I am Shwetha Shivaprasad, a postdoctoral researcher in the laboratory of Dr.Peter Sarnow, Department of Microbiology and Immunology, Stanford University.

Originally I hail from a small town in Southern India, Hassan which is in the state of Karnataka. It is a place well known for its delightful coffee and skillful stonework architecture. I completed my schooling in Hassan and moved to Manipal University in Karnataka for my Bachelors in Biotechnology. The degree included a six month project in immunology that I carried out in the Biochemistry department of the Indian Institute of Science (IISc). IISc is ranked first among all the research institutes in India. After my Bachelors, I pursued a Masters degree in M.S.University of Baroda in the state of Gujarat, where I was awarded the gold medal for obtaining the highest GPA. I also secured an All India Rank of 3 and a five year scholarship for PhD studies awarded by the Government of India.

I was a PhD candidate in the Department of Microbiology and Cell Biology at the Indian Institute of Science. My research in the field of virology under the guidance of Dr. Saumitra Das revealed novel regulators of viral replication and pathogenesis and I published my findings in several peer reviewed journals. At Stanford, I continue to work on virus-host interactions with specific emphasis on the dengue virus.

Honors & Awards

  • Kishore Vaigyanik Protsahan Yojna scholarship for research in the Basic Sciences, Department of Science and Technology, Government of India (2005-2010)
  • Gold medal for highest GPA, Maharaja Sayajirao University of Baroda, India (2010)
  • Graduate student research fellowship, Council of Scientific and Industrial research, Government of India (2010-2015)
  • Best poster award in the 4th Molecular Virology Meet, Rajiv Gandhi Centre for Biotechnology, India (04/2015)

Professional Education

  • Doctor of Philosophy, Indian Institute of Science (2016)
  • Master of Science, Maharaja Sayajirao University Baroda (2010)
  • Bachelor of Science, Manipal University (2008)

Stanford Advisors

Current Research and Scholarly Interests

The Flaviviridae family of viruses are arthropod-borne human pathogens predominant in tropical regions of the world. Their ability to thrive in both vertebrate and invertebrate hosts make them ideal candidates to study cross species barriers to viral propagation and species specific adaptations in the viral genome. Some of the best examples of structural and functional adaptations of the virus to different hosts can be seen with the Dengue virus.

Dengue is a mosquito borne flavivirus that affects upto 340 million people in a year. The dengue positive strand RNA genome is highly structured with several long range RNA-RNA interactions. These structures act as riboswitches to regulate the viral life cycle. For example, the 5’ and 3’ ends of the viral genome have complementary regions that allow the RNA to alternate between linear and circular conformations, thereby regulating the translation replication switch. There are many examples of such cis acting elements dispersed throughout the 11kb Dengue genome that regulate viral infection. These RNA structures are also involved in interactions with host RNA and protein molecules in a structure and/or sequence dependent manner. Through such interactions, dengue virus is able to subvert the biochemical machineries of both mammalian and mosquito cells and establish successful infection in two different host organisms. Since the physiological and biochemical processes in humans and arthropods are fundamentally different, the virus faces different selective pressures in the two hosts. As the virus replicates, it generates a genetically diverse population from which different variants are selected for in a host specific manner. The dengue 3’UTR contains a regulatory RNA sequence which evolves differently in mosquitoes and mammalian cells. During transmission from humans to mosquitoes, large deletions and mutations accumulate in the 3’UTR which affect the immunomodulatory ability of the virus. They promote survival in mosquito cells but are rapidly cleared in mammalian cells because they generate a higher immune response. In my project, I plan to study the structural and mechanistic determinants of dengue virus adaptation to human and mosquito hosts.

Goals of my study:

1. Global mapping of RNA structures and interactions in Dengue infected mammalian and mosquito cells using in vivo crosslinking (PARIS).

Base pairing between different regions of the dengue RNA (structures) and between dengue RNA and host RNA molecules (interactions) are known to modulate the viral life cycle and viral pathogenesis. Dengue RNA adopts alternative RNA structures that bring distant regulatory motifs of the genome together to facilitate viral translation and replication. At the same time, interactions between the dengue RNA and specific host RNA molecules such as microRNAs adds additional levels of regulation to the viral life cycle. Our goal is to generate a global map of RNA duplexes that are formed in virus infected cells, which could potentially uncover many new structures and interactions that are of consequence to viral propagation.

2. Identification of host proteins interacting with mammalian and mosquito adapted variants of Dengue using the RAPID assay.

Host switching generates different clonal variants of dengue in mammalian cells and mosquito cells. Most of the variants contain mutations in the stem loop 2 of the 3’UTR. These mutations alter the pattern of subgenomic viral RNA fragments (sfRNAs) that are generated in the mosquito and mammalian cells leading to differential triggering of the immune response in the two hosts. In our experiments, we aim to identify host proteins that interact differentially with the mammalian and mosquito adapted variants of dengue genomic RNA, with specific emphasis on the 3’ untranslated region. The findings from our study will help us understand the mechanistic determinants of viral fitness in different hosts.

All Publications

  • 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