Ranjith-Kumar, C. T. | bioRxiv Science

bioRxiv2025

Chikungunya virus non-structural protein 2 (nsP2) inhibits RIG-I and TLR-mediated immune response

Chikungunya virus (CHIKV) is a single-stranded positive-sense RNA virus that employs various strategies to evade the hosts immune response. The CHIKV non-structural protein 2 (nsP2) is one of the viral-encoded proteins essential for viral replication as well as modulation of the immune response. In this study, we demonstrate that CHIKV nsP2 suppresses both RIG-I-like receptors (RLR) and Toll-like receptors (TLR) signaling pathways. Domain mapping of the nsP2 identified the N-terminal region encompassing the N-terminal domain and the helicase domain (NH) is responsible for the inhibition. Furthermore, site-directed mutagenesis experiments showed that functional helicase is necessary for inhibiting interferon production, but the C-terminal V-Loop region, previously implicated in host transcriptional shutoff is not. Lastly, we demonstrate that nsP2 disrupts two key immune signaling pathways, RLR and TLRs, by interfering with common proteins, TBK1 and IRF3, involved in both signaling pathways. These findings enhance our understanding of CHIKV immune evasion strategies and offer potential targets for the development of antiviral therapeutics.

immunology↗

bioRxiv2022

RNA-protein interactome at the Hepatitis E virus internal ribosome entry site

Multiple processes exist in a cell to ensure continuous production of essential proteins either through cap-dependent or cap-independent translation processes. Viruses depend on the host translation machinery for viral protein synthesis. Therefore, viruses have evolved clever strategies to utilize the host translation machinery. Earlier studies have shown that genotype 1-Hepatitis E virus (g1-HEV) utilizes both cap-dependent and cap-independent translation machineries for its replication and proliferation. Cap-independent translation in g1-HEV is driven by an eighty seven nucleotide-long RNA element which acts as a noncanonical, internal ribosome entry site like (IRESl) element. Here, we have identified the RNA-protein interactome of the HEV IRESl element and characterized the functional significance of some of its components. Our study reveals indispensable roles of host ribosomal protein RPL5 and DHX9 (RNA helicase A) in mediating efficient translation from the IRESl element and establish the function of HEV IRESl as a bonafide internal ribosome entry site. Author summaryProtein synthesis is a fundamental process for survival and proliferation of all living organisms. Majority of cellular proteins are produced through cap-dependent translation. Cells also utilize a variety of cap-independent translation processes to synthesize essential proteins during stress. Viruses depend on the host cell translation machinery to synthesize their own proteins. Hepatitis E virus is a major cause of hepatitis worldwide. The viral genome is a capped positive strand RNA. Viral non-structural and structural proteins are synthesized through a cap-dependent translation process. An earlier study from our laboratory reported the presence of a fourth ORF in genotype 1-HEV, which produced the ORF4 protein using a cap-independent internal ribosome entry site-like (IRESl) element. In the current study, we identified the host proteins that associate with the HEV-IRESl RNA and generated the RNA-protein interactome. Through a variety of experimental approaches, our data proves that HEV-IRESl is a bonafide internal ribosome entry site.

microbiology↗