The AFT1 transcriptional factor is differentially required for expression of high-affinity iron uptake genes in Saccharomyces cerevisiae

Two ferrous iron transporter-like proteins independently participate in asexual development under iron limitation and virulence in Beauveria bassiana

Reductive assimilation pathway involves ferric reductase and ferrous iron transporter, which is integral for fungal iron acquisition. A family of ferric reductase-like proteins has been functionally characterized in the filamentous entomopathogenic fungus Beauveria bassiana. In this investigation, two ferrous iron transporter-like proteins (Ftr) were functionally annotated in B. bassiana. BbFtr1 and BbFtr2 displayed high similarity in structure and were associated with the plasma and nuclear membrane. Their losses had no negatively influence on fungal growth on various nutrients and development under the iron-replete condition. Single mutants of BbFTR1 and BbFTR2 displayed the iron-availability dependent developmental defects, and double mutant exhibited the significantly impaired developmental potential under the iron-limited conditions. In insect bioassay, the double mutant also showed the weaker virulence than either of two single disruption mutants. These results suggested that two ferrous iron transporter-like proteins function independently in fungal physiologies under the iron-deficient condition. Intriguingly, a bZIP transcription factor BbHapX was required for expression of BbFTR1 and BbFTR2 under iron-depleted conditions. This study enhances our understanding of the iron uptake system in the filamentous entomopathogenic fungi.

Essential roles of ferric reductase-like proteins in growth, development, stress response, and virulence of the filamentous entomopathogenic fungus Beauveria bassiana

In yeasts, ferric reductase catalyzes reduction of ferric ion to ferrous form, which is essential for the reductive iron assimilation system. However, the physiological roles of ferric reductases remain largely unknown in the filamentous fungi. In this study, genome-wide annotation revealed thirteen ferric reductase-like (Fre) proteins in the filamentous insect pathogenic fungus Beauveria bassiana, and all their functions were genetically characterized. Ferric reductase family proteins exhibit different sub-cellular distributions (e.g., cell periphery and vacuole), which was due to divergent domain architectures. Fre proteins had a synergistic effect on fungal virulence, which was ascribed to their distinct functions in different physiologies. Ten Fre proteins were not involved in reduction of ferric ion in submerged mycelia, but most proteins contributed to blastospore development. Only two Fre proteins significantly contributed to B. bassiana vegetative growth under the chemical-induced iron starvation, but most Fre proteins were involved in resistance to osmotic and oxidative stresses. Notably, a bZIP-type transcription factor HapX bound to the promoter regions of all FRE genes in B. bassiana, and displayed varying roles in the transcription activation of these genes. This study reveals the important role of BbFre family proteins in development, stress response, and insect pathogenicity, as well as their distinctive role in the absorption of ferric iron from the environment.

Overexpression of a novel gene Aokap2 affects the growth and kojic acid production in Aspergillus oryzae

BACKGROUND

Aspergillus oryzae is an industrially important filamentous fungus for the production of fermentative food, commercial enzyme and valuable secondary metabolites. Although the whole genome of A. oryzae has been sequenced in 2005, there is currently not enough research on functional genes that affect the growth and secondary metabolites of A. oryzae. This study aimed to identify and characterize functional genes involved in the growth and secondary metabolites of A. oryzae.

METHODS AND RESULTS

Our previous work on the developmental transcriptome of A. oryzae found that an uncharacterized gene Aokap2 was repressed during the development of A. oryzae. In this study, the gene expression pattern was verified by qRT-PCR. Phylogenetic analysis revealed that AoKAP2 has the species specificity of Aspergillus. Furthermore, Aokap2 was overexpressed using the A. oryzae amyB promoter and overexpression of Aokap2 caused the inhibition in mycelium growth, conidia formation and biomass. Additionally, overexpression of Aokap2 increased the production of kojic acid. In accordance with the enhanced kojic acid, the overexpression of Aokap2 led to elevated transcription levels of the key kojic acid synthesis gene kojA and the global transcriptional regulator gene of secondary metabolism laeA. Moreover, the expression of Aokap2 was down-regulated significantly in the laeA mutant. Meanwhile, overexpression of Aokap2 in the kojA disrupted strain resulted in a ΔkojA strain-like phenotype with significant inhibition in kojic acid production.

CONCLUSION

Taken together, these data suggest that a novel gene Aokap2 is involved in the growth and overexpression of Aokap2 increased kojic acid production through affecting the expression of laeA and kojA. The identification of Aokap2 provides a new target for genetic modification of the growth and the production of kojic acid in A. oryzae.

Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae

The development of high-performance xylose-fermenting yeast is essential to achieve feasible conversion of biomass-derived sugars in lignocellulose-based biorefineries. However, engineered C5-strains of Saccharomyces cerevisiae still present low xylose consumption rates under anaerobic conditions. Here, we explore alternative metabolisms involved in metal homeostasis, which positively affect C5 fermentation and analyse the non-obvious regulatory network connection of both metabolisms using time-course transcriptome analysis. Our results indicated the vacuolar Fe2+ /Mn2+ transporter CCC1, and the protein involved in heavy metal ion homeostasis BSD2, as promising new targets for rational metabolic engineering strategies, enhancing xylose consumption in nine and 2.3-fold compared with control. Notably, intracellular metal concentration levels were affected differently by mutations and the results were compared with positive controls isu1Δ, a Fe-S cluster scaffold protein, and ssk2Δ, a component of HOG pathway. Temporal expression profiles indicate a metabolic remodelling in response to xylose, demonstrating changes in the main sugar sensing signalling pathways.

The MAPK Slt2/Mpk1 plays a role in iron homeostasis through direct regulation of the transcription factor Aft1

Iron is an essential element for life. Cells develop mechanisms to tightly regulate its homeostasis, in order to avoid abnormal accumulation and the consequent cell toxicity. In budding yeast, the high affinity iron regulon is under the control of the transcription factor Aft1. We present evidence demonstrating that the MAPK Slt2 of the cell wall integrity pathway (CWI), phosphorylates and negatively regulates Aft1 activity upon the iron depletion signal, both in fermentative or respiratory conditions. The lack of Slt2 provokes Aft1 dysfunction leading to a shorter chronological life span. The signal of iron scarcity is not transmitted to Slt2 through other signalling pathways such as TOR1, PKA, SNF1 or TOR2/YPK1. The observation that Slt2 physically binds Aft1 rather suggests a direct regulation.

