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The Ryegrass mottle virus genome codes for a sobemovirus 3C-like serine protease and RNA-dependent RNA polymerase translated via −1 ribosomal frameshifting

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Abstract

In the course of sobemovirus gene cloning the complete genome of Ryegrass mottle virus (RGMoV) was sequenced. Sequence analysis revealed differences including missing and extraneous nucleotides in comparison to the previously published sequence (Zhang, Toriyama, Takanashi, J. Gen. Plant Pathol. 67, 63 (2001)). A gene coding for a typical sobemovirus 3C-like serine protease was identified in ORF2a after multiple sequence alignment analysis. The newly identified 57-amino-acid stretch in ORF2a showed similarities ranging from 38.5 to 50.9% among sequenced genes of sobemovirus proteases. ORF analysis of the RGMoV polyprotein coding sequence demonstrated the arrangement of ORF2b coding for RNA-dependent RNA polymerase (RdRP) in the −1 frame in regard to ORF2a. The localization of conserved among sobemoviruses slippery sequence (UUUAAAC) at the 3′-end of ORF2a suggests the translation of RdRP via a −1 ribosomal frameshifting mechanism, allowing to include the RGMoV in the sobemovirus group with a Cocksfoot mottle virus-like (CfMV-like) genome organization.

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Acknowledgements

We thank Prof. P. Pumpens for fruitful discussions and critical reading of the manuscript. This work was supported by Latvian Science Council grant No. 04.1149 and EU Project No.VPD1/ERAF/CFLA/05/APK/2.5.1./000031/016.

Author information

Correspondence to Andris Zeltins.

Additional information

The nucleotide sequence data reported in this paper have been submitted to the Genbank nucleotide sequence database and have been assigned the accession number EF091714.

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Balke, I., Resevica, G. & Zeltins, A. The Ryegrass mottle virus genome codes for a sobemovirus 3C-like serine protease and RNA-dependent RNA polymerase translated via −1 ribosomal frameshifting . Virus Genes 35, 395–398 (2007). https://doi.org/10.1007/s11262-007-0087-y

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Keywords

  • Sobemovirus
  • Ryegrass mottle virus
  • Genome organization