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Zhang Y, Luo J, Gui X, Zheng Y, Schaar E, Liu G, Shi J. Bioengineered nanotechnology for nucleic acid delivery. J Control Release 2023; 364:124-141. [PMID: 37879440 PMCID: PMC10838211 DOI: 10.1016/j.jconrel.2023.10.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/15/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
Nucleic acid-based therapy has emerged as a promising therapeutic approach for treating various diseases, such as genetic disorders, cancers, and viral infections. Diverse nucleic acid delivery systems have been reported, and some, including lipid nanoparticles, have exhibited clinical success. In parallel, bioengineered nucleic acid delivery nanocarriers have also gained significant attention due to their flexible functional design and excellent biocompatibility. In this review, we summarize recent advances in bioengineered nucleic acid delivery nanocarriers, focusing on exosomes, cell membrane-derived nanovesicles, protein nanocages, and virus-like particles. We highlight their unique features, advantages for nucleic acid delivery, and biomedical applications. Furthermore, we discuss the challenges that bioengineered nanocarriers face towards clinical translation and the possible avenues for their further development. This review ultimately underlines the potential of bioengineered nanotechnology for the advancement of nucleic acid therapy.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China; Center for Nanomedicine and Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Luo
- Department of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiran Gui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yating Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Eric Schaar
- Center for Nanomedicine and Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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2
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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Loiko N, Tereshkina K, Kovalenko V, Moiseenko A, Tereshkin E, Sokolova OS, Krupyanskii Y. DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation. BIOLOGY 2023; 12:853. [PMID: 37372138 DOI: 10.3390/biology12060853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5-8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA-Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA-Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.
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Affiliation(s)
- Nataliya Loiko
- Winogradsky Institute of Microbiology, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ksenia Tereshkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Kovalenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey Moiseenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Eduard Tereshkin
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yurii Krupyanskii
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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Park JH, Lee ES, Jung YJ. Functional characterization of the DNA-binding protein from starved cells (DPS) as a molecular chaperone under heat stress. Biochem Biophys Res Commun 2023; 667:180-185. [PMID: 37229826 DOI: 10.1016/j.bbrc.2023.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
The DNA-binding protein from starved cells, known as DPS, has been characterized as a crucial factor in protecting E. coli from external stresses. The DPS functions in various cellular processes, including protein-DNA binding, ferroxidase activity, compaction of chromosome and regulation of stress resistance gene expression. DPS proteins exist as oligomeric complexes; however, the specific biochemical activity of oligomeric DPS in conferring heat shock tolerance has not been fully understood. Therefore, we investigated the novel functional role of DPS under heat shock. To elucidate the functional role of DPS under heat shock conditions, we purified recombinant GST-DPS protein and demonstrated its thermostability and existence in its highly oligomeric form. Furthermore, we discovered that the hydrophobic region of GST-DPS influenced the formation of oligomers, which exhibited molecular chaperone activity, thereby preventing the aggregation of substrate proteins. Collectively, our findings highlight the novel functional role of DPS, as a molecular chaperone and may confer thermotolerance to E. coli.
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Affiliation(s)
- Joung Hun Park
- Division of Ecological Safety, National Institute of Ecology, Seocheon, Republic of Korea
| | - Eun Seon Lee
- Division of Ecological Safety, National Institute of Ecology, Seocheon, Republic of Korea
| | - Young Jun Jung
- Division of Ecological Safety, National Institute of Ecology, Seocheon, Republic of Korea.
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Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis. Int J Mol Sci 2022; 24:ijms24010469. [PMID: 36613913 PMCID: PMC9820295 DOI: 10.3390/ijms24010469] [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: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H2O2 treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.
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Oetke S, Scheidig AJ, Krupinska K. WHIRLY1 of Barley and Maize Share a PRAPP Motif Conferring Nucleoid Compaction. PLANT & CELL PHYSIOLOGY 2022; 63:234-247. [PMID: 34792609 DOI: 10.1093/pcp/pcab164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
WHIRLY1 in barley was shown to be a major architect of plastid nucleoids. Its accumulation in cells of Escherichia coli coincided with an induction of nucleoid compaction and growth retardation. While WHIRLY1 of maize had similar effects on E. coli cells, WHIRLY1 proteins of Arabidopsis and potato as well as WHIRLY2 proteins had no impact on nucleoid compaction in E. coli. By mutagenesis of HvWHIRLY1 the PRAPP motif at the N-terminus preceding the highly conserved WHIRLY domain was identified to be responsible for the nucleoid compacting activity of HvWHIRLY1 in bacteria. This motif is found in WHIRLY1 proteins of most members of the Poaceae family, but neither in the WHIRLY2 proteins of the family nor in any WHIRLY protein of eudicot species such as Arabidopsis thaliana. This finding indicates that a subset of the monocot WHIRLY1 proteins has acquired a specific function as nucleoid compacters by sequence variation in the N-terminal part preceding the conserved WHIRLY domain and that in different groups of higher plants the compaction of nucleoids is mediated by other proteins.
