Karl Ocius

J Immunol. 2025 Aug 18:vkaf204. doi: 10.1093/jimmun/vkaf204. Online ahead of print.

ABSTRACT

NOD2 is primarily recognized as a cytosolic bacterial sensor of peptidoglycan, activating a downstream Rip2/NF-κB-mediated antimicrobial signaling pathway and playing a vital role in host defense against bacterial infections. NOD2 also appears to play a critical role in immune homeostasis, as NOD2 variants have been linked to multiple human inflammatory diseases, including common polymorphisms that increase the risk of Crohn's disease and rare mutations that cause Blau syndrome. The cellular mechanisms through which mutated NOD2 contributes to disease remain unclear and are currently under investigation. A T cell-intrinsic role for Nod2 in infection and inflammation was suggested almost 15 years ago, leading to intense scrutiny in this research area. This review highlights recent studies establishing a T cell-intrinsic role for NOD2 downstream of T-cell receptor and co-receptor signaling and delineates how NOD2 shapes T-cell responses in both homeostasis and disease, with implications for Blau syndrome and Crohn's disease.

PMID:40824708 | DOI:10.1093/jimmun/vkaf204

ACS Infect Dis. 2025 Aug 18. doi: 10.1021/acsinfecdis.5c00233. Online ahead of print.

ABSTRACT

Infections with Mycobacterium tuberculosis (Mtb) cause tuberculosis (TB), which requires at least 6 months of treatment with multiple antibiotics. There is emergent interest in using β-lactam antibiotics to improve treatment outcomes for patients. These drugs target cell wall biosynthesis, but a comprehensive list of enzymes inhibited by β-lactams in Mtb is lacking. In the current study, we sought to identify and characterize Mtb enzymes inhibited by β-lactam antibiotics using physiological conditions representative of both acute and chronic TB disease. We used new activity-based probes based on the β-lactam antibiotic meropenem due to its approval by the World Health Organization for TB treatment. Activity-based probes label enzymes based on both substrate specificity and catalytic mechanism, enabling precise identification of drug targets. We identified previously undiscovered targets of meropenem in addition to known cell wall biosynthetic enzymes. We validated β-lactam binding and hydrolysis for six newly identified targets: Rv1723, Rv2257c, Rv0309, DapE (Rv1202), MurI (Rv1338), and LipD (Rv1923). Our results demonstrate that there are at least 30 enzymes in Mtb vulnerable to inhibition by meropenem. This is many more β-lactam targets than historically described, suggesting that efficacy in Mtb is a direct result of polypharmacology.

PMID:40824748 | DOI:10.1021/acsinfecdis.5c00233

bioRxiv [Preprint]. 2025 Aug 4:2025.08.04.668434. doi: 10.1101/2025.08.04.668434.

ABSTRACT

BACKGROUND: Anti-CD4 autoantibodies in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART) appear to prevent CD4+ T cell reconstitution, yet the mechanisms underlying their production remain unclear. Emerging evidence implicates Staphylococcus aureus and its peptidoglycan (PGN) in autoimmunity.

METHODS: Plasma from 32 ART-naive PWH, 53 ART-treated PWH, and 32 HIV- negative controls was analyzed for IgG autoantibodies and markers of S. aureus translocation. Causality was examined in EcoHIV-infected mice administered PGN from S. aureus or Bacillus subtilis . PGN structure was analyzed via mass spectrometry.

RESULTS: Among 87 autoantibodies, 40% were elevated in ART-naive PWH and largely normalized by ART; however, anti-CD4 IgGs remained elevated in PWH on ART. Anti- CD4 IgG levels inversely correlated with CD4+ T cell counts in ART-treated PWH and positively with S. aureus translocation. In mice, S. aureus PGN induced anti-CD4 IgGs, reduced gut CD4+ T cells, and promoted surface IgG binding and apoptosis in CD4+ T cells.

CONCLUSION: S. aureus and its PGN translocation may contribute to anti-CD4 autoimmunity and hinder immune recovery in ART-treated PWH, representing a potential therapeutic target.

PMID:40799576 | PMC:PMC12340865 | DOI:10.1101/2025.08.04.668434

bioRxiv [Preprint]. 2025 Jul 25:2025.07.25.666485. doi: 10.1101/2025.07.25.666485.

