%0 Journal Article
%T Unusual Loop-Sequence Flexibility of the Proximal RNA Replication Element in EMCV
%A Jan Zoll
%A Marc M. Hahn
%A Paul Gielen
%A Hans A. Heus
%A Willem J. G. Melchers
%A Frank J. M. van Kuppeveld
%J PLOS ONE
%D 2011
%I Public Library of Science (PLoS)
%R 10.1371/journal.pone.0024818
%X Picornaviruses contain stable RNA structures at the 5กไ and 3กไ ends of the RNA genome, OriL and OriR involved in viral RNA replication. The OriL RNA element found at the 5กไ end of the enterovirus genome folds into a cloverleaf-like configuration. In vivo SELEX experiments revealed that functioning of the poliovirus cloverleaf depends on a specific structure in this RNA element. Little is known about the OriL of cardioviruses. Here, we investigated structural aspects and requirements of the apical loop of proximal stem-loop SL-A of mengovirus, a strain of EMCV. Using NMR spectroscopy, we showed that the mengovirus SL-A apical loop consists of an octaloop. In vivo SELEX experiments demonstrated that a large number of random sequences are tolerated in the apical octaloop that support virus replication. Mutants in which the SL-A loop size and the length of the upper part of the stem were varied showed that both stem-length and stability of the octaloop are important determinants for viral RNA replication and virus reproduction. Together, these data show that stem-loop A plays an important role in virus replication. The high degree of sequence flexibility and the lack of selective pressure on the octaloop argue against a role in sequence specific RNA-protein or RNA-RNA interactions in which octaloop nucleotides are involved.
%U http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024818