Biology subjects

Boocock, D. J.

Publications and source records attributed to Boocock, D. J..

4 recordsLinked to original sources

bioRxiv2025

The Omp85 family protein, TamA, exhibits characteristics 1 of a suitable drug target against Pseudomonas aeruginosa

The outer membrane (OM) of Gram-negative bacteria is crucial for cell stability and virulence and acts as a permeability barrier. The biogenesis, assembly, and regulation of proteins in the OM are therefore attractive areas of study that could lead to identifying novel drug targets. The Translocation and Assembly Module (TAM), composed of TamA and TamB, facilitates the insertion of some {beta}-barrel proteins into the OM of Escherichia coli and Klebsiella pneumoniae, and has also been implicated in lipid homeostasis. However, its role in Pseudomonas aeruginosa remains mostly uncharacterized. To investigate the TAMs function and drug target potential in P. aeruginosa, we generated both single- and double-gene TAM knockouts and assessed their fitness using competition growth assays against wild-type (WT) strains. The WT significantly outcompeted the TAM mutants, indicating a fitness defect. Proteomic analysis revealed surprisingly similar profiles between WT and the double knockout strains, while single knockouts showed changes in OM proteins and reduced expression of flagellar components consistent with attenuated swimming motility observed in {Delta}tamA. Single mutants exhibited differential levels of expression of lipoproteins of the {beta}-barrel assembly machinery suggesting compensatory OM remodelling. In vivo infection assays using Galleria mellonella larvae demonstrated significantly higher survival rates when infected with TAM mutants, with tamA mutants showing the greatest attenuation in virulence. Our findings demonstrate a role the TAM plays in P. aeruginosa virulence and identify TamA as a potential drug target for the development of new antimicrobial therapies. Data summaryThe RNAseq data reported on in this article are available from ArrayExpress: E-MTAB-15348 The mass spectrometry proteomics data have been deposited to the ProteomeXchange with the dataset identifier PXD06704.

microbiology↗

bioRxiv2025

Podocalyxin and ciliary neurotrophic factor receptor are novel components of the surfaceome of chondrogenic cells

BackgroundOsteoarthritis is a degenerative joint disease characterized by progressive loss of articular cartilage and limited capacity for intrinsic repair. A major barrier to developing effective regenerative strategies is the incomplete understanding of the molecular mechanisms regulating chondrogenesis and cartilage maintenance. Cell surface proteins are key mediators of extracellular communication, adhesion, and signaling, yet the chondrogenic surfaceome remains incompletely mapped, with prior studies focusing primarily on mature or cytokine-activated chondrocytes. The aim of this study was to provide a temporal profile of the surfaceome during in vitro chondrogenic differentiation and to identify novel membrane proteins with potential roles in cartilage biology. MethodsWe applied a sialoglycoprotein-targeted glycocapture strategy to selectively enrich plasma membrane proteins from chick embryonic limb bud-derived micromass cultures undergoing chondrogenesis. Enriched samples underwent high-resolution shotgun proteomic analysis, and differentially expressed candidates were validated by western blotting, immunocytochemistry, and transient gene silencing. Functional effects on extracellular matrix gene regulation were assessed by quantitative RT-PCR and matrix histochemistry. ResultsThis approach generated the first temporal surfaceome map of chondrogenic progenitors. Among identified candidates, two proteins not previously linked to chondrogenesis, podocalyxin (PODXL) and ciliary neurotrophic factor receptor (CNTFR), were detected at the plasma membrane and confirmed at the protein and transcript levels. Both proteins exhibited time-dependent downregulation during differentiation. Targeted knockdown revealed differential regulation of the fibrocartilage marker COL1A1 expression, indicating non-redundant roles in cell-matrix signaling and survival pathways. Single-cell transcriptomic meta-analysis confirmed expression of both proteins in discrete human articular chondrocyte subpopulations. ConclusionsThis study expands the molecular framework of chondrogenesis, identifying PODXL and CNTFR as novel, temporally regulated surfaceome components with distinct roles in extracellular matrix signaling. These findings complement prior proteomic analyses of cytokine-activated mature articular chondrocytes and suggest new candidates for developmental cartilage biomarkers and therapeutic targets for osteoarthritis. Our results provide a resource for future cross-species surfaceome studies and highlight key pathways for further investigation into cartilage lineage specification and matrix adaptation. Plain English SummaryOsteoarthritis is the most common joint disease worldwide, causing pain, stiffness, and reduced mobility as the smooth cartilage that covers the ends of bones gradually breaks down. Cartilage has a very limited ability to heal itself, and there are currently no treatments that can stop or reverse the disease. Scientists are working on new ways to repair or replace damaged cartilage, but to do this effectively, they need to understand the molecular "language" that cartilage-forming cells use to develop and maintain healthy tissue. In this study, we examined the set of proteins that are present on the surface of cartilage-forming cells, known as the "surfaceome." These surface proteins play important roles in how cells connect to their surroundings, receive signals, and work together to build the cartilage matrix. Using a method to selectively capture and analyze these proteins, we discovered two that had never been linked to cartilage development: podocalyxin and ciliary neurotrophic factor receptor. We found that these two proteins may have opposite effects on cartilage quality. Because they can be detected on the outside of cells, they could be developed into markers for early osteoarthritis detection or as targets for new therapies. Our findings open the door to new strategies for diagnosing and treating joint disease by focusing on cell-surface communication.

