Biology subjects

Jablonska, J.

Publications and source records attributed to Jablonska, J..

15 recordsLinked to original sources

bioRxiv2026

Alternatively polarized neutrophils metabolically restrain macrophage-driven inflammation

Macrophage-driven inflammation underlies many inflammatory diseases, yet the mechanisms that restrain macrophage activation within inflamed tissues remain poorly understood. Using mouse models of foreign body granuloma formation and macrophage activation syndrome, we show that neutrophils accumulate at sites of inflammation and metabolically restrain macrophage-driven pathology. Neutrophil depletion or genetic impairment exacerbated tissue pathology, whereas induced neutrophilia attenuated inflammatory damage. Tissue-infiltrating neutrophils acquired an alternatively polarized state characterized by high arginase 1 activity that was regulated by an IL4Ra-STAT3-NOX2 signaling axis. Functionally, polarized neutrophils depleted extracellular arginine in an arginase 1-dependent manner, thereby limiting macrophage effector programs. Human neutrophils exhibited conserved regulation of arginase activity, and alternatively polarized neutrophils were detected in patients with sarcoidosis and macrophage activation syndrome. Together, these findings identify an arginine-dependent metabolic mechanism through which alternatively polarized neutrophils restrain macrophage-driven inflammation and reveal a previously unrecognized immune-regulatory role for these cells in chronic inflammatory disease.

immunology↗

bioRxiv2026

Distinct protein synthesis requirements for coupled excitatory and inhibitory long-term co-plasticity in mouse hippocampus

The functioning of neuronal networks critically depends on the coordinated interaction between excitation and inhibition. The properties of glutamatergic and GABAergic synapses are finely tuned by network activity, and the heterosynaptic nature of inhibitory plasticity further emphasizes their functional coupling. Although the dependence of glutamatergic plasticity on protein synthesis is well established, the role of translation in inhibitory plasticity remains unclear. Herein, we investigated how protein synthesis supports the concurrent plasticity at inhibitory and excitatory inputs onto CA1 pyramidal neurons. To this end, we applied a high-frequency stimulation protocol of CA3-CA1 input combined with prolonged postsynaptic depolarization of principal cells. This induced both glutamatergic long-term potentiation (LTP) and inhibitory LTP (iLTP) at synapses formed by somatostatin-expressing interneurons onto pyramidal neurons. Although LTP was observed in slices from both juvenile ([≤]45 days) and adult (>45 days) mice, iLTP was only present in the adult group, revealing an unusual developmental profile. Moreover, in adult animals, excitatory LTP was required for the induction of iLTP but did not determine its magnitude. We found that bath application of translation inhibitor cycloheximide (CHX) strongly attenuated LTP and converted co-occurring iLTP into iLTD. However, when CHX was restricted to the recorded postsynaptic neuron, the initial phase of iLTP proceeded normally, but GABAergic currents gradually returned to baseline levels, indicating intact induction but impaired maintenance. In contrast, postsynaptic CHX left excitatory LTP unaffected. Together, these findings identify two distinct translational mechanisms: a postsynaptic one necessary for strengthening inhibition and a non-postsynaptic process required to potentiate excitation.

neuroscience↗

bioRxiv2026

Integrated kidney and urine proteomics define encrypted antimicrobial peptides as effectors of host defence in human pyelonephritis

Antimicrobial peptides (AMPs) are key effectors of host defence, however, their functional deployment across renal tissue and urine in pyelonephritis (PN) remains incompletely understood. Here, we integrate kidney and urine proteomics with urinary peptidomics and computational prediction to define AMP organisation and function. Proteomic analysis indicated coordinated induction of multiple AMPs in infected kidneys. These patterns were recapitulated in the urinary proteome, where AMP abundance correlated with leukocyte counts. Multiplex immunofluorescence microscopy localised these AMPs to myeloid cells, identifying them as central effector sources. Importantly, analysis of the urine peptidome revealed multiple encrypted AMPs (EPs), which arise from proteolytic processing of precursor proteins. To systematically assess their relevance for host defence, we applied an ensemble of machine learning-based predictors to prioritise candidates with activity in the urinary environment. This approach identified several potential EPs, among which the S100A12-derived peptide Calcitermin was confirmed in patient urine. Furthermore, it exerts antibacterial activity against uropathogenic E. coli (UPEC) and modulates myeloid cell responses. Together, these findings define a coordinated and compartmentalised AMP defence programme in human PN that extends beyond increased peptide expression, highlighting EPs as functionally relevant effectors with therapeutic potential.

