Internal initiation by the cucumber necrosis virus RNA-dependent RNA polymerase is facilitated by promoter-like sequences

T. Panavas, J. Pogany, P. D. Nagy

Research output: Contribution to journalArticlepeer-review

41 Citations (SciVal)


Tombusviruses, small positive sense RNA viruses of plants, are replicated by the viral-coded RNA-dependent RNA polymerase (RdRp) in infected cells. An unusual feature of the tombusvirus RdRp that is partially purified from cucumber necrosis virus (CNV)-infected plants is the ability to initiate complementary RNA synthesis from several internal positions on minus-strand templates derived from DI RNAs (Nagy and Pogany, 2000). In this study, we used template deletion, mutagenesis, and oligo-based inhibition of RNA synthesis to map the internal initiation sites observed with the in vitro CNV RdRp system. Comparing sequences around the internal initiation sites reveals that they have either (i) similar sequences to the core minus-strand initiation promoter; or (ii) similar structures to the core plus-strand initiation promoter. In addition, we find similarities among the internal initiation sites and the subgenomic RNA initiation sites. These similarities suggest that the mechanism of internal initiation is similar to initiation from the terminal core promoters or the putative subgenomic promoter sequences. We propose that internal initiation on full-length RNA templates may be important in defective interfering (DI) RNA formation/evolution by producing intermediate templates for RNA recombination in tombusviruses. This may explain why tombusviruses are frequently associated with DI RNAs.

Original languageEnglish
Pages (from-to)275-287
Number of pages13
Issue number2
StatePublished - 2002

Bibliographical note

Funding Information:
We thank Dr. Tom Pirone for critical reading of the manuscript and for very helpful suggestions. This work was supported by NSF (MCB0078152) and by the University of Kentucky. This study is Publication No. 01-12-139 of the Kentucky Agricultural Experiment Station.


  • Defective interfering RNA
  • Internal initiation
  • Plant virus
  • Plus-strand synthesis
  • RNA promoter
  • RdRp
  • Replication

ASJC Scopus subject areas

  • Virology


Dive into the research topics of 'Internal initiation by the cucumber necrosis virus RNA-dependent RNA polymerase is facilitated by promoter-like sequences'. Together they form a unique fingerprint.

Cite this