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Affiliation(s)
- Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of Kiel, Am Botanischen Garten 7, 24118 Kiel, Germany
| | - Axel J Scheidig
- Institute of Zoology, Christian-Albrechts-University of Kiel, Am Botanischen Garten 7, 24118 Kiel, Germany
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Am Botanischen Garten 7, 24118 Kiel, Germany
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When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nat Rev Microbiol 2021; 19:774-785. [PMID: 34183820 PMCID: PMC9191689 DOI: 10.1038/s41579-021-00583-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
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Almeida AV, Carvalho AJ, Pereira AS. Encapsulin nanocages: Protein encapsulation and iron sequestration. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Zhang Y, Li Y, Zhang J, Chen X, Zhang R, Sun G, Jiang B, Fan K, Li Z, Yan X. Nanocage-Based Capture-Detection System for the Clinical Diagnosis of Autoimmune Disease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101655. [PMID: 34028968 DOI: 10.1002/smll.202101655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/13/2021] [Indexed: 06/12/2023]
Abstract
The detection of autoantibodies is critical for diagnosis of autoimmune diseases. However, the sensitivity is often limited by the properties of the antigens and the detection systems such as enzyme-linked immunosorbent assay (ELISA). Here, employing the multidisplay ability of ferritin, a highly sensitive nanocage-based capture-detection system is designed, of which the sensitivity is 100-1000-fold higher than that of conventional ELISA methods. The capture nanocages are constructed by displaying the primary Sjögren's syndrome (pSS)-related antigenic peptides on ferritin nanocage, which present epitopes effectively and high affinity, leading to tenfold higher capture capability for autoantibodies. Human IgG Fc-binding peptides are also engineered on ferritin nanocage, which enable high binding affinity and efficient horseradish peroxidase (HRP)-labeling. Compared with commercial HRP-conjugated anti-human IgG antibody, the nanocage-based detecting probe exhibited more than tenfold increased sensitivity. Autoantibodies are then examined in 91 sera from patients with pSS, 51 from rheumatoid arthritis, 54 from systemic lupus erythematosus, and 55 from healthy individuals by using the nanocage-based ELISA. The results indicate that the nanocage-based capture-detection system is an effective detection platform and provide a novel and more sensitive method for the diagnosis of autoimmune diseases.
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Affiliation(s)
- Yanan Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingni Li
- Department of Rheumatology and Immunology, Peking University People's Hospital and Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Jianlin Zhang
- Experimental Center of Advanced Materials, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuehui Chen
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guoming Sun
- Nanjing Nanozyme Tech Co., Ltd., Nanjing, 211500, China
| | - Bing Jiang
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Peking University People's Hospital and Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
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10
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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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11
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Li H, Xia X, Tan X, Zang J, Wang Z, Ei-Seedi HR, Du M. Advancements of nature nanocage protein: preparation, identification and multiple applications of ferritins. Crit Rev Food Sci Nutr 2021; 62:7117-7128. [PMID: 33860692 DOI: 10.1080/10408398.2021.1911925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Ferritin is an important iron storage protein, which is widely existed in all forms of life. Ferritin can regulate iron homeostasis when iron ions are lacking or enriched in the body, so as to avoid iron deficiency diseases and iron poisoning. Ferritin presents a hollow nanocage, which can store ions or other small molecular substances in the cavity. Therefore, ferritin shows its potential as a functional nanomaterial that can deliver nutrients or drugs in a targeted manner to improve bioavailability. Due to the special structure, the research on ferritin has attracted more and more attention in recent years. In this paper, the structural characteristics of ferritin were introduced, and the natural purification and prokaryotic expression methods of ferritin from different sources were described. At the same time, ferritin can bind to small molecules, so that it has the activity of small molecules, to construct a new type of ferritin. As a result, ferritin plays an important role as a nutrient substance, in targeted transport, and disease monitoring, etc. In conclusion, the yield of ferritin can be improved by means of molecular biology. Meanwhile, molecular modification can be used to make ferritin have unique activity and function, which lays a foundation for subsequent research. HighlightsThe molecular and structural properties of ferritins were clearly described.Isolation and purification technologies of ferritin were compared.Characterization, functions and molecular modifications mechanism of ferritin were reviewed.The applications of ferritin in pharmaceutical and food industry were prospected.
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Affiliation(s)
- Han Li
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xiaoyu Xia
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhenyu Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Hesham R Ei-Seedi
- Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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Dubrovin EV, Dadinova LA, Petoukhov MV, Soshinskaya EY, Mozhaev AA, Klinov DV, Schäffer TE, Shtykova EV, Batishchev OV. Spatial organization of Dps and DNA-Dps complexes. J Mol Biol 2021; 433:166930. [PMID: 33713674 DOI: 10.1016/j.jmb.2021.166930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 02/04/2023]
Abstract
DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA-Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA-Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA-Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA-Dps complexes. Angle analysis has demonstrated that in DNA-Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.
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Affiliation(s)
- Evgeniy V Dubrovin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia; Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| | - Liubov A Dadinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Ekaterina Yu Soshinskaya
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Tilman E Schäffer
- University of Tübingen, Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Oleg V Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
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13
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Genetically engineered magnetic nanocages for cancer magneto-catalytic theranostics. Nat Commun 2020; 11:5421. [PMID: 33110072 PMCID: PMC7591490 DOI: 10.1038/s41467-020-19061-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
The clinical applications of magnetic hyperthermia therapy (MHT) have been largely hindered by the poor magnetic-to-thermal conversion efficiency of MHT agents. Herein, we develop a facile and efficient strategy for engineering encapsulin-produced magnetic iron oxide nanocomposites (eMIONs) via a green biomineralization procedure. We demonstrate that eMIONs have excellent magnetic saturation and remnant magnetization properties, featuring superior magnetic-to-thermal conversion efficiency with an ultrahigh specific absorption rate of 2390 W/g to overcome the critical issues of MHT. We also show that eMIONs act as a nanozyme and have enhanced catalase-like activity in the presence of an alternative magnetic field, leading to tumor angiogenesis inhibition with a corresponding sharp decrease in the expression of HIF-1α. The inherent excellent magnetic-heat capability, coupled with catalysis-triggered tumor suppression, allows eMIONs to provide an MRI-guided magneto-catalytic combination therapy, which may open up a new avenue for bench-to-bed translational research of MHT. The clinical application of magnetic hyperthermia therapy (MHT) is limited by the poor magnetic-to-thermal conversion efficiency of MHT agents. Here, the authors develop encapsulin-produced magnetic iron oxide nanocomposites (eMIONs) with excellent magnetic-heat capability and catalysis-triggered tumor suppression ability to overcome the critical issues of MHT.
