Biology subjects

Chande, A.

Publications and source records attributed to Chande, A..

11 recordsLinked to original sources

bioRxiv2026

ViralEpiBase: a manually curated repository of epitranscriptomic modification sites across viral RNA genomes and virus-encoded transcripts

Post-transcriptional chemical modifications of RNA, collectively termed the epitranscriptome, have emerged as critical regulatory layers governing viral replication, pathogenicity, and host- virus interactions. Despite the rapid accumulation of experimental data on viral RNA modifications, no dedicated, freely accessible resource existed for systematically cataloguing these sites across diverse viral species. Here we present ViralEpiBase, a manually curated database of epitranscriptomic modification sites identified in viral RNA genomes and virus-encoded transcripts at single-nucleotide resolution. ViralEpiBase currently integrates seven chemically distinct RNA modification types: N6-methyladenosine (m6A), N1-methyladenosine (m1A), pseudouridine ({Psi}), 5-methylcytosine (m5C), 2'-O-methylation (2'OMe), inosine and N4-acetylcytidine (ac4C); across 12 viral species encompassing both DNA and RNA viruses of clinical and biological significance. Each entry is linked to its primary literature source or deposited dataset and is retrievable by modification type, genomic coordinates, or viral taxonomy. The database is freely accessible through an intuitive web interface and is updated continuously as new experimental evidence becomes available. ViralEpiBase thus provides the first unified platform dedicated exclusively to viral epitranscriptomics and is designed to facilitate mechanistic investigation of RNA modification functions in viral biology.

bioinformatics↗

bioRxiv2026

HIV-1 virions selectively package circESYT2 to sculpt an actin scaffold that constraints egress

Retroviruses such as HIV-1 package both viral and host RNAs, yet whether circular RNAs (circRNAs) enter virions has remained unknown. Here, we capture the HIV-1 RNA packageome and show the evidence that circRNAs represent a previously unrecognized class of selectively encapsidated host RNAs. Using nanopore sequencing of purified virions, we identify fourteen host-encoded circRNAs that are packaged and focus on the abundant species circESYT2. Expression of HIV-1 Gag alone is sufficient to drive circESYT2 incorporation into virus-like particles, indicating that circRNA incorporation is an intrinsic property of the assembly machinery. Proximity-labeling, mass spectrometry and network analysis of the proteins reveal that circESYT2 is embedded in a filamentous cytoskeleton and interacts predominantly with actin, and functional perturbation in a T-cell line shows that circESYT2 depletion destabilizes actin assembly, reduces actin incorporation into virions and enhances viral egress. Extending this analysis to other retroviruses demonstrates that circESYT2 is more efficiently packaged by murine leukaemia virus than by HIV-1, whereas foamy virus excludes it, indicating virus-specific selectivity in circRNAs capture. These findings suggest circRNAs as bona fide components of retroviral particles and uncover a host RNA-cytoskeleton axis in late replication as an unanticipated layer to host-virus crosstalk.

microbiology↗

bioRxiv2026

circDiscoverer: A resource for curated and predicted circRNA-Protein interactions with experimental support tools

Circular RNAs (circRNAs) regulate various cellular processes by interacting with miRNAs, proteins, and by encoding peptides. Compared to circRNA-miRNA interactions, circRNA-protein interactions (CPIs) and circRNA modifications have been relatively less explored. Here, we developed a comprehensive user-friendly web resource, CircDiscoverer, to explore CPIs and modification landscapes across multiple species, including Homo sapiens, Mus musculus, Drosophila melanogaster, and Arabidopsis thaliana. CircDiscoverer integrates manually curated literature-supported CPIs with computationally predicted interactions. Furthermore, it offers comprehensive insights into protein-binding profiles and detailed information on interacting circRNAs, including qRT-PCR primer sequences, guide RNAs for experimental validation and potential RNA modifications, thereby providing an integrated platform for further research. CircDiscoverer is available at https://aclab.iiserb.ac.in.

bioinformatics↗

bioRxiv2025

SERINC5 Is the Primary Target of Retroviral Antagonists Among Human SERINC Paralogs and Requires a Tri-Cysteine Motif for Its Counteraction by HIV-1 Nef

