Abstract
Biogenesis of iron-sulfur (Fe/S) proteins in eukaryotes is an essential process involving the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries and the cytosolic iron/sulfur protein assembly (CIA) apparatus. To define the integration of Fe/S protein biogenesis into cellular homeostasis, we compared the global transcriptional responses to defects in the three biogenesis systems in Saccharomyces cerevisiae using DNA microarrays. Depletion of a member of the CIA machinery elicited only weak (up to 2-fold) alterations in gene expression with no clear preference for any specific cellular process. In contrast, depletion of components of the mitochondrial ISC assembly and export systems induced strong and largely overlapping transcriptional responses of more than 200 genes (2-100-fold changes). These alterations were strikingly similar, yet not identical, to the transcriptional profiles developed upon iron starvation. Hence, mitochondria and their ISC systems serve as primary physiological regulators exerting a global control of numerous iron-dependent processes. First, ISC depletion activates the iron-responsive transcription factors Aft1/2p leading to increased cellular iron acquisition. Second, respiration and heme metabolism are repressed ensuring the balanced utilization of iron by the two major iron-consuming processes, iron-sulfur protein and heme biosynthesis. Third, the decreased respiratory activity is compensated by induction of genes involved in glucose acquisition. Finally, transcriptional remodeling of the citric acid cycle and the biosyntheses of ergosterol and biotin reflect the iron dependence of these pathways. Together, our data suggest a model in which mitochondria perform a global regulatory role in numerous cellular processes linked to iron homeostasis.
Highlights
We have performed a comparative analysis of the global transcriptional consequences of functional defects in the three cellular Fe/S protein biogenesis systems in S. cerevisiae
Defects in mitochondrial Fe/S protein maturation are associated with a substantial accumulation of iron within the mitochondria and the constitutive expression of the yeast iron regulon, observations that indicated a de-regulation of cellular iron homeostasis [18, 19, 29, 60]
Our systematic analyses considerably extend this conclusion in that they revealed that yeast cells depleted of members of the mitochondrial iron-sulfur cluster (ISC) assembly and export apparatus show strong and largely similar transcriptional responses, which substantially overlap with the transcriptional response of yeast to iron deprivation [48, 49, 61]
Summary
Yeast Strains and Cell Growth—Yeast strains used in this study are listed in supplemental Table SIV. Strains were cultivated in SC medium supplemented with 2% glucose (SD) for 40 h (WT, Gal-ATM1, Gal-NBP35) or 48 h (Gal-YAH1). Microarray Analysis—Strains were cultivated in parallel in SD medium supplemented with the minimal set of amino acids required for growth of the wild type strain [30]. RNA was extracted from cells that were diluted from overnight cultures to an A600 nm of 0.2 and cultivated in parallel to an A600 nm of 0.5– 0.6 using the RNeasy kit (Qiagen). Nbp35p, wild type and the corresponding mutants were cultivated in parallel in minimal medium supplemented with glucose and a minimal set of amino acids. RNA was isolated, and genes showing an altered expression level with respect to the wild type control cells were identified by DNA microarray analyses
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