Translational recoding is the process by which ribosomes are directed into an alternate reading frame of an mRNA to synthesize a different protein. Most retroviruses, and some coronaviruses, utilize translational recoding in the form of an RNA programmed -1 frameshift, which increases the viral genomic coding capacity and regulates expression of essential genes. It is also now becoming clear that translational recoding regulates cellular gene expression in many organisms, including humans. This proposal will examine RNA structures from viruses and cellular mRNAs that recode the reading frame, thus providing insights into the fundamental strategies of how RNA structures direct translational recoding in cells. We will measure for the first time the thermodynamic relationship between HIV-1 mRNA structure and frameshift efficiency in vivo. We will explore how novel, high affinity compounds bind to the HIV-1 frameshift site, stimulate frameshifting, and inhibit HIV replication. Using the tools we have developed for HIV, we will investigate the structure and function of the human CCR5 mRNA frameshift site, which regulates expression of the HIV co-receptor and is stimulated by microRNAs through an unknown mechanism. Finally, we will determine the structural basis for +1 frame recoding, using the well-studied Israeli Acute Paralysis Virus internal ribosome entry site as a model system. These studies will significantly advance our understanding of how mRNAs program translational recoding in human cells, and may eventually lead to the development of novel antiviral therapies.
We aim to broadly understand how viral and cellular mRNA structures program translational recoding events in the form of -1 and +1 frameshifts. This project has direct relevance to public health because it will elucidate the molecular basis of HIV-1 frameshifting and how this process can be targeted with small molecules that inhibit viral replication.
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