1
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Rohaun SK, Sethu R, Imlay JA. Microbes vary strategically in their metalation of mononuclear enzymes. Proc Natl Acad Sci U S A 2024; 121:e2401738121. [PMID: 38743623 PMCID: PMC11127058 DOI: 10.1073/pnas.2401738121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Studies have determined that nonredox enzymes that are cofactored with Fe(II) are the most oxidant-sensitive targets inside Escherichia coli. These enzymes use Fe(II) cofactors to bind and activate substrates. Because of their solvent exposure, the metal can be accessed and oxidized by reactive oxygen species, thereby inactivating the enzyme. Because these enzymes participate in key physiological processes, the consequences of stress can be severe. Accordingly, when E. coli senses elevated levels of H2O2, it induces both a miniferritin and a manganese importer, enabling the replacement of the iron atom in these enzymes with manganese. Manganese does not react with H2O2 and thereby preserves enzyme activity. In this study, we examined several diverse microbes to identify the metal that they customarily integrate into ribulose-5-phosphate 3-epimerase, a representative of this enzyme family. The anaerobe Bacteroides thetaiotaomicron, like E. coli, uses iron. In contrast, Bacillus subtilis and Lactococcus lactis use manganese, and Saccharomyces cerevisiae uses zinc. The latter organisms are therefore well suited to the oxidizing environments in which they dwell. Similar results were obtained with peptide deformylase, another essential enzyme of the mononuclear class. Strikingly, heterologous expression experiments show that it is the metal pool within the organism, rather than features of the protein itself, that determine which metal is incorporated. Further, regardless of the source organism, each enzyme exhibits highest turnover with iron and lowest turnover with zinc. We infer that the intrinsic catalytic properties of the metal cannot easily be retuned by evolution of the polypeptide.
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Affiliation(s)
| | | | - James A. Imlay
- Department of Microbiology, University of Illinois, Urbana, IL61801
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2
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Bradley JM, Bugg Z, Sackey A, Andrews SC, Wilson MT, Svistunenko DA, Moore GR, Le Brun NE. The Ferroxidase Centre of Escherichia coli Bacterioferritin Plays a Key Role in the Reductive Mobilisation of the Mineral Iron Core. Angew Chem Int Ed Engl 2024; 63:e202401379. [PMID: 38407997 DOI: 10.1002/anie.202401379] [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: 01/19/2024] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Ferritins are multimeric cage-forming proteins that play a crucial role in cellular iron homeostasis. All H-chain-type ferritins harbour a diiron site, the ferroxidase centre, at the centre of a 4 α-helical bundle, but bacterioferritins are unique in also binding 12 hemes per 24 meric assembly. The ferroxidase centre is known to be required for the rapid oxidation of Fe2+ during deposition of an immobilised ferric mineral core within the protein's hollow interior. In contrast, the heme of bacterioferritin is required for the efficient reduction of the mineral core during iron release, but has little effect on the rate of either oxidation or mineralisation of iron. Thus, the current view is that these two cofactors function in iron uptake and release, respectively, with no functional overlap. However, rapid electron transfer between the heme and ferroxidase centre of bacterioferritin from Escherichia coli was recently demonstrated, suggesting that the two cofactors may be functionally connected. Here we report absorbance and (magnetic) circular dichroism spectroscopies, together with in vitro assays of iron-release kinetics, which demonstrate that the ferroxidase centre plays an important role in the reductive mobilisation of the bacterioferritin mineral core, which is dependent on the heme-ferroxidase centre electron transfer pathway.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Zinnia Bugg
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Aaren Sackey
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Simon C Andrews
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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3
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Wang W, Xiang Y, Yin G, Hu S, Cheng J, Chen J, Du G, Kang Z, Wang Y. Construction of 5-Aminolevulinic Acid Microbial Cell Factories through Identification of Novel Synthases and Metabolic Pathway Screens and Transporters. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8006-8017. [PMID: 38554273 DOI: 10.1021/acs.jafc.4c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
5-Aminolevulinic acid (5-ALA) plays a pivotal role in the biosynthesis of heme and chlorophyll and has garnered great attention for its agricultural applications. This study explores the multifaceted construction of 5-ALA microbial cell factories. Evolutionary analysis-guided screening identified a novel 5-ALA synthase from Sphingobium amiense as the best synthase. An sRNA library facilitated global gene screening that demonstrated that trpC and ilvA repression enhanced 5-ALA production by 74.3% and 102%, respectively. Subsequently, efflux of 5-ALA by the transporter Gdx increased 5-ALA biosynthesis by 25.7%. To mitigate oxidative toxicity, DNA-binding proteins from starved cells were employed, enhancing cell density and 5-ALA titer by 21.1 and 4.1%, respectively. Combining these strategies resulted in an Escherichia coli strain that produced 5-ALA to 1.51 g·L-1 in shake flask experiments and 6.19 g·L-1 through fed-batch fermentation. This study broadens the repertoire of available 5-ALA synthases and transporters and provides a new platform for optimizing 5-ALA bioproduction.
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Affiliation(s)
- Wenqiu Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiaxing Institute of Future Food, Jiaxing 314050, China
| | - Yulong Xiang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shan Hu
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiaxing Institute of Future Food, Jiaxing 314050, China
| | - Jian Cheng
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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4
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Hu J, Sha X, Li Y, Wu J, Ma J, Zhang Y, Yang R. Multifaceted Applications of Ferritin Nanocages in Delivering Metal Ions, Bioactive Compounds, and Enzymes: A Comprehensive Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19903-19919. [PMID: 37955969 DOI: 10.1021/acs.jafc.3c05510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Ferritin, a distinctive iron-storage protein, possesses a unique cage-like nanoscale structure that enables it to encapsulate and deliver a wide range of biomolecules. Recent advances prove that ferritin can serve as an efficient 8 nm diameter carrier for various bioinorganic nutrients, such as minerals, bioactive polyphenols, and enzymes. This review offers a comprehensive summary of ferritin's structural features from different sources and emphasizes its functions in iron supplementation, calcium delivery, single- and coencapsulation of polyphenols, and enzyme package. Additionally, the influence of innovative food processing technologies, including manothermosonication, pulsed electric field, and atmospheric cold plasma, on the structure and function of ferritin are examined. Furthermore, the limitations and prospects of ferritin in food and nutritional applications are discussed. The exploration of ferritin as a multifunctional protein with the capacity to load various biomolecules is crucial to fully harnessing its potential in food applications.
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Affiliation(s)
- Jiangnan Hu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xinmei Sha
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yue Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jincan Wu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Junrui Ma
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yuyu Zhang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China
| | - Rui Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
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5
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Liang A, Zhou W, Zhang H, Zhang J, Zhang XE, Fang T, Li F. Effects of Individual Amino Acids on the Blood Circulation of Biosynthetic Protein Nanocages: Toward Guidance on Surface Engineering. Adv Healthc Mater 2023; 12:e2300502. [PMID: 37067183 DOI: 10.1002/adhm.202300502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Protein nanocages (PNCs) hold great promise for developing multifunctional nanomedicines. Long blood circulation is a key requirement of PNCs for most in vivo application scenarios. In addition to the classical PEGylation strategy, short peptides with a specific sequence screened via phage display are also very effective in prolonging the blood half-life (t1/2 ) of PNCs. However, there is a lack of knowledge on how individual amino acids affect the circulation of PNCs. Here the effects of the 20 proteinogenic amino acids in the form of an X3 or X5 tag (X represents an amino acid) are explored on the pharmacokinetics of PNCs, which lead to the formation of a heatmap illustrating the extent of t1/2 prolongation by each proteinogenic amino acid. Significantly, oligo-lysine and oligo-arginine can effectively prolong the t1/2 of strongly negatively charged PNCs through charge neutralization, while oligo-cysteine can also do so, but via a different mechanism, mediating the covalent binding of PNCs with plasma albumin as a stealth material. These findings are extendible and offer guidance for surface-engineering biosynthetic PNCs and other nanoparticles.
