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The genome of Bunyamwera virus (BUN; family Bunyaviridae) consists of three segments of negative-sense, single-stranded RNA that are called L (large), M (medium) and S (small), according to their size. The genomic RNAs are encapsidated by the viral nucleocapsid protein to form ribonucleoprotein complexes (RNPs). The terminal 3' and 5' non-coding sequences are complementary and interact to give a panhandle-like structure to the RNP. Located within these non-coding sequences are elements that control replication and transcription. The sequences of the terminal 11 nt are conserved among the genome segments and are followed by shorter, complementary nucleotide motifs that are conserved on a segment-specific basis. Here, a detailed analysis of the 3' and 5' non-coding regions of the BUN S segment is presented. By using a mini-replicon system, it was shown that a functional BUN S promoter requires complementarity, as well as defined sequences, within the terminal 15 nt of either end. It was also shown that the minimal requirement for transcription is localized within the terminal 32 nt of the S segment. A comparison of known strong BUN promoters led to the prediction of a structural element outside the terminal 15 nt; introduction of this motif into the BUN S sequence resulted in increased antigenome and mRNA levels and increased expression of S segment proteins, as shown by mini-replicon assays, as well as recovery of a recombinant virus.

Bunyaviruses have a genome comprising three segments of negative-sense RNA. The smallest RNA segment, S, encodes the nucleocapsid protein, N, and a nonstructural protein, NSs, in overlapping reading frames. The sequences of the S genome RNA segments of seven bunyaviruses (Batai, Cache Valley, Guaroa, Kairi, Main Drain, Northway and Lumbo) were determined from cloned cDNAs obtained using a one-step reverse transcription-PCR protocol. These sequences were compared to those of six viruses previously published, reinforcing earlier conclusions about relationships of the bunyaviruses. Sequence homologies between N proteins correlated with the subdivision of these viruses into three serogroups, Bunyamwera, California and Simbu. The encoded N proteins are either 233 or 235 amino acids in length, depending on the serogroup, whereas the NSs proteins are more variable (83 to 109 amino acids). Certain nucleotide sequence motifs are conserved in the S segments of the Bunyamwera and California serogroup viruses, including the spacing of the AUG initiation codons for the N and NSs proteins (except Guaroa virus), and a CA-rich motif in the virion-sense RNA just downstream of the predicted mRNA termination site. A duplicated sequence was observed in the 3' non-coding region of the Lumbo virus S segment, which accounts for the significantly longer S genome segment of this virus.