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Nucleic Acids Research 2006 34(10):2953-2965; doi:10.1093/nar/gkl349
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Published online 31 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-element

Mark J. M. van Ooij, Charlotta Polacek3, Dirk H. R. F. Glaudemans, Judith Kuijpers, Frank J. M. van Kuppeveld, Raul Andino3, Vadim I. Agol1,2 and Willem J. G. Melchers*

Department of Medical Microbiology Nijmegen Center for Molecular Life Science, Radboud University Nijmegen Medical Centre PO Box 9101, 6500 HB Nijmegen, The Netherlands 1 M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences Moscow Region 142782, Russia 2 Moscow State University Moscow 119899, Russia 3 University of California, San Francisco, Mission Bay Genentech Hall, UCSF Department of Microbiology 600 16th Street, PO Box 2280, San Francisco, CA 94143, USA

*To whom correspondence should be addressed. Tel: +31 24 3614356; Fax: +31 24 3540216; Email: w.melchers{at}ncmls.ru.nl

Received February 2, 2006. Revised March 28, 2006. Accepted April 19, 2006.

Genomes and antigenomes of many positive-strand RNA viruses contain 3'-poly(A) and 5'-poly(U) tracts, respectively, serving as mutual templates. Mechanism(s) controlling the length of these homopolymeric stretches are not well understood. Here, we show that in coxsackievirus B3 (CVB3) and three other enteroviruses the poly(A) tract is ~80–90 and the poly(U) tract is ~20 nt-long. Mutagenesis analysis indicate that the length of the CVB3 3'-poly(A) is determined by the oriR, a cis-element in the 3'-noncoding region of viral RNA. In contrast, while mutations of the oriR inhibit initiation of (–) RNA synthesis, they do not affect the 5'-poly(U) length. Poly(A)-lacking genomes are able to acquire genetically unstable AU-rich poly(A)-terminated 3'-tails, which may be generated by a mechanism distinct from the cognate viral RNA polyadenylation. The aberrant tails ensure only inefficient replication. The possibility of RNA replication independent of oriR and poly(A) demonstrate that highly debilitated viruses are able to survive by utilizing ‘emergence’, perhaps atavistic, mechanisms.


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