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  • Journal article
    Hards K, Cheung C-Y, Waller N, Adolph C, Keighley L, Tee ZS, Harold LK, Menorca A, Bujaroski RS, Buckley BJ, Tyndall JDA, McNeil MB, Rhee KY, Opel-Reading HK, Krause K, Preiss L, Langer JD, Meier T, Hasenoehrl EJ, Berney M, Kelso MJ, Cook GMet al., 2022,

    An amiloride derivative is active against the F1Fo-ATP synthase and cytochrome bd oxidase of Mycobacterium tuberculosis.

    , Commun Biol, Vol: 5

    Increasing antimicrobial resistance compels the search for next-generation inhibitors with differing or multiple molecular targets. In this regard, energy conservation in Mycobacterium tuberculosis has been clinically validated as a promising new drug target for combatting drug-resistant strains of M. tuberculosis. Here, we show that HM2-16F, a 6-substituted derivative of the FDA-approved drug amiloride, is an anti-tubercular inhibitor with bactericidal properties comparable to the FDA-approved drug bedaquiline (BDQ; Sirturo®) and inhibits the growth of bedaquiline-resistant mutants. We show that HM2-16F weakly inhibits the F1Fo-ATP synthase, depletes ATP, and affects the entry of acetyl-CoA into the Krebs cycle. HM2-16F synergizes with the cytochrome bcc-aa3 oxidase inhibitor Q203 (Telacebec) and co-administration with Q203 sterilizes in vitro cultures in 14 days. Synergy with Q203 occurs via direct inhibition of the cytochrome bd oxidase by HM2-16F. This study shows that amiloride derivatives represent a promising discovery platform for targeting energy generation in drug-resistant tuberculosis.

  • Journal article
    Mohamed NAN, Han Y, Hector AL, Houghton AR, Hunter-Sellars E, Reid G, Williams DR, Zhang Wet al., 2022,

    Increasing the Diameter of Vertically Aligned, Hexagonally Ordered Pores in Mesoporous Silica Thin Films

    , LANGMUIR, Vol: 38, Pages: 2257-2266, ISSN: 0743-7463
  • Journal article
    Guo M, Chang ZH, Liang E, Mitchell H, Zhou L, Yin Q, Guinn EJ, Heng JYYet al., 2022,

    The effect of chain length and side chains on the solubility of peptides in water from 278.15 K to 313.15 K: a case study in glycine homopeptides and dipeptides

    , Journal of Molecular Liquids, Vol: 352, Pages: 1-14, ISSN: 0167-7322

    The thermodynamic properties of peptides are significant in terms of the crystallization conditions of biomaterials. In this work, we seek to understand and explain the effect of side chains and chain length on the solubility of peptides. The amino acid residues of dipeptides investigated here were chosen based on their difference in side chain properties. The modified Apelblat equation was used to correlate the relationship between the solubility in water and temperature. In order to explore solute–solvent interactions, the solvation free energies of these peptides were calculated by Molecular Dynamic simulations. This work gives an indication of the effects of side chains and chain length on the solubility of amino acids and peptides in water under different temperatures, which not only provides the thermodynamic data for peptides, but is also critical in the prediction of peptide solubility using Statistical Associating Fluid Theory (SAFT).

  • Journal article
    Demmer J, Phillips B, Uhrig L, Filloux A, Allsopp L, Bublitz M, Meier Tet al., 2022,

    Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii

    , Science Advances, Vol: 8, ISSN: 2375-2548

    The global spread of multi-drug resistant Acinetobacter baumannii infections urgently calls for the identification of novel drug targets. We solved the cryo- electron microscopy structure of the F1Fo-ATP synthase from A. baumannii in three distinct conformational states. The nucleotide-converting F1 sub-complex reveals a specific self-inhibition mechanism, which supports a uni-directional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded Fo complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen.

