Biology subjects

Bhattacharyya, D.

Publications and source records attributed to Bhattacharyya, D..

11 recordsLinked to original sources

bioRxiv2026

Oxidative Stress Susceptibility, Complement Dysregulation, and Metabolic Reprogramming in CFH Y402H Patient-Derived Choriocapillaris Endothelial Cells

Age-related macular degeneration (AMD) is a leading cause of central vision loss. Immunofluorescence and gene expression studies in human donor eyes have shown that choriocapillaris endothelial cells (CECs) are lost before retinal pigment epithelium (RPE) degeneration, leaving extracellular matrix-filled empty lumens known as "ghost vessels." To investigate disease mechanisms, we generated CECs from patient-specific induced pluripotent stem cells (iPSCs) carrying the high-risk CFH Y402H variant and CRISPR-Cas9-corrected isogenic controls. The iPSC-derived CECs expressed canonical endothelial markers, formed fenestrations, maintained barrier function, and assembled capillary-like structures. Although baseline metabolism was preserved, Y402H CECs showed heightened sensitivity to hydroquinone-induced oxidative stress, with increased cytotoxicity and deposition of the complement membrane attack complex (C5b-9). RNA sequencing revealed oxidative stress-driven upregulation of lipid biosynthesis, mTORC signalling, endothelial-to-mesenchymal transition, and angiogenic pathways, alongside an imbalance in the complement pathway. These findings demonstrate that the CFH Y402H polymorphism increases CEC vulnerability to environmental stress, linking complement dysregulation and metabolic reprogramming to choriocapillaris dysfunction in AMD and highlighting CECs as a potential therapeutic target.

Cell Biology↗

bioRxiv2026

Adaptive Focused Acoustics-integrated proteome profiling of macrophages uncovers low abundant proteins associated with immune homeostasis, inflammatory response, and transport

Efficient and reproducible protein extraction is a critical step in mass spectrometry-based proteomics workflows, particularly for complex host-pathogen systems where low-abundance immune-associated proteins are difficult to detect. Probe sonication methods used for cell lysis requiring mitigation of excessive heat generation, to prevent degradation of biologically important proteins, while also limiting throughput and potentially introducing sample-to-sample variability. In this study, we evaluated adaptive focused acoustics (AFA) technology as an alternative approach for macrophage lysis and protein extraction and digestion within a standard proteomics workflow coupled with mass spectrometry. We observed that AFA technology reduced hands-on processing times and overall workflow timelines and single-sample AFA technology improves proteome coverage, dynamic range, and reproducibility. We also evaluated multiplexed AFA technology for lysis, and we observed an exclusive macrophage proteome and influence on replicate reproducibility and dynamic range detection for low abundant proteins. Moreover, multiplexed AFA technology for macrophage lysis and digestion further increased protein identifications, replicate reproducibility, and dynamic range. Considering the AFA-exclusive proteome, 86 proteins were detected across all AFA-based lysis and digestion methods, including low-abundance proteins associated with macrophage homeostasis, inflammatory response, and transport. Together, these findings demonstrate that AFA technology enhances reproducibility, throughput, and proteome depth for macrophage protein extraction while enabling the detection of biologically relevant low-abundance immune-associated proteins. These improvements provide a strong foundation for future investigation of host-pathogen infection models, where pathogen-derived proteins remain challenging to detect within complex host proteomes.

immunology↗

bioRxiv2026

Rv0783c of Mycobacterium tuberculosis acts as a proton-motive force dependent multidrug efflux transporter involved in the efflux of structurally unrelated antibiotics and enhancing biofilm formation

