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  • Journal article
    Valentini M, Filloux A, 2016,

    Biofilms and cyclic di-GMP (c-di-GMP) signaling: lessons from Pseudomonas aeruginosa and other bacteria

    , Journal of Biological Chemistry, Vol: 291, Pages: 12547-12555, ISSN: 1083-351X

    The cyclic-di-GMP (c-di-GMP) second messenger represents a signaling system that regulates many bacterial behaviors and is of key importance for driving the lifestyle switch between motile loner cells and biofilm formers. This review provides an up-to-date compendium of c-di-GMP pathways connected to biofilm formation, biofilm-associated motilities and other functionalities in the ubiquitous and opportunistic human pathogen Pseudomonas aeruginosa. This bacterium is frequently adopted as model organism to study bacterial biofilm formation. Importantly, its versatility and adaptation capabilities are linked with a broad range of complex regulatory networks, including a large set of genes involved in c-di-GMP biosynthesis, degradation and transmission.

  • Journal article
    Taylor JD, Hawthorne WJ, Lo J, Dear A, Jain N, Meisl G, Andreasen M, Fletcher C, Koch M, Darvill N, Scull N, Escalera-Maurer A, Sefer L, Wenman R, Lambert S, Jean J, Xu Y, Turner B, Kazarian SG, Chapman MR, Bubeck D, de Simone A, Knowles TPJ, Matthews SJet al., 2016,

    Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones

    , Scientific Reports, Vol: 6, ISSN: 2045-2322

    Polypeptide aggregation into amyloid is linked with several debilitating human diseases.Despite the inherent risk of aggregation-induced cytotoxicity, bacteria control the export ofamyloid-prone subunits and assemble adhesive amyloid fibres during biofilm formation. AnEscherichia protein, CsgC potently inhibits amyloid formation of curli amyloid proteins.Here we unlock its mechanism of action, and show that CsgC strongly inhibits primarynucleation via electrostatically-guided molecular encounters, which expands theconformational distribution of disordered curli subunits. This delays the formation of higherorder intermediates and maintains amyloidogenic subunits in a secretion-competent form.New structural insight also reveal that CsgC is part of diverse family of bacterial amyloidinhibitors. Curli assembly is therefore not only arrested in the periplasm, but the preservationof conformational flexibility also enables efficient secretion to the cellsurface. Understanding how bacteria safely handle amyloidogenic polypeptides contributetowards efforts to control aggregation in disease-causing amyloids and amyloid-based biotechnological applications.

  • Journal article
    Miliara X, Matthews S, 2016,

    Structural comparison of yeast and human intra-mitochondrial lipid transport systems

    , Biochemical Society Transactions, Vol: 44, Pages: 479-485, ISSN: 1470-8752

    Mitochondria depend on a tightly regulated supply of phospholipids. The protein of relevant evolutionary and lymphoid interest (PRELI)/Ups1 family together with its mitochondrial chaperones [TP53-regulated inhibitor of apoptosis 1 (TRIAP1)/Mdm35] represents a unique heterodimeric lipid-transfer system that is evolutionary conserved from yeast to man. Recent X-ray crystal structures of the human and yeast systems are compared and discuss here and shed new insight into the mechanism of the PRELI/Ups1 system.

  • Journal article
    O'Neill A, Thurston T, Holden D, 2016,

    Cytosolic Replication of Group A Streptococcus in Human Macrophages

    , mBio, Vol: 7, ISSN: 2161-2129

    As key components of innate immune defense, macrophages are essential in controlling bacterial pathogens, includinggroup A Streptococcus (GAS). Despite this, only a limited number of studies have analyzed the recovery of GAS from withinhuman neutrophils and macrophages. Here, we determined the intracellular fate of GAS in human macrophages by using severalquantitative approaches. In both U937 and primary human macrophages, the appearance over time of long GAS chains revealedthat despite GAS-mediated cytotoxicity, replication occurred in viable, propidium iodide-negative macrophages. Whereas themajor virulence factor M1 did not contribute to bacterial growth, a GAS mutant strain deficient in streptolysin O (SLO) was impairedfor intracellular replication. SLO promoted bacterial escape from the GAS-containing vacuole (GCV) into the macrophagecytosol. Up to half of the cytosolic GAS colocalized with ubiquitin and p62, suggesting that the bacteria were targeted bythe autophagy machinery. Despite this, live imaging of U937 macrophages revealed proficient replication of GAS after GCV rupture,indicating that escape from the GCV is important for growth of GAS in macrophages. Our results reveal that GAS can replicatewithin viable human macrophages, with SLO promoting GCV escape and cytosolic growth, despite the recruitment of autophagyreceptors to bacteria.

