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      Ferritinophagy via NCOA4 is required for erythropoiesis and is regulated by iron dependent HERC2-mediated proteolysis

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          Abstract

          NCOA4 is a selective cargo receptor for the autophagic turnover of ferritin, a process critical for regulation of intracellular iron bioavailability. However, how ferritinophagy flux is controlled and the roles of NCOA4 in iron-dependent processes are poorly understood. Through analysis of the NCOA4-FTH1 interaction, we demonstrate that direct association via a key surface arginine in FTH1 and a C-terminal element in NCOA4 is required for delivery of ferritin to the lysosome via autophagosomes. Moreover, NCOA4 abundance is under dual control via autophagy and the ubiquitin proteasome system. Ubiquitin-dependent NCOA4 turnover is promoted by excess iron and involves an iron-dependent interaction between NCOA4 and the HERC2 ubiquitin ligase. In zebrafish and cultured cells, NCOA4 plays an essential role in erythroid differentiation. This work reveals the molecular nature of the NCOA4-ferritin complex and explains how intracellular iron levels modulate NCOA4-mediated ferritinophagy in cells and in an iron-dependent physiological setting.

          DOI: http://dx.doi.org/10.7554/eLife.10308.001

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          The cells of nearly all organisms need iron as this metal plays an important role in a wide range of biological processes. However, iron can also trigger the formation of harmful molecules that can damage cells. It is therefore crucial that the amount of iron in cells is tightly controlled and that any extra iron is safely stored away. Most of the iron in the body is stored within a protein called ferritin, which is then broken down to release iron as it is needed, in a process known as ferritinophagy.

          Cells use several systems to break down proteins, one of which, called autophagy, has been linked to ferritinophagy. During autophagy, a bubble-like structure called an autophagosome engulfs proteins that need to be removed and delivers them to a compartment in the cell where they can be broken down. In 2014, researchers showed that a protein called NCOA4 on the surface of autophagosomes targets ferritin for destruction. When iron levels are high in the cell, the amount of NCOA4 on the autophagosomes is low. This leads to fewer ferritin molecules being broken down. In contrast, low iron levels lead to an increase of NCOA4 on autophagosomes, which promotes ferritinophagy and increases the amount of iron in the cell.

          Now, Mancias, Vaites et al—including several of the researchers involved in the 2014 work—investigate the role of NCOA4 in ferritinophagy in more detail. Biochemical experiments revealed that a region of NCOA4 directly interacts with a particular subunit of ferritin and this interaction is necessary to deliver ferritin to autophagosomes.

          Mancias, Vaites et al. then used laboratory grown-cells to investigate why the amount of NCOA4 changes in response to the amount of iron in the cell. The experiments show the amount of NCOA4 varies depending on whether it interacts with another protein called HERC2, which targets proteins for destruction by a structure called the proteasome. HERC2 only binds to NCOA4 when iron levels are high, which leads to NCOA4 being broken down by the proteasome. When iron levels are low, HERC2 does not interact with NCOA4. The presence of more NCOA4 then leads to more ferritinophagy, and so increases the amount of iron in the cell.

          Mancias, Vaites et al. also found that red blood cells, which depend highly on iron, do not develop properly in zebrafish that have lower amounts of the NCOA4 protein. Further work is needed to see whether NCOA4 is also important for the development of other cells and tissues.

          DOI: http://dx.doi.org/10.7554/eLife.10308.002

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          Most cited references26

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          Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy

          Autophagy, the process by which proteins and organelles are sequestered in double-membrane structures called autophagosomes and delivered to lysosomes for degradation, is critical in diseases such as cancer and neurodegeneration 1,2 . Much of our understanding of this process has emerged from analysis of bulk cytoplasmic autophagy, but our understanding of how specific cargo including organelles, proteins, or intracellular pathogens are targeted for selective autophagy is limited 3 . We employed quantitative proteomics to identify a cohort of novel and known autophagosome-enriched proteins, including cargo receptors. Like known cargo receptors, NCOA4 was highly enriched in autophagosomes, and associated with ATG8 proteins that recruit cargo-receptor complexes into autophagosomes. Unbiased identification of NCOA4-associated proteins revealed ferritin heavy and light chains, components of an iron-filled cage structure that protects cells from reactive iron species 4 but is degraded via autophagy to release iron 5,6 through an unknown mechanism. We found that delivery of ferritin to lysosomes required NCOA4, and an inability of NCOA4-deficient cells to degrade ferritin leads to decreased bioavailable intracellular iron. This work identifies NCOA4 as a selective cargo receptor for autophagic turnover of ferritin (ferritinophagy) critical for iron homeostasis and provides a resource for further dissection of autophagosomal cargo-receptor connectivity.
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            Systematic and quantitative assessment of the ubiquitin-modified proteome.

