The p92 polymerase coding region contains an internal RNA element required at an early step in Tombusvirus genome replication.

Abstract:

:The replication of positive-strand RNA viral genomes involves various cis-acting RNA sequences. Generally, regulatory RNA sequences are present at or near genomic termini; however, internal replication elements (IREs) also exist. Here we report the structural and functional characterization of an IRE present in the readthrough portion of the p92 polymerase gene of Tomato bushy stunt virus. Analysis of this element in the context of a noncoding defective interfering RNA revealed a functional core structure composed of two noncontiguous segments of sequence that interact with each other to form an extended helical conformation. IRE activity required maintenance of several base-paired sections as well as two distinct structural features: (i) a short, highly conserved segment that can potentially form two different and mutually exclusive structures and (ii) an internal loop that contains a critical CC mismatch. The IRE was also shown to play an essential role within the context of the viral genome. In vivo analysis with novel RNA-based temperature-sensitive genomic mutants and translationally active subgenomic viral replicons revealed the following about the IRE: (i) it is active in the positive strand, (ii) it is dispensable late in the viral RNA replication process, and (iii) it is functionally inhibited by active translation over its sequence. Together, these results suggest that IRE activity is required in the cytosol at an early step in the viral replication process, such as template recruitment and/or replicase complex assembly.

journal_name

J Virol

journal_title

Journal of virology

authors

Monkewich S,Lin HX,Fabian MR,Xu W,Na H,Ray D,Chernysheva OA,Nagy PD,White KA

doi

10.1128/JVI.79.8.4848-4858.2005

subject

Has Abstract

pub_date

2005-04-01 00:00:00

pages

4848-58

issue

8

eissn

0022-538X

issn

1098-5514

pii

79/8/4848

journal_volume

79

pub_type

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