The human transmembrane protein SERINC5 incorporates into budding HIV-1 particles and inhibits their fusion with new target cells. Among the five members of the SERINC family, SERINC3 and SERINC1 exhibit modest antiviral activity, whereas SERINC2 lacks this function. HIV-1 counteracts SERINC5 by promoting its endocytosis in a Nef- dependent manner. SERINC5 is also downregulated by glycoGag of Moloney murine leukaemia virus (MoMLV) and by the S2 glycoprotein of equine infectious anaemia virus (EIAV). Here, we demonstrate that all human SERINCs, despite their differing antiviral potencies, are incorporated into HIV-1 virions. SERINC5 is the most sensitive to viral antagonists, whereas its paralogs display moderate (SERINC2, SERINC3) or no (SERINC1) susceptibility, suggesting that SERINC5 has exerted stronger selective pressure on retroviral evolution. To identify the determinants of SERINC5 sensitivity to Nef, we performed structure- guided mutagenesis and identified a critical tri-cysteine motif (Cys355, Cys356, Cys358) within intracellular loop 4 (ICL4) required for Nef-mediated downregulation. Substitution of these residues with glutamines conferred resistance to Nef antagonism. While this motif is essential for SERINC5 internalization by diverse HIV-1 and SIV Nef alleles, it is dispensable for downregulation by MoMLV glycoGag and EIAV S2, indicating that these viral antagonists exploit distinct structural features of SERINC5. Finally, we show that SERINC5 is palmitoylated at the tri-cysteine motif, raising the possibility that this modification modulates its sensitivity to Nef. Together, these results confirm the central role of SERINC5 as a target of retroviral counteraction and highlight the crucial importance of ICL4 in mediating its engagement by Nef. ImportanceThe SERINC family of multipass transmembrane proteins includes host factors capable of restricting retrovirus infectivity. Among the five human paralogs, SERINC5 displays the strongest antiviral activity and is the only member efficiently targeted by all known retroviral antagonists, including HIV-1 Nef, MLV glycoGag, and the EIAV S2. This selectivity indicates that the evolutionary pressure exerted by SERINC proteins on retroviruses has been primarily driven by SERINC5 rather than by its relatives. Through structure-guided mutagenesis, we identified a tri-cysteine motif within intracellular loop 4 as a crucial determinant for SERINC5 downregulation by Nef, providing a molecular explanation for its distinctive susceptibility. These findings establish SERINC5 as the principal target of viral counteraction and suggest that its molecular features have contributed to shaping the adaptation of primate lentiviral Nef proteins to the host.

microbiology↗

bioRxiv2024

TGF-β signaling promotes the expression of proviral circular RNA ciTRAN in HIV-1 infection

Circular RNA (circRNA) expression is widespread in immune cells infected by HIV-1, but the crosstalk between circRNA expression and various cellular signaling pathways remains unclear. We report that HIV-1 Vpr triggers TGF-{beta} signaling, which we linked to the increased expression of ciTRAN, a proviral circRNA encoded by SMARCA5. Consistent with this finding, we observed that the essential intracellular TGF-{beta} receptor signaling component SMAD2/3 was recruited to the SMARCA5 promoter in a Vpr-dependent manner. SMARCA5 promoter analysis and functional assays further revealed that the SAMD2/3 binding motif is crucial for ciTRAN upregulation. In response to treatment with DNA-damaging agents or the exogenous addition of recombinant TGF-{beta}, the TGF-{beta}-SMAD axis upregulated the expression of ciTRAN as well as the parental SMARCA5 mRNA. Finally, pharmacological targeting of TGF-{beta} signaling or genetic ablation of TGFBR1 can reduce the ability of HIV-1 Vpr to induce the expression of ciTRAN and viral genes. These results offer crucial mechanistic insights into the regulation of ciTRAN expression by TGF-{beta} signaling and suggest a strategy to inhibit circRNA expression during infection by small molecules.

