Imagine a bustling food market, with hawkers and food trucks. They would have to try and make as many sales as possible. To do that, they might prioritise cooking some food items over others, depending both on its demand and on the ease of making the item. They would also need to prioritise and replenish the high-demand items.

Cells are similar to this busy market and are constantly metabolizing molecules, synthesizing some and breaking down others. One of these molecules are amino acids—the building blocks of proteins and important for metabolism. Cells have to ensure they maintain their levels to achieve homeostasis. In the event that cells are deprived of amino acids and therefore have to synthesize them, would they prioritise restoring some amino acids over others?

A study published in Nature Communications using yeast has shown that cells indeed prioritise the restoration of specific amino acid groups over others—akin to a market. Amino acids with a low supply cost and high demand are prioritised and restored first.

"Experiments thus far have focused on amino acids as a group. However, amino acids are distinct from each other chemically and are produced by different metabolic pathways. This makes it important to look at them individually", said Sunil Laxman, Associate Professor, iBRIC-inStem, the corresponding author on this study.

As the first step, the researchers classified amino acids into groups based on their metabolic origins, i.e., how they are synthesized in cells and their chemical nature. To test how cells prioritise the restoration of amino acids, they used yeast cells that can synthesize all amino acids. By moving cells from growth medium containing all amino acids to growth medium lacking all amino acids they could set up experiments to monitor how cells restored amino acids. Cells appeared to take a calculated approach in restoring the levels of amino acids.

To detect the restoration response of the cells, the scientists led by Ritu Gupta, a former Postdoctoral Fellow at iBRIC-inStem and Swagata Adhikary, a current PhD student at iBRIC-inStem, co-first authors on this study, made a simple reporter of amino acid biosynthesis. For this, they used a transcription factor, Gcn4—which functions during amino acid starvation to restore their levels. The researchers found that the reporter showed different responses when methionine, cystine, leucine, isoleucine, valine, arginine, proline, lysine, and histidine were dropped out of the medium. Of these, the reporter response was highest when the medium lacked the glutamate-derived amino acids, i.e., arginine, proline, lysine. But why does this group of amino acids show such a strong response? The response could be determined either by costs to make the amino acid, or by the demand cells had for an amino acid. The researchers set out to test these possibilities next.

"We developed a cost calculator and a relative scoring-scale to calculate the supply cost of individual amino acids. We accounted for what all goes into making these amino acids. Ultimately this came down to how much energy is involved in supplying individual amino acids," said Adhikary.

The glutamate-derived amino acids as a group emerged as the ones with the lowest supply costs. Of these, arginine was the clear winner, with very low costs, while lysine followed suit, and proline had high supply costs. What about the demand component? The demand for amino acids is both in protein synthesis and in metabolism. The amino acids that are enriched in the most abundant proteins in the cell would be in high demand. As expected, the researchers found that lysine and arginine were highly enriched in the most abundant proteins in the cell. Further, they found that while the demand for lysine in protein synthesis is high, its metabolic demand is far lower than arginine. Arginine is required to synthesize highly abundant metabolites in cells. With a low supply cost and high demand, cells thus prioritise the restoration of arginine levels.

Amino acid supply is an inherent property in a given environment. So, the major driver of restoration responses is the demand for a specific amino acid. This follows from classical economics and the law of demand, that states that if supply is inherent, then demand drives the economy.

"This study leads to a question: Why have cells evolved to utilize the glutamate-derived amino acids far more than other amino acids? Further, this study can be extended to studying other metabolites and metabolic pathways," said Adhikary.