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14
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Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells. PLoS One 2020; 15:e0231562. [PMID: 33006967 PMCID: PMC7531825 DOI: 10.1371/journal.pone.0231562] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022] Open
Abstract
One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of the Dps protein is tightly bound to nucleoid DNA. The dps-null cells contained only one type of condensed DNA structure, liquid crystalline, thus, differing from those with Dps. The results obtained here shed some light on the phenomenon of DNA condensation in dormant prokaryotic cells and on the general problem of developing a response to stress. We demonstrated that the population of dormant cells is structurally heterogeneous, allowing them to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.
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15
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Zhou J, Zhou J, Wu ZQ, Goyal H, Xu HG. A novel prognostic model for adult patients with Hemophagocytic Lymphohistiocytosis. Orphanet J Rare Dis 2020; 15:215. [PMID: 32819431 PMCID: PMC7439554 DOI: 10.1186/s13023-020-01496-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Hemophagocytic Lymphohistiocytosis (HLH) is a type of rare disease with low survival rate. We aimed to develop a model to evaluate the six-month prognosis in adult HLH patients. The data at discharge (will be called as post-treatment) for newly diagnosed adult HLH patients was collected and independent prognostic variables were selected for inclusion in the model. RESULTS Three laboratory markers were confirmed to be the independent risk factors (ferritin: hazard ratio (HR) 0.101, 95% confidence interval (CI) 0.036-0.282, P<0.001; platelets: HR 4.799, 95% CI 1.884-12.223, P = 0.001; alanine aminotransferase (ALT): HR 0.423, 95% CI 0.180-0.997, P = 0.049). These were included in the final clinical prediction model. Receiver operating characteristic (ROC) curves disclosed that this model had a better discrimination (area under the curve (AUC) = 0.842, 95% CI 0.773-0.910, P < 0.001) than each of them alone and the calibration curves aligned completely with the model predictions and actual observations. Kaplan-Meier curves revealed a significant difference in the overall survival (OS) in patients stratified by the model with higher values associated with a better OS. CONCLUSION These results point out that serum ferritin, platelets and ALT levels are independent elements of OS in adult patients with HLH, and that the proposed model have a better prognostic value than any of these markers alone.
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Affiliation(s)
- Jun Zhou
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Zhou
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi-Qi Wu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hemant Goyal
- The Wright Center of Graduate Medical Education, Scranton, USA
| | - Hua-Guo Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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16
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Pedone E, Fiorentino G, Bartolucci S, Limauro D. Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea. Antioxidants (Basel) 2020; 9:antiox9080703. [PMID: 32756530 PMCID: PMC7465337 DOI: 10.3390/antiox9080703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2-.) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
- Correspondence:
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17
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Smith MJ, Fowler M, Naftalin RJ, Siow RCM. UVA irradiation increases ferrous iron release from human skin fibroblast and endothelial cell ferritin: Consequences for cell senescence and aging. Free Radic Biol Med 2020; 155:49-57. [PMID: 32387586 DOI: 10.1016/j.freeradbiomed.2020.04.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022]
Abstract
UVA irradiation of human dermal fibroblasts and endothelial cells induces an immediate transient increase in cytosolic Fe(II), as monitored by the fluorescence Fe(II) reporters, FeRhonox1 in cytosol and MitoFerroGreen in mitochondria. Both superoxide dismutase (SOD) inhibition by tetrathiomolybdate (ATM) and catalase inhibition by 3-amino-1, 2, 4-triazole (ATZ) increase and prolong the cytosolic Fe(II) signal after UVA irradiation. SOD inhibition with ATM also increases mitochondrial Fe(II). Thus, mitochondria do not source the UV-dependent increase in cytosolic Fe(II), but instead reflect and amplify raised cytosolic labile Fe(II) concentration. Hence control of cytosolic ferritin iron release is key to preventing UVA-induced inflammation. UVA irradiation also increases dermal endothelial cell H2O2, as monitored by the adenovirus vector Hyper-DAAO-NES(HyPer). These UVA-dependent changes in intracellular Fe(II) and H2O2 are mirrored by increases in cell superoxide, monitored with the luminescence probe L-012. UV-dependent increases in cytosolic Fe(II), H2O2 and L-012 chemiluminescence are prevented by ZnCl2 (10 μM), an effective inhibitor of Fe(II) transport via ferritin's 3-fold channels. Quercetin (10 μM), a potent membrane permeable Fe(II) chelator, abolishes the cytosolic UVA-dependent FeRhonox1, Fe(II) and HyPer, H2O2 and increase in MitoFerroGreen Fe(II) signals. The time course of the quercetin-dependent decrease in endothelial H2O2 correlates with the decrease in FeRhox1 signal and both signals are fully suppressed by preloading cells with ZnCl2. These results confirm that antioxidant enzyme activity is the key factor in controlling intracellular iron levels, and hence maintenance of cell antioxidant capacity is vitally important in prevention of skin aging and inflammation initiated by labile iron and UVA.
