The Bloomsbury Colleges

Mapping The Ultrastructural Topology of Septin Cage ‎‎‎‎‎Entrapment

Principal Supervisor: Professor Serge Mostowy, London School of Hygiene and Tropical Medicine (LSHTM)
Co-Supervisor: Professor Carolyn Moores, Birkbeck College

Project Description

Background

Shigella, a Gram-negative enteroinvasive bacterial pathogen, causes ~200 million cases of bacillary dysentery each year, and due to antibiotic resistance the World Health Organisation (WHO) has listed Shigella among its top pathogens requiring urgent action. Shigella is also recognised as an exceptional model pathogen to study key issues in cell biology and innate immunity.

Cell-autonomous immunity, the ability of a host cell to eliminate an invasive infectious agent, is a first line of host defence against bacterial pathogens. Recent studies of host-pathogen interactions have shown that cytoskeletal components are important for cell-autonomous immunity, yet underlying determinants are only beginning to emerge. We discovered that host cells prevent the actin-based motility of Shigella by entrapping bacteria targeted to autophagy inside ‘septin cages’, a mechanism of host defence that restricts bacterial dissemination. We showed that septins, a cytoskeletal component essential for many morphogenetic and signaling events, are recruited with autophagy proteins to cytosolic bacteria and counteract actin tail formation. Our results were first to highlight septins as structural determinants of host defence, and suggest that a comprehensive understanding of septin cage entrapment will have important consequences for understanding bacterial pathophysiology and its control.

Work which has led up to the project

We discovered that septins, which recognise and assemble on membranes presenting micron scale curvature, recognise membrane curvature of Shigella to arrest bacterial cell division, introducing bacterial cell shape as a danger signal triggering cell-autonomous immunity. Considering that septins have many roles in normal cell physiology, we used bottom-up cellular microbiology to create a cell-free platform for investigation of septin cage entrapment in isolation. We reconstituted the Shigella-septin cage in vitro using purified proteins, transforming our understanding of septin-bacteria interactions and its translational potential. It is next of great interest to understand how septins interact with the bacterial cell surface, and how septin cage entrapment is coordinated on the bacterial cell surface with other host factors (including actin, ubiquitin, autophagosomes) for Shigella infection control.

For this PhD project, we will combine cell-free reconstitution platforms (Prof. Mostowy) with innovative structural biology approaches (Prof. Moores) to study Shigella-septin cage entrapment. Building from results recently published, we will address fundamental gaps in knowledge through 2 synergistic research Aims.

Aim 1: Determine how septins interact with the Shigella cell surface

We discovered that septins recognise membrane curvature of Shigella to arrest bacterial cell division. From this, we hypothesise that host cells employ septins to sense intracellular bacteria based on biophysical cues as a new danger signal for cell-autonomous immunity. In combination with state-of-the-art microscopy techniques we will test this using our cell-free reconstitution system to reduce complexity and identify biophysical cues responsible for septin recruitment and cage assembly. Biophysical cues identified using Shigella may serve as universal danger signals presented by other intracellular bacterial pathogens (Gram-negative, Gram-positive) or damaged organelles (mitochondria, ER).

Considering that septin filament orientation at the yeast bud neck is linked to force generation in cell division, septin filament orientation may suggest a mechanical function for septins in inhibiting cell elongation or blocking septum constriction. To study this, we will perform cryo-EM. In-depth structural studies, using either single-particle reconstruction or cryo-ET according to the requirements of the sample, will determine how septin filaments self-assemble into higher-order oligomers upon bacterial surfaces in vitro. Together, investigation of biophysical cues promises identification of novel determinants modulating septin assembly and entrapment of Shigella into cages. Moreover, it can yield fundamental insights into septin biology and its links with membrane.

Aim 2: How do septins organise and functionalise the Shigella cell surface?

