A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation

Abstract

Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, 3-'5' exoribonucleases comprise up to eight distinct enzymes. Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. However, the molecular basis of Orn's unique cellular function remained unclear. Here we show that Orn exhibits exquisite substrate preference for diribonucleotides. Crystal structures of substrate-bound Orn reveal an active site optimized for diribonucleotides. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, Orn is the one and only diribonucleotidase that completes the terminal step of RNA degradation. Together, our studies indicate RNA degradation as a step-wise process with a dedicated enzyme for the clearance of a specific intermediate pool, diribonucleotides, that affects cellular physiology and viability.

Data availability

The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID codes 6N6A, 6N6C, 6N6D, 6N6E, 6N6F, 6N6G, 6N6H, 6N6I, 6N6J, and 6N6K). Source data files have been provided for Figures.

The following data sets were generated

Article and author information

Author details

  1. Soo-Kyoung Kim

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Justin D Lormand

    Department of Molecular Medicine, Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Cordelia A Weiss

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Karin A Eger

    Department of Molecular Medicine, Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Husan Turdiev

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Asan Turdiev

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Wade C Winkler

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    For correspondence
    wwinkler@umd.edu
    Competing interests
    The authors declare that no competing interests exist.
  8. Holger Sondermann

    Department of Molecular Medicine, Cornell University, Ithaca, United States
    For correspondence
    hs293@cornell.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2211-6234
  9. Vincent T Lee

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    For correspondence
    vtlee@umd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3593-0318

Funding

National Institute of Allergy and Infectious Diseases (R01AI110740)

  • Vincent T Lee

National Institute of General Medical Sciences (R01GM123609)

  • Holger Sondermann

National Science Foundation (MCB1051440)

  • Wade C Winkler

Cystic Fibrosis Foundation (LEE16G0)

  • Vincent T Lee

National Institute of Diabetes and Digestive and Kidney Diseases (R01AI110740)

  • Vincent T Lee

National Institute of General Medical Sciences (T32-GM080201)

  • Cordelia A Weiss

National Institute of Allergy and Infectious Diseases (R01AI142400)

  • Wade C Winkler
  • Holger Sondermann
  • Vincent T Lee

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Bryce E Nickels, Rutgers University, United States

Version history

  1. Received: February 22, 2019
  2. Accepted: June 14, 2019
  3. Accepted Manuscript published: June 21, 2019 (version 1)
  4. Version of Record published: July 8, 2019 (version 2)
  5. Version of Record updated: July 10, 2019 (version 3)
  6. Version of Record updated: July 16, 2019 (version 4)
  7. Version of Record updated: January 28, 2022 (version 5)

Copyright

© 2019, Kim et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Soo-Kyoung Kim
  2. Justin D Lormand
  3. Cordelia A Weiss
  4. Karin A Eger
  5. Husan Turdiev
  6. Asan Turdiev
  7. Wade C Winkler
  8. Holger Sondermann
  9. Vincent T Lee
(2019)
A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation
eLife 8:e46313.
https://doi.org/10.7554/eLife.46313

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https://doi.org/10.7554/eLife.46313

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