cell biology↗

bioRxiv2021

Astrocytic extracellular vesicles modulate neuronal calcium homeostasis via transglutaminase-2

We have uncovered a novel role for astrocytes-derived extracellular vesicles (EVs) in controlling intraneuronal Ca2+ concentration ([Ca2+]i) and identified transglutaminase-2 (TG2) as a surface-cargo of astrocytes-derived EVs. Incubation of hippocampal neurons with primed astrocyte-derived EVs have led to an increase in [Ca2+]i, unlike EVs from TG2-knockout astrocytes. Exposure of neurons or brain slices to extracellular TG2 promoted a [Ca2+]i rise, which was reversible upon TG2 removal and was dependent on Ca2+ influx through the plasma membrane. Patch-clamp and calcium imaging recordings revealed TG2-dependent neuronal membrane depolarisation and activation of inward currents, due to the opening of L-type-VOCCs and to Na+/Ca2+ -exchanger (NCX) operation in the reverse mode, as indicated by VOCCs/NCX pharmacological inhibitors. A subunit of Na+/K+-ATPase was selected by comparative proteomics and identified as being functionally inhibited by extracellular TG2, implicating Na+/K+-ATPase inhibition in NCX reverse mode-switching leading to Ca2+ influx and higher basal [Ca2+]i. These data suggest that reactive astrocytes control intraneuronal [Ca2+]i through release of EVs with TG2 as responsible cargo, which could have a significant impact on synaptic activity in brain inflammation.

neuroscience↗

bioRxiv2019

Exercise does not induce browning of WAT at thermoneutrality and induces an oxidative, myogenic signature in BAT

Background and aimExercise training elicits diverse effects on brown (BAT) and white adipose tissue (WAT) physiology in rodents. However, these animals are typically housed below their thermoneutral zone (i.e. 28-32{degrees}C). In these conditions, BAT is chronically hyperactive and, unlike human residence, closer to thermoneutrality. Therefore, we set out to determine the effects of exercise training in obese animals at 28{degrees}C (i.e. thermoneutrality) on BAT and WAT in its basal (i.e. inactive) state.\n\nMethodsSprague-Dawley rats (n=12) were housed at thermoneutrality from 3 weeks of age and fed a high-fat diet (HFD). At 12 weeks of age half these animals were randomised to 4-weeks of exercise exercise training, i.e. swim-training (1 hour/day, 5 days per week). Metabolic assessment was undertaken during the final 48h and was followed by interscapular and perivascular BAT and inguinal (I)WAT sampling for the analysis of thermogenic genes and the proteome.\n\nResultsExercise attenuated weight gain but did not affect fat mass or general metabolic parameters (i.e. fasting insulin and glucose). Interestingly, although BAT mass was increased, there was no change in thermogenic gene expression. Differentially regulated proteins in BAT enriched gene ontology (GO) terms including 2-oxoglutarate metabolic process, cytochrome-c activity and mitochondrial respiratory chain complex IV. This was accompanied by an upregulation of multiple proteins and GO terms involved in skeletal muscle physiology suggesting an adipocyte to myocyte switch in BAT. UCP1 mRNA was undetectable in IWAT despite an increase in classical browning markers (i.e. PGC1a and ADRB3) with exercise. Enriched GO terms in IWAT included DNA binding and positive regulation of apoptosis. Impact analysis highlighted carbon metabolism and OXPHOS pathways were regulated by exercise in BAT whilst HIF-1 signalling and cytokine-cytokine receptor interaction were among those modified in IWAT.\n\nConclusionExercise training reduces weight gain in obese animals at thermoneutrality and is accompanied by an oxidative, myogenic signature in BAT, rather than induction of thermogenic genes. This may represent a new, UCP1-independent pathway through which BAT regulates body weight at thermoneutrality.

physiology↗