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Eren E, Watts NR, Montecinos F, Wingfield PT. Encapsulated Ferritin-like Proteins: A Structural Perspective. Biomolecules 2024; 14:624. [PMID: 38927029 PMCID: PMC11202242 DOI: 10.3390/biom14060624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell's interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology.
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Affiliation(s)
| | | | | | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Masison J, Mendes P. Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. PLoS One 2023; 18:e0281401. [PMID: 36745660 PMCID: PMC9901743 DOI: 10.1371/journal.pone.0281401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/22/2023] [Indexed: 02/07/2023] Open
Abstract
Computational models can be created more efficiently by composing them from smaller, well-defined sub-models that represent specific cellular structures that appear often in different contexts. Cellular iron metabolism is a prime example of this as multiple cell types tend to rely on a similar set of components (proteins and regulatory mechanisms) to ensure iron balance. One recurrent component, ferritin, is the primary iron storage protein in mammalian cells and is necessary for cellular iron homeostasis. Its ability to sequester iron protects cells from rising concentrations of ferrous iron limiting oxidative cell damage. The focus of the present work is establishing a model that tractably represents the ferritin iron sequestration kinetics such that it can be incorporated into larger cell models, in addition to contributing to the understanding of general ferritin iron sequestration dynamics within cells. The model's parameter values were determined from published kinetic and binding experiments and the model was validated against independent data not used in its construction. Simulation results indicate that FT concentration is the most impactful on overall sequestration dynamics, while the FT iron saturation (number of iron atoms sequestered per FT cage) fine tunes the initial rates. Finally, because this model has a small number of reactions and species, was built to represent important details of FT kinetics, and has flexibility to include subtle changes in subunit composition, we propose it to be used as a building block in a variety of specific cell type models of iron metabolism.
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Affiliation(s)
- Joseph Masison
- Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT, United States of America
| | - Pedro Mendes
- Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT, United States of America
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3
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Eren E, Wang B, Winkler DC, Watts NR, Steven AC, Wingfield PT. Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism. Structure 2022; 30:551-563.e4. [PMID: 35150605 PMCID: PMC8995368 DOI: 10.1016/j.str.2022.01.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/22/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical applications. Encapsulin shell proteins are structurally similar to HK97 bacteriophage capsid protein and their function depends on the encapsulated cargos. The Myxococcus xanthus encapsulin system comprises EncA and three cargos: EncB, EncC, and EncD. EncB and EncC are similar to bacterial ferritins that can oxidize Fe+2 to less toxic Fe+3. We analyzed EncA, EncB, and EncC by cryo-EM and X-ray crystallography. Cryo-EM shows that EncA cages can have T = 3 and T = 1 symmetry and that EncA T = 1 has a unique protomer arrangement. Also, we define EncB and EncC binding sites on EncA. X-ray crystallography of EncB and EncC reveals conformational changes at the ferroxidase center and additional metal binding sites, suggesting a mechanism for Fe oxidation and storage within the encapsulin shell.
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Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Baslé A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem 2020; 295:15511-15526. [PMID: 32878987 DOI: 10.1074/jbc.ra120.014502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/24/2020] [Indexed: 11/06/2022] Open
Abstract
Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.
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Affiliation(s)
- Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Didi He
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Kelly J Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Will A Stanley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laurène Adam
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin J Waldron
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland.
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Fei DQ, Yu HZ, Xu JP, Zhang SZ, Wang J, Li B, Yang LA, Hu P, Xu X, Zhao K, Shahzad T. Isolation of ferritin and its interaction with BmNPV in the silkworm, Bombyx mori. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 86:130-137. [PMID: 29793044 DOI: 10.1016/j.dci.2018.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Ferritin is a ubiquitous iron storage protein that plays an important role in host defence against pathogen infections. In the present study, native ferritin was isolated from the hemolymph of Bombyx mori using native-polyacrylamide gel electrophoresis (native-PAGE) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results revealed that ferritin consisted of two subunits, designated as BmFerHCH and BmFerLCH. Previously integrated previous transcriptome and iTRAQ data showed that the two subunits were down-regulated in resistant silkworm strain BC9 and there was no obvious change in the expression levels of the subunits in susceptible silkworm strain P50 after BmNPV infection. Virus overlay assays revealed that B. mori ferritin as the form of heteropolymer had an interaction with B. mori nucleopolyhedrovirus (BmNPV), but it can't interact with BmNPV after depolymerisation. What's more, reverse transcription quantitative PCR (RT-qPCR) analysis suggested that BmFerHCH and BmFerLCH could be induced by bacteria, virus and iron. This is the first study to extract B. mori ferritin successfully and confirms their roles in the process of BmNPV infection. All these results will lay a foundation for further research the function of B. mori ferritin.
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Affiliation(s)
- Dong-Qiong Fei
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Hai-Zhong Yu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China; National Navel Orange Engineering and Technology Research Center, Gannan Normal University, Ganzhou, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China.
| | - Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Li-Ang Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Xin Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Kang Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
| | - Toufeeq Shahzad
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Development Center of Sericulture Resources Utilization, China
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Hagen WR, Hagedoorn PL, Honarmand Ebrahimi K. The workings of ferritin: a crossroad of opinions. Metallomics 2018; 9:595-605. [PMID: 28573266 DOI: 10.1039/c7mt00124j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biochemistry of the essential element iron is complicated by radical chemistry associated with Fe(ii) ions and by the extremely low solubility of the Fe(iii) ion in near-neutral water. To mitigate these problems cells from all domains of life synthesize the protein ferritin to take up and oxidize Fe(ii) and to form a soluble storage of Fe(iii) from which iron can be made available for physiology. A long history of studies on ferritin has not yet resulted in a generally accepted mechanism of action of this enzyme. In fact strong disagreement exists between extant ideas on several key steps in the workings of ferritin. The scope of this review is to explain the experimental background of these controversies and to indicate directions towards their possible resolution.