Despite multiple treatment strategies and extensive research on resistance mechanisms, tuberculosis (TB) remains a major global health threat, largely because of the rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. Among various mechanisms complicating the situation, active antibiotic export via efflux pumps is particularly significant, yet largely unexplored. Mycobacterium sp. encodes numerous transporters, many of which are overexpressed in clinical isolates or under drug stress. Here, we examined the possible role of Rv0783c, a putative transporter that is reportedly overexpressed in drug-stressed conditions. Rv0783c conferred resistance to multiple structurally diverse antibiotics, fluoroquinolones and anti-TB drugs in the heterologous hosts, namely, Escherichia coli and Mycobacterium smegmatis. Reduced drug accumulation and active efflux of ethidium bromide (EtBr) confirmed its transport activity, which in turn gets nullified upon using the proton-motive force blocker, CCCP. On the other hand, its expression enhanced biofilm formation, linking antibiotic resistance to persistence-associated phenotype. Furthermore, site-directed mutagenesis confirmed the presence of crucial interacting residues with antibiotics that were identified by in silico analysis. Overall, we demonstrate the role of Rv0783c in the extrusion of first and second-line anti-TB drugs and enhancing biofilm formation.

microbiology↗

bioRxiv2026

Targeting activated IL-23 signaling in Scleroderma by tildrakizumab

The pathogenesis of systemic sclerosis (SSc) involves immune system dysregulation and progressive multi-organ fibrosis. Aberrant interleukin-23 (IL-23) function is linked to many inflammatory conditions. Tildrakizumab, a humanized monoclonal antibody that binds to the p19 subunit of IL-23 to block its interaction with the IL-23 receptor, is FDA-approved for treating psoriasis. IL-23 levels are increased in SSc patients with lung involvement, but the pathogenic role of IL-23 in SSc fibrosis remains unclear. We examined IL-23 expression in SSc skin biopsies and assessed the effects of IL-23 inhibition in an in vivo fibrosis model. We found increased IL-23 expression in SSc compared to healthy skin biopsies. Pharmacological blockade of IL-23 signaling using tildrakizumab reversed experimental skin and lung fibrosis. Our findings support a pathogenic role of IL-23 in SSc and suggest that tildrakizumab could be a novel antifibrotic treatment strategy for SSc and related fibrotic disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/701821v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@777c8aorg.highwire.dtl.DTLVardef@9163f5org.highwire.dtl.DTLVardef@1399a54org.highwire.dtl.DTLVardef@c30ec2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

A magnesium transporter CorA of Mycobacterium smegmatis enhances the tolerance of structurally unrelated antibiotics in the host cells

Ion transporters or channels are involved in maintaining metal homeostasis in bacterial cells by aiding the movement of metal ions across the cell, which might also facilitate the export of antimicrobials. Ubiquitous magnesium transporter, CorA of Mycobacterium smegmatis is well known for its role in maintaining magnesium homeostasis. However, little is known about its involvement in exerting antimicrobial resistance. Here, with the help of molecular genetics, in vivo and in silico studies we tried to envisage the role of CorA of M. smegmatis in antimicrobial resistance of M. smegmatis and E. coli. Expression of corA in M. smegmatis and E. coli increased the tolerance of the host cells towards various structurally unrelated antibiotics and anti-tubercular drugs. In addition, a significantly lower accumulation of norfloxacin and ofloxacin by the host cells expressing corA further indicated its role in enhancing the efflux pump activity. Moreover, the presence of a sub-inhibitory concentration of Mg2+ resulted in increased low-level tolerance towards the tested drugs. Furthermore, CorA enhanced the biofilm-forming ability of cells expressing it. Overall, we speculate that magnesium transporter CorA facilitates multi-drug efflux activity of the host cells where Mg2+ might act as a facilitator in the process. IMPORTANCEMagnesium acts as a co-factor for various biochemical and physiological reactions, such as protein synthesis, cell membrane integrity, nucleic acid synthesis, etc. Metal transporters maintain metal homeostasis by regulating the uptake, efflux, or transportation of metals in certain necessary cellular compartments. In bacteria, magnesium ion (Mg2+) is mainly supplied by the CorA protein which is a ubiquitous family of transport proteins and extensively studied in E. coli and Salmonella sp. However, little is known about the functional relationship of metal transporters of Mycobacterium sp with extrusion of antibiotics, and their involvement in stress tolerance. Here, we report CorA (MSMEG_5056), a magnesium transporter of Mycobacterium smegmatis in influencing the extrusion of multiple structurally unrelated classes of drugs and enhancing the biofilm formation of E. coli and Mycobacterium smegmatis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/602764v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@11a5f5corg.highwire.dtl.DTLVardef@6ac8f9org.highwire.dtl.DTLVardef@b083dcorg.highwire.dtl.DTLVardef@a0fb8a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Hypothetical model of Antibiotic export by CorA. Antibiotics bind to the closed state of the protein (left). During the transition to the open state (right), the to-and-fro motion between multiple open states drives the efflux of the antibiotic while facilitating the import of Mg2+. The colors of the models correspond to the chain ID. The bottom views of both the closed and open states are shown in the rectangular box, with the color indicated by their respective chain IDs. C_FIG