  • Journal article
    Zhang Y, Matthews S, Wu D, Zou Yet al., 2022,

    Interactions between successive high-velocity impact droplets during plasma spraying

    , SURFACE & COATINGS TECHNOLOGY, Vol: 431, ISSN: 0257-8972
  • Conference paper
    Beltran L, Seddon C, Frankel G, Beis K, Egelman EHet al., 2022,

    Stabilizing bacterial conjugation via conjugation junction proteins

    , 66th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 462A-462A, ISSN: 0006-3495
  • Conference paper
    Kreutzberger MA, Sobe R, Sauder AB, Chatterjee S, Wang F, Kiessling V, Conticello V, Frankel G, Kendall M, Scharf B, Egelman EHet al., 2022,

    Cryo-EM of bacterial flagellar filaments with screw-like surfaces and outer domain sheaths

    , 66th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 131-131, ISSN: 0006-3495
  • Journal article
    Fantuzzi A, Allgower F, Baker H, McGuire G, Teh WK, Gamiz-Hernandez AP, Kaila VRI, Rutherford Aet al., 2022,

    Bicarbonate-controlled reduction of oxygen by the QA semiquinone in Photosystem II in membranes

    , Proceedings of the National Academy of Sciences of USA, Vol: 119, ISSN: 0027-8424

    Photosystem II (PSII), the water/plastoquinone photo-oxidoreductase, plays a key energy input role in the biosphere. Q∙−A, the reduced semiquinone form of the nonexchangeable quinone, is often considered capable of a side reaction with O2, forming superoxide, but this reaction has not yet been demonstrated experimentally. Here, using chlorophyll fluorescence in plant PSII membranes, we show that O2 does oxidize Q∙−A at physiological O2 concentrations with a t1/2 of 10 s. Superoxide is formed stoichiometrically, and the reaction kinetics are controlled by the accessibility of O2 to a binding site near Q∙−A, with an apparent dissociation constant of 70 ± 20 µM. Unexpectedly, Q∙−A could only reduce O2 when bicarbonate was absent from its binding site on the nonheme iron (Fe2+) and the addition of bicarbonate or formate blocked the O2-dependant decay of Q∙−A. These results, together with molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations, indicate that electron transfer from Q∙−A to O2 occurs when the O2 is bound to the empty bicarbonate site on Fe2+. A protective role for bicarbonate in PSII was recently reported, involving long-lived Q∙−A triggering bicarbonate dissociation from Fe2+ [Brinkert et al., Proc. Natl. Acad. Sci. U.S.A. 113, 12144–12149 (2016)]. The present findings extend this mechanism by showing that bicarbonate release allows O2 to bind to Fe2+ and to oxidize Q∙−A. This could be beneficial by oxidizing Q∙−A and by producing superoxide, a chemical signal for the overreduced state of the electron transfer chain.

  • Working paper
    David S, Wong JLC, Sanchez-Garrido J, Kwong H-S, Low WW, Morecchiato F, Giani T, Rossolini GM, Brett SJ, Clements A, Beis K, Aanensen D, Frankel Get al., 2022,

    Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of <i>Klebsiella pneumoniae</i>

    <jats:title>Abstract</jats:title> <jats:p> Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, <jats:italic>Klebsiella pneumoniae</jats:italic> (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact <jats:italic>ompK36</jats:italic> gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. In a murine pneumonia model, KP mutants harbouring L3 insertions have a competitive disadvantage relative to a strain expressing wild-type OmpK36 in the absence of antibiotics. This explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanis

  • Journal article
    Wong G, Lim LR, Tan YQ, Go MK, Bell DJ, Freemont PS, Yew WSet al., 2022,

    Reconstituting the complete biosynthesis of <i>D</i>-lysergic acid in yeast

    , NATURE COMMUNICATIONS, Vol: 13
  • Journal article
    Hao M, Ye F, Jovanovic M, Kotta-Loizou I, Xu Q, Qin X, Buck M, Zhang X, Wang Met al., 2022,

    Structures of Class I and Class II transcription complexes reveal the molecular basis of RamA-dependent transcription activation

    , Advanced Science, Vol: 9, Pages: 1-10, ISSN: 2198-3844

    Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In bacteria, σ70, together with activators, controls the majority of genes by recruiting RNA polymerase (RNAP) to the promoter regions. RNAP and σ70 form a holoenzyme that recognizes -35 and -10 promoter DNA consensus sites. Many activators bind upstream from the holoenzyme and can be broadly divided into two classes. RamA acts as a class I activator on acrA and class II activator on micF, respectively. The authors present biochemical and structural data on RamA in complex with RNAP-σ70 at the two promoters and the data reveal the molecular basis for how RamA assembles and interacts with core RNAP and activates transcription that contributes to antibiotic resistance. Further, comparing with CAP/TAP complexes reveals common and activator-specific features in activator binding and uncovers distinct roles of the two C-terminal domains of RNAP α subunit.

