Identification and Primary Structure of the Gene Encoding the Berne Virus Nucleocapsid Protein

This study identified and characterized the nucleocapsid (N) protein gene of Berne virus (BEV), a prototype member of the proposed Toroviridae family. Using cDNA cloning from infected cells, researchers sequenced the N gene and predicted it encodes an 18.3 kilodalton protein, which closely matches the experimentally determined 19K size of the viral nucleocapsid protein. The N protein was identified through in vitro transcription and translation followed by immunoprecipitation, and confirmed by metabolic labeling showing that cysteine residues are absent from the N protein sequence. The analysis revealed the presence of multiple downstream AUG codons within the N gene that can serve as alternative translation initiation sites, explaining the smaller N-related polypeptides frequently observed in BEV-infected cell lysates. These smaller proteins are likely aberrant translation products rather than functional viral components. The N protein is highly basic with clustered arginine residues, suggesting roles in RNA binding and virion assembly. The study also identified the 3' untranslated region containing a potential stem-loop structure that may function in viral RNA synthesis.

Key findings

• The BEV N protein gene encodes an 18.3 kilodalton basic protein that comprises approximately 80% of virion protein mass and possesses RNA-binding properties.
• The absence of cysteine residues in the N protein sequence was confirmed through metabolic labeling experiments using [35S]cysteine incorporation into other viral proteins.
• Smaller N-related polypeptides found in infected cells result from aberrant translation initiated at multiple internal AUG codons within the N gene rather than from proteolytic processing.
• The N protein contains two clusters of basic amino acid residues, including 15 consecutive arginines, suggesting important roles in nucleic acid binding and virion architecture.
• The 3' untranslated region contains a large predicted stem-loop structure that likely functions as a recognition signal for negative-strand RNA synthesis.