Mitochondria utilize iron, but the transporters that mediate mitochondrial iron uptake and efflux are largely unknown. Cells with a deletion in the vacuolar iron/manganese transporter Ccc1p are sensitive to high iron. Overexpression of MRS3 or MRS4 suppresses the high iron sensitivity of ⌬ccc1 cells. MRS3 and MRS4 have recently been suggested to encode mitochondrial iron transporters. We demonstrate that deletion of MRS3 and MRS4 severely affects cellular and mitochondrial metal homeostasis, including a reduction in cytosolic and mitochondrial iron acquisition. We show that vacuolar iron transport is increased in ⌬mrs3⌬mrs4 cells, resulting in decreased cytosolic iron and activation of the iron-sensing transcription factor Aft1p. Activation of Aft1p leads to increased expression of the high affinity iron transport system and increased iron uptake. Deletion of CCC1 in ⌬mrs3⌬mrs4 cells restores cellular and mitochondrial iron homeostasis to near normal levels. ⌬mrs3⌬mrs4 cells also show increased resistance to cobalt but decreased resistance to copper and cadmium. These phenotypes are also corrected by deletion of CCC1 in ⌬mrs3⌬mrs4 cells. Decreased copper resistance in ⌬mrs3⌬mrs4 cells results from activation of Aft1p by Ccc1p-mediated iron depletion, as deletion of CCC1 or AFT1 in ⌬mrs3⌬mrs4 cells restores copper resistance. These results suggest that deletion of mitochondrial proteins can alter vacuolar metal homeostasis. The data also indicate that increased expression of the AFT1-regulated gene(s) can disrupt copper homeostasis.Two important aspects of cellular iron metabolism are localized to mitochondria, heme synthesis and iron-sulfur cluster synthesis. Both synthetic pathways require iron import into mitochondria, but little is known about mitochondrial transporters for either import or export of iron. Recent studies have shown that deletion of both MRS3 and MRS4, members of the mitochondrial carrier family, results in decreased mitochondrial iron content. Double deletion strains (⌬mrs3⌬mrs4) demonstrate a low iron growth defect and decreased heme and iron-sulfur cluster synthesis (1, 2). Furthermore, Foury and Roganti (1) deleted MRS3 and MRS4 in a strain lacking Yfh1p, the yeast frataxin homologue. Loss of Yfh1p leads to defects in iron-sulfur cluster synthesis (3-5) and excessive mitochondrial iron accumulation (6). ⌬yfh1 cells are protected from mitochondrial iron toxicity when MRS3 and MRS4 are deleted (1). Deletion of these genes does not completely abrogate mitochondrial iron uptake, leading to the suggestion that they encode mitochondrial iron transporters whose function only becomes apparent under low iron conditions (2).Other characteristics of ⌬mrs3⌬mrs4 cells are inconsistent with a role for these genes simply as mitochondrial iron transporters, as broad effects on transition metal metabolism have been observed. In particular, ⌬mrs3⌬mrs4 cells show increased cellular iron acquisition due to up-regulation of the iron regulon (1, 2). Disruption of the MRS3/MRS4 homologue in Cryptococcus neoforma...