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De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner
doi: https://doi.org/10.1101/521872
Bahar Behsaz
1Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, USA
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Hosein Mohimani
2Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
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Alexey Gurevich
3Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
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Andrey Prjibelski
3Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
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Mark F. Fisher
4The University of Western Australia, School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
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Larry Smarr
2Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
5California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, USA
6Center for Microbiome Innovation, University of California at San Diego, La Jolla, USA
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Pieter C. Dorrestein
6Center for Microbiome Innovation, University of California at San Diego, La Jolla, USA
7Department of Pharmacology, University of California at San Diego, La Jolla, USA
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Joshua S. Mylne
4The University of Western Australia, School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
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Pavel A. Pevzner
2Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
3Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
6Center for Microbiome Innovation, University of California at San Diego, La Jolla, USA
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ABSTRACT

Cyclic and branch cyclic peptides (cyclopeptides) represent an important class of bioactive natural products that include many antibiotics and anti-tumor compounds. However, little is known about cyclopeptides in the human gut, despite the fact that humans are constantly exposed to them. To address this bottleneck, we developed the CycloNovo algorithm for de novo cyclopeptide sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms. CycloNovo reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. Our benchmarking revealed a vast hidden cyclopeptidome in the human gut and other environments and suggested that CycloNovo offers a much-needed step-change for cyclopeptide discovery. Furthermore, CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.

SIGNIFICANCE The golden age of antibiotics was followed by a decline in the pace of antibiotics discovery in the 1990s. The key prerequisite for the resurgence of antibiotics research is the development of a computational discovery pipeline for antibiotics sequencing. We describe such pipeline for cyclic and branch cyclic peptides (cyclopeptides) that represent an important class of bioactive natural products such as antibiotics and anti-tumor compounds. Our CycloNovo algorithm for cyclopeptide sequencing reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 20, 2019.
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De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner
bioRxiv 521872; doi: https://doi.org/10.1101/521872
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De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner
bioRxiv 521872; doi: https://doi.org/10.1101/521872

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