Biological consequences of deletions within the 3 '-untranslated region offlaviviruses may be due to rearrangements of RNA secondary structure

It was previously reported that deletions introduced into the 3'-untranslat ed region (3'-UTR) of dengue type 4 (DEN 4) virus (Men, R., Bray, M., Clark , D., Chanock, R.M., Lai, C.J., 1996. DEN 4 virus mutants containing deleti ons in the 3'-noncoding region of the RNA genome: analysis of growth restri ction in cell culture and altered viremia pattern and immunogenicity in Rhe sus monkeys. J. Virol. 70, 3930-3937), tick-borne encephalitis (TBE) virus (Mandl, C.W., Holzmann, H., Meixner, T., Rauscher, S., Stadler, P.F., Allis on, S.L., Heinz, F.X., 1998. Spontaneous and engineered deletions in the 3' -noncoding region of TBE virus: construction of highly attenuated mutants o f a flavivirus. J. Virol. 72, 2132-2140) and subgenomic replicons of Kunjin virus (Khromykh, A.A., Westaway, E.G., 1997. Subgenomic replicons of the f lavivirus Kunjin: construction and applications. J. Virol. 71, 1497-1505) a ltered the infectivity of the mutants and reduced the efficiency of RNA rep lication. Here, these deletions were superimposed onto the models of second ary structure we constructed previously and the folding of the modified 3'- UTR sequences was simulated. The analysis showed that most of the deletions disrupted or reshaped conserved elements of secondary structure and that t he biological effects of these deletions are likely to represent structural rearrangements in the 3'-UTR, rather than the loss of sequence motifs. The analysis also suggested that the overall structural integrity of the flavi viral 3'-UTR is essential for optimal performance of its promotor function, although two distinct parts can be defined: the most 3'-terminal structure s and sequences which may be critical for the initiation of minus-strand RN A synthesis, and more proximal structures and sequences that possibly funct ion as enhancers of viral RNA replication. The functional significance of c ertain structural elements and their possible effect on the efficiency of v iral replication in different cells are also discussed. (C) 1999 Elsevier S cience B.V. All rights reserved.