Molecular strategies to increase yeast iron accumulation and resistance

All eukaryotic organisms rely on iron as an essential micronutrient for life because it participates as a redox-active cofactor in multiple biological processes. However, excess iron can generate reactive oxygen species that damage cellular macromolecules. The low solubility of ferric iron under physiological conditions increases the prevalence of iron deficiency anemia. A common strategy to treat iron deficiency consists of dietary iron supplementation. The baker's yeast Saccharomyces cerevisiae is used as a model eukaryotic organism, but also as a feed supplement. In response to iron deficiency, the yeast Aft1 transcription factor activates cellular iron acquisition. However, when constitutively active, Aft1 inhibits growth probably due to iron toxicity. In this report, we have studied the consequences of using hyperactive AFT1 alleles, including AFT1-1UP, to increase yeast iron accumulation. We first characterized the iron sensitivity of cells expressing different constitutively active AFT1 alleles. We rescued the high iron sensitivity conferred by the AFT1 alleles by deleting the sphingolipid signaling kinase YPK1. We observed that the deletion of YPK1 exerts different effects on iron accumulation depending on the AFT1 allele and the environmental iron. Moreover, we determined that the impairment of the high-affinity iron transport system partially rescues the high iron toxicity of AFT1-1UP-expressing cells. Finally, we observed that AFT1-1UP inhibits oxygen consumption through activation of the RNA-binding protein Cth2. Deletion of CTH2 partially rescues the AFT1-1UP negative respiratory effect. Collectively, these results contribute to understand how the Aft1 transcription factor functions and the multiple consequences derived from its constitutive activation.

Cancer-associated isocitrate dehydrogenase mutations induce mitochondrial DNA instability

A major advance in understanding the progression and prognostic outcome of certain cancers, such as low-grade gliomas, acute myeloid leukaemia, and chondrosarcomas, has been the identification of early-occurring mutations in the NADP⁺-dependent isocitrate dehydrogenase genes IDH1 and IDH2 These mutations result in the production of the onco-metabolite D-2-hydroxyglutarate (2HG), thought to contribute to disease progression. To better understand the mechanisms of 2HG pathophysiology, we introduced the analogous glioma-associated mutations into the NADP⁺isocitrate dehydrogenase genes (IDP1, IDP2, IDP3) in Saccharomyces cerevisiae Intriguingly, expression of the mitochondrial IDP1^R148H mutant allele results in high levels of 2HG production as well as extensive mtDNA loss and respiration defects. We find no evidence for a reactive oxygen-mediated mechanism mediating this mtDNA loss. Instead, we show that 2HG production perturbs the iron sensing mechanisms as indicated by upregulation of the Aft1-controlled iron regulon and a concomitant increase in iron levels. Accordingly, iron chelation, or overexpression of a truncated AFT1 allele that dampens transcription of the iron regulon, suppresses the loss of respirative capacity. Additional suppressing factors include overexpression of the mitochondrial aldehyde dehydrogenase gene ALD5 or disruption of the retrograde response transcription factor RTG1 Furthermore, elevated α-ketoglutarate levels also suppress 2HG-mediated respiration loss; consistent with a mechanism by which 2HG contributes to mtDNA loss by acting as a toxic α-ketoglutarate analog. Our findings provide insight into the mechanisms that may contribute to 2HG oncogenicity in glioma and acute myeloid leukaemia progression, with the promise for innovative diagnostic and prognostic strategies and novel therapeutic modalities.

Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery

Iron-sulfur (Fe-S) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. The combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables Fe-S clusters to participate in numerous biological processes. Fe-S clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i.e. cellular iron homeostasis and oxidative stress response), and to the replication and maintenance of the nuclear genome. Fe-S cluster biogenesis is a multistep process that involves a complex sequence of catalyzed protein-protein interactions and coupled conformational changes between the components of several dedicated multimeric complexes. Intensive studies of the assembly process have clarified key points in the biogenesis of Fe-S proteins. However several critical questions still remain, such as: what is the role of frataxin? Why do some defects of Fe-S cluster biogenesis cause mitochondrial iron overload? How are specific Fe-S recipient proteins recognized in the process of Fe-S transfer? This review focuses on the basic steps of Fe-S cluster biogenesis, drawing attention to recent advances achieved on the identification of molecular features that guide selection of specific subsets of nascent Fe-S recipients by the cochaperone HSC20. Additionally, it outlines the distinctive phenotypes of human diseases due to mutations in the components of the basic pathway. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Yeast Dun1 kinase regulates ribonucleotide reductase inhibitor Sml1 in response to iron deficiency

Iron is an essential micronutrient for all eukaryotic organisms because it participates as a redox-active cofactor in many biological processes, including DNA replication and repair. Eukaryotic ribonucleotide reductases (RNRs) are Fe-dependent enzymes that catalyze deoxyribonucleoside diphosphate (dNDP) synthesis. We show here that the levels of the Sml1 protein, a yeast RNR large-subunit inhibitor, specifically decrease in response to both nutritional and genetic Fe deficiencies in a Dun1-dependent but Mec1/Rad53- and Aft1-independent manner. The decline of Sml1 protein levels upon Fe starvation depends on Dun1 forkhead-associated and kinase domains, the 26S proteasome, and the vacuolar proteolytic pathway. Depletion of core components of the mitochondrial iron-sulfur cluster assembly leads to a Dun1-dependent diminution of Sml1 protein levels. The physiological relevance of Sml1 downregulation by Dun1 under low-Fe conditions is highlighted by the synthetic growth defect observed between dun1Δ and fet3Δ fet4Δ mutants, which is rescued by SML1 deletion. Consistent with an increase in RNR function, Rnr1 protein levels are upregulated upon Fe deficiency. Finally, dun1Δ mutants display defects in deoxyribonucleoside triphosphate (dNTP) biosynthesis under low-Fe conditions. Taken together, these results reveal that the Dun1 checkpoint kinase promotes RNR function in response to Fe starvation by stimulating Sml1 protein degradation.

Brain iron homeostasis: from molecular mechanisms to clinical significance and therapeutic opportunities

Iron has emerged as a significant cause of neurotoxicity in several neurodegenerative conditions, including Alzheimer's disease (AD), Parkinson's disease (PD), sporadic Creutzfeldt-Jakob disease (sCJD), and others. In some cases, the underlying cause of iron mis-metabolism is known, while in others, our understanding is, at best, incomplete. Recent evidence implicating key proteins involved in the pathogenesis of AD, PD, and sCJD in cellular iron metabolism suggests that imbalance of brain iron homeostasis associated with these disorders is a direct consequence of disease pathogenesis. A complete understanding of the molecular events leading to this phenotype is lacking partly because of the complex regulation of iron homeostasis within the brain. Since systemic organs and the brain share several iron regulatory mechanisms and iron-modulating proteins, dysfunction of a specific pathway or selective absence of iron-modulating protein(s) in systemic organs has provided important insights into the maintenance of iron homeostasis within the brain. Here, we review recent information on the regulation of iron uptake and utilization in systemic organs and within the complex environment of the brain, with particular emphasis on the underlying mechanisms leading to brain iron mis-metabolism in specific neurodegenerative conditions. Mouse models that have been instrumental in understanding systemic and brain disorders associated with iron mis-metabolism are also described, followed by current therapeutic strategies which are aimed at restoring brain iron homeostasis in different neurodegenerative conditions. We conclude by highlighting important gaps in our understanding of brain iron metabolism and mis-metabolism, particularly in the context of neurodegenerative disorders.

Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2

The paralogous iron-responsive transcription factors Aft1 and Aft2 (activators of ferrous transport) regulate iron homeostasis in Saccharomyces cerevisiae by activating expression of iron-uptake and -transport genes when intracellular iron is low. We present the previously unidentified crystal structure of Aft2 bound to DNA that reveals the mechanism of DNA recognition via specific interactions of the iron-responsive element with a Zn(2+)-containing WRKY-GCM1 domain in Aft2. We also show that two Aft2 monomers bind a [2Fe-2S] cluster (or Fe(2+)) through a Cys-Asp-Cys motif, leading to dimerization of Aft2 and decreased DNA-binding affinity. Furthermore, we demonstrate that the [2Fe-2S]-bridged heterodimer formed between glutaredoxin-3 and the BolA-like protein Fe repressor of activation-2 transfers a [2Fe-2S] cluster to Aft2 that facilitates Aft2 dimerization. Previous in vivo findings strongly support the [2Fe-2S] cluster-induced dimerization model; however, given the available evidence, Fe(2+)-induced Aft2 dimerization cannot be completely ruled out as an alternative Aft2 inhibition mechanism. Taken together, these data provide insight into the molecular mechanism for iron-dependent transcriptional regulation of Aft2 and highlight the key role of Fe-S clusters as cellular iron signals.

Iron sparing and recycling in a compartmentalized cell

This review focuses on economizing, prioritizing and recycling iron in Chlamydomonas, a reference organism for discovering mechanisms of acclimation to poor iron nutrition in the plant lineage. The metabolic flexibility of Chlamydomonas offers a unique opportunity to distinguish the impact of iron nutrition on photosynthetic versus respiratory metabolism, and the contribution of subcellular compartments to iron storage and mobilization. Mechanisms of iron sparing include down regulation of protein abundance by transcript reduction or protein degradation. Two well-studied examples of hierarchical iron allocation are the maintenance of FeSOD in the plastid and heterotrophic metabolism in acetate-grown cells at the expense of photosynthetic metabolism. The latter implicates the existence of a pathway for inter-compartment iron recycling when access to iron becomes limiting.

A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription

Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology, and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors, including the CAF-1 complex, Spt10, and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning, and these data provide a valuable resource for future studies.

The genome in eukaryotic cells is packaged into nucleosomes, which play critical roles in regulating where and when different genes are expressed. For example, nucleosomes can physically block access of transcription factor to sites on DNA or direct regulatory proteins to DNA. Consistent with these roles, nucleosomes assume a stereotypical pattern around genes: they are depleted at the promoter region that marks the start of genes and assume a regularly spaced array within genes. To identify factors involved in this organization, we generated high-resolution nucleosome and transcriptome maps for 50 loss-of-function mutants with known or suspected roles in nucleosome biology in budding yeast. We show that nucleosome organization is determined by the combined effects of many factors that often exert opposing forces on nucleosomes. We further demonstrate that specific nucleosomes can be positioned independently within genes and that repositioning of nucleosomes at the start of genes may affect expression of these genes in response to environmental stimuli. Data mining of this extensive resource allowed us to show that general transcription factors act as insulators at diverging promoters to prevent the formation of cryptic transcripts, and also revealed 36 novel transcripts regulated by the Tup1/Cyc8 complex.

Monothiol glutaredoxins and A-type proteins: partners in Fe-S cluster trafficking

Monothiol glutaredoxins (Grxs) are proposed to function in Fe-S cluster storage and delivery, based on their ability to exist as apo monomeric forms and dimeric forms containing a subunit-bridging [Fe(2)S(2)](2+) cluster, and to accept [Fe(2)S(2)](2+) clusters from primary scaffold proteins. In addition yeast cytosolic monothiol Grxs interact with Fra2 (Fe repressor of activation-2), to form a heterodimeric complex with a bound [Fe(2)S(2)](2+) cluster that plays a key role in iron sensing and regulation of iron homeostasis. In this work, we report on in vitro UV-visible CD studies of cluster transfer between homodimeric monothiol Grxs and members of the ubiquitous A-type class of Fe-S cluster carrier proteins ((Nif)IscA and SufA). The results reveal rapid, unidirectional, intact and quantitative cluster transfer from the [Fe(2)S(2)](2+) cluster-bound forms of A. thaliana GrxS14, S. cerevisiae Grx3, and A. vinelandii Grx-nif homodimers to A. vinelandii(Nif)IscA and from A. thaliana GrxS14 to A. thaliana SufA1. Coupled with in vivo evidence for interaction between monothiol Grxs and A-type Fe-S cluster carrier proteins, the results indicate that these two classes of proteins work together in cellular Fe-S cluster trafficking. However, cluster transfer is reversed in the presence of Fra2, since the [Fe(2)S(2)](2+) cluster-bound heterodimeric Grx3-Fra2 complex can be formed by intact [Fe(2)S(2)](2+) cluster transfer from (Nif)IscA. The significance of these results for Fe-S cluster biogenesis or repair and the cellular regulation of the Fe-S cluster status are discussed.

Iron content of Saccharomyces cerevisiae cells grown under iron-deficient and iron-overload conditions

Fermenting cells were grown under Fe-deficient and Fe-overload conditions, and their Fe contents were examined using biophysical spectroscopies. The high-affinity Fe import pathway was active only in Fe-deficient cells. Such cells contained ~150 μM Fe, distributed primarily into nonheme high-spin (NHHS) Fe(II) species and mitochondrial Fe. Most NHHS Fe(II) was not located in mitochondria, and its function is unknown. Mitochondria isolated from Fe-deficient cells contained [Fe(4)S(4)](2+) clusters, low- and high-spin hemes, S = (1)/(2) [Fe(2)S(2)](+) clusters, NHHS Fe(II) species, and [Fe(2)S(2)](2+) clusters. The presence of [Fe(2)S(2)](2+) clusters was unprecedented; their presence in previous samples was obscured by the spectroscopic signature of Fe(III) nanoparticles, which are absent in Fe-deficient cells. Whether Fe-deficient cells were grown under fermenting or respirofermenting conditions had no effect on Fe content; such cells prioritized their use of Fe to essential forms devoid of nanoparticles and vacuolar Fe. The majority of Mn ions in wild-type yeast cells was electron paramagnetic resonance-active Mn(II) and not located in mitochondria or vacuoles. Fermenting cells grown on Fe-sufficient and Fe-overloaded medium contained 400-450 μM Fe. In these cells, the concentration of nonmitochondrial NHHS Fe(II) declined 3-fold, relative to that in Fe-deficient cells, whereas the concentration of vacuolar NHHS Fe(III) increased to a limiting cellular concentration of ~300 μM. Isolated mitochondria contained more NHHS Fe(II) ions and substantial amounts of Fe(III) nanoparticles. The Fe contents of cells grown with excessive Fe in the medium were similar over a 250-fold change in nutrient Fe levels. The ability to limit Fe import prevents cells from becoming overloaded with Fe.

