Rna-protein interaction analysis of sars-cov-2 59 and 39 untranslated regions reveals a role of lysosome-associated membrane protein-2a during viral infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive- strand RNA virus. The viral genome is capped at the 59 end, followed by an untranslated region (UTR). There is a poly(A) tail at the 39 end, preceded by a UTR. The self-interaction between the RNA regulatory elements present within the 59 and 39 UTRs and their interaction with host/virus-encoded proteins mediate the function of the 59 and 39 UTRs. Using an RNA-protein interaction detection (RaPID) assay coupled to liquid chromatography with tandem mass spectrometry, we identified host interaction partners of SARS-CoV-2 59 and 39 UTRs and generated an RNA-protein interaction network. By combining these data with the previously known protein-protein interaction data proposed to be involved in virus replication, we generated the RNA-proteinprotein interaction (RPPI) network, likely to be essential for controlling SARS-CoV-2 replication. Notably, bioinformatics analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism. Lysosome-associated membrane protein-2a (Lamp2a), the receptor for chaperone-mediated autophagy, is one of the host proteins that interact with the 59 UTR. Further studies showed that the Lamp2 level is upregulated in SARS-CoV-2-infected cells and that the absence of the Lamp2a isoform enhanced the viral RNA level whereas its overexpression significantly reduced the viral RNA level. Lamp2a and viral RNA colocalize in the infected cells, and there is an increased autophagic flux in infected cells, although there is no change in the formation of autophagolysosomes. In summary, our study provides a useful resource of SARS-CoV-2 59 and 39 UTR binding proteins and reveals the role of Lamp2a protein during SARS-CoV-2 infection. © 2021 Verma et al.