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Affiliation(s)
- Wilfred R Hagen
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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First biochemical and crystallographic characterization of a fast-performing ferritin from a marine invertebrate. Biochem J 2017; 474:4193-4206. [PMID: 29127253 DOI: 10.1042/bcj20170681] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 01/31/2023]
Abstract
Ferritin, a multimeric cage-like enzyme, is integral to iron metabolism across all phyla through the sequestration and storage of iron through efficient ferroxidase activity. While ferritin sequences from ∼900 species have been identified, crystal structures from only 50 species have been reported, the majority from bacterial origin. We recently isolated a secreted ferritin from the marine invertebrate Chaetopterus sp. (parchment tube worm), which resides in muddy coastal seafloors. Here, we present the first ferritin from a marine invertebrate to be crystallized and its biochemical characterization. The initial ferroxidase reaction rate of recombinant Chaetopterus ferritin (ChF) is 8-fold faster than that of recombinant human heavy-chain ferritin (HuHF). To our knowledge, this protein exhibits the fastest catalytic performance ever described for a ferritin variant. In addition to the high-velocity ferroxidase activity, ChF is unique in that it is secreted by Chaetopterus in a bioluminescent mucus. Previous work has linked the availability of Fe2+ to this long-lived bioluminescence, suggesting a potential function for the secreted ferritin. Comparative biochemical analyses indicated that both ChF and HuHF showed similar behavior toward changes in pH, temperature, and salt concentration. Comparison of their crystal structures shows no significant differences in the catalytic sites. Notable differences were found in the residues that line both 3-fold and 4-fold pores, potentially leading to increased flexibility, reduced steric hindrance, or a more efficient pathway for Fe2+ transportation to the ferroxidase site. These suggested residues could contribute to the understanding of iron translocation through the ferritin shell to the ferroxidase site.
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Yu HZ, Zhang SZ, Ma Y, Fei DQ, Li B, Yang LA, Wang J, Li Z, Muhammad A, Xu JP. Molecular Characterization and Functional Analysis of a Ferritin Heavy Chain Subunit from the Eri-Silkworm, Samia cynthia ricini. Int J Mol Sci 2017; 18:ijms18102126. [PMID: 29036914 PMCID: PMC5666808 DOI: 10.3390/ijms18102126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/16/2023] Open
Abstract
Ferritins are conserved iron-binding proteins that are primarily involved in iron storage, detoxification and the immune response. Despite the importance of ferritin in organisms, little is known about their roles in the eri-silkworm (Samia cynthia ricini). We previously identified a ferritin heavy chain subunit named ScFerHCH in the S. c. ricini transcriptome database. The full-length S. c. ricini ferritin heavy chain subunit (ScFerHCH) was 1863 bp and encoded a protein of 231 amino acids with a deduced molecular weight of 25.89 kDa. Phylogenetic analysis revealed that ScFerHCH shared a high amino acid identity with the Bombyx mori and Danaus plexippus heavy chain subunits. Higher ScFerHCH expression levels were found in the silk gland, fat body and midgut of S. c. ricini by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blotting. Injection of Staphylococcus aureus and Pseudomonas aeruginosa was associated with an upregulation of ScFerHCH in the midgut, fat body and hemolymph, indicating that ScFerHCH may contribute to the host’s defense against invading pathogens. In addition, the anti-oxidation activity and iron-binding capacity of recombinant ScFerHCH protein were examined. Taken together, our results suggest that the ferritin heavy chain subunit from eri-silkworm may play critical roles not only in innate immune defense, but also in organismic iron homeostasis.
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Affiliation(s)
- Hai-Zhong Yu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Yan Ma
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Dong-Qiong Fei
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Li-Ang Yang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Zhen Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Azharuddin Muhammad
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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Honarmand Ebrahimi K, Bill E, Hagedoorn P, Hagen WR. Spectroscopic evidence for the presence of a high-valent Fe(IV) species in the ferroxidase reaction of an archaeal ferritin. FEBS Lett 2017; 591:1712-1719. [PMID: 28542723 PMCID: PMC5519934 DOI: 10.1002/1873-3468.12697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/10/2017] [Accepted: 05/21/2017] [Indexed: 12/20/2022]
Abstract
A high‐valent Fe(IV) species is proposed to be generated from the decay of a peroxodiferric intermediate in the catalytic cycle at the di‐iron cofactor center of dioxygen‐activating enzymes such as methane monooxygenase. However, it is believed that this intermediate is not formed in the di‐iron substrate site of ferritin, where oxidation of Fe(II) substrate to Fe(III) (the ferroxidase reaction) occurs also via a peroxodiferric intermediate. In opposition to this generally accepted view, here we present evidence for the occurrence of a high‐valent Fe(IV) in the ferroxidase reaction of an archaeal ferritin, which is based on trapped intermediates obtained with the freeze‐quench technique and combination of spectroscopic characterization. We hypothesize that a Fe(IV) intermediate catalyzes oxidation of excess Fe(II) nearby the ferroxidase center.
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Affiliation(s)
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion (MPI‐CEC)MülheimGermany
| | | | - Wilfred R. Hagen
- Department of BiotechnologyDelft University of TechnologyThe Netherlands
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Diversity of Fe 2+ entry and oxidation in ferritins. Curr Opin Chem Biol 2017; 37:122-128. [DOI: 10.1016/j.cbpa.2017.02.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 01/08/2023]
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