Biology subjects

Chowdhury, C.

Publications and source records attributed to Chowdhury, C..

3 recordsLinked to original sources

bioRxiv2026

Characterization of PduU Reveals a Modular Tool for Tuning Microcompartment Permeability

Bacterial microcompartments (MCPs) are versatile proteinaceous organelles that compartmentalize metabolic pathways, offering promising scaffolds for synthetic biology and metabolic engineering. However, designing customized nanobioreactors requires distinguishing structurally indispensable shell proteins from those that can be modified or deleted to tune shell permeability without disrupting core organelle assembly. In this study, we performed a systematic biophysical and metabolic characterization of the hexameric shell protein PduU to evaluate its potential as a modular platform for synthetic organelle engineering. We tested whether deleting pduU or selectively truncating its N-terminal {beta}-barrel domain preserves shell assembly, metabolite flux, and intermediate confinement. Our results demonstrate that PduU modifications alter shell permeability while fully maintaining organelle structural integrity, monodispersity, and electrostatic colloidal stability. Crucially, this modulation in permeability redirects internal metabolic flux toward the energy-generating propionate pathway, resulting in elevated cell biomass and significantly increased yields of propionate, an economically vital industrial platform chemical. By establishing that PduU is a non-essential structural component whose modification tunes small-molecule flux, this work highlights PduU as a flexible locus for shell engineering, providing a scalable strategy for biomanufacturing of high-value bio-based products in tailor-made MCP nanobioreactors.

bioengineering↗

bioRxiv2026

Deciphering the role of the non-active site ancillary residues in maintaining the activity and substrate specificity of OXA-232 beta-lactamase

OXA-232, an OXA-48 like carbapenemase stands amongst newly identified beta-lactamases that causes of the extensive of beta-lactam resistance. While active-site residues are well characterised, the contributions of conserved non-active-site residues in exerting enzymatic activity remain unexplored, limiting our understanding about the roles of these residues in the overall OXA-232 function. To address these gaps, the conserved residues S118, V120, L158, and D159 of OXA-232 positioned adjacent to the active-site motifs and within the omega-like loop were substituted with alanine. Substitutions of S118A and D159A rendered the expressing cells susceptible to penicillins, cephalosporins, and carbapenems, whereas the cells harbouring OXA-232V120A and OXA-232L158A proteins exhibited substrate-selective susceptibility changes. Kinetic analysis with purified proteins revealed the reduction in catalytic efficiency of all the mutants compared to wild-type protein. Though the L158A and D159A mutated proteins become deacylation-deficient, the mutations S118A and V120A exhibited selective acylation defects without trapping intermediates. It is evident from circular dichroism spectroscopy and molecular dynamics simulations that OXA-232S118A, OXA-232V120A, and OXA-232L158A nearly retained their secondary structures and compactness, except for OXA-232D159A, which presumably triggered a misfolding leading to destabilisation of the omega-loop. Interestingly, bicarbonate supplementation partially rescued the lost activities in soluble mutants, underscoring the carbamylation dependence. Taken together, these findings establish S118 and D159 as essential for core catalysis and structural integrity, with V120 and L158 modulating substrate-specific turnover and orientation. The current study reappraised the mechanistic insights of OXA-48-like carbapenemases, providing significant resources in rationally designing future therapeutics to combat carbapenem resistance.

molecular biology↗

bioRxiv2025

Deletion of major shell protein of ethanolamine utilization microcompartment reduces intrinsic antibiotic resistance, biofilm and intracellular survival of Salmonella Typhimurium

With the high rise in Salmonella infection and emergence of antibiotic-resistant variants, developing a novel strategy to control the pathogen is imperative. Earlier studies revealed that Salmonella deploys ethanolamine (EA) metabolic machinery to disseminate in the intestine. Salmonella with a defect in EA metabolism manifests with lower intestinal colonization efficiency. Remarkably, the potential of EA metabolism as a therapeutic target is yet to explore. Our study revealed that supplementation of EA and vitamin B12 in both rich and minimal media enhanced biofilm formation, increased motility, and increased tolerance of Salmonella to some antibiotics. Conversely, mutants deficient in EA metabolic enzymes exhibited no physiological fitness. In Salmonella, EA metabolic enzymes are localized within a proteinaceous microcompartment (MCP) shell composed of thousands of copies of shell proteins encoded by five genes from the eut operon. Fascinatingly, bacterial cells with defective MCP shell due to mutation in the major shell proteins showed enhanced susceptibility towards a number of antibiotics in minimal media. The mutants were unable to form biofilm, produced lower curli expression and were defective in flagellar motility. Also, mutation in one of the major shell proteins reduced intramacrophagic viability of Salmonella. Notably, phenotypes were restored upon ectopic expression of corresponding genes. It was evident that mutation in the MCP shell proteins downregulated the expression of genes related to pathogenicity. Overall, this study sheds new light on understanding the relationship between EA metabolism and bacterial physiology that would pave the way for developing novel therapeutic interventions against Salmonella.

microbiology↗