Synthesis of subgenomic (SG) messenger RNAs (mRNAs) by (+)strand RNA viruses allows the differential expression of specific virus genes, both quantitatively and temporally. SG RNAs have the following properties:
- They are made in infected cells but do not interfere with the normal course of virus replication
- The SG RNA sequences are shorter than their cognate genomic RNAs
- Their sequences are usually co-terminal with the 3′ genomic sequence but sometimes are co-terminal with the 5′ sequences. Yet other viruses make SG RNAs which contain a 5′ co-terminal leader joined to a 3′ co-terminal sequence
- Typically, whether a messenger SG RNA contains only one ORF, or multiple ORFs, with some rare exceptions, only the 5′ ORF is translated. Although most SG RNAs function as messengers and are translated, other SG RNAs, generally those with 5′ co-terminal sequences, have other functions.
Subgenomic messenger RNAs: mastering regulation of (+)-strand RNA virus life cycle. Virology. 2011 412(2):245-255
Many (+)-strand RNA viruses use subgenomic (SG) RNAs as messengers for protein expression, or to regulate their viral life cycle. Three different mechanisms have been described for the synthesis of SG RNAs. The first mechanism involves internal initiation on a (-)-strand RNA template and requires an internal SGP promoter. The second mechanism makes a prematurely terminated (-)-strand RNA which is used as template to make the SG RNA. The third mechanism uses discontinuous RNA synthesis while making the (-)-strand RNA templates. Most SG RNAs are translated into structural proteins or proteins related to pathogenesis: however other SG RNAs regulate the transition between translation and replication, function as riboregulators of replication or translation, or support RNA-RNA recombination. In this review we discuss these functions of SG RNAs and how they influence viral replication, translation and recombination.