IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v6y2015i1d10.1038_ncomms9421.html
   My bibliography  Save this article

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

Author

Listed:
  • Chad W. Johnston

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

  • Michael A. Skinnider

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

  • Morgan A. Wyatt

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

  • Xiang Li

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

  • Michael R. M. Ranieri

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

  • Lian Yang

    (The David R. Cheriton School of Computer Science, University of Waterloo)

  • David L. Zechel

    (Department of Chemistry; Queens University
    Queens University)

  • Bin Ma

    (The David R. Cheriton School of Computer Science, University of Waterloo)

  • Nathan A. Magarvey

    (M. G. DeGroote Institute for Infectious Disease Research
    McMaster University
    M. G. DeGroote Institute for Infectious Disease Research, McMaster University)

Abstract

Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC–MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products.

Suggested Citation

  • Chad W. Johnston & Michael A. Skinnider & Morgan A. Wyatt & Xiang Li & Michael R. M. Ranieri & Lian Yang & David L. Zechel & Bin Ma & Nathan A. Magarvey, 2015. "An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products," Nature Communications, Nature, vol. 6(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9421
    DOI: 10.1038/ncomms9421
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms9421
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms9421?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Donghui Yan & Muqing Zhou & Abhinav Adduri & Yihao Zhuang & Mustafa Guler & Sitong Liu & Hyonyoung Shin & Torin Kovach & Gloria Oh & Xiao Liu & Yuting Deng & Xiaofeng Wang & Liu Cao & David H. Sherman, 2024. "Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9421. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.