Identification and functional characterization of mitochondrial carrier Mrs4 in Candida albicans

Iron is an essential nutrient required for the growth and metabolism in Candida albicans. Here, we for the first time identified Mrs4 as a new member of mitochondrial carrier family in C. albicans. Our experiments revealed that C. albicans Mrs4 (CaMrs4) is localized to the mitochondria and required for mitochondrial morphology. We found that CaMrs4 is required for cell growth, and the mrs4Δ/Δ mutant showed a more severe growth defect in iron deficiency. Deletion of MRS4 affected cellular iron content by altering the expression of iron regulon genes in C. albicans, such as AFT2, SMF3, FTR1 and ISU1. Candida albicans Aft2 factor functions as a negative regulator of MRS4 expression through the CACCC Aft-type sequence in a gene dose-dependent fashion. In addition, the mrs4Δ/Δ mutant exhibited hypersensitivity to oxidants and most metal ions, but decreased sensitivity to cobalt. Exogenous iron could suppress the sensitivity of the mrs4Δ/Δ mutant to oxidants and most metal ions, suggesting that the role of CaMrs4 is partially mediated by iron availability. Furthermore, deletion of MRS4 resulted in delayed filamentation under tested conditions. Taken together, these findings characterize a new mitochondrial carrier and provide a novel insight into the role of CaMrs4 in mitochondrial function.

Monothiol CGFS glutaredoxins and BolA-like proteins: [2Fe-2S] binding partners in iron homeostasis

Monothiol glutaredoxins (Grxs) with a signature CGFS active site and BolA-like proteins have recently emerged as novel players in iron homeostasis. Elegant genetic and biochemical studies examining the functional and physical interactions of CGFS Grxs in the fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe have unveiled their essential roles in intracellular iron signaling, iron trafficking, and the maturation of Fe-S cluster proteins. Biophysical and biochemical analyses of the [2Fe-2S] bridging interaction between CGFS Grxs and a BolA-like protein in S. cerevisiae provided the first molecular-level understanding of the iron regulation mechanism in this model eukaryote and established the ubiquitous CGFS Grxs and BolA-like proteins as novel Fe-S cluster-binding regulatory partners. Parallel studies focused on Escherichia coli and human homologues for CGFS Grxs and BolA-like proteins have supported the studies in yeast and provided additional clues about their involvement in cellular iron metabolism. Herein, we review recent progress in uncovering the cellular and molecular mechanisms by which CGFS Grxs and BolA-like proteins help regulate iron metabolism in both eukaryotic and prokaryotic organisms.

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information

Background

Inference of causal regulators responsible for gene expression changes under different conditions is of great importance but remains rather challenging. To date, most approaches use direct binding targets of transcription factors (TFs) to associate TFs with expression profiles. However, the low overlap between binding targets of a TF and the affected genes of the TF knockout limits the power of those methods.

Results

We developed a TF-centered downstream gene set enrichment analysis approach to identify potential causal regulators responsible for expression changes. We constructed hierarchical and multi-layer regulation models to derive possible downstream gene sets of a TF using not only TF-DNA interactions, but also, for the first time, post-translational modifications (PTM) information. We verified our method in one expression dataset of large-scale TF knockout and another dataset involving both TF knockout and TF overexpression. Compared with the flat model using TF-DNA interactions alone, our method correctly identified five more actual perturbed TFs in large-scale TF knockout data and six more perturbed TFs in overexpression data. Potential regulatory pathways downstream of three perturbed regulators— SNF1, AFT1 and SUT1 —were given to demonstrate the power of multilayer regulation models integrating TF-DNA interactions and PTM information. Additionally, our method successfully identified known important TFs and inferred some novel potential TFs involved in the transition from fermentative to glycerol-based respiratory growth and in the pheromone response. Downstream regulation pathways of SUT1 and AFT1 were also supported by the mRNA and/or phosphorylation changes of their mediating TFs and/or “modulator” proteins.

Conclusions

The results suggest that in addition to direct transcription, indirect transcription and post-translational regulation are also responsible for the effects of TFs perturbation, especially for TFs overexpression. Many TFs inferred by our method are supported by literature. Multiple TF regulation models could lead to new hypotheses for future experiments. Our method provides a valuable framework for analyzing gene expression data to identify causal regulators in the context of TF-DNA interactions and PTM information.

Role of Candida albicans Aft2p transcription factor in ferric reductase activity, morphogenesis and virulence

The ability of Candida albicans to act as an opportunistic fungal pathogen is linked to its ability to switch among different morphological forms. This conversion is an important feature of C. albicans and is correlated with its pathogenesis. Many conserved positive and negative transcription factors regulate morphogenetic transition of C. albicans. Here, we show the results of functional analysis of CaAFT2, which is an orthologue of the Saccharomyces cerevisiae AFT2 gene. We have cloned CaAFT2 which has an ability to complement the S. cerevisiae aft1Δ mutant strain growth defect. Interestingly, although disruption of the AFT2 gene did not affect cell growth in solid and liquid iron-limited conditions, the cell surface ferric reductase activity was significantly decreased. Importantly, deletion of AFT2 in C. albicans led to growth of a smooth colony with no peripheral hyphae. Moreover, virulence of an aft2Δ/aft2Δ mutant was markedly attenuated in a mouse model. Our results suggest that CaAft2p represents a novel activator and that it functions in ferric reductase activity, morphogenesis and virulence in C. albicans.

Functional genomics analysis of the Saccharomyces cerevisiae iron responsive transcription factor Aft1 reveals iron-independent functions

The Saccharomyces cerevisiae transcription factor Aft1 is activated in iron-deficient cells to induce the expression of iron regulon genes, which coordinate the increase of iron uptake and remodel cellular metabolism to survive low-iron conditions. In addition, Aft1 has been implicated in numerous cellular processes including cell-cycle progression and chromosome stability; however, it is unclear if all cellular effects of Aft1 are mediated through iron homeostasis. To further investigate the cellular processes affected by Aft1, we identified >70 deletion mutants that are sensitive to perturbations in AFT1 levels using genome-wide synthetic lethal and synthetic dosage lethal screens. Our genetic network reveals that Aft1 affects a diverse range of cellular processes, including the RIM101 pH pathway, cell-wall stability, DNA damage, protein transport, chromosome stability, and mitochondrial function. Surprisingly, only a subset of mutants identified are sensitive to extracellular iron fluctuations or display genetic interactions with mutants of iron regulon genes AFT2 or FET3. We demonstrate that Aft1 works in parallel with the RIM101 pH pathway and the role of Aft1 in DNA damage repair is mediated by iron. In contrast, through both directed studies and microarray transcriptional profiling, we show that the role of Aft1 in chromosome maintenance and benomyl resistance is independent of its iron regulatory role, potentially through a nontranscriptional mechanism.

