Nucleotide and amino acid sequence analysis of the rotavirus nonstructural RNA-binding protein NS35

NS35, a basic protein encoded by gene 8 of SA11 rotavirus, possesses RNA-binding activity and is essential for genome replication. To identify conserved regions in the NS35 gene and its protein product, we determined the nucleotide sequences of the NS35 gene for the mammalian and avian rotaviruses Wa, DS1, SA11 (Patton and Ramig strains), NCDV, and Ty-1 and compared them and their deduced amino acid sequences to those reported for SA11 (Both strain), OSU, and UK. The results indicated that the NS35 genes of the mammalian rotaviruses are 1058-1059 bases in length and encode proteins of 317 amino acids that exhibit high levels of sequence conservation (> or = 83%). The NS35 gene of the turkey rotavirus Ty-1 differed from those of the mammalian rotaviruses with respect to size of the predicted protein (315 amino acids) and of the gene (1042 bases). NS35 of Ty-1 exhibited a relatively low degree of amino acid homology (52-57%) with NS35 of the mammalian viruses. Phylogenetic analysis of the NS35 gene indicated that avian (TY-1) and mammalian rotaviruses are distantly related. Comparison of the predicted sequences of NS35 showed that all possessed a conserved basic domain of 37 amino acids at residues 205-241 that may serve as the RNA-binding domain. Electrophoretic examination showed that NS35 contains a disulfide bond probably located in the amino-terminal half of the protein. Comparison of NS35 genes at the nucleotide level revealed two regions of extensive conservation, (i) a 75-base (b) sequence that includes the 35-base 5'-noncoding region and the first 30 bases of the open reading frame for NS35, and (ii) a 28-b sequence in the 3'-noncoding region of the gene. Secondary structure predictions for the NS35 mRNA suggest that the 75-base sequence can fold to produce a stem double-loop structure. Such a structure may serve as a packaging signal for the assortment of NS35 mRNA into replicase particles.