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Discover: How the not-so-lowly fruit fly can be a powerful weapon in the fight against deadly viruses

Dr. Thomas Merritt, Canada research chair in genomics and bioinformatics, explains how the fruit fly genetic code could hold the secret to building better vaccines

The current pandemic, and maybe even more importantly the next one, will be beaten in the laboratory, by strong fundamental science and stronger public policy and medical response based on this science.

To be perfectly clear, the most important thing right now is for everyone who can to stay home and, when you do have to go out, to follow up-to-date health and safety guidelines. Peoples’ lives are literally at stake. Only go out if you have to – but what if one of those times you have to go out is to the research laboratory?

As we face the COVID-19 pandemic, the global research community is galvanized to do whatever possible to save lives, to fight this virus and the suffering it brings. Sometimes, this fight means working to create a new vaccine, developing ways to reuse personal protective equipment (PPE), or devising better treatments for people who have been infected. Sometimes this fight means maintaining the basic research structure that we will need when we return to the lab after this pandemic to better fight, or avoid, the next one.

Around the globe, scientists are working to ensure that irreplaceable resources are still available after the pandemic.

In my research group, we are maintaining lines of fruit flies, essentially fly families, that we have spent decades creating. We have flies in my lab that literally do not exist anywhere else in the world. If these fly lines die out, some could not be replaced without years of work, while others simply could not be replaced. Why does that matter? They’re just flies, after all. 

It matters because these flies are helping us understand the very foundation of biology and could help us be better prepared for, and better fight, the next pandemic. 

One of the major issues in fighting the COVID-19 pandemic is that we simply don’t understand why SARS-CoV-2, the corona virus that causes the disease, is so deadly. We do know that its deadly nature is a function of small genetic changes, called mutations, which distinguish it from other viruses. But which mutations? SARS-CoV-2 is a close relative of SARS-CoV, the virus that caused the 2005 SARS outbreak. Even between these closely related viruses, however, there are around 6,000 genetic differences (a staggering 20 per cent of the genome). Between these two SARS viruses and other far less deadly corona viruses there are even more.

Which of these changes, or combination of these changes, makes the virus so deadly? Answering this question may also help us create a vaccine. SARS-CoV-2 has 14 genes in its genome, coding for 27 proteins (we often think of one gene giving one protein, but in some cases, especially in viruses, a single gene codes for more than one protein). Proteins are simply folded chains of amino acids and those 6,000 genetic differences result in 380 amino acid changes. It’s the changes in amino acids, and what those changes do to protein function, that give each virus its unique characteristics.

SARS-CoV-2 is, like other coronaviruses, a sphere with spikes radiating out of it. In electron microscope images of the virus, these spikes form a crown – the corona – that gives these viruses their name. The sphere and the spikes are made of proteins. In infection, the spikes attach to human cells and control the virus genes entering the cells. Different coronavirus spikes bind to different receptors on the cell surface. SARS-CoV-2 and SARS-CoV, for example, bind to different receptors than the MERS virus. This distinct binding is part of the difference in pathology that exists between different viruses. 

Variation in these spikes is also a challenge, but also a possible solution, to creating a SARS-CoV-2 vaccine. Vaccines allow your immune system to attack and destroy a virus or bacteria before it can infect your body. Our immune system is incredibly complex – and specific – an immune response is to a single threat. Vaccines work by training your immune system to recognize a specific pathogen, to recognize a part, generally on the surface, of that pathogen – an antigen. A challenge for creating a SARS-CoV-2 vaccine, or any vaccine, is that because virus surfaces vary so much, antigens change and a vaccine for one virus doesn’t recognize another. But, if we can identify something that we know is on the surface of a virus, we can possibly create a vaccine that specifically recognizes this feature. With SARS-CoV-2, its unique spike protein is just such a possible candidate, and work characterizing this protein is underway.

Why do different spikes have different biology? We know that differences in spike binding and shape are a function of those amino acid changes, but we don’t know which ones. In part, our lack of understanding lies in our ignorance of how simple amino acid changes affect protein shape and function – and this is where those fly lines in my lab come in.