The yeast iron regulatory proteins Grx3/4 and Fra2 form heterodimeric complexes containing a [2Fe-2S] cluster with cysteinyl and histidyl ligation

The transcription of iron uptake and storage genes in Saccharomyces cerevisiae is primarily regulated by the transcription factor Aft1. Nucleocytoplasmic shuttling of Aft1 is dependent upon mitochondrial Fe-S cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (Grx3 and Grx4) and the BolA homologue Fra2. However, the interactions between these proteins and the iron-dependent mechanism by which they control Aft1 localization are unclear. To reconstitute and characterize components of this signaling pathway in vitro, we have overexpressed yeast Fra2 and Grx3/4 in Escherichia coli. We have shown that coexpression of recombinant Fra2 with Grx3 or Grx4 allows purification of a stable [2Fe-2S](2+) cluster-containing Fra2-Grx3 or Fra2-Grx4 heterodimeric complex. Reconstitution of a [2Fe-2S] cluster on Grx3 or Grx4 without Fra2 produces a [2Fe-2S]-bridged homodimer. UV-visible absorption and CD, resonance Raman, EPR, ENDOR, Mossbauer, and EXAFS studies of [2Fe-2S] Grx3/4 homodimers and the [2Fe-2S] Fra2-Grx3/4 heterodimers indicate that inclusion of Fra2 in the Grx3/4 Fe-S complex causes a change in the cluster stability and coordination environment. Taken together, our analytical, spectroscopic, and mutagenesis data indicate that Grx3/4 and Fra2 form a Fe-S-bridged heterodimeric complex with Fe ligands provided by the active site cysteine of Grx3/4, glutathione, and a histidine residue. Overall, these results suggest that the ability of the Fra2-Grx3/4 complex to assemble a [2Fe-2S] cluster may act as a signal to control the iron regulon in response to cellular iron status in yeast.

Regulation of Metallothionein Gene Expression

Organisms from bacteria to humans use elaborate systems to regulate levels of bioavailable zinc, copper, and other essential metals. An excess of them, or even traces of non-essential metals such as cadmium and mercury, can be highly toxic. Metallothioneins (MTs), short, cysteine-rich proteins, play pivotal roles in metal homeostasis and detoxification. With their sulfhydryl groups they avidly bind toxic metals and also play a role in cellular redox balance and radical scavenging. The intracellular concentration of MTs is adjusted to cellular demand primarily via regulated transcription. Especially upon heavy metal load, metallothionein gene transcription is strongly induced. From insects to mammals, the major regulator of MT transcription is MTF-1 (metal-responsive transcription factor 1), a zinc finger protein that binds to specific DNA sequence motifs (MREs) in the promoters of MT genes and other metal-regulated genes. This chapter provides an overview of our current knowledge on the expression and regulation of MT genes in higher eukaryotes, with some reference also to fungi which apparently have independently evolved their own regulatory systems.

Iron acquisition: a novel perspective on mucormycosis pathogenesis and treatment

PURPOSE OF REVIEW

Mucormycosis is an increasingly common fungal infection with an unacceptably high mortality despite first-line antifungal therapy. Iron acquisition is a critical step in the causative organisms' pathogenetic mechanism. Therefore, abrogation of fungal iron acquisition is a promising therapeutic strategy to impact clinical outcomes for this deadly disease.

RECENT FINDINGS

The increased risk of mucormycosis in patients with renal failure receiving deferoxamine iron chelation therapy is explained by the fact that deferoxamine actually acts as a siderophore for the agents of mucormycosis, supplying previously unavailable iron to the fungi. The iron liberated from deferoxamine is likely transported into the fungus by the high-affinity iron permease. In contrast, two other iron chelators, deferiprone and deferasirox, do not supply iron to the fungus and were shown to be cidal against Zygomycetes in vitro. Further, both iron chelators were shown to effectively treat mucormycosis in animal models, and one has been successfully used as salvage therapy for a patient with rhinocerebral mucormycosis.

SUMMARY

Further investigation and development of iron chelators as adjunctive therapy for mucormycosis is warranted.

Iron source preference and regulation of iron uptake in Cryptococcus neoformans

The level of available iron in the mammalian host is extremely low, and pathogenic microbes must compete with host proteins such as transferrin for iron. Iron regulation of gene expression, including genes encoding iron uptake functions and virulence factors, is critical for the pathogenesis of the fungus Cryptococcus neoformans. In this study, we characterized the roles of the CFT1 and CFT2 genes that encode C. neoformans orthologs of the Saccharomyces cerevisiae high-affinity iron permease FTR1. Deletion of CFT1 reduced growth and iron uptake with ferric chloride and holo-transferrin as the in vitro iron sources, and the cft1 mutant was attenuated for virulence in a mouse model of infection. A reduction in the fungal burden in the brains of mice infected with the cft1 mutant was observed, thus suggesting a requirement for reductive iron acquisition during cryptococcal meningitis. CFT2 played no apparent role in iron acquisition but did influence virulence. The expression of both CFT1 and CFT2 was influenced by cAMP-dependent protein kinase, and the iron-regulatory transcription factor Cir1 positively regulated CFT1 and negatively regulated CFT2. Overall, these results indicate that C. neoformans utilizes iron sources within the host (e.g., holo-transferrin) that require Cft1 and a reductive iron uptake system.

Opportunistic fungal pathogens and other invading microbes must overcome extreme iron limitation to proliferate in the mammalian host. It is not yet known which iron sources are preferred by fungal pathogens of mammals, although the mechanisms of acquisition are beginning to be explored. Some fungi produce iron-chelating siderophores to capture iron from host proteins, while others appear to require a membrane-bound iron permease–ferroxidase system. We describe the ability of the encapsulated yeast Cryptococcus neoformans to use host iron sources including transferrin and heme, and we identify an iron permease that is required for full disease progression in experimental mouse models. The permease is required for iron utilization from transferrin but not heme during growth in laboratory culture. This result when combined with the observed slow growth of the permease mutant during the experimental infections implicates transferrin as an important iron source in the host. However, we find that mutants lacking the permease eventually do cause disease, thus revealing that additional iron sources such as heme and other uptake mechanisms are available to C. neoformans. Finally, we noted that the permease mutant showed particularly poor growth in the brains of infected animals, suggesting that transferrin may be an especially important iron source in this tissue.

Candida albicans ferric reductases are differentially regulated in response to distinct forms of iron limitation by the Rim101 and CBF transcription factors

Iron is an essential nutrient that is severely limited in the mammalian host. Candida albicans encodes a family of 15 putative ferric reductases, which are required for iron acquisition and utilization. Despite the central role of ferric reductases in iron acquisition and mobilization, relatively little is known about the regulatory networks that govern ferric reductase gene expression in C. albicans. Here we have demonstrated the differential regulation of two ferric reductases, FRE2 and FRP1, in response to distinct iron-limited environments. FRE2 and FRP1 are both induced in alkaline-pH environments directly by the Rim101 transcription factor. However, FRP1 but not FRE2 is also induced by iron chelation. We have identified a CCAAT motif as the critical regulatory sequence for chelator-mediated induction and have found that the CCAAT binding factor (CBF) is essential for FRP1 expression in iron-limited environments. We found that a hap5Delta/hap5Delta mutant, which disrupts the core DNA binding activity of CBF, is unable to grow under iron-limited conditions. C. albicans encodes three CBF-dependent transcription factors, and we identified the Hap43 protein as the CBF-dependent transcription factor required for iron-limited responses. These studies provide key insights into the regulation of ferric reductase gene expression in the fungal pathogen C. albicans.

