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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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52
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Kamnev AA, Tugarova AV. Bioanalytical applications of Mössbauer spectroscopy. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
Data on the applications of Mössbauer spectroscopy in the transmission (mainly on 57Fe nuclei) and emission (on 57Co nuclei) variants for analytical studies at the molecular level of metal-containing components in a wide range of biological objects (from biocomplexes and biomacromolecules to supramolecular structures, cells, tissues and organisms) and of objects that are participants or products of biological processes, published in the last 15 years are discussed and systematized. The prospects of the technique in its biological applications, including the developing fields (emission variant, use of synchrotron radiation), are formulated.
The bibliography includes 248 references.
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53
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Bradley JM, Fair J, Hemmings AM, Le Brun NE. Key carboxylate residues for iron transit through the prokaryotic ferritin SynFtn. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34825885 PMCID: PMC8743623 DOI: 10.1099/mic.0.001105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ferritins are proteins forming 24meric rhombic dodecahedral cages that play a key role in iron storage and detoxification in all cell types. Their function requires the transport of Fe2+ from the exterior of the protein to buried di-iron catalytic sites, known as ferroxidase centres, where Fe2+ is oxidized to form Fe3+-oxo precursors of the ferritin mineral core. The route of iron transit through animal ferritins is well understood: the Fe2+ substrate enters the protein via channels at the threefold axes and conserved carboxylates on the inner surface of the protein cage have been shown to contribute to transient binding sites that guide Fe2+ to the ferroxidase centres. The routes of iron transit through prokaryotic ferritins are less well studied but for some, at least, there is evidence that channels at the twofold axes are the major route for Fe2+ uptake. SynFtn, isolated from the cyanobacterium Synechococcus CC9311, is an atypical prokaryotic ferritin that was recently shown to take up Fe2+ via its threefold channels. However, the transfer site carboxylate residues conserved in animal ferritins are absent, meaning that the route taken from the site of iron entry into SynFtn to the catalytic centre is yet to be defined. Here, we report the use of a combination of site-directed mutagenesis, absorbance-monitored activity assays and protein crystallography to probe the effect of substitution of two residues potentially involved in this pathway. Both Glu141 and Asp65 play a role in guiding the Fe2+ substrate to the ferroxidase centre. In the absence of Asp65, routes for Fe2+ to, and Fe3+ exit from, the ferroxidase centre are affected resulting in inefficient formation of the mineral core. These observations further define the iron transit route in what may be the first characterized example of a new class of ferritins peculiar to cyanobacteria.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Joshua Fair
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.,Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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Identification of FtpA, a Dps-like protein involved in anti-oxidative stress and virulence in Actinobacillus pleuropneumoniae. J Bacteriol 2021; 204:e0032621. [PMID: 34807725 DOI: 10.1128/jb.00326-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have evolved a variety of enzymes to eliminate endogenous or host-derived oxidative stress factors. The Dps protein, first identified in Escherichia coli, contains a ferroxidase center and protects bacteria from reactive oxygen species damage. There is a lack of knowledge of the role of Dps-like proteins in bacterial pathogenesis. Actinobacillus pleuropneumoniae causes pleuropneumonia, a respiratory disease of swine. The A. pleuropneumoniae ftpA gene is up-regulated during a shift to anaerobiosis, in biofilms and, as found in this study, also by H2O2. An A. pleuropneumoniae ftpA deletion mutant (△ftpA) had increased H2O2 sensitivity, less intracellular viability in macrophages, and decreased virulence in a mouse infection model. Expression of ftpA in an E. coli dps mutant restored wild-type resistance to H2O2. FtpA possesses a conserved ferritin domain containing a ferroxidase site. Recombinant rFtpA bound and oxidized Fe2+ reversibly. Under aerobic conditions, compared with the wild-type strain, the viability of an △ftpA mutant was reduced after extended culture, transition from anaerobic to aerobic conditions, and upon supplementation with Fenton reaction substrates. Under anaerobic conditions, additional H2O2 resulted in a more severe growth defect of △ftpA than under aerobic conditions. Therefore, by oxidizing and mineralizing Fe2+, FtpA alleviates oxidative damage mediated by intracellular Fenton reactions. Furthermore, by mutational analysis, two residues were confirmed to be critical for Fe2+ binding and oxidization, as well as for A. pleuropneumoniae H2O2 resistance. Taken together, this study demonstrates that A. pleuropneumoniae FtpA is a Dps-like protein, playing critical roles in oxidative stress resistance and virulence. IMPORTANCE As a ferroxidase, Dps of Escherichia coli can protect bacteria from reactive oxygen species damage, but its role in bacterial pathogenesis has received little attention. In this study, FtpA of the swine respiratory pathogen A. pleuropneumoniae was identified as a new Dps-like protein. It facilitated A. pleuropneumoniae resistance to H2O2, survival in macrophages, and infection in vivo. FtpA could bind and oxidize Fe2+ through two important residues in its ferroxidase site and protected the bacteria from oxidative damage mediated by the intracellular Fenton reaction. These findings provide new insights into the role of the FtpA-based antioxidant system in the pathogenesis of A. pleuropneumoniae, and the conserved Fe2+ binding ligands in Dps/FtpA provide novel drug target candidates for disease prevention.
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55
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Jacobs AB, Banerjee R, Deweese DE, Braun A, Babicz JT, Gee LB, Sutherlin KD, Böttger LH, Yoda Y, Saito M, Kitao S, Kobayashi Y, Seto M, Tamasaku K, Lipscomb JD, Park K, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of the Fe(IV) 2 Intermediate Q in Methane Monooxygenase and Its Reactivity. J Am Chem Soc 2021; 143:16007-16029. [PMID: 34570980 PMCID: PMC8631202 DOI: 10.1021/jacs.1c05436] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.
