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Journal articleManchinu MF, Congiu M, Massidda M, et al., 2026, , Neurobiol Dis, Vol: 226
Amyotrophic lateral sclerosis (ALS) lacks reliable, disease-specific, and minimally invasive biomarkers, representing a major barrier to early diagnosis and patient stratification. The primary aim of this translational pilot study was to identify a disease-specific, TDP-43-related, gene-microRNA (miRNA) signature in peripheral blood mononuclear cells (PBMCs) of ALS patients with potential diagnostic value. To this end, we first identified differentially expressed disease-specific genes (dsDEGs) using a TDP-43-based rat model of ALS, generated by stereotaxic infusion of full-length (FL) TAR DNA-binding protein 43 (TDP-43) into the motor cortex. Transcriptomic profiling of the motor cortex revealed candidate dsDEGs, which were subsequently validated by RT-qPCR in motor cortex, spinal cord, and PBMCs from the same animals. To assess translational relevance, expression levels of these dsDEGs were analyzed in PBMCs from early- to mid-stage ALS patients and matched healthy controls, while disease specificity was evaluated using Parkinson's disease (PD) samples. In parallel, conserved miRNAs predicted to target the identified dsDEGs were examined in both rat and human PBMCs. Five dsDEGs, Mctp1, Penk, Mt2A, Drd1, and Rasgrp2, were consistently dysregulated across central and peripheral tissues in the TDP-43 rat model. RT-qPCR analysis of human PBMCs confirmed significant and selective dysregulation of these genes in ALS, but not in PD, supporting disease specificity. Moreover, exposure of human neuroblastoma cells and healthy PBMCs to TDP-43 recapitulated the ALS-like expression changes. Computational and experimental analyses identified seven conserved miRNAs targeting these dsDEGs, of which four were significantly downregulated in ALS PBMCs, supporting a coordinated regulatory network. Receiver operating characteristic (ROC) analyses demonstrated strong discriminative performance for both the gene signature (AUC 0.87-1.00) and the associated miRNAs (AUC 0.95-1.00). Togeth
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Journal articleLau R, Giblin S, Sugar A, et al., 2026,
SpyCEP dismantles neutrophil immunity via disorder-drivenchemokine remodeling and GAG targeting
, Proceedings of the National Academy of Sciences of the United States of America, ISSN: 0027-8424Streptococcus pyogenes (Group A Streptococcus; GAS) employs sophisticated virulence strategies to evade human immunity, including secretion of the cell envelope protease SpyCEP, which cleaves and inactivates key neutrophil鈥慳ttracting chemokines such as CXCL8. Here, we integrate cryo鈥慹lectron microscopy (cryo鈥慐M), nuclear magnetic resonance (NMR) spectroscopy, and native mass spectrometry (MS) to investigate how SpyCEP disrupts CXCL8 function. We demonstrate that a disordered aromatic and acidic region within the cleaved autocatalytic maturation loop (CAML) of SpyCEP mimics receptor N-domains and binds an allosteric site on CXCL8. The resulting interaction forms a dynamic fuzzy complex and is coupled to dimer dissociation, consistent with enhanced access to the cleavage site. This disorder鈥憁ediated substrate engagement differs from classical protease mechanisms that rely on rigid recognition interfaces. Additionally, glycan microarray and NMR analyses show that the CAML region mediates glycosaminoglycan (GAG) binding, suggesting a means to recruit SpyCEP and maximize encounters with GAG鈥慹nriched CXCL8 reservoirs. Together, these findings provide a structural and biophysical framework for understanding how SpyCEP combines substrate engagement with GAG targeting to dismantle chemokine gradients and inhibit neutrophil recruitment. More broadly, this work highlights the role of intrinsic disorder in protease recognition and suggests new avenues for anti鈥憊irulence therapies and vaccine strategies targeting SpyCEP.
