Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

Biswas, Subhajit and Li, Wilson and Manktelow, Emily and Lever, Jonathan and Easton, Laura E. and Lukavsky, Peter J. and Desselberger, Ulrich and Lever, Andrew M. (2014) Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS). Archives of Virology, 159 (2). pp. 235-248. ISSN 0304-8608

Full content URL: http://dx.doi.org/10.1007/s00705-013-1802-8

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Abstract

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties.

Keywords:Virus mutation, DNA virus, Rotavirus, tRNA, Genome packaging, RNA, JCOpen
Subjects:C Biological Sciences > C540 Virology
C Biological Sciences > C521 Medical Microbiology
Divisions:College of Science > School of Life Sciences
ID Code:11272
Deposited On:22 Jul 2013 07:50

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