  • Journal article
    Helaine S, holden DW, sampson SL, Mouton JMet al., 2016,

    Elucidating population-wide mycobacterial replication dynamics at the single-cell level

    , Microbiology, Vol: 162, Pages: 966-978, ISSN: 1350-0872

    Mycobacterium tuberculosis infections result in a spectrum of clinical outcomes, and frequently the infection persists in a latent, clinically asymptomatic state. The within-host bacterial population is likely to be heterogeneous, and it is thought that persistent mycobacteria arise from a small population of viable, but non-replicating (VBNR) cells. These are likely to be antibiotic tolerant and necessitate prolonged treatment. Little is known about these persistent mycobacteria, since they are very difficult to isolate. To address this, we have successfully developed a replication reporter system for use in M. tuberculosis. This approach, termed fluorescence dilution, exploits 2 fluorescent reporters; a constitutive reporter allows the tracking of bacteria, while an inducible reporter enables the measurement of bacterial replication. The application of fluorescent single-cell analysis to characterise intracellular M. tuberculosis identified a distinct subpopulation of non-growing mycobacteria in murine macrophages. The presence of VBNR and actively replicating mycobacteria was observed within the same macrophage after 48 hours of infection. Furthermore, our results suggest that macrophage uptake resulted in enrichment of non- or slowly replicating bacteria (as revealed by DCS treatment); this population is likely to be highly enriched for persisters, based on its drug tolerant phenotype. These results demonstrate the successful application of the novel dual fluorescent reporter system both in vitro and in macrophage infection models to provide a window into mycobacterial population heterogeneity.

  • Journal article
    Pratap CB, Scanu T, Spaapen RM, Bakker JM, Wu L-E, Hofland I, Broeks A, Shukla VK, Kumar M, Janssen H, Song J-Y, Riele HT, Holden DW, Nath G, Neefjes Jet al., 2016,

    Salmonella manipulation of host signalling pathways promotes cellular transformation and cancer of infected tissues

    , International Journal of Infectious Diseases, Vol: 45, Pages: 145-145, ISSN: 1201-9712
  • Journal article
    Larrouy-Maumus GJ, Leonardo B Marino, Ashoka V R Madduri, T J Ragan, Debbie M Hunt, Lucrezia Bassano, Maximiliano G Gutierrez, D Branch Moody, Fernando R Pavan, Luiz Pedro S de Carvalhoet al., 2016,

    Cell-Envelope Remodeling as a Determinant of Phenotypic Antibacterial Tolerance in Mycobacterium tuberculosis

    , ACS Infectious Diseases, Vol: 2, Pages: 352-360, ISSN: 2373-8227

    The mechanisms that lead to phenotypic antibacterial tolerance in bacteria remain poorly understood. We investigate whether changes in NaCl concentration toward physiologically higher values affect antibacterial efficacy against Mycobacterium tuberculosis (Mtb), the causal agent of human tuberculosis. Indeed, multiclass phenotypic antibacterial tolerance is observed during Mtb growth in physiologic saline. This includes changes in sensitivity to ethionamide, ethambutol, d-cycloserine, several aminoglycosides, and quinolones. By employing organism-wide metabolomic and lipidomic approaches combined with phenotypic tests, we identified a time-dependent biphasic adaptive response after exposure of Mtb to physiological levels of NaCl. A first rapid, extensive, and reversible phase was associated with changes in core and amino acid metabolism. In a second phase, Mtb responded with a substantial remodelling of plasma membrane and outer lipid membrane composition. We demonstrate that phenotypic tolerance at physiological concentrations of NaCl is the result of changes in plasma and outer membrane lipid remodeling and not changes in core metabolism. Altogether, these results indicate that physiologic saline-induced antibacterial tolerance is kinetically coupled to cell envelope changes and demonstrate that metabolic changes and growth arrest are not the cause of phenotypic tolerance observed in Mtb exposed to physiologic concentrations of NaCl. Importantly, this work uncovers a role for bacterial cell envelope remodeling in antibacterial tolerance, alongside well-documented allterations in respiration, metabolism, and growth rate.

