IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32993-8.html
   My bibliography  Save this article

Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase

Author

Listed:
  • Ruonan Wu

    (Pacific Northwest National Laboratory)

  • Clyde A. Smith

    (Stanford University)

  • Garry W. Buchko

    (Pacific Northwest National Laboratory
    Washington State University)

  • Ian K. Blaby

    (Lawrence Berkeley National Laboratory)

  • David Paez-Espino

    (Mammoth Biosciences)

  • Nikos C. Kyrpides

    (Lawrence Berkeley National Laboratory)

  • Yasuo Yoshikuni

    (Lawrence Berkeley National Laboratory)

  • Jason E. McDermott

    (Pacific Northwest National Laboratory
    Oregon Health & Science University)

  • Kirsten S. Hofmockel

    (Pacific Northwest National Laboratory)

  • John R. Cort

    (Pacific Northwest National Laboratory
    Washington State University)

  • Janet K. Jansson

    (Pacific Northwest National Laboratory)

Abstract

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

Suggested Citation

  • Ruonan Wu & Clyde A. Smith & Garry W. Buchko & Ian K. Blaby & David Paez-Espino & Nikos C. Kyrpides & Yasuo Yoshikuni & Jason E. McDermott & Kirsten S. Hofmockel & John R. Cort & Janet K. Jansson, 2022. "Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32993-8
    DOI: 10.1038/s41467-022-32993-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32993-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-32993-8?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
    ---><---

    References listed on IDEAS

    as
    1. Debbie Lindell & Jacob D. Jaffe & Zackary I. Johnson & George M. Church & Sallie W. Chisholm, 2005. "Photosynthesis genes in marine viruses yield proteins during host infection," Nature, Nature, vol. 438(7064), pages 86-89, November.
    Full references (including those not matched with items on IDEAS)

    Citations

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


    Cited by:

    1. Ruonan Wu & Michelle R. Davison & William C. Nelson & Montana L. Smith & Mary S. Lipton & Janet K. Jansson & Ryan S. McClure & Jason E. McDermott & Kirsten S. Hofmockel, 2023. "Hi-C metagenome sequencing reveals soil phage–host interactions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Javier Lopez-Simon & Marina Vila-Nistal & Aleksandra Rosenova & Daniele Corte & Federico Baltar & Manuel Martinez-Garcia, 2023. "Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Zihao Zhao & Chie Amano & Thomas Reinthaler & Federico Baltar & Mónica V. Orellana & Gerhard J. Herndl, 2024. "Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean," 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:13:y:2022:i:1:d:10.1038_s41467-022-32993-8. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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.