immunology↗

bioRxiv2026

Histone neutralization protects the ischemic brain against stroke-associated pneumonia

Bacterial pneumonia aggravates ischemic stroke via mechanisms that still remain to be determined. In ischemic stroke patients and mice exposed to middle cerebral artery occlusion, we show that stroke-associated pneumonia markedly worsens clinical stroke outcome. In mice, pneumonia induced 3 days after stroke impaired neurological recovery and increased brain neutrophil infiltrates, blood-brain barrier breakdown, cerebral microvascular thrombosis, and progressive brain atrophy. The antibiotic amoxicillin only partially ameliorated pneumonia-associated neurological deficits and neutrophil infiltrates. Neutrophils were critical mediators of pneumonia-induced blood-brain barrier breakdown and microvascular thrombosis. Notably, administration of a neutralizing anti-histone antibody during pneumonia--unlike degradation or blockade of neutrophil extracellular trap formation or myeloperoxidase inhibition--restored long-term neurological recovery and prevented brain atrophy in stroke-associated pneumonia mice. This study identifies extracellular histones as key drivers of secondary inflammatory brain injury and establishes histone neutralization as a therapeutic strategy with an extended treatment window in the post-acute stroke phase. One Sentence SummaryNeutralizing extracellular histones reverses pneumonia-driven secondary brain injury and restores long-term recovery after ischemic stroke.

neuroscience↗

bioRxiv2025

TSP1/TGF-β1 drives arachidonic acid metabolism to orchestrate neutrophil swarming

Neutrophil swarming has emerged as a conserved multicellular behaviour observed across tissues and pathological contexts. Yet, the molecular cues and the spatially coordinated cellular circuits that drive the process of neutrophil swarming leading to cluster formation remain poorly understood. Here, we combine spatial proteomics and lipid profiling in a model of urinary tract infection to define the epithelial-immune circuits driving neutrophil cluster formation. We identify thrombospondin-1 (TSP1)-mediated activation of transforming growth factor beta 1 (TGF-{beta}1) as key epithelial signal licensing neutrophil clustering and enhancing bacterial control. Spatial lipid analysis further reveals that TSP1/TGF-{beta}1 signalling locally activates arachidonic acid metabolism in epithelial neutrophils, with 5-lipoxygenase dependent leukotriene synthesis required for swarm formation and infection clearance. These findings uncover a spatially coordinated defence mechanism in which epithelial-derived TSP1/TGF-{beta}1 engages neutrophil lipid metabolism to orchestrate neutrophil swarming behaviour and reinforce antibacterial immunity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/688397v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@114ea92org.highwire.dtl.DTLVardef@345244org.highwire.dtl.DTLVardef@10520baorg.highwire.dtl.DTLVardef@1a7c0fe_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

immunology↗

bioRxiv2025

Serpins A1/A3 within tumor-derived extracellular vesicles support pro-tumoral bias of neutrophils in cancer

Neutrophils are known to play an important regulatory role during tumor progression in several types of cancer. However, the mechanisms responsible for their tumorigenic bias and extended lifespan in cancer are not clear to date. This study uncovers a previously unknown mechanism by which tumor-derived small extracellular vesicles (sEVs), via their serpin cargo, reprogram neutrophils to adopt a tumor-supporting phenotype. We demonstrated here an elevated content of plasma sEVs during head and neck cancer progression, and their significant cargo enrichment with inhibitors of neutrophil serine proteases: serpins A1 and A3. Mechanistically, neutrophils educated with serpin-rich tumor-derived sEVs displayed typical pro-tumoral characteristics, including prolonged lifespan and activated CD62Llow CD11bhigh PDL1high phenotype. Functionally, such neutrophils demonstrated a strong ability to promote the epithelial-to-mesenchymal transition of tumor cells. Moreover, such neutrophils induced remarkable suppression of cytotoxic CD8 T cells, significantly reducing their tumor cell-killing capacity. Importantly, serpin cargo was essential for this activity, as serpin-depleted sEVs failed to reprogram neutrophils. These findings again highlight the clinical significance of sEVs and suggest their serpin content as important mediators of pro-tumoral functionality. Targeting the biogenesis or uptake of such immunosuppressive sEVs, or modifying their cargo, could potentially serve as a potent adjuvant anti-cancer therapy.

