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Journal articlePark Y, Sisley TA, Corrigan RM, et al., 2025,
SpbR controls lipoteichoic acid length by directly inhibiting signal peptidase SpsB in <i>Staphylococcus aureus<i>
, Proceedings of the National Academy of Sciences of USA, Vol: 122, ISSN: 0027-8424Staphylococcus aureus is a Gram-positive pathogen that causes life threatening infections. Its cell envelope contains anionic polymers called teichoic acids that are required for cell viability. Teichoic acids come in two forms and are made by different biosynthetic pathways. One form, lipoteichoic acid (LTA), is anchored in the cell membrane; the other form, wall teichoic acid (WTA), is covalently linked to the peptidoglycan cell wall. Although the LTA and WTA biosynthetic pathways have been characterized, regulation of teichoic acid production is not well understood. Here, we identified SpbR (SAOUHSC_00965), a polytopic membrane protein similar to a eukaryotic CAAX protease, as a new factor that controls LTA levels in S. aureus cells. We show that loss of SpbR results in short LTAs and a synthetically sick phenotype when WTA biosynthesis is prevented, whereas overexpressing SpbR results in elongated LTAs. Mechanistically, we find that SpbR physically associates with the type I signal peptidase SpsB, which cleaves LtaS, thepolymerase that assembles LTA on the extracellular side of the membrane, and we show that this physical interaction inhibits SpsB cleavage of LtaS both in vivo and in vitro. Although the phenotypes investigated here are dominated by SpbR’s effects on LtaS, it also inhibits cleavage of other SpsB substrates. Based on its role in regulating the activity of SpsB, we named this factor SpbR (Signal peptidase b Regulator). To the best of our knowledge, SpbR is the first known factor that directly modulates the activity of a type Isignal peptidase in bacteria.
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Journal articleKim H, Hillson NJ, Cho B-K, et al., 2025,
Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications
, Nature Communications, Vol: 16, ISSN: 2041-1723Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.
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Journal articleBickel JK, Ahmed AIS, Pidd AB, et al., 2025,
Macrocyclic peptide probes for immunomodulatory protein CD59: potent modulators of bacterial toxin activity and antibody‐dependent cytotoxicity
, Angewandte Chemie International Edition, Vol: 64, ISSN: 1433-7851CD59 is an immunomodulatory cell surface receptor associated with human disease. Despite its importance in complement regulation and bacterial pathogenesis, CD59 remains a challenging therapeutic target. Research to date has focused on antibody or protein-based strategies. Here we present a new approach to target CD59 using macrocyclic peptides with low nanomolar affinity for CD59. Through X-ray crystallographic studies and structure-activity relationship (SAR) studies, we identify key interactions that are essential for binding and activity. We find that the macrocyclic peptide CP-06 adopts a beta-hairpin structure and binds CD59 through an intermolecular beta-sheet, mimicking protein–protein interactions of biologically relevant CD59 interaction partners. We create dimeric and lipidated macrocyclic peptide conjugates as enhanced cell-active CD59 inhibitors and show that these probes can be used to modulate both complement-mediated killing of human cells and lytic activity of bacterial virulence factors. Together, our data provide a starting point for future development of macrocyclic peptides to target CD59 activity in diverse cellular contexts.
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Journal articleNajmudin S, Pan X-S, Wang B, et al., 2025,
Structural basis of topoisomerase targeting by delafloxacin
, Nature Communications, Vol: 16, ISSN: 2041-1723Delafloxacin is a potent anionic fluoroquinolone approved for the treatment of respiratory infections that acts by trapping the DNA cleavage complexes of bacterial topoisomerase IV and gyrase. Its N-1-pyridinyl-, C-7-azetidinyl- and C-8-chlorine substituents confer enhanced antibiotic activity against bacteria resistant to other fluoroquinolones, but its mode of action is unclear. Here we present the X-ray crystal structures of a delafloxacin-DNA cleavage complex obtained by co-crystallization with Streptococcus pneumoniae topo IV using a graphene nucleant and solved at 2.0 and 2.4 Å resolution. The two Mg2+-chelated delafloxacin molecules intercalated at the DNA cleavage site are bound in an unusual conformation involving interacting out-of-plane N-1-aromatic- and C-8-chlorine- substituents. The unprecedented resolution allows comprehensive imaging of water-metal ion links integrating enzyme and DNA through drug-bound and active-site Mg2+ ions plus the discovery of enzyme-bound K+ ions. Our studies on delafloxacin action suggest that intrinsic target affinity contributes to its activity against quinolone-resistant bacteria.
