Signals for ribosomal frameshifting in the rous sarcoma virus gag-pol region

Abstract

The gag-pol protein of Rous sarcoma virus (RSV), the precursor to the enzymes responsible for reverse transcription and integration, is expressed from two genes that lie in different translational reading frames by ribosomal frameshifting. Here, we localize the site of frameshifting and show that the frameshifting reaction is mediated by slippage of two adjacent tRNAs by a single nucleotide in the 5' direction. The gag terminator, which immediately follows the frameshift site, is not required for frameshifting. Other suspected retroviral frameshift sites mediate frameshifting when placed at the end of RSV gag. Mutations in RSV pol also affect synthesis of the gag-pol protein in vitro. The effects of these mutations best correlate with the potential to form an RNA stem-loop structure adjacent to the frameshift site. A short sequence of RSV RNA, 147 nucleotides in length, containing the frameshift site and stem-loop structure, is sufficient to direct frameshifting in a novel genetic context.

Mechanical Unfolding of the Beet Western Yellow Virus −1 Frameshift Signal

“…The Beet Western Yellow Virus (BWYV) belongs to the family of plant luteoviruses regulating the expression of its RNA-dependent RNA polymerase by programmed -1 frameshifting in a fashion identical to the well-known gag-pol retroviral frameshifting (54,55). Replication of BWYV genomic RNA requires two virus-encoded functions, a structural capsid protein P1 and an RNA polymerase P2 (18).…”

A code in the protein coding genes

“…Several trinucleotides which may direct −1 frameshift, have been reported, e.g. AAG (E. coli dnaX gene: Tsuchihashi and Brown, 1992;Lindsley and Gallant, 1993; the prokaryotic insertion sequence IS150: Vö gele et al, 1991), AGC (Bruce et al, 1986), CCG (Dayhuff et al, 1986) and TTA (Jacks et al, 1988;ten Dam et al, 1990). As these trinucleotides belong to X 1 and as X 1 is deduced by one circular permutation of X 0 , the theoretical frame 0 is retrieved with − 1 frameshift, as expected with the examples mentioned.…”

Amino acid sequence similarity between the terminal protein of hepatitis B virus and predicted hepatitis delta virus gene product

“…2), which suggests the formation of a stable secondary structure within this mRNA region. Strong hairpin structures are also known to occur near frame shifting sites [20]. These data demonstrate the possibility for the synthesis of a new protein encoded by HDAg mRNA.…”

“…We did not, however, find sequences resembling canonical splice sites; consequently, frame shifting seems to be a more plausible mechanism. Such a mechanism for protein synthesis is known to be widely used in viral genome expression [20]. It has been shown that protein coding sequences can carry an additional message in the form of a universal 3-base periodical pattern (G-nonG-N)m. At recognized slippage sites the G-periodical pattern has been found to be interrupted.…”

“…A stretch of four G residues is exactly placed within this region. Frameshifts are known to occur often in sites containing stretches of identical nucleotides [20]. Furthermore, the whole 3 '-terminal part of 0RF5 is saturated with reverse repeats ( fig.…”