Immediately after the infection of a cell within the throat or lungs, the SARS-CoV-2 virus works very hard to copy, using the human cell’s metabolic pathways to provide its proteins and make sure that that its genetic material (the RNA genome) is copied. The RNA genome is then packaged very compactly into latest virus particles which are released from the cell to contaminate more cells.

One viral protein, called the nucleocapsid protein (N), is especially vital for rapid and efficient replication. It wraps across the RNA genome within the virus and ensures that the very long RNA is tightly coiled up. When it penetrates the cell, N detaches itself from the RNA genome and assumes an entire range of functions during viral replication: When the RNA is translated into viral proteins, N protects the RNA from being destroyed by the cell’s antiviral defense mechanism (“RNA interference”). N also contributes on to the transcription of RNA into viral proteins, and at last it collects the replicated viral RNA within the cell and coils it up in order that latest viral particles can form.

Like a Swiss army knife, N has several tools at its disposal for all these functions: Firstly, N must give you the option to differentiate between cellular and viral RNA and to coil up the latter in a spiral shape. That’s the reason N can bind viral RNA in a comparatively non-specific manner. To steer the transcription of viral RNA into viral proteins (translation), for instance, N must, nevertheless, equally give you the option to acknowledge specific positions on the viral RNA, called RNA motifs.

Researchers led by Dr. Sophie Korn and Dr. Andreas Schlundt from the Institute for Molecular Biosciences and the Center for Biomolecular Magnetic Resonance (BMRZ) at Goethe University Frankfurt have now make clear exactly how this specific binding through one in all N’s tools, often called the N-terminal domain (NTD), works. Their results construct on preliminary studies by the COVID19-NMR consortium established in Frankfurt through the pandemic. Within the work now presented, Korn and her colleagues used nuclear magnetic resonance (NMR) spectroscopy, by which the atoms of the NTD tool and of the sure RNA are exposed to a powerful magnetic field and in this manner reveal something about their spatial arrangement during binding. As well as, a special X-ray technique (small-angle X-ray scattering, SAXS) delivered precise information concerning the stability of the newly formed molecular complexes.

The result: Each the sequence of the RNA constructing blocks (bases) and the spatial folding of the RNA are vital for binding, whereby the positively charged a part of the NTD binds the negatively charged RNA in a really unspecific way. Several “fingers” of the NTD then explore the RNA in the hunt for motifs that the NTD can use to bind more stably. What attracted the researchers’ attention was that the NTD prefers motifs that are present in lung cells at body temperature in a selected spatial folding that’s lost when the temperature increases by just a number of degrees. This not only identifies them as their very own goal motifs but additionally binds them way more tightly, which may lead to the NTD exercising latest functions.

Although our data are only a primary step, they suggest that the virus could switch between replication and packaging into latest virus particles in this manner: At normal body temperature, the cell predominantly produces constructing blocks for brand new viruses. If we develop a fever in the middle of the infection because our immune system recognizes and fights the virus, the virus might switch to replication as a direct result and make sure that the viral RNA is packaged more and released in the shape of latest virus particles. It’s the viral RNA motifs themselves that provide the switch, which is then triggered by the human defense system.”

Dr. Sophie Korn, Goethe University Frankfurt

Andreas Schlundt is convinced: “With the mix of NMR spectroscopy and SAXS, we’ve got established an experimental method that we are able to use to quickly assess which binding partners N prefers, and this may probably be transposed to other viral proteins. This will probably be useful each within the study of emerging viruses and viral variants in addition to in the event of antiviral drugs that systematically disable the virus, minimizing uncomfortable side effects in the method.”

Source:

Goethe University Frankfurt

Journal reference:

Korn, S. M., et al. (2023). The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements. Nature Communications. doi.org/10.1038/s41467-023-38882-y