Biology subjects

Ocius, K.

Publications and source records attributed to Ocius, K..

4 recordsLinked to original sources

bioRxiv2026

Non-canonical peptidoglycan cross-linking is essential for Mycobacterium tuberculosis acid resistance

Mycobacterium tuberculosis withstands acidic conditions to survive and replicate within macrophages. To define the genetic determinants of this adaptation, we performed a transposon screen in a lipid-rich, acidic medium that mimics the host environment and supports robust M. tuberculosis growth. This screen identified ldtB, encoding an L,D-transpeptidase, as essential for growth and survival under acid stress. Loss of LdtB decreased 3-3 peptidoglycan cross-linking, disrupted cell wall architecture, and impaired intrabacterial pH homeostasis, resulting in increased susceptibility to cell wall-active antibiotics. Notably, M. tuberculosis lacking LdtB displayed heightened sensitivity to meropenem within macrophages, suggesting that targeting this enzyme could potentiate {beta}-lactam efficacy during infection. These findings establish LdtB as a key mediator linking peptidoglycan homeostasis to acid stress resistance and underscores the importance of in vitro culture models that recapitulate the host microenvironment for uncovering new in vivo active therapeutic targets. TeaserDisabling a key peptidoglycan cross-linking enzyme compromises M. tuberculosis survival under acidic stress and antibiotic exposure.

microbiology↗

bioRxiv2025

Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition

Cytotoxic T lymphocytes recognize infected and transformed cells through peptide antigens presented by MHC-I. Peptide sequence is assumed to dictate recognition, yet non-enzymatic post-translational modifications (PTMs) installed by reactive electrophiles can render a peptide chemically distinct from the form against which tolerance was established. Here we show that non-enzymatic PTMs arising from oxidative, inflammatory, metabolic, and carbonyl stress alter peptide-MHC-I stability and frequently disrupt recognition by a cognate TCR despite preserved MHC-I binding. Using a thioester probe, we demonstrate proof-of-concept capture of acylation-susceptible MHC-I ligands from the cellular immunopeptidome. Environmental chemicals, pharmaceuticals, and dietary isothiocyanates likewise modify antigenic peptides and impair T cell activation, and chemically distinct adducts at a single residue span the range from complete loss to full retention. Finally, methylglyoxal glycation impairs antigen-specific activation, and scavenging by creatine prevents it. Antigenic identity therefore reflects not only sequence but a peptides cumulative chemical history.

immunology↗

bioRxiv2025

Identification and Evaluation of Benzimidazole- Agonists of Innate Immune Receptor NOD2

Emerging evidence has demonstrated the importance of pattern recognition receptors (PRRs), including the nucleotide-binding and oligomerization domain receptor 2 (NOD2), in human health and disease states. NOD2 activation has shown promise with aiding malnutrition recovery, lessening irritable bowel disease (IBD) symptoms, and increasing the efficacy of cancer immunotherapy. Currently, most NOD2 agonists are derivatives or analogs of the endogenous agonist derived from bacterial peptidoglycan, muramyl dipeptide (MDP). These MDP-based agonists can suffer from low oral bioavailability and cause significant adverse side effects. With the goal of broadly improving NOD2 therapeutic interventions, we sought to discover a novel small molecule capable of activating NOD2 by screening a library of total 1917 FDA approved drugs in a phenotypic assay. We identified a class of compounds, benzimidazoles, that act as NOD2 agonists, with the most potent member of this class being nocodazole. Nocodazole activates NOD2 with nanomolar potency and causes the release of cytokines canonically associated with MDP-induced NOD2 activation, suggesting its potential to elicit similar therapeutic immune effects as MDP and potentially offer improved pharmacological properties.

immunology↗

bioRxiv2023

A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice

Mechanisms by which Mycobacterium tuberculosis (Mtb) evades pathogen recognition receptor activation during infection may offer insights for the development of improved tuberculosis (TB) vaccines. Whilst Mtb elicits NOD-2 activation through host recognition of its peptidoglycan-derived muramyl dipeptide (MDP), it masks the endogenous NOD-1 ligand through amidation of glutamate at the second position in peptidoglycan sidechains. As the current BCG vaccine is derived from pathogenic mycobacteria, a similar situation prevails. To alleviate this masking ability and to potentially improve efficacy of the BCG vaccine, we used CRISPRi to inhibit expression of the essential enzyme pair, MurT-GatD, implicated in amidation of peptidoglycan sidechains. We demonstrate that depletion of these enzymes results in reduced growth, cell wall defects, increased susceptibility to antibiotics and altered spatial localization of new peptidoglycan. In cell culture experiments, training of monocytes with this recombinant BCG yielded improved control of Mtb growth. In the murine model of TB infection, we demonstrate that depletion of MurT-GatD in BCG, resulting in unmasking of the D-glutamate diaminopimelate (iE-DAP) NOD-1 ligand, yields superior prevention of TB disease compared to the standard BCG vaccine. This work demonstrates the feasibility of gene regulation platforms such as CRISPRi to alter antigen presentation in BCG in a bespoke manner that tunes immunity towards more effective protection against TB disease.

microbiology↗