Ribosomal frameshifting is a signature process in many viruses, particularly retroviruses, used to proliferate inside hosts. Now, researchers have developed detailed imaging technology and computational tools to visualize, quantify, and understand frameshifting mechanisms in unprecedented detail in living cells. Details of the study are published in Molecular Cell.
When a virus has infected a host cell, it manipulates host ribosomes to make viral proteins. In a frameshift mutation, a ribosome that’s translating an RNA slips one spot backward or forward along a nucleotide sequence, which leads to the creation of an entirely new protein sequence.
To get a closer look at what is happening during this process, Tim Stasevich, a Colorado State University scientist, and his team engineered protein tags to bind and fluoresce in different colors when RNA translation occurs. They monitored the translation of single RNAs into two, unique protein chains during frameshifting, in a partial HIV-1 virus.
The team observed frameshifting to occur in bursts of activity, following a longer period of non-frameshifting. For example, it is known that HIV virus outputs frameshifted proteins approximately 5% of the time. While it might be expected that lots of RNAs would frameshift occasionally, it was instead observed that 8% of the RNA frameshift at incredibly high rates, thus demonstrating that frameshifting happens only in a small subset of RNA.
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Computer modeling from another Colorado State University researcher revealed that fluctuations in the fluorescent data observed as part of the study could only occur if ribosomes involved in viral frameshifting sometimes pause at the frameshift site. This model suggests that this could cause ribosomal “traffic jams” that maintain production of frameshifted proteins long after regular translation has stopped.
While it is still unclear what exactly distinguishes frameshifting RNA from others, the observations offer hope that this special subset of viral RNA could provide a target for antiviral therapies.
Image: Ribosomes (trains) frameshift (change tracks) at the HIV-1 frameshift sequence (yellow sign), producing large amounts of frameshifted protein (blue smoke) compared to non-frameshifted protein (green smoke). Image courtesy of Keith Rein/Salt & Paper House.