Iron and siderophores in fungal-host interactions

Most fungi and bacteria express specific mechanisms for the acquisition of iron from the hosts they infect for their own survival. This is primarily because iron plays a key catalytic role in various vital cellular reactions in conjunction with the fact that iron is not freely available in these environments due to host sequestration. High-affinity iron uptake systems, such as siderophore-mediated iron uptake and reductive iron assimilation, enable fungi to acquire limited iron from animal or plant hosts. Regulating iron uptake is crucial to maintain iron homeostasis, a state necessary to avoid iron-induced toxicity from iron abundance, while simultaneously supplying iron required for biochemical demand. Siderophores play diverse roles in fungal-host interactions, many of which have been principally delineated from gene deletions in non-ribosomal peptide synthetases, enzymes required for siderophore biosynthesis. These analyses have demonstrated that siderophores are required for virulence, resistance to oxidative stress, asexual/sexual development, iron storage, and protection against iron-induced toxicity in some fungal organisms. In this review, the strategies fungi employ to obtain iron, siderophore biosynthesis, and the regulatory mechanisms governing iron homeostasis will be discussed with an emphasis on siderophore function and relevance for fungal organisms in their interactions with their hosts.

Mechanism underlying the iron-dependent nuclear export of the iron-responsive transcription factor Aft1p in Saccharomyces cerevisiae

Aft1p is an iron-responsive transcriptional activator that plays a central role in maintaining iron homeostasis in Saccharomyces cerevisiae. Aft1p is regulated primarily by iron-induced shuttling of the protein between the nucleus and cytoplasm, but its nuclear import is not regulated by iron. Here, we have shown that the nuclear export of Aft1p is promoted in the presence of iron and that Msn5p is the nuclear export receptor (exportin) for Aft1p. Msn5p recognizes Aft1p in the iron-replete condition. Phosphorylation of S210 and S224 in Aft1p, which is not iron dependent, and the iron-induced intermolecular interaction of Aft1p are both essential for its recognition by Msn5p. Mutation of Cys291 of Aft1p to Phe, which causes Aft1p to be retained in the nucleus and results in constitutive activation of Aft1-target genes, disrupts the intermolecular interaction of Aft1p. Collectively, these results suggest that iron induces a conformational change in Aft1p, in which Aft1p Cys291 plays a critical role, and that, in turn, Aft1p is recognized by Msn5p and exported into the cytoplasm in an iron-dependent manner.

Glutaredoxins Grx3 and Grx4 regulate nuclear localisation of Aft1 and the oxidative stress response in Saccharomyces cerevisiae

Grx3 and Grx4, two monothiol glutaredoxins of Saccharomyces cerevisiae, regulate Aft1 nuclear localisation. We provide evidence of a negative regulation of Aft1 activity by Grx3 and Grx4. The Grx domain of both proteins played an important role in Aft1 translocation to the cytoplasm. This function was not, however, dependent on the availability of iron. Here we demonstrate that Grx3, Grx4 and Aft1 interact each other both in vivo and in vitro, which suggests the existence of a functional protein complex. Interestingly, each interaction occurred independently on the third member of the complex. The absence of both Grx3 and Grx4 induced a clear enrichment of G1 cells in asynchronous cultures, a slow growth phenotype, the accumulation of intracellular iron and a constitutive activation of the genes regulated by Aft1. The grx3grx4 double mutant was highly sensitive to the oxidising agents hydrogen peroxide and t-butylhydroperoxide but not to diamide. The phenotypes of the double mutant grx3grx4 characterised in this study were mainly mediated by the Aft1 function, suggesting that grx3grx4 could be a suitable cellular model for studying endogenous oxidative stress induced by deregulation of the iron homeostasis. However, our results also suggest that Grx3 and Grx4 might play additional roles in the oxidative stress response through proteins other than Aft1.

The Iron/Lead Transporter Superfamily of Fe3+/Pb2+ Uptake Systems

Oxidase-dependent ferrous iron uptake transporters of the OFeT family and lead uptake transporters of the PbrT family comprise the iron/lead transporter (ILT) superfamily (transporter classification No. 9.A.10). All sequenced homologues of the ILT superfamily were multiply aligned, and conserved motifs, including fully conserved acidic residues in putative transmembrane segments (TMSs) 1 and 4, previously implicated in heavy metal binding, were identified. Topological analyses confirmed the presence of 7 conserved TMSs in a 3 + 3 + 1 arrangement where the two 3 TMS elements are internally repeated. Phylogenetic analyses revealed the presence of several sequence divergent clusters of orthologous proteins that group roughly according to the phylogenes of the organisms of origin. The results serve to characterize and provide evolutionary insight into a novel superfamily of heavy metal uptake transporters.

Identification and functional characterization of a novel Candida albicans gene CaMNN5 that suppresses the iron-dependent growth defect of Saccharomyces cerevisiae aft1Delta mutant

In Saccharomyces cerevisiae, the transcription factor Aft1p plays a central role in regulating many genes involved in iron acquisition and utilization. An aft1Delta mutant exhibits severely retarded growth under iron starvation. To identify the functional counterpart of AFT1 in Candida albicans, we transformed a C. albicans genomic DNA library into aft1Delta to isolate genes that could allow the mutant to grow under iron-limiting conditions. In the present paper, we describe the unexpected discovery in this screen of CaMNN5. CaMnn5p is an alpha-1,2-mannosyltransferease, but its growth-promoting function in iron-limiting conditions does not require this enzymatic activity. Its function is also independent of the high-affinity iron transport systems that are mediated by Ftr1p and Fth1p. We obtained evidence suggesting that CaMnn5p may function along the endocytic pathway, because it cannot promote the growth of end4Delta and vps4Delta mutants, where the endocytic pathway is blocked at an early and late step respectively. Neither can it promote the growth of a fth1Delta smf3Delta mutant, where the vacuole-cytosol iron transport is blocked. Expression of CaMNN5 in S. cerevisiae specifically enhances an endocytosis-dependent mechanism of iron uptake without increasing the uptake of Lucifer Yellow, a marker for fluid-phase endocytosis. CaMnn5p contains three putative Lys-Glu-Xaa-Xaa-Glu iron-binding sites and co-immunoprecipitates with 55Fe. We propose that CaMnn5p promotes iron uptake and usage along the endocytosis pathway under iron-limiting conditions, a novel function that might have evolved in C. albicans.