cancer biology↗

bioRxiv2025

Divergent granulopoiesis at extramedullary sites safeguards host defense

Extramedullary organs such as the spleen can assume granulopoiesis as a supportive mechanism to cope with the demands during persistent inflammation. However, the quantitative output of extramedullary granulopoiesis is limited, thus raising the question if the spleen in fact provides neutrophils of a qualitative difference rather than merely contributing to neutrophil numbers. Here we report splenic stress granulopoiesis with distinct production and differentiation trajectories. Myeloid progenitors in the spleen engage in accelerated production of neutrophils with an immature phenotype. Yet, neutrophils generated during persistent stress granulopoiesis are fully competent to exert antimicrobial functions and are necessary to contain bacterial invasion. Activation of type I interferon signaling in the spleen is required for splenic neutrophil production and its loss impairs host defense. Thus, the spleen provides an immunological environment for stress-induced rapid production and priming of highly active neutrophils to meet the demands during infection.

immunology↗

bioRxiv2025

Rubisco is slow across the tree of life

Rubisco is the main gateway through which inorganic carbon enters the biosphere, catalyzing the vast majority of carbon fixation on Earth. This pivotal enzyme has long been observed to be kinetically constrained. Yet, this impression is based on kinetic measurements heavily focused on eukaryotic rubiscos, a rather conserved group of low genetic diversity. Moreover, the fastest rubiscos that we know of so far were found among the sparsely sampled prokaryotes. Could there be yet faster rubiscos among the uncharted regions of rubiscos phylogenetic diversity? Here, we perform a characterization of more than 250 rubiscos from a wide range of bacteria and archaea, thereby doubling the coverage of the diversity of this key enzyme. We assess the distribution of the carboxylation rates at saturating levels of CO2, and establish that rubisco is a relatively slow enzyme across the tree of life, never exceeding {approx}30 reactions per second at 30{degrees}C. We show that relatively faster subclades share similar evolutionary contexts, involving micro-oxygenic environments or a CO2 concentrating mechanism. Leveraging a simple machine learning model trained on this dataset, we predict the carboxylation rate for all {approx}68,000 sequenced rubisco variants found in nature to date. This study provides the largest and most diverse dataset of natural variants for an enzyme and their associated rates, establishing a solid benchmark for future efforts to predict catalytic rates from sequence data. SignificanceDiscovering a fast carboxylating rubisco has been a long-standing challenge in the scientific community, given its potential impact on sustainable food and fuel production. Yet, only a small fraction of rubiscos natural diversity has been kinetically characterized. Here, we present a large-scale kinetic survey covering the entire spectrum of rubiscos diversity found in nature. Focusing on genetic clusters with above-average rates, we show that rubiscos catalytic rate does not exceed {approx}30 reactions per second at 30{degrees}C. Supported by a machine-learning predictive model, we extend this finding to all sequenced natural variants. Our study provides the most comprehensive kinetic dataset for a single enzyme to date.

systems biology↗

bioRxiv2025

NMDA-dependent coplasticity in VIP interneuron-driven inhibitory circuits

Inhibitory plasticity is emerging as a key regulator of excitation/inhibition (E/I) balance, a fundamental determinant of brain network dynamics. While significant progress has been made in understanding inhibitory plasticity at synapses targeting excitatory principal neurons (I[->]E), the mechanisms and functional implications of plasticity at interneuron-interneuron (I[->]I) synapses remain largely unexplored. Herein, we investigated the properties and plasticity of inhibitory inputs from vasoactive intestinal peptide (VIP) interneurons onto stratum oriens interneurons (soINs) in the hippocampal CA1 region. Using optogenetics, patch-clamp electrophysiology, and morphological reconstructions, we characterized the kinetics, short-term plasticity, and NMDA receptor-dependent long-term plasticity at VIP[->]soIN synapses in two distinct soIN subtypes: fast-spiking (FS) and oriens-lacunosum moleculare (OLM)/bistratified interneurons. Optogenetically evoked VIP[->]soIN IPSCs showed faster rise times and slower decay kinetics in FS interneurons compared to OLM/bistratified cells, although both subtypes exhibited similar short-term plasticity profiles. Brief NMDA receptor activation (1 min) induced long-term depression (iLTD) at VIP[->]OLM/bistratified synapses, but not at VIP[->]FS synapses, underscoring subtype-specific plasticity. However, prolonged NMDA exposure (2 min) elicited iLTD in both interneuron subtypes. Interestingly, excitatory inputs to soINs demonstrated NMDA-induced long-term potentiation (E[->]I LTP) after brief NMDA exposure, but not after prolonged application. Notably, coplasticity analysis in individual soINs revealed asymmetric co-expression of I[->]I LTD and E[->]I LTP in OLM/bistratified interneurons. In contrast, FS interneurons exhibited a duration-dependent transition between asymmetric and symmetric coplasticity. These findings reveal a target-cell-specific landscape of inhibitory I[->]I plasticity and its co-expression with excitatory plasticity, highlighting VIP interneurons as key modulators of E/I balance within local hippocampal circuits.

