Biology subjects

Choudhary, I.

Publications and source records attributed to Choudhary, I..

3 recordsLinked to original sources

bioRxiv2026

Structural basis of substrate recognition and conformational gating in the bacteriophage M15 metalloendopeptidase LysPH

The rapid emergence of antimicrobial resistance has led to a surge in multidrug-resistant strains, jeopardising the efficacy of frontline and last-resort antibiotics and thereby aggravating the antimicrobial resistance crisis. Bacteriophage-derived endolysins represent a promising class of next-generation antimicrobials. Here, we report the isolation of a novel bacteriophage, PA_Ganga_001, targeting multidrug-resistant Pseudomonas aeruginosa. Genomic sequencing of this phage identified a previously uncharacterised endolysin LysPH, a zinc-dependent globular endolysin that exhibits antibacterial activity against multiple multidrug-resistant Gram-negative pathogens, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Site-directed mutagenesis of the endolysin LysPH suggests that His77, Asp84, His159, Arg41, and Asp156 are essential for catalysis and substrate accommodation. To understand the structural basis of substrate binding and catalysis, we determined the crystal structures of the apo-enzyme (1.8 [A]) and the catalytically attenuated D156A mutant in complex with a synthetic pentapeptide stem (PGX) of peptidoglycan (2.0 [A]). The pentapeptide-bound complex revealed a defined substrate-binding groove, and a pronounced displacement of the Thr42-Ser75 loop was observed. This led to an approximately six-fold volumetric expansion of the catalytic cleft, indicative of a substrate-induced transition to an open, catalytically competent conformation. Notably, a distinctive C-terminal helical element, which diverges sequentially from characterised M15 homologues, is predicted to interact with the NAG-NAM scaffold and may contribute to the positioning of the stem pentapeptide for Zn2+ dependent catalysis. These distinct structural features establish the molecular basis for L-Ala-D-Glu hydrolysis by M15 bacteriophage endolysins and provide a foundational framework for the rational design and engineering of the next generation of antimicrobial enzymes.

biochemistry↗

bioRxiv2025

Single-cell transcriptomics reveal alveolar macrophages-specific responses in single-hit ozone exposure model in mice

Alveolar macrophages (AMs), a highly plastic immune cell population, are among the first responders to the inhaled ozone (O3) and ozonized products in the lung airspaces. However, the complete understanding of how AMs respond to O3, particularly to different concentrations, remains elusive. Accordingly, we exposed C57BL/6J male adult mice to filtered air (FA), 1 ppm O3, or 1.5 ppm O3 for 3 hours. As compared to FA-exposed mice, O3-exposed mice exhibited increased recruitment of alveolar macrophages and neutrophils in the lung airspaces, which was consistent with the elevated levels of macrophage- and neutrophil-specific chemokines, i.e., MIP-2, MCP-3, and MCP-5. Next, to profile AM transcriptome from O3-exposed mice and understand the relevance of these transcriptomic changes in relation to their population heterogeneity and functionality, we performed single-cell RNA sequencing (scRNA-seq) analyses. The differentially expressed genes (DEGs) analyses on AM population identified significant changes in 1 ppm-exposed and 1.5 ppm O3-exposed mice. As compared to AMs from FA-exposed group, AMs from 1 ppm O3- and 1.5 ppm O3-exposed groups displayed enrichment of pathways including oxidative phosphorylation, EIF2 signaling, and non-canonical NF-kB signaling. Furthermore, AMs from 1 ppm O3-exposed mice showed enrichment of IL-10 signaling pathway. On the other hand, AMs from 1.5 ppm O3-exposed mice were uniquely enriched in DNA damage bypass and repair pathways. Interestingly, UMAP analyses on annotated AMs resulted in five distinct subclusters. DEGs and ingenuity pathways (IP) analyses on each subcluster revealed O3 concentration-dependent enrichment of pathways relevant to protein translation, cholesterol biosynthesis and mitochondrial biogenesis. Further analyses revealed that O3 exposure results in cluster-specific alterations to the expression of gene signatures associated with macrophage activation. Finally, AMs from 1.5 ppm O3-exposed mice displayed elevated expression of proliferation-associated gene signatures. Taken together, this study identifies O3 concentration-dependent alterations in AMs transcriptome and associated functional modulations at a single-cell resolution.

pharmacology and toxicology↗

bioRxiv2020

Ozone exposure upregulates the expression of host susceptibility protein TMPRSS2 to SARS-CoV-2

BackgroundSARS-CoV-2, a novel coronavirus, and the etiologic agent for the current global health emergency, causes acute infection of the respiratory tract leading to severe disease and significant mortality. Ever since the start of SARS-CoV-2, also known as COVID-19 pandemic, countless uncertainties have been revolving around the pathogenesis and epidemiology of the SARS-CoV-2 infection. While air pollution has been shown to be strongly correlated to increased SARS-CoV-2 morbidity and mortality, whether environmental pollutants such as ground level ozone affects the susceptibility of individuals to SARS-CoV-2 is not yet established. ObjectiveTo investigate the impact of ozone inhalation on the expression levels of signatures associated with host susceptibility to SARS-CoV-2. MethodsWe analyzed lung tissues collected from mice that were sub-chronically exposed to air or 0.8ppm ozone for three weeks (4h/night, 5 nights/week), and analyzed the expression of signatures associated with host susceptibility to SARS-CoV-2. ResultsSARS-CoV-2 entry into the host cells requires proteolytic priming by the host-derived protease, transmembrane protease serine 2 (TMPRSS2). The TMPRSS2 protein and Tmprss2 transcripts were significantly elevated in the extrapulmonary airways, parenchyma, and alveolar macrophages from ozone-exposed mice. A significant proportion of additional known SARS-CoV-2 host susceptibility genes were upregulated in alveolar macrophages and parenchyma from ozone-exposed mice. ConclusionsOur data indicate that the unhealthy levels of ozone in the environment may predispose individuals to severe SARS-CoV-2 infection. Given the severity of this pandemic, and the challenges associated with direct testing of host-environment interactions in clinical settings, we believe that this mice-ozone-exposure based study informs the scientific community of the potentially detrimental effects of the ambient ozone levels determining the host susceptibility to SARS-CoV-2.

pharmacology and toxicology↗