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Affiliation(s)
- Ariel B. Jacobs
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Dory E. Deweese
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Leland B. Gee
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578 Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo, 679-5148, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States,Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, 94025, United States
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56
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Abstract
Increasing efficiency is an important driving force behind cellular organization and often achieved through compartmentalization. Long recognized as a core principle of eukaryotic cell organization, its widespread occurrence in prokaryotes has only recently come to light. Despite the early discovery of a few microcompartments such as gas vesicles and carboxysomes, the vast majority of these structures in prokaryotes are less than 100 nm in diameter - too small for conventional light microscopy and electron microscopic thin sectioning. Consequently, these smaller-sized nanocompartments have therefore been discovered serendipitously and then through bioinformatics shown to be broadly distributed. Their small uniform size, robust self-assembly, high stability, excellent biocompatibility, and large cargo capacity make them excellent candidates for biotechnology applications. This review will highlight our current knowledge of nanocompartments, the prospects for applications as well as open question and challenges that need to be addressed to fully understand these important structures.
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57
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Morvan C, Folgosa F, Kint N, Teixeira M, Martin-Verstraete I. Responses of Clostridia to oxygen: from detoxification to adaptive strategies. Environ Microbiol 2021; 23:4112-4125. [PMID: 34245087 DOI: 10.1111/1462-2920.15665] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022]
Abstract
Clostridia comprise bacteria of environmental, biotechnological and medical interest and many commensals of the gut microbiota. Because of their strictly anaerobic lifestyle, oxygen is a major stress for Clostridia. However, recent data showed that these bacteria can cope with O2 better than expected for obligate anaerobes through their ability to scavenge, detoxify and consume O2 . Upon O2 exposure, Clostridia redirect their central metabolism onto pathways less O2 -sensitive and induce the expression of genes encoding enzymes involved in O2 -reduction and in the repair of oxidized damaged molecules. While Faecalibacterium prausnitzii efficiently consumes O2 through a specific extracellular electron shuttling system requiring riboflavin, enzymes such as rubrerythrins and flavodiiron proteins with NAD(P)H-dependent O2 - and/or H2 O2 -reductase activities are usually encoded in other Clostridia. These two classes of enzymes play indeed a pivotal role in O2 tolerance in Clostridioides difficile and Clostridium acetobutylicum. Two main signalling pathways triggering O2 -induced responses have been described so far in Clostridia. PerR acts as a key regulator of the O2 - and/or reactive oxygen species-defence machinery while in C. difficile, σB , the sigma factor of the general stress response also plays a crucial role in O2 tolerance by controlling the expression of genes involved in O2 scavenging and repair systems.
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Affiliation(s)
- Claire Morvan
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Nicolas Kint
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
- Institut Universitaire de France, Paris, France
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58
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Gijsbers A, Zhang Y, Gao Y, Peters PJ, Ravelli RBG. Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development. Acta Crystallogr D Struct Biol 2021; 77:1077-1083. [PMID: 34342280 PMCID: PMC8329864 DOI: 10.1107/s2059798321007233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022] Open
Abstract
The use of cryo-EM continues to expand worldwide and calls for good-quality standard proteins with simple protocols for their production. Here, a straightforward expression and purification protocol is presented that provides an apoferritin, bacterioferritin B (BfrB), from Mycobacterium tuberculosis with high yield and purity. A 2.12 Å resolution cryo-EM structure of BfrB is reported, showing the typical cage-like oligomer constituting of 24 monomers related by 432 symmetry. However, it also contains a unique C-terminal extension (164-181), which loops into the cage region of the shell and provides extra stability to the protein. Part of this region was ambiguous in previous crystal structures but could be built within the cryo-EM map. These findings and this protocol could serve the growing cryo-EM community in characterizing and pushing the limits of their electron microscopes and workflows.
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Affiliation(s)
- Abril Gijsbers
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Yue Zhang
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Ye Gao
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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59
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Caldas Nogueira ML, Pastore AJ, Davidson VL. Diversity of structures and functions of oxo-bridged non-heme diiron proteins. Arch Biochem Biophys 2021; 705:108917. [PMID: 33991497 PMCID: PMC8165033 DOI: 10.1016/j.abb.2021.108917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O2 or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.
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Affiliation(s)
- Maria Luiza Caldas Nogueira
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Anthony J Pastore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
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60
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Sun X, Hong Y, Gong Y, Zheng S, Xie D. Bioengineered Ferritin Nanocarriers for Cancer Therapy. Int J Mol Sci 2021; 22:7023. [PMID: 34209892 PMCID: PMC8268655 DOI: 10.3390/ijms22137023] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022] Open
Abstract
Ferritin naturally exists in most organisms and can specifically recognize the transferrin 1 receptor (TfR1), which is generally highly expressed on various types of tumor cells. The pH dependent reversible assembling and disassembling property of ferritin renders it as a suitable candidate for encapsulating a variety of anticancer drugs and imaging probes. Ferritins external surface is chemically and genetically modifiable which can serve as attachment site for tumor specific targeting peptides or moieties. Moreover, the biological origin of these protein cages makes it a biocompatible nanocarrier that stabilizes and protects the enclosed particles from the external environment without provoking any toxic or immunogenic responses. Recent studies, further establish ferritin as a multifunctional nanocarrier for targeted cancer chemotherapy and phototherapy. In this review, we introduce the favorable characteristics of ferritin drug carriers, the specific targeted surface modification and a multifunctional nanocarriers combined chemotherapy with phototherapy for tumor treatment. Taken together, ferritin is a potential ideal base of engineered nanoparticles for tumor therapy and still needs to explore more on its way.
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Affiliation(s)
- Xuanrong Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (Y.H.); (Y.G.); (S.Z.); (D.X.)
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61
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Rodríguez JM, Allende-Ballestero C, Cornelissen JJLM, Castón JR. Nanotechnological Applications Based on Bacterial Encapsulins. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1467. [PMID: 34206092 PMCID: PMC8229669 DOI: 10.3390/nano11061467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.
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Affiliation(s)
- Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Carolina Allende-Ballestero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Jeroen J. L. M. Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands;
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, 28049 Madrid, Spain
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62
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Wang W, Zhang Y, Zhao G, Wang H. Ferritin with Atypical Ferroxidase Centers Takes B-Channels as the Pathway for Fe 2+ Uptake from Mycoplasma. Inorg Chem 2021; 60:7207-7216. [PMID: 33852289 DOI: 10.1021/acs.inorgchem.1c00265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here, we present a 1.9 Å resolution crystal structure of Mycoplasma Penetrans ferritin, which reveals that its ferroxidase center is located on the inner surface of ferritin but not buried within the four-helix of each subunit. Such a ferroxidase center exhibits a lower iron oxidation activity as compared to the reported ferritin. More importantly, we found that Fe2+ enters into the center via the rarely reported B-channels rather than the normal 3- or 4-fold channels. All these findings may provide the structural bases to explore the new iron oxidation mechanism adopted by this special ferritin, which is beneficial for understanding the relationship between the structure and function of ferritin.