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Affiliation(s)
- Matthew J Smith
- King's BHF Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, Faculty of Life Sciences & Medicine, 150 Stamford Street, London, SE1 9NH, UK
| | - Mark Fowler
- Unilever Colworth Science Park, Bedfordshire, UK
| | - Richard J Naftalin
- King's BHF Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, Faculty of Life Sciences & Medicine, 150 Stamford Street, London, SE1 9NH, UK.
| | - Richard C M Siow
- King's BHF Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, Faculty of Life Sciences & Medicine, 150 Stamford Street, London, SE1 9NH, UK
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18
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Uchida M, Maier B, Waghwani HK, Selivanovitch E, Pay SL, Avera J, Yun EJ, Sandoval RM, Molitoris BA, Zollman A, Douglas T, Hato T. The archaeal Dps nanocage targets kidney proximal tubules via glomerular filtration. J Clin Invest 2020; 129:3941-3951. [PMID: 31424427 DOI: 10.1172/jci127511] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
Nature exploits cage-like proteins for a variety of biological purposes, from molecular packaging and cargo delivery to catalysis. These cage-like proteins are of immense importance in nanomedicine due to their propensity to self-assemble from simple identical building blocks to highly ordered architecture and the design flexibility afforded by protein engineering. However, delivery of protein nanocages to the renal tubules remains a major challenge because of the glomerular filtration barrier, which effectively excludes conventional size nanocages. Here, we show that DNA-binding protein from starved cells (Dps) - the extremely small archaeal antioxidant nanocage - is able to cross the glomerular filtration barrier and is endocytosed by the renal proximal tubules. Using a model of endotoxemia, we present an example of the way in which proximal tubule-selective Dps nanocages can limit the degree of endotoxin-induced kidney injury. This was accomplished by amplifying the endogenous antioxidant property of Dps with addition of a dinuclear manganese cluster. Dps is the first-in-class protein cage nanoparticle that can be targeted to renal proximal tubules through glomerular filtration. In addition to its therapeutic potential, chemical and genetic engineering of Dps will offer a nanoplatform to advance our understanding of the physiology and pathophysiology of glomerular filtration and tubular endocytosis.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Bernhard Maier
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
| | | | | | - S Louise Pay
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
| | - John Avera
- Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA
| | - EJun Yun
- Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Ruben M Sandoval
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
| | - Bruce A Molitoris
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
| | - Amy Zollman
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Takashi Hato
- Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA
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19
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Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans. Microorganisms 2020; 8:microorganisms8030451. [PMID: 32210096 PMCID: PMC7143949 DOI: 10.3390/microorganisms8030451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans.
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20
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Pacheco MR, Jacinto JP, Penas D, Calmeiro T, Almeida AV, Colaço M, Fortunato E, Jones NC, Hoffmann SV, Pereira MMA, Tavares P, Pereira AS. Supramolecular protein polymers using mini-ferritin Dps as the building block. Org Biomol Chem 2020; 18:9300-9307. [DOI: 10.1039/d0ob01702g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Production of long polymer chains with iron oxidation and storage activity, built from protein nanocages using a click chemistry approach.
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21
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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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22
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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: 22] [Impact Index Per Article: 4.4] [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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23
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Listeria innocua Dps as a nanoplatform for bioluminescence based photodynamic therapy utilizing Gaussia princeps luciferase and zinc protoporphyrin IX. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 20:102005. [PMID: 31048084 PMCID: PMC6712498 DOI: 10.1016/j.nano.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022]
Abstract
Listeria innocua DNA binding protein from starved cells (LiDps) belongs to the ferritin family and provides a promising self-assembling spherical 12-mer protein scaffold for the generation of functional nanomaterials. We report the creation of a Gaussia princeps luciferase (Gluc)-LiDps fusion protein, with chemical conjugation of Zinc (II)-protoporphyrin IX (ZnPP) to lysine residues on the fusion protein (giving Gluc-LiDps-ZnPP). The Gluc-LiDps-ZnPP conjugate is shown to generate reactive oxygen species (ROS) via Bioluminescence Resonance Energy Transfer (BRET) between the Gluc (470-490 nm) and ZnPP. In vitro, Gluc-LiDps-ZnPP is efficiently taken up by tumorigenic cells (SKBR3 and MDA-MB-231 breast cancer cells). In the presence of coelenterazine, this construct inhibits the proliferation of SKBR3 due to elevated ROS levels. Following exposure to Gluc-LiDps-ZnPP, migration of surviving SKBR3 cells is significantly suppressed. These results demonstrate the potential of the Gluc-LiDps-ZnPP conjugate as a platform for future development of an anticancer photodynamic therapy agent.
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24
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Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME JOURNAL 2019; 13:2150-2161. [PMID: 31024152 DOI: 10.1038/s41396-019-0418-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 11/09/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635-560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood-Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
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Affiliation(s)
- Minglei Ren
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Xiaoyuan Feng
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | | | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.,National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA
| | - Miguel M Fonseca
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - David Posada
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | | | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China.
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25
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Monti DM, Ferraro G, Merlino A. Ferritin-based anticancer metallodrug delivery: Crystallographic, analytical and cytotoxicity studies. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 20:101997. [PMID: 31028889 DOI: 10.1016/j.nano.2019.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/28/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022]
Abstract
The encapsulation of anticancer metal-based drugs within a protein nanocage represents a valuable strategy to improve the efficacy and selectivity of these compounds towards cancer cells. The preparation, characterization of the in vitro cytotoxicity and X-ray structures of several ferritin-metallodrug nanocomposites (mainly containing platinum-, ruthenium- and gold-based anticancer agents) are here reviewed. The molecular mechanisms of action of these Ft-metallodrug adducts are discussed and future directions in the field are outlined.
