The Ribosomal Shunt Translation Strategy of Cauliflower Mosaic Virus Has Evolved from Ancient Long Terminal Repeats

Abstract

We have screened portions of the large intergenic region of the Cauliflower mosaic virus (CaMV) genome for promoter activity in baker's yeast (Saccharomyces cerevisiae) and have identified an element that contributes to promoter activity in yeast but has negligible activity in plant cells when expressed in an agroinfiltration assay. A search of the yeast genome sequence revealed that the CaMV element had sequence similarity with the R region of the long terminal repeat (LTR) of the yeast Ty1 retrotransposon, with significant statistical confidence. In plants, the same CaMV sequence has been shown to have an essential role in the ribosomal shunt mechanism of translation, as it forms the base of the right arm of the stem-loop structure that is required for the ribosomal shunt. Since the left arm of the stem-loop structure must represent an imperfect reverse copy of the right arm, we propose that the ribosomal shunt has evolved from a pair of LTRs that have become incorporated end to end into the CaMV genome.Cauliflower mosaic virus (CaMV), the type member of the caulimovirus group, is a pararetrovirus; it replicates by reverse transcription, but replication does not require the integration of the CaMV genome into host chromosomes. The lack of an integration step is one feature that distinguishes the replication strategy of CaMV from that of other plant retrotransposons or the animal retroviruses, and this is reflected in the structure of the CaMV genome (50). The CaMV genome is composed of circular, double-stranded DNA that is approximately 8,000 bp in size (Fig. 1A). The replication intermediate that serves as the template for reverse transcription is the CaMV 35S RNA (Fig. 1A) (47). The 35S RNA is formed when the host RNA polymerase II initiates transcription at nucleotide (nt) position 7435. A transcript termination signal at nucleotide 7613 is initially bypassed such that the RNA Pol II synthesizes viral RNA over the full length of the viral genome until it reaches the transcript termination signal for a second time, at which point transcription stops. Consequently, the first 179 bp of the 5Ј end of the 35S RNA are reiterated on the 3Ј end of the 35S RNA (50).The terminal redundancy in the 35S RNA is required for the template switch that occurs during the synthesis of the first strand of viral DNA by the CaMV reverse transcriptase. In this capacity, the terminal redundancies of the 35S RNA fulfill the function of the R region present in the long terminal repeats (LTRs) of retrotransposons and retroviruses. The structure and function of LTRs are most easily visualized in the retrotransposon forms that are integrated into host chromosomes (Fig. 1B). For example, the integrated form of Ty1 consists of two complete LTRs that flank the open reading frames (ORFs), and each of the LTRs is composed of three distinct regions: U3, R, and U5 (4, 5, 13). Transcription is initiated within the leftward LTR at the junction of U3 and R and is terminated at the junction of R and U5 in the rightward LTR (Fig. 1B). The resultant...

Cross-Species Functionality of Pararetroviral Elements Driving Ribosome Shunting

“…It has been proposed that the ascending and descending arms of the CaMV leader stem section 1 have evolved through head-to-head incorporation of long terminal repeats of an ancient retrotransposon found in the yeast genome [38] . However, the primary sequences building the stem section 1 in RTBV ( Fig.…”