ABSTRACT

The Gram-negative cell envelope is a vital interface between the bacterial cell and its environment. It acts as a selective barrier, blocking harmful agents while permitting nutrient uptake. Additionally, it enables environmental sensing and adaptive responses. Structurally, it is composed of the outer membrane, the cytoplasmic (inner) membrane, and the periplasm, which contains the peptidoglycan layer. Peptidoglycan is a conserved polymer that provides structural integrity, allowing the cell to withstand the internal turgor. It consists of glycan strands connected by short peptides, forming a mesh-like structure. In Gram-negative bacteria, the majority of the peptidoglycan subunits contain tetrapeptides. Tetrapeptides are generated through the action of DD-carboxypeptidases (DD-CPases), which cleave the terminal D-alanine from pentapeptides. Gram-negative bacteria encode multiple DD-CPases, but their precise role in maintaining cell shape and structural integrity remain poorly understood. The nosocomial pathogen Acinetobacter baumannii encodes three putative DD-CPases. To investigate the role of these enzymes, we generated single mutants, as well as double mutants in dacC , dacD, and pbpG, which encode the homologs of Escherichia coli DD-CPases PBP5, PBP6a, PBP6b, and the endopeptidase (DD-EPase) PBP7, respectively. We assessed the mutants for changes in cell morphology, growth dynamics, and stress tolerance. Additionally, we analyzed the composition of their peptidoglycan layers to determine the biochemical consequences of their inactivation. Each mutant exhibited distinct alterations in coccobacillary morphology and growth. Peptidoglycan analysis confirmed the enzymes possess DD-CPase activity, and PBP6b also demonstrated endopeptidase activity. Together, our results demonstrate that each peptidoglycan-modifying enzyme contributes uniquely to cell growth and morphology. These findings underscore their non-redundant functions and suggest their specific activities may serve as valuable targets for developing new antimicrobial therapies.

IMPORTANCE: DD-peptidases, including carboxypeptidases and endopeptidases are crucial for maintaining cell envelope homeostasis, with distinct roles for each enzyme in cell wall biogenesis and structural integrity. The enzymatic characterization presented in this study not only advance our understanding of fundamental A. baumannii biology but also highlight these enzymatic activities as targets for development of innovative therapeutic strategies to combat infections caused by this multidrug-resistant microbe.

PMID:40777447 | PMC:PMC12330690 | DOI:10.1101/2025.07.25.666485

bioRxiv [Preprint]. 2025 Jul 21:2025.07.21.665895. doi: 10.1101/2025.07.21.665895.

ABSTRACT

Enterococcus faecium is a Gram-positive bacterium that is resident to the intestines of animals including humans. E. faecium is also an opportunistic pathogen that causes multidrug resistant (MDR) infections. Bacteriophages (phages) have been proposed as therapeutics for the treatment of MDR infections, however, an obstacle for phage therapy is the emergence of phage resistance. Despite this, the development of phage resistance can impact bacterial fitness, thus, understanding the molecular basis of fitness costs associated with phage resistance can likely be leveraged as an antimicrobial strategy. We discovered that phage resistant E. faecium harbor mutations in the cell wall hydrolase gene sagA . SagA cleaves crosslinked peptidoglycan (PG) involved in PG remodeling. We show that mutations in sagA compromise E. faecium PG hydrolysis rendering them sensitive to β-lactam antibiotics. sagA mutants have cell envelope integrity defects, increased cellular permeability, and aberrant distribution of penicillin binding proteins. This corresponds to a growth defect where cells have abnormal division septa, membrane blebbing, and the formation of mini cells. The dysregulation of the cell envelope in sagA mutants alters the binding of phages to the E. faecium cell surface. Our data support a model where phage infection of E. faecium requires phages to localize to sites of peptidoglycan remodeling at the cell poles and division septa. Our findings show that by altering the function of a single PG hydrolase, E. faecium loses intrinsic β-lactam resistance. This indicates that phage therapy could help revive certain antibiotics when used in combination.

PMID:40777461 | PMC:PMC12330477 | DOI:10.1101/2025.07.21.665895