Notes on Genus: Sobemovirus
Type member: Southern bean mosaic virus
The genus Sobemovirus
(named from the type member, so
saic virus) has isometric particles of about 30 nm in diameter and a monopartite genome. They have some similarities to the members of the family Tombusviridae
in size of virion and genome but they differ in the molecular weights of their capsid proteins and in genome organisation. Most of the better know members (but not all) are beetle-transmitted, and some are also transmitted through seed.
Some sobemoviruses encapsidate a viroid-like Circular satellite RNA of 220-390nt, which is dependent on the helper virus for replication.
Virions isometric (icosahedral), not enveloped, 30 nm in diameter. The surface capsomere arrangement is obvious (T=3), with 32 capsomeres per nucleocapsid (180 protein subunits).
Monopartite, linear, single stranded, positive sense RNA about 4100 to 4500 nucleotides long. The 3' terminus has neither a poly(A) tract nor a tRNA-like structure. The 5' terminus has a genome-linked protein (VPg) which is probably essential for infectivity.
Genus Genomic Organization
There are three or four open reading frames:
- ORF1 encodes a protein of 11-24 kDa that may be a movement protein.
- ORF2 encodes a polyprotein of c. 100kDa; in most members this is a continuous ORF, but in CfMV there are two overlapping parts and the polyprotein is expressed through a -1 ribosomal frameshift mechanism. This polyprotein contains a serine protease-like domain, the VPg and an RNA-dependent RNA polymerase domain.
- Most members (except CfMV) have a nested ORF (ORF3) potentially encoding a protein of 10-18 kDa; this may be expressed as an ORF2-ORF3 transframe fusion protein.
- The 3'-proximal ORF (usually ORF4) encodes the 21-30 kDa coat protein, which is translated from a 3'-coterminal subgenomic RNA.
N.B. Recent results suggest that all members may actually follow the CfMV pattern of gene expression but this is not represented in most of the sequence files.
Type Member Genomic Organization
It has generally been thought that there are four open reading frames. The sequence L34672 has proved to be rather abnormal compared with other isolates (and other viruses in the genus) so this description is based on the Arkansas isolate (AF055888):
|1. ||17.2 kDa||possible movement protein|
|2. ||106.5 kDa ||polyprotein, including a serine protease-like domain, the VPg and an RNA-dependent RNA polymerase domain|
|3. ||14.8 kDa||unknown function but may be expressed as a frame-shift fusion with the 5'-part of ORF2|
|4. ||28.6 kDa||coat protein, expressed from subgenomic RNA of about 1000 nucleotides|
N.B. Recent results suggest that all members may actually follow the CfMV pattern of gene expression but this is not yet represented in the sequence files.