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Nucleocapsids of the Rift Valley fever virus ambisense S segment contain an exposed RNA element in the center that overlaps with the intergenic region

Author

Listed:
  • Lyudmila Shalamova

    (Justus-Liebig University)

  • Patrick Barth

    (Justus-Liebig University
    University of Regensburg)

  • Matthew J. Pickin

    (Justus-Liebig University)

  • Kiriaki Kouti

    (Justus-Liebig University)

  • Benjamin Ott

    (Justus-Liebig University)

  • Katharina Humpert

    (Justus-Liebig University
    Philipps-University)

  • Stefan Janssen

    (Justus-Liebig University)

  • Gema Lorenzo

    (Centro de Investigación en Sanidad Animal (CISA-INIA/CSIC))

  • Alejandro Brun

    (Centro de Investigación en Sanidad Animal (CISA-INIA/CSIC))

  • Alexander Goesmann

    (Justus-Liebig University)

  • Torsten Hain

    (Justus-Liebig University)

  • Roland K. Hartmann

    (Philipps-University Marburg)

  • Oliver Rossbach

    (Justus-Liebig University)

  • Friedemann Weber

    (Justus-Liebig University)

Abstract

Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen. Its RNA genome consists of two negative-sense segments (L and M) with one gene each, and one ambisense segment (S) with two opposing genes separated by the noncoding “intergenic region” (IGR). These vRNAs and the complementary cRNAs are encapsidated by nucleoprotein (N). Using iCLIP2 (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to map all N-vRNA and N-cRNA interactions, we detect N coverage along the L and M segments. However, the S segment vRNA and cRNA each contain approximately 100 non-encapsidated nucleotides stretching from the IGR into the 5’-adjacent reading frame. These exposed regions are RNase-sensitive and predicted to form stem-loop structures with the mRNA transcription termination motif positioned near the top. Moreover, optimal S segment transcription and replication requires the entire exposed region rather than only the IGR. Thus, the RVFV S segment contains a central, non-encapsidated RNA region with a functional role.

Suggested Citation

  • Lyudmila Shalamova & Patrick Barth & Matthew J. Pickin & Kiriaki Kouti & Benjamin Ott & Katharina Humpert & Stefan Janssen & Gema Lorenzo & Alejandro Brun & Alexander Goesmann & Torsten Hain & Roland , 2024. "Nucleocapsids of the Rift Valley fever virus ambisense S segment contain an exposed RNA element in the center that overlaps with the intergenic region," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52058-2
    DOI: 10.1038/s41467-024-52058-2
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    References listed on IDEAS

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    1. Graham D. Williams & Dana Townsend & Kristine M. Wylie & Preston J. Kim & Gaya K. Amarasinghe & Sebla B. Kutluay & Adrianus C. M. Boon, 2018. "Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    2. Smriti Mallapaty, 2024. "The pathogens that could spark the next pandemic," Nature, Nature, vol. 632(8025), pages 488-488, August.
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