Researchers in the US have provided a detailed catalog of the interactions that occur between host cell proteins and RNA and the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the course of infection.
SARS-CoV-2 is the causative agent of the current 2019 Coronavirus Disease (COVID-19) pandemic, which is increasingly a threat to global public health and the global economy.
By integrating the analysis across time points, species, and other positive single-stranded RNA viruses, the researchers identified both common and SARS-CoV-2-specific patterns of RNA-host-protein interactions.
The Stanford University and Yale University team says the results could help inform future studies aimed at understanding viral pathogenesis and possible therapeutic strategies to combat SARS-CoV-2 infection.
A pre-print version of the paper is available on the bioRxiv * server while the article is being peer-reviewed.
Researchers are urgently trying to understand host cell infection and antiviral immunity
As the COVID-19 pandemic continues to hit the world with no vaccine or effective treatment in sight, researchers are urgently trying to understand the molecular mechanisms required for host cell infection and antiviral immunity.
Although the genomes of positive single-stranded RNA viruses have similar replication strategies, there are notable differences in the health outcomes that these pathogens cause.
For example, mosquito-borne flaviviruses such as dengue and zika cause systemic disease, while human coronaviruses such as SARS-CoV-2 generally cause respiratory symptoms.
The infection process is complex and often very specific to the individual virus.
After a virus binds to and enters a host cell, the viral genome rebuilds the host’s cellular pathways to express, replicate, and produce new virions.
Once viral RNA transcripts are deposited in host cells, they eventually produce viral protein products.
“Together, these RNA and protein species remodel the cell to facilitate the viral life cycle,” write Ryan Flynn (Stanford University) and colleagues.
Some studies have recently described the virus products encoded by SARS-CoV-2 RNA and their interactions with host partners, but the exact interactions of SARS-CoV-2 virus RNA (vRNA) with host partners are not well understood.
Cellular context of extended interactomes across viruses. Selected groups of proteins, their accumulation in SARS-CoV-2, Zika, Dengue and Rhinovirus ChIRP and their approximate subcellular localization. Heat map colors indicate the log 2 ChIRP-MS enrichment values. Each heat map has a separate scale bar.
What did the current study include?
Now, Flynn and colleagues have used extensive identification of RNA-binding proteins by mass spectrometry (ChIRP-ms) to define both the common and SARS-CoV-2 specific host pathways that associate with vRNAs.
The team identified 309 host proteins that interact with SARS-CoV-2 RNA during the course of infection.
By comparing the data with ChIRP-MS data for three other positive sense RNA viruses (Zika, Dengue and Rhinovirus) as well as with genome-wide CRISPR screens (Clustered Regular Interspaced Short Palindromic Repeats), the researchers identified both shared and SARS – CoV-2-specific patterns of RNA-host-protein interactions.
For example, the SARS-CoV-2, Dengue, and Zika vRNAs are all associated with the Rab proteins RAB10 and RAB2A, which are involved in subcellular trafficking, and these proteins are required for virus replication and virus-induced cell death.
Although both human coronaviruses and flaviviruses require these Rab glycoproteins to produce new infectious virions, the interaction of SARS-CoV-2 vRNA with the translational apparatus and the Sec / Translocon / OST complexes was compared to Dengue and Zika limited.
“These data suggest that flaviviruses can physically use the translocon complex, while both form membrane-enclosed replication complexes, while SARS-CoV-2 uses other domains of the ERGIC [ER-Golgi intermediate compartment]) “, Writes the team.
An unexpected finding was that vRNA-binding proteins protected the host
An unexpected finding was that the vast majority (116/138) of the vRNA-binding proteins protected the host from virus-induced cell death and did not act as pro-viral factors.
Most of these antiviral factors were linked to multiple families of viruses, but the researchers also identified 31 that were specific for SARS-CoV-2.
“These results show that host cells use a wide and diverse range of proteins to physically detect and counteract viral infections,” say Flynn and colleagues.
SARS-CoV-2 RNA got into the mitochondria
Finally, the researchers also identified a physical link between SARS-CoV-2 vRNA and host mitochondria, which was validated by electron microscopic data that showed changes in the shape and size of the mitochondria after infection.
The team suggests that other viruses, including HIV, may enter the mitochondria, suggesting that vRNA may gain access to the mitochondria during infection.
Mitochondria, which are vital to maintaining cell health, play an important role in perceiving and transmitting signals during cellular stress, and are critical to innate immune signaling.
“We propose that RNA viruses can follow a certain logic in causing mitochondrial stress. That is, many viruses can interact with and disrupt this organelle, but the exact way in which stress is caused and thus signals appear is virus-specific, ”the researchers write.
The results can help inform future studies
According to Flynn and colleagues, the study provides an RNA-centered view of the host proteins and RNAs that interact with SARS-CoV-2 RNA during active infection, and has both common and SARS-CoV-2-specific patterns of RNA – Host protein interactions identified.
“Overall, these data provide a comprehensive catalog of SARS-CoV-2 RNA host-protein interactions that may influence future studies to understand the mechanisms of viral pathogenesis and to nominate host pathways that may be suitable for therapeutic use “concludes the team.
* Important NOTE
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guide clinical practice / health-related behavior, or be treated as established information.