Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae

Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA.
BMC Genomics (Impact Factor: 4.04). 04/2009; 10(1):130. DOI: 10.1186/1471-2164-10-130
Source: PubMed

ABSTRACT Iron-deficiency anemia is the most prevalent form of anemia world-wide. The yeast Saccharomyces cerevisiae has been used as a model of cellular iron deficiency, in part because many of its cellular pathways are conserved. To better understand how cells respond to changes in iron availability, we profiled the yeast genome with a parallel analysis of homozygous deletion mutants to identify essential components and cellular processes required for optimal growth under iron-limited conditions. To complement this analysis, we compared those genes identified as important for fitness to those that were differentially-expressed in the same conditions. The resulting analysis provides a global perspective on the cellular processes involved in iron metabolism.
Using functional profiling, we identified several genes known to be involved in high affinity iron uptake, in addition to novel genes that may play a role in iron metabolism. Our results provide support for the primary involvement in iron homeostasis of vacuolar and endosomal compartments, as well as vesicular transport to and from these compartments. We also observed an unexpected importance of the peroxisome for growth in iron-limited media. Although these components were essential for growth in low-iron conditions, most of them were not differentially-expressed. Genes with altered expression in iron deficiency were mainly associated with iron uptake and transport mechanisms, with little overlap with those that were functionally required. To better understand this relationship, we used expression-profiling of selected mutants that exhibited slow growth in iron-deficient conditions, and as a result, obtained additional insight into the roles of CTI6, DAP1, MRS4 and YHR045W in iron metabolism.
Comparison between functional and gene expression data in iron deficiency highlighted the complementary utility of these two approaches to identify important functional components. This should be taken into consideration when designing and analyzing data from these type of studies. We used this and other published data to develop a molecular interaction network of iron metabolism in yeast.

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Available from: Adam P Arkin, Jul 30, 2015
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    • "Also, conventional growth assays (on elevated calcium or zinc) do not differentiate between wild-type yeast and yeast lacking STV1, as the vacuolar isoform compensates for a loss of the Stv1p-containing complex (Figure 3A). However, a recent report described a phenotypic difference between wild-type yeast and stv1∆ mutant yeast on media containing the iron chelator, BPS (Jo et al., 2009). "
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    • "Some coincidences are observed between our results with RNA binding protein mutants (Table S2) and the above studies. Thus, the sky1 and not3 mutants were also hypersensitive to BPS in Jo et al. (2009). Also, the ccr4 mutant, which displays hypersensitivity to BPS in our study, is moderately compromised for ferrous uptake in Lesuisse et al. (2005). "
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    • "DISCUSSION Genome-wide genetic screens identify diverse cellular roles for Aft1: In an effort to further define the cellular functions of Aft1, SGA methodology was used to perform complementary genome-wide SL and SDL screens (Tables 2 and Tables 3). As expected, the genetic interaction map identified genes encoding proteins implicated in processes previously linked to Aft1 including iron regulation (reviewed in Rutherford and Bird 2004), chromosome stability (Measday et al. 2005), cellcycle progression (Philpott et al. 1998; Jorgensen et al. 2002; White et al. 2009), and DNA damage repair (Lee et al. 2005; Kimura et al. 2007). Further, the AFT1 genetic interaction map also predicts possible functional roles for Aft1 in cell-wall assembly, protein transport, and the mitochondria. "
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