Mutational analyses of the non-conserved sequences in the Bunyamwera orthobunyavirus S segment untranslated regions

Bunyamwera virus (BUNV) is the prototype of the genus Orthobunyavirus and the family Bunyaviridae. BUNV has a tripartite genome of negative-sense RNA composed of small (S), medium (M), and large (L) segments. Partially complementary untranslated regions (UTRs) flank the coding region of each segment. The terminal 11 nucleotides of these UTRs are conserved between the three segments and throughout the genus, while the internal regions are unique to each segment and largely nonconserved between different viruses. To investigate the functions of the UTR sequences, we constructed a series of BUNV S segment cDNA clones with deletions in the 3' and/or 5' UTR and then attempted to rescue these segments into recombinant viruses. We found that the genomic 5' UTR was much more sensitive to mutation than the 3' UTR and, in general, sequences proximal to the termini were more important than those flanking the coding region. Northern blot analyses of infected-cell RNA showed that the internal, nonconserved sequences of the S segment 3' UTR play a role in the regulation of transcription and replication and the balance between these two processes. In contrast, deletions in the 5' UTR caused attenuation of the recombinant virus but did not specifically affect levels of S segment RNAs or the encoded nucleocapsid protein. Thus, the internal regions of both UTRs are functional: most of the 5' UTR is essential to viral growth, and, while nonessential, the internal 3' UTR is important to the regulation of viral RNA synthesis.