RNA-Protein Interaction Analysis of SARS-CoV-2 5′ and 3′ Untranslated Regions Reveals a Role of Lysosome-Associated Membrane Protein-2a during Viral Infection

Verma, Rohit; Saha, Sandhini; Kumar, Shiv; Mani, Shailendra; Maiti, Tushar Kanti; Surjit, Milan

doi:10.1128/msystems.00643-21

Cited by 26 publications

(40 citation statements)

References 59 publications

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“…RNA - protein interaction detection assay (RaPID assay) involves biotinylation of IRES interacting proteins, followed by their identification by liquid chromatography with tandem mass spectroscopy (LC-MS-MS) (28). RaPID assay was optimized in our laboratory (29). 87 nucleotides of the g1-HEV genome (Genbank ID: AF444002.1) corresponding to the IRESl region was cloned into the pRMB vector between the BirA ligase binding stem-loop (RMB-SLI, RMB-SLII) sequences (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…43 and 8 host proteins identified as interaction partners of the HEV-IRESl RNA by RaPID and Y3H assay, respectively, were clubbed and imported to Cytoscape to generate the RNA-Protein-Protein interaction (RPPI) network, as described earlier (29). Analysis of the different network characteristics revealed that the HEV IRESl-RPPI network contained 51 nodes and 74 edges, the average node degree being 3.36.…”

Section: Identification Of Host Proteins That Interact With the Hev I...mentioning

confidence: 99%

“…The RaPID assay was done as described, following similar conditions (29). To identify the HEV IRESl-interacting host proteins, HEK 293T cells were co-transfected with the pRMB HEV IRESl and BASU plasmids (in 6:1 ratio) using lipofectamine 2000 (1:1 ratio).…”

Section: Rapid Assaymentioning

confidence: 99%

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

Kumar

Verma

Saha

et al. 2022

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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 capindependent 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.

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Section: Resultsmentioning

confidence: 99%

Section: Identification Of Host Proteins That Interact With the Hev I...mentioning

confidence: 99%

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

Kumar

Verma

Saha

et al. 2022

Preprint

Self Cite

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“…Viruses can mimic the host’s mRNAs, which contains 5’ cap, 3’ polyadenylated tail, and untranslated regions (UTRs) on the 5’ and 3’ ends to take advantage of the host’s translational machinery ( 46 , 58 – 60 ). The 5’ and 3’ UTRs in the genome RNA play essential regulatory roles in virus replication, viral gRNA stability, host immunoregulation, and viral genome encapsulation ( 61 ). The SARS-CoV-2 genome has an m7G-cap structure, m7GpppA1, on the genome 5’ end, and a ~30-60-nt-long (47nts in median length) poly(A) tail on the 3’end for viral genome stability and preventing cellular exoribonuclease digestion ( 16 , 62 , 63 ).…”

Section: Proteins Encoded By Coronavirus Genomementioning

confidence: 99%

Translational Control of COVID-19 and Its Therapeutic Implication

et al. 2022

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.

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“…Another study investigated the interaction between 5′ and 3′ UTR of SARS-CoV-2 RNA and host proteins, revealing an enriched expression of proteins involved in RNA metabolism and translation initiation [ 134 ]. The study also identified Lysosome-associated membrane protein-2a (Lamp2a) as one of the 5′-UTR interacting proteins.…”

Section: Introductionmentioning

confidence: 99%

Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components

et al. 2021

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid evolution has led to a global health crisis. Increasing mutations across the SARS-CoV-2 genome have severely impacted the development of effective therapeutics and vaccines to combat the virus. However, the new SARS-CoV-2 variants and their evolutionary characteristics are not fully understood. Host cellular components such as the ACE2 receptor, RNA-binding proteins (RBPs), microRNAs, small nuclear RNA (snRNA), 18s rRNA, and the 7SL RNA component of the signal recognition particle (SRP) interact with various structural and non-structural proteins of the SARS-CoV-2. Several of these viral proteins are currently being examined for designing antiviral therapeutics. In this review, we discuss current advances in our understanding of various host cellular components targeted by the virus during SARS-CoV-2 infection. We also summarize the mutations across the SARS-CoV-2 genome that directs the evolution of new viral strains. Considering coronaviruses are rapidly evolving in humans, this enables them to escape therapeutic therapies and vaccine-induced immunity. In order to understand the virus’s evolution, it is essential to study its mutational patterns and their impact on host cellular machinery. Finally, we present a comprehensive survey of currently available databases and tools to study viral–host interactions that stand as crucial resources for developing novel therapeutic strategies for combating SARS-CoV-2 infection.

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RNA-Protein Interaction Analysis of SARS-CoV-2 5′ and 3′ Untranslated Regions Reveals a Role of Lysosome-Associated Membrane Protein-2a during Viral Infection

Cited by 26 publications

References 59 publications

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

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

Translational Control of COVID-19 and Its Therapeutic Implication

Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components

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