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Affiliation(s)
- Dara Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
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26
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Ashraf N, Ahmad F, Da-Wei L, Zhou RB, Feng-Li H, Yin DC. Iron/iron oxide nanoparticles: advances in microbial fabrication, mechanism study, biomedical, and environmental applications. Crit Rev Microbiol 2019; 45:278-300. [PMID: 30985230 DOI: 10.1080/1040841x.2019.1593101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbially synthesized iron oxide nanoparticles (FeONPs) hold great potential for biomedical, clinical, and environmental applications owing to their several unique features. Biomineralization, a process that exists in almost every living organism playing a significant role in the fabrication of FeONPs through the involvement of 5-100 nm sized protein compartments such as dodecameric (Dps), ferritin, and encapsulin with their diameters 9, 12, and ∼32 nm, respectively. This contribution provides a detailed overview of the green synthesis of FeONPs by microbes and their applications in biomedical and environmental fields. The first part describes our understanding in the biological fabrication of zero-valent FeONPs with special emphasis on ferroxidase (FO) mediated series of steps involving in the translocation, oxidation, nucleation, and storage of iron in Dps, ferritin, and encapsulin protein nano-compartments. Secondly, this review elaborates the significance of biologically synthesized FeONPs in biomedical science for the detection, treatment, and prevention of various diseases. Thirdly, we tried to provide the recent advances of using FeONPs in the environmental process, e.g. detection, degradation, remediation and treatment of toxic pesticides, dyes, metals, and wastewater.
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Affiliation(s)
- Noreen Ashraf
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
| | - Fiaz Ahmad
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
| | - Li Da-Wei
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
| | - Ren-Bin Zhou
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
| | - He Feng-Li
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
| | - Da-Chuan Yin
- a Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University , Xi'an , PR China
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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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28
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Spanka DT, Konzer A, Edelmann D, Berghoff BA. High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells. Front Microbiol 2019; 10:378. [PMID: 30894840 PMCID: PMC6414554 DOI: 10.3389/fmicb.2019.00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial populations produce phenotypic variants called persisters to survive harmful conditions. Persisters are highly tolerant to antibiotics and repopulate environments after the stress has vanished. In order to resume growth, persisters have to recover from the persistent state, but the processes behind recovery remain mostly elusive. Deciphering these processes is an essential step toward understanding the persister phenomenon in its entirety. High-throughput proteomics by mass spectrometry is a valuable tool to assess persister physiology during any stage of the persister life cycle, and is expected to considerably contribute to our understanding of the recovery process. In the present study, an Escherichia coli strain, that overproduces the membrane-depolarizing toxin TisB, was established as a model for persistence by the use of high-throughput proteomics. Labeling of TisB persisters with stable isotope-containing amino acids (pulsed-SILAC) revealed an active translational response to ampicillin, including several RpoS-dependent proteins. Subsequent investigation of the persister proteome during postantibiotic recovery by label-free quantitative proteomics identified proteins with importance to the recovery process. Among them, AhpF, a component of alkyl hydroperoxide reductase, and the outer membrane porin OmpF were found to affect the persistence time of TisB persisters. Assessing the role of AhpF and OmpF in TisB-independent persisters demonstrated that the importance of a particular protein for the recovery process strongly depends on the physiological condition of a persister cell. Our study provides important insights into persister physiology and the processes behind recovery of depolarized cells.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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Penas D, Pereira AS, Tavares P. Direct Evidence for Ferrous Ion Oxidation and Incorporation in the Absence of Oxidants by Dps from Marinobacter hydrocarbonoclasticus. Angew Chem Int Ed Engl 2019; 58:1013-1018. [PMID: 30481405 DOI: 10.1002/anie.201809584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/15/2018] [Indexed: 11/09/2022]
Abstract
Dps proteins (DNA-binding protein from starved cells) are hollow-sphere-shaped, dodecameric enzymes found in bacteria and archaeal species. They can oxidize ferrous iron in a controlled manner using hydrogen peroxide or molecular oxygen as co-substrate, and most of them confer physical protection through DNA binding. Oxidized iron is stored, as a mineral core, in a central cavity. Direct evidence is now provided that, furthermore, Dps proteins containing small mineral cores can oxidize and mineralize toxic ferrous ions in anaerobic conditions and in the absence of any additional aqueous oxidant co-substrate. Dps proteins containing cores of 24 irons per dodecamer can oxidize about 5 ferrous irons per dodecamer, with that number approximately doubling for protein particles containing in average 96 irons per protein. This additional activity carries importance as it can be a detoxification mechanism present during anaerobic or oxygen-limited growth conditions.
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Affiliation(s)
- Daniela Penas
- Molecular Biophysics Lab., UCIBIO/Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Alice S Pereira
- Molecular Biophysics Lab., UCIBIO/Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Pedro Tavares
- Molecular Biophysics Lab., UCIBIO/Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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31
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Penas D, Pereira AS, Tavares P. Direct Evidence for Ferrous Ion Oxidation and Incorporation in the Absence of Oxidants by Dps from Marinobacter hydrocarbonoclasticus. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniela Penas
- Molecular Biophysics Lab.UCIBIO/RequimteDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade Nova de Lisboa 2829-516 Caparica Portugal
| | - Alice S. Pereira
- Molecular Biophysics Lab.UCIBIO/RequimteDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade Nova de Lisboa 2829-516 Caparica Portugal
| | - Pedro Tavares
- Molecular Biophysics Lab.UCIBIO/RequimteDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade Nova de Lisboa 2829-516 Caparica Portugal
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Reductive Mobilization of Iron from Intact Ferritin: Mechanisms and Physiological Implication. Pharmaceuticals (Basel) 2018; 11:ph11040120. [PMID: 30400623 PMCID: PMC6315955 DOI: 10.3390/ph11040120] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/18/2023] Open
Abstract
Ferritins are highly conserved supramolecular protein nanostructures composed of two different subunit types, H (heavy) and L (light). The two subunits co-assemble into a 24-subunit heteropolymer, with tissue specific distributions, to form shell-like protein structures within which thousands of iron atoms are stored as a soluble inorganic ferric iron core. In-vitro (or in cell free systems), the mechanisms of iron(II) oxidation and formation of the mineral core have been extensively investigated, although it is still unclear how iron is loaded into the protein in-vivo. In contrast, there is a wide spread belief that the major pathway of iron mobilization from ferritin involves a lysosomal proteolytic degradation of ferritin, and the dissolution of the iron mineral core. However, it is still unclear whether other auxiliary iron mobilization mechanisms, involving physiological reducing agents and/or cellular reductases, contribute to the release of iron from ferritin. In vitro iron mobilization from ferritin can be achieved using different reducing agents, capable of easily reducing the ferritin iron core, to produce soluble ferrous ions that are subsequently chelated by strong iron(II)-chelating agents. Here, we review our current understanding of iron mobilization from ferritin by various reducing agents, and report on recent results from our laboratory, in support of a mechanism that involves a one-electron transfer through the protein shell to the iron mineral core. The physiological significance of the iron reductive mobilization from ferritin by the non-enzymatic FMN/NAD(P)H system is also discussed.