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Affiliation(s)
- Wenming Wang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.,Shanxi Key Laboratory of Pharmaceutical Biotechnology, Taiyuan 030006, China
| | - Yao Zhang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongfei Wang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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63
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Khademian M, Imlay JA. How Microbes Evolved to Tolerate Oxygen. Trends Microbiol 2021; 29:428-440. [PMID: 33109411 PMCID: PMC8043972 DOI: 10.1016/j.tim.2020.10.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
Ancient microbes invented biochemical mechanisms and assembled core metabolic pathways on an anoxic Earth. Molecular oxygen appeared far later, forcing microbes to devise layers of defensive tactics that fend off the destructive actions of both reactive oxygen species (ROS) and oxygen itself. Recent work has pinpointed the enzymes that ROS attack, plus an array of clever protective strategies that abet the well known scavenging systems. Oxygen also directly damages the low-potential metal centers and radical-based mechanisms that optimize anaerobic metabolism; therefore, committed anaerobes have evolved customized tactics that defend these various enzymes from occasional oxygen exposure. Thus a more comprehensive, detailed, and surprising view of oxygen toxicity is coming into view.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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64
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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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65
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Jenkins MC, Lutz S. Encapsulin Nanocontainers as Versatile Scaffolds for the Development of Artificial Metabolons. ACS Synth Biol 2021; 10:857-869. [PMID: 33769792 DOI: 10.1021/acssynbio.0c00636] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The construction of non-native biosynthetic pathways represents a powerful, modular strategy for the production of valuable synthons and fine chemicals. Accordingly, artificially affixing enzymes that catalyze sequential reactions onto DNAs, proteins, or synthetic scaffolds has proven to be an effective route for generating de novo metabolons with novel functionalities and superior efficiency. In recent years, nanoscale microbial compartments known as encapsulins have emerged as a class of robust and highly engineerable proteinaceous containers with myriad applications in biotechnology and synthetic biology. Herein we report the concurrent surface functionalization and internal packaging of encapsulins from Thermotoga maritima to generate a catalytically competent two-enzyme metabolon. Encapsulins were engineered to covalently sequester up to 60 copies of a dihydrofolate reductase (DHFR) enzyme variant on their exterior surfaces using the SpyCatcher bioconjugation system, while their lumens were packaged with a tetrahydrofolate-dependent demethylase enzyme using short peptide affinity tags abstracted from the encapsulin's native protein cargo. Successful cross-talk between the two colocalized enzymes was confirmed as tetrahydrofolate produced by externally tethered DHFR was capable of driving the demethylation of a lignin-derived aryl substrate by packaged demethylases, albeit slowly. The subsequent introduction of a previously reported pore-enlarging deletion in the encapsulin shell was shown to enhance metabolite exchange such that the encapsulin-based metabolon functioned at speeds equivalent to those of the two enzymes freely dispersed in solution. Our work thus further emphasizes the engineerability of encapsulins and their potential use as flexile scaffolds for biocatalytic applications.
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Affiliation(s)
- Matthew C. Jenkins
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - Stefan Lutz
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- Codexis Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
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66
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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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67
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Bradley JM, Svistunenko DA, Wilson MT, Hemmings AM, Moore GR, Le Brun NE. Bacterial iron detoxification at the molecular level. J Biol Chem 2021; 295:17602-17623. [PMID: 33454001 PMCID: PMC7762939 DOI: 10.1074/jbc.rev120.007746] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Indexed: 01/18/2023] Open
Abstract
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
| | | | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom; Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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68
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Liu JJ, Sniezko RA, Zamany A, Williams H, Omendja K, Kegley A, Savin DP. Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis Underlying Cronartium ribicola vcr2 Virulence. Front Microbiol 2021; 12:602812. [PMID: 33776951 PMCID: PMC7990074 DOI: 10.3389/fmicb.2021.602812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/01/2021] [Indexed: 12/25/2022] Open
Abstract
Breeding programs of five-needle pines have documented both major gene resistance (MGR) and quantitative disease resistance (QDR) to Cronartium ribicola (Cri), a non-native, invasive fungal pathogen causing white pine blister rust (WPBR). WPBR is one of the most deadly forest diseases in North America. However, Cri virulent pathotypes have evolved and can successfully infect and kill trees carrying resistance (R) genes, including vcr2 that overcomes MGR conferred by the western white pine (WWP, Pinus monticola) R gene (Cr2). In the absence of a reference genome, the present study generated a vcr2 reference transcriptome, consisting of about 20,000 transcripts with 1,014 being predicted to encode secreted proteins (SPs). Comparative profiling of transcriptomes and secretomes revealed vcr2 was significantly enriched for several gene ontology (GO) terms relating to oxidation-reduction processes and detoxification, suggesting that multiple molecular mechanisms contribute to pathogenicity of the vcr2 pathotype for its overcoming Cr2. RNA-seq-based bulked segregant analysis (BSR-Seq) revealed genome-wide DNA variations, including about 65,617 single nucleotide polymorphism (SNP) loci in 7,749 polymorphic genes shared by vcr2 and avirulent (Avcr2) pathotypes. An examination of the distribution of minor allele frequency (MAF) uncovered a high level of genomic divergence between vcr2 and Avcr2 pathotypes. By integration of extreme-phenotypic genome-wide association (XP-GWAS) analysis and allele frequency directional difference (AFDD) mapping, we identified a set of vcr2-associated SNPs within functional genes, involved in fungal virulence and other molecular functions. These included six SPs that were top candidate effectors with putative activities of reticuline oxidase, proteins with common in several fungal extracellular membrane (CFEM) domain or ferritin-like domain, polysaccharide lyase, rds1p-like stress responsive protein, and two Cri-specific proteins without annotation. Candidate effectors and vcr2-associated genes provide valuable resources for further deciphering molecular mechanisms of virulence and pathogenicity by functional analysis and the subsequent development of diagnostic tools for monitoring the virulence landscape in the WPBR pathosystems.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, Cottage Grove, OR, United States
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Kangakola Omendja
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Angelia Kegley
- USDA Forest Service, Dorena Genetic Resource Center, Cottage Grove, OR, United States
| | - Douglas P Savin
