The structure and function of the rous sarcoma virus RNA stability element

Abstract

For simple retroviruses, such as the Rous sarcoma virus (RSV), post-transcriptional control elements regulate viral RNA splicing, export, stability, and packaging into virions. These RNA sequences interact with cellular host proteins to regulate and facilitate productive viral infections. One such element, known as the RSV stability element (RSE), is required for maintaining stability of the full-length unspliced RNA. This viral RNA serves as the mRNA for the Gag and Pol proteins and also as the genome packaged in progeny virions. When the RSE is deleted from the viral RNA, the unspliced RNA becomes unstable and is degraded in a Upf1-dependent manner. Current evidence suggests that the RSE inhibits recognition of the viral gag termination codon by the nonsense-mediated mRNA decay (NMD) pathway. We believe that the RSE acts as an insulator to NMD, thereby preventing at least one of the required functional steps that target an mRNA for degradation. Here, we discuss the history of the RSE and the current model of how the RSE is interacting with cellular NMD factors.

Fig. 1

The RSV genome and viral mRNAs. RSV contains three uORFS and four ORFs (gag, pol, env, and src) that are expressed from the proviral DNA in three RNA isoforms. The direct repeats (DRs) are required for export of the unspliced RNA. The long terminal repeats (LTRs) contain the sequences required for gene expression, including the promoter, enhancer elements and transcription start site.

Fig. 2

Structure and summary of mutation studies of the RSE. Nucleotides on the main structure are according to accession number NC_001407. The structure shown was determined by S.H.A.P.E. chemistry and RNase digestion in vitro. The −1 frameshift pseudoknot was reprinted with permission [Marczinke et al., 1998]. The white letters on a black background represent the pseudoknot pairing. The gag stop codon is indicated in white letters on a red background. Arrow brackets indicate the 5′ and 3′ boundary of the minimal RSE (2,577–2,732) and the RSE C fragment (2,660–2,880). Mutations made to the RSE are indicated with the color of the letter representing the level of mutant RNA relative to wild-type RSV unspliced RNA levels.

Fig. 3

The RSE inhibits Upf1 to prevent NMD recognition of the gag termination codon. The RSE interferes with Upf1 binding to eRF3, ATPase activity or NMD RNP remodeling. These steps may be inhibited by direct interaction of the RSE with the NMD factors or through recruitment of a secondary, yet unidentified protein.