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Affiliation(s)
- Ao Liang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Juan Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ti Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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Rivera M. Mobilization of iron stored in bacterioferritin, a new target for perturbing iron homeostasis and developing antibacterial and antibiofilm molecules. J Inorg Biochem 2023; 247:112306. [PMID: 37451083 DOI: 10.1016/j.jinorgbio.2023.112306] [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: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Antibiotic resistance is a global public health threat. The care of chronic infections is complicated by bacterial biofilms. Biofilm embedded cells can be up to 1000-fold more tolerant to antibiotic treatment than planktonic cells. Antibiotic tolerance is a condition which does not involve mutation and enables bacteria to survive in the presence of antibiotics. The antibiotic tolerance of biofilm-cells often renders antibiotics ineffective, even against strains that do not carry resistance-impairing mutations. This review discusses bacterial iron homeostasis and the strategies being developed to target this bacterial vulnerability, with emphasis on a recently proposed approach which aims at targeting the iron storage protein bacterioferritin (Bfr) and its physiological partner, the ferredoxin Bfd. Bfr regulates cytosolic iron concentrations by oxidizing Fe2+ and storing Fe3+ in its internal cavity, and by forming a complex with Bfd to reduce Fe3+ in the internal cavity and release Fe2+ to the cytosol. Blocking the Bfr-Bfd complex in P. aeruginosa cells causes an irreversible accumulation of Fe3+ in BfrB and simultaneous cytosolic iron depletion, which leads to impaired biofilm maintenance and biofilm cell death. Recently discovered small molecule inhibitors of the Bfr-Bfd complex, which bind Bfr at the Bfd binding site, inhibit iron mobilization, and elicit biofilm cell death.
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Affiliation(s)
- Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA.
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7
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Williams SM, Chatterji D. Dps Functions as a Key Player in Bacterial Iron Homeostasis. ACS OMEGA 2023; 8:34299-34309. [PMID: 37779979 PMCID: PMC10536872 DOI: 10.1021/acsomega.3c03277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Iron plays a vital role in the maintenance of life, being central to various cellular processes, from respiration to gene regulation. It is essential for iron to be stored in a nontoxic and readily available form. DNA binding proteins under starvation (Dps) belong to the ferritin family of iron storage proteins and are adept at storing iron in their hollow protein shells. Existing solely in prokaryotes, these proteins have the additional functions of DNA binding and protection from oxidative stress. Iron storage proteins play a functional role in storage, release, and transfer of iron and therefore are central to the optimal functioning of iron homeostasis. Here we review the multifarious properties of Dps through relevant biochemical and structural studies with a focus on iron storage and ferroxidation. We also examine the role of Dps as a possible candidate as an iron donor to iron-sulfur (Fe-S) clusters, which are ubiquitous to many biological processes.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute
of Structural and Molecular Biology, Birkbeck,
University of London, Malet Street, London WC1E
7HX, United Kingdom
| | - Dipankar Chatterji
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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8
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Hop HT, Huy TXN, Lee HJ, Kim S. Intracellular growth of Brucella is mediated by Dps-dependent activation of ferritinophagy. EMBO Rep 2023; 24:e55376. [PMID: 37503678 PMCID: PMC10481649 DOI: 10.15252/embr.202255376] [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: 05/09/2022] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Bacteria of the genus Brucella cause brucellosis, one of the world's most common zoonotic diseases. A major contributor to Brucella's virulence is the ability to circumvent host immune defense mechanisms. Here, we find that the DNA-binding protein Dps from Brucella is secreted within the macrophage cytosol, modulating host iron homeostasis and mediating intracellular growth of Brucella. In addition to dampening iron-dependent production of reactive oxygen species (ROS), a key immune effector required for immediate bacterial clearance, cytosolic Dps mediates ferritinophagy activation to elevate intracellular free-iron levels, thereby promoting Brucella growth and inducing host cell necrosis. Inactivation of the ferritinophagy pathway by Ncoa4 gene knockout significantly inhibits intracellular growth of Brucella and host cell death. Our study uncovers an unconventional role of bacterial Dps, identifying a crucial virulence mechanism used by Brucella to adapt to the harsh environment inside macrophages.
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Affiliation(s)
- Huynh Tan Hop
- University Center for Bioscience and BiotechnologyNational Cheng Kung UniversityTainanTaiwan
| | | | - Hu Jang Lee
- College of Veterinary MedicineGyeongsang National UniversityJinjuKorea
| | - Suk Kim
- College of Veterinary MedicineGyeongsang National UniversityJinjuKorea
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9
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João J, Prazeres DMF. Manufacturing of non-viral protein nanocages for biotechnological and biomedical applications. Front Bioeng Biotechnol 2023; 11:1200729. [PMID: 37520292 PMCID: PMC10374429 DOI: 10.3389/fbioe.2023.1200729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Protein nanocages are highly ordered nanometer scale architectures, which are typically formed by homo- or hetero-self-assembly of multiple monomers into symmetric structures of different size and shape. The intrinsic characteristics of protein nanocages make them very attractive and promising as a biological nanomaterial. These include, among others, a high surface/volume ratio, multi-functionality, ease to modify or manipulate genetically or chemically, high stability, mono-dispersity, and biocompatibility. Since the beginning of the investigation into protein nanocages, several applications were conceived in a variety of areas such as drug delivery, vaccine development, bioimaging, biomineralization, nanomaterial synthesis and biocatalysis. The ability to generate large amounts of pure and well-folded protein assemblies is one of the keys to transform nanocages into clinically valuable products and move biomedical applications forward. This calls for the development of more efficient biomanufacturing processes and for the setting up of analytical techniques adequate for the quality control and characterization of the biological function and structure of nanocages. This review concisely covers and overviews the progress made since the emergence of protein nanocages as a new, next-generation class of biologics. A brief outline of non-viral protein nanocages is followed by a presentation of their main applications in the areas of bioengineering, biotechnology, and biomedicine. Afterwards, we focus on a description of the current processes used in the manufacturing of protein nanocages with particular emphasis on the most relevant aspects of production and purification. The state-of-the-art on current characterization techniques is then described and future alternative or complementary approaches in development are also discussed. Finally, a critical analysis of the limitations and drawbacks of the current manufacturing strategies is presented, alongside with the identification of the major challenges and bottlenecks.
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Affiliation(s)
- Jorge João
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Duarte Miguel F. Prazeres
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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10
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Guerra JPL, Penas D, Tavares P, Pereira AS. Influence of Cupric (Cu 2+) Ions on the Iron Oxidation Mechanism by DNA-Binding Protein from Starved Cells (Dps) from Marinobacter nauticus. Int J Mol Sci 2023; 24:10256. [PMID: 37373403 DOI: 10.3390/ijms241210256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by oxidizing and storing ferrous ions within their cavity, using either hydrogen peroxide or molecular oxygen as the co-substrate, thus reducing the toxic effects of Fenton reactions. Interestingly, the interaction between Dps and transition metals (other than iron) is a known but relatively uncharacterized phenomenon. The impact of non-iron metals on the structure and function of Dps proteins is a current topic of research. This work focuses on the interaction between the Dps from Marinobacter nauticus (a marine facultative anaerobe bacterium capable of degrading petroleum hydrocarbons) and the cupric ion (Cu2+), one of the transition metals of greater biological relevance. Results obtained using electron paramagnetic resonance (EPR), Mössbauer and UV/Visible spectroscopies revealed that Cu2+ ions bind to specific binding sites in Dps, exerting a rate-enhancing effect on the ferroxidation reaction in the presence of molecular oxygen and directly oxidizing ferrous ions when no other co-substrate is present, in a yet uncharacterized redox reaction. This prompts additional research on the catalytic properties of Dps proteins.
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Affiliation(s)
- João P L Guerra
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Daniela Penas
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro Tavares
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alice S Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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11
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Rajapaksha N, Soldano A, Yao H, Donnarumma F, Kashipathy MM, Seibold S, Battaile KP, Lovell S, Rivera M. Pseudomonas aeruginosa Dps (PA0962) Functions in H 2O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity. Int J Mol Sci 2023; 24:4669. [PMID: 36902100 PMCID: PMC10002758 DOI: 10.3390/ijms24054669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe2+ utilizing H2O2 (not O2) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H2O2-mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H2O2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H2O2 or O2 but requires divalent cations and 12-mer Pa Dps.