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Journal articleFenn J, Koycheva A, Kundu R, et al., 2025,
Early de novo T cell expansion following SARS-CoV-2 infection predicts favourable clinical and virological outcomes
, eBioMedicine, Vol: 117, ISSN: 2352-3964BackgroundDe novo T cell expansion to a novel viral infection is assumed to confer protection, but empirical evidence in humans is limited. The SARS-CoV-2 pandemic provided a unique opportunity to investigate de novo T cell-mediated protection in antigen-naïve individuals without the confounding effects of preexisting immune memory.MethodsWe leveraged a prospective household contact study to recruit new COVID-19 cases a median of 4 days post-SARS-CoV-2 exposure. We longitudinally enumerated SARS-CoV-2 antigen-specific functional T cell subsets using dual IFN-γ/IL-2 fluorescence-linked immunospot (FLISpot) assays. We then correlated T cell dynamics with detailed clinical and virological outcomes derived from longitudinal measurement of symptom burden and viral load.FindingsEarly expansion (day 0–7) of SARS-CoV-2-specific IFN-γ-secreting T cells correlated with lower peak viral load and symptom burden. Conversely, late T cell expansion (day 7–28) correlated with higher symptom burden. Neither pre-existing cross-reactive T cells nor early antibody induction correlated with virological outcomes.InterpretationThese findings provide empiric evidence for early antigen-specific T cell expansion being protective against naturally acquired viral infection in humans.FundingThis work is supported by the NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London in partnership with the UK Health Security Agency (Grant number: NIHR200927; AL) and the Medical Research Council (Grant number: MR/X004058/1).
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Journal articleVijayrajratnam S, Patkowski JB, Khorsandi J, et al., 2025,
Optimized <i>Legionella</i> expression strain for affinity purification of His-tagged membrane proteins eliminates major multimeric contaminant
, Microbiology Spectrum, Vol: 13, ISSN: 2165-0497Polyhistidine tags are frequently used for isolating proteins through nickel-nitrilotriacetic acid (Ni-NTA) affinity purification. However, proteins rich in histidine can also bind to the Ni-NTA resin, leading to contamination of the purification with undesired proteins. While attempting to purify the Legionella pneumophila Dot/Icm type IVB secretion system complex for single particle analysis, we encountered an unknown contaminant protein that bound to the Ni-NTA resin and formed uniform particles visible in negative stain electron microscopy (EM). Mass spectrometry identified this protein, which is encoded by the Legionella gene lpg1596 as a homolog of enoyl-CoA hydratase. Modeling of Lpg1596 revealed surface-exposed histidine clusters, which likely explains its ability to bind to the Ni-NTA resin. Moreover, since enoyl-CoA hydratase homologs are known to multimerize, multimers of Lpg1596 would be large enough to be visible by negative stain EM. To address the problematic issue of Lpg1596 binding to the Ni-NTA resin, we constructed and analyzed a L. pneumophila ∆lpg1596 mutant strain. Notably, Ni-NTA affinity purification of lysates from the ∆lpg1596 strain did not contain the contaminant protein or generate observable particles. Since the ∆lpg1596 mutant strain exhibited replication capabilities similar to the wild-type L. pneumophila in macrophages, its deletion will likely not affect pathogenesis studies. To facilitate the deletion of lpg1596 in other Legionella strains, we developed a set of natural transformation vectors with various antibiotic resistance markers. In summary, we present a strategy for removing a common Ni-NTA resin binding protein contaminant in L. pneumophila, which improves single particle analysis outcomes.
