Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis

Abstract

SummaryOrganelle transporters define metabolic compartmentalization and how this metabolite transport process can be modulated is poorly explored. Here, we discovered that SLC25A39, a mitochondrial transporter critical for mitochondrial glutathione uptake, is a short-lived protein under dual regulation at the protein level. Co-immunoprecipitation mass spectrometry and CRISPR KO in cells identified that mitochondrialm-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. SLC25A39 senses mitochondrial iron-sulfur cluster using four matrix cysteine residues and inhibits its degradation. SLC25A39 protein regulation is robust in developing and mature neurons. This dual transporter regulation, by protein quality control and metabolic sensing, allows modulating mitochondrial glutathione level in response to iron homeostasis, opening new avenues to explore regulation of metabolic compartmentalization. Neuronal SLC25A39 regulation connects mitochondrial protein quality control, glutathione and iron homeostasis, which were previously unrelated biochemical features in neurodegeneration.

The iAAA-mitochondrial protease YME1L1 regulates the degradation of the short-lived mitochondrial transporter SLC25A38

“…This aligns with a previously published proteomics dataset showing that SLC25A38 accumulates in YME1L1 KO cells, along with other YME1L1 substrates 21 . Thus, together with other recent studies 11,12 , our research establishes degradation by mitochondrial proteases as a mechanism regulating the abundance of transporters in the IMM. While our results indicate a direct interaction between YME1L1 and SLC25A38, further experiments are required to determine whether YME1L1 directly degrades SLC25A38, or if YME1L1 indirectly influences SLC25A38 stability through the degradation of other proteases 22,23 , as reported for OMA1.…”

“…Gene ontology annotations associate SLC25A38 with erythrocyte differentiation, and loss-of-function mutations in SLC25A38 lead to congenital sideroblastic anemia 24 . Given that glycine import is the rate-limiting step in heme synthesis, we expected that changes in glycine and heme availability would trigger a compensatory mechanism to fine-tune SLC25A38 abundance on the IMM, analogous to the proteolytic regulation of SLC25A39 by mitochondrial glutathione levels 11,12 . However, perturbation of heme biosynthesis and levels -such as inhibition of ALA dehydratase, cofactor PLP starvation, or addition of hemin-did not affect SLC25A38 turnover.…”

“…1a), suggesting potential regulation of their synthesis or degradation. Indeed, SLC25A39, the mitochondrial glutathione transporter 9,10 , has recently been reported as a short-lived protein regulated by proteolysis 11,12 . Based on this, we hypothesized that SLC25A38 protein is also rapidly turned over under steady-state conditions.…”

Transcriptomic profile of premature ovarian insufficiency with RNA-sequencing

“…Therefore, the gene product of SLC25A39 plays a pivotal role in mitochondrial function by facilitating the transport of glutathione into mitochondria, which is essential for antioxidant defense and maintaining cellular redox balance (Slabbaert et al, 2016). Dysfunction in this transport mechanism, regulated by AFG3L2 and iron, may compromise mitochondrial health (Shi et al, 2024), resulting in oxidative stress within oocytes and potentially contributing to the development of POI. This underscores the significance of SLC25A39 in preserving oocyte quality and sustaining cellular energy metabolism critical for fertility.…”