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Affiliation(s)
- Nimesha Rajapaksha
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Anabel Soldano
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Huili Yao
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | - Steve Seibold
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | | | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
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12
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Codolo G, Coletta S, D’Elios MM, de Bernard M. HP-NAP of Helicobacter pylori: The Power of the Immunomodulation. Front Immunol 2022; 13:944139. [PMID: 35844568 PMCID: PMC9277015 DOI: 10.3389/fimmu.2022.944139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
The miniferritin HP-NAP of Helicobacter pylori was originally described as a neutrophil-activating protein because of the capacity to activate neutrophils to generate oxygen radicals and adhere to endothelia. Currently, the main feature for which HP-NAP is known is the ability to promote Th1 responses and revert the immune suppressive profile of macrophages. In this review, we discuss the immune modulating properties of the protein regarding the H. pylori infection and the evidence that support the potential clinical application of HP-NAP in allergy and cancer immunotherapy.
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Affiliation(s)
- Gaia Codolo
- Department of Biology, University of Padova, Padova, Italy
| | - Sara Coletta
- Department of Biology, University of Padova, Padova, Italy
| | - Mario Milco D’Elios
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
- *Correspondence: Marina de Bernard, ; Mario Milco D’Elios,
| | - Marina de Bernard
- Department of Biology, University of Padova, Padova, Italy
- *Correspondence: Marina de Bernard, ; Mario Milco D’Elios,
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13
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Shtykova EV, Petoukhov MV, Mozhaev AA. Formation of Iron Oxide Nanoparticles in the Internal Cavity of Ferritin-Like Dps Protein: Studies by Anomalous X-Ray Scattering. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:511-523. [PMID: 35790408 DOI: 10.1134/s0006297922060037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
DNA-binding protein from starved cells (Dps) takes a special place among dodecamer mini-ferritins. Its most important function is protection of bacterial genome from various types of destructive external factors via in cellulo Dps-DNA co-crystallization. This protective response results in the emergence of bacterial resistance to antibiotics and other drugs. The protective properties of Dps have attracted a significant attention of researchers. However, Dps has another equally important functional role. Being a ferritin-like protein, Dps acts as an iron depot and protects bacterial cells from the oxidative damage initiated by the excess of iron. Here we investigated formation of iron oxide nanoparticles in the internal cavity of the Dps dodecamer. We used anomalous small-angle X-ray scattering as the main research technique, which allows to examine the structure of metal-containing biological macromolecules and to analyze the size distribution of metal nanoparticles formed in them. The contributions of protein and metal components to total scattering were distinguished by varying the energy of the incident X-ray radiation near the edge of the metal atom absorption band (the K-band for iron). We examined Dps specimens containing 50, 500, and 2000 iron atoms per protein dodecamer. Analysis of the particle size distribution showed that, depending on the iron content in the solution, the size of the nanoparticles formed inside the protein molecule was 2 to 4 nm and the growth of metal nanoparticles was limited by the size of the protein inner cavity. We also found some amount of iron ions in the Dps surface layer. This layer is very important for the protein to perform its protective functions, since the surface-located N-terminal domains determine the nature of interactions between Dps and DNA. In general, the results obtained in this work can be useful for the next step in studying the Dps phenomenon, as well as in creating biocompatible and solution-stabilized metal nanoparticles.
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Affiliation(s)
- Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia.
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
- National Research University Higher School of Economics, Moscow, 101000, Russia
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14
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Wang R, Chi W, Wan F, Wei J, Ping H, Zou Z, Xie J, Wang W, Fu Z. Nanocage Ferritin Reinforced Polyacrylamide Hydrogel for Wearable Flexible Strain Sensors. ACS APPLIED MATERIALS & INTERFACES 2022; 14:21278-21286. [PMID: 35471924 DOI: 10.1021/acsami.2c00317] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biocomposite hydrogels are promising for applications in wearable flexible strain sensors. Nevertheless, the existing biocomposite hydrogels are still hard to meet all requirements, which limits the practical application. Here, inspired by the structure and composition of natural ferritin, we design a PAAm-Ferritin hybrid hydrogel through a facile method. Ferritin is uniformly distributed in the cross-linking networks and acts as a nanocage spring model, leading to the enhanced tensile strength of the hydrogel. The fracture stress is 99 kPa at 1400% maximum elongation. As fabricated PAAm-Ferritin hybrid hydrogels exhibit high toughness and low elastic modulus (21 kPa). The PAAm-Ferritin hybrid hydrogels present excellent biocompatibility and increased conductivity compared with PAAm hydrogel. Impressively, as a wearable flexible strain sensor, the PAAm-Ferritin hybrid hydrogels have high sensitivity (gauge factor = 2.06), excellent reliability, and cycling stability. This study indicates the feasibility of utilizing ferritin to synthesize functional materials, which is conducive to expanding the use of protein synthesis of materials technology and application fields.
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Affiliation(s)
- Rongjie Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Wenhao Chi
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Fuqiang Wan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Jingjiang Wei
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Hang Ping
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Zhaoyong Zou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Jingjing Xie
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Weimin Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
| | - Zhengyi Fu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P.R. China
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15
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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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16
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Distinct structural characteristics define a new subfamily of Mycoplasma ferritin. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Identification of FtpA, a Dps-like protein involved in anti-oxidative stress and virulence in Actinobacillus pleuropneumoniae. J Bacteriol 2021; 204:e0032621. [PMID: 34807725 DOI: 10.1128/jb.00326-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have evolved a variety of enzymes to eliminate endogenous or host-derived oxidative stress factors. The Dps protein, first identified in Escherichia coli, contains a ferroxidase center and protects bacteria from reactive oxygen species damage. There is a lack of knowledge of the role of Dps-like proteins in bacterial pathogenesis. Actinobacillus pleuropneumoniae causes pleuropneumonia, a respiratory disease of swine. The A. pleuropneumoniae ftpA gene is up-regulated during a shift to anaerobiosis, in biofilms and, as found in this study, also by H2O2. An A. pleuropneumoniae ftpA deletion mutant (△ftpA) had increased H2O2 sensitivity, less intracellular viability in macrophages, and decreased virulence in a mouse infection model. Expression of ftpA in an E. coli dps mutant restored wild-type resistance to H2O2. FtpA possesses a conserved ferritin domain containing a ferroxidase site. Recombinant rFtpA bound and oxidized Fe2+ reversibly. Under aerobic conditions, compared with the wild-type strain, the viability of an △ftpA mutant was reduced after extended culture, transition from anaerobic to aerobic conditions, and upon supplementation with Fenton reaction substrates. Under anaerobic conditions, additional H2O2 resulted in a more severe growth defect of △ftpA than under aerobic conditions. Therefore, by oxidizing and mineralizing Fe2+, FtpA alleviates oxidative damage mediated by intracellular Fenton reactions. Furthermore, by mutational analysis, two residues were confirmed to be critical for Fe2+ binding and oxidization, as well as for A. pleuropneumoniae H2O2 resistance. Taken together, this study demonstrates that A. pleuropneumoniae FtpA is a Dps-like protein, playing critical roles in oxidative stress resistance and virulence. IMPORTANCE As a ferroxidase, Dps of Escherichia coli can protect bacteria from reactive oxygen species damage, but its role in bacterial pathogenesis has received little attention. In this study, FtpA of the swine respiratory pathogen A. pleuropneumoniae was identified as a new Dps-like protein. It facilitated A. pleuropneumoniae resistance to H2O2, survival in macrophages, and infection in vivo. FtpA could bind and oxidize Fe2+ through two important residues in its ferroxidase site and protected the bacteria from oxidative damage mediated by the intracellular Fenton reaction. These findings provide new insights into the role of the FtpA-based antioxidant system in the pathogenesis of A. pleuropneumoniae, and the conserved Fe2+ binding ligands in Dps/FtpA provide novel drug target candidates for disease prevention.
