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Nucleotide sequence of the simian rotavirus SA11 genome segment 3.

Rotaviruses are the most significant cause of severe gastroenteritis in young children and animals (1). Genome segment 3 of the simian rotavirus SAIl codes for a minor component, VP3, of the viral inner core (2). Sequences for all rotavirus genome segments except genome segment 3 have been published (3). We have isolated a cDNA clone of the SAl 1 gene 3 from a pUC 13 library and determined its nucleotide sequence by the dideoxy chain termination method. The sequence of 16 bases at the 5'- terminus of the gene (which were missing in the cDNA clone) was determined by primer extension of SA II mRNAs and genomic RNAs with AMV reverse transcriptase. The SAl 1 genome segment 3 is 2591 base pairs long and it contains one long open reading frame (bases 50 to 2553) of 835 amino acids coding for a protein of 98,120 molecular weight. The deduced polypeptide is basic with a net positive charge of 12.5 at pH 7.0 and many stretches of amino acid doublets and triplets are found throughout the sequence. A homology comparison of the deduced VP3 protein sequence with Genebank protein databases (Molecular Biology Information Resource, Eugene Software Package, Baylor College of Medicine) showed scattered short stretches of similarity between the predicted VP3 protein sequence and various viral polymerases including the L protein of vesicular stomatitis virus, polymerase proteins of HTLV III and other retroviruses, DNA-directed RNA polymerase of vaccinia virus, DNA polymerase of cytomegalovirus, and mastadenoviruses h2 and h5. These similarities and the fact that temperature sensitive mutants that map to this gene are defective in RNA synthesis (5) indicate that VP3 is a viral RNA polymerase or part of the RNA polymerase complex. 1