Comparative analysis of the rotavirus NS53 gene: conservation of basic and cysteine-rich regions in the protein and possible stem-loop structures in the RNA.

NS53, the product of rotavirus gene 5, is an RNA-binding protein that contains a cysteine-rich region and is a component of early replication intermediates. To gain information about the structure of NS53 and its RNA, we determined the nucleotide sequence of gene 5 for the human viruses Wa (serotype 1) and DS1 (2) and the simian virus SA11 (3) (Patton strain) and compared them and their deduced amino acid sequences to those reported for the bovine viruses UK (6) and RF (6), SA11 (3) (Both strain), the human virus Rohivg803, and the group C porcine virus PRV. The results showed that gene 5 for human, simian, and bovine strains have lengths of 1564-1567, 1611, and 1579-1581 nucleotides (nt) and encode proteins of 486, 495, and 491 amino acids, respectively. Comparison of the protein sequences for NS53 among different serotypes showed that they are extremely divergent with many sharing amino acid homologies of only 36-38%. Even NS53 from viruses isolated from the same species possessed relatively poor homology, e.g., DS1 versus Wa was 68%. The first 150 amino acids of NS53 exhibited a greater degree of conservation than the rest of the protein. Near the amino terminus, NS53 contains three basic regions and a cysteine-rich domain, suggesting that this area is responsible for the RNA-binding activity of the protein. Present in the cysteine-rich domain of all group A and C viruses was the motif C-X2-C-X8-C-X2-C-X3-H-X-C-X2-C-X5-C. Although this motif may form one or two zinc fingers, the fact that it is highly conserved indicates that it plays a critical role in the function of protein. Comparison of the nucleotide sequences for gene 5 showed that the entire 5'-noncoding region and the first 24 nt of the NS53 ORF are conserved. RNA-folding predictions suggest that this region of the NS53 mRNA can interact with itself, producing a stem-loop structure similar to that found near the 5'-terminus of the NS35 mRNA. Thus, such structures may be common to all rotavirus mRNAs, perhaps functioning as signals for packaging of RNAs into replication intermediates or regulating mRNA translation.