Summary auto-generated
This study determined the complete 3879-nucleotide genome sequence of saguaro cactus carmovirus (SCV), a small RNA virus infecting giant saguaro cacti in Arizona. The genome contains five open reading frames (ORFs) organized as follows: the 5'-proximal ORF encodes a 26 kDa protein (p26) with an amber termination codon that undergoes readthrough to produce an 86 kDa fusion protein (p86); two overlapping internal ORFs encode 6 kDa (p6) and 9 kDa (p9) proteins; and the 3'-proximal ORF encodes a 37 kDa capsid protein (p37). The researchers identified two subgenomic RNAs (sg RNAs) of 1.6 kb and 1.4 kb produced during infection. The larger sg RNA expresses both p6 and p9 proteins, while the smaller sg RNA expresses only the capsid protein. In vitro translation studies confirmed that all predicted protein products are expressed from SCV RNA. The nucleotide sequence analysis shows SCV is most closely related to carnation mottle virus among the genus Carmovirus in family Tombusviridae, supporting its taxonomic classification. These findings reveal the complete gene expression strategy and genome organization of this plant virus.
Key findings
- SCV genome is 3879 nucleotides containing five major ORFs: p26, readthrough p86, p6, p9, and p37 capsid protein
- Two subgenomic RNAs (1.6 kb and 1.4 kb) are produced during infection; the larger one encodes p6 and p9, the smaller one encodes only capsid protein
- All five predicted ORFs are expressed in vitro, with p26 and p37 being the most abundant products
- SCV is most closely related to carnation mottle virus (53.8% nucleotide identity) and belongs to genus Carmovirus, family Tombusviridae
- The p6 and p9 proteins are expressed from a single bicistronic subgenomic RNA, supporting a previously untested hypothesis about carmovirus gene expression
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Abstract
The complete sequence of the single-stranded, (+)-sense RNA genome of saguaro cactus carmovirus (SCV) has been determined. The 3879 nucleotide genome contains five open reading frames (ORFs). The 5'- proximal ORF encodes a 26 kDa protein (p26) and terminates with an amber codon which is readthrough into an in-frame p57 ORF to generate an 86 kDa fusion protein (p86). Two small, centrally located ORFs encode a 6 kDa protein (p6) and a 9 kDa protein (p9), respectively. The 3'-proximal ORF encodes a 37 kDa (p37) capsid protein (CP). Analysis of the nucleotide and predicted amino acid sequences supports the classification of SCV in the genus Carmovirus in the family Tombusviridae. All predicted SCV proteins are expressed in an in vitro translation system. SCV p26 and the readthrough fusion protein p86 are synthesized from the genomic RNA while p6, p9 and p37 CP ORFs at the 3' half of the genome are expressed from two subgenomic (sg) RNAs. The 5' termini of both sg RNAs have been mapped. The large 1614 nucleotide sg RNA contains the p6 and p9 ORFs as the first and the second ORFs respectively from its 5' end. It directs the synthesis of abundant p6 but a small amount of p9. While a synthetic transcript with the p9 ORF at the 5' end is a more efficient messenger for p9, no corresponding sg RNA has been identified in vivo. The smaller 1396 nucleotide sg RNA contains only the p37 ORF and directs the synthesis of SCV CP.