- USDA Forest Service, Dorena Genetic Resource Center, Cottage Grove, OR, United States
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69
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Beier N, Kucklick M, Fuchs S, Mustafayeva A, Behringer M, Härtig E, Jahn D, Engelmann S. Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA. PLoS One 2021; 16:e0248865. [PMID: 33780465 PMCID: PMC8007024 DOI: 10.1371/journal.pone.0248865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/05/2021] [Indexed: 11/23/2022] Open
Abstract
Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed the adaptation of D. shibae to different kinds of oxidative stress using a GeLC-MS/MS approach. D. shibae was grown in artificial seawater medium in the dark with succinate as sole carbon source and exposed to hydrogen peroxide, paraquat or diamide. We quantified 2580 D. shibae proteins. 75 proteins changed significantly in response to peroxide stress, while 220 and 207 proteins were differently regulated by superoxide stress and thiol stress. As expected, proteins like thioredoxin and peroxiredoxin were among these proteins. In addition, proteins involved in bacteriochlophyll biosynthesis were repressed under disulfide and superoxide stress but not under peroxide stress. In contrast, proteins associated with iron transport accumulated in response to peroxide and superoxide stress. Interestingly, the iron-responsive regulator RirA in D. shibae was downregulated by all stressors. A rirA deletion mutant showed an improved adaptation to peroxide stress suggesting that RirA dependent proteins are associated with oxidative stress resistance. Altogether, 139 proteins were upregulated in the mutant strain. Among them are proteins associated with protection and repair of DNA and proteins (e. g. ClpB, Hsp20, RecA, and a thioredoxin like protein). Strikingly, most of the proteins involved in iron metabolism such as iron binding proteins and transporters were not part of the upregulated proteins. In fact, rirA deficient cells were lacking a peroxide dependent induction of these proteins that may also contribute to a higher cell viability under these conditions.
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Affiliation(s)
- Nicole Beier
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | - Martin Kucklick
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | | | - Ayten Mustafayeva
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | - Maren Behringer
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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70
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Tan Z, Lu P, Adewole D, Diarra M, Gong J, Yang C. Iron requirement in the infection of Salmonella and its relevance to poultry health. J APPL POULTRY RES 2021. [DOI: 10.1016/j.japr.2020.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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71
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Li X, Wang L, Wang M, Zhang Z, Ma C, Ma X, Na X, Liang W. Global analysis of protein succinylation modification of Nostoc flagelliforme in response to dehydration. J Proteomics 2021; 237:104149. [PMID: 33588108 DOI: 10.1016/j.jprot.2021.104149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 11/29/2022]
Abstract
Nostoc flagelliforme is a type of terrestrial cyanobacteria that is distributed in arid or semi-arid steppes in China. To research the molecular mechanisms underlying the adaptation of N. flagelliforme to drought stress, the succinylated expression profile and changes in N. flagelliforme that resulted as a response to dehydration were analyzed by label-free proteomics. A total of 1149 succinylated sites, 1128 succinylated peptides, and 396 succinylated proteins were identified. Succinylated proteins were differentially involved in photosynthesis and energy metabolism, as well as in reactive oxygen species (ROS) scavenging. Motif-X analysis of succinylated sites determined a succinylation motif [KxxG]. N. flagelliforme adapts to dehydration by increasing glucose metabolism and pentose phosphate pathway flux, and decreasing photosynthetic rate, which some of the key proteins were succinylated. ROS scavenging was mainly involved in the regulation of the enzyme antioxidant defense system and non-enzymatic antioxidant defense system through succinylation modification, thus eliminating excessive ROS. Protein succinylation of N. flagelliforme may play an important regulatory role in response to dehydration. The results are foundational, as they can inform future research into the mechanisms involved in the succinylation regulation mechanism of N. flagelliforme in response to dehydration. SIGNIFICANCE: The global succinylation network involved in response to dehydration in N. flagelliforme has been established. We found that many succinylated proteins were involved in photosynthesis, glucose metabolism and antioxidation. The global survey of succinylated proteins and the changes of succinylated levels in response to dehydration provided effective information for the drought tolerance mechanism in N. flagelliforme.
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Affiliation(s)
- Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Zheng Zhang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Caixia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaorong Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaofan Na
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China.
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72
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Zhang N, Yu X, Xie J, Xu H. New Insights into the Role of Ferritin in Iron Homeostasis and Neurodegenerative Diseases. Mol Neurobiol 2021; 58:2812-2823. [PMID: 33507490 DOI: 10.1007/s12035-020-02277-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022]
Abstract
Growing evidence has indicated that iron deposition is one of the key factors leading to neuronal death in the neurodegenerative diseases. Ferritin is a hollow iron storage protein composed of 24 subunits of two types, ferritin heavy chain (FTH) and ferritin light chain (FTL), which plays an important role in maintaining iron homeostasis. Recently, the discovery of extracellular ferritin and ferritin in exosomes indicates that ferritin might be not only an iron storage protein within the cell, but might also be an important factor in the regulation of tissue and body iron homeostasis. In this review, we first described the structural characteristics, regulation and the physiological functions of ferritin. Secondly, we reviewed the current evidence concerning the mechanisms underlying the secretion of ferritin and the possible role of secreted ferritin in the brain. Then, we summarized the relationship between ferritin and the neurodegenerative diseases including Parkinson's disease (PD), Alzheimer's disease (AD) and neuroferritinopathy (NF). Given the importance and relationship between iron and neurodegenerative diseases, understanding the role of ferritin in the brain can be expected to contribute to our knowledge of iron dysfunction and neurodegenerative diseases.
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Affiliation(s)
- Na Zhang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.,Institute of Brain Science and Disease, Qingdao University, Qingdao, 266071, China
| | - Xiaoqi Yu
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.,Institute of Brain Science and Disease, Qingdao University, Qingdao, 266071, China
| | - Junxia Xie
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, School of Basic Medicine, Qingdao University, Qingdao, 266071, China. .,Institute of Brain Science and Disease, Qingdao University, Qingdao, 266071, China.
| | - Huamin Xu
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, School of Basic Medicine, Qingdao University, Qingdao, 266071, China. .,Institute of Brain Science and Disease, Qingdao University, Qingdao, 266071, China.
