Biology subjects

Ratra, Y.

Publications and source records attributed to Ratra, Y..

6 recordsLinked to original sources

bioRxiv2025

A dominant role of cell death in limiting Chandipura virus propagation at cell-saturating high multiplicity of infection

Viruses transit from a low to high multiplicity of infection (MOI) regime in infected tissues. Type-1 interferons (IFNs) enforce a cellular state refractory to virus multiplication, while the death of infected cells eliminates viral replicative niche. Here, we investigated how these two innate antiviral mechanisms cooperate at various MOIs upon cell infection by Chandipura virus (CHPV), a cytopathic RNA virus implicated in several outbreaks of acute encephalitis in India. We found that as expected, a gradual increase in the input MOI from 0.02 to 2 led to a proportionate surge in the viral yield. Surprisingly, a further rise to MOI 20 caused a reduction in the progeny titer. Our mathematical modeling together with ex vivo infection studies involving mutant cells suggested that cell death - more so than virus-induced type-1 IFNs - restricted CHPV propagation at cell-saturating high MOIs, leading to a net fall in the yield at MOI 20. We argue that the distinct involvement of innate immune pathways at varied MOIs imparts robust cellular defense against cytopathic viruses. Significance sentenceCell death - more so than type-1 interferons - limits Chandipura virus propagation at cell-saturating high multiplicity of infection. Highlights# Type-1 IFNs and cell death cooperate at varied MOI in limiting CHPV multiplication. # At sub-saturating low MOI, type-1 IFNs play a dominant role in controlling CHPV propagation. # At cell-saturating high MOI, cell death determines the progeny yield.

systems biology↗

bioRxiv2023

Downregulation of a cell polarity protein potentiates Chikungunya Virus infection in host cells

During cellular infections, alphaviruses produce a 6 kDa membrane protein (6K) and a transframe variant (TF) of 6K through ribosomal frameshifting. The role of these proteins in alphavirus biology is largely unknown. Here, we show that TF of Chikungunya virus plays a unique and critical role in promoting virus propagation by manipulating host cell boundaries. TF achieves this by targeting and downregulating human Scribble, a component of the polarity complex that controls cellular morphology and apoptosis, leading to its punctate localization, ubiquitination, and subsequent degradation via the proteasomal pathway. The TF-Scribble interaction is mediated by a newly discovered PDZ-domain binding motif (PBM) in TF, with the PDZ domains of Scribble, as demonstrated by co-localization during viral infection and further by co-immunoprecipitation and proteomics analysis. This PBM is unique to TF and is absent in 6K; thus, 6K cannot modulate Scribble localization in infected cells. shRNA-mediated knockdown of Scribble potentiates CHIKV propagation highlighting the requirement of TF for the downregulation of Scribble. While wildtype CHIKV drastically alters cell-cell boundaries, a mutated version of CHIKV generated through reverse genetics ({Delta}TF CHIKV), which produces 6K but not TF, is unable to trigger similar morphological alterations due to its inability to engage Scribble, ultimately resulting in suboptimal virus propagation. A cryoEM reconstruction of {Delta}TF CHIKV at a global resolution of 3.6 [A], one of the highest reported among all alphavirus structures, indicates that the assembly of glycoprotein spikes and nucleocapsid is unaffected. Thus, the loss of TF affects the ultimate stage of cellular egress in the virus life cycle, and not earlier stages such as entry, replication or assembly. Our work thus establishes a novel function for the TF component of alphaviruses in modulating host morphology, potentiating virus transmission, and also distinguishes the functionality of TF from that of 6K in alphavirus biology. TeaserA novel functionality of Chikungunya Virus in modulating cell boundaries to allow efficient virus propagation

cell biology↗

bioRxiv2021

A vitamin D-RelB/NF-κB pathway limits Chandipura virus multiplication by rewiring the homeostatic state of autoregulatory type 1 interferon-IRF7 signaling

Besides its functions in the skeletomuscular system, vitamin D also promotes protective immunity against viral pathogens. Viral sensing by mammalian cells triggers nuclear activation of RelA/NF-{kappa}B and IRF3 factors, which collaborate in mediating the early induction of antiviral type 1 interferons (T1-IFNs). Autocrine T1-IFN signaling further accumulates otherwise negligibly expressed IRF7 in virus-infected cells that then sustains T1-IFN production in a positive feedback. Surprisingly, prior cell-culture studies revealed that vitamin D actually suppresses signal-induced RelA activation. Indeed, it remains unclear how vitamin D limits viral multiplication in a cell-autonomous manner. Here, we examined the role of vitamin D in controlling cellular infections by the Chandipura virus (CHPV), a cytoplasmic RNA virus implicated in human epidemics. We found that vitamin D conditioning produced an altered cell state less permissive for CHPV multiplication because of the heightened expression of T1-IFNs. It is thought that viruses also induce a distinct RelB/NF-{kappa}B activity, which counteracts RelA-driven T1-IFN expressions in infected cells. Our analyses instead characterized a basal nuclear RelB activity, which was downregulated upon vitamin D-mediated suppression of RelB synthesis. Interestingly, this vitamin D-RelB pathway provoked IRF7-mediated positive autoregulation augmenting constitutive T1-IFN expressions even in the absence of viral infections. Accordingly, RelB deficiency rendered redundant, while IRF7 depletion abrogated antiviral vitamin D actions. In sum, our study suggests that the homeostatic state of the signaling circuitry comprising of the NF-{kappa}B and T1-IFN pathways connects micronutrients to antiviral immunity at the cellular level. Significance statementVitamin D limits viral infections, but the underlying mechanism remains unclear. Linking micronutrients to antiviral immunity, Ratra et al. characterize an immune signaling circuitry engaged by vitamin D that generates a cellular state less permissive to infections by Chandipura virus, a pathogen of public health importance.