            Despite the diverse biological pathways known to be regulated by ubiquitylation, global identification of substrates that are targeted for ubiquitylation has remained a challenge. To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides following trypsin digestion. We identify ~19,000 diGly-modified lysine residues within ~5000 proteins. Using quantitative proteomics we monitored temporal changes in diGly site abundance in response to both proteasomal and translational inhibition, indicating both a dependence on ongoing translation to observe alterations in site abundance and distinct dynamics of individual modified lysines in response to proteasome inhibition. Further, we demonstrate that quantitative diGly proteomics can be utilized to identify substrates for cullin-RING ubiquitin ligases. Interrogation of the ubiquitinome allows for not only a quantitative assessment of alterations in protein homeostasis fidelity, but also identification of substrates for individual ubiquitin pathway enzymes. Copyright © 2011 Elsevier Inc. All rights reserved.
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              Mammalian iron metabolism and its control by iron regulatory proteins.

              Cellular iron homeostasis is maintained by iron regulatory proteins 1 and 2 (IRP1 and IRP2). IRPs bind to iron-responsive elements (IREs) located in the untranslated regions of mRNAs encoding protein involved in iron uptake, storage, utilization and export. Over the past decade, significant progress has been made in understanding how IRPs are regulated by iron-dependent and iron-independent mechanisms and the pathological consequences of IRP2 deficiency in mice. The identification of novel IREs involved in diverse cellular pathways has revealed that the IRP-IRE network extends to processes other than iron homeostasis. A mechanistic understanding of IRP regulation will likely yield important insights into the basis of disorders of iron metabolism. This article is part of a Special Issue entitled: Cell Biology of Metals. Copyright © 2012 Elsevier B.V. All rights reserved.
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                Author and article information

                Contributors
                Role: Reviewing editor
                Journal
                eLife
                eLife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                2050-084X
                05 October 2015
                2015
                : 4
                : e10308
                Affiliations
                [1 ]deptDepartment of Cell Biology , Harvard Medical School , Boston, United States
                [2 ]deptDivision of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston, United States
                [3 ]deptGastroenterology Division, Brigham and Women's Hospital , Harvard Medical School , Boston, United States
                [4 ]deptGenetics Division , Brigham and Women's Hospital , Boston, United States
                [5 ]deptDepartment of Radiation Oncology , Beth Israel Deaconess Medical Center , Harvard Medical School , Boston, United States
                [6 ]Dana-Farber Cancer Institute , Boston, United States
                [7 ]Harvard Stem Cell Institute , Cambridge, United States
                [8 ]Broad Institute of MIT and Harvard , Cambridge, United States
                Goethe University Medical School , Germany
                Goethe University Medical School , Germany
                Author notes
                [* ]For correspondence: Alec_Kimmelman@ 123456dfci.harvard.edu (ACK);
                [†]

                These authors contributed equally to this work.

                Article
                10308
                10.7554/eLife.10308
                4592949
                26436293
                c7296b26-c93c-4446-976d-c7a866f30f10
                © 2015, Mancias et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 23 July 2015
                : 05 September 2015
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health (NIH);
                Award ID: GM095567
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute (NCI);
                Award ID: R01CA157490
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000048, American Cancer Society (ACS);
                Award ID: RSG-13-298-01-TBG
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100005979, Lustgarten Foundation;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100001960, American Society for Radiation Oncology (ASTRO);
                Award ID: JF2013-2
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000861, Burroughs Wellcome Fund (BWF);
                Award ID: Career Award for Medical Scientists
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100001021, Damon Runyon Cancer Research Foundation (Damon Runyon);
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute (NCI);
                Award ID: R01CA188048
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health (NIH);
                Award ID: GM070565
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health (NIH);
                Award ID: KL2 TR001100
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health (NIH);
                Award ID: DK105326-01
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Cell Biology
                Custom metadata
                2.3
                NCOA4, the ferritin autophagy receptor, is regulated by HERC2 in an iron-dependent manner and is critical for red blood cell development.

                Life sciences
                ncoa4,autophagy,iron metabolism,erythropoiesis,herc2,human,zebrafish
                Life sciences
                ncoa4, autophagy, iron metabolism, erythropoiesis, herc2, human, zebrafish

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