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73
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Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
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Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Williams SM, Chatterji D. An Overview of Dps: Dual Acting Nanovehicles in Prokaryotes with DNA Binding and Ferroxidation Properties. Subcell Biochem 2021; 96:177-216. [PMID: 33252729 DOI: 10.1007/978-3-030-58971-4_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA binding proteins under starvation (Dps) are proteins belonging to the ferritin family with the capacity for DNA binding, in addition to iron storage and ferroxidation. Present only in the prokaryotes, these multifaceted proteins have been assigned with a number of roles, from pathogenesis to nucleoid condensation and protection. They have a significant role in protecting the cells from free radical assaults, indirectly by sequestration of iron and by directly binding to the DNA. Due to their symmetry, stability and biomineralization capacity, these proteins have ever increasing potential applications in biotechnology and drug delivery. This chapter tries to bring together all these aspects of Dps in the view of current understanding and older perspectives by studies of our group as well as other experts in the field.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, United Kingdom.
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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75
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Honarmand Ebrahimi K. Ferritin as a Platform for Creating Antiviral Mosaic Nanocages: Prospects for Treating COVID-19. Chembiochem 2020; 22:1371-1378. [PMID: 33350032 DOI: 10.1002/cbic.202000728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/25/2020] [Indexed: 11/11/2022]
Abstract
Infectious diseases are a continues threat to human health and the economy worldwide. The latest example is the global pandemic of COVID-19 caused by SARS-CoV-2. Antibody therapy and vaccines are promising approaches to treat the disease; however, they have bottlenecks: they might have low efficacy or narrow breadth due to the continuous emergence of new strains of the virus or antibodies could cause antibody-dependent enhancement (ADE) of infection. To address these bottlenecks, I propose the use of 24-meric ferritin for the synthesis of mosaic nanocages to deliver a cocktail of antibodies or nanobodies alone or in combination with another therapeutic, like a nucleotide analogue, to mimic the viral entry process and deceive the virus, or to develop mosaic vaccines. I argue that available data showing the effectiveness of ferritin-antibody conjugates in targeting specific cells and ferritin-haemagglutinin nanocages in developing influenza vaccines strongly support my proposals.
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Simão M, Leite RB, Cancela ML. Expression of four new ferritins from grooved carpet shell clam Ruditapes decussatus challenged with Perkinsus olseni and metals (Cd, Cu and Zn). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 229:105675. [PMID: 33197689 DOI: 10.1016/j.aquatox.2020.105675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Iron has a fundamental role in life and in its biochemical reactions but, when in excess, it can promote the formation of free radicals which can lead to cell death. Therefore, managing the levels of iron is essential to regulate the production of oxidative stress related to iron, and ferritins are one of the main protein families involved in this process. Ferritins are ≈480 kDa multimeric proteins composed by 24 subunits, each with 19-26 kDa, which can accumulate up to 4500 iron atoms. Besides their role in managing iron bioavailability, they have also developed a role in organism immunity and defence present throughout evolution. In this work, we identified and characterized, for the first time, four different ferritin subunits in the clam Ruditapes decussatus, a bivalve commercially and ecologically important along the south Atlantic coast and in the Mediterranean basin, which is a major target of the parasitic protozoa Perkinsus olseni, considered one of the main causes of high levels of clam mortality. Following phylogenetic annotation, the four ferritins subunits identified were subdivided into two cytosolic and two secreted forms. All four subunits maintain the canonical ferritin structure with four main helices α (A-D) and a small helix (E), but the secreted ferritins present an additional helix in their N-terminal region (F), located after the signal peptide and with possible antimicrobial properties. Additionally, we identified in ferritin 4 an extra helix α (G) located between helices B and C. These alpha helix domains revealed high degree of similarity with antimicrobial peptides associated with antibacterial and antifungal activities. Analysis of the expression of these subunits showed that ferritins 1 and 2 are ubiquitously expressed while ferritins 3 and 4 are present mainly in visceral mass. Ferritin 1 lacked a putative functional iron response element (IRE) and appeared to be under a tight regulation. Ferritins 2 and 3 showed a strong response to infection by parasite Perkinsus olseni in contrast to ferritin 4, whose main response was related to exposure to a combination of metals. The synergistic effect between metals and infection promoted a general upregulation of the four ferritins. In conclusion, our results suggest that ferritins, besides their function in iron and metals detoxification, may play a determinant role in clam immune response.
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Affiliation(s)
- Márcio Simão
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal; Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal.
| | - Ricardo B Leite
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal; Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal; Algarve Biomedical Center (ABC) and Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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77
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Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus. Genes (Basel) 2020; 11:genes11121392. [PMID: 33255299 PMCID: PMC7760498 DOI: 10.3390/genes11121392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/22/2022] Open
Abstract
Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.
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78
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Sorribes-Dauden R, Peris D, Martínez-Pastor MT, Puig S. Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi. Comput Struct Biotechnol J 2020; 18:3712-3722. [PMID: 33304466 PMCID: PMC7714665 DOI: 10.1016/j.csbj.2020.10.044] [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: 09/10/2020] [Revised: 10/28/2020] [Accepted: 10/31/2020] [Indexed: 02/06/2023] Open
Abstract
Iron is an essential micronutrient for most living beings since it participates as a redox active cofactor in many biological processes including cellular respiration, lipid biosynthesis, DNA replication and repair, and ribosome biogenesis and recycling. However, when present in excess, iron can participate in Fenton reactions and generate reactive oxygen species that damage cells at the level of proteins, lipids and nucleic acids. Organisms have developed different molecular strategies to protect themselves against the harmful effects of high concentrations of iron. In the case of fungi and plants, detoxification mainly occurs by importing cytosolic iron into the vacuole through the Ccc1/VIT1 iron transporter. New sequenced genomes and bioinformatic tools are facilitating the functional characterization, evolution and ecological relevance of metabolic pathways and homeostatic networks across the Tree of Life. Sequence analysis shows that Ccc1/VIT1 homologs are widely distributed among organisms with the exception of animals. The recent elucidation of the crystal structure of a Ccc1/VIT1 plant ortholog has enabled the identification of both conserved and species-specific motifs required for its metal transport mechanism. Moreover, recent studies in the yeast Saccharomyces cerevisiae have also revealed that multiple transcription factors including Yap5 and Msn2/Msn4 contribute to the expression of CCC1 in high-iron conditions. Interestingly, Malaysian S. cerevisiae strains express a partially functional Ccc1 protein that renders them sensitive to iron. Different regulatory mechanisms have been described for non-Saccharomycetaceae Ccc1 homologs. The characterization of Ccc1/VIT1 proteins is of high interest in the development of biofortified crops and the protection against microbial-derived diseases.
