A(T) contribution towards a SARS-CoV-2 human interactome map

Until a vaccine against SARS-CoV-2 is generally available, basic research that promotes a detailed understanding of how to intervene in the SARS-CoV-2 life cycle is one of the best options for fighting COVID-19 at the molecular level. A SARS-CoV- 2 - human protein interaction map that contains high quality viral host protein interactions will provide a useful framework to identify host components which are critical for the viral life cycle and which causally alter host functions. Such a map can guide the prioritization of new points of intervention for drug target research and testing and can directly lead to the repurposing of approved drugs. The acute project will provide an Austrian data contribution to a highly reliable binary virus-human interaction network. This interaction map will be created within an international consortium of research groups who will team employing complementary interaction mapping approaches. The cooperative approach that integrates research work of several laboratories through joining data analysis and data validation is essential in order to quickly and competitively achieve research results and validated research output.

SARS-CoV-2 infection of human cell elicits a substantial cellular phospho-proteome response. However, even after more than 200000 SARS-CoV-2 research papers, this response is not well understood and direct interactions between SARS-CoV-2 proteins and human kinases are largely elusive. We investigated direct interactions between human protein kinases and SARS-CoV-2 proteins to better understand the impact of the virus on cellular signaling. Employing a targeted yeast two-hybrid matrix, we discovered 51 direct interactions involving 14 SARS-CoV-2 proteins and 29 human kinases. Notably, we observed a relatively high number of interactions for CAMK and GMGC kinase families, as well as non-receptor tyrosine kinases. Integrating interactions identified in our screen with transcriptomics and phospho-proteomics data revealed connections between SARS-CoV-2 protein interactions, kinase activity changes, and the cellular phospho-response to infection. We identified altered activity patterns in infected cells for a set of human kinases: AURKB, CDK4, CDK7, ABL2, PIM2, and CDK2. Using a yeast system, we demonstrated a direct inhibition of a FER human tyrosine kinase activity through interaction with a SARS-CoV-2 auxiliary protein, ORF6. ORF6 is involved in suppressing the innate immune response to the virus and FER phosphorylates one of the key transcription factors in innate immune response. Our findings shed light on dysregulated kinase signaling during SARS-CoV-2 infection, and guides our understanding of ORF6 upregulation observed in recent SARS-CoV-2 strains. This study expands our understanding of SARS-CoV-2-host interactions, emphasizing the critical role of kinase-mediated signaling pathways during viral infection.