Viruses need the resources of an infected cell to replicate, then infect other cells and transfer to other individuals. An essential step in the viral life cycle is the production of new viral proteins based on the instructions of the viral RNA genome. As a result of these blueprints, the cell’s own protein synthesis machine, called a ribosome, produces viral proteins.
In the absence of viral infection, the ribosome moves along the RNA in strictly defined steps, reading three letters of RNA at a time. This three letter code defines the corresponding amino acid which is attached to the growing protein. It almost never happens that the ribosome slides one or two letters of RNA forward or backward instead of following the regular three-letter steps. When such a ribosome shift occurs, it is called a “frame shift” and it leads to an incorrect reading of the genetic code.
Frame shift almost never occurs in our cells. This would lead to dysfunctional cellular proteins; however, some viruses, such as coronaviruses and HIV, depend on a frame change event to regulate viral protein levels. For example, SARS-CoV-2 – the virus that causes COVID-19 – critically depends on the frame shift promoted by unusual and complex folding of viral RNA.
Therefore, since frame shift is essential for the virus but hardly ever occurs in our organism, any compound that inhibits frame shift by targeting this RNA fold could potentially be useful as a medicine to fight infection. However, so far there is no information on how viral RNA interacts with the ribosome to promote frame shifting, which would be important for drug development.
Detailed image of a process essential for the replication of the coronavirus
A team of researchers from ETH Zurich and the Universities of Bern, Lausanne (Switzerland) and Cork (Ireland) have for the first time succeeded in revealing the interactions between the viral genome and the ribosome during frame shifting. Their results have just been published in the journal La science.
Using sophisticated biochemical experiments, the researchers succeeded in capturing the ribosome at the frame shift site of the SARS-CoV-2 RNA genome. They could then study this molecular complex using cryo-electron microscopy.
The results provided a molecular description of the process in unprecedented detail and revealed a number of unexpected new features. The frame shift event causes the generally dynamic ribosome machine to assume a tense conformation, which has helped provide one of the sharpest and most accurate images of a mammalian ribosome, visualized in the process of frame shift when reading viral genome information. The researchers then continued their structural discoveries with in vitro and in vivo experiments, including exploring how this process can be targeted with chemical compounds. Nenad Ban, professor of molecular biology at ETH Zurich and co-author of the study, points out that “the results presented here on SARS-CoV-2 will also be useful in understanding the mechanisms of frame change in other RNA virus ”.
Possible target for development of antiviral drugs
The dependence of SARS-CoV-2 on this ribosomal frame shift event could be used to develop antiviral drugs. Previous studies have reported that several compounds are able to inhibit frame shift in coronaviruses, however, this study now provides information on the effects of these compounds on SARS-CoV-2 levels in infected cells.
In their experiments, both compounds reduced viral replication by three to four orders of magnitude and were not toxic to the treated cells. However, one of the two reduced viral replication by inhibiting the ribosomal frame shift, while the other might act through a different mechanism.
Although these compounds are currently not potent enough to be used as therapeutic drugs, this study demonstrates that inhibition of ribosomal frame shift has a profound effect on viral replication, paving the way for the development of better compounds. Since all coronaviruses depend on this conserved frame shift mechanism, a drug that targets this process may even be useful for treating infections with coronaviruses further afield. “Our future work will focus on understanding the cellular defense mechanisms that suppress the viral frame shift, as this could be useful for the development of small compounds with similar activity,” says Ban.
Bhatt PR et al. Structural basis of the ribosomal frame shift during the translation of the SARS-CoV-2 RNA genome, La science, published online 13 May 2021. DOI: 10.1126 / science.abf3546
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