All Publications

  • Cross-species microRNA transmission modulates flavivirus growth in mosquitoes. Trends in parasitology Shivaprasad, S., Sarnow, P. 2022


    Mosquitoes can be infected with a variety of RNA viruses. Recently,Zhu et al. demonstrated that human microRNA hsa-miR-150-5p is acquired by mosquitoes during blood meals and protects the Dengue virus by downregulation of chymotrypsin AaCT-1 mRNA. This finding suggests the use of microRNA antagomirs as an antiviral approach in mosquitoes.

    View details for DOI 10.1016/

    View details for PubMedID 35246384

  • The tale of two flaviviruses: subversion of host pathways by RNA shapes in dengue and hepatitis C viral RNA genomes. Current opinion in microbiology Shivaprasad, S., Sarnow, P. 2020; 59: 79–85


    Pathogenic RNA viruses continue to emerge owing to their rapid evolutionary rates. The family of the Flaviviridae contains enveloped, single-stranded, positive-sense RNA viruses that include mosquito borne viruses such as dengue virus and the blood-borne hepatitis C virus. Upon infection, the genomic viral RNA needs to first compete with a sea of host mRNAs for host ribosomes that synthesize the viral proteins. Then, the positive-sense template needs to be amplified and packaged into newly assembled virions. To accomplish these tasks, the virus subverts several biochemical machineries from the host. The participation of specific structures in the viral RNA mediates specific RNA-RNA and RNA-protein interactions that dictate many viral subversion strategies. In this review, we shall focus on the various mechanisms by which RNA elements in the dengue virus and hepatitis C virus untranslated regions aid the viral infectious cycle and contribute to viral fitness.

    View details for DOI 10.1016/j.mib.2020.08.007

    View details for PubMedID 33070015

  • Interaction of miR-125b-5p with Human antigen R mRNA: Mechanism of controlling HCV replication. Virus research Shwetha, S., Sharma, G., Raheja, H., Goel, A., Aggarwal, R., Das, S. 2018; 258: 1-8


    Cellular miRNAs influence Hepatitis C virus (HCV) infection in multiple ways. In this study, we demonstrate that miR-125b-5p is upregulated in HCV infected patient serum samples as well as in HCV infected liver carcinoma cells and is involved in translational regulation of one of its predicted targets, Human antigen R (HuR). We used miRNA mimics and antagomiRs to confirm that HuR is a bonafide miR-125b target. Previously, we have shown that HuR is a positive regulator of HCV replication, whereas we noticed that miR-125b is a negative regulator of HCV infection. As a connecting link between these two observations, we showed that knockdown of miR-125b-5p increased HuR protein levels and rescued HCV replication when the availability of HuR in the cytoplasm was compromised using siRNAs against HuR or an inhibitor of HuR export to the cytoplasm. Overall, the study sheds light on the ability of host cell to use a miRNA as a tool to control virus propagation.

    View details for DOI 10.1016/j.virusres.2018.09.006

    View details for PubMedID 30253192

  • Reversible HuR-microRNA binding controls extracellular export of miR-122 and augments stress response EMBO REPORTS Mukherjee, K., Ghoshal, B., Ghosh, S., Chakrabarty, Y., Shwetha, S., Das, S., Bhattacharyya, S. N. 2016; 17 (8): 1184-1203


    microRNAs (miRNAs), the tiny but stable regulatory RNAs in metazoan cells, can undergo selective turnover in presence of specific internal and external cues to control cellular response against the changing environment. We have observed reduction in cellular miR-122 content, due to their accelerated extracellular export in human hepatic cells starved for small metabolites including amino acids. In this context, a new role of human ELAV protein HuR has been identified. HuR, a negative regulator of miRNA function, accelerates extracellular vesicle (EV)-mediated export of miRNAs in human cells. In stressed cells, HuR replaces miRNPs from target messages and is both necessary and sufficient for the extracellular export of corresponding miRNAs. HuR could reversibly bind miRNAs to replace them from Ago2 and subsequently itself gets freed from bound miRNAs upon ubiquitination. The ubiquitinated form of HuR is predominantly associated with multivesicular bodies (MVB) where HuR-unbound miRNAs also reside. These MVB-associated pool of miRNAs get exported out via EVs thereby delimiting cellular miR-122 level during starvation. Therefore, by modulating extracellular export of miR-122, HuR could control stress response in starved human hepatic cells.