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Key Words
- BLOSUM, BLOcks SUbstitution Matrix
- CBC, CCAAT-binding core complex
- CRD, Cysteine-rich domain
- CS, Consistency score
- Ccc1
- Cg, Candida glabrata
- Eg, Eucalyptus grandis
- Fe, Iron
- Fungi
- H, Helix
- Hap, Heme activator protein
- ISC, Iron-sulfur luster
- Iron detoxification
- Iron regulation
- Iron transport
- MAFFT, Multiple Alignment using Fast Fourier Transform
- MBD, Metal-binding domain
- ML, Maximum-likelihood
- NRAMP, Natural Resistance-Associated Macrophage Protein
- Plants
- ROS, Reactive oxygen species
- TMD, Transmembrane domain
- VIT, Vacuolar iron transporter
- VIT1
- VTL, Vacuolar iron transporter-like
- Vacuole
- YRE, Yap response elements
- Yeast
- bZIP, basic leucine-zipper
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Affiliation(s)
- Raquel Sorribes-Dauden
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - David Peris
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | | | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
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79
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Golan MP, Piłsyk S, Muszewska A, Wawrzyniak A. Ferritins in Chordata: Potential evolutionary trajectory marked by discrete selective pressures: History and reclassification of ferritins in chordates and geological events' influence on their evolution and radiation. Bioessays 2020; 43:e2000207. [PMID: 33226145 DOI: 10.1002/bies.202000207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/11/2022]
Abstract
Ferritins (FTs) are iron storage proteins that are involved in managing iron-oxygen balance. In our work, we present a hypothesis on the putative effect of geological changes that have affected the evolution and radiation of ferritin proteins. Based on sequence analysis and phylogeny reconstruction, we hypothesize that two significant factors have been involved in the evolution of ferritin proteins: fluctuations of atmospheric oxygen concentrations, altering redox potential, and changing availability of water rich in bioavailable ferric ions. Fish, ancient amphibians, reptiles, and placental mammals developed the broadest repertoire of singular FTs, attributable to embryonic growth in aquatic environments containing low oxygen levels and abundant forms of soluble iron. In contrast, oviparous land vertebrates, like reptiles and birds, that have developed in high oxygen levels and limited levels of environmental Fe2+ exhibit a lower diversity of singular FTs, but display a broad repertoire of subfamilies, particularly notable in early reptiles.
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Affiliation(s)
- Maciej P Golan
- Department of Neuropathology, Institute of Psychiatry and Neurology, Warszawa, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Agata Wawrzyniak
- Morphological Sciences Department, College for Medical Sciences of University of Rzeszów, Rzeszów, Poland
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80
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Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Baslé A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem 2020; 295:15511-15526. [PMID: 32878987 DOI: 10.1074/jbc.ra120.014502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/24/2020] [Indexed: 11/06/2022] Open
Abstract
Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.
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Affiliation(s)
- Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Didi He
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Kelly J Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Will A Stanley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laurène Adam
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin J Waldron
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland.
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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81
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Mak WS, Wang X, Arenas R, Cui Y, Bertolani S, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB. Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily. Biochemistry 2020; 59:3834-3843. [PMID: 32935984 DOI: 10.1021/acs.biochem.0c00665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To complement established rational and evolutionary protein design approaches, significant efforts are being made to utilize computational modeling and the diversity of naturally occurring protein sequences. Here, we combine structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs), an enzyme family that has significant implications in synthetic biology and chemoenzymatic synthesis. Through these efforts, we discovered latent ADO-like function across the ferritin-like superfamily in various species of Bacteria and Archaea. We created a machine learning model that uses protein structural features to discriminate ADO-like activity. Computational enzyme design tools were then utilized to introduce ADO-like activity into the small subunit of Escherichia coli class I ribonucleotide reductase. The integrated approach of genomic mining, structural biology, molecular modeling, and machine learning has the potential to be utilized for rapid discovery and modulation of functions across enzyme families.
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Affiliation(s)
- Wai Shun Mak
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - XiaoKang Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Rigoberto Arenas
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Steve Bertolani
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wen Qiao Deng
- California College of Arts, 1111 Eighth Street, San Francisco, California 94107, United States
| | - Ilias Tagkopoulos
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States.,Department of Computer Science, University of California, Davis, Davis, California 95616, United States
| | - David K Wilson
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
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82
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Yang J, Pan X, Xu Y, Li Y, Xu N, Huang Z, Ye J, Gao D, Guo M. Agrobacterium tumefaciens ferritins play an important role in full virulence through regulating iron homeostasis and oxidative stress survival. MOLECULAR PLANT PATHOLOGY 2020; 21:1167-1178. [PMID: 32678502 PMCID: PMC7411545 DOI: 10.1111/mpp.12969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 05/23/2023]
Abstract
Ferritins are a large family of iron storage proteins, which are used by bacteria and other organisms to avoid iron toxicity and as a safe iron source in the cytosol. Agrobacterium tumefaciens, a phytopathogen, has two ferritin-encoding genes: atu2771 and atu2477. Atu2771 is annotated as a Bfr-encoding gene (Bacterioferritin, Bfr) and atu2477 as a Dps-encoding gene (DNA binding protein from starved cells, Dps). Three deletion mutants (Δbfr, Δdps, and bfr-dps double-deletion mutant ΔbdF) of these two ferritin-encoding genes were constructed to investigate the effects of ferritin deficiency on the iron homeostasis, oxidative stress resistance, and pathogenicity of A. tumefaciens. Deficiency of two ferritins affects the growth of A. tumefaciens under iron starvation and excess. When supplied with moderate iron, the growth of A. tumefaciens is not affected by the deficiency of ferritin. Deficiency of ferritin significantly reduces iron accumulation in the cells of A. tumefaciens, but the effect of Bfr deficiency on iron accumulation is severer than Dps deficiency and the double mutant ΔbdF has the least intracellular iron content. All three ferritin-deficient mutants showed a decreased tolerance to 3 mM H2 O2 in comparison with the wild type. The tumour induced by each of three ferritin-deficient mutants is less than that of the wild type. Complementation reversed the effects of ferritin deficiency on the growth, iron homeostasis, oxidative stress resistance, and tumorigenicity of A. tumefaciens. Therefore, ferritin plays an important role in the pathogenesis of A. tumefaciens through regulating iron homeostasis and oxidative stress survival.