neuroscience↗

bioRxiv2024

Extracellular matrix integrity regulates GABAergic plasticity in the hippocampus

The brains extracellular matrix (ECM) is crucial for neural circuit functionality, synaptic plasticity, and learning. While the role of the ECM in excitatory synapses has been extensively studied, its influence on inhibitory synapses, particularly on GABAergic long-term plasticity, remains poorly understood. This study aims to elucidate the effects of ECM components on inhibitory synaptic transmission and plasticity in the hippocampal CA1 region. We focus on the roles of chondroitin sulfate proteoglycans (CSPGs) and hyaluronic acid in modulating inhibitory postsynaptic currents (IPSCs) at two distinct inhibitory synapses formed by somatostatin (SST)-positive and parvalbumin (PV)-positive interneurons onto pyramidal cells (PCs). Using optogenetic stimulation in brain slices, we observed that acute degradation of ECM constituents by hyaluronidase or chondroitinase-ABC did not affect basal inhibitory synaptic transmission. However, short-term plasticity, particularly burst-induced depression, was enhanced at PV[->]PC synapses following enzymatic treatments. Long-term plasticity experiments demonstrated that CSPGs are essential for NMDA-induced iLTP at SST[->]PC synapses, whereas the digestion of hyaluronic acid by hyaluronidase impaired iLTP at PV[->]PC synapses. This indicates a synapse-specific role of CSPGs and hyaluronic acid in regulating GABAergic plasticity. Additionally, we report the presence of cryptic GABAergic plasticity at PV[->]PC synapses induced by prolonged NMDA application, which became evident after CSPG digestion and was absent under control conditions. Our results underscore the differential impact of ECM degradation on inhibitory synaptic plasticity, highlighting the synapse-specific interplay between ECM components and specific GABAergic synapses. This offers new perspectives in studies on learning and critical period timing.

neuroscience↗

bioRxiv2024

Heat shock alters the distribution and in vivo interaction of major nuclear structural proteins, lamin and DNA topoisomerase II, with nucleic acids

Lamins and topoisomerases play a critical role in the structural support of cell nuclei, in the regulation of chromatin structure, chromatin distribution, topology of DNA, gene expression, transcription, splicing and transport. Here, we report the role of lamins and Top2 during transition from normal conditions (N), in heat shock (HS) and recovery (R) in Drosophila since the fly genome contains a single gene for B-type lamin (lamin Dm), for A-type lamin (lamin C) and Top2. Heat shock increases transient phosphorylation of lamin Dm on S25, induces changes in solubility of lamin Dm, Top2, HSF, HDAC1 and HP1 proteins, especially in S2 cells and relocates Top2 and chromatin closer to the nuclear lamina with induction of granular staining for Top2 in Kc, S2 and embryonic cells. Lamin Dm interacts with Top2 protein and HS increases the interaction. In vivo photocrosslinking and immunoprecipitation revealed a significant increase in binding to chromatin and nucleic acids upon HS induction for Top2 and lamin Dm. All the detected changes in the properties and location of proteins returned to "normal" after recovery from heat shock. This suggests an important role for lamin Dm, Top2 and their complexes in nuclear functions during HS and recovery. We propose a model in which relocation of Top2 chromatin complexes closer to the nuclear lamina and lamin Dm may help to rearrange the gene expression pattern by tethering HS inactivated genes to nuclear lamina and NPCs which might also help to bind nuclear fraction of non-HS-related transcripts at the nuclear lamina/NPCs area.

