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Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

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Tuplin, Andrew, Evans, D. J. (David J.), Buckley, A., Jones, I. M. (Ian M.), Gould, E. and Gritsun, T. S.. (2011) Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus. Nucleic Acids Research, Vol.39 (No.16). pp. 7034-7048. ISSN 0305-1048

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Official URL: http://dx.doi.org/10.1093/nar/gkr237

Abstract

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem-loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology > QR355 Virology
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	DNA replication, Tick-borne encephalitis viruses -- Genetics
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
ISSN:	0305-1048
Date:	September 2011
Volume:	Vol.39
Number:	No.16
Page Range:	pp. 7034-7048
Identification Number:	10.1093/nar/gkr237
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Sixth Framework Programme (European Commission) (FP6), Medical Research Council (Great Britain) (MRC)
Grant number:	BBS/B/00697 (BBSRC), LSHG-CT-2004-511960 (FP6), 87652 (MRC)
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URI:	http://wrap.warwick.ac.uk/id/eprint/38430