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Journal articleengelman A, Grandgenett DP, Maertens G, et al., 2025,
Retrointegration2023—papers from the 7th InternationalConference on Retroviral Integration
, Viruses, Vol: 17, ISSN: 1999-4915The integration of retroviral DNA into host chromosomal DNA is a landmark event that demarcates the transition from the early steps of virus replication to post-integration gene expression and the assembly of new virus particles. Becoming a permanent part of the host cell’s genome, transcriptionally latent proviruses are impervious to highly active antiretroviral therapy and present the greatest barrier to a cure for HIV. Integrase, the viral enzyme that mediates integration, has risen in prominence to a high-value antiretroviral target over the past two decades, with strand transfer inhibitors now widely prescribed for people living with HIV. Allosteric integrase inhibitors (ALLINIs), which potently inhibit virus particle morphogenesis, are being evaluated in phase II clinical trials and are also investigated for “block-and-lock” cure strategies. Papers addressing these subjects and other integration-related research topics were presented and discussed at the 7th International Conference on Retroviral Integration, which was held in Boulder, Colorado during the summer of 2023. In this Editors’ overview, we discuss the papers since published in this dedicated Viruses Special Issue, and briefly touch upon other talks of significant interest.Retrointegration2023 marked the seventh time that the retroviral community had convened at an international conference dedicated to the science of integrase and viral DNA integration. We five served as the meeting co-organizers, with Dr. Kvaratskhelia serving as the local lead organizer. The conference consisted of seven oral sessions and one poster session, with 36 talks given by invited speakers and 11 short talks selected from submitted abstracts (Table 1). Four papers were published as part of the Viruses Special Issue [1,2,3,4]. One of these manuscripts, which expanded upon Dr. Grandgenett’s outro presentation at the end of the conference (Table 1), gave an overview of the field of retroviral inte
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Journal articlePenades JR, Seed KD, Chen J, et al., 2025,
Genetics, ecology and evolution of phage satellites
, NATURE REVIEWS MICROBIOLOGY, Vol: 23, Pages: 410-422, ISSN: 1740-1526- Cite
- Citations: 2
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Journal articleEinenkel R, Qin K, Schmidt J, et al., 2025,
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation
, NATURE MICROBIOLOGY, Vol: 10, ISSN: 2058-5276 -
Journal articleSpeck C, Reuter LM, 2025,
Compact Origins and Where to Find Them: ORC's Guide to Genome-Wide Licensing
, BIOESSAYS, Vol: 47, ISSN: 0265-9247 -
Journal articleDrobnic T, Cohen EJ, Calcraft T, et al., 2025,
In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque
, NATURE MICROBIOLOGY, Vol: 10, ISSN: 2058-5276- Cite
- Citations: 2
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Journal articleAllgower F, Sirohiwal A, Gamiz-Hernandez AP, et al., 2025,
Modified chlorophyll pigment at ChlD₁ tunes photosystem II beyond the red-light limit
, Chemical Science, Vol: 16, Pages: 11270-11279, ISSN: 2041-6520Photosystem II (PSII) is powered by the light-capturing properties of chlorophyll a pigments that define the spectral range of oxygenic photosynthesis. Some photosynthetic cyanobacteria can acclimate to growth in longer wavelength light by replacing five chlorophylls with long wavelength pigments in specific locations, including one in the reaction center (RC) (Science, 2018, 360, 1210–1213). However, the exact location and the nature of these long wavelength pigments still remain uncertain. Here we have addressed the color-tuning mechanism of the far-red light PSII (FRL-PSII) by excited state calculations at both the ab initio correlated (ADC2) and linear-response time-dependent density functional theory (LR-TDDFT) levels in combination with large-scale hybrid quantum/classical (QM/MM) simulations and atomistic molecular dynamics. We show that substitution of a single chlorophyll pigment (ChlD1) at the RC by chlorophyll d leads to a spectral shift beyond the far-red light limit, as a result of the protein electrostatic, polarization and electronic coupling effects that reproduce key structural and spectroscopic observations. Pigment substitution at the ChlD1 site further results in a low site energy within the RC that could function as a sink for the excitation energy and initiate the primary charge separation reaction, driving the water oxidation. Our findings provide a basis for understanding color-tuning mechanisms and bioenergetic principles of oxygenic photosynthesis at the far-red light limit.
