Studying mitochondrial DNA sheds light on the importance of vitamins

In a very real sense, you are what you eat — at least, your cells are. The nutrients inside your food create some of the most important molecules in your cells. Scientists are looking at how not having enough of some vitamins can affect one of these essential molecules, DNA. 

“You need to create more DNA if you're going to make new cells, and you need to create more RNA for those cells to do their job,” said Lawrence Brody, Ph.D., a senior scientist at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. “That's the raw material for the work of cells.” 

Vitamins like vitamin B12 and folate are linked to creating the building blocks of DNA and RNA, and not having enough of these vitamins can interfere with this process.

Most people know about vitamin B12 and folate for the health problems caused by vitamin deficiencies. Low levels of folate in pregnancy can cause spina bifida and other issues in closing the neural tube, the structure that eventually forms into the infant’s spinal cord and brain. 

“That’s why in 1998, the U.S. began fortifying milled grains with folic acid, a stable form of folate,” said Dr. Brody. “It's a big public health effort, and research shows that this program has prevented almost 40% of neural tube defects.”

Could these same vitamins contribute to changes in DNA? Dr. Brody and his collaborator Anne Parle-McDermott, Ph.D., a professor of genetics at Dublin City University, decided to investigate. 

You need to create more DNA if you're going to make new cells, and you need to create more RNA for those cells to do their job. That's the raw material for the work of cells.

DNA is made up of nucleotides, chemical building blocks often referred to as “letters” that spell out the DNA sequence. There are four types of nucleotides, dubbed A, T, C and G. Strung together in different combinations, the order of the letters along the DNA molecule is important for orchestrating how cells function.

To create new DNA molecules, cells are grabbing from a pool of nucleotides made through a metabolic process involving B12 and folate. Not having enough of these vitamins can limit the pool of available nucleotides and may contribute to changes to the DNA sequence, also known as mutations.

Imagine fishing tiles out of the bag in a Scrabble game. At the start of the game, more tiles are available for you to choose from, so it is easier to spell words. However, as the game goes on, the remaining tiles might not be the ones you’re hoping for; similarly, with deficiencies in vitamin B12 and folate, there are not as many nucleotides for cells to grab. The cell then struggles to spell out the DNA sequence correctly because the nucleotides aren’t available in the right ratios, just as you would be hard pressed to spell out a word if all that’s left is a Q and three Es.

These impacts have been studied in the human genome. However, Drs. Brody and Parle-McDermott aimed to look at how these deficiencies may affect the cell’s second, much smaller genome, which exists in the mitochondria. This work was led by NHGRI’s David Bernard and Darren Walsh, a graduate student at Dublin City University, and the group recently published their findings in PNAS Nexus.

Mitochondria are a type of cellular structure called an organelle and are popularly known as “the powerhouses of the cell” because they are responsible for generating the majority of the body’s energy. Mitochondria are also the only organelles that have their own genomes. 

Compared to the human genome, which resides in the cell’s nucleus, the mitochondrial genome is tiny, just 17,000 letters of DNA. This is about 353,000 times smaller than the human genome (that’s like comparing the thickness of a couple of pieces of paper to the length of a football field). While it’s always challenging to find mutations, tinier genomes are easier to scan for differences compared to the larger human genome.

“And I'm a stickler about when we use the term mutation,” Dr. Brody added. “A mutation is a new change in the DNA. What we’re looking for is something that didn't exist when the organism was born, but then changed during the organism’s life.”

The researchers first searched for mutations in mice that were bred to be genetically identical. That way, when the researchers sequenced the rodents’ mitochondrial DNA, they would know they were looking at mutations and not variations in the genome that were already present.

“You could think of all the mice we studied as being large groups of identical twins,” Dr. Brody said. “The traits and characteristics we were looking at in the mice reflect a combination of genes and environment, so in these experiments, we were controlling the genes by using identical mice and controlling the environment in the form of diet. This helps us understand how these two things interact.”

In some of the mice, the researchers manipulated one gene to make it harder to absorb vitamin B12, mimicking a vitamin deficiency. All the mice, however, were on strictly controlled diets to regulate how much vitamin B12 and folate they received.

Because each cell has many copies of the mitochondrial genome, the team carried out a very thorough DNA sequencing technique called “deep sequencing.” This way, the researchers could examine 50,000 to 100,000 mitochondrial genomes in each sample. 

The researchers found that vitamin B12 deficiency increased the number of mutations in the mitochondrial genomes of the mice. This was especially true for older mice. When the researchers manipulated the amount of folate in the mice’s diet, they found very slightly increased mitochondrial genome mutations in the mice with the highest folate diet.

“We’ve often thought of nutrient status as important when you’re either pregnant or young and developing, but here we see it can be important throughout life,” Dr. Parle-McDermott said.

To see if similar effects could be found in humans, the researchers then examined data from the Framingham Heart Study, a long-term research effort conducted in the U.S. These data included measurements of vitamin B12 and folate levels from some participants’ blood samples along with their genome sequences.

Compared to the mice, the human data told a different story. While mice had increased mutations with high folate, the human data showed that instead low folate slightly increased the mitochondrial genome mutation rate. Additionally, the differences the researchers saw in humans were very small. 

We’ve often thought of nutrient status as important when you’re either pregnant or young and developing, but here we see it can be important throughout life.

“The Framingham study wasn’t originally looking at mitochondrial DNA,” said Dr. Parle McDermott. “When you sequence a genome, you sometimes get some mitochondrial DNA, though the quality isn’t as good, so the findings are less certain. In the future, we need bigger human studies using more updated techniques.”

Human studies will also always be more challenging. Unlike genetically identical mice, people are not genetically identical, which increases the background noise in looking for mutations.

“We also don’t know if this has any biological impact,” Dr. Parle-McDermott emphasized. “One very important thing to remember is that there are thousands of mitochondria per cell. We don’t know the threshold of how many mitochondria need to have a specific mutation to cause a disease.”

Future studies are needed to look more directly at the impact that these mutations have on the function of the mitochondria and if there are any effects in humans. However, this study is important in showing how the mitochondria can be used as a tool in genomics research. By studying the tiny, mitochondrial genome, researchers can assess the potential effects of nutrients and other environmental exposures on DNA.