Ebolavirus polymerase uses an unconventional genome replication mechanism

Laure R. Deflubé, Tessa N. Cressey, Adam J. Hume, Judith Olejnik, Elaine Haddock, Friederike Feldmann, Hideki Ebihara, Rachel Fearns, Elke Mühlberger

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Most nonsegmented negative strand (NNS) RNA virus genomes have complementary 3′ and 5′ terminal nucleotides because the promoters at the 3′ ends of the genomes and antigenomes are almost identical to each other. However, according to published sequences, both ends of ebolavirus genomes show a high degree of variability, and the 3′ and 5′ terminal nucleotides are not complementary. If correct, this would distinguish the ebolaviruses from other NNS RNA viruses. Therefore, we investigated the terminal genomic and antigenomic nucleotides of three different ebolavirus species, Ebola (EBOV), Sudan, and Reston viruses. Whereas the 5′ ends of ebolavirus RNAs are highly conserved with the sequence ACAGG-5′, the 3′ termini are variable and are typically 3′-GCCUGU, ACCUGU, or CCUGU. A small fraction of analyzed RNAs had extended 3′ ends. The majority of 3′ terminal sequences are consistent with a mechanism of nucleotide addition by hairpin formation and back-priming. Using single-round replicating EBOV minigenomes, we investigated the effect of the 3′ terminal nucleotide on viral replication and found that the EBOV polymerase initiates replication opposite the 3′-CCUGU motif regardless of the identity of the 3′ terminal nucleotide(s) and of the position of this motif relative to the 3′ end. Deletion or mutation of the first residue of the 3′-CCUGU motif completely abolished replication initiation, suggesting a crucial role of this nucleotide in directing initiation. Together, our data show that ebolaviruses have evolved a unique replication strategy among NNS RNA viruses resulting in 3′ overhangs. This could be a mechanism to avoid antiviral recognition.

Original languageEnglish (US)
Pages (from-to)8535-8543
Number of pages9
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number17
DOIs
StatePublished - Jan 1 2019

Keywords

  • Ebola virus genome ends
  • Ebola virus replication
  • Ebolavirus replication initiation
  • Nonsegmented negative strand RNA virus replication
  • Variable 3′ genome ends

ASJC Scopus subject areas

  • General

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  • Cite this

    Deflubé, L. R., Cressey, T. N., Hume, A. J., Olejnik, J., Haddock, E., Feldmann, F., Ebihara, H., Fearns, R., & Mühlberger, E. (2019). Ebolavirus polymerase uses an unconventional genome replication mechanism. Proceedings of the National Academy of Sciences of the United States of America, 116(17), 8535-8543. https://doi.org/10.1073/pnas.1815745116