A yeast model for a severe neurometabolic disorder

It may not be obvious why scientists sometimes use simple, unicellular organisms such as yeast to study complex human disorders. But yeast and humans share fundamental cell biology. More than 50 percent of yeast genes have a human homolog, and about 25 percent of human-disease related genes have a close yeast homolog. These strong similarities have made yeast a model system for understanding cellular processes such as protein degradation, synthesis, quality control, secretion, vesicular trafficking, oxidative stress, and cell survival and death. Rapid growth rate and ease of genetic manipulation also have made yeast useful for high-throughput genetic and chemical screening.

Yeast was chosen by Carole Linster and her team at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg and collaborators at the Luxembourg Institute of Science and Technology to study the rare neurometabolic disorder 2-hydroxyglutaric aciduria. Caused by elevated levels of 2-hydroxyglutarate, or 2HG, the disorder is characterized by delayed development, seizures, weak muscle tone and cerebral white matter abnormalities. In severe cases of the disorder, breathing and feeding problems can lead to death in infancy or early childhood. High 2HG levels also more recently have been found in certain cancers, hence the qualification of 2HG as an oncometabolite.

Although mutations have been identified in metabolite repair enzymes that degrade the two forms of 2HG, D-2HG and L-2HG, the main source of the oncometabolite D-2HG in humans has remained unclear. In a recent issue of the Journal of Biological Chemistry, Linster’s group shares the discovery of a novel enzymatic activity that degrades D-2HG along with enzymes involved in the formation of the metabolite in the baker’s yeast Saccharomyces cerevisiae.

The researchers identified Dld2 and Dld3 as the yeast homologs of the human enzyme that degrades D-2HG. They showed that deletion of DLD2 or DLD3 led to elevation of D-2HG levels of up to two-and twentyfold, respectively, in the yeast mutants. When they restored DLD3 expression in the mutant, D-2HG levels decreased almost to wild-type levels and further decreased by 50 percent when they overexpressed this gene.

The researchers subsequently proved that just like their human homolog, Dld2 and Dld3 convert D-2HG to alpha-ketoglutarate by serving as dehydrogenases. In addition, they discovered that both yeast enzymes also degrade D-2HG through a novel enzymatic mechanism by acting as transhydrogenases. Importantly, the transhydrogenase activity of the cytosolic Dld3 enzyme, which forms D-lactate as one of the products, suggests the existence of a coupling between cytosolic D-2HG metabolism and the mitochondrial respiratory chain.

Linster and her team went on to investigate the main enzymes that catalyze the formation of D-2HG. Since the expression profiles of the yeast 3-phosphoglycerate dehydrogenase Ser33 and Dld3 are highly correlated, and because Ser3 (paralog of Ser33), Ser33 and Dld3 are co-localized within the yeast cytosol, they tested the effect of overexpression and then deletion of SER3 or SER33 on D-2HG levels. They reported that overexpressing either gene further increased the accumulation of D-2HG and that deleting each gene partially reduced synthesis of the metabolite. Their observation that a double deletion of SER3 and SER33 reduced D-2HG levels by more than 80 percent compared with wild-type levels led them to conclude that Ser3 and Ser33 are major enzymes responsible for D-2HG formation in yeast.

The researchers plan to cultivate the yeast under different growth conditions and with different genetic backgrounds and then look for phenotypic changes associated with D-2HG accumulation. Since it is the primary enzyme that breaks down D-2HG, they are also keen to elucidate the roles of Dld3 in the retrograde response to mitochondrial dysfunction. Finally, they want to investigate how D-2HG accumulation may affect the structure of the yeast chromatin, its gene expression profiles and its lifespan.

According to Linster, “An obvious advantage of finding any phenotypic effects of D-2HG in yeast is that it can be followed up by high-throughput screens to pinpoint intracellular targets of D-2HG or to find chemicals that can rescue the phenotype. If conserved mechanisms are involved, the findings may then translate into advances in our understanding and treatment of human diseases characterized by D-2HG accumulation.”

Vivian Tang Vivian Tang is a graduate student at the School of Pathology and Laboratory Medicine at the University of Western Australia.