microbiology↗

bioRxiv2022

HIV-1 Vpr induces ciTRAN to prevent transcriptional silencing of the provirus

The functional relevance of circular RNA (circRNA) expression in HIV-1 infection remains unclear. By developing a customized protocol involving direct RNA nanopore sequencing here, we captured circRNAs in their native state from HIV-1 infected T cells and identified ciTRAN, a circRNA modulator of HIV-1 Transcription. We show that HIV-1 infection of monocytic, T cell lines and primary CD4+ T cells induces ciTRAN expression in a Vpr-dependent manner. ciTRAN protein interactome analysis by proximity biotinylation and mass spectrometry identified SRSF-1 as a prominent interactor of the circular RNA. SRSF-1 is known to negatively regulate HIV-1 transcription, which the virus overcomes by a yet unknown mechanism. We demonstrate that HIV-1 Vpr induced ciTRAN sequesters SRSF1 away from the viral transcriptional complex to promote efficient viral transcription. Accordingly, ciTRAN depletion by CRISPR-Cas phenocopied the effects of SRSF1 overexpression and improved SRSF1 association with HIV-1 transcriptional complex. Finally, we show that an SRSF-1-inspired competing peptide can inhibit HIV-1 transcription regardless of ciTRAN induction. The hijacking of a host circRNA thus represents a new facet of primate lentiviruses in overcoming transmission bottlenecks.

microbiology↗

bioRxiv2021

B.1.617.3 SARS CoV-2 spike E156G/Δ157-158 mutations contribute to reduced neutralization sensitivity and increased infectivity

SARS CoV-2 variants raise significant concerns due to their ability to cause vaccine breakthrough infections. Here, we sequence-characterized the spike gene, isolated from a breakthrough infection, that corresponded to B.1.617.3 lineage. Delineating the functional impact of spike mutations using reporter pseudoviruses (PV) revealed that N-terminal domain (NTD)-specific E156G/{Delta}157-158 contributed to increased infectivity and reduced sensitivity to ChAdOx1 nCoV-19 vaccine (Covishield)-elicited neutralizing antibodies. A six-nucleotide deletion (467-472) in the spike coding region introduced this change in the NTD. We confirmed the presence of E156G/{Delta}157-158 in the RT-PCR-positive cases concurrently screened, in addition to other circulating spike (S1) mutations like T19R, T95I, L452R, E484Q, and D614G. Notably, E156G/{Delta}157-158 was present in more than 85% of the sequences reported from the USA, UK, and India in August 2021. The spike PV bearing combination of E156G/{Delta}157-158 and L452R further promoted infectivity and conferred immune evasion. Additionally, increased cell-to-cell fusion was observed when spike harbored E156G/{Delta}157-158, L452R, and E484Q, suggesting a combinatorial effect of these mutations. Notwithstanding, the plasma from a recovered individual robustly inhibited mutant spike PV, indicating the increased breadth of neutralization post-recovery. Our data highlights the importance of spike NTD-specific changes in determining infectivity and immune escape of variants.

microbiology↗

bioRxiv2021

SARS CoV-2 nucleoprotein enhances the infectivity of lentiviral spike particles

The establishment of SARS CoV-2 spike-pseudotyped lentiviral (LV) systems has enabled the rapid identification of entry inhibitors and neutralizing agents, alongside allowing for the study of this emerging pathogen in BSL-2 level facilities. While such frameworks recapitulate the cellular entry process in ACE2+ cells, they are largely unable to factor in supplemental contributions by other SARS CoV-2 genes. To address this, we performed an unbiased ORF screen and identified the nucleoprotein (N) as a potent enhancer of spike-pseudotyped LV particle infectivity. We further demonstrate that this augmentation by N renders LV spike particles less vulnerable to the neutralizing effects of a human IgG-Fc fused ACE2 microbody. Biochemical analysis revealed that the spike protein is better enriched in virions when the particles are produced in the presence of SARS CoV-2 nucleoprotein. Importantly, this improvement in infectivity is achieved without a concomitant increase in sensitivity towards RBD binding-based neutralization. Our results hold important implications for the design and interpretation of similar LV pseudotyping-based studies.