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19
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Yamanaka M, Mashima T, Ogihara M, Okamoto M, Uchihashi T, Hirota S. Construction of ferritin hydrogels utilizing subunit-subunit interactions. PLoS One 2021; 16:e0259052. [PMID: 34731167 PMCID: PMC8565734 DOI: 10.1371/journal.pone.0259052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022] Open
Abstract
Various proteins form nanostructures exhibiting unique functions, making them attractive as next-generation materials. Ferritin is a hollow spherical protein that incorporates iron ions. Here, we found that hydrogels are simply formed from concentrated apoferritin solutions by acid denaturation and subsequent neutralization. The water content of the hydrogel was approximately 80%. The apoferritin hydrogel did not decompose in the presence of 1 M HCl, 2-mercaptoethanol, or methanol but was dissolved in the presence of 1 M NaOH, by heating at 80°C, or by treatment with trypsin or 6 M guanidine hydrochloride. The Young’s modulus of the hydrogel was 20.4 ± 12.1 kPa according to local indentation experimentes using atomic force microscopy, indicating that the hydrogel was relatively stiff. Transition electron microscopy measurements revealed that a fibrous network was constructed in the hydrogel. The color of the hydrogel became yellow-brown upon incubation in the presence of Fe3+ ions, indicating that the hydrogel adsorbed the Fe3+ ions. The yellow-brown color of the Fe3+-adsorbed hydrogel did not change upon incubation in pure water, whereas it became pale by incubating it in the presence of 100 mM ethylenediaminetetraacetic acid (EDTA). The apoferritin hydrogel also adsorbed Co2+ and Cu2+ ions and released them in the presence of EDTA, while it adsorbed less Ni2+ ions; more Fe3+ ions adsorbed to the apoferritin hydrogel than other metal ions, indicating that the hydrogel keeps the iron storage characteristic of ferritin. These results demonstrate a new property of ferritin: the ability to form a hydrogel that can adsorb/desorb metal ions, which may be useful in designing future biomaterials.
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Affiliation(s)
- Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Michio Ogihara
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Mei Okamoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- * E-mail:
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20
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Dps-DNA interaction in Marinobacter hydrocarbonoclasticus protein: effect of a single-charge alteration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:513-521. [PMID: 33900431 DOI: 10.1007/s00249-021-01538-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/06/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
DNA-binding proteins from starved cells (Dps) are members of the ferritin family of proteins found in prokaryotes, with hollow rounded cube-like structures, composed of 12 equal subunits. These protein nanocages are bifunctional enzymes that protect the cell from the harmful reaction of iron and peroxide (Fenton reaction), thus preventing DNA damage by oxidative stress. Ferrous ions are oxidized at specific iron-binding sites in the presence of the oxidant and stored in its cavity that can accommodate up to ca. 500 iron atoms. DNA-binding properties of Dps are associated with the N-terminal, positive charge rich, extensions that can promote DNA binding and condensation, apparently by a cooperative binding mechanism. Here, we describe the binding and protection activities of Marinobacter hydrocarbonoclasticus Dps using Electrophoretic Mobility Shift Essays (EMSA), and synchrotron radiation circular dichroism (SRCD) spectroscopy. While no DNA condensation was observed in the tested conditions, it was possible to determine a Dps-DNA complex formation with an apparent dissociation constant of 6.0 ± 1.0 µM and a Hill coefficient of 1.2 ± 0.1. This interaction is suppressed by the inclusion of a single negative charge in the N-terminal region by point mutation. In Dps proteins containing a ferric mineral core (above 96 Fe/protein), DNA binding was impaired. SRCD data clearly showed that no significant modification existed either in secondary structure or protein stability of WT, Q14E variant and core containing proteins. It was, however, interesting to note that, in our experimental conditions, thermal denaturation induced protein aggregation that caused artifacts in thermal denaturation curves, which were dependent on radiation flux and vertical arrangement of the CD cell.
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21
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Bradley JM, Svistunenko DA, Wilson MT, Hemmings AM, Moore GR, Le Brun NE. Bacterial iron detoxification at the molecular level. J Biol Chem 2021; 295:17602-17623. [PMID: 33454001 PMCID: PMC7762939 DOI: 10.1074/jbc.rev120.007746] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Indexed: 01/18/2023] Open
Abstract
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
| | | | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom; Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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22
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Zhu W, Fang T, Zhang W, Liang A, Zhang H, Zhang ZP, Zhang XE, Li F. A ROS scavenging protein nanocage for in vitro and in vivo antioxidant treatment. NANOSCALE 2021; 13:4634-4643. [PMID: 33616146 DOI: 10.1039/d0nr08878a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Elevated levels of reactive oxygen species (ROS) are implicated in the onset and progression of many diseases, e.g., virus infection, ischemic stroke and neurodegenerative diseases. ROS-scavenging nanomaterials have attracted particular interest. Here, we report the development of a natural protein nanocage named Dps for in vitro and in vivo antioxidant treatment by inhibiting the Fenton reaction, a critical step in ROS generation and interconversion. Systematic surface engineering enabled cell penetration, good colloidal stability, and facile purification of Dps. With its intrinsic ferroxidase activity consuming both H2O2 and Fe2+, Dps not only protects human cells from oxidative stress but also effectively alleviates ROS-induced inflammation in a mouse dermatitis model. The protection is triggered by elevated H2O2 and thereby, in principle, avoids ROS imbalances. Thus, Dps has potential as a new bionano platform for different purposes, such as antiaging, anti-inflammation and cosmetics.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ti Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ao Liang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Xian-En Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
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23
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Williams SM, Chatterji D. An Overview of Dps: Dual Acting Nanovehicles in Prokaryotes with DNA Binding and Ferroxidation Properties. Subcell Biochem 2021; 96:177-216. [PMID: 33252729 DOI: 10.1007/978-3-030-58971-4_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA binding proteins under starvation (Dps) are proteins belonging to the ferritin family with the capacity for DNA binding, in addition to iron storage and ferroxidation. Present only in the prokaryotes, these multifaceted proteins have been assigned with a number of roles, from pathogenesis to nucleoid condensation and protection. They have a significant role in protecting the cells from free radical assaults, indirectly by sequestration of iron and by directly binding to the DNA. Due to their symmetry, stability and biomineralization capacity, these proteins have ever increasing potential applications in biotechnology and drug delivery. This chapter tries to bring together all these aspects of Dps in the view of current understanding and older perspectives by studies of our group as well as other experts in the field.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, United Kingdom.
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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24
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Demchuk AM, Patel TR. The biomedical and bioengineering potential of protein nanocompartments. Biotechnol Adv 2020; 41:107547. [PMID: 32294494 DOI: 10.1016/j.biotechadv.2020.107547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Protein nanocompartments (PNCs) are self-assembling biological nanocages that can be harnessed as platforms for a wide range of nanobiotechnology applications. The most widely studied examples of PNCs include virus-like particles, bacterial microcompartments, encapsulin nanocompartments, enzyme-derived nanocages (such as lumazine synthase and the E2 component of the pyruvate dehydrogenase complex), ferritins and ferritin homologues, small heat shock proteins, and vault ribonucleoproteins. Structural PNC shell proteins are stable, biocompatible, and tolerant of both interior and exterior chemical or genetic functionalization for use as vaccines, therapeutic delivery vehicles, medical imaging aids, bioreactors, biological control agents, emulsion stabilizers, or scaffolds for biomimetic materials synthesis. This review provides an overview of the recent biomedical and bioengineering advances achieved with PNCs with a particular focus on recombinant PNC derivatives.
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Affiliation(s)
- Aubrey M Demchuk
- Department of Neuroscience, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming, School of Medicine, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada; Li Ka Shing Institute of Virology and Discovery Lab, Faculty of Medicine & Dentistry, University of Alberta, 6-010 Katz Center for Health Research, Edmonton, AB T6G 2E1, Canada.
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25
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Lei J, Liu H, Yin D, Zhou L, Liu JA, Chen Q, Cui X, He R, Duan T, Zhu W. Boosting the Loading of Metal Single Atoms via a Bioconcentration Strategy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905920. [PMID: 31916700 DOI: 10.1002/smll.201905920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Increasing the mass loading of transition metal single atoms coordinated with nitrogen in carbon-based materials (M-N-C) is still challenging. Herein, inspired by the bioconcentration effect in the living body, a biochemistry strategy for the synthesis of Fe-N-C single atoms is demonstrated. Through introducing ferrous glycinate into the growth of fungus, the Fe atoms are bioconcentrated in hyphae. The highly dispersed Fe-N-C single atoms in hyphae-derived carbon fibers (labeled as Fe-N-C SA/HCF) are prepared by the pyrolysis of Fe-riched hyphae. In the bioconcentration process, the uptake of Fe ions by hyphae promotes the secretion of glutathione and ferritin, which provides additional coordination sites for Fe ions. Accordingly, the mass content of Fe in bioconcentrated Fe-N-C SA/HCF reaches 4.8%, which is 5.3 times larger than that of the sample prepared by the conventional pyrolysis process. The present bioconcentration strategy is further extended to the preparation of Co, Ni, and Mn single atoms. Owing to the high content of Fe-N-C single atoms, Fe-N-C SA/HCF shows the onset potential (Eonset ) of 0.931 V versus reversible hydrogen electrode (RHE) and half-wave potential (E1/2 ) of 0.802 V versus RHE in oxygen reduction reaction measurements, which is comparable to the commercial Pt/C catalysts.