Septin filaments directly associate with membranes, where they act as diffusion barriers and serve as scaffolds to concentrate essential signaling molecules. We will use reductionist bottom-up cellular microbiology to study septin-mediated organization and function of the Shigella cell surface. In vitro reconstitution of the actin tail is a hallmark of cellular microbiology, and we will investigate the coordination of actin (tail) polymerization and septin (cage) assembly in vitro using bacterial surfaces and purified proteins. Studying how these processes are coordinated with each other, and also with other cellular processes (such as ubiquitination, autophagosome formation), will be necessary for a complete understanding of cell-autonomous immunity. We will use our cell-free platform, biochemistry and high-resolution microscopy techniques (super resolution, cryo-ET) to study coordination of host factors on the bacterial surface.

Perspectives

This project will provide the student with an opportunity to gain first-hand experience with cutting edge research on bacterial pathogens, cell free reconstitution systems, and advanced cryo-EM imaging techniques, significantly advancing our understanding of septin roles in health and disease. Through this project, they will receive extensive training in cell and molecular biology and imaging techniques, as well as invaluable experience working in the ISMB Electron Microscopy facility. Furthermore, both the Mostowy and Moores groups are engaged in several different London, UK, and international collaborations, exposing the PhD candidate to a wide range of interdisciplinary research and exciting opportunities for career advancement.

Subject areas/keywords

Subject Area: cell biology, structural biology, infection biology, microscopy, Shigella, septins, host defence

Keywords: cryo-electron microscopy, cytoskeleton, host-pathogen interactions

Key References

  • Krokowski S, et al. (2018) Septins recognize and entrap dividing bacterial cells for delivery to lysosomes. Cell Host Microbe 24, 866-874. PMID: 30543779
  • Manka SW, Moores CA (2018) Microtubule structure by cryo-EM: snapshots of dynamic instability. Essays in Biochem 62, 737. PMID: 30315096
  • Lobato-Márquez D, et al. (2021) Mechanistic insight into bacterial entrapment by septin cage reconstitution. Nat Commun 12, 4511. PMID: 34301939
  • Atherton J, et al. CA (2022) Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. J Cell Sci 135, jcs259234. PMID: 35383828
  • Liu T, et al. (2025) Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers. Nat Struct Mol Biol 32, 2262-2271. PMID: 40954369

Further details about the project may be obtained from:

Principal Supervisor: Professor Serge Mostowy, serge.mostowy@lshtm.ac.uk

Co-Supervisor: Professor Carolyn Moores, c.moores@bbk.ac.uk

Further information about PhDs at LSHTM is available from:

Applying for a Research degree | How to apply | LSHTM

How to Apply

The application process has two steps. To be considered for the funding, applicants must meet all eligibility criteria and complete both steps outlined below by the scholarship deadline stated for the project they are applying for.

  • Step 1
    Submit an application for research degree study via the LSHTM application portal. Applicants should apply via the Faculty of Infectious & Tropical Diseases (ITD).
    • Students should submit a research proposal based on the advertisement for their project.
    • Incomplete applications will not be considered for this studentship.
  • Step 2Once you have submitted an application to study you should receive an automated email from the Scholarships Team (scholarships@lshtm.ac.uk) providing you with the link to our online scholarships application portal.
    • This will provide you with a temporary password to use the first time you login (via e-vision), which you should then update.
    • Please search for ‘Bloomsbury PhD Studentship’ if you wish to apply for this funding, and then answer the questions online to indicate your interest in one of the two funded PhD projects available.  Once you are happy with your responses you can press submit and should receive a confirmation of receipt email at your contact email address.
    • The scholarships portal will not be able to accept applications after the relevant project deadline (see below).
    • The Scholarships team will be in touch with an outcome in due course.

Applications for this project will only be reviewed and processed after the deadline. All applications that are submitted before the deadline will be considered equally, regardless of submission date.   

Applicants must meet the School’s minimum English language proficiency requirements if shortlisted for this funding by Monday 15 June 2026. Failure to do so may result in any scholarship offer being withdrawn and offered to a reserve candidate instead.

By submitting an application for this funding applicants agree to its Terms & Conditions.

Closing date for applications is:

16:00 (GMT) on 1 March 2026