Using a new screening assay and experiments with cell lines, the international team of scientists discovered that SARS-CoV-2 proteins can cut host proteins.
Proteases are proteins with enzymatic activity to cut other proteins. Viruses rely on proteases to cut up large chains of newly synthesised viral proteins into individual functional units during their replication process.
In a study published in Emerging Microbes and Infections recently, the team discovered new functions for SARS-CoV-2’s two proteases, called NSP3 and NSP5. They demonstrate that the viral proteases also cleaved host proteins that orchestrate antiviral immunity, interferon regulatory factor 3 (IRF3) being a key one.
Dr Emma Sierecki and Dr Yann Gambin of UNSW Medicine & Health’s Single Molecule Science co-led the study with Mt Sinai Hospital’s Professor Benhur Lee, who is also known widely as “The Virus Whisperer”.
To identify which human proteins interact with SARS-CoV-2 proteases, the researchers used a screening assay where purified viral proteases were combined with a library of immune proteins. This approach identified protein targets, the cleavage of which were then validated in human cell lines infected with SARS-CoV-2.
After the UNSW Sydney researchers discovered the targets in their screen, they reached out to collaborators in New York and Texas where the laboratories were set up for work on infectious agents.
“It was a nervous wait, but when the results came back and we saw that IRF3 was completely wiped out by SARS-CoV-2, it was such an exciting reward for the team,” Dr Gambin said.
Dr Sierecki explained that using full-length proteins that are correctly folded in their protease assay overcomes some limitations of other screening methods that rely on protein fragments or sequence analysis to find protease cleavage sites.
“There’s a lot of information there that helps you understand the biology – information that is lost when you’re looking at a fragment of the protein rather than the whole protein,” Dr Sierecki said.
“Sometimes the binding site is present, but in the correctly folded protein, it may be hidden away in deep folds and can’t be reached by the proteases in the natural environment.”
This study sheds more light on virus-host interactions and a possible way SARS-CoV-2 could affect host cells. The authors believe that these observations reveal a potential mechanism the virus may use to try to temper the host’s innate immune defence.
“We knew very little about the SARS-CoV-2 at the beginning of the pandemic. The more information we have about this virus, the better equipped we are at finding ways to treat COVID-19 and to develop better vaccine strategies,” Dr Sierecki said.
[Feature image: Colourised scanning electron micrograph of a cell (green) heavily infected with SARS-CoV-2 (purple); image credit: NIAID]