Genome 3′-end repair in dengue virus type 2
- 30 October 2008
- journal article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 14 (12), 2645-2656
- https://doi.org/10.1261/rna.1051208
Abstract
Genomes of RNA viruses encounter a continual threat from host cellular ribonucleases. Therefore, viruses have evolved mechanisms to protect the integrity of their genomes. To study the mechanism of 3′-end repair in dengue virus-2 in mammalian cells, a series of 3′-end deletions in the genome were evaluated for virus replication by detection of viral antigen NS1 and by sequence analysis. Limited deletions did not cause any delay in the detection of NS1 within 5 d. However, deletions of 7–10 nucleotides caused a delay of 9 d in the detection of NS1. Sequence analysis of RNAs from recovered viruses showed that at early times, virus progenies evolved through RNA molecules of heterogeneous lengths and nucleotide sequences at the 3′ end, suggesting a possible role for terminal nucleotidyl transferase activity of the viral polymerase (NS5). However, this diversity gradually diminished and consensus sequences emerged. Template activities of 3′-end mutants in the synthesis of negative-strand RNA in vitro by purified NS5 correlate well with the abilities of mutant RNAs to repair and produce virus progenies. Using the Mfold program for RNA structure prediction, we show that if the 3′ stem–loop (3′ SL) structure was abrogated by mutations, viruses eventually restored the 3′ SL structure. Taken together, these results favor a two-step repair process: non-template-based nucleotide addition followed by evolutionary selection of 3′-end sequences based on the best-fit RNA structure that can support viral replication.Keywords
This publication has 39 references indexed in Scilit:
- Specific requirements for elements of the 5′ and 3′ terminal regions in flavivirus RNA synthesis and viral replicationVirology, 2008
- Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymeraseBMC Molecular Biology, 2007
- Catalytic Core of Alphavirus Nonstructural Protein nsP4 Possesses Terminal Adenylyltransferase ActivityJournal of Virology, 2006
- A 5′ RNA element promotes dengue virus RNA synthesis on a circular genomeGenes & Development, 2006
- Screening of the Yeast yTHC Collection Identifies Essential Host Factors Affecting Tombusvirus RNA RecombinationJournal of Virology, 2006
- Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegansNature, 2005
- In Vitro RNA Synthesis from Exogenous Dengue Viral RNA Templates Requires Long Range Interactions between 5′- and 3′-Terminal Regions That Influence RNA StructurePublished by Elsevier BV ,2001
- Determination of the 5' end of the lactate dehydrogenase-elevating virus genome by two independent approachesJournal of General Virology, 1994
- Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNAGene, 1991
- Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequencesJournal of Molecular Biology, 1987