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Journal articleSpeck C, Reuter M, Weekes C, 2026,
Mechanisms of MCM2-7 helicase activation and initial DNA melting at near base-pair resolution
, Nature Communications, ISSN: 2041-1723 -
Journal articleGottweis J, Weng W-H, Daryin A, et al., 2026, , Nature, ISSN: 0028-0836
Scientific discovery is driven by scientists generating hypotheses for complex problems that undergo rigorous experimental validation. To augment this process, we introduce Co-Scientist, a multi-agent artificial intelligence (AI) system built on Gemini for structured scientific thinking and hypothesis generation. Co-Scientist aims to help scientists discover new original knowledge. Conditioned on their research objectives and previous scientific evidence, it formulates demonstrably novel research hypotheses for experimental verification. The system’s design involves agents continuously generating, critiquing and refining hypotheses accelerated by scaling test-time compute. Key contributions include (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling, and (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute scaling, improving hypothesis quality over time. Although this is a general-purpose system, we focus the validation in three biomedical applications: drug repurposing; novel-target discovery1; and explaining mechanisms of antimicrobial resistance2. Specifically, Co-Scientist helped to identify new drug-repurposing candidates and synergistic combination therapies for acute myeloid leukaemia that were validated through in vitro experiments. These real-world validations demonstrate the potential of Co-Scientist to accelerate scientific discovery and usher in an era of AI-empowered scientists.
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Journal articleLi X, Xu L, He F, et al., 2026, , Crystal Growth & Design, Vol: 26, Pages: 5242-5251, ISSN: 1528-7483
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Journal articleEttema TW, Inaba-Inoue S, Thangaratnarajah C, et al., 2026,
Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters
, Nature Communications, Vol: 17, ISSN: 2041-1723SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and 61 secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC trans- porters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.
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Journal articleHobbs B, Limmer N, Clenshaw GL, et al., 2026, , Phys Chem Chem Phys
Intrinsically disordered, low-complexity regions frequently cooperate with folded domains to mediate protein-protein interactions, yet accurately describing these mixed folded-disordered systems remains challenging. To visualize these mixed folded proteins, experimentally guided coarse-grained (CG) molecular dynamics simulations are often employed to extend the timescales required to capture the complex dynamics in play. However, the minimalistic nature of these approaches often compromises structural accuracy and can lead to inaccurate inter-domain interactions. Here we introduce backbone dihedral terms directly derived from NMR chemical shift data in CG-simulations to characterize the open state of a mixed-folded construct of the anti-aggregation chaperone DNAJB6 that contains a folded J-domain and a disordered GF linker. By tuning residue-specific backbone dihedral parameters to match NMR-derived secondary-structure propensities of the linker in CG-simulations, we generate conformational ensembles that yield accurate interdomain contact maps. In agreement with analysis of NMR relaxation data, the resulting ensembles show that even in the nominally open state the linker experiences motions that resemble those of the closed state driven by hydrophobic residues in GF. More generally, we show that by expanding CG-simulations to allow them to capture both local and global structural properties, physically relevant interdomain contacts can be retrieved.
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Journal articleZhao Z, Vercellino I, Whitelegge JP, et al., 2026, , Nature Communications, ISSN: 2041-1723
Robust oxygenic photosynthesis requires the efficient assembly and repair of the multi-subunit oxygen-evolving photosystem II (PSII) complex. Previous cryogenic electron microscopy (cryo-EM) structures of PSII assembly/disassembly intermediates have relied on the analysis of deletion mutants or removal of PSII subunits in vitro. Here we determine the cryo-EM structures of naturally occurring dimeric PSII intermediates from the cyanobacterium Thermosynechococcus vestitus at a resolution of about 2.2 Å. These intermediates contain inactive dimers lacking the oxygen-evolving complex (OEC) and semi-active dimers with the OEC present in one of the two monomers. Our structural data provide a mechanism for how assembly and disassembly of the Mn4CaO5 cluster is coordinated with the binding and release of the extrinsic proteins: restructuring of the C-terminal tail of D1 subunit during assembly or disassembly of the Mn cluster triggers conformational changes in D2, CP47 and CP43 to drive the binding/release of the extrinsic proteins. A combination of structural and mass spectrometry data also suggests that the inactive PSII complexes may include damaged complexes containing oxidized D1-His332, a monodentate ligand to one of the Mn ions of the OEC.
