Biology subjects

Maulik, A.

Publications and source records attributed to Maulik, A..

3 recordsLinked to original sources

bioRxiv2026

hnRNPA1 Remodels SARS-CoV-2 Genomic G-Quadruplexes through Its UP1 Domain

The single-stranded RNA genome of SARS-CoV-2 contains several predicted G-quadruplex (G4) forming sequences. Pharmacological stabilisation of these structures has been shown to suppress viral replication, suggesting that their resolution may be required for efficient viral replication. However, the roles of host proteins in stabilization or destabilization of G4 structures have remained largely unexplored. Human hnRNPA1, one of the most abundant RNA-binding proteins in eukaryotic cells, is a G-quadruplex unfolding protein and has independently been identified as a SARS-CoV-2 genome-binding protein. However, whether it acts on the G-quadruplexes within the SARS-CoV-2 genome has not been examined. Here, we screened eight putative G-quadruplex forming sequences conserved across SARS-related coronaviruses and identified two sequences that fold into G4 structures, confirmed by circular dichroism (CD) spectroscopy and thioflavin T (ThT) fluorescence-based experiments. Furthermore, we showed that the UP1 and UP1+RGG domains of hnRNPA1 specifically bind and unfold these two viral RNA G-quadruplexes. Both UP1 and UP1+RGG unfold viral RNA G-quadruplexes to similar extent, indicating that recognition and unfolding of these viral G-quadruplexes are mediated mainly by the UP1 domain of hnRNPA1. Together, these findings identify hnRNPA1 as a host factor capable of binding and remodelling SARS-CoV-2 genomic RNA G-quadruplexes and suggest a mechanism by which the virus may exploit an abundant host protein to resolve G4 structures within its genome.

biophysics↗

bioRxiv2021

Sequence and phylogenetic analysis revealed structurally conserved domains and motifs in lincRNA-p21

Long Intergenic Non-coding RNAs (lincRNAs) are the largest class of long non-coding RNAs in the eukaryotes, which originate from the intergenic regions of the genome. A ~4kb long lincRNA-p21 is derived from a transcription unit next to the p21/Cdkn1a gene locus. LincRNA-p21 plays key regulatory roles in p53 dependent transcriptional repression and translational repression through its physical association with proteins such as hnRNP-K and HuR.It is also involved in the aberrant gene expression in different cancers. However, detailed information on its structure, recognition, and trans-regulation by proteins is not well known. In this study, we have carried out a complete gene analysis and annotation of lincRNA-p21. This analysis showed that lincRNA-p21 is highly conserved in primates, and its conservation drops significantly in lower organisms. Furthermore, our analysis has revealed two structurally conserved domains in the 5 and 3 terminal regions of lincRNA-p21. Phylogenetic analysis has revealed discrete evolutionary dynamics in these conserved domains for orthologous sequences of lincRNA-p21, which have evolved slowly across primates compared to other mammals. Using Infernal based covariance analysis, we have computed the secondary structures of these domains. The secondary structures were further validated by energy minimization criteria for individual orthologous sequences as well as the full-length human lincRNA-p21. In summary, this analysis has led to the identification of sequence and structural motifs in the conserved fragments, indicating the functional importance for these regions.

bioinformatics↗

bioRxiv2019

Extended insight into the preponderance of LRRs - a docking & simulation study with members of the TLR1 subfamily

The widespread structural motif of Leucine-rich repeats (LRR) constitute the extracellular part of the Toll-like receptor (TLR) family preceded by an intracellular Toll/interleukin-1 receptor (TIR) domain at the C-terminus. The benefit of using LRRs in these pattern recognition receptors (PRR) that are responsible for early detection of pathogens to elicit inflammatory/innate immune response still remains elusive. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) of nine TLR (TLR 1-9) genes from 36 mammals reconfirmed the existence of two distinct clades, one (TLR1/2/6) for recognizing bacterial cell wall derivatives and another (TLR7/8/9) for various nucleic acids. TLR3, TLR4 and TLR5 showed independent line of evolution. The distinction of the TLR1 subfamily to form heterodimers within its members and the existence of the paralogs TLR1 and TLR6 therein, was appealing enough to carry out further studies with the extracellular recognition domain. Dimerizing and ligand binding residues from the crystal structures of TLR1 and TLR6 were interchanged to generate chimeric proteins. The dimer forming ability of these variants with their common partner, TLR2, were checked before running MD simulations. The chimeras were compared with wild type dimers to find no significant alterations in the overall structure. Finally, interchanged ligands were docked to the variants to ratify reversal of the binding function. Intriguingly, sequence change in substantial numbers, 16 in TLR1 and 18 in TLR6, preserves the native scaffold offered by LRRs. This exercise thus depicts how the LRR motif has been advantageous to be selected as an evolutionarily conserved motif for essential cellular processes.

bioinformatics↗