatenated TIGRFAM core genome sequence alignment, all dated BEAST species trees, extracted gene/domain family sequences, annotated gene/domain families, gene/domain family alignments, gene/domain family trees and all reconciliations (scheme A00, A10, B00, B10, C01 and C03) are available at http://github.com/waglecn/GPA_evolution.

Code availability

Reconciliations were visualized by overlaying the reconciled nodes of each gene tree to the species tree using a custom Python script, which is available at http://github.com/waglecn/GPA_evolution.

References

  1. Thaker, M. N. et al. Identifying producers of antibacterial compounds by screening for antibiotic resistance. Nat. Biotechnol. 31, 922–927 (2013).

    Article  CAS  PubMed  Google Scholar 

  2. Weber, T. et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W237–W243 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Skinnider, M. A., Merwin, N. J., Johnston, C. W. & Magarvey, N. A. PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. Nucleic Acids Res. 45, W49–W54 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cruz-Morales, P. et al. Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes. Genome Biol. Evol. 8, 1906–1916 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Marshall, C. G., Broadhead, G., Leskiw, B. K. & Wright, G. D. d-Ala-d-Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB. Proc. Natl Acad. Sci. USA 94, 6480–6483 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nicolaou, K. C., Boddy, C. N., Brase, S. & Winssinger, N. Chemistry, biology, and medicine of the glycopeptide antibiotics. Angew. Chem. Int. Ed. 38, 2096–2152 (1999).

    Article  CAS  Google Scholar 

  7. Chen, H., Tseng, C. C., Hubbard, B. K. & Walsh, C. T. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc. Natl Acad. Sci. USA 98, 14901–14906 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Yim, G., Thaker, M. N., Koteva, K. & Wright, G. Glycopeptide antibiotic biosynthesis. J. Antibiot. 67, 31–41 (2014).

    Article  CAS  Google Scholar 

  9. Lo Grasso, L. et al. Two master switch regulators trigger A40926 biosynthesis in Nonomuraea sp. strain ATCC 39727. J. Bacteriol. 197, 2536–2544 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kilian, R., Frasch, H. J., Kulik, A., Wohlleben, W. & Stegmann, E. The VanRS homologous two-component system VnlRSAb of the glycopeptide producer Amycolatopsis balhimycina activates transcription of the vanHAX Sc genes in Streptomyces coelicolor, but not in A. balhimycina. Micro. Drug Resist. 22, 499–509 (2016).

    Article  CAS  Google Scholar 

  11. Chevrette, M. G. & Currie, C. R. Emerging evolutionary paradigms in antibiotic discovery. J. Ind. Microbiol. Biotechnol. 46, 257–271 (2018).

  12. Selengut, J. D. et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 35, D260–D264 (2007).

    Article  CAS  PubMed  Google Scholar 

  13. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jombart, T., Kendall, M., Almagro-Garcia, J. & Colijn, C. treespace: statistical exploration of landscapes of phylogenetic trees. Mol. Ecol. Resour. 17, 1385–1392 (2017).

  17. Battistuzzi, F. U., Feijao, A. & Hedges, S. B. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4, 44 (2004).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. McDonald, B. R. & Currie, C. R. Lateral gene transfer dynamics in the ancient bacterial genus Streptomyces. mBio 8, 00644-17 (2017).

  19. Cimermancic, P. et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412–421 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Goodman, M., Czelusniak, J., Moore, G. W., Romero-Herrera, A. E. & Matsuda, G. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Biol. 28, 132–163 (1979).

    Article  CAS  Google Scholar 

  21. Stolzer, M., Siewert, K., Lai, H., Xu, M. & Durand, D. Event inference in multidomain families with phylogenetic reconciliation. BMC Bioinform. 16, S8 (2015).

  22. Libeskind-Hadas, R., Wu, Y. C., Bansal, M. S. & Kellis, M. Pareto-optimal phylogenetic tree reconciliation. Bioinformatics 30, i87–i95 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jacox, E., Chauve, C., Szollosi, G. J., Ponty, Y. & Scornavacca, C. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32, 2056–2058 (2016).

    Article  CAS  PubMed  Google Scholar 

  24. Stinchi, S. et al. A derivative of the glycopeptide A40926 produced by inactivation of the β-hydroxylase gene in Nonomuraea sp. ATCC39727. FEMS Microbiol. Lett. 256, 229–235 (2006).

    Article  CAS  PubMed  Google Scholar 

  25. Hoertz, A. J., Hamburger, J. B., Gooden, D. M., Bednar, M. M. & McCafferty, D. G. Studies on the biosynthesis of the lipodepsipeptide antibiotic Ramoplanin A2. Bioorg. Med. Chem. 20, 859–865 (2012).