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Krupyanskii YF, Loiko NG, Sinitsyn DO, Tereshkina KB, Tereshkin EV, Frolov IA, Chulichkov AL, Bokareva DA, Mysyakina IS, Nikolaev YA, El’-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN. Biocrystallization in Bacterial and Fungal Cells and Spores. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518040144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Hagen WR, Hagedoorn PL, Honarmand Ebrahimi K. The workings of ferritin: a crossroad of opinions. Metallomics 2018; 9:595-605. [PMID: 28573266 DOI: 10.1039/c7mt00124j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biochemistry of the essential element iron is complicated by radical chemistry associated with Fe(ii) ions and by the extremely low solubility of the Fe(iii) ion in near-neutral water. To mitigate these problems cells from all domains of life synthesize the protein ferritin to take up and oxidize Fe(ii) and to form a soluble storage of Fe(iii) from which iron can be made available for physiology. A long history of studies on ferritin has not yet resulted in a generally accepted mechanism of action of this enzyme. In fact strong disagreement exists between extant ideas on several key steps in the workings of ferritin. The scope of this review is to explain the experimental background of these controversies and to indicate directions towards their possible resolution.
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Affiliation(s)
- Wilfred R Hagen
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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35
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Loiko NG, Suzina NE, Soina VS, Smirnova TA, Zubasheva MV, Azizbekyan RR, Sinitsyn DO, Tereshkina KB, Nikolaev YA, Krupyanskii YF, El’-Registan GI. Biocrystalline structures in the nucleoids of the stationary and dormant prokaryotic cells. Microbiology (Reading) 2017. [DOI: 10.1134/s002626171706011x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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36
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Sinitsyn DO, Loiko NG, Gularyan SK, Stepanov AS, Tereshkina KB, Chulichkov AL, Nikolaev AA, El-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN, Krupyanskii YF. Biocrystallization of bacterial nucleoid under stress. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117050128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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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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Voet ARD, Tame JRH. Protein-templated synthesis of metal-based nanomaterials. Curr Opin Biotechnol 2017; 46:14-19. [DOI: 10.1016/j.copbio.2016.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/24/2016] [Indexed: 01/07/2023]
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SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions. J Mol Biol 2017; 429:667-687. [PMID: 28088481 DOI: 10.1016/j.jmb.2017.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 02/06/2023]
Abstract
The radiation-resistant bacterium Deinococcus radiodurans contains two DNA-binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction and manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterised N-terminal extensions. In the case of DrDps1, these extensions have been proposed to be involved in DNA interactions, while in DrDps2, their function has yet to be established. The reported data reveal the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps. The low-resolution small angle X-ray scattering (SAXS) results show that the N-terminal extensions protrude from the spherical shell of both proteins. The SAXS envelope of a truncated form of DrDps1 without the N-terminal extensions appears as a dodecameric sphere, contrasting strongly with the protrusions observed in the full-length models. The effect of iron incorporation into DrDps2 was investigated by static and stopped-flow SAXS measurements, revealing dynamic structural changes upon iron binding and core formation, as reflected by a quick alteration of its radius of gyration. The truncated and full-length versions of DrDps were also compared on the basis of their interaction with DNA to analyse functional roles of the N-terminal extensions. DrDps1 N-terminal protrusions appear to be directly involved with DNA, whilst those from DrDps2 are indirectly associated with DNA binding. Furthermore, detection of DrDps2 in the D. radiodurans membrane fraction suggests that the N-terminus of the protein interacts with the membrane.
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40
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Turishchev SY, Antipov SS, Novolokina NV, Chuvenkova OA, Melekhov VV, Ovsyannikov R, Senkovskii BV, Timchenko AA, Ozoline ON, Domashevskaya EP. A soft X-ray synchrotron study of the charge state of iron ions in the ferrihydrite core of the ferritin Dps protein in Escherichia coli. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916050286] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Arnold AR, Grodick MA, Barton JK. DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016; 23:183-197. [PMID: 26933744 DOI: 10.1016/j.chembiol.2015.11.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 11/30/2022]
Abstract
The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.