    View details for DOI 10.15252/embr.201541930

    View details for Web of Science ID 000380990300012

    View details for PubMedID 27402548

  • HuR Displaces Polypyrimidine Tract Binding Protein To Facilitate La Binding to the 3 ' Untranslated Region and Enhances Hepatitis C Virus Replication JOURNAL OF VIROLOGY Shwetha, S., Kumar, A., Mullick, R., Vasudevan, D., Mukherjee, N., Das, S. 2015; 89 (22): 11356-11371


    HuR is a ubiquitous, RNA binding protein that influences the stability and translation of several cellular mRNAs. Here, we report a novel role for HuR, as a regulator of proteins assembling at the 3' untranslated region (UTR) of viral RNA in the context of hepatitis C virus (HCV) infection. HuR relocalizes from the nucleus to the cytoplasm upon HCV infection, interacts with the viral polymerase (NS5B), and gets redistributed into compartments of viral RNA synthesis. Depletion in HuR levels leads to a significant reduction in viral RNA synthesis. We further demonstrate that the interaction of HuR with the 3' UTR of the viral RNA affects the interaction of two host proteins, La and polypyrimidine tract binding protein (PTB), at this site. HuR interacts with La and facilitates La binding to the 3' UTR, enhancing La-mediated circularization of the HCV genome and thus viral replication. In addition, it competes with PTB for association with the 3' UTR, which might stimulate viral replication. Results suggest that HuR influences the formation of a cellular/viral ribonucleoprotein complex, which is important for efficient initiation of viral RNA replication. Our study unravels a novel strategy of regulation of HCV replication through an interplay of host and viral proteins, orchestrated by HuR.Hepatitis C virus (HCV) is highly dependent on various host factors for efficient replication of the viral RNA. Here, we have shown how a host factor (HuR) migrates from the nucleus to the cytoplasm and gets recruited in the protein complex assembling at the 3' untranslated region (UTR) of HCV RNA. At the 3' UTR, it facilitates circularization of the viral genome through interaction with another host factor, La, which is critical for replication. Also, it competes with the host protein PTB, which is a negative regulator of viral replication. Results demonstrate a unique strategy of regulation of HCV replication by a host protein through alteration of its subcellular localization and interacting partners. The study has advanced our knowledge of the molecular mechanism of HCV replication and unraveled the complex interplay between the host factors and viral RNA that could be targeted for therapeutic interventions.

    View details for DOI 10.1128/JVI.01714-15

    View details for Web of Science ID 000363467200017

    View details for PubMedID 26339049

    View details for PubMedCentralID PMC4645635

  • The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function NUCLEIC ACIDS RESEARCH Bhat, P., Shwetha, S., Sharma, D. K., Joseph, A. P., Srinivasan, N., Das, S. 2015; 43 (5): 2888-2901


    Translation initiation in Hepatitis C Virus (HCV) is mediated by Internal Ribosome Entry Site (IRES), which is independent of cap-structure and uses a limited number of canonical initiation factors. During translation initiation IRES-40S complex formation depends on high affinity interaction of IRES with ribosomal proteins. Earlier, it has been shown that ribosomal protein S5 (RPS5) interacts with HCV IRES. Here, we have extensively characterized the HCV IRES-RPS5 interaction and demonstrated its role in IRES function. Computational modelling and RNA-protein interaction studies demonstrated that the beta hairpin structure within RPS5 is critically required for the binding with domains II and IV. Mutations disrupting IRES-RPS5 interaction drastically reduced the 80S complex formation and the corresponding IRES activity. Computational analysis and UV cross-linking experiments using various IRES-mutants revealed interplay between domains II and IV mediated by RPS5. In addition, present study demonstrated that RPS5 interaction is unique to HCV IRES and is not involved in 40S-3' UTR interaction. Further, partial silencing of RPS5 resulted in preferential inhibition of HCV RNA translation. However, global translation was marginally affected by partial silencing of RPS5. Taken together, results provide novel molecular insights into IRES-RPS5 interaction and unravel its functional significance in mediating internal initiation of translation.

    View details for DOI 10.1093/nar/gkv110

    View details for Web of Science ID 000352487100040

    View details for PubMedID 25712089

  • Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator JOURNAL OF GENERAL VIROLOGY Gouthamchandra, K., Kumar, A., Shwetha, S., Mukherjee, A., Chandra, M., Ravishankar, B., Khaja, M. N., Sadhukhan, P. C., Das, S. 2014; 95: 1654-1667


    Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20 % of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.

    View details for DOI 10.1099/vir.0.062430-0

    View details for Web of Science ID 000341070400006

    View details for PubMedID 24784414

  • Circulating miRNA profile in HCV infected serum: novel insight into pathogenesis SCIENTIFIC REPORTS Shwetha, S., Gouthamchandra, K., Chandra, M., Ravishankar, B., Khaja, M. N., Das, S. 2013; 3


    Changes in circulating miRNA profiles have been associated with different diseases. Here we demonstrate the circulating miRNA profile in serum of HCV infected individuals using a microRNA array that profiles the expression of 940 miRNAs. Serum samples from two HCV genotype - 1 and two HCV genotype - 3 infected individuals were compared with healthy controls. Expression levels of miR-134, miR-198, miR-320c and miR-483-5p that were commonly upregulated in case of both genotypes were validated in 36 individual patient serum samples. Serum miR-134, miR-320c and miR-483-5p were significantly upregulated during HCV infection. miR-320c and miR-483-5p were also upregulated in HCV- JFH1 infected cells and cell culture supernatant. Pathway analysis of putative target genes of these miRNAs indicated involvement of PI3K-Akt, NFKB and MAPK signaling pathways. Results revealed novel insights on the role of circulating miRNAs in mediating pathogenesis in HCV-infected cells.

    View details for DOI 10.1038/srep01555

    View details for Web of Science ID 000316982600001

    View details for PubMedID 23549102