A replication silencer element in a plus-strand RNA virus

Judit Pogany, Marc R. Fabian, K. Andrew White, Peter D. Nagy

Research output: Contribution to journalArticlepeer-review

115 Scopus citations


Replication represents a key step in the infectious cycles of RNA viruses. Here we describe a regulatory RNA element, termed replication silencer, that can down-regulate complementary RNA synthesis of a positive-strand RNA virus via an RNA-RNA interaction. This interaction occurs between the 5-nucleotide-long, internally positioned replication silencer and the extreme 3′-terminus of the viral RNA comprising part of the minimal minus-strand initiation promoter. Analysis of RNA synthesis in vitro, using model defective interfering (DI) RNA templates of tomato bushy stunt virus and a partially purified, RNA-dependent RNA polymerase preparation from tombusvirus-infected plants, revealed that this interaction inhibits minus-strand synthesis 7-fold. This functional interaction was supported further by: (i) RNA structure probing; (ii) phylogenetic analysis; (iii) inhibition of activity by short complementary DNAs; and (iv) compensatory mutational analysis. The silencer was found to be essential for accumulation of DI RNAs in protoplasts, indicating that it serves an important regulatory role(s) in vivo. Because similar silencer-promoter interactions are also predicted in other virus genera, this type of RNA-based regulatory mechanism may represent a widely utilized strategy for modulating replication.

Original languageEnglish
Pages (from-to)5602-5611
Number of pages10
JournalEMBO Journal
Issue number20
StatePublished - Oct 15 2003


  • Cis-acting RNA element
  • RNA promoter
  • RNA synthesis
  • RNA-dependent RNA polymerase
  • Virus replication

ASJC Scopus subject areas

  • General Neuroscience
  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


Dive into the research topics of 'A replication silencer element in a plus-strand RNA virus'. Together they form a unique fingerprint.

Cite this