Study of Polyribosomal Effects on Frameshifting

Abstract

Frameshifting (FS) is a mechanism that enables the cell to use the same gene transcript to translate into different protein products. Frameshifting has been found mostly in prokaryotes and viruses. In prokaryotes, the mRNA for frameshifting usually contains three elements: a secondary structure (e.g., a hairpin), a slippery sequence and a Shine-Dalgarno (SD) sequence. When the ribosome is decoding the slippery sequence and stalled by the downstream structure and the upstream SD sequence, translocation of the ribosome may be affected and it will move backward by one base, resulting in −1 frameshifting.In our research, we use the FS motif from the E. coli dnaX gene as the model. We include three tandem repeats of the FS motif. It has been shown that the FS efficiency is about 80%. However, our experiments show that the efficiency was only about 30% at the first FS site, and about 80% at second and third FS sites. We speculate that polyribosomes may play a role for the results; when one ribosome still occupies the hairpin sequence and prevents its refolding, the following ribosome will encounter no structures and thus the FS efficiency is decreased. With a mutated sequence that effectively reduces the density of ribosomes on the mRNA, the FS efficiency of the first site was recovered back to 80%. Other experiments that change the extent of polyribosomes are ongoing to further explore the effects of polyribosomes on frameshifting.