How bacteria survive with almost no oxygen
Researchers in Leiden have, for the first time, observed how a specialised enzyme helps bacteria stay alinve when oxygen levels are low, and how that process can be blocked. The discovery opens up new possibilities for targeted antibiotics.
It really exists: a secret trick that allows bacteria to survive with very little oxygen. This also applies to bacteria that can make us sick. ‘Like us, these bacteria need oxygen to survive,’ says PhD candidate Tijn van der Velden. ‘But unlike humans, they have a special enzyme called cytochrome bd that allows them to keep producing energy even when oxygen levels are very low.’ Because the enzyme is so important for bacterial survival, it is an promising target for new antibiotics, including potential treatments for tuberculosis.
More time to observe, a clearer picture
For years, scientists have been trying to understand exactly how cytochrome bd works and how existing inhibitors block the enzyme. But studying it has been difficult because the relevant part of the enzyme is highly flexible and constantly moving, making it hard to capture clearly. ‘We needed to find a way to stabilise it,’ Van der Velden explains.
The breakthrough came thanks to the new Glacios microscope, funded through the Oncode Accelerator project (see box below). Using the microscope, the researchers were able to study the enzyme at atomic level. They carried out the work in E. coli, a bacterium commonly used in laboratory research.
Previously, the team used the advanced Krios microscope at the national imaging centre NeCEN. ‘But that microscope is often booked solid, so you only get one or two chances to collect data, and everything has to work immediately,’ says supervisor Lars Jeuken. ‘Now we could repeat experiments, adjust our methods, and improve the process step by step.’
Gentler method reveals a more stable enzyme
In the end, the key turned out to be changing the way the enzyme was removed from the bacterium’s fatty cell membrane – a necessary step before it can be studied. Chemists normally use a fairly strong detergent for this, but the researchers chose a milder alternative.
That made a major difference. ‘With this detergent, the enzymes came out as dimers: pairs of identical proteins that remain attached to each other,’ says Van der Velden. With stronger detergents, the enzyme probably fell apart, leaving only unstable single proteins behind.
The dimers turned out to be more stable and less mobile, allowing the researchers to clearly examine the flexible part of the enzyme for the first time. ‘That finally allowed us to see how this enzyme works,’ says Van der Velden. ‘No one had managed that before,’ Jeuken adds.
An inhibitor that changes the shape of the enzyme
The researchers also discovered how an inhibitor shuts the enzyme down. For this, they used a known inhibitor of E. coli.
‘It’s an unusual way of blocking an enzyme, and we do not see it very often.’
Inhibitors often resemble the natural substance that normally binds to an enzyme and is then processed by it. They block the binding site, preventing the enzyme from doing its job. But in this case, something unusual happened.
‘The inhibitor does more than just block the binding site – it actually changes the shape of the enzyme,’ says Van der Velden. The inhibitor forces the enzyme to fold differently, squeezing shut the area where the reaction normally takes place. ‘It’s an unusual way of blocking an enzyme, and we do not see it very often.’
A step towards targeted antibiotics
The inhibitor used in the study is not itself suitable as a medicine. ‘The compound is also harmful to human cells,’ says Jeuken. ‘It kills bacteria, but unfortunately it is also lethal to humans.’
Even so, the inhibitor is highly useful for research. ‘For the first time, we have been able to see at atomic scale what happens inside this type of protein, how it provides bacteria with the energy they need to survive, and how the process can be blocked,’ says Van der Velden. ‘Other researchers can now use this refolding mechanism to develop new inhibitors that are harmless to humans but toxic to bacteria. We are gradually learning more about how to selectively switch off these crucial enzymes.’
Scientific paper
Tijn T. van der Velden et al. Visualizing the mechanism of quinol oxidation and inhibition of a bd-type oxidase using cryo-EM. Science Advances 12, eaec9946 (2026). DOI: 10.1126/sciadv.aec9946
Oncode Accelerator microscope at NeCEN
The Glacios microscope was installed in 2024 at the Netherlands Centre for Electron Nanoscopy (NeCEN) in Leiden. The investment came from the Oncode Accelerator programme. This public-private partnership is partially funded by the Dutch National Growth Fund, aiming to innovate and accelerate the development of new cancer therapies by placing cancer patients at the core of preclinical therapy development. It is a collaboration between six coordinating partners: Leiden University, Leiden University Medical Center, the Netherlands Cancer Institute, Princess Máxima Center, UMC Utrecht and the Oncode Accelerator Foundation.
For who?
The Glacios microscope can be used within Demonstrator Projects, collaborative oncology preclinical development projects that focus on advancing a small molecule, biologic, cell and gene therapy, or therapeutic vaccine and run on Oncode Accelerator’s unique infrastructure. Drug developers worldwide can apply for Demonstrator Projects to gain access to translational expertise, state-of-the-art facilities and technologies, up to €1.5 million in co-funding, and hands-on project coordination.
To maximise the scientific and societal impact of this investment, the microscope can also be used for other drug research projects. Researchers are, for example, using it to work on inhibitors against the tuberculosis bacterium.
About the Glacios microscope
To make biological structures visible, samples are rapidly frozen in liquid ethane at around -180 °C. This prevents ice crystals from forming and instead creates ‘vitreous’ ice, in which molecules are effectively frozen in place. The microscope then sends electrons through the frozen sample at speeds of up to around 70% of the speed of light. This makes it possible to observe details as small as around 2.2 ångströms (0.22 nanometres – about a billionth of a metre).
More technical details can be found on the NeCEN website.