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Journal articleGroff A, Lu Y, Feeney M, et al., 2026,
Sustainable production of myoglobin meat protein in plant chloroplasts
, Frontiers in Plant Science, ISSN: 1664-462XAlternative routes for producing animal proteins are crucial for reducing the reliance on traditional livestock farming, which contributes significantly to greenhouse gas emissions, deforestation, and water consumption. Myoglobin (Mb) is an important oxygen-binding hemoprotein found in vertebrate muscle, that enhances the nutritional and sensorial properties of meat. Due to its unique functionality, Mb has been heterologously expressed in a variety of organisms, although only transient expression in Nicotiana benthamiana has been reported for higher plants. In this study, we used chloroplast transformation technology to express porcine Mb in higher plants (tobacco, a non-edible model plant, and lettuce, an edible host) and bovine Mb in the green alga Chlamydomonas reinhardtii. Mb accumulation was estimated by immunoblotting and found to be much higher in tobacco (2.7% total soluble protein (TSP)) and lettuce (1.5% TSP) than Chlamydomonas reinhardtii (<0.25% TSP). The expression in tobacco chloroplasts is also superior to tobacco nuclear expression (using either the cauliflower mosaic virus 35S promoter or Arabidopsis thaliana ubiquitin promoter). Total heme levels were elevated in myoglobin-producing mutants compared to control plants, although porcine Mb purified from tobacco leaves exhibited approximately 35% heme-binding (compared to 80% heme-binding in E. coli-expressed Mb), despite being correctly folded, suggesting that heme availability might be a bottleneck. Overall, our work describes the first report of stable Mb production in higher plants and its effect on photosynthesis and heme levels. This provides a foundation for future plant-made animal proteins for food applications.
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Conference paperPessina D, Heng JYY, Papathanasiou MM, 2026, , The 36th European Symposium on Computer Aided Process Engineering, Publisher: PSE Press, Pages: 631-639, ISSN: 2818-4734
<jats:p>Crystallisation is a promising and scalable alternative to chromatography for biologics purification. However biologics such as proteins and peptides often crystallise only in narrow operating windows, limiting process flexibility. Template-induced crystallisation can lower supersaturation requirements and expand feasible operating ranges, yet the template dependence of nucleation and growth kinetics remains difficult to parametrise mechanistically. To address this, we develop and experimentally validate uncertainty-aware hybrid models for lysozyme crystallisation on hydroxyl- and carboxyl-functionalised silica templates. A mechanistic population-balance model is coupled to a data-driven regressor that maps operating conditions and template variables to effective nucleation and growth rates. We compare a neural network baseline against a structured neural power-law surrogate, which embeds a supersaturation-dependent power-law form. Both hybrid models are trained in-the-loop via differentiable simulation, and variational inference is used to obtain posterior parameter distributions and calibrated predictive uncertainty. Across cross-validation and off-grid tests at previously unseen combinations of temperature and template loading, the hybrid models accurately reproduce solute concentration dynamics and capture key particle-size trends, while the neural power-law surrogate provides improved robustness and faster uncertainty quantification. These results support hybrid, uncertainty-aware PBMs as practical tools for prediction, design-space exploration, and comparison of template-enabled protein crystallisation processes.</jats:p>
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Journal articleFrankel G, 2026, , Nature Communications, ISSN: 2041-1723
Bacterial conjugation, the process of horizontal gene transfer between bacteria, is initiated by mating pair formation (MPF) via a conjugative pilus. Conjugation of the IncP RP4 plasmid is mediated by short mating pili. Here, we report the cryo-EM structure of the RP4 pilus at 2.74 Å resolution. Uniquely, both the structural and quantitative mass spectral analyses revealed that the cyclic TrbC pilin subunit is not lipidated. Consistently, an E. coli pgsA mutant lacking phosphatidylglycerol (PG) can serve as a donor of RP4 but not of F- (pKpQIL), H- (R27) or W- (R388) pili, whose biogenesis and DNA transfer is PG-dependent. RP4 is the first example of a lipid-independent functional mating pilus. This discovery suggests that an amphipathic lipid moiety is not universally essential for the biogenesis of conjugative pili and MPF, providing an alternative model for their assembly and function. These data expand our understanding of the diverse bacterial mechanisms employ to transfer genetic material.