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Affiliation(s)
- Anna R Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Zeth K, Hoiczyk E, Okuda M. Ferroxidase-Mediated Iron Oxide Biomineralization: Novel Pathways to Multifunctional Nanoparticles. Trends Biochem Sci 2016; 41:190-203. [DOI: 10.1016/j.tibs.2015.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 11/29/2022]
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Abstract
Iron, a major protein cofactor, is essential for most organisms. Despite the well-known effects of O2 on the oxidation state and solubility of iron, the impact of O2 on cellular iron homeostasis is not well understood. Here we report that in Escherichia coli K-12, the lack of O2 dramatically changes expression of genes controlled by the global regulators of iron homeostasis, the transcription factor Fur and the small RNA RyhB. Using chromatin immunoprecipitation sequencing (ChIP-seq), we found anaerobic conditions promote Fur binding to more locations across the genome. However, by expression profiling, we discovered that the major effect of anaerobiosis was to increase the magnitude of Fur regulation, leading to increased expression of iron storage proteins and decreased expression of most iron uptake pathways and several Mn-binding proteins. This change in the pattern of gene expression also correlated with an unanticipated decrease in Mn in anaerobic cells. Changes in the genes posttranscriptionally regulated by RyhB under aerobic and anaerobic conditions could be attributed to O2-dependent changes in transcription of the target genes: aerobic RyhB targets were enriched in iron-containing proteins associated with aerobic energy metabolism, whereas anaerobic RyhB targets were enriched in iron-containing anaerobic respiratory functions. Overall, these studies showed that anaerobiosis has a larger impact on iron homeostasis than previously anticipated, both by expanding the number of direct Fur target genes and the magnitude of their regulation and by altering the expression of genes predicted to be posttranscriptionally regulated by the small RNA RyhB under iron-limiting conditions. Microbes and host cells engage in an “arms race” for iron, an essential nutrient that is often scarce in the environment. Studies of iron homeostasis have been key to understanding the control of iron acquisition and the downstream pathways that enable microbes to compete for this valuable resource. Here we report that O2 availability affects the gene expression programs of two Escherichia coli master regulators that function in iron homeostasis: the transcription factor Fur and the small RNA regulator RyhB. Fur appeared to be more active under anaerobic conditions, suggesting a change in the set point for iron homeostasis. RyhB preferentially targeted iron-containing proteins of respiration-linked pathways, which are differentially expressed under aerobic and anaerobic conditions. Such findings may be relevant to the success of bacteria within their hosts since zones of reduced O2 may actually reduce bacterial iron demands, making it easier to win the arms race for iron.
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Arutyunov D, Szymanski CM. A novel DNA-binding protein from Campylobacter jejuni bacteriophage NCTC12673. FEMS Microbiol Lett 2015; 362:fnv160. [PMID: 26363017 DOI: 10.1093/femsle/fnv160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 12/21/2022] Open
Abstract
We previously suggested that the double-stranded genomic DNA of Campylobacter jejuni bacteriophage NCTC12673 was complexed with proteins. Mass spectrometry of peptides obtained from tryptic digests of purified phage DNA indicated that phage protein Gp001 co-purified with the DNA. Gp001 is an acidic protein that lacks any obvious homology or conserved domains found in known DNA-binding proteins. The DNA-binding ability of recombinant Gp001 was examined using an electrophoretic mobility shift assay. Slow DNA-Gp001 complex formation was observed at pH 5.5, but not at neutral or basic pH. This nucleoprotein complex had difficulty entering agarose gels used in the assay while proteinase K pretreatment released the DNA from the complex. No mobility shift was observed when the DNA was immediately subjected to electrophoresis after mixing with Gp001, even if both components were separately pre-incubated at pH 5.5. The complexed DNA was unable to transform chemically competent Escherichia coli cells and was less susceptible to degradation by nucleases. The formation of Gp001-DNA complexes at low pH may provide a mechanism for maintaining DNA integrity while the phage pursues its host through the gastrointestinal tract. Also, this feature can potentially be used to improve DNA delivery protocols applied in gene therapy.
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Affiliation(s)
- Denis Arutyunov
- Department of Biological Sciences and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Christine M Szymanski
- Department of Biological Sciences and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
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Roles of RpoS in Yersinia pseudotuberculosis stress survival, motility, biofilm formation and type VI secretion system expression. J Microbiol 2015; 53:633-42. [DOI: 10.1007/s12275-015-0099-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 07/16/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022]
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Melekhov VV, Shvyreva US, Timchenko AA, Tutukina MN, Preobrazhenskaya EV, Burkova DV, Artiukhov VG, Ozoline ON, Antipov SS. Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy. PLoS One 2015; 10:e0126504. [PMID: 25978038 PMCID: PMC4433220 DOI: 10.1371/journal.pone.0126504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/02/2015] [Indexed: 11/18/2022] Open
Abstract
Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.
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Affiliation(s)
- Vladislav V. Melekhov
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Uliana S. Shvyreva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Alexander A. Timchenko
- Department of Physics of Nucleoproteids, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Maria N. Tutukina
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | | | - Diana V. Burkova
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
| | - Valiriy G. Artiukhov
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
| | - Olga N. Ozoline
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
| | - Sergey S. Antipov
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
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Sanchuki HBS, Valdameri G, Moure VR, Oliveira MA, Pedrosa FO, Souza EM, Korolik V, Huergo LF. Purification of the Campylobacter jejuni Dps protein assisted by its high melting temperature. Protein Expr Purif 2015; 111:105-10. [PMID: 25707373 DOI: 10.1016/j.pep.2014.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/17/2022]
Abstract
Dps proteins (DNA binding protein from starved cell) form a distinct group within the ferritin superfamily. All Dps members are composed of 12 identical subunits that assemble into a conserved spherical protein shell. Dps oxidize Fe(2+) in a conserved ferroxidase center located at the interface between monomers, the product of the reaction Fe(3+), is then stored inside the protein shell in the form of non-reactive insoluble Fe2O3. The Campylobacter jejuni Dps (CjDps) has been reported to play a plethora of functions, such as DNA binding and protection, iron storage, survival in response to hydrogen peroxide and sulfatide binding. CjDps is also important during biofilm formation and caecal colonization in poultry. In order to facilitate in vitro characterisation of CjDps, it is important to have a simple and reproducible protocol for protein purification. Here we report an observation that CjDps has an unusual high melting temperature. We exploited this property for protein purification by introducing a thermal treatment step which allowed achieving homogeneity by using only two chromatographic steps. Gel filtration chromatography, circular dichroism, mass spectrometry, DNA-binding and iron oxidation analysis confirmed that the CjDps structure and function were unaffected.