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Affiliation(s)
- Jia Lei
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
- Sichuan Co-Innovation Center for New Energetic Materials, Mianyang, Sichuan, 621010, P. R. China
| | - Huanhuan Liu
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Dingrui Yin
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Linghao Zhou
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Ji-An Liu
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Qiang Chen
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Xudong Cui
- Sichuan New Materials Research Center, Institute of Chemical Materials, China Academy of Engineering Physics, Chengdu, Sichuan, 610200, P. R. China
| | - Rong He
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Tao Duan
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
- Sichuan Co-Innovation Center for New Energetic Materials, Mianyang, Sichuan, 621010, P. R. China
| | - Wenkun Zhu
- State Key Laboratory of Environment-Friendly Energy Materials, National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, School of National Defense Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
- Sichuan Co-Innovation Center for New Energetic Materials, Mianyang, Sichuan, 621010, P. R. China
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26
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Min X, Fang T, Li L, Li C, Zhang ZP, Zhang XE, Li F. AIE nanodots scaffolded by mini-ferritin protein for cellular imaging and photodynamic therapy. NANOSCALE 2020; 12:2340-2344. [PMID: 31934693 DOI: 10.1039/c9nr09788k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photodynamic therapy (PDT) is one of the most elegant cancer treatment strategies that can be controlled by a beam of light with non-invasion, precise control, and high spatiotemporal accuracy. An ideal photosensitizer (PS) is the key to ensure the efficacy of PDT. Due to their hydrophobic and rigid planar structures, most traditional PSs are prone to aggregate under physiological conditions, which causes fluorescence quenching and significantly reduces reactive oxygen species (ROS) generation. Fortunately, the emergence of aggregation-induced emission (AIE) dyes offers a potential opportunity to overcome these limitations. When AIE PS molecules are in the aggregation state, the fluorescence intensity and ROS production can be increased. We herein use red AIE PS molecules to prepare stable AIE nanodots for cell imaging and PDT via a simple method with a highly negatively charged mini-ferritin protein as the scaffold. The as-prepared protein-AIE nanodots show strong fluorescence emission and efficient singlet oxygen generation, with good stability, relatively long wavelengths of absorption and emission, and negligible dark toxicity. The mini-ferritin-AIE system may be useful in developing novel functional probes for tumour nanotheranostics.
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Affiliation(s)
- Xuehong Min
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Ti Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Lingling Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Chaoqun Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China.
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27
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Akyüz E, Başkan KS, Tütem E, Apak R. Novel Iron(III)−Induced Prooxidant Activity Measurement Using a Solid Protein Sensor in Comparison with a Copper(II)−Induced Assay. ANAL LETT 2020. [DOI: 10.1080/00032719.2019.1710180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Esin Akyüz
- Faculty of Engineering, Department of Chemistry, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Kevser Sözgen Başkan
- Faculty of Engineering, Department of Chemistry, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Esma Tütem
- Faculty of Engineering, Department of Chemistry, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Reşat Apak
- Faculty of Engineering, Department of Chemistry, Istanbul University-Cerrahpasa, Istanbul, Turkey
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28
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Liu Y, Yang R, Liu J, Meng D, Zhou Z, Zhang Y, Blanchard C. Fabrication, structure, and function evaluation of the ferritin based nano-carrier for food bioactive compounds. Food Chem 2019; 299:125097. [DOI: 10.1016/j.foodchem.2019.125097] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 12/13/2022]
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29
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Zeth K, Sancho-Vaello E, Okuda M. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps. Inorg Chem 2019; 58:11351-11363. [PMID: 31433627 DOI: 10.1021/acs.inorgchem.9b00301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron storage in biology is carried out by cage-shaped proteins of the ferritin superfamily, one of which is the dodecameric protein Dps. In Dps, four distinct steps lead to the formation of metal nanoparticles: attraction of ion-aquo complexes to the protein matrix, passage of these complexes through translocation pores, oxidation of these complexes at ferroxidase centers, and, ultimately, nanoparticle formation. In this study, we investigated Dps from Listeria innocua to structurally characterize these steps for Co2+, Zn2+, and La3+ ions. The structures reveal that differences in their ion coordination chemistry determine alternative metal ion-binding sites on the areas of the surface surrounding the translocation pore that captures nine La3+, three Co2+, or three Zn2+ ions as aquo clusters and passes them on for translocation. Inside these pores, ion-selective conformational changes at key residues occur before a gating residue to actively move ions through the constriction zone. Ions upstream of the Asp130 gate residue are typically hydrated, while ions downstream directly interact with the protein matrix. Inside the cavity, ions move along negatively charged residues to the ferroxidase center, where seven main residues adapt to the three different ions by dynamically changing their conformations. In total, we observed more than 20 metal-binding sites per Dps monomer, which clearly highlights the metal-binding capacity of this protein family. Collectively, our results provide a detailed structural description of the preparative steps for amino acid-assisted biomineralization in Dps proteins, demonstrating unexpected protein matrix plasticity.
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Affiliation(s)
- Kornelius Zeth
- Roskilde University , Department of Science and Environment , Universitetsvej 1 , 4000 Roskilde , Denmark.,Universidad del Pais Vasco (UPV/EHU) , 48940 Leioa , Basque Country , Spain
| | - Enea Sancho-Vaello
- Unidad de Biofisica, Consejo Superior de Investigaciones Científicas , Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU) , Barrio Sarriena s/n, Leioa , 48940 Leioa , Basque Country , Spain
| | - Mitsuhiro Okuda
- Unidad de Biofisica, Consejo Superior de Investigaciones Científicas , Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU) , Barrio Sarriena s/n, Leioa , 48940 Leioa , Basque Country , Spain.,CIC nanoGUNE , 20018 Donostia-San Sebastian , Basque Country , Spain.,IKERBASQUE , Basque Foundation for Science , 48011 Bilbao , Basque Country , Spain
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30
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Structural diffusion properties of two atypical Dps from the cyanobacterium Nostoc punctiforme disclose interactions with ferredoxins and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148063. [PMID: 31419396 DOI: 10.1016/j.bbabio.2019.148063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Ferritin-like proteins, Dps (DNA-binding protein from starved cells), store iron and play a key role in the iron homeostasis in bacteria, yet their iron releasing machinery remains largely unexplored. The electron donor proteins that may interact with Dps and promote the mobilization of the stored iron have hitherto not been identified. Here, we investigate the binding capacity of the two atypical Dps proteins NpDps4 and NpDps5 from Nostoc punctiforme to isolated ferredoxins. We report NpDps-ferredoxin interactions by fluorescence correlation spectroscopy (FCS) and fluorescence resonance energy transfer (FRET) methods. Dynamic light scattering, size exclusion chromatography and native gel electrophoresis results show that NpDps4 forms a dodecamer at both pH 6.0 and pH 8.0, while NpDps5 forms a dodecamer only at pH 6.0. In addition, FCS data clearly reveal that the non-canonical NpDps5 interacts with DNA at pH 6.0. Our spectroscopic analysis shows that [FeS] centers of the three recombinantly expressed and isolated ferredoxins are properly incorporated and are consistent with their respective native states. The results support our hypothesis that ferredoxins could be involved in cellular iron homeostasis by interacting with Dps and assisting the release of stored iron.