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Journal articleRibardo DA, Singh NK, Beeby M, et al., 2026, , Proc Natl Acad Sci U S A, Vol: 123
Campylobacter jejuni is an intestinal commensal of birds and animals and a leading cause of bacterial diarrheal disease in humans. In hosts, C. jejuni primarily resides in the mucus layer atop the lower intestinal epithelium. Persistence in this niche requires a single flagellar motor at both C. jejuni poles that generates high torque for flagellar rotation to facilitate motility and high swimming velocities. Unlike many bacterial flagellates, C. jejuni swimming velocity increases as external viscosity increases. We identified a complex formed by FlgV, VidA, and VidC (Cjj81176_1732) positioned near the MS-ring-rotor junction in the flagellar motor we annotated as the V-ring. Viscosity-influenced growth, modulation of swimming velocity, and transcription of iron/heme acquisition, respiratory, and energy-generating systems were dependent on the V-ring. C. jejuni ΔflgV and ΔvidC populations lacking a complete V-ring were motile, but could not optimally modulate swimming velocity. Like nonmotile flagellar stator or filament mutants, motile V-ring mutants had in vivo and in vitro growth and viability defects and dysregulated transcription of genes likely impacting physiology. Because the V-ring mutants behaved similarly as nonmotile mutants that experience little to no viscous drag on the filament, we propose C. jejuni V-ring mutants cannot detect viscous drag on their rotating filaments. We propose the V-ring evolved in C. jejuni and potentially other bacteria producing high torque flagellar motors to monitor external viscosity information via viscous drag on the rotating flagellar filament to adjust swimming velocity, transcription, and physiology for optimal fitness in different host lower intestinal niches.
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Journal articleDe Chiara A, Giachino C, Pirillo MF, et al., 2026, , Mol Ther Nucleic Acids, Vol: 37, ISSN: 2162-2531
The continuous evolution of SARS-CoV-2 variants, driven by mutations in the spike protein undermines viral recognition by antibodies elicited through prior infection or vaccination with the ancestral Wuhan strain. Original antigenic sin of SARS-CoV-2 ancestral virus or vaccine led to a weakened neutralizing antibody response against successive variants upon administration of an updated vaccine. On the contrary, T cells retain cross-reactivity thanks to the high density of conserved epitopes. We designed mRNA vaccines encoding single-chain heterotrimers of the receptor-binding domain (RBD) natural variants of interest (VOI), (RBD-VOI) and of phylogenetically informed consensus representing the major variant lineages RBD-consensus (RBD-Cons). We demonstrate a broad neutralizing activity against omicron subvariants and mitigated immune imprinting when RBD-Cons was used as a booster after conventional Wuhan spike priming. To enhance cellular immunity, we designed a second mRNA vaccine component encoding the viral polymerase NSP12 able to induce a cross-reactive T cell response to be combined with the heterotrimeric RBD vaccine. Our results offer a rational strategy for next-generation, imprinting-resistant vaccines.
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Journal articleOliver TJ, Elias E, Consoli G, et al., 2026, , Sci Adv, Vol: 12
Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium Acaryochloris marina pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, unexpectedly lacks low-energy chlorophylls ("red forms") in photosystem I, limiting absorption beyond 740 nanometers. Here, we show that another strain, A. marina NIES-2412, has evolved a strategy to absorb far-red photons up to 760 nanometers. Combining time-resolved fluorescence spectroscopy with cryo-electron microscopy at 2.64-angstrom resolution, we identify two distinct classes of chlorophyll d red forms in its photosystem I. One class originates from classical charge-transfer-exciton mixing, while the other arises purely from excitonic interactions. Mapping all 96 chlorophylls d reveals the precise pigments responsible for these far-red states. We also uncover a previously unreported subunit, PsaX2, which stabilizes the photosystem I complex and shapes pigment geometry and energetics to enable the formation of red forms. Last, we show that the protein modifications responsible for binding and tuning these red forms are widespread across the Acaryochloris genus but not within the model MBIC11017 strain. Far-red photons lie close to the energetic limit of oxygenic photosynthesis; their efficient use therefore requires fine-tuning of the photosynthetic machinery. To our knowledge, our findings provide the structural and mechanistic basis of one of the most red-shifted photosystem I complexes identified to date, highlighting a distinct adaptive strategy in far-red light environments and offering design principles for extending photosynthesis in crops into the infrared.
