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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
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    References listed on IDEAS

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    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.
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    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.

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