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31
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Howe C, Moparthi VK, Ho FM, Persson K, Stensjö K. The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria. PLoS One 2019; 14:e0218300. [PMID: 31369577 PMCID: PMC6675082 DOI: 10.1371/journal.pone.0218300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 11/18/2022] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) have been found to detoxify H2O2. At their catalytic centers, the ferroxidase center (FOC), Dps proteins utilize Fe2+ to reduce H2O2 and therefore play an essential role in the protection against oxidative stress and maintaining iron homeostasis. Whereas most bacteria accommodate one or two Dps, there are five different Dps proteins in Nostoc punctiforme, a phototrophic and filamentous cyanobacterium. This uncommonly high number of Dps proteins implies a sophisticated machinery for maintaining complex iron homeostasis and for protection against oxidative stress. Functional analyses and structural information on cyanobacterial Dps proteins are rare, but essential for understanding the function of each of the NpDps proteins. In this study, we present the crystal structure of NpDps4 in its metal-free, iron- and zinc-bound forms. The FOC coordinates either two iron atoms or one zinc atom. Spectroscopic analyses revealed that NpDps4 could oxidize Fe2+ utilizing O2, but no evidence for its use of the oxidant H2O2 could be found. We identified Zn2+ to be an effective inhibitor of the O2-mediated Fe2+ oxidation in NpDps4. NpDps4 exhibits a FOC that is very different from canonical Dps, but structurally similar to the atypical one from DpsA of Thermosynechococcus elongatus. Sequence comparisons among Dps protein homologs to NpDps4 within the cyanobacterial phylum led us to classify a novel FOC class: the His-type FOC. The features of this special FOC have not been identified in Dps proteins from other bacterial phyla and it might be unique to cyanobacterial Dps proteins.
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Affiliation(s)
- Christoph Howe
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Vamsi K. Moparthi
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Felix M. Ho
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karina Persson
- Department of Chemistry, Umeå University, Umeå, Sweden
- * E-mail: (KS); (KP)
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail: (KS); (KP)
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32
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Dadinova LA, Chesnokov YM, Kamyshinsky RA, Orlov IA, Petoukhov MV, Mozhaev AA, Soshinskaya EY, Lazarev VN, Manuvera VA, Orekhov AS, Vasiliev AL, Shtykova EV. Protective Dps-DNA co-crystallization in stressed cells: an in vitro structural study by small-angle X-ray scattering and cryo-electron tomography. FEBS Lett 2019; 593:1360-1371. [PMID: 31090064 DOI: 10.1002/1873-3468.13439] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/14/2023]
Abstract
Under severe or prolonged stress, bacteria produce a nonspecific DNA-binding protein (Dps), which effectively protects DNA against damaging agents both in vitro and in vivo by forming intracellular biocrystals. The phenomenon of protective crystallization of DNA in living cells has been intensively investigated during the last two decades; however, the results of studies are somewhat contradictory, and up to now, there has been no direct determination of a Dps-DNA crystal structure. Here, we report the in vitro analysis of the vital process of Dps-DNA co-crystallization using two complementary structural methods: synchrotron small-angle X-ray scattering in solution and cryo-electron tomography. Importantly, for the first time, the DNA in the co-crystals was visualized, and the lattice parameters of the crystalline Dps-DNA complex were determined.
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Affiliation(s)
- Liubov A Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Yurii M Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Roman A Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan A Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia.,European Molecular Biology Laboratory, EMBL Hamburg Outstation, Germany
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Yu Soshinskaya
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Vassili N Lazarev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Valentin A Manuvera
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Anton S Orekhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Alexander L Vasiliev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
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33
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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34
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Nihei M, Ida H, Nibe T, Moeljadi AMP, Trinh QT, Hirao H, Ishizaki M, Kurihara M, Shiga T, Oshio H. Ferrihydrite Particle Encapsulated within a Molecular Organic Cage. J Am Chem Soc 2018; 140:17753-17759. [DOI: 10.1021/jacs.8b10957] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Masayuki Nihei
- Faculty of Pure and Applied Sciences, Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan
| | - Hiromichi Ida
- Faculty of Pure and Applied Sciences, Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan
| | - Takayuki Nibe
- Faculty of Pure and Applied Sciences, Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan
| | | | - Quang Thang Trinh
- Cambridge Centre for Advanced Research and Education in Singapore, Nanyang Technological University, 1 Create Way, Singapore 138602
| | - Hajime Hirao
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
| | - Manabu Ishizaki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Masato Kurihara
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Takuya Shiga
- Faculty of Pure and Applied Sciences, Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan
| | - Hiroki Oshio
- Faculty of Pure and Applied Sciences, Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan
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35
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Diaz D, Care A, Sunna A. Bioengineering Strategies for Protein-Based Nanoparticles. Genes (Basel) 2018; 9:E370. [PMID: 30041491 PMCID: PMC6071185 DOI: 10.3390/genes9070370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP's intrinsic properties and to impart them with novel functionalities.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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36
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Ardini M, Howes BD, Fiorillo A, Falvo E, Sottini S, Rovai D, Lantieri M, Ilari A, Gatteschi D, Spina G, Chiancone E, Stefanini S, Fittipaldi M. Study of manganese binding to the ferroxidase centre of human H-type ferritin. J Inorg Biochem 2018; 182:103-112. [PMID: 29454149 DOI: 10.1016/j.jinorgbio.2018.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/11/2018] [Accepted: 02/04/2018] [Indexed: 01/15/2023]
Abstract
Ferritins are ubiquitous and conserved proteins endowed with enzymatic ferroxidase activity, that oxidize Fe(II) ions at the dimetal ferroxidase centre to form a mineralized Fe(III) oxide core deposited within the apo-protein shell. Herein, the in vitro formation of a heterodimetal cofactor constituted by Fe and Mn ions has been investigated in human H ferritin (hHFt). Namely, Mn and Fe binding at the hHFt ferroxidase centre and its effects on Fe(II) oxidation have been investigated by UV-Vis ferroxidation kinetics, fluorimetric titrations, multifrequency EPR, and preliminary Mössbauer spectroscopy. Our results show that in hHFt, both Fe(II) and Mn(II) bind the ferroxidase centre forming a Fe-Mn cofactor. Moreover, molecular oxygen seems to favour Mn(II) binding and increases the ferroxidation activity of the Mn-loaded protein. The data suggest that Mn influences the Fe binding and the efficiency of the ferroxidation reaction. The higher efficiency of the Mn-Fe heterometallic centre may have a physiological relevance in specific cell types (i.e. glia cells), where the concentration of Mn is the same order of magnitude as iron.
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Affiliation(s)
- Matteo Ardini
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Barry D Howes
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Elisabetta Falvo
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Silvia Sottini
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Donella Rovai
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Lantieri
- ISC-CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Dante Gatteschi
- INSTM, Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia, 3-13 50019 Sesto Fiorentino, Florence, Italy
| | - Gabriele Spina
- INSTM, Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Emilia Chiancone
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; CNR-Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Simonetta Stefanini
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.
| | - Maria Fittipaldi
- INSTM, Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Florence, Italy.
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37
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Zang J, Chen H, Zhao G, Wang F, Ren F. Ferritin cage for encapsulation and delivery of bioactive nutrients: From structure, property to applications. Crit Rev Food Sci Nutr 2018; 57:3673-3683. [PMID: 26980693 DOI: 10.1080/10408398.2016.1149690] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Ferritin is a class of naturally occurring iron storage proteins, which is distributed widely in animal, plant, and bacteria. It usually consists of 24 subunits that form a hollow protein shell with high symmetry. One holoferritin molecule can store up to 4500 iron atom within its inner cavity, and it becomes apoferritin upon removal of iron from the cavity. Recently, scientists have subverted these nature functions and used reversibly self-assembled property of apoferritin cage controlled by pH for the encapsulation and delivery of bioactive nutrients or anticancer drug. In all these cases, the ferritin cages shield their cargo from the influence of external conditions and provide a controlled microenvironment. More importantly, upon encapsulation, ferritin shell greatly improved the water solubility, thermal stability, photostability, and cellular uptake activity of these small bioactive compounds. This review aims to highlight recent advances in applications of ferritin cage as a novel vehicle in the field of food science and nutrition. Future outlooks are highlighted with the aim to suggest a research line to follow for further studies.