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Affiliation(s)
- Heloisa B S Sanchuki
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Glaucio Valdameri
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Vivian R Moure
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Marco A Oliveira
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Fábio O Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Emanuel M Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, Australia
| | - Luciano F Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil.
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He D, Marles-Wright J. Ferritin family proteins and their use in bionanotechnology. N Biotechnol 2015; 32:651-7. [PMID: 25573765 PMCID: PMC4571993 DOI: 10.1016/j.nbt.2014.12.006] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/05/2014] [Accepted: 12/16/2014] [Indexed: 01/20/2023]
Abstract
We discuss bionanotechnology applications of ferritin family proteins. Ferritin family proteins are able to mineralise a range of metal ions. The ferritin and DPS cages can be used in semi-conductor patterning. We explore a commercial application of ferritin as a phosphate removal system for water purification. We examine how the superparamagnetic properties of iron-loaded ferritin can be used in medical imaging.
Ferritin family proteins are found in all kingdoms of life and act to store iron within a protein cage and to protect the cell from oxidative damage caused by the Fenton reaction. The structural and biochemical features of the ferritins have been widely exploited in bionanotechnology applications: from the production of metal nanoparticles; as templates for semi-conductor production; and as scaffolds for vaccine design and drug delivery. In this review we first discuss the structural properties of the main ferritin family proteins, and describe how their organisation specifies their functions. Second, we describe materials science applications of ferritins that rely on their ability to sequester metal within their cavities. Finally, we explore the use of ferritin as a container for drug delivery and as a scaffold for the production of vaccines.
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Affiliation(s)
- Didi He
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
| | - Jon Marles-Wright
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom.
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Hitchings MD, Townsend P, Pohl E, Facey PD, Jones DH, Dyson PJ, Del Sol R. A tale of tails: deciphering the contribution of terminal tails to the biochemical properties of two Dps proteins from Streptomyces coelicolor. Cell Mol Life Sci 2014; 71:4911-26. [PMID: 24915944 PMCID: PMC11113173 DOI: 10.1007/s00018-014-1658-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/07/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
Dps proteins are members of an extensive family of proteins that oxidise and deposit iron in the form of ferric oxide, and are also able to bind DNA. Ferroxidation centres are formed at the interface of anti-parallel dimers, which further assemble into dodecameric nanocages with a hollow core where ferric oxide is deposited. Streptomyces coelicolor encodes three Dps-like proteins (DpsA, B and C). Despite sharing the conserved four-helix bundle organisation observed in members of the Dps family, they display significant differences in the length of terminal extensions, or tails. DpsA possess both N- and C-terminal tails of different lengths, and their removal affects quaternary structure assembly to varying degrees. DpsC quaternary structure, on the other hand, is heavily dependent on its N-terminal tail as its removal abolishes correct protein folding. Analysis of the crystal structure of dodecamers from both proteins revealed remarkable differences in the position of tails and interface surface area; and provides insight to explain the differences in biochemical behaviour observed while comparing DpsA and DpsC.
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Affiliation(s)
| | - Philip Townsend
- Department of Chemistry, School of Biological and Biomedical Sciences, University Science Laboratories, Durham University, South Road, Durham, DH1 3LE UK
| | - Ehmke Pohl
- Department of Chemistry, School of Biological and Biomedical Sciences, University Science Laboratories, Durham University, South Road, Durham, DH1 3LE UK
| | - Paul D. Facey
- College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - D. Hugh Jones
- College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Paul J. Dyson
- College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Ricardo Del Sol
- College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
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50
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Theil EC. IRE mRNA riboregulators use metabolic iron (Fe(2+)) to control mRNA activity and iron chemistry in animals. Metallomics 2014; 7:15-24. [PMID: 25209685 DOI: 10.1039/c4mt00136b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A family of noncoding RNAs bind Fe(2+) to increase protein synthesis. The structures occur in messenger RNAs encoding animal proteins for iron metabolism. Each mRNA regulatory sequence, ∼30 ribonucleotides long, is called an IRE (Iron Responsive Element), and folds into a bent, A-RNA helix with a terminal loop. Riboregulatory RNAs, like t-RNAs, r-RNAs micro-RNAs, etc. contrast with DNA, since single-stranded RNA can fold into a variety of complex, three-dimensional structures. IRE-RNAs bind two types of proteins: (1) IRPs which are protein repressors, sequence-related to mitochondrial aconitases. (2) eIF-4F, which bind ribosomes and enhances general protein biosynthesis. The competition between IRP and eIF-4F binding to IRE-RNA is controlled by Fe(2+)-induced changes in the IRE-RNA conformation. Mn(2+), which also binds to IRE-RNA in solution, is a convenient experimental proxy for air-sensitive Fe(2+) studies of in vitro protein biosynthesis and protein binding. However, only Fe(2+) has physiological effects on protein biosynthesis directed by IRE-mRNAs. The structures of the IRE-RNA riboregulators is known indirectly from effects of base substitutions on function, from solution NMR of the free RNA, and of X-ray crystallography of the IRE-RNA-IRP repressor complex. However, the inability to date, to crystallize the free IRE-RNA, and the dissociation of the IRE-RNA-IRP complex when metal binds, have hampered direct identification and characterization of the RNA-metal binding sites. The high conservation of the primary sequence in IRE-mRNA control elements has facilitated their identification and analysis of metal-assisted riboregulator function. Expansion of RNA search analyses beyond primary will likely reveal other, metal-dependent families of mRNA riboregulators.
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Affiliation(s)
- Elizabeth C Theil
- The Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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