microbiology↗

bioRxiv2020

Integrated role of microRNA-30e-5p through targeting negative regulators of innate immune pathways during HBV infection and SLE

Precise regulation of innate immunity is crucial for the development of appropriate host immunity against microbial infections and the maintenance of immune homeostasis. The microRNAs are small non-coding RNA, post-transcriptional regulator of multiple genes and act as a rheostat for protein expression. Here, we identified microRNA(miR)-30e-5p (miR-30e) induced by the hepatitis B virus (HBV) and other viruses that act as a master regulator for innate immune responses. Moreover, pegylated type I interferons treatment to HBV patients for viral reduction also reduces the miRNA. Additionally, we have also shown the immuno-pathological effects of miR-30e in systemic lupus erythematous (SLE) patients and SLE mouse model. Mechanistically, the miR-30e targets multiple negative regulators namely TRIM38, TANK, ATG5, ATG12, BECN1, SOCS1, SOCS3 of innate immune signaling pathways and enhances innate immune responses. Furthermore, sequestering of endogenous miR-30e in PBMCs of SLE patients and SLE mouse model respectively by the introduction of antagomir and locked nucleic acid based inhibitor significantly reduces type I interferon and pro-inflammatory cytokines. Collectively, our study demonstrates the novel role of miR-30e in innate immunity and its prognostic and therapeutic potential in infectious and autoimmune diseases.

immunology↗

bioRxiv2020

Coevolution of retroviruses with SERINCs following whole-genome duplication divergence

The SERINC gene family comprises of five paralogs in humans of which SERINC3 and SERINC5 inhibit HIV-1 infectivity and are counteracted by Nef. The origin of this anti-retroviral activity, its prevalence among the remaining paralogs, and its ability to target retroviruses remain largely unknown. Here we show that despite their early divergence, the anti-retroviral activity is functionally conserved among four human SERINC paralogs with SERINC2 being an exception. The lack of activity in human SERINC2 is associated with its post-whole genome duplication (WGD) divergence, as evidenced by the ability of pre-WGD orthologs from yeast, fly, and a post-WGD-proximate SERINC2 from coelacanth to inhibit nef-defective HIV-1. Intriguingly, potent retroviral factors from HIV-1 and MLV are not able to relieve the SERINC2-mediated particle infectivity inhibition, indicating that such activity was directed towards other retroviruses that are found in coelacanth (like foamy viruses). However, foamy-derived vectors are intrinsically resistant to the action of SERINC2, and we show that a foamy virus envelope confers this resistance. Despite the presence of weak arms-race signatures, the functional reciprocal adaptation among SERINC2 and SERINC5 and, in response, the emergence of antagonizing ability in foamy virus appears to have resulted from a long-term conflict with the host.

microbiology↗

bioRxiv2018

A hypothetical new role for single-stranded DNA binding proteins in the immune system

The breadth of the host range of single-stranded DNA (ssDNA) viruses is roughly comparable to the host range of double-stranded DNA viruses (dsDNA). Yet, general ssDNA sensing receptors that activate the immune system have not been unequivocally identified while numerous dsDNA sensing receptors are known. Here, we hypothesize that some of the Single-Stranded DNA Binding (SSB) proteins may act as receptors that detect single-stranded DNA from pathogens and activate the innate immune system. As the first test of our hypothesis, we checked whether human genes that are known to bind to ssDNA are potentially interferon-regulated. Out of the 102 human genes that are known to have ssDNA binding ability 23 genes show a more than two-fold increase in gene expression upon interferon treatment. Single-stranded DNA viruses are pathogens of not only animals but also of plants and protozoans. We used this information to further prioritize our candidate list to ssDNA binding genes that are common between the model plant Arabidopsis thaliana and humans. Based on these strategies, we shortlist several promising candidate genes including the HMGB1 gene which could act as a ssDNA sensor that activates the immune system. Agreeably though we cannot establish a definitive role for these genes as ssDNA sensors of the immune system as yet, our preliminary analysis suggests the potential existence of ssDNA binding protein-like receptors (SLRs) that are worth investigating further.

immunology↗