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Journal articleKang Y, Liu Y, Zhou H, et al., 2025,
A temperature-driven DNA discrimination strategy to distinguish E. coli DNA and phage 5hmC-modified DNA
, Nucleic Acids Research, Vol: 53, ISSN: 0305-1048The arms race between phages and bacteria is dynamic and ongoing, with both continuously acquiring new strategies to outcompete each other during co-evolution. Here, we report bacteriophage T4 exonuclease DexA and an uncharacterized Escherichia coli exonuclease as a rare pair of attack and defense duo arising from the same mechanism. DexA, highly conserved among phages, has two well-characterized biological roles: host DNA scavenging and intron homing. Unmodified DNA is the substrate during host DNA scavenging, whereas cleavage of 5hmC (5-hydroxymethylcytosine)-modified phage DNA is required for intron homing. We reveal a temperature-driven quaternary fold switch between DexA dimer and tetramer that facilitates cleavage of distinct DNA forms, namely 5hmC-modified phage DNA and unmodified host DNA. As a countermeasure, bacteria produce DexA variants for defense against phage that only targets 5hmC-modified DNA. Thus, both phages and bacteria compete using HmC-Recognizing EXonuclease strategies (designated as HREX).
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Journal articleConsoli G, Leong HF, Davis GA, et al., 2025,
Structure of a stripped-down and tuned-up far-red phycobilisome
, Communications Biology, Vol: 8, ISSN: 2399-3642A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm–800 nm). To achieve this, all the main light-driven components of the photosynthetic apparatus, including their allophycocyanin antenna, are replaced with red-shifted paralogues. Recent studies based on the structure of an incomplete complex provided some insights into the tuning of the far-red phycobiliproteins. Here, we solved the structure of the intact bicylindrical allophycocyanin complex from the cyanobacterium Chroococcidiopsis thermalis PCC 7203 at a resolution of 2.51 Å determined by Cryo-electron microscopy single particle analysis. A comparison between conserved structural features in far-red and white light allophycocyanin cores provides insight on the evolutionary adaptations needed to optimize excitation energy transfer in the far-red light adapted photosynthetic apparatus. The reduction in antenna size in far-red photosynthesis suggests a need to optimize membrane packing to increase the number of photosystems and tune the ratio between chlorophyll f molecules and bilin pigments, while the wider spread in the absorption range of the bilins suggests faster and more efficient excitation energy transfer to far-red Photosystem II by limiting backflow of excitation from the reaction centres to the far-red bilin pigments.
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Journal articlePessina D, De Anda JC, Heffernan C, et al., 2025,
Integrated <i>In Vitro</i>/<i>In Silico</i> Uncertainty Quantification Method for Protein Crystallization Models
, INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, Vol: 64, Pages: 12025-12035, ISSN: 0888-5885 -
Journal articleTajadura-Ortega V, Chai W, Roberts LA, et al., 2025,
Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes
, Nature Communications, Vol: 16, ISSN: 2041-1723Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.
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Journal articleKadeřábková N, Furniss RCD, Maslova E, et al., 2025,
Antibiotic potentiation and inhibition of cross-resistance in pathogens associated with cystic fibrosis.
, bioRxivCritical Gram-negative pathogens, like Pseudomonas, Stenotrophomonas and Burkholderia, have become resistant to most antibiotics. Complex resistance profiles together with synergistic interactions between these organisms increase the likelihood of treatment failure in distinct infection settings, for example in the lungs of cystic fibrosis (CF) patients. Here, we discover that cell envelope protein homeostasis pathways underpin both antibiotic resistance and cross-protection in CF-associated bacteria. We find that inhibition of oxidative protein folding inactivates multiple species-specific resistance proteins. Using this strategy, we sensitize multidrug-resistant Pseudomonas aeruginosa to β-lactam antibiotics and demonstrate promise of new treatment avenues for the recalcitrant emerging pathogen Stenotrophomonas maltophilia. The same approach also inhibits cross-protection between resistant S. maltophilia and susceptible P. aeruginosa, allowing eradication of both commonly co-occurring CF-associated organisms. Our results provide the basis for the development of next-generation strategies that target antibiotic resistance, while also impairing specific interbacterial interactions that enhance the severity of polymicrobial infections.