immunology↗

bioRxiv2021

Selective estrogen receptor modulators limit alphavirus infection by targeting the viral capping enzyme nsP1

Alphaviruses cause animal or human diseases that are characterized by febrile illness, debilitating arthralgia, or encephalitis. Selective estrogen receptor modulators (SERMs), a class of FDA-approved drugs, have been shown to possess antiviral activities against multiple viruses, including Hepatitis C virus, Ebola virus, dengue virus, and vesicular stomatitis virus. Here, we evaluated three SERM compounds, namely 4-hydroxytamoxifen, tamoxifen, and clomifene, for plausible antiviral properties against two medically important alphaviruses, chikungunya virus (CHIKV) and Sindbis virus (SINV). In cell culture settings, these SERMs displayed potent activity against CHIKV and SINV at non-toxic concentrations with EC50 values ranging between 400 nM and 3.9 M. Further studies indicated that these compounds inhibit a post-entry step of the alphavirus life cycle, while enzymatic assays involving purified recombinant proteins confirmed that these SERMs target the enzymatic activity of non-structural protein 1 (nsP1), the capping enzyme of alphaviruses. Finally, tamoxifen treatment restrained CHIKV growth in the infected mice and diminished musculoskeletal pathologies. Combining biochemical, cell culture-based studies, and in vivo analyses, we strongly argue that SERM compounds, or their derivatives, may provide for attractive therapeutic options against alphaviruses.

immunology↗

bioRxiv2019

Chandipura virus requires pro-survival RelA NF-κB function for its propagation

In response to infection by RNA viruses, mammalian cells typically activate RelA-containing NF-{kappa}B heterodimers, which induce genes encoding interferon-{beta} and other antiviral mediators. Therefore, RelA is commonly thought to function as an anti-viral transcription factor. Notably, virus-specific mechanisms often modify mainstay immune pathways. Despite its human health relevance, how Chandipura virus (CHPV) per se interacts with the cellular signaling machinery has not been investigated. Here, we report that RelA deficiency abrogated antiviral gene expressions and yet surprisingly caused diminished growth of CHPV in mouse embryonic fibroblasts. Our experimental studies clarified that RelA-dependent synthesis of pro-survival factors restrained infection-inflicted cell death, and that exacerbated cell death processes prevented multiplication of CHPV in RelA-deficient cells. In sum, we identify a pro-viral function of the immune-activating transcription factor RelA NF-{kappa}B linked to its pro-survival properties.\n\nHighlightsO_LILack of RelA NF-{kappa}B leads to reduced growth of CHPV ex vivo\nC_LIO_LIRelA deficiency exacerbates cell-death processes upon CHPV infection\nC_LIO_LIInhibition of cell-death processes restores CHPV multiplication in RelA-deficient MEFs\nC_LI

immunology↗

bioRxiv2018

Immune differentiation regulator p100 tunes NF-κB responses to TNF

Stringent regulation of TNF signaling prevents aberrant inflammation. TNF engages the canonical NF-{kappa}B pathway for activating the RelA:p50 heterodimer, which mediates specific expressions of pro-inflammatory and immune response genes. Importantly, the NF-{kappa}B system discriminates between time-varied TNF inputs. Negative feedback regulators of the canonical pathway, including I{kappa}B, are thought to ensure transient RelA:p50 responses to brief TNF stimulations. The noncanonical NF-{kappa}B pathway controls a separate RelB activity associated with immune differentiation. In a systems modeling approach, we uncovered an unexpected role of p100, a constituent of the noncanonical pathway, in TNF signaling. Brief TNF stimulation of p100-deficient cells produced an additional late NF-{kappa}B activity consisted of the RelB:p50 heterodimer, which distorted the TNF-induced gene-expression program. Periodic TNF pulses augmented this RelB:p50 activity, which was reinforced by NF-{kappa}B-dependent RelB synthesis. In sum, the NF-{kappa}B system seems to engage distantly related molecules for enforcing dynamical and gene controls of immune-activating TNF signaling.

systems biology↗