The food we eat may influence our genes

A recent study from the University of Cambridge and the Francis Crick Institute in London has provided evidence that almost all of our genes may be influenced by the food we eat.

In the study, which was published in Nature Microbiology this month, Markus Ralser and his international team of researchers used yeast cells to model some of the body’s most basic processes and concluded that the nutrients available to our cells can influence our genes.

The researchers decided to use yeast as a model organism because yeast cells have very similar fundamental cellular mechanisms to those of human cells, and the former are much simpler to manipulate. The yeast cells were studied at different levels of important metabolites and then examined to determine how the quantity of these metabolites affected the various genes and molecules the cells produced. The researchers found that the cells’ products were affected by changes in cellular metabolism in nearly nine out of 10 genes.

“Cellular metabolism plays a far more dynamic role in the cells than we previously thought,” Ralser said in a press release. “Nearly all of a cell’s genes are influenced by changes to the nutrients they have access to. In fact, in many cases the effects were so strong that changing a cell’s metabolic profile could make some of its genes behave in a completely different manner.”

Metabolism has been previously studied largely as a combination of the activity of genes and chemical reactions needed to maintain cells. It was found that metabolism works in two directions, first by breaking down molecules to provide energy for the body and second by producing all of the compounds needed by cells.

Ralser and his team regard this two-directional metabolic pathway as “dual dependency.” They found that transcriptional changes that follow metabolic oscillations of yeast cells could comprise more than 50 percent of the genome. The group focused its study on four markers for genetic expression: HIS3, LEU2, URA3 and MET15. They found that even when growth was restored by external nutrient supplementation, gene expression was affected in a metabolism-dependent manner.

Gene regulation is primarily linked to the genome, or the DNA blueprint, of an organism. Though this map can provide a substantial amount of information about how an organism will look, there are other ways that genes can be regulated by other genes or by epigenetic modifiers. In fact, it has even been shown that gene regulation may exist within the metabolic network. The metabolic reactions that occur within an organism depend on nutrients, which are, in turn, derived from the foods we consume.

Ralser and his team have found that the way nutrients break down affects how our genes behave and interact. Ralser believes that the findings could spark further questions about our responses to certain drugs.

For example, cancer cells contain genetic mutations that change the metabolic network of cells. These mutations could explain the behavior of genes and show why some drugs fail to work for some individuals.

Ralser and his team found that the metabolic background of the cells affected up to 85 percent of the coding genome and 88 percent of transcriptional interactions. In other words, deleting the same metabolic gene in a different background could cause an entirely different response. Therefore, the tendencies of metabolic background have profound implications when it comes to gene expression on the genome.

“Another important aspect of our findings is a practical one for scientists,” Ralser said in a press release. “Biological experiments are often not reproducible between laboratories and we often blame sloppy researchers for that. It appears, however, that small metabolic differences can change the outcomes of the experiments. We need to establish new laboratory procedures that control better for differences in metabolism. This will help us to design better and more reliable experiments.”