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Journal articleCarver A, Zhang B, Zhang X, 2025,
Structures and mechanisms of AAA plus protein complexes in DNA processing
, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 92, ISSN: 0959-440X -
Journal articleNolan LM, Webber MA, Filloux A, 2025,
Throwing a spotlight on genomic dark matter: The power and potential of transposon-insertion sequencing
, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 301 -
Journal articleGyamfi E, Baum J, 2025,
Malaria parasite phenotypic heterogeneity and the power of single-cell technologies.
, Trends Parasitol, Vol: 41, Pages: 460-470The two-host life cycle of the malaria parasite, combined with its ability to regulate gene expression and protein translation within a single clonal genotype, results in a remarkable potential for phenotypic heterogeneity. This heterogeneity presents underappreciated challenges to antimalarial interventions such as vaccines, drugs, and diagnostic tools, with parasites able to evolve resistance rapidly. Here we summarise current knowledge of the different mechanisms driving parasite phenotypic heterogeneity both at the gene and protein level. Centred on the most virulent human malaria parasite, Plasmodium falciparum, we explore the consequences of this diversity for antimalarial interventions and how single-cell technologies present an opportunity to study inter- and intra-clonal heterogeneity to better design future-proofed intervention strategies against this ancient disease.
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Journal articleHobbs B, Limmer N, Ossa F, et al., 2025,
A low-complexity linker as a driver of intra- and intermolecular interactions in DNAJB chaperones
, Nature Communications, Vol: 16, ISSN: 2041-1723J-domain proteins ( JDPs) act as major regulators of the proteostasis network by driving the specificity of the Hsp70 machine. Their important functions are mediated by a low-complexity glycine-/phenylalanine-rich region (GF-linker) that links the folded J-domain with the substrate binding domain. Recently, we and others have shown that in an autoinhibited JDP state, an α-helix formed within the GF-linker blocks the Hsp70 binding site on the J-domain. However, the role of the disordered GF-linker in autoinhibition and how the latter is released, are still not understood. Here, using autoinhibited DNAJB1 and DNAJB6 constructs, we show that in combination with the J-domain, the GF-linker creates a hydrophobic, partially collapsed cluster that shows a remarkable degree of long-range structural communication, disruption of which can lead to destabilisation of autoinhibition. Apart from this crucial intramolecular role, we reveal that the GF-linker can also be recognised by the substrate-binding domain of Hsp70 and dictate the lifetime of the entire JDP–Hsp70 complex. Strikingly, the GF-linkers of DNAJB1 and DNAJB6 display distinct structural properties that lead to different Hsp70 binding kinetics, showing that the behaviour of the GF-linker can vary dramatically even within the same class of JDPs.
