Novel Approaches to Study Metals in Molecular Biology

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Iron-tracking strategies: Chaperones capture iron in the cytosolic labile iron pool
Caroline C. Philpott
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Amber J. Tietgens
Schematic overview of three high throughput workflows for screening interacting intracellular iron trafficking proteins. Affinity purification (left panel): the flag tagged bait protein is pulled down from cell lysates (mild conditions) using an anti-Flag agarose resin. Only tightly interacting proteins forming stable complexes with the bait are coimmunoprecipitated. Interacting proteins are identified via mass spectrometry. Proximity labeling BioID (central panel): the bait protein is expressed fused to the biotin ligase BirA, which biotinylates proteins located in close proximity to the bait, including tightly and transiently interacting proteins. Biotinylated proteins are purified using streptavidin resin and identified via mass spectrometry. Bioinformatics analysis of interactomes (bottom left panel): the obtained proteomic data are filtered to separate non-specific interactors and contaminants from true interactors. Interactomes are then visualized in networks and analyzed for enriched canonical pathways related to iron trafficking and metabolism. Cysteine reactivity to identify Fe-S binding residues in proteomes (right panel): Cysteines in Fe-S cluster binding sites of proteins are analyzed proteome-wide under Fe-S permissive (control conditions that favor the formation of Fe-S clusters) and Fe-S impaired conditions (i.e. treatment with iron chelator or perturbation of Fe-S biogenesis pathway to impair Fe-S cluster formation). The existence of holo or apo forms of the Fe-S proteins is tested by isotopically labeling free cysteines using light (L) and heavy (H) iodoacetamide (IA), one per condition. The presence of the cluster in holo proteins protects the cysteines from IA-alkylation (No labeling). In turn, the Fe-S binding cysteines in apo proteins are available for IA-alkylation (Labeling). The L/H ratio is determined via quantitative proteomics to measure the reactivity of the cysteines in the Fe-S proteins. A parallel proteomic quantification accounts for any change in protein abundance between treatments. Net increases in cysteine reactivity under “Fe-S” impaired conditions compared to control, are indicative of the loss of Fe-S clusters. Figured adapted from (96).

Cells express hundreds of iron-dependent enzymes that rely on the iron cofactors heme, iron-sulfur clusters, and mono-or di-nuclear iron centers for activity. Cells require systems for both the assembly and the distribution of iron cofactors to their cognate enzymes. Proteins involved in the binding and trafficking of iron ions in the cytosol, called cytosolic iron chaperones, have been identified and characterized in mammalian cells. The first identified iron chaperone, poly C-binding protein 1 (PCBP1), has also been studied in mice using genetic models of conditional deletion in tissues specialized for iron handling. Studies of iron trafficking in mouse tissues have necessitated the development of new approaches, which have revealed new roles for PCBP1 in the management of cytosolic iron. These approaches can be applied to investigate use of other nutrient metals in mammals.

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