  • Journal article
    Beal J, Telmer CA, Vignoni A, Boada Y, Baldwin GS, Hallett L, Lee T, Selvarajah V, Billerbeck S, Brown B, Cai G-N, Cai L, Eisenstein E, Kiga D, Ross D, Alperovich N, Sprent N, Thompson J, Young EM, Endy D, Haddock-Angelli Tet al., 2022,

    Multicolor plate reader fluorescence calibration

    , SYNTHETIC BIOLOGY, Vol: 7
  • Journal article
    Azmi LHM, Cherukupally P, Hunter-Sellars E, Ladewig PB, Williams RDet al., 2022,

    Fabrication of MIL-101-polydimethylsiloxane composites for environmental toluene abatement from humid air

    , CHEMICAL ENGINEERING JOURNAL, Vol: 429, ISSN: 1385-8947
  • Journal article
    Mullineaux Sanders C, Kozik Z, Sanchez Garrido J, Hopkins EGD, Choudhary JS, Frankel Get al., 2022,

    Citrobacter rodentium infection induces persistent molecular changes and interferon gamma-dependent major histocompatibility complex class II expression in the colonic epithelium

    , mBio, Vol: 13, Pages: 1-18, ISSN: 2150-7511

    Most studies of infections at mucosal surfaces have focused on the acute phase of the disease. Consequently, little is known about the molecular processes that underpin tissue recovery and the long-term consequences postinfection. Here, we conducted temporal deep quantitative proteomic analysis of colonic intestinal epithelial cells (cIECs) from mice infected with the natural mouse pathogen Citrobacter rodentium over time points corresponding to the late steady-state phase (10 days postinfection [DPI]), the clearance phase (13 to 20 DPI), and 4 weeks after the pathogen has been cleared (48 DPI). C. rodentium, which relies on a type III secretion system to infect, is used to model infections with enteropathogenic and enterohemorrhagic Escherichia coli. We observe a strong upregulation of inflammatory signaling and nutritional immunity responses during the clearance phase of the infection. Despite morphological tissue recovery, chromogranin B (ChgB)-positive endocrine cells remained significantly below baseline levels at 48 DPI. In contrast, we observed an increased abundance of proteins involved in antigen processing and presentation 4 weeks after pathogen clearance. In particular, long-term changes were characterized by a persistent interferon gamma (IFN-γ) response and the expression of major histocompatibility complex class II (MHCII) molecules in 60% of the EpCAM+ cIECs, which were not seen in Ifnγ−/− mice. Nonetheless, both wild-type and Ifnγ−/− mice mounted similar systemic and colonic IgG responses to C. rodentium and were equally protected from rechallenge, suggesting that cIEC MHCII is not necessary for protective immunity against C. rodentium.

  • Journal article
    Matthews S, Kennett J, 2022,

    Respecting Agency in Dementia Care: When Should Truthfulness Give Way?

    , JOURNAL OF APPLIED PHILOSOPHY, Vol: 39, Pages: 117-131, ISSN: 0264-3758
  • Journal article
    Zhong Q, Chatterjee S, Choudhary JS, Frankel Get al., 2022,

    EPEC-induced activation of the Ca<SUP>2+</SUP> transporter TRPV2 leads to pyroptotic cell death

    , MOLECULAR MICROBIOLOGY, Vol: 117, Pages: 480-492, ISSN: 0950-382X
  • Journal article
    Singanayagam A, Hakki S, Dunning J, Madon KJ, Crone MA, Koycheva A, Derqui-Fernandez N, Barnett JL, Whitfield MG, Varro R, Charlett A, Kundu R, Fenn J, Cutajar J, Quinn V, Conibear E, Barclay W, Freemont PS, Taylor GP, Ahmad S, Zambon M, Ferguson NM, Lalvani A, ATACCC Study Investigatorset al., 2022,

    Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study.

