D-alanine is linked to gluconeogenesis in the kidney and the circadian clock

It was only recently discovered that amino acids, the building blocks of proteins, exist in two different forms: L- and D-forms. While all natural proteins are composed exclusively of L-amino acids, the function of D-amino acids has remained poorly understood, despite the fact that they are present in the foods we eat every day.

Now, a multi-institutional research team led by Osaka University has revealed a function of a D-form amino acid: D-alanine. So what does it do and how did they uncover its function? To understand, we need some basic information.

The circadian clock, a natural oscillation in our bodies that aligns with the 24-hour cycle of day and night, affects many biological processes. One of these is gluconeogenesis, in which new glucose can be created to maintain energy levels instead of carbohydrate intake. While gluconeogenesis was known to vary with circadian rhythm, the reason was unknown.

However, there were some clues. D-alanine is found in tissues that metabolize glucose, and traces of D-alanine in blood and urine have been reported to vary with circadian rhythm. Using special equipment and advanced analytical technique, the researchers were able to detect and quantify traces of the rare amino acid. The team could then verify that D-alanine levels reliably change with the circadian clock. The fluctuations are caused by the elimination of D-alanine through the urine, a process controlled by the kidneys. They also showed that sleep was key in regulating D-alanine levels.

We decided to see which genes are expressed when the kidney is exposed to D-alanine. We used deep learning analysis with an iterative random forest algorithm to identify target genes. “We found that D-alanine up-regulates both genes linked to gluconeogenesis and genes known to be associated with circadian rhythm.”

Shinsuke Sakai, lead author of the study

Analysis of transcription factors, which are proteins that regulate gene expression, showed that the changes caused by D-alanine were mediated by a protein called Cry2, which is known to be a key circadian regulator. In conditions of disturbed circadian rhythm, D-alanine treatment improved the diurnal rhythm.

“Through these experiments, we were able to show that D-alanine is a link between gluconeogenesis in the kidney and the circadian clock,” says senior author Tomonori Kimura, “and that D-alanine activates gluconeogenesis through the circadian transcription network”.

Uncovering the relationship between D-alanine and the circadian clock represents a major step forward in our understanding of these rare D-amino acids. An exciting possibility is new treatments for diseases related to glucose, eg diabetes, and the circadian clock, eg. Sleep Disorders.