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Affiliation(s)
- Jing Yang
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Xiaoyue Pan
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Yujuan Xu
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Yuan Li
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Nan Xu
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Zhiwei Huang
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Jingyang Ye
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Dawei Gao
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Minliang Guo
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
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83
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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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84
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Abreu I, Mihelj P, Raimunda D. Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles. Metallomics 2020; 11:735-755. [PMID: 30734808 DOI: 10.1039/c8mt00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
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Affiliation(s)
- Isidro Abreu
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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85
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de Alcântara NR, de Oliveira FM, Garcia W, Dos Santos OAL, Junqueira-Kipnis AP, Kipnis A. Dps protein is related to resistance of Mycobacterium abscessus subsp. massiliense against stressful conditions. Appl Microbiol Biotechnol 2020; 104:5065-5080. [PMID: 32253472 DOI: 10.1007/s00253-020-10586-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) belongs to the Mycobacterium abscessus complex and is a rapidly growing non-tuberculous mycobacterium. The chronic pulmonary, skin, and soft tissue infections that it causes may be difficult to treat due to its intrinsic resistance to the commonly used antimicrobial drugs, making it a serious world public health problem. Iron is an essential nutrient for the growth of microorganisms; nonetheless, it can be toxic when in excess. Thus, bacteria require an iron homeostasis mechanism to succeed in different environments. DNA-binding proteins from starved cells (Dps) are miniferritins with the property to act as additional iron storage proteins but also can bind to DNA, protecting it against hydroxyl radical. Annotation of the Mycma genome revealed the gene mycma_03135 with 79% sequential identity when compared to MSMEG_3242 gene from M. smegmatis mc2 155, which codifies for a known Dps. Recombinant Dps from M. abscessus (rMaDps) was produced in Escherichia coli, purified in soluble form and shown to form high mass oligomers in solution with ferroxidase activity, DNA binding, and protection against damage. The expression of the mycma_03135 gene was induced during Mycma growth in the presence of hydrogen peroxide (H2O2). Additionally, the expression of rMaDps by E. coli conferred greater resistance to H2O2. Thus, this study is the first to identify and characterize a Dps from M. abscessus. KEY POINTS: Mycobacterium abscessus subsp. massiliense express a miniferritin protein (Dps). Mycma Dps binds to DNA and protects against oxidative stress.
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Affiliation(s)
| | - Fábio Muniz de Oliveira
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | | | | | - André Kipnis
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil.
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86
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Pinto G, D'Acierno M, Illiano A, Petruk G, Ferraro G, Merlino A, Monti DM, Godovac-Zimmermann J, Amoresano A. Label-free quantitative proteomics of the MCF-7 cellular response to a ferritin–metallodrug complex. Mol Omics 2020; 16:165-173. [DOI: 10.1039/c9mo00158a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Schematic summary of the experimental workflow based on label-free quantitative proteomics.
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Affiliation(s)
- Gabriella Pinto
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
| | | | - Anna Illiano
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
| | - Ganna Petruk
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
| | - Giarita Ferraro
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
- Department of Chemistry Ugo Schiff
| | - Antonello Merlino
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
| | - Daria Maria Monti
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
| | | | - Angela Amoresano
- Department of Chemical Sciences
- University of Naples Federico II
- Napoli
- Italy
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87
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Kamyshinsky R, Chesnokov Y, Dadinova L, Mozhaev A, Orlov I, Petoukhov M, Orekhov A, Shtykova E, Vasiliev A. Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering. Biomolecules 2019; 10:biom10010039. [PMID: 31888079 PMCID: PMC7023142 DOI: 10.3390/biom10010039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/01/2022] Open
Abstract
Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization—one of the most curious processes in the area of life science at the moment. However, the actual structure of the Dps–DNA co-crystals remained uncertain in the details for more than two decades. Cryo-electron tomography and small-angle X-ray scattering revealed polymorphous modifications of the co-crystals depending on the buffer parameters. Two different types of the Dps–DNA co-crystals are formed in vitro: triclinic and cubic. Three-dimensional reconstruction revealed DNA and Dps molecules in cubic co-crystals, and the unit cell parameters of cubic lattice were determined consistently by both methods.
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Affiliation(s)
- Roman Kamyshinsky
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
- Correspondence: ; Tel.: +7-916-356-3963
| | - Yury Chesnokov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry of Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Ivan Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Maxim Petoukhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Leninsky prospect, 31, 119071 Moscow, Russia
| | - Anton Orekhov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Alexander Vasiliev
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
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88
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Mebs S, Srinivas V, Kositzki R, Griese JJ, Högbom M, Haumann M. Fate of oxygen species from O 2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148060. [PMID: 31394094 DOI: 10.1016/j.bbabio.2019.148060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Oxygen (O2) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O2 cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only 57Fe(II) or Mn(II) plus 57Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including 16/18O and H/D exchange. 57Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H2O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas 18O from 18O2 cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O2 reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O2 cleavage route in an enzyme.