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Affiliation(s)
- Jiachen Zang
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , College of Food Science and Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing , P. R. China
| | - Hai Chen
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , College of Food Science and Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing , P. R. China
| | - Guanghua Zhao
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , College of Food Science and Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing , P. R. China
| | - Fudi Wang
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , College of Food Science and Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing , P. R. China
| | - Fazheng Ren
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , College of Food Science and Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing , P. R. China.,b Beijing Laboratory for Food Quality and Safety , Beijing , P. R. China
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Devaraj A, Buzzo J, Rocco CJ, Bakaletz LO, Goodman SD. The DNABII family of proteins is comprised of the only nucleoid associated proteins required for nontypeable Haemophilus influenzae biofilm structure. Microbiologyopen 2017; 7:e00563. [PMID: 29230970 PMCID: PMC6011942 DOI: 10.1002/mbo3.563] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 11/20/2022] Open
Abstract
Biofilms play a central role in the pathobiology of otitis media (OM), bronchitis, sinusitis, conjunctivitis, and pneumonia caused by nontypeable Haemophilus influenzae (NTHI). Our previous studies show that extracellular DNA (eDNA) and DNABII proteins are essential components of biofilms formed by NTHI. The DNABII protein family includes integration host factor (IHF) and the histone‐like protein HU and plays a central role in NTHI biofilm structural integrity. We demonstrated that immunological targeting of these proteins during NTHI‐induced experimental OM in a chinchilla model caused rapid clearance of biofilms from the middle ear. Given the essential role of DNABII proteins in maintaining the structure of an NTHI biofilm, we investigated whether any of the other nucleoid associated proteins (NAPs) expressed by NTHI might play a similar role, thereby serving as additional target(s) for intervention. We demonstrated that although several NAPs including H‐NS, CbpA, HfQ and Dps are present within the biofilm extracellular matrix, only the DNABII family of proteins is critical for the structural integrity of the biofilms formed by NTHI. We have also demonstrated that IHF and HU are located at distinct regions within the extracellular matrix of NTHI biofilms formed in vitro, indicative of independent functions of these two proteins.
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Affiliation(s)
- Aishwarya Devaraj
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
| | - John Buzzo
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
| | - Christopher J Rocco
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
| | - Steven D Goodman
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
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Antipov SS, Tutukina MN, Preobrazhenskaya EV, Kondrashov FA, Patrushev MV, Toshchakov SV, Dominova I, Shvyreva US, Vrublevskaya VV, Morenkov OS, Sukharicheva NA, Panyukov VV, Ozoline ON. The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. PLoS One 2017; 12:e0182800. [PMID: 28800583 PMCID: PMC5553809 DOI: 10.1371/journal.pone.0182800] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/25/2017] [Indexed: 11/18/2022] Open
Abstract
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.
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Affiliation(s)
- S. S. Antipov
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Biophysics and Biotechnology, Voronezh State University, Voronezh, Russian Federation
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - M. N. Tutukina
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain
- Department of Evolutionary Genomics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - E. V. Preobrazhenskaya
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - F. A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain
- Department of Evolutionary Genomics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain
| | - M. V. Patrushev
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - S. V. Toshchakov
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - I. Dominova
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - U. S. Shvyreva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - V. V. Vrublevskaya
- Department of Cell Culture and Cell Engeneering, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - O. S. Morenkov
- Department of Cell Culture and Cell Engeneering, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - N. A. Sukharicheva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - V. V. Panyukov
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Bioinformatics, Institute of Mathematical Problems of Biology—the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - O. N. Ozoline
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
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Hingston P, Chen J, Allen K, Truelstrup Hansen L, Wang S. Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes. PLoS One 2017; 12:e0180123. [PMID: 28662112 PMCID: PMC5491136 DOI: 10.1371/journal.pone.0180123] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/11/2017] [Indexed: 11/19/2022] Open
Abstract
The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA) profiling to characterize the bacterium's cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3×) were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431) and magnitude (>1,000-fold) of differentially expressed genes (>2-fold, p<0.05) in response to cold. A core set of 22 genes was upregulated at all growth phases, including nine genes required for branched-chain fatty acid (BCFA) synthesis, the osmolyte transporter genes opuCBCD, and the internalin A and D genes. Genes suppressed at 4°C were largely associated with cobalamin (B12) biosynthesis or the production/export of cell wall components. Antisense transcription accounted for up to 1.6% of total mapped reads with higher levels (2.5×) observed at 4°C than 20°C. The greatest number of upregulated antisense transcripts at 4°C occurred in early lag phase, however, at both temperatures, antisense expression levels were highest in late stationary-phase cells. Cold-induced FA membrane changes included a 15% increase in the proportion of BCFAs and a 15% transient increase in unsaturated FAs between lag and exponential phase. These increases probably reduced the membrane phase transition temperature until optimal levels of BCFAs could be produced. Collectively, this research provides new information regarding cold-induced membrane composition changes in L. monocytogenes, the growth-phase dependency of its cold-stress regulon, and the active roles of antisense transcripts in regulating its cold stress response.
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Affiliation(s)
- Patricia Hingston
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica Chen
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Allen
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Siyun Wang
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
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Abstract
Iron is very important in many biological processes and the ferritin protein family has evolved to store iron and to maintain cellular iron homeostasis. The deletion of the coding gene for the H subunit of ferritin leads to early embryonic death in mice and mutations in the gene for the L subunits in humans has been observed in neurodegenerative diseases, such as neuroferritinopathy. Thus, understanding how ferritin works is imperative and many studies have been conducted to delineate the molecular mechanism of ferritins and bacterioferritins. In the ferritin protein family, it is clear that a catalytic center for iron oxidation, the routes for iron to reach this center and the ability to nucleate an iron core, are common requirements for all ferritins. However, there are differences in the structural and mechanistic details of iron oxidation and mineralization. Although a common mechanism has been proposed for all ferritins, this mechanism needs to be further explored. There is a mechanistic diversity related to structural variation in the ferritin protein family. It is clear that other factors appear to affect the mechanism of iron oxidation and mineralization. This review focusses on the structural features of the ferritin protein family and its role in the mechanism of iron mineralization.
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Affiliation(s)
- Alejandro Yévenes
- Departamento de Química Física, Facultad de Química, Pontificia Universidad Católica de Chile, Santiago, Chile.
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42
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Meyer AS, Grainger DC. The Escherichia coli Nucleoid in Stationary Phase. ADVANCES IN APPLIED MICROBIOLOGY 2016; 83:69-86. [PMID: 23651594 DOI: 10.1016/b978-0-12-407678-5.00002-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compaction of DNA is an essential phenomenon that affects all facets of cellular biology. Surprisingly, given the abundance and apparent simplicity of bacteria, our understanding of chromosome organization in these ancient organisms is inadequate. In this chapter we will focus on arguably the best understood aspect of DNA folding in the model bacterium Escherichia coli: the supercondensation of the chromosome that occurs during periods of starvation and stress.
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Affiliation(s)
- Anne S Meyer
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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43
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Kumar KS, Pasula RR, Lim S, Nijhuis CA. Long-Range Tunneling Processes across Ferritin-Based Junctions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1824-30. [PMID: 26708136 DOI: 10.1002/adma.201504402] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/13/2015] [Indexed: 05/23/2023]
Abstract
The mechanism of long-range charge transport across tunneling junctions with monolayers of ferritin is investigated. It is shown that the mechanism can be switched between coherent tunneling, sequential tunneling, and hopping by changing the iron content inside the ferritin. This study shows that ferritins are an interesting class of biomolecules to control charge transport.
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Affiliation(s)
| | - Rupali Reddy Pasula
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
- NTU-Northwestern Institute for Nanomedicine, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Christian A Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
- Centre for Advanced 2D Materials and Graphene Research Centre, National University of Singapore, 6 Science Drive 2, 117546, Singapore
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Sanchuki HBS, Valdameri G, Moure VR, Rodriguez JA, Pedrosa FO, Souza EM, Korolik V, Ribeiro RR, Huergo LF. Conserved histidine residues at the ferroxidase centre of the Campylobacter jejuni Dps protein are not strictly required for metal binding and oxidation. MICROBIOLOGY-SGM 2015; 162:156-163. [PMID: 26555736 DOI: 10.1099/mic.0.000210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Iron is an essential micronutrient for living organisms as it is involved in a broad variety of important biological processes. However, free iron inside the cell could be potentially toxic, generating hydroxyl radicals through the Fenton reaction. Dps (DNA-binding protein from starved cells) belongs to a subfamily of ferritins and can store iron atoms inside the dodecamer. The presence of a ferroxidase centre, composed of highly conserved residues, is a signature of this protein family. In this study, we analysed the role of two conserved histidine residues (H25 and H37) located at the ferroxidase centre of the Campylobacter jejuni Dps protein by replacing them with glycine residues. The C. jejuni H25G/H37G substituted variant showed reduced iron binding and ferroxidase activities in comparison with wt Dps, while DNA-binding activity remained unaffected. We also found that both CjDps wt and CjDps H25G/H37G were able to bind manganese atoms. These results indicate that the H25 and H37 residues at the ferroxidase centre of C. jejuni Dps are not strictly required for metal binding and oxidation.