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Journal articleSauthof L, Szczepek M, Schmidt A, et al., 2025,
Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes
, SCIENCE ADVANCES, Vol: 11- Cite
- Citations: 1
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Conference paperXu V, Barritt J, Bubeck D, et al., 2025,
Countdown to Package: Molecular Insights into the Rep-mediated Adenoassociated-virus Packaging Machinery
, 28th Annual Meeting of the American-Society-of-Gene-and-Cell-Therapy (ASGCT), Publisher: CELL PRESS, ISSN: 1525-0016 -
Journal articleGiblin SP, McKenna S, Matthews S, et al., 2025,
The N-terminal ELR+ motif of the neutrophil attractant CXCL8 confers susceptibility to degradation by the Group A Streptococcal protease, SpyCEP
, Journal of Biological Chemistry, Vol: 301, ISSN: 0021-9258Streptococcus pyogenes (Group A Streptococcus or GAS) is a major human pathogen for which an effective vaccine is highly desirable. Invasive S. pyogenes strains evade the host immune response in part by producing a cell envelope protease, SpyCEP. This neutralizes chemokines containing an N-terminal Glu-Leu-Arg motif (ELR+ chemokines) by cleavage at a distal C-terminal site within the chemokine. SpyCEP is a component of several S. pyogenes vaccines, yet the molecular determinants underlying substrate selectivity are poorly understood. We hypothesized that chemokine recognition and cleavage is a multistep process involving distinct domains of both substrate and enzyme. We generated a panel of recombinant CXCL8 variants where domains of the chemokine were exchanged or mutated. Chemokine degradation by SpyCEP was assessed by SDS-PAGE, Western blot, and ELISA. Extension of the CXCL8 N-terminus was found to inhibit chemokine cleavage. Reciprocal exchanges of the N-termini of CXCL8 with that of the ELR- chemokine CXCL4 resulted in the generation of loss of function and gain of function substrates. This suggested a key role for the ELR motif in substrate recognition, which was supported directly by alanine substitution of the ELR motif of CXCL8, impairing the parameters, KM, Vmax, and Kcat in kinetic assays with SpyCEP. Collectively, our findings identify the N-terminal ELR motif as a major determinant for recognition by SpyCEP and expose a vulnerability in the mechanism by which the protease recognises its substrates. This likely presents potential avenues for therapeutic intervention via targeted vaccine design and small molecule inhibition.
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Journal articleKim TD, Pretorius D, Murray JW, et al., 2025,
Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree
, Physiologia Plantarum, Vol: 177, ISSN: 0031-9317Although our knowledge of photosystem II has expanded to include time-resolved atomic details, the diversity of experimental structures of the enzyme remains limited. Recent advances in protein structure prediction with AlphaFold offer a promising approach to fill this gap in structural diversity in non-model systems. This study used AlphaFold to predict the structures of the D1 protein, the core subunit of photosystem II, across a broad range of photosynthetic organisms. The prediction produced high-confidence structures, and structural alignment analyses highlighted conserved regions across the different D1 groups, which were in line with high pLDDT scoring regions. In contrast, varying pLDDT in the DE loop and terminal regions appears to correlate with different degrees of structural flexibility or disorder. Subsequent structural phylogenetic analysis using Foldtree provided a tree that is in good agreement with previous sequence-based studies. Moreover, the phylogeny supports a parsimonious scenario in which far-red D1 and D1INT evolved from an ancestral form of G4 D1. This work demonstrates the potential of AlphaFold and Foldtree to study the molecular evolution of photosynthesis.
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Journal articleGao F, Ye F, Buck M, et al., 2025,
Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ54. σ54 recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ54-mediated open complex formation requires specific AAA+ proteins (ATPases Associated with diverse cellular Activities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ54 unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ54 into the bEBP hexamer central pore causing the partial unfolding of σ54, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family.
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Journal articleZhang X, 2025,
Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling
, Proceedings of the National Academy of Sciences of USA, ISSN: 0027-8424 -
Journal articleIshimoto N, Wong JLC, He S, et al., 2025,
Cryo-EM structure of the conjugation H-pilus reveals the cyclic nature of the TrhA pilin
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Conjugation, the major driver of the spread of antimicrobial resistance genes, relies on a conjugation pilus for DNA transfer. Conjugative pili, such as the F-pilus, are dynamic tubular structures, composed of a polymerized pilin, that mediate the initial donor–recipient interactions, a process known as mating pair formation (MPF). IncH are low-copy-number plasmids, traditionally considered broad host range, which are found in bacteria infecting both humans and animals. The reference IncHI1 plasmid R27, isolated from Salmonella enterica serovar Typhi, encodes the conjugative H-pilus subunit TrhA containing 74 residues after cleavage of the signal sequence. Here, we show that the H-pilus forms long filamentous structures that mediate MPF and describe its cryoelectron-microscopic (cryo-EM) structure at 2.2 Å resolution. Like the F pilus, the H-pilin subunits form helical assemblies with phospholipid molecules at a stoichiometric ratio of 1:1. While there were previous reports that the T-pilus from Agrobacterium tumefaciens was composed of cyclic subunits, three recent cryo-EM structures of the T-pilus found no such cyclization. Here, we report that the H-pilin is cyclic, with a covalent bond connecting the peptide backbone between the N and C termini. Both the cryo-EM map and mass spectrometry revealed cleavage of the last five residues of the pilin, followed by cyclization via condensation of the amine and carboxyl residues. Mutagenesis experiments revealed that loss of cyclization abolished pilus biogenesis and efficient plasmid transfer. The cyclic nature of the pilin could stabilize the pilus and may explain the high incidence of IncH plasmid dissemination.