  • Journal article
    Buckley AM, Jukes C, Candlish D, Irvine JJ, Spencer J, Fagan RP, Roe AJ, Christie JM, Fairweather NF, Douce GRet al., 2016,

    Lighting Up Clostridium Difficile: Reporting Gene Expression Using Fluorescent Lov Domains

    , Scientific Reports, Vol: 6, ISSN: 2045-2322

    The uses of fluorescent reporters derived from green fluorescent protein have proved invaluable for the visualisation of biological processes in bacteria grown under aerobic conditions. However, their requirement for oxygen has limited their application in obligate anaerobes such as Clostridium difficile. Fluorescent proteins derived from Light, Oxygen or Voltage sensing (LOV) domains have been shown to bridge this limitation, but their utility as translational fusions to monitor protein expression and localisation in a strict anaerobic bacterium has not been reported. Here we demonstrate the utility of phiLOV in three species of Clostridium and its application as a marker of real-time protein translation and dynamics through genetic fusion with the cell division protein, FtsZ. Time lapse microscopy of dividing cells suggests that Z ring assembly arises through the extension of the FtsZ arc starting from one point on the circumference. Furthermore, through incorporation of phiLOV into the flagella subunit, FliC, we show the potential of bacterial LOV-based fusion proteins to be successfully exported to the extracellular environment.

  • Journal article
    Hergott CB, Roche AM, Tamashiro E, Clarke TB, Bailey AG, Laughlin A, Bushman FD, Weiser JNet al., 2016,

    Detection of peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.

    , Blood, Vol: 127, Pages: 2460-2471, ISSN: 1528-0020

    Maintenance of myeloid cell homeostasis requires continuous turnover of phagocytes from the bloodstream, yet whether environmental signals influence phagocyte longevity in the absence of inflammation remains unknown. Here, we show that the gut microbiota regulates the steady-state cellular lifespan of neutrophils and inflammatory monocytes, the two most abundant circulating myeloid cells and key contributors to inflammatory responses. Treatment of mice with broad-spectrum antibiotics, or with the gut-restricted aminoglycoside neomycin alone, accelerated phagocyte turnover and increased the rates of their spontaneous apoptosis. Metagenomic analyses revealed that neomycin altered the abundance of intestinal bacteria bearing γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP), a ligand for the intracellular peptidoglycan sensor Nod1. Accordingly, signaling through Nod1 was both necessary and sufficient to mediate the stimulatory influence of the flora on myeloid cell longevity. Stimulation of Nod1 signaling increased the frequency of lymphocytes in the murine intestine producing the pro-inflammatory cytokine interleukin 17A (IL-17A), and liberation of IL-17A was required for transmission of Nod1-dependent signals to circulating phagocytes. Together, these results define a mechanism through which intestinal microbes govern a central component of myeloid homeostasis and suggest perturbations of commensal communities can influence steady-state regulation of cell fate.

  • Journal article
    So EC, Schroeder GN, Carson D, Mattheis C, Mousnier A, Broncel M, Tate EW, Frankel GMet al., 2016,

    The Rab-binding profiles of bacterial virulence factors during infection

    , Journal of Biological Chemistry, Vol: 291, Pages: 5832-5843, ISSN: 1083-351X

    Legionella pneumophila, the causativeagent of Legionnaire’s disease, uses its typeIV secretion system to translocate over 300effector proteins into host cells. Theseeffectors subvert host cell signalingpathways to ensure bacterial proliferation.Despite their importance for pathogenesis,the roles of most of the effectors are yet tobe characterized. Key to understanding thefunction of effectors is the identification ofhost proteins they bind during infection. Wepreviously developed a novel tandemaffinitypurification (TAP) approach usinghexahistidine and BirA-specificbiotinylation tags for isolating translocatedeffector complexes from infected cellswhose composition were subsequentlydeciphered by mass spectrometry. Here wefurther advanced the workflow for the TAPapproach and determined the infectiondependentinteractomes of the effectorsSidM and LidA, which were previouslyreported to promiscuously bind multiple RabGTPases in vitro. In this study we defined astringent subset of Rab GTPases targeted bySidM and LidA during infection, comprisingof Rab1A, 1B, 6 and 10; in addition, LidAtargets Rab14 and 18. Taken together, thisstudy illustrates the power of this approachto profile the intracellular interactomes ofbacterial effectors during infection

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