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The nucleotide sequence and genome organization of Sclerophthora macrospora virus A
Toshiro Yokoi1, Shuichi Yamashita, Tadaaki Hibi
1Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
Abstract:
Sclerophthora macrospora virus A (SmV A) found in S. macrospora, the pathogenic fungus responsible for downy mildew of gramineous plants, is a small icosahedral virus containing three segments (RNAs 1, 2, and 3) of the positive-strand ssRNA genome. In the present study we report the complete nucleotide sequence of the SmV A genome. The viral genome RNA 1 consists of 2928 nucleotides (nt) and has two open reading frames (ORFs 1a and 1b). ORF 1a contains the motifs of RNA-directed RNA polymerase (RdRp). The function of ORF 1b is unknown. RNA 2 consists of 1981 nt and single ORF (ORF 2). ORF 2 encodes a capsid protein. RNA 3 consists of 977 nt but not any ORFs, suggesting it as a satellite RNA. The deduced amino acid sequence of ORF 1a shows some similarity to those of RdRp of certain positive-strand RNA viruses, especially to the members of the family Nodaviridae, and that of ORF 2 to CP of the members in the family Tombusviridae. The nucleotide sequence of RNA 3 shows a 40-nucleotide length of partial similarity to S. macrospora virus B (SmV B) RNA. The capsid of SmV A is composed of two capsid proteins, CP 1 (p43) and CP 2 (p39), both encoded in ORF 2. CP 2 is apparently derived from CP 1 via proteolytic cleavage at the N-terminus. The genome organization of SmV A is characteristic and distinct from those of other known fungal RNA viruses, including SmV B. These results suggest that SmV A should be classified into a new group of mycoviruses.
Insights
Sclerophthora macrospora virus A (SmV A), a fungal virus causing downy mildew, has a unique genome structure. Its RNA segments encode key proteins, suggesting SmV A represents a new mycovirus group.
Area of Science:
- Mycology
- Virology
- Plant Pathology
Background:
- Sclerophthora macrospora causes downy mildew in gramineous plants.
- Sclerophthora macrospora virus A (SmV A) is an icosahedral virus with a positive-strand ssRNA genome.
- The complete genome sequence of SmV A was previously uncharacterized.
Purpose of the Study:
- To determine and analyze the complete nucleotide sequence of the Sclerophthora macrospora virus A (SmV A) genome.
- To investigate the genome organization and identify potential open reading frames (ORFs) and their encoded proteins.
- To compare SmV A's genetic features with other known mycoviruses.
Main Methods:
- Complete nucleotide sequencing of the SmV A genome.
- Bioinformatic analysis to identify ORFs and predict protein functions.
- Sequence comparison with known RNA viruses and viral families.
Main Results:
- The SmV A genome comprises three RNA segments (RNA 1, RNA 2, RNA 3).
- RNA 1 (2928 nt) contains ORFs for RNA-directed RNA polymerase (RdRp) and an unknown function.
- RNA 2 (1981 nt) encodes capsid proteins (CP 1 and CP 2), with CP 2 derived from CP 1.
- RNA 3 (977 nt) lacks ORFs, suggesting it is a satellite RNA with partial similarity to SmV B RNA.
- SmV A's genome organization is distinct from other fungal RNA viruses, including SmV B.
Conclusions:
- SmV A possesses a unique genome organization distinct from known fungal RNA viruses.
- The deduced protein sequences show similarities to RdRp of Nodaviridae and CP of Tombusviridae.
- These findings support the classification of SmV A into a novel group of mycoviruses.