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Journal articleYoun T, Kim G, Hariharan P, et al., 2025,
Improved pendant-bearing glucose-neopentyl glycols for membrane protein stability
, Bioconjugate Chemistry, Vol: 36, Pages: 707-717, ISSN: 1043-1802Membrane proteins are biologically and pharmaceutically significant, and determining their 3D structures requires a membrane-mimetic system to maintain protein stability. Detergent micelles are widely used as membrane mimetics; however, their dynamic structures often lead to the denaturation and aggregation of encapsulated membrane proteins. To address the limitations of classical detergents in stabilizing membrane proteins, we previously reported a class of glucose-neopentyl glycols (GNGs) and their pendant-bearing versions (P-GNGs), several of which proved more effective than DDM in stabilizing membrane proteins. In this study, we synthesized additional GNG derivatives by varying the lengths of the pendant (P-GNGs), and by introducing hemifluorinated pendants to the GNG scaffold (fluorinated pendant-bearing GNGs or FP-GNGs). The synthetic flexibility of the GNG chemical architecture allowed us to create a diverse range of derivatives, essential for the effective optimization of detergent properties. When tested with two model membrane proteins (a transporter and a G-protein coupled receptor (GPCR)), most of the new (F)P-GNGs demonstrated superior stabilization of these membrane proteins compared to DDM, the original GNG (OGNG)), and a previously developed P-GNG (i.e., GNG-3,14). Notably, several P-GNGs synthesized in this study were as effective as or even better than lauryl maltose neopentyl glycol (LMNG) in stabilizing a human GPCR, beta2 adrenergic receptor (β2AR). Enhanced protein stability was particularly observed for the P-GNGs with a butyl (C4) or pentyl (C5) pendant, indicating that these pendant sizes are optimal for membrane protein stability. The volumes of these pendants appear to minimize the empty spaces in the micelle interiors, thereby enhancing detergent-detergent interactions in micelles complexed with the membrane proteins. Additionally, we identified one FP-GNG that was more efficient at extracting the transporter and more effective at st
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Journal articleSadaf A, Yun HS, Lee H, et al., 2025,
Multiple pendants-bearing triglucosides for membrane protein studies: effects of pendant length and number on micelle interior hydration and protein stability
, Biomacromolecules, Vol: 26, Pages: 2565-2579, ISSN: 1525-7797Membrane proteins play central roles in cell physiology and are the targets of over 50% of FDA-approved drugs. In the present study, we prepared single alkyl-chained triglucosides decorated with multiple pendants, designated multiple pendant-bearing glucosides (MPGs), to enhance membrane protein stability. The new detergents feature two and four pendants of varying size at the hydrophilic–lipophilic interfaces, designated MPG-Ds and MPG-Ts, respectively. When tested with model membrane proteins, including the human adrenergic receptor (β2AR), the tetra-pendant-bearing MPGs (MPG-Ts) demonstrated superior performance compared to the dipendant analogs (MPG-Ds) and the gold standard DDM. All-atom molecular dynamics (MD) simulations results reveal that the four-pendant configuration of this detergent is remarkably effective in excluding water from the hydrophobic micelle interiors compared to the dipendant MPGs and DDM, an unprecedented feature of this new detergent. Our findings provide a novel strategy for designing water-resistant detergents, advancing the field of membrane protein research.
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