Post-transcriptional Regulation of the Yeast High Affinity Iron Transport System

Saccharomyces cerevisiae transcriptionally regulates the expression of the plasma membrane high affinity iron transport system in response to iron need. This transport system is comprised of the products of the FET3 and FTR1 genes. We show that Fet3p and Ftr1p are post-translationally regulated by iron. Incubation of cells in high iron leads to the internalization and degradation of both Fet3p and Ftr1p. Yeast strains defective in endocytosis (Deltaend4) show a reduced iron-induced loss of Fet3p-Ftr1p. In cells with a deletion in the vacuolar protease PEP4, high iron medium leads to the accumulation of Fet3p and Ftr1p in the vacuole. Iron-induced degradation of Fet3p-Ftr1p is significantly reduced in strains containing a deletion of a gene, VTA1, which is involved in multivesicular body (MVB) sorting in yeast. Sorting through the MVB can involve ubiquitination. We demonstrate that Ftr1p is ubiquitinated, whereas Fet3p is not ubiquitinated. Iron-induced internalization and degradation of Fet3p-Ftr1p occurs in a mutant strain of the E3 ubiquitin ligase RSP5 (rsp5-1), suggesting that Rsp5p is not required. Internalization of Fet3p-Ftr1p is specific for iron and requires both an active Fet3p and Ftr1p, indicating that it is the transport of iron through the iron permease Ftr1p that is responsible for the internalization and degradation of the Fet3p-Ftr1p complex.

Activation of the Iron Regulon by the Yeast Aft1/Aft2 Transcription Factors Depends on Mitochondrial but Not Cytosolic Iron-Sulfur Protein Biogenesis

Two transcriptional activators, Aft1 and Aft2, regulate iron homeostasis in Saccharomyces cerevisiae. These factors induce the expression of iron regulon genes in iron-deficient yeast but are inactivated in iron-replete cells. Iron inhibition of Aft1/Aft2 is abrogated in cells defective for Fe-S cluster biogenesis within the mitochondrial matrix (Chen, O. S., Crisp, R. J., Valachovic, M., Bard, M., Winge, D. R., and Kaplan, J. (2004) J. Biol. Chem. 279, 29513-29518). To determine whether iron sensing by Aft1/Aft2 requires the function of the mitochondrial Fe-S export and cytosolic Fe-S protein assembly systems, we evaluated the expression of the iron regulon in cells depleted of glutathione and in cells depleted of Atm1, Nar1, Cfd1, and Nbp35. The iron regulon is induced in cells depleted of Atm1 with Aft1 largely responsible for the induced gene expression. Aft2 is activated at a later time in Atm1-depleted cells. Likewise, the iron regulon is induced in cells depleted of glutathione. In contrast, repression of NAR1, CFD1, or NBP35 fails to induce the iron regulon despite strong inhibition of cytosolic/nuclear Fe-S protein assembly. Thus, iron sensing by Aft1/Aft2 is not linked to the maturation of cytosolic/nuclear Fe-S proteins, but the mitochondrial inner membrane transporter Atm1 is important to transport the inhibitory signal. Although Aft1 and Aft2 sense a signal emanating from the Fe-S cluster biogenesis pathway, there is no indication that the proteins are inhibited by direct binding of an Fe-S cluster.

Copper and iron are the limiting factors for growth of the yeast Saccharomyces cerevisiae in an alkaline environment

Exposure of the yeast Saccharomyces cerevisiae to an alkaline environment represents a stress situation that negatively affects growth and results in an adaptive transcriptional response. We screened a collection of 4825 haploid deletion mutants for their ability to grow at mild alkaline pH, and we identified 118 genes, involved in numerous cellular functions, whose absence results in reduced growth. The list includes several key genes in copper and iron homeostasis, such as CCC2, RCS1, FET3, LYS7, and CTR1. In contrast, a screen of high-copy number plasmid libraries for clones able to increase tolerance to alkaline pH revealed only two genes: FET4 (encoding a low affinity transporter for copper, iron, and zinc) and CTR1 (encoding a high affinity copper transporter). The beneficial effect of overexpression of CTR1 requires a functional high affinity iron transport system, as it was abolished by deletion of FET3, a component of the high affinity transport system, or CCC2, which is required for assembly of the transport system. The growth-promoting effect of FET4 was not modified in these mutants. These results suggest that the observed tolerance to alkaline pH is because of improved iron uptake and indicate that both iron and copper are limiting factors for growth under alkaline pH conditions. Addition to the medium of micromolar concentrations of copper or iron ions drastically improved growth at high pH. Supplementation with iron improved somewhat the tolerance of a fet3 strain but was ineffective in a ctr1 mutant, suggesting the existence of additional copper-requiring functions important for tolerance to an alkaline environment.

The Snf1 protein kinase controls the induction of genes of the iron uptake pathway at the diauxic shift in Saccharomyces cerevisiae

In Saccharomyces cerevisiae the transition between the fermentative and the oxidative metabolism, called the diauxic shift, is associated with major changes in gene expression. In this study, we characterized a novel family of five genes whose expression is induced during the diauxic shift. These genes, FET3, FTR1, TIS11, SIT1, and FIT2, are involved in the iron uptake pathway. We showed that their induction at the diauxic shift is positively controlled by the Snf1/Snf4 kinase pathway. The transcriptional factor Aft1p, which is known to control their induction in response to iron limitation, is also required for their induction during the diauxic shift. The increase of the extracellular iron concentration does not affect this induction, indicating that glucose exhaustion by itself would be the signal. The possibility that the Snf1/Snf4 pathway was also involved in the induction of the same set of genes in response to iron starvation was considered. We demonstrate here that this is not the case. Thus, the two signals, glucose exhaustion and iron starvation, use two independent pathways to activate the same set of genes through the Aft1p transcriptional factor.

Iron requirement for GAL gene induction in the yeast Saccharomyces cerevisiae

Iron is an essential nutrient. Its deficiency hinders the synthesis of ATP and DNA. We report that galactose metabolism is defective when iron availability is restricted. Our data support this connection because 1) galactose-mediated induction of GAL promoter-dependent gene expression was diminished by iron limitation, and 2) iron-deficient mutants grew slowly on galactose-containing medium. These two defects were immediately corrected by iron replacement. Inherited defects in human galactose metabolism are characteristic of the disease called galactosemia. Our findings suggest that iron-deficient galactosemic individuals might be more severely compromised than iron-replete individuals. This work shows that iron homeostasis and galactose metabolism are linked with one another.

A specific role of the yeast mitochondrial carriers MRS3/4p in mitochondrial iron acquisition under iron-limiting conditions

The yeast genes MRS3 and MRS4 encode two members of the mitochondrial carrier family with high sequence similarity. To elucidate their function we utilized genome-wide expression profiling and found that both deletion and overexpression of MRS3/4 lead to up-regulation of several genes of the "iron regulon." We therefore analyzed the two major iron-utilizing processes, heme formation and Fe/S protein biosynthesis in vivo, in organello (intact mitochondria), and in vitro (mitochondrial extracts). Radiolabeling of yeast cells with 55Fe revealed a clear correlation between MRS3/4 expression levels and the efficiency of these biosynthetic reactions indicating a role of the carriers in utilization and/or transport of iron in vivo. Similar effects on both heme formation and Fe/S protein biosynthesis were seen in organello using mitochondria isolated from cells grown under iron-limiting conditions. The correlation between MRS3/4 expression levels and the efficiency of the two iron-utilizing processes was lost upon detergent lysis of mitochondria. As no significant changes in the mitochondrial membrane potential were observed upon overexpression or deletion of MRS3/4, our results suggest that Mrs3/4p carriers are directly involved in mitochondrial iron uptake. Mrs3/4p function in mitochondrial iron transport becomes evident under iron-limiting conditions only, indicating that the two carriers do not represent the sole system for mitochondrial iron acquisition.