cell biology↗

bioRxiv2023

Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif

Antibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNAIle for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 103-fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.

biochemistry↗

bioRxiv2022

The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation

How protein translation evolved from a simple beginning to its complex and accurate contemporary state is unknown. Aminoacyl-tRNA synthetases (AARSs) define the genetic code by activating amino acids and loading them onto cognate tRNAs. As such, their evolutionary history can shed light on early translation. Using structure-based alignments of the conserved core of Class I AARSs, we reconstructed their phylogenetic tree and ancestral states. Unexpectedly, AARSs charging amino acids that are assumed to have emerged later - such as TrpRS and TyrRS or LysRS and CysRS - appear as the earliest splits in the tree; conversely, those AARSs charging abiotic, early-emerging amino acids, e.g. ValRS, seem to have diverged most recently. Furthermore, the inferred Class I ancestor (excluding TrpRS and TyrRS) lacks the residues that mediate selectivity in contemporary AARSs, and appears to be a generalist that could charge a wide range of amino acids. This ancestor subsequently diverged to two clades: "charged" (which gave rise to ArgRS, GluRS, and GlnRS) and "hydrophobics", which includes CysRS and LysRS as its outgroups. The ancestors of both clades maintain a wide-accepting pocket that could readily diverge to the contemporary, specialized families. Overall, our findings suggest a "generalist-maintaining" model of class I AARS evolution, in which early statistical translation was kept active by a generalist AARS while the evolution of a specialized, accurate translation system took place. SignificanceAminoacyl-tRNA synthetases (AARS) define the genetic code by linking amino acids with their cognate tRNAs. While contemporary AARSs leverage exquisite molecular recognition and proofreading to ensure translational fidelity, early translation was likely less stringent and operated on a different pool of amino acids. The co-emergence of translational fidelity and the amino acid alphabet, however, is poorly understood. By inferring the evolutionary history of Class I AARSs we found seemingly conflicting signals: Namely, the oldest AARSs apparently operate on the youngest amino acids. We also observed that the early ancestors had broad amino acid specificities, consistent with a model of statistical translation. Our data suggests that a generalist AARS was actively maintained until complete specialization, thereby resolving the age paradox.

bioinformatics↗

bioRxiv2020

On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment

Dating back to the last universal common ancestor (LUCA), the P-loop NTPases and Rossmanns now comprise the most ubiquitous and diverse enzyme lineages. Intriguing similarities in their overall architecture and phosphate binding motifs suggest common ancestry; however, due to a lack of sequence identity and some fundamental structural differences, these families are considered independent emergences. To address this longstanding dichotomy, we systematically searched for bridge proteins with structure and sequence elements shared by both lineages. We detected homologous segments that span the first {beta}{beta} segment of both lineages and include two key functional motifs: (i) a phosphate binding loop - the Walker A motif of P-loop NTPases or the Rossmann equivalent, both residing at the N-terminus of 1; and (ii) an Asp at the tip of {beta}2. The latter comprises the Walker B aspartate that chelates the catalytic metal in P-loop NTPases, or the canonical Rossmann {beta}2-Asp that binds the cofactors ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the {beta}2-Asp to take either one of these two roles. We conclude that common P-loops/Rossmann ancestry is plausible, although convergence cannot be completely ruled out. Regardless, both lineages most likely emerged from a polypeptide comprising a {beta}{beta} segment carrying the above two functional motifs, a segment that comprises the core of both enzyme families to this very day.

evolutionary biology↗

bioRxiv2020

Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion

De novo emergence, and emergence of the earliest proteins specifically, demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can peptides confer evolutionary relevant functions, let alone with minimal abiotic amino acid alphabets? How can such polypeptides evolve into mature proteins? Specifically, while nucleic acids binding is presumed a primordial function, it demands basic amino acids that do not readily form abiotically. To address these questions, we describe an experimentally-validated trajectory from a phase-separating polypeptide to a dsDNA-binding protein. The intermediates comprise sequence-duplicated, functional proteins made of only 10 amino acid types, with ornithine, which can form abiotically, as the only basic amino acid. Statistical, chemical modification of ornithine sidechains to arginine promoted structure and function. The function concomitantly evolved - from phase separation with RNA (coacervates) to avid and specific dsDNA binding - thereby demonstrating a smooth, gradual peptide-to-protein transition with respect to sequence, structure, and function.

biochemistry↗