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Journal articleBiswas P, Mishra V, Sanchez-Garrido J, et al., 2026, , Cellular and Molecular Gastroenterology and Hepatology (CMGH), ISSN: 2352-345X
Background & AimsPrior intestinal inflammation can leave durable immune and epithelial alterations, yet how these changes influence responses to subsequent injury remains unclear. Infectious and sterile colitis share core features, including barrier disruption and cytokine secretion. We therefore investigated whether the nature of the initial inflammatory event shapes protection or susceptibility during later intestinal insult.MethodsWe used reciprocal mouse models of Citrobacter rodentium (CR) infection and dextran sodium sulphate (DSS)-induced colitis to define how prior infectious versus sterile colitis shapes secondary disease. Barrier integrity, immune cell populations, cytokine production, and susceptibility to wild-type and CR mutants that cause limited epithelial barrier disruption were assessed.ResultsMice recovered from CR infection were protected against DSS-induced colitis, displaying reduced weight loss, preserved epithelial architecture, and lower inflammatory pathology. This protection required type III secretion system effector-mediated epithelial injury during primary infection and was associated with sustained IL-17A signalling, which contributed to the protective phenotype. In contrast, mice recovered from DSS colitis exhibited persistent epithelial barrier defects, chronic colonic neutrophilia, and heightened susceptibility to CR infection despite elevated IL-17A. Infection with CR mutants that cause minimal epithelial damage still resulted in severe disease in DSS-experienced mice, indicating that unresolved epithelial barrier dysfunction is a major contributor to vulnerability.ConclusionsThe nature of the primary colitis is associated with distinct epithelial and immune programs that persist beyond resolution of inflammation. Infectious colitis is associated with a protective mucosal state where IL-17A is a key contributor in a broader protective response, whereas sterile colitis is associated with persistent epithelial barrier dysfunction
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Journal articleBennison DJ, Chaudhary I, Chaudhuri D, et al., 2026, , EMBO Journal, ISSN: 0261-4189
The IFNγ-induced GTPase guanylate-binding protein 1 (GBP1) binds to lipopolysaccharide (LPS) on cytosolic gram-negative bacteria and promotes pyroptosis via the recruitment and activation of caspase-4 on the bacterial outer membrane. Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC, respectively) are extracellular pathogens that adhere to host cells and stimulate dense actin polymerisation underneath their attachment sites, generating structures described as actin-rich pedestals. Here, we show that GBP1 traffics to actin-rich pedestals in human cells infected with EPEC or EHEC in vitro and mouse colonocytes infected with the EPEC-like murine pathogen Citrobacter rodentium in vivo. GBP1 promotes caspase-4 recruitment to actin-rich pedestals, leading to pyroptosis and IL-18 release. GBP1 mutants defective in LPS coatomer formation also localise to EPEC pedestals. A novel assay that mimics pathogenic effector activity reveals GBP1 recruitment to sterile actin polymerisation sites. We conclude that cytosolic GBP1 is mobilised to sites of pathogen-induced actin remodelling independently of LPS. Our study establishes that GBP1 not only operates as a pattern-recognition receptor but also orchestrates effector-triggered immunity against pathogens that hijack the actin cytoskeleton.
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Journal articleDewan D, Wang Y, De Simone A, et al., 2026, , J Chem Theory Comput, Vol: 22, Pages: 5827-5837
Most biomolecular simulations depend on the quality of empirical force fields, and the use of hybrid restraint potentials has emerged as a promising approach. In this contribution, we extend the application of hybrid potentials to membrane proteins by developing optimized restraints derived from experimentally determined NMR data. NMR chemical shift, chemical shift anisotropy, dipolar coupling, and NOE distance information are combined with appropriately weighted empirical force fields to study two transmembrane systems, namely sarcolipin and phospholamban. To remedy the problems of rare events and broken ergodicity, the energy landscape framework, including basin-hopping global optimization and discrete path sampling, is employed for exploring the underlying energy landscapes. Much of the appeal of the hybrid potential approach is the ability to study membrane proteins in the absence of conventional explicit or implicit solvent and lipid molecules, thereby simplifying the sampling of complex biomolecular conformational spaces. Our results suggest that the hybridization of NMR constraints as penalty energies with empirical force fields improves global optimization and energy landscape analysis by excluding experimentally incompatible structures.