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Affiliation(s)
- Heloisa B S Sanchuki
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Glaucio Valdameri
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Vivian R Moure
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Jorge A Rodriguez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Guadalajara, Mexico
| | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | | | - Luciano F Huergo
- Setor Litoral, UFPR, Matinhos, PR, Brazil.,Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Brazil
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45
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Yang R, Zhou Z, Sun G, Gao Y, Xu J. Ferritin, a novel vehicle for iron supplementation and food nutritional factors encapsulation. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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46
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Ma L, Li F, Fang T, Zhang J, Wang Q. Controlled Self-Assembly of Proteins into Discrete Nanoarchitectures Templated by Gold Nanoparticles via Monovalent Interfacial Engineering. ACS APPLIED MATERIALS & INTERFACES 2015; 7:11024-11031. [PMID: 25943563 DOI: 10.1021/acsami.5b02823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Designed rational assembly of proteins promises novel properties and functionalities as well as new insights into the nature of life. De novo design of artificial protein nanostructures has been achieved using protein subunits or peptides as building blocks. However, controlled assembly of protein nanostructures into higher-order discrete nanoarchitectures, rather than infinite arrays or aggregates, remains a challenge due to the complex or symmetric surface chemistry of protein nanostructures. Here we develop a facile strategy to control the hierarchical assembly of protein nanocages into discrete nanoarchitectures with gold nanoparticles (AuNPs) as scaffolds via rationally designing their interfacial interaction. The protein nanocage is monofunctionalized with a polyhistidine tag (Histag) on the external surface through a mixed assembly strategy, while AuNPs are modified with Ni(2+)-NTA chelates, so that the protein nanocage can controllably assemble onto the AuNPs via the Histag-Ni(2+) affinity. Discrete protein nanoarchitectures with tunable composition can be generated by stoichiometric control over the ratio of protein nanocage to AuNP or change of AuNP size. The methodology described here is extendable to other protein nanostructures and chemically synthesized nanomaterials, and can be borrowed by synthetic biology for biomacromolecule manipulation.
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Affiliation(s)
- Lingzhi Ma
- †Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou 215123, P. R. China
| | - Feng Li
- ‡State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44, Xiaohongshan, Wuhan 430071, P. R. China
| | - Ti Fang
- ‡State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44, Xiaohongshan, Wuhan 430071, P. R. China
| | - Jianting Zhang
- †Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou 215123, P. R. China
| | - Qiangbin Wang
- †Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou 215123, P. R. China
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Uchida M, LaFrance B, Broomell CC, Prevelige PE, Douglas T. Higher order assembly of virus-like particles (VLPs) mediated by multi-valent protein linkers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:1562-1570. [PMID: 25641768 DOI: 10.1002/smll.201402067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/14/2014] [Indexed: 06/04/2023]
Abstract
Two- and three-dimensional assembly of nanoparticles has generated significant interest because these higher order structures could exhibit collective behaviors/properties beyond those of the individual nanoparticles. Highly specific interactions between molecules, which biology exploits to regulate molecular assemblies such as DNA hybridization, often provide inspiration for the construction of higher order materials using bottom-up approaches. In this study, higher order assembly of virus-like particles (VLPs) derived from the bacteriophage P22 is demonstrated by using a small adaptor protein, Dec, which binds to symmetry specific sites on the P22 capsid. Two types of connector proteins, which have different number of P22 binding sites and different geometries (ditopic linker with liner geometry and tetratopic linker with tetrahedral geometry) have been engineered through either a point mutation of Dec or genetic fusion with another protein, respectively. Bulk assembly and layer-by-layer deposition of P22 VLPs from solution was successfully achieved using both of the engineered multi-topic linker molecules, while Dec with only a single binding site does not mediate P22 assembly. Beyond the two types of linkers developed in this study, a wide range of different connector geometries could be envisioned using a similar engineering approach. This is a powerful strategy to construct higher order assemblies of VLP based nanomaterials.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA; Department of Chemistry and Biochemistry, Montana State University, CBB103, Bozeman, MT, 59717, USA
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48
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Jutz G, van Rijn P, Santos Miranda B, Böker A. Ferritin: a versatile building block for bionanotechnology. Chem Rev 2015; 115:1653-701. [PMID: 25683244 DOI: 10.1021/cr400011b] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Günther Jutz
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Lehrstuhl für Makromolekulare Materialien und Oberflächen, RWTH Aachen University , Forckenbeckstrasse 50, D-52056 Aachen, Germany
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49
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Arenas-Salinas M, Townsend PD, Brito C, Marquez V, Marabolli V, Gonzalez-Nilo F, Matias C, Watt RK, López-Castro JD, Domínguez-Vera J, Pohl E, Yévenes A. The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family. Biochimie 2014; 106:39-47. [PMID: 25079050 DOI: 10.1016/j.biochi.2014.07.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 07/18/2014] [Indexed: 12/19/2022]
Abstract
Ferritins are ubiquitous iron-storage proteins found in all kingdoms of life. They share a common architecture made of 24 subunits of five α-helices. The recombinant Chlorobium tepidum ferritin (rCtFtn) is a structurally interesting protein since sequence alignments with other ferritins show that this protein has a significantly extended C-terminus, which possesses 12 histidine residues as well as several aspartate and glutamic acid residues that are potential metal ion binding residues. We show that the macromolecular assembly of rCtFtn exhibits a cage-like hollow shell consisting of 24 monomers that are related by 4-3-2 symmetry; similar to the assembly of other ferritins. In all ferritins of known structure the short fifth α-helix adopts an acute angle with respect to the four-helix bundle. However, the crystal structure of the rCtFtn presented here shows that this helix adopts a new conformation defining a new assembly of the 4-fold channel of rCtFtn. This conformation allows the arrangement of the C-terminal region into the inner cavity of the protein shell. Furthermore, two Fe(III) ions were found in each ferroxidase center of rCtFtn, with an average FeA-FeB distance of 3 Å; corresponding to a diferric μ-oxo/hydroxo species. This is the first ferritin crystal structure with an isolated di-iron center in an iron-storage ferritin. The crystal structure of rCtFtn and the biochemical results presented here, suggests that rCtFtn presents similar biochemical properties reported for other members of this protein family albeit with distinct structural plasticity.
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Affiliation(s)
- Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Philip D Townsend
- Department of Chemistry & School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK
| | - Christian Brito
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Valeria Marquez
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Vanessa Marabolli
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Fernando Gonzalez-Nilo
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Cata Matias
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Richard K Watt
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Juan D López-Castro
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - José Domínguez-Vera
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Ehmke Pohl
- Department of Chemistry & School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK
| | - Alejandro Yévenes
- Departamento de Química Física, Facultad de Química, Pontificia Universidad Católica de Chile, Santiago, Chile.
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50
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Structures and metal-binding properties of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center. Biomolecules 2014; 4:600-15. [PMID: 24971723 PMCID: PMC4192664 DOI: 10.3390/biom4030600] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 01/24/2023] Open
Abstract
Helicobacter pylori causes severe diseases, such as chronic gastritis, peptic ulcers, and stomach cancers. H. pylori neutrophil-activating protein (HP-NAP) is an iron storage protein that forms a dodecameric shell, promotes the adhesion of neutrophils to endothelial cells, and induces the production of reactive oxygen radicals. HP-NAP belongs to the DNA-protecting proteins under starved conditions (Dps) family, which has significant structural similarities to the dodecameric ferritin family. The crystal structures of the apo form and metal-ion bound forms, such as iron, zinc, and cadmium, of HP-NAP have been determined. This review focused on the structures and metal-binding properties of HP-NAP. These metal ions bind at the di-nuclear ferroxidase center (FOC) by different coordinating patterns. In comparison with the apo structure, metal loading causes a series of conformational changes in conserved residues among HP-NAP and Dps proteins (Trp26, Asp52, and Glu56) at the FOC. HP-NAP forms a spherical dodecamer with 23 symmetry including two kinds of pores. Metal ions have been identified around one of the pores; therefore, the negatively-charged pore is suitable for the passage of metal ions.
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