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Daan van Tol - Order in the chaos: an almanac for enzymes

During the first lockdown all the lab work for biology students suddenly came to a standstill. Bachelor’s student Daan van Tol was forced to change his research plans and decided to map out the evolutionary history of an important type of enzyme. ‘By gathering together all this information, I hope I can help other researchers bring more focus to their research.’ Daan is one of the four nominees for the Young Star Award 2020.

Living with oxygen

It is one of the most important developments in the creation of life on earth: the ability to use oxygen. It may sound strange, but, without the right tools, oxygen can be very harmful for an organism. Daan: ‘That’s because oxygen is highly reactive: it reacts with almost every existing element. This reactivity can seriously damage an organism.’  But ultimately the first life forms learned to handle oxygen and even to use it to their advantage. They did this by ‘inventing’ Cytochrome p450: ‘An enzyme that would change life on earth for ever,’ Dan says.

Cytochrome p450 enzymes, or CYPs,  as they are more commonly known, ensure that oxygen is no longer harmful, but rather beneficial to organisms. ‘They allow reactions to take place more rapidly, and make sure that oxygen can only bring about minor changes,’ Daan explains. ‘CYPs split an oxygen molecule – which is made up of two oxygen atoms – in two. The enzyme then places one oxygen atom in another molecule, and uses the other oxygen atom to produce water.’  Because this reaction is so simple, you find it in almost all organisms. Plants use CYPs for example to make substances that repel herbivores. ‘Over millions of years, an enormous family of enzymes has developed.’

Overview of evolution

And it’s that last point that makes research on CYPs difficult, says Daan. ‘There is a mass of information around about CYPs, but you won’t find a clear overview of this information anywhere. I wanted to change that.’ Daan collected all the literature on CYPs in one big document, thus mapping the evolutionary history of CYPs and their many functions. ‘I hope this will help other researchers to make their research more specific and more manageable. All the information they need is now in one place. Research can now be more focused and it is more feasible to use CYPs on a large scale, for example in the bio industry.’

'I want to use enormous potential of nature to develop something that can really benefit people around me.’

Changes plans

Making an almanac was not Daan’s original plan, but the first lockdown in March meant that his planned lab work wasn’t possible. He didn’t want to postpone the research, so he changed his plan.  Daan: ‘Rather than looking at the role of ten specific CYP genes that can be found in Ragwort, I focused on the role of all CYPs that are found in plants.’ Daan hopes that other researchers will add their own findings to the ‘CYP almanac’ and he has future plans to completely digitise his almanac in a CYP search programme.

Solutions from nature

Daan is now studying for a Master’s in Biology in Leiden. ‘I decided to study Biology to learn about the enormous possibilities of nature,’ he explains. ‘Evolution is unbelievably innovative and it’s constantly presenting researchers with surprises. I think it’s fantastic to use this enormous potential to develop something that can really benefit people around me.’

This is also the reason that Daan wants to carry on with synthetic biology. ‘In this field, you study products from nature and think up new applications for them.’ At the moment he is focusing on fungi, which are able to produce all kinds of useful enzymes. ‘What I most want to do is to make industry more sustainable. Applying biological processes means we can make production more efficient and more environmentally friendly. Nature offers enormous possibilities for improving our society and that’s something I want to contribute to.’

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