Taking a Closer Look at Microbial-Environmental Interactions With Cryo-EM

No microbe is an island. Understanding how they interact with each other and their surrounding environment is important to harness their beneficial properties and combat harmful behavior.

Observing microbes at the molecular and even individual protein level can reveal the details of how microbes are able to avoid danger, seek out their preferred environments and adapt to make the most of their surroundings. In order to do this, tools, such as electron cryotomography (ECT) and cryogenic electron microscopy (cryo-EM) are vital.

We spoke to Ariane Briegel, Professor of Ultrastructural Biology at the Institute of Biology at Leiden University and the Centre of Microbial Cell Biology about her group’s work in the field of microbial structural elucidation and the role that cryo-EM plays.

Karen Steward (KS): How important is cryo-EM to your work, what difference does it make to the capabilities of your team?

Ariane Briegel (AB): Our research is focused on understanding the structure and function of macromolecular complexes involved in bacterial behavior. We are for example interested in the molecular structure of chemoreceptor arrays that guide motile bacteria to preferential environments, and more generally how bacteria structurally adjust in changing environments. ECT is the central tool we use to study the macromolecular complexes three-dimensionally at the molecular level, both inside intact cells and in vitro. We complement ECT with other methods such as for example genetics, bioinformatics, and molecular dynamics.

KS: Why is it important that we understand how microbes interact with their environment? What are the possible implications or outcomes of improving our knowledge in this area?

AB: Bacteria structurally and metabolically adjust to their surrounding environment. Consequently, cells of the same species may have vastly different morphological and behavioral characteristics depending on the environment they are in. The susceptibility to stressors such as antibiotics and phage infection also may vary dramatically depending on cell morphology. Due to this innate adaptability, it is necessary to form a detailed understanding of how the cells structurally remodel to counter and thrive despite often dramatically changing conditions. This structural insight may be a crucial prerequisite for designing novel drugs aiming to target the specific molecular machines during infection.

KS: Could you tell us about one of the most interesting discoveries or observations that you and your team have made that has been facilitated by cryo-EM?

AB: I was among the first to discover that chemoreceptors are arranged in honeycomb-like arrays. We have since contributed significantly to understand how the arrays form and how the enzyme that sends signals to the motility apparatus is controlled by the chemoreceptors. We are also looking at the structure of additional chemotaxis systems in the cells, some of which are not anchored in the membrane and form double-layered arrays inside the cells.

We have also uncovered distinct differences in chemoreceptor arrays between the main model organism (Escherichia coli) and the pathogen Vibrio cholerae, highlighting the need to study non-model systems.

We recently analyzed the dramatic structural and metabolic changes Vibrio cholerae cells undergo when they are exposed to prolonged unfavorable environmental conditions (low nutrients and low temperatures).

KS: Could the information you gather contribute to improved targeted therapies, or environmental management and screening, for example, in the case of pathogenic bacteria?

AB: Our work mainly involves addressing fundamental questions on how bacteria structurally adapt and interact with their environment using molecular machines, and understand their structure and function. However, we do hope that our research on the structural architecture of pathogens will indeed help identify for example new drug targets, and also uncover the cell susceptibility to treatments between different morphological states in order to develop more specific treatments for infections.

KS: Where do you feel there are currently unmet needs with cryo-EM capabilities where future developments could be usefully focused?

AB: I think that the new frontier of cryo-EM is certainly the aim to investigate more complex biological material. In essence, harnessing the power of cryo-EM to look into how cells interact with each other for example in tissues and whole organisms. Therefore, I think there is urgent development needed to make such samples accessible for this methodology. The FIB-SEM instruments are a big step forward, but to make it really useful for a broader science community, the workflows and tools to prepare such samples are still extremely difficult at the moment. For example, the necessary high-pressure freezers are quite ancient technology and rather inflexible in the samples that can be processed. So, I would say the most urgent need is instrumentation that will facilitate the preprocessing of complex biological specimens to prepare them for cryo-EM.

Professor Ariane Briegel was speaking to Dr Karen Steward, Science Writer for Technology Networks.