    Article  CAS  PubMed  Google Scholar 

  26. Chen, H. et al. Deoxysugars in glycopeptide antibiotics: enzymatic synthesis of TDP-l-epivancosamine in chloroeremomycin biosynthesis. Proc. Natl Acad. Sci. USA 97, 11942–11947 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Thibodeaux, C. J., Melancon, C. E.III & Liu, H. W. Natural-product sugar biosynthesis and enzymatic glycodiversification. Angew. Chem. Int. Ed. 47, 9814–9859 (2008).

    Article  CAS  Google Scholar 

  28. Medema, M. H., Cimermancic, P., Sali, A., Takano, E. & Fischbach, M. A. A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PLoS Comput. Biol. 10, e1004016 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Banik, J. J., Craig, J. W., Calle, P. Y. & Brady, S. F. Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products. J. Am. Chem. Soc. 132, 15661–15670 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Yim, G., Wang, W., Thaker, M. N., Tan, S. & Wright, G. D. How to make a glycopeptide: a synthetic biology approach to expand antibiotic chemical diversity. ACS Infect. Dis. 2, 642–650 (2016).

    Article  CAS  PubMed  Google Scholar 

  31. Truman, A. W. et al. Chimeric glycosyltransferases for the generation of hybrid glycopeptides. Chem. Biol. 16, 676–685 (2009).

    Article  CAS  PubMed  Google Scholar 

  32. Truman, A. W., Robinson, L. & Spencer, J. B. Identification of a deacetylase involved in the maturation of teicoplanin. Chembiochem 7, 1670–1675 (2006).

    Article  CAS  PubMed  Google Scholar 

  33. Stegmann, E., Frasch, H. J., Kilian, R. & Pozzi, R. Self-resistance mechanisms of actinomycetes producing lipid II-targeting antibiotics. Int. J. Med. Microbiol. 305, 190–195 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Baltz, R. Antibiotic discovery from actinomycetes: will a renaissance follow the decline and fall? SIM News 55, 186–196 (2005).

    Google Scholar 

  35. Joynt, R. & Seipke, R. F. A phylogenetic and evolutionary analysis of antimycin biosynthesis. Microbiology 164, 28–39 (2018).

    Article  CAS  PubMed  Google Scholar 

  36. Kirst, H. A., Thompson, D. G. & Nicas, T. I. Historical yearly usage of vancomycin. Antimicrob. Agents Chemother. 42, 1303–1304 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Leclercq, R., Derlot, E., Duval, J. & Courvalin, P. Plasmid-mediated resistance to vancomycin and teicoplanin in Enterococcus faecium. N. Engl. J. Med. 319, 157–161 (1988).

    Article  CAS  PubMed  Google Scholar 

  38. Jiang, H., Lei, R., Ding, S. W. & Zhu, S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinform. 15, 182 (2014).

    Article  Google Scholar 

  39. Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).

    Article  CAS  PubMed  Google Scholar 

  42. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Blin, K. et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45, W36–W41 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).

    Article  CAS  Google Scholar 

  45. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    Article  CAS  PubMed  Google Scholar 

  46. Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642 (2014).

    Article  CAS  PubMed  Google Scholar 

  48. Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ayres, D. L. et al. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 61, 170–173 (2012).

    Article  PubMed  Google Scholar 

  50. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  52. To, T. H., Jacox, E., Ranwez, V. & Scornavacca, C. A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality. BMC Bioinform. 16, 384 (2015).

    Article  Google Scholar 

Download references

Acknowledgements

C. Groves provided valuable input on the figures. This research was funded by the Canadian Institutes of Health Research (grant no. MT-14981) and by a Canada Research Chair (to G.D.W.). N.W. was supported by a Canadian Institutes of Health Research graduate scholarship. A.G.M. holds a Cisco Research Chair in Bioinformatics, supported by Cisco Systems Canada, Inc. Some computer resources were provided by the McMaster Service Lab and Repository computing cluster, funded in part by grants from the Canadian Foundation for Innovation (grant no. 34531 to A.G.M.).

Author information

Authors and Affiliations

  1. David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada

    Nicholas Waglechner, Andrew G. McArthur & Gerard D. Wright

Authors
  1. Nicholas Waglechner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew G. McArthur
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gerard D. Wright
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

N.W. and G.D.W. conceived the project. N.W., G.D.W. and A.G.M. designed the experiments. N.W. collected and analysed the sequences, and constructed phylogenies and phylogenetic reconciliations. N.W., A.G.M. and G.D.W. interpreted the results and wrote the manuscript.

Corresponding author

Correspondence to Gerard D. Wright.

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 Figs. 1–7, Supplementary Table 3, Supplementary Table 4 and Supplementary References.

Reporting Summary

Supplementary Table 1

Description of organisms, clusters, sequences used in this study.

Supplementary Table 2

Time tree node details.

Supplementary Table 5

Node reconciliation details.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Waglechner, N., McArthur, A.G. & Wright, G.D. Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance. Nat Microbiol 4, 1862–1871 (2019). https://doi.org/10.1038/s41564-019-0531-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-019-0531-5

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

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