microbiology↗

bioRxiv2024

Morphological Reprogramming of Primary Cilia Length Mitigates the Fibrotic Phenotype in fibroblasts across diverse fibrotic conditions

Fibrosis is a hallmark of systemic sclerosis (SSc) and many diverse and incurable diseases. Myofibroblast activation, a common cellular phenomenon shared across fibrotic diseases, is marked by actin polymerization known to affect primary cilia (PC) length. We discovered that fibroblasts from diverse fibrotic conditions display significantly reduced PC length ex vivo. Treatment of healthy fibroblasts with profibrotic TGF-{beta}1 induced PC shortening, while silencing ACTA2 in SSc skin fibroblasts caused PC elongation. Importantly, we found that PC length is negatively correlated with cellular expression of -SMA in TGF-{beta}1-stimulated healthy fibroblasts, or pharmacologically de-differentiated myofibroblasts. PC elongation by microtubule polymerization induction in SSc skin fibroblasts using LiCl or the HDAC6 inhibitor tubacin, reversed and mitigated fibrotic responses. Our results implicate a key role for microtubule polymerization in restraining fibrotic responses and suggest that modulation of PC dynamics may represent a potential therapeutic strategy for SSc and other treatment-resistant diseases associated with fibrosis. Teaser. PC length shortening is a hallmark of fibrosis.

cell biology↗

bioRxiv2022

Microdynamics of lamin A Ig-fold domain regulates higher order assembly of the protein

Lamins maintain the shape and rigidity of the nucleus in the form of a proteinaceous scaffold underneath the inner nuclear membrane (INM) and provide anchorage to chromatin and other nuclear proteins. Mutations in the human LMNA gene encoding lamin A/C cause about 16 different diseases with distinct phenotypes collectively termed as laminopathies which affect primarily the muscle tissues as well as adipose tissues, neuromuscular junctions and multiple other organs in progeroid syndromes. Lamins contain several domains of which Ig-fold is one of the well characterized and structured domains that harbours many mutations leading to deleterious interactions with other nuclear proteins. In this work, we have elucidated the effects of 3 such mutations namely R453W, W498C and W498R on the dynamics and flexibility of the Ig-fold domain and the consequent effect on the assembly into lamina by live cell imaging, fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. From our experimental observations, we concluded that R453W has somewhat increased flexibility compared to the other mutants but lower than that of the wild type. This might be attributed due to an alteration of the salt bridges in the Ig fold domain of the mutant. This is the first report where such an alteration in the full length has been documented by gross changes in diffusional properties as a sequel to a mutation in the Ig fold domain

biochemistry↗

bioRxiv2021

Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional requirements

With wide ranging diversity in their geometries, binding strengths and chemical properties, noncanonical base pairs are equipped to intricately regulate and control the structural dynamics of RNA molecules. Protonation of nucleobases adds to the diversity. Compared to the unprotonated scenario, on one hand they open up new alternatives for base pairing interactions (Class I) while on the other, they modulate the geometry and stability of existing base pairing interactions (Class II). In both cases, compensation of the energetic cost associated with nucleobase protonation at physiological pH, can be understood in terms of protonation induced restructuring of charge distribution. This not only leads to modifications in existing base-base interactions but often also leads to additional stabilizing interactions, resulting in the formation of protonated base triples. Here we report our detailed quantum chemical studies, in conjunction with structural bioinformatics based analysis of RNA crystal and NMR structure datasets, probing into the contribution of such protonated triples in the structural dynamics of RNA. Our studies revealed more than 55 varieties of protonated triples in RNA, some of which occur recurrently within conserved structural motifs present in rRNAs, tRNAs and in other synthetic RNAs. Our studies suggest that high occurrence frequencies are associated with protonated triples which satisfy the specific structural requirements of conserved motifs where they occur. For example, protonated triples with flexible geometries are involved in the formation of tertiary contacts between different distant motifs. Stabilization of protonated base pairs, through the induction of additional energetically cooperative interactions, appears to be another factor. These results provide significant insights into the sequence-structure-function relationships in RNA.