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Journal articleLeong M, Consoli G, Davis G, et al., 2026, , Nature Communications, ISSN: 2041-1723
Far-red light photoacclimation enables some cyanobacteria to survive in white-light-depleted environments by extending the red limit of photosynthesis. In far-red Photosystem II, paralogous subunits replace their canonical counterparts, allowing the incorporation of some chlorophyll f molecules and one chlorophyll d that are red-shifted and spectrally distinct from the chlorophyll a manifold, and from each other. Here, we present a comparative study of far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203 and Calothrix sp. NIES-3974. In C. thermalis, the cryo-electron microscopy structure reveals the far-red-exclusive subunit, PsbH2’, which forms part of a chlorophyll f binding site. We also assign four chlorophyll f sites using sequence comparisons and electrostatic potential analyses. In Calothrix, psbH2’ is absent, and the same analyses show that only two of these chlorophyll f sites are present. Comparative phylogenetic, structural, and spectroscopic analyses allow the assignment of specific wavelengths to all the red-shifted chlorophylls. This provides the framework needed to model excitation energy transfer in far-red Photosystem II, and to understand the conserved features that allow survival under far-red light.
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Journal articleKelwick R, Webb A, Heliot A, et al., 2026, , Trends in Biotechnology, ISSN: 0167-7799
Extracellular vesicles (EVs) are lipid-delimited particles produced by most cell types that can have therapeutic effects. Cell-free gene expression systems can be used to produce membrane proteins in vitro, which can integrate with exogenously added EVs. To advance this type of cell-free EV engineering, we established an end-to-end cell-free EV engineering workflow. Firstly, human embryonic kidney (HEK293) cells were cultured within a hollow-fibre bioreactor to generate several batches of HEK293 EVs. Subsequently, these EVs were successfully cell-free engineered with several CD63-based membrane fusion proteins. Nano-flow cytometry analyses revealed that, under optimal conditions, up to 4.83 × 1011 /ml of HEK293 EVs were successfully cell-free engineered to incorporate CD63 I-shaped membrane-insertion topology transmembrane helix 3 (CD63ITM3)-monomeric green lantern membrane fusion proteins. Finally, we demonstrated that cell-free engineered EVs can be functionally assessed using nano-flow cytometry and cell-based assays. We envision that, in the future, cell-free EV engineering workflows could be used to help accelerate future EV discoveries and advancements in EV therapeutics.
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Journal articleKeskin Erdogan Z, Desai K, Baldwin GS, et al., 2026, , Trends Biotechnol, Vol: 44, Pages: 1576-1588
The emerging field of biosensors exploits the abilities of cells to identify specific molecules, presenting improved sensitivity, specificity, and limit of detection. Whole-cell biosensors (WCB) are organisms specifically engineered to detect a target analyte and express a reporter in response. In biomanufacturing, they can be used for monitoring of key substrate and metabolite concentrations or strain engineering, while in medicine, they can be used to diagnose disease or report on human-microbe interactions. Many applications require WCB to coexist with mammalian cells where a key challenge is to keep separate cell populations viable while still allowing them to interact. In this review, we highlight key considerations when encapsulating WCB to engineer controlled microenvironments that enable collaboration and coexistence of different populations.
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Journal articleWong LH, Mitchell NA, Heng JYY, 2026, , Chemical Engineering 91桃色 and Design, ISSN: 0263-8762
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Journal articleParacuellos P, Bexter A, Patkowski JB, et al., 2026, , Nature Microbiology, ISSN: 2058-5276
Type VI secretion systems (T6SSs) are widespread bacterial nanomachines that deliver effectors into prokaryotic and eukaryotic cells. How an effector cargo is recruited and loaded into the Hcp ring assemblies that form the tube injected by the T6SS remains poorly understood. Pseudomonas aeruginosa has four T6SSs, each associated with a different Hcp protein. Here we use cryo-electron microscopy to resolve the structure of the Tce1 cargo loaded into a Hcp3 ring from the P. aeruginosa H3-T6SS. We show that a single Tce1 monomer interacts asymmetrically with, and is enclosed by, two hexameric Hcp3 rings, engaging key residues lining the inner surface of the Hcp3 disc. Our data indicate a stepwise loading mechanism, where an initial heterodimeric Hcp–cargo complex forms before ring encapsulation around the effector. Structural modelling suggests similar effector–Hcp3 interactions for a second T6SS effector, Tce2, which has antifungal activity. We propose that this mechanism enables coordinated delivery of a broad payload into target cells.
