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Elucidating the mechanisms of outer membrane biogenesis in Gram-negative bacteria

Primary Supervisor: Dr Tim Knowles, School of Biosciences

Secondary supervisor: Dr Andrew Lovering

PhD project title: Elucidating the mechanisms of outer membrane biogenesis in Gram-negative bacteria

University of Registration: University of Birmingham

Project outline:

Projects within the Knowles laboratory focus on the biophysical characterisation of the mechanisms involved in outer membrane biogenesis in Gram-negative bacteria with the overall aim of identifying novel targets for the development of the next generation of antimicrobials.

The emergence of bacteria that are resistant to available antibiotics represents an enormous and growing global threat requiring new targets and strategies to combat infection. Multidrug resistance is most serious for Gram-negative bacteria, with essentially few antibiotics under development or likely to be available for clinical use in the near future.

Gram-negative bacteria are generally more resistant than Gram-positive bacteria to antibiotics, detergents, and other toxic chemicals because of the presence of an additional membrane surrounding the cell, the outer membrane (OM). This membrane contains a sophisticated asymmetry of lipids with LPS in the outer leaflet and phospholipid in the inner leaflet. It makes for a highly effective permeability barrier, both by acting as a barrier to hydrophilic molecules but also by acting to slow the penetration of small hydrophobic molecules, explaining their increased resistance to hydrophobic antibiotics and detergents. Whilst the proteins present within the outer membrane are the prime instruments of microbial warfare and play key roles in microbial pathogenesis, virulence and multidrug resistance, mediating many of the lethal processes responsible for infection and disease progression. Outer membrane proteins (OMPs) are also essential for cellular homeostasis allowing excretion of toxic substances, such as antibiotics, and uptake of nutrients.

The research in the laboratory of Dr Tim Knowles is focused on elucidating the mechanisms involved in the fundamental processes of OM biogenesis in Gram-negative bacteria and has several important objectives: (1) to provide fundamental information about how Gram-negative bacteria form and therefore by proxy mitochondria and chloroplasts. (2) To provide new opportunities to attenuate bacteria in the pursuit of anti-infective strategies. Current antibiotics predominantly target peptidoglycan synthesis and have been very effective in the past. Targeting OM biogenesis offers the potential for a whole new class of antimicrobials urgently required to stay ahead of bacterial resistance. 

Projects are available in two research areas.

Focus - Phospholipid transport to the outer membrane

Recently three protein pathways, the Mla, PqiABC and YebST pathways, have been identified that have components in the inner membrane, periplasm and outer membrane and all bind phospholipid suggesting they may be involved in phospholipid transport. Indeed our recent research in to the Mla pathway (Nature Microbiology) has shown that this pathway can function to transport phospholipids towards the outer membrane and is the first evidence of a phospholipid transport pathway to the outer membrane in Gram-negative bacteria. How these pathways transport phospholipid and the molecular mechanisms involved in transport still remain to be elucidated however. To answer these questions we are using the latest structural biology techniques including cryo-electron microscopy, X-ray crystallography, nuclear magnetic resonance, neutron reflectometry as well as developing our own novel in house biophysical tools to study these fascinating pathways. Using this approach potential druggable pockets will be identified and allow the identification of compounds that will not only abolish virulence but also impede the restoration of a damaged OM and therefore increase the effectiveness of already available antibiotics.

Focus - The Bam complex

A single OM complex, the β-Barrel assembly machine (Bam) complex, has been recognized as essential for the efficient insertion of almost all OMPs into the OM. It is ubiquitous throughout Gram-negative bacteria, however little is known about how it functions. The structures of the individual components have been identified but little information about how the components function as part of the complex nor how this complex can insert the myriad OMPs targeted to the OM has been determined. We are using a multidisciplinary approach, working in both the fields of biophysics and molecular biology to probe the structure of this complex and how it functions. This understanding is critical as the design of compounds that inhibit this process would impede OMP biogenesis and therefore essential physiological, pathogenic and drug resistance functions.

References:

  1. Hughes, G, et al. (2019), Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system Nature Microbiology. doi: 10.1038/s41564-019-0481-y [epub ahead of print]
  2. Browning, D.F., et al., Cross-species chimeras reveal BamA POTRA and beta-barrel domains must be fine-tuned for efficient OMP insertion. Mol Microbiol, 2015. 97(4): p. 646-59.
  3. Knowles, T.J., et al., Structure and function of BamE within the outer membrane and the beta-barrel assembly machine. EMBO Rep, 2011. 12(2): p. 123-8.

BBSRC Strategic Research Priority: Understanding the Rules of Life: Microbiology & Structural Biology & Systems Biology

    Techniques that will be undertaken during the project:

    X-ray crystallography, Cryo-electron microscopy, Nuclear Magnetic Resonance spectroscopy, neutron Scattering, X-ray Scattering, novel polymer solubilisation techniques, mass spectrometry, quartz crystal microbalance, linear dichroism, circular dichroism, analytical ultracentrifugation, isothermal titration calorimetry, surface plasmon resonance, protein expression and purification, mutagenesis, SMALPs, enzymatic activity, ligand screening assays, protein structure calculation and modelling, cell-based assays, western blots, SDS_PAGE, genome sequencing.

    Contact: Dr Tim Knowles, University of Birmingham