One of the things we study in my research group is how amino acid substitutions change protein function and biology. A lot of this work focuses on a metabolic protein called malic enzyme, a critical protein that is found in essentially all living organisms, including Drosophila melanogaster, the fruit fly we study that converts malate to pyruvate, two critical metabolites. Like every protein, Drosophila Malic enzyme is a string of amino acids folded into a 3D form. You can picture this like a ball made up of rubber bands – if the rubber bands were all one long string, and the ball wasn’t necessarily round (and also not necessarily funny – thanks Raising Arizona). 

This ‘not round’ aspect is important; the shape that a protein takes depends on the amino acids in that chain. The links in this chain, the amino acids, are different because different amino acids take up more or less space or fit next to each other more or less tightly. There are only 20 different naturally occurring amino acids; proteins are simply chains of hundreds of these links strung in a specific sequence. The shape of the protein, then, depends on the specific sequence of amino acids and shape determines function, determines how proteins work. This hierarchy – amino acids determine shape, shape determines function – holds whether we are looking at a metabolic enzyme or a viral spike protein. Determining how amino acid changes influence one gets us closer to understanding those changes in the other.

Drosophila malic enzyme is made up of a little fewer than 600 amino acids, which is a little larger, but not much, than a typical animal protein. Strikingly, only two of these amino acids have ever differed in the thousands of flies that we have looked at from around the globe. Position 113 (the first site) is either a glycine or an alanine, and position 351 (the second site) is either a leucine or a methione. The other amino acids never vary. This small number of variable sites, and limited variation at those sites, is a stark contrast to what we see in viruses, but makes the system experimentally much more manageable. We can look at how this small amount of variation affects protein function and then extrapolate out to more complicated, and variable, systems like a viral protein coat or spike. 

So, what do changes in these two amino acids do to protein function? When we ask this question, we get different answers for each site, and different in interesting and telling ways. 

At the first site, the two amino acids that we find are fairly similar to each other, but substituting between the two actually changes the  enzyme by almost 30 per cent and in biology 30 per cent is a big deal. A closer look at this site may explain the difference in activity. It is at the edge of the active site of the protein, the pocket in which the enzyme breaks down malate, and part of a helix, a twirl of amino acids forming a spiral staircase-like structure. Alanines form spirals, but glycines do not. 

That 30-per-cent difference in activity is likely a function of a slightly short spiral at the edge of the protein active site, a small difference leading to a subtle change in shape but very different biochemistry. Understanding this connection tells us quite a bit about what to expect from simple amino acid changes.

The second site tells us a little more. At this site, the two amino acids are also fairly similar to each other, but again we see a difference in biochemistry: there is about a 40-per-cent difference in the strength with which the enzyme binds to malate. The second site is further away from the active site and, in fact, isn’t particularly near to any known structure. We do know, however, that this is in a region of the protein in which the amino acids lie down in a sheet, interacting to form a pleated surface similar to a pleated skirt, but a pleated skirt that can twist and roll. The subtle difference between a leucine and a methionine likely changes the shape of this sheet, resulting in the difference in binding biochemistry. 

Understanding both of these small differences helps us understand, in general, how proteins work, and how amino acid variation leads to changes in protein function. This understanding allows us to predict how other changes may alter the function of the protein we find them in.

How does this get us closer to beating the COVID-19 pandemic? The short answer is that it doesn’t, but it may get us closer to beating the next one. As we get better and better at understanding protein variation, through good fundamental science, we will get better at predicting which viruses have the potential to be deadly and better at designing new vaccines

Our fly work is a part of this progress, so, about once every five days, I go to my lab and check on my fly stocks.

For now, stay home, wash your hands, support your local food banks and charities, and buy local whenever you can. When this pandemic is over, we can all get back to some version of what we were doing before March 2020. For my research group, this will be trying to understand how simple and small genetic changes can lead to complicated and substantial changes in how proteins work.

Dr. Thomas Merritt is the Canada Research Chair in Genomics and Bioinformatics at Laurentian University.