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Journal articleGrimaldi A, Hobbs B, Stofella M, et al., 2026, , ACS Phys Chem Au, Vol: 6, Pages: 446-450
Hydrogen-deuterium exchange (HDX) of protein backbone amides provides a powerful probe of conformational dynamics. However, when experiments are performed in H2O/D2O mixtures, quantitative interpretation is hindered by back exchange and isotope effects not captured by the classical Linderstro谭m-Lang (LL) model. We introduce a generalized Linderstro谭m-Lang (GLL) framework that explicitly accounts for forward and reverse exchange and for changes in protection upon isotopic substitution. Analytical solutions describe equilibrium enrichment (fractionation) and protection factors in mixtures, reducing to the LL model in pure D2O. Application to HDX/NMR of the molecular chaperone DNAJB1 in 50% D2O demonstrates that the GLL model recovers protection factors at 100% D2O. Ignoring back exchange (i.e., using the LL model), protection factors are systematically underestimated. A particularly powerful feature of our approach is that a single HDX experiment in a mixture (e.g., 50% D2O) simultaneously provides protection factors that report on conformational dynamics and local stability and fractionation factors that are sensitive to the local hydrogen-bonding environment.
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Journal articleHolden D, 2026,
MAP4Ks drive cell death in response to Salmonella SpvB-induced actin depolymerisation
, mBio, ISSN: 2161-2129Many pathogens target the host actin cytoskeleton through the delivery of actin depolymerizing toxins, including mono-ADP-ribosyltransferases (mART), ultimately triggering host cell death. Despite the importance of mARTs in pathogen virulence, it remains unclear whether actin ribosylation is required for mART-dependent cell death, and how actin depolymerization leads to cell death. Using the non-typhoidal Salmonella enterica Typhimurium-encoded mART, SpvB, we report that cell death is induced exclusively through ribosylation of actin. We found cell death to be morphologically and mechanistically distinct from apoptosis as well as any previously reported mode of cell death. Instead, our data identify the Hippo signaling MAP4Ks as the essential host cell sensors of actin depolymerization signaling through JNK to facilitate vacuolization and host cell death. Cell death following treatment of cells with the actin depolymerizing agent latrunculin A followed the same pathway, identifying a conserved mechanism of cell death. Therefore, we identify MAP4K family members as key regulators of an atypical caspase-independent cell death induced by actin depolymerization, building on our understanding of host-cell death signaling and mechanisms of bacterial virulence
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Journal articleRost酶l JT, Chmielowska C, Marina A, et al., 2026, , Nat Rev Microbiol
Temperate bacteriophages (phages) are ubiquitous viruses that co-evolve with their bacterial hosts. They are defined by their ability to undergo two distinct life cycles: the lytic cycle, in which the phage produces more viral copies and kills the host, and the lysogenic cycle, in which the temperate phage exists as a prophage in the host. Temperate phages have long served as fundamental models in microbiology, genetics and evolutionary biology research, and their life cycles are among the most thoroughly characterized in virology. Historically, the phage life cycle was viewed primarily through the lens of how excision, replication and packaging drive the formation of infective particles. Although it captures the central processes of the phage life cycle, this narrow perspective overlooks the full range of interactions with the host and with other mobile genetic elements. In this Review, we re-examine the temperate phage life cycle in light of emerging insights that expand on this framework with unanticipated complexities. We argue that many properties of (pro)phages should be viewed as integral parts of their life cycle instead of being discussed separately. This holistic view is important to fully appreciate the intricacies of the temperate phage life cycle and the key roles of these viruses in microbiology and biotechnological applications.