biophysics↗

bioRxiv2020

Fruit bromelain derived peptides destabilize growth of amyloidal fibrils

{beta}-Amyloid deposition as fibrillar plaques in brain is the primary cause of Alzheimers disease. We report potency of cysteine protease fruit bromelain from pineapple in destabilising A{beta} fibrils. Bromelain peptide pool (Mw<500 Da) obtained mimicking human alimentary tract digestion inhibited fibrillation from monomeric and oligomeric states of A and irreversibly dissociated preformed fibrils into small oligomers of varied sizes. Time kinetics was followed by Thioflavin-T assay and microscopic imaging. Synthetic bromelain peptides corresponding to A{beta} sticky region found using ClustalW analysis revealed specificity of peptides in destabilisation of amyloidal structures. Spectra of different molecular states of A{beta} obtained from application of 8-anilino-1-naphthalenesulfonic acid, circular dichroism and Fourier-Transformed Infrared spectroscopy collectively indicated interaction dependent structural change. Probable mechanism for fibril dissociation was thus predicted. Peptides relieved A{beta} cytotoxicity on pheochromcytoma cells and dissociated plaques in AD-type rats prepared by bilateral intracerebroventricular administration of A{beta} in rat brain cortex. Pineapple being a phytoceutical, its efficiency to disaggregate amyloid bodies warrant further investigation. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biochemistry↗

bioRxiv2017

Reverse Watson-Crick purine-purine base pairs : the Sharp-turn motif and other structural consequences in functional RNAs

Identification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse Watson-Crick purine-purine base pairs (A:A, G:G&A:GW:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1'-C1' distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a Sharp-turn motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

biophysics↗

bioRxiv2017

How does Mg2+ modulate the RNA folding mechanism - a case study of G:C W:W Trans base pair.

Reverse Watson-Crick G:C base pairs (G:C W:W Trans) occur frequently in different functional RNAs. It is one of the few base pairs whose gas phase optimized isolated geometry is inconsistent with the corresponding experimental geometry. Several earlier studies indicate that accumulation of positive charge near N7 of guanine, through posttranscriptional modification, direct protonation or coordination with Mg2+, can stabilize the experimental geometry. Interestingly, recent studies reveal significant variation in the position of putatively bound Mg2+. This, in conjunction with recently raised doubts regarding some of the Mg2+ assignments near the imino nitrogen of guanine, is suggestive of the existence of multiple Mg2+ binding modes for this base pair. Our detailed investigation of Mg2+ bound G:C W:W Trans pairs, occurring in high resolution RNA crystal structures, show that they occur in 14 different contexts, 8 out of which display Mg2+ binding at the Hoogsteen edge of guanine. Further examination of occurrences in these 8 contexts led to the characterization of three different Mg2+ binding modes, (i) direct binding via N7 coordination, (ii) direct binding via O6 coordination and (iii) binding via hydrogen bonding interaction with the first shell water molecules. In the crystal structures, the latter two modes are associated with a buckled and propeller twisted geometry of the base pair. Interestingly, respective optimized geometries of these different Mg2+ binding modes (optimized at B3LYP) are consistent with their corresponding experimental geometries. Subsequent interaction energy calculations at MP2 level, and decomposition of its components, suggest that for G:C W:W Trans, Mg2+ binding can fine tune the base pair geometries without compromising with their stability. Our results, therefore, underline the importance of the mode of binding of Mg2+ ions in shaping RNA structure, folding and function.

biophysics↗