SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation

• Published in: Nature communications Vol. 16; no. 1; pp. 978 - 19
• Main Authors: Pena, Izabella A., Shi, Jeffrey S., Chang, Sarah M., Yang, Jason, Block, Samuel, Adelmann, Charles H., Keys, Heather R., Ge, Preston, Bathla, Shveta, Witham, Isabella H., Sienski, Grzegorz, Nairn, Angus C., Sabatini, David M., Lewis, Caroline A., Kory, Nora, Vander Heiden, Matthew G., Heiman, Myriam
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.01.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 13/1; 14/19; 140/58; 38/77; 45/44; 45/47; 49/40; 631/208/191; 631/208/4041; 631/337/4041/3196; 631/45/320; 692/4017; 82/58; Accumulation; Amino acids; Anemia; Anemia, Sideroblastic - genetics; Anemia, Sideroblastic - metabolism; Carbon; Cell Proliferation; Chemical reactions; CRISPR; CRISPR-Cas Systems; Enzymes; Erythroleukemia; Erythropoiesis; Genetic Diseases, X-Linked; Genomes; Glycine; Glycine Hydroxymethyltransferase - metabolism; Humanities and Social Sciences; Humans; K562 Cells; Mammals; Metabolism; Metabolomics; Mitochondria; Mitochondria - metabolism; Mitochondrial Membrane Transport Proteins - genetics; Mitochondrial Membrane Transport Proteins - metabolism; Mitochondrial Proteins - genetics; Mitochondrial Proteins - metabolism; Molecular machines; multidisciplinary; Nucleotides; Ornithine-aminotransferase; Phosphate; Phosphates; Physiology; Polyamines; Proteins; Pyridoxal Phosphate - metabolism; Pyridoxine; Science; Science (multidisciplinary); Serine; Sideroblastic anemia; Synthesis; Vitamin B 6 - metabolism; Vitamin B6
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-025-56130-3

Many essential proteins require pyridoxal 5’-phosphate, the active form of vitamin B6, as a cofactor for their activity. These include enzymes important for amino acid metabolism, one-carbon metabolism, polyamine synthesis, erythropoiesis, and neurotransmitter metabolism. A third of all mammalian pyridoxal 5’-phosphate-dependent enzymes are localized in the mitochondria; however, the molecular machinery involved in the regulation of mitochondrial pyridoxal 5’-phosphate levels in mammals remains unknown. In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5’-phosphate. Loss of SLC25A38 causes depletion of mitochondrial, but not cellular, pyridoxal 5’-phosphate, and impairs cellular proliferation under both physiological and low vitamin B6 conditions. Metabolic changes associated with SLC25A38 loss suggest impaired mitochondrial pyridoxal 5’-phosphate-dependent enzymatic reactions, including serine to glycine conversion catalyzed by serine hydroxymethyltransferase-2 as well as ornithine aminotransferase. The proliferation defect of SLC25A38-null K562 cells in physiological and low vitamin B6 media can be explained by the loss of serine hydroxymethyltransferase-2-dependent production of one-carbon units and downstream de novo nucleotide synthesis. Our work points to a role for SLC25A38 in mitochondrial pyridoxal 5’-phosphate accumulation and provides insights into the pathology of congenital sideroblastic anemia. Pyridoxal 5’-phosphate (PLP, vitamin B6) is crucial for various metabolic processes. Here, the authors identified SLC25A38 as a key regulator of mitochondrial PLP levels using a genome-wide CRISPRi screen and organellar metabolomics, with insights into congenital sideroblastic anemia.