    , The Lancet. Infectious diseases, Vol: 22, Pages: 183-195, ISSN: 1473-3099

    <h4>Background</h4>The SARS-CoV-2 delta (B.1.617.2) variant is highly transmissible and spreading globally, including in populations with high vaccination rates. We aimed to investigate transmission and viral load kinetics in vaccinated and unvaccinated individuals with mild delta variant infection in the community.<h4>Methods</h4>Between Sept 13, 2020, and Sept 15, 2021, 602 community contacts (identified via the UK contract-tracing system) of 471 UK COVID-19 index cases were recruited to the Assessment of Transmission and Contagiousness of COVID-19 in Contacts cohort study and contributed 8145 upper respiratory tract samples from daily sampling for up to 20 days. Household and non-household exposed contacts aged 5 years or older were eligible for recruitment if they could provide informed consent and agree to self-swabbing of the upper respiratory tract. We analysed transmission risk by vaccination status for 231 contacts exposed to 162 epidemiologically linked delta variant-infected index cases. We compared viral load trajectories from fully vaccinated individuals with delta infection (n=29) with unvaccinated individuals with delta (n=16), alpha (B.1.1.7; n=39), and pre-alpha (n=49) infections. Primary outcomes for the epidemiological analysis were to assess the secondary attack rate (SAR) in household contacts stratified by contact vaccination status and the index cases' vaccination status. Primary outcomes for the viral load kinetics analysis were to detect differences in the peak viral load, viral growth rate, and viral decline rate between participants according to SARS-CoV-2 variant and vaccination status.<h4>Findings</h4>The SAR in household contacts exposed to the delta variant was 25% (95% CI 18-33) for fully vaccinated individuals compared with 38% (24-53) in unvaccinated individuals. The median time between second vaccine dose and study recruitment in fully vaccinated contacts was longer for infected individuals (medi

  • Journal article
    Sperandio V, Frankel G, 2022,

    Editorial overview: Host-microbe interactions: friends, foes and frenemies

    , CURRENT OPINION IN MICROBIOLOGY, Vol: 65, Pages: VIII-X, ISSN: 1369-5274
  • Journal article
    Yahiya S, Jordan S, Smith HX, Gaboriau DCA, Famodimu MT, Dahalan FA, Churchyard A, Ashdown GW, Baum Jet al., 2022,

    Live-cell fluorescence imaging of microgametogenesis in the human malaria parasite <i>Plasmodium falciparum</i>

    , PLOS PATHOGENS, Vol: 18, ISSN: 1553-7366
  • Journal article
    MacGregor-Chatwin C, Nurnberg DJ, Jackson PJ, Vasilev C, Hitchcock A, Ho M-Y, Shen G, Gisriel CJ, Wood WHJ, Mahbub M, Selinger VM, Johnson MP, Dickman MJ, Rutherford AW, Bryant DA, Hunter CNet al., 2022,

    Changes in supramolecular organization of cyanobacterial thylakoid membrane complexes in response to far-red light photoacclimation

    , SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548
  • Journal article
    Amin H, Ilangovan A, Costa TRD, 2022,

    Publisher Correction: Architecture of the outer-membrane core complex from a conjugative type IV secretion system.

    , Nature Communications, Vol: 13, Pages: 1-1, ISSN: 2041-1723
  • Journal article
    Mandela E, Stubenrauch CJ, Ryoo D, Hwang H, Cohen EJ, Torres VL, Deo P, Webb CT, Huang C, Schittenhelm RB, Beeby M, Gumbart JC, Lithgow T, Hay IDet al., 2022,

    Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability

    , ELIFE, Vol: 11, ISSN: 2050-084X
  • Journal article
    Velasquez-Hernandez MDJ, Lopez-Cervantes VB, Martinez-Ahumada E, Tu M, Hernandez-Balderas U, Martinez-Otero D, Williams DR, Martis V, Sanchez-Gonzalez E, Chang J-S, Lee JS, Balmaseda J, Ameloot R, Ibarra IA, Jancik Vet al., 2022,

    CCIQS-1: A Dynamic Metal-Organic Framework with Selective Guest-Triggered Porosity Switching

    , CHEMISTRY OF MATERIALS, Vol: 34, Pages: 669-677, ISSN: 0897-4756
  • Journal article
    Dwijayanti A, Storch M, Stan G-B, Baldwin GSet al., 2022,

