Unzipping the Secrets of DNA Repair

Our bodies are experts at looking after our DNA and are continuously monitoring for any damage that needs to be repaired to keep us healthy. Parts of DNA that are very repetitive, like the sequence causing Huntington’s disease (HD), are very tricky to look after and our body can try and fix them but make it worse! This can make the repeat sequences longer and even more toxic to our cells.  In this study led by the CHDI foundation, researchers look in detail at the proteins responsible for making those sequences longer in HD, so we can get a better idea of how they work, and how we might be able to stop them. Let’s, take a closer look.

The Faulty Zipper: How DNA repair fuels HD

DNA is made up of four letters:  A,T,G and C. Sequences of these letters make up the instructions to tell our body how to make all the different proteins we need to function and be healthy. In HD there is a longer stretch of C-A-G letter repeats in the sequence for the  Huntingtin gene. Throughout life, the size of these repeats can get longer in some of the brain cells most affected by HD. This process is called somatic expansion.

Imagine the DNA in your cells is like the zipper on a jacket, and the zipper teeth are the letters of DNA. Normally the zipper moves up and down smoothly but there can be weak patches where it is easy for a bump or loop to form. 

You have a tailor who fixes zipper mistakes, and most of the time they are extremely helpful. But at the weak spot in the zipper, the tailor sometimes makes the problem worse, and instead of flattening the bump, they add in extra teeth to the zipper. 

Now every time the zipper is opened and closed the weak spot has a chance to get bigger. In HD, the weak spot is like the C-A-G repeats in the Huntingtin DNA, and the tailor is the DNA repair machinery in the cell. This is an important guardian of the DNA in our cells, particularly for preventing changes to our DNA sequence, which could cause cancer. Despite this, long C-A-G repeats, like those involved in HD, can confuse the repair response sometimes, causing the repeats to get even longer. This process is called somatic expansion and some scientists think this can cause some brain cells to get sick. 

An important part of the DNA repair tailor involved in expansion are two proteins called MSH2 and MSH3. They work together as a team and are collectively known as MutSβ (pronounced mute-ess-behta). Previous analysis of the DNA from thousands of individuals with HD has shown us that MutSβ can impact the age that symptoms begin. Because of this MutSβ has become an exciting area of HD research, which has shown that stopping MutSβ from acting on the damaged DNA zipper might help to slow somatic expansion and progression of the disease. 

Research studies are increasingly showing us that inhibiting MSH3, or reducing the amount of MSH3 in the brain, can prevent C-A-G repeats from getting longer and may even reduce C-A-G length, making it an exciting target for new potential HD therapies. 

Taking a sneak peek at how the mismatch repair proteins work

To better understand how the MutSβ complex can make the DNA zipper worse, the authors used a technique called cryo-electron microscopy (cryo-EM). This is a way of looking at the shape and structure of protein molecules – like taking a snapshot of what they look like at at a specific moment in time. 

Imagine you want to see what a snowflake really looks like. If you let it sit on your glove for too long after it has landed, it will melt or change shape before you get to see all its intricate details. 

Cryo-EM works like a camera for tiny biological “snowflakes”. Samples are frozen quickly so that the protein is trapped in its natural shape. Many snapshots are taken, which can capture different shapes and positions the protein may form. This helps us to piece together how the proteins change conformations to carry out their jobs. 

In this study, the scientists used cryo-EM to take a picture of MutSβ both before and after it is bound to DNA.  They were able to produce 9 distinct images of MutSβ, including the following conditions:

• When it’s not stuck to DNA
• When bound to normal error-free DNA
• When bound to DNA with mismatched DNA

These images show how the MutSβ complex moves and changes shape when it spots errors in DNA. Normally, this helps the cell repair the DNA, but in the case of HD, it can make matters worse. 

The researchers found that the shape and position of MutSβ depend on whether it is stuck to DNA as well as small energy molecules like ATP. ATP molecules are like the cell’s energy packets, a bit like fuel for an engine, which can keep everything running. Both parts of MutSβ, MSH2 and MSH3, can grab ATP and use it to do repairs on DNA.  

The snapshots of MutSβ from this study show that it starts out in an open clamp shape. This open clamp can grab onto DNA and scan along it, looking for errors in the DNA zipper. When a mistake is found, the clamp snaps shut, and can slide along DNA, powered by ATP. This kicks off the next steps of the repair process. Once its job is done, MutSβ uses more ATP to get itself off the DNA. 

Why do we care about the MutSβ structure?

By figuring out the shape of MutSβ in as fine detail as possible, especially when carrying out its job repairing DNA, we can find pockets on the protein surface which a future drug could stick onto to stop this process working. Like looking for the right key which perfectly fits a specific keyhole. If we know what the protein looks like, we can perfectly design a drug that should bind somewhere tightly on the protein and stop it from working. Ultimately being able to stop or even reverse C-A-G repeat expansion could be a great therapeutic route for HD, as well as other diseases which are also caused by repeat expansion, including several spinocerebellar ataxias and spinal and bulbar muscular atrophy. 

Summary:

• MutSβ (MSH2 + MSH3) is a DNA repair machine that normally helps prevent cancer-causing mutations.
• In HD, MutSβ can sometimes accidentally make CAG repeats in the HTT gene longer which is thought to lead to neuronal death and faster disease progression. 
• New data about the 3D structure of the MutSβ proteins and how this molecular machine works will aid the design of drugs which can inhibit its activity, preventing the elongation of CAG repeats.

Learn More

Original research article, “Elucidation of multiple high-resolution states of human MutSβ by cryo-EM reveals interplay between ATP/ADP binding and heteroduplex DNA recognition” (open access).