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Journal articleWan Y, Katie H, 2026,
Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam
, BMC Genomic Data, ISSN: 2730-6844Background Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital. Methods Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation. Mutagenesis experiments were performed to verify predicted functional alterations. Results All isolates belonged to clone ST8134 and carried blaKPC-2 alleles (KpMVR1: blaKPC-157; KpMVS1 and KpMVS2: blaKPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a frameshift mutation in KpMVR1’s ompK36 gene, reducing susceptibility to meropenem-vaborbactam and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact, iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate. ConclusionsKpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance profile
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Conference paperChen J, Leung VCH, Wang R, et al., 2026, , ICASSP 2026 - 2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Publisher: IEEE, Pages: 11567-11571
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Journal articleMurray JW, 2026, , Plant J, Vol: 126
Photosystem II (PSII) is the membrane protein-pigment complex responsible for the light-driven oxidation of water to molecular oxygen, a reaction that enables the aerobic biosphere and powers biological carbon fixation. Over the past two decades, structural biology has transformed our understanding of PSII from low-resolution outlines of its protein chains and cofactors to near-atomic resolution models. Early X-ray crystallographic structures from thermophilic cyanobacteria established the architecture of the reaction centre and the Mn4CaO5 oxygen-evolving complex (OEC), defining the protein ligands and cofactor network that support charge separation and water oxidation. The advent of high-resolution single-particle cryo-EM microscopy has expanded structural coverage across taxa, assembly and repair intermediates, and PSII-antenna supercomplexes that are beyond crystallisation. CryoEM now routinely achieves sub-2.5 Å resolution. In situ cryo-EM tomography further bridges atomic models to the native thylakoid membrane environment, exposing the supramolecular organisation of PSII in cells. X-ray free electron laser (XFEL) pump-probe experiments provide time-resolved snapshots of the Kok S-state cycle, revealing substrate water insertion, metal-oxo rearrangements and approaches O-O bond formation. Despite these advances, key challenges remain, including unambiguous assignment of manganese oxidation states, direct localisation of hydrogen atoms and complete structural characterisation of transient S-state intermediates. Integration of structural methods with spectroscopy, computation and emerging protein design approaches promises not only deeper mechanistic insight into biological water oxidation, but also guidance for the development of robust, earth-abundant catalysts.
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Journal articleGovada L, Wang B, Li Y, et al., 2026, , International Journal of Molecular Sciences, Vol: 27, ISSN: 1661-6596
X-ray crystallography is still the most widely used and versatile method for structural studies of biological macromolecules. This study concerns the application of nanogels to facilitate protein crystallization, a prerequisite for X-ray crystallography. Nanogels (NGs) are nano-sized, highly crosslinked polymeric particles that have been extensively studied for chemical catalysis and drug delivery but not for protein crystal nucleation. The efficacy of six types of nanogels (three N-isopropylacrylamide-based and three acrylamide-based) was tested, with promising results. They were subsequently functionalised with active hydroxyl groups for further testing. Both functionalised and non-functionalised nanogels were tested on model (trypsin, thaumatin, proteinase K, ferritin and catalase) and target proteins (glulisine, α-crustacyanin and acriflavine resistance protein subunit AcrB) using both manual and automated techniques. All nanogels were found to be effective in promoting protein crystallization in both screening and optimization trials, giving crystal 'hits' that would have otherwise been missed. Overall, the functionalised nanogels were more effective. Nanogel effects are proposed to be due to a combination of surface porosity and surface chemistry.
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Journal articleBubeck D, Noone DP, 2026,
Advances in cryo-EM that have shaped mechanistic models of membrane attack complex assembly and regulation
, IUCrJ, ISSN: 2052-2525The complement system is a blood-based immune network that plays a crucial role in fighting infection and maintaining immune homeostasis. The membrane attack complex (MAC) is a pore assembled from complement proteins that creates holes in cells when the immune system is activated. Over the last 10 years, advances in cryo electron microscopy (cryo-EM) have enabled key molecular insights into how MAC assembles, remodels membranes, and is regulated. These new tools revealed the inherent flexibility of complement complexes. By adapting computational approaches that disentangle diverse conformations, these studies have provided detailed mechanisms for MAC activity that could underpin novel complement-targeted therapeutics. Now accelerated by AI-driven image analysis and advances in structural cell biology, the next revolution in cryo-EM o ers new opportunities to understand the cellular consequences of immune activation.
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