Reconstructing ancient proteins

Warning signs greet you as you go through the green doors and enter what can only be described as a jungle. The warm air feels weird in your lungs as you enter a room full of machines and laboratory desks. In amongst the proliferation of measuring equipment, bushels of pipettes, chemicals, and computers, stand several large bottles filled with bacteria containing proteins that haven’t seen daylight in millions of years. The only thing missing is a sign saying ‘WELCOME TO JURASSIC PROTEIN PARK’.

Creator of these prehistoric proteins and lord and master of this laboratory is Gautier Bailleul, adventurer, avid festival-goer, and gamer, but above all: researcher. He’s a young French scientist with a passion for DNA and green chemistry, ‘as well as prehistory’.  

Toxins

The past few years he’s been focused on figuring out how flavin-containing monooxygenases (FMOs) work. These are special proteins that break down toxins in organs such as the liver, lungs and kidneys. And they are sorely needed. 

These proteins are like machines

Almost all substances that enter your body travel through your organs and past your body’s checkpoints: the FMOs. But these FMOs are not particularly friendly. They’re aggressive proteins that break down foreign substances in an effort to cleanse the body. ‘They’re like machines’, says Bailleul.  

This is great if you’ve been drinking or taking drugs. You want the FMOs to clean up. Unfortunately, the kill-and-destroy proteins don’t always distinguish between wanted and unwanted foreign substances. That means they sometimes take care of medication before it’s had a chance to do its job. That’s not good. 

Clump together

Bailleul wants to try to prevent this by figuring out how these molecular exterminators work. ‘Until now, however, FMOs couldn’t be studied’, he says. 

One problem that’s interfered with research is that FMO structures are basically indecipherable. Normally, researchers study proteins by making them clump together to form crystals. They then fire x-rays at these crystals and use a computer to determine what the proteins look like.  

FMOs, however, apparently don’t want to clump together. While most proteins are natural swimmers that feel at home in a pool of solvent and come together with no issue, human FMOs just keep floating around. 

FMOs are anchored in the endoplasmic reticulum, an organ-like part of a cell. This type of protein, membrane proteins, will sometimes clump together if researchers add a substance to calm them down. But even this has failed to work on FMOs so far.  

Brilliant thought

For years, scientists were at a loss, until the team of researchers from Italy, Argentina and the Netherlands that Bailleul is a part of had a brilliant thought. ‘We realised that older versions of FMOs might be more stable’, he says. ‘That would mean it would be easier to crystallise them.’ 

The reason for this is that for a large part of the past, the average temperature on earth was much higher. In what geologists call the Devonian period, approximately 410 million years ago, when the first fish started to crawl onto land, it was about five degrees hotter than it is now. The FMOs inside animals back then were probably more heat-resistant and more durable than modern ones, the team figured.

We realised older versions might be more stable

Argentinian researcher Laura Mascotti concentrated on studying the similarities in the genetic code of FMOs in large groups of animals. This enabled her to figure out which codes were present in the common ancestor of these animals. 

Implant

When she found a location where the genetic codes differed, she used probability calculations, which resulted in several probable sequences. In the end, the team was able to not just figure out the most likely genes of our ancestor, but also to reconstruct their entire genealogical tree. They keyed the code into the computer, which could then fabricate the DNA for them. 

Next, they focused on implanting the DNA in bacteria. ‘We’re using the bacteria like little factories that make the protein machines’, says Bailleul. ‘They’ll use the DNA like an instruction manual to create these ancient FMOs. Once we’d created and cleaned the FMOs, we found out that these did clump together and crystallise.’  

And now he’s got jars full of bacteria containing prehistoric proteins. Like it’s absolutely no big deal that there’s life that’s millions of years old just standing around on a Groningen researcher’s lab table.  

Genetic code

The research is promising. Bailleul has already proven that his Devonian proteins respond to various substances the same way their modern counterparts do. Their genetic code and predicted appearance are more than ninety percent identical to the extant human ones. That means they can be used to learn more about our own FMOs. 

Bacteria will use the DNA like an instruction manual

This could form the basis for new insights into medication and diseases. Pharmaceutical companies could design drugs to be resistant to destruction by FMOs, or to be activated by them. 

Always a researcher, Bailleul has already gone back to his laboratory jungle full of equipment, pipettes, chemicals, and computers.  

What’s next for the researcher? Bailleul is passionate and always trying to learn more. He smiles: ‘I’m already researching an even older protein.’ Is it a Velociraptor FMO, or a T.rex or Brontosaurus protein? If Bailleul can help it, something a little more applicable to modern life. ‘An opportunity to make the world a little bit better.’

Dutch