    A modular RNA interference system for multiplexed gene regulation

    , Nucleic Acids Research, Vol: 50, ISSN: 0305-1048

    The rational design and realisation of simple-to-use genetic control elements that are modular, orthogonal and robust is essential to the construction of predictable and reliable biological systems of increasing complexity. To this effect, we introduce modular Artificial RNA interference (mARi), a rational, modular and extensible design framework that enables robust, portable and multiplexed post-transcriptional regulation of gene expression in Escherichia coli. The regulatory function of mARi was characterised in a range of relevant genetic contexts, demonstrating its independence from other genetic control elements and the gene of interest, and providing new insight into the design rules of RNA based regulation in E. coli, while a range of cellular contexts also demonstrated it to be independent of growth-phase and strain type. Importantly, the extensibility and orthogonality of mARi enables the simultaneous post-transcriptional regulation of multi-gene systems as both single-gene cassettes and poly-cistronic operons. To facilitate adoption, mARi was designed to be directly integrated into the modular BASIC DNA assembly framework. We anticipate that mARi-based genetic control within an extensible DNA assembly framework will facilitate metabolic engineering, layered genetic control, and advanced genetic circuit applications.

  • Journal article
    Vickers CE, Freemont PS, 2022,

    Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time COMMENT

    , NATURE COMMUNICATIONS, Vol: 13
  • Journal article
    Matthews S, 2022,

    Secondary structure and X-ray crystallographic analysis of the Glideosome-Associated Connector (GAC) from Toxoplasma gondii

    , Crystals, Vol: 12, Pages: 1-6, ISSN: 2073-4352

    A model for parasitic motility has been proposed in which parasite filamentous actin (F-actin) is attached to surface adhesins by a large component of the glideosome, known as the glideosome-associated connector protein (GAC). This large 286 kDa protein interacts at the cytoplasmic face of the plasma membrane with the phosphatidic acid-enriched inner leaflet and cytosolic tails of surface adhesins to connect them to the parasite actomyosin system. GAC is observed initially to the conoid at the apical pole and re-localised with the glideosome to the basal pole in gliding parasite. GAC presumably functions in force transmission to surface adhesins in the plasma membrane and not in force generation. Proper connection between F-actin and the adhesins is as important for motility and invasion as motor operation itself. This notion highlights the need for new structural information on GAC interactions, which has eluded the field since its discovery. We have obtained crystals that diffracted to 2.6–2.9 Å for full-length GAC from Toxoplasma gondii in native and selenomethionine-labelled forms. These crystals belong to space group P212121; cell dimensions are roughly a = 119 Å, b = 123 Å, c = 221 Å, α = 90°, β = 90° and γ = 90° with 1 molecule per asymmetric unit, suggesting a more compact conformation than previously proposed

  • Journal article
    Allsopp LP, Collins ACZ, Hawkins E, Wood TE, Filloux Aet al., 2022,

    RpoN/Sfa2-dependent activation of the <i>Pseudomonas aeruginosa</i> H2-T6SS and its cognate arsenal of antibacterial toxins

    , NUCLEIC ACIDS RESEARCH, Vol: 50, Pages: 227-243, ISSN: 0305-1048
  • Journal article
    Haines MC, Carling B, Marshall J, Shenshin VA, Baldwin GS, Storch M, Freemont Pet al., 2022,

    basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

    <jats:title>Abstract</jats:title> <jats:p> Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These features facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein engineering and multiplexed gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App ( <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://basicsynbio.web.app/">https://basicsynbio.web.app/</jats:ext-link> ) and Python Package ( <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/LondonBiofoundry/basicsynbio">https://github.com/LondonBiofoundry/basicsynbio</jats:ext-link> ). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Users can export sequence data and create build instructions for manual or acoustic liquid-handling platforms. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serializable in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection is compatib

  • Journal article
    Nagaraj M, Najarzadeh Z, Pansieri J, Biverstal H, Musteikyte G, Smirnovas V, Matthews S, Emanuelsson C, Johansson J, Buxbaum JN, Morozova-Roche L, Otzen DEet al., 2022,

    Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation

    , CHEMICAL SCIENCE, Vol: 13, Pages: 536-553, ISSN: 2041-6520
  • Journal article
    Filloux A, Ramos JL, 2022,

    Preface

    , Advances in Experimental Medicine and Biology, Vol: 1386, Pages: v-x, ISSN: 0065-2598

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