Combat7

Uncovering bacteria’s secret weapons

Project Description

For years, scientists thought specialised secretion systems were exclusive to Gram-negative bacteria. But Gram-positive bacteria, including harmful pathogens like Mycobacterium tuberculosis, have a powerful exception: the type VII secretion system (T7SS). This complex machinery does not just export proteins involved in infection; it also plays a surprising role in microbial warfare between bacteria. The ERC-funded CombaT7 project brings together top researchers to decode the mysteries of T7SS in important mycobacterial pathogens like M. tuberculosis and M. abscessus. Using cutting-edge tools like cryo-EM and lung-on-a-chip models, the team will map the system’s structure, identify new protein targets, and uncover how it influences both disease and bacterial competition, laying the groundwork for new ways to fight infection.

Objectives

Bacteria interact with their environment via specialised secretion systems that deliver proteins outside of the cell. Due to a bias in research efforts, for many years such systems were assumed to be unique to Gram-negative bacteria. A major exception is the type VII secretion system (T7SS), which is widespread in Gram-positive bacteria and actinobacteria, including the important human pathogen Mycobacterium tuberculosis. The T7SS is a complex secretion apparatus that exports folded proteins and even protein complexes. While secreted substrates are well-known for being crucial players in host-pathogen interactions, our recent data indicate that specific substrates of the relevant opportunistic pathogen Mycobacterium abscessus and the fish pathogen Mycobacterium marinum are also involved in interbacterial antagonism. This makes T7SSs important factors to understand microbial interactions, also for the understudied part of the microbial world.

While the mechanism of secretion via T7SSs remains little understood, our preliminary data show that not only their roles but also their substrates are more diverse than thus far thought. Here, we unite leading experts in microbiology, structural biology, cell biology, and biophysics to spearhead research on mycobacterial T7SSs and their roles in both interbacterial and host-pathogen interactions. In this unique consortium, we will (i) define the full trans-envelope T7SS by atomic force microscopy and cryo-electron microscopy, (ii) study the mechanism of transport by creating translocation intermediates, (iii) expand the set of T7SS substrates by extensive proteomics and bioinformatics analysis, and (iv) visualise the role of T7SS in bacterial warfare and host-pathogen interactions using microfluidics, innovative lung-on-a-chip infection models and time-lapse microscopy. This will deliver a deep mechanistic understanding of the diverse roles of mycobacterial T7SSs and provide clues to exploit these systems to combat infections.

Teams Involved

Prof. John McKinney

EPFL

Prof. Georg Fantner

EPFL

Prof. Tracy Palmer

University of Newcastle

Prof. Thomas Marlovits

Universitätsklinikum Hamburg-Eppendorf

Prof. Wilbert Bitter

Vrije Universiteit Amsterdam

Prof. Edith Houben

Vrije Universiteit Amsterdam

Members

Théo ASPERT, PhD

Research interests: Human tissue models, Microfabrication, Microfluidics, Timelapse microscopy, Host-pathogen interactions.

To fully understand the T7SS's role in both bacterial warfare and host-pathogen interactions, we require dynamic and controlled models. Microfluidic systems are essential as they allow for precise visualization of bacteria-bacteria antagonism and, when integrated with platforms like the lung-on-a-chip, enable the study of complex host-bacteria interactions in an in vivo-like context. My efforts are concentrated on developing and utilizing these microfluidic models to observe and quantify the T7SS mechanisms in action.

Pit ENGLING, PhD

Research interests: Interbacterial antagonism, Bacterial secretion systems, Mycobacterial pathogenesis, Timelapse microscopy.

My work focuses on the mechanistic characterization of ESX-4–mediated interbacterial antagonism in mycobacteria and on identifying predator-prey interaction dynamics at single-cell level. Central to this effort is timelapse imaging at single-cell resolution, supported by machine-learning–based image analysis. This enables us to resolve the mode of action, sequence of events, and dynamic outcomes of ESX-4-driven cell–cell antagonism. To achieve this, we incorporate custom-made microfluidic and lung-on-chip platforms providing controlled environments and physiologically relevant contexts for these single-cell mechanistic studies.

Luca Schlotheuber, PhD

As a crucial resident immune cell in the Alveolar of the lung, immune cells, specifically Macrophages represent the first line of defense against Tuberculosis. During infection, however, the lung pathogen TB can infect, high-jack and kill Macrophages in a complex interplay between secreted proteins of the T7 Secretion system, host receptors, and intracellular factors. As part of the Comba T7 I am investigating this interplay and the mechanisms that drive the killing of Macrophages and the dissemination of Mycobacteria in the lung.

Rory Hennell James, PhD

Research interests:CryoEM, CryoET, Secretion systems, Cellular structure, Microbiology.