1. Microbiology and Infectious Disease
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A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation

  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  Is a corresponding author
  8. Holger Sondermann  Is a corresponding author
  9. Vincent T Lee  Is a corresponding author
  1. University of Maryland, United States
  2. Cornell University, United States
Research Article
  • Cited 6
  • Views 1,509
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Cite this article as: eLife 2019;8:e46313 doi: 10.7554/eLife.46313

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

Publication 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)

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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Further reading

    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics
    Justin D Lormand et al.
    Research Advance

    RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC employs similar structural features that distinguish these two classes as dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases indicates convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.

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