PhD project

Supervisor: Georgia Isom

Antimicrobial resistant (AMR) micro-organisms cause a major global threat to modern medicine, contributing to almost 5 million deaths a year. Gram-negative, double-membraned bacteria (such as Escherichia coli) are particularly difficult to treat, in part because they have an outer membrane that acts as a barrier against antibiotics. Therefore, it is critical to understand how bacteria build and maintain their outer membrane, potentially allowing for novel therapeutic approaches that disrupt this barrier.

The Gram-negative bacterial cell envelope consists of an inner membrane and an outer membrane separated by an aqueous periplasmic space. To build and maintain this outer membrane, bacteria must transport lipids and hydrophobic proteins across the aqueous periplasm. Increasingly, evidence suggests that membrane components are transported via bridges or tunnels that directly connect the two membranes (Ekiert et al., 2017, Isom et al., 2020, Coudray et al., 2020). Understanding how these proteins function provide new insights into how bacteria build the outer membrane, and potentially enable us to design new drugs targeting this membrane.

The Isom lab group focuses on understudied proteins that transport of outer membrane components in E. coli (Ekiert et al., 2017, Isom et al., 2020, Coudray et al., 2020). A PhD in the Isom lab give you the opportunity to learn state-of-the-art techniques, including structural biology, biochemistry and/or microbial genetics. A project will be carved around the interest of the incoming PhD student, centred around the following outstanding questions:

• How do proteins that transport outer membrane components function mechanistically? We can use a combination of cryo-EM and X-ray crystallography to solve the structure of proteins/protein complexes.
• What are the substrates of these proteins? Understanding which molecules the proteins interact with will allow us to determine what exactly they are transporting. We will use a combination of biochemical approaches including protein-substrate binding assays, mass spectrometry, and in vivo
• What are the phenotypes of bacteria that lack these proteins? We will construct gene knockouts in coli and assess changes in cell morphology, sensitivity to outer membrane stresses/antibiotics, and outer membrane lipid and protein composition.

Publications:

• *Isom, G.L., *Coudray, N., MacRae, M.R., McManus, C.T., Ekiert, D.C., Bhabha, G., (2020). LetB Structure Reveals a Tunnel for Lipid Transport across the Bacterial Envelope. Cell
• *Coudray, N., *Isom, G.L., *MacRae, M.R., Saiduddin, S.N., Bhabha, G., and Ekiert, D.C.. (2020). Structure of Bacterial Phospholipid Transporter MlaFEDB with Substrate Bound. eLife
• Isom, G.L., Davies, N.J., Chong, Z.-S., Bryant, J.A., Jamshad, M., Sharif, M., Cunningham, A.F., Knowles, T.J., Chng, S.-S., Cole, J.A., Henderson, I.R., (2017). MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane. Scientific reports
• Ekiert, D.C., Bhabha, G., Isom, G.L., Greenan, G., Ovchinnikov, S., Henderson, I.R., Cox, J.S., Vale, R.D., (2017). Architectures of Lipid Transport Systems for the Bacterial Outer Membrane. Cell