Exploratory and confirmatory gene expression profiling of mac1Delta

Exploratory outlier identification methods and confirmatory gene expression studies showed induction of the iron regulon in Saccharomyces cerevisiae lacking Mac1p, a copper-responsive transcription factor. The Aft1p/Aft2p binding motif was the most discriminating motif between up- and down-regulated genes, and we identified new genes potentially regulated by Aft1p/Aft2p. In addition, multiple genes encoding proteins containing Fe-S clusters were down-regulated suggesting metabolic reorganization to conserve iron in mac1Delta. Null mutants of each of the differentially expressed genes were characterized for copper- or iron-related phenotypes. New or additional support for a role in copper and iron homeostasis is provided in this study for the gene products of AKR1, MRS4, PCA1, SSU1, TIS11, YBR047W, YHL035C, YHR045W, YLR047C, YLR126C, and YTP1.

Pse1p mediates the nuclear import of the iron-responsive transcription factor Aft1p in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the iron-responsive transcription factor Aft1p plays a critical role in maintaining iron homeostasis. The activity of Aft1p is induced in response to iron starvation and as a consequence the expression of the iron-regulon is increased. We have shown previously that Aft1p is localized to the cytoplasm under iron-replete conditions but that it is localized to the nucleus under iron-depleted conditions. In this study, we identified the transport receptor that mediates the import of Aft1p into the nucleus, located the nuclear localization signal (NLS) sequences of Aft1p, and examined whether the nuclear import of Aft1p is affected by iron status. In pse1-1 cells, which bear a temperature-sensitive mutation of PSE1, Aft1p was misdirected to the cytoplasm during iron starvation at the restrictive temperature. Aft1p could also directly bind to Pse1p and was dissociated from the complex by Ran-GTP in vitro. These results indicate that Aft1p is imported into the nucleus by Pse1p. Supporting this is that the induction of an Aft1p target gene, FTR1, in response to iron starvation was greatly reduced in pse1-1 cells. Furthermore, we demonstrated that the nuclear localization of a mutant Aft1 protein that contains an NLS derived from SV40 was regulated by iron status regardless of whether Pse1p could interact with Aft1p. This suggests that the interaction between Aft1p and Pse1p is not a critical step that controls the iron-regulated nucleo-cytoplasmic transport of Aft1p.

Aft1p and Aft2p mediate iron-responsive gene expression in yeast through related promoter elements

The transcription factors Aft1p and Aft2p from Saccharomyces cerevisiae regulate the expression of genes that are involved in iron homeostasis. In vitro studies have shown that both transcription factors bind to an iron-responsive element (FeRE) that is present in the upstream region of genes in the iron regulon. We have used DNA microarrays to distinguish the genes that are activated by Aft1p and Aft2p and to establish for the first time that each factor gives rise to a unique transcriptional profile due to the differential expression of individual iron-regulated genes. We also show that both Aft1p and Aft2p mediate the in vivo expression of FET3 and FIT3 through a consensus FeRE. In addition, both proteins regulate MRS4 via a variant FeRE with Aft2p being the stronger activator from this particular element. Like other paralogous pairs of transcription factors within S. cerevisiae, Aft1p and Aft2p are able to interact with the same promoter elements while maintaining specificity of gene activation.

Iron transport and signaling in plants

Cellular and whole organism iron homeostasis must be balanced to supply enough iron for metabolism and to avoid excessive, toxic levels. To perform iron uptake from the environment, iron distribution to various organs and tissues, and iron intracellular compartmentalization, various membranes must be crossed by this metal. The uptake and transport of iron under physiological conditions require particular processes such as chelation or reduction because ferric iron has a very low solubility. The molecular actors involved in iron acquisition from the soil have recently been characterized. A few candidates belonging to various gene families are hypothesized to play major roles in iron distribution throughout the plant. All these transport activities are tightly regulated at transcriptional and posttranslational levels, according to the iron status of the plant. These coordinated regulations result from an integration of local and long-distance transduction pathways.

The yeast iron regulon is induced upon cobalt stress and crucial for cobalt tolerance

To identify yeast genes involved in cobalt detoxification, we performed RNA expression profiling experiments and followed changes in gene activity upon cobalt stress on a genome-wide scale. We found that cobalt stress specifically results in an immediate and dramatic induction of genes involved in iron uptake. This response is dependent on the Aft1 protein, a transcriptional factor known to regulate a set of genes involved in iron uptake and homeostasis (iron regulon). Like iron starvation, cobalt stress induces accumulation of the Aft1 protein in the nucleus to activate transcription of its target genes. Cells lacking the AFT1 gene (aft1) are hypersensitive to cobalt as well as to other transition metals, whereas expression of the dominant AFT1-1(up) allele, which results in up-regulation of AFT1-controlled genes, confers resistance. Cobalt resistance correlates with an increase in intracellular iron in AFT1-1(up) cells, and sensitivity of aft1 cells is associated with a lack of iron accumulation. Furthermore, elevated iron levels in the growth medium suppress the cobalt sensitivity of the aft1 mutant cells, even though they increase cellular cobalt. Results presented indicate that yeast cells acquire cobalt tolerance by activating the Aft1p-dependent iron regulon and thereby increasing intracellular iron levels.

Combinatorial control of yeast FET4 gene expression by iron, zinc, and oxygen

Acquisition of metals such as iron, copper, and zinc by the yeast Saccharomyces cerevisiae is tightly regulated. High affinity uptake systems are induced under metal-limiting conditions to maintain an adequate supply of these essential nutrients. Low affinity uptake systems function when their substrates are in greater supply. The FET4 gene encodes a low affinity iron and copper uptake transporter. FET4 expression is regulated by several environmental factors. In this report, we describe the molecular mechanisms underlying this regulation. First, we found that FET4 expression is induced in iron-limited cells by the Aft1 iron-responsive transcriptional activator. Second, FET4 is regulated by zinc status via the Zap1 transcription factor. We present evidence that FET4 is a physiologically relevant zinc transporter and this provides a rationale for its regulation by Zap1. Finally, FET4 expression is regulated in response to oxygen by the Rox1 repressor. Rox1 attenuates activation by Aft1 and Zap1 in aerobic cells. Derepression of FET4 may allow the Fet4 transporter to play an even greater role in metal acquisition under anaerobic conditions. Thus, Fet4 is a multisubstrate metal ion transporter under combinatorial control by iron, zinc, and oxygen.