De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments

peer-reviewed · Cell Systems · 2020

peer-reviewed · Cell Systems · 2020. Bahar Behsaz et al. Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that…
Date 2020-01-22
Type peer-reviewed
Venue Cell Systems
Publisher Elsevier BV
Contribution algorithm
DOI 10.1016/j.cels.2019.11.007
Citations (OpenAlex) 43
Venue 2-year citedness 6.21

Preprint version: De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments (2019-01-16, bioRxiv)

Abstract

Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo.

Authors

  1. Bahar Behsaz · University of California San Diego
  2. Hosein Mohimani · Carnegie Mellon University, University of California San Diego
  3. Alexey Gurevich · St Petersburg University, St. Petersburg State University
  4. Andrey Prjibelski · St Petersburg University, St. Petersburg State University
  5. Mark Fisher · ARC Centre of Excellence in Plant Energy Biology, University of Western Australia
  6. Fernando Vargas · University of California San Diego
  7. Larry Smarr · University of California San Diego
  8. Pieter C. Dorrestein · Scripps Institution of Oceanography, University of California San Diego, University of California System
  9. Joshua S. Mylne · ARC Centre of Excellence in Plant Energy Biology, University of Western Australia
  10. Pavel A. Pevzner · Max Planck Institute of Molecular Cell Biology and Genetics, Saint Petersburg Academic University, St Petersburg University, St. Petersburg State University, University of California San Diego, University of Southern California

Methods and tools

Data used

  • GNPS - KendrickMassFilter_EvaluationDataset_PUBLIC (as deposited) · MSV000081544
  • GNPS - Streptomyces on A1, MS and R5 agar (as deposited) · MSV000078839

Cites (3)

Cited by (5)

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