This new study from researchers at IISER Pune delves into the potential biological function of an ‘orphan enzyme’ using a variety of biochemical, molecular, and structural techniques. Siddhesh Kamat, the Principal Investigator who led this project was recently awarded the EMBO Young Investigators Award as well as the Merck Young Scientist Award.
A team of researchers led by Siddhesh Kamat, Associate Professor at the Indian Institute of Science Education and Research (IISER), Pune has discovered the function of an orphan enzyme named ABHD14B. The study has laid a foundation for investigating this enzyme’s role in metabolic pathways and its connection to human diseases like cancer.
Enzymes are proteins that catalyse biochemical reactions within the body. Enzymes have specific amino acid sequences which fold in a particular manner, forming specific pockets (active sites) where biochemical reactions take place. While the amino acid sequences of almost all enzymes are known, a vast majority of them lack any known biological function, and are hence classified as “orphan enzymes”.
Many of these orphan enzymes have been associated with various disease conditions and therefore, investigating the function of such enzymes is of utmost importance. With the use of computational tools, researchers can compare the amino acid sequences of orphan enzymes with enzymes whose functions are known, to try to predict their biological function. However, the lack of experimental evidence to confirm such computational predictions somewhat hinders researchers from understanding the biological roles of these enzymes.
Kamat’s lab works on assigning functions to enzymes and finding their mode of action. ABHD14B is one such orphan enzyme. While the structure of this enzyme was deduced almost a decade ago, nothing is known about its function except for its association with cancer cell progression and survival. Its biological substrate(s) and the physiological pathways that it regulates have, until recently, been a mystery.
“Data from whole-genome sequencing has made it clear that a significant proportion of enzymes lack any functional annotation, and assigning function to them is of great biomedical importance, as several of these are associated with human diseases. This spiked our interest in this enzyme, and we decided to pursue this further,” says Kamat.
Using a chemical proteomics technique called activity-based protein profiling (ABPP), as well as metabolomics, biochemical assays, and structural modelling studies, the team successfully identified ABHD14B as a novel lysine deacetylase enzyme that transfers an acetyl group from the lysine residue of protein substrates and makes the biologically important molecule acetyl-CoA in the process. The study was done in collaboration with Jennifer Bridwell-Rabb’s lab from the University of Michigan.
Addition of acetyl groups (acetylation) or their removal (deacetylation) is an important post-translational modification via which protein function can be modulated. This balance of acetylation and deacetylation is critical as it plays a major role in cell metabolism, signalling and gene expression.
Until now only two enzyme families have been known to deacetylate protein lysine residues: (i) sirtuins and (ii) histone deacetylases. Both these enzyme families have unique mechanisms to remove acetyl groups from acetylated-protein lysine residues. Through this study, Kamat’s team has described a third mechanism of lysine deacetylation.
Sunil Laxman, Scientist at the Institute of Stem Cell Science and Regenerative Medicine (inStem), Bangalore, who was not involved in this study says, “This third class or family of deacetylases has tremendous possible implications. It immediately suggests that there are additional ways by which acetylation can be controlled.”
“Moving forward, we think this enzyme plays an important role in controlling key steps in metabolism and cellular energetics, and we are interested in understanding this mechanistically,” says Kamat. Supporting ABHD14B’s potential role in regulating metabolic pathways, the researchers found high concentrations of it in the liver and kidney. “It is early days, but the likelihood of this protein being important in several diseases is high,” says Laxman.