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Archives of Virology

, Volume 142, Issue 5, pp 1029–1033 | Cite as

Conserved vRNA end sequences of Thogoto-orthomyxovirus suggest a new panhandle structure

  • F. Weber
  • O. Haller
  • G. Kochs
Brief Report

Summary

Panhandles are dsRNA structures formed by conserved sequences at the 5 and 3 ends of the influenza virus genomic RNA. They consist of two stems separated by a flexible bulge and serve as promoter for the viral polymerase. In the outer stem, melting of base pairs is a prerequisite for initiation of transcription. We compared the terminal sequences of Thogoto virus (THOV), a tick-borne orthomyxovirus, with those of influenza virus. Despite their overall similarity, the first U downstream of the 5 end of the panhandle (position 3 in influenza virus) is found at position 8 in the THOV sequence. This shift from position 3 to position 8 results in a radical change of the predicted secondary structure. In the outer stem, intra-strand base pairings are clearly favoured above inter-strand hybridizations. As this secondary structure can explain the functioning of a mutant promoter of influenza virus with twice the activity of the wild-type, we propose a general validity of our “hook-like” panhandle structure.

Keywords

Influenza Virus Virus Membrane Protein dsRNA Structure Outer Stem Panhandle Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag 1997

Authors and Affiliations

  • F. Weber
    • 1
  • O. Haller
    • 1
  • G. Kochs
    • 1
  1. 1.Abteilung Virologie, Institut für Medizinische Mikrobiologie und Hygiene, Universität Freiburg, Freiburg, Federal Republic of GermanyDE

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