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Affiliation(s)
- Stefan Mebs
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Ramona Kositzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Julia J Griese
- Department of Cell and Molecular Biology, Structural Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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89
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Manganese Is Required for the Rapid Recovery of DNA Synthesis following Oxidative Challenge in Escherichia coli. J Bacteriol 2019; 201:JB.00426-19. [PMID: 31570529 DOI: 10.1128/jb.00426-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 11/20/2022] Open
Abstract
Divalent metals such as iron and manganese play an important role in the cellular response to oxidative challenges and are required as cofactors by many enzymes. However, how these metals affect replication after oxidative challenge is not known. Here, we show that replication in Escherichia coli is inhibited following a challenge with hydrogen peroxide and requires manganese for the rapid recovery of DNA synthesis. We show that the manganese-dependent recovery of DNA synthesis occurs independent of lesion repair, modestly improves cell survival, and is associated with elevated rates of mutagenesis. The Mn-dependent mutagenesis involves both replicative and translesion polymerases and requires prior disruption by H2O2 to occur. Taking these findings together, we propose that replication in E. coli is likely to utilize an iron-dependent enzyme(s) that becomes oxidized and inactivated during oxidative challenges. The data suggest that manganese remetallates these or alternative enzymes to allow genomic DNA replication to resume, although with reduced fidelity.IMPORTANCE Iron and manganese play important roles in how cell's cope with oxygen stress. However, how these metals affect the ability of cells to replicate after oxidative challenges is not known. Here, we show that replication in Escherichia coli is inhibited following a challenge with hydrogen peroxide and requires manganese for the rapid recovery of DNA synthesis. The manganese-dependent recovery of DNA synthesis occurs independently of lesion repair and modestly improves survival, but it also increases the mutation rate in cells. The results imply that replication in E. coli is likely to utilize an iron-dependent enzyme(s) that becomes oxidized and inactivated during oxidative challenges. We propose that manganese remetallates these or alternative enzymes to allow genomic DNA replication to resume, although with reduced fidelity.
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90
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Romero-Afrima L, Zelmanovich V, Abergel Z, Zuckerman B, Shaked M, Abergel R, Livshits L, Smith Y, Gross E. Ferritin is regulated by a neuro-intestinal axis in the nematode Caenorhabditis elegans. Redox Biol 2019; 28:101359. [PMID: 31677552 PMCID: PMC6920132 DOI: 10.1016/j.redox.2019.101359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/24/2023] Open
Abstract
Iron is vital for the life of most organisms. However, when dysregulated, iron can catalyze the formation of oxygen (O2) radicals that can destroy any biological molecule and thus lead to oxidative injury and death. Therefore, iron metabolism must be tightly regulated at all times, as well as coordinated with the metabolism of O2. However, how is this achieved at the whole animal level is not well understood. Here, we explore this question using the nematode Caenorhabditis elegans. Exposure of worms to O2 starvation conditions (i.e. hypoxia) induces a major upregulation in levels of the conserved iron-cage protein ferritin 1 (ftn-1) in the intestine, while exposure to 21% O2 decreases ftn-1 level. This O2-dependent inhibition is mediated by O2-sensing neurons that communicate with the intestine through neurotransmitter and neuropeptide signalling, and requires the activity of hydroxylated HIF-1. By contrast, the induction of ftn-1 in hypoxia appears to be HIF-1-independent. This upregulation provides protection against Pseudomonas aeruginosa bacteria and oxidative injury. Taken together, our studies uncover a neuro-intestine axis that coordinates O2 and iron responses at the whole animal level. The expression of ferritin 1 (ftn-1) is tightly regulated by O2 tension. O2-sensing neurons inhibit the expression of ftn-1 in the intestine at 21% O2. Hydroxylated–HIF–1 inhibits the expression of ftn-1 at 21% O2. ftn-1 is important for protecting against Pseudomonas aeruginosa bacteria.
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Affiliation(s)
- Leonor Romero-Afrima
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Veronica Zelmanovich
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Zohar Abergel
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Binyamin Zuckerman
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Maayan Shaked
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Rachel Abergel
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Leonid Livshits
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University - Hadassah Medical School, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Einav Gross
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem. P.O. Box 12271, Jerusalem, 9112102, Israel.
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91
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Vijayan V, Mohapatra A, Uthaman S, Park IK. Recent Advances in Nanovaccines Using Biomimetic Immunomodulatory Materials. Pharmaceutics 2019; 11:E534. [PMID: 31615112 PMCID: PMC6835828 DOI: 10.3390/pharmaceutics11100534] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/09/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
The development of vaccines plays a vital role in the effective control of several fatal diseases. However, effective prophylactic and therapeutic vaccines have yet to be developed for completely curing deadly diseases, such as cancer, malaria, HIV, and serious microbial infections. Thus, suitable vaccine candidates need to be designed to elicit appropriate immune responses. Nanotechnology has been found to play a unique role in the design of vaccines, providing them with enhanced specificity and potency. Nano-scaled materials, such as virus-like particles, liposomes, polymeric nanoparticles (NPs), and protein NPs, have received considerable attention over the past decade as potential carriers for the delivery of vaccine antigens and adjuvants, due to their beneficial advantages, like improved antigen stability, targeted delivery, and long-time release, for which antigens/adjuvants are either encapsulated within, or decorated on, the NP surface. Flexibility in the design of nanomedicine allows for the programming of immune responses, thereby addressing the many challenges encountered in vaccine development. Biomimetic NPs have emerged as innovative natural mimicking biosystems that can be used for a wide range of biomedical applications. In this review, we discuss the recent advances in biomimetic nanovaccines, and their use in anti-bacterial therapy, anti-HIV therapy, anti-malarial therapy, anti-melittin therapy, and anti-tumor immunity.
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Affiliation(s)
- Veena Vijayan
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju 58128, Korea.
| | - Adityanarayan Mohapatra
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju 58128, Korea.
| | - Saji Uthaman
- Department of Polymer Science and Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - In-Kyu Park
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju 58128, Korea.
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92
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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93
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Johnson LA, Hug LA. Distribution of reactive oxygen species defense mechanisms across domain bacteria. Free Radic Biol Med 2019; 140:93-102. [PMID: 30930298 DOI: 10.1016/j.freeradbiomed.2019.03.032] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/06/2019] [Accepted: 03/26/2019] [Indexed: 11/25/2022]
Abstract
Bacteria are the most diverse and numerous organisms on the planet, inhabiting environments from the deep subsurface to particles in clouds. Across this range of conditions, bacteria have evolved a diverse suite of enzymes to mitigate cellular damage from reactive oxygen species (ROS). Here, we review the diversity and distribution of ROS enzymatic defense mechanisms across the domain Bacteria, using both peer-reviewed literature and publicly available genome databases. We describe the specific strategies used by well-characterized organisms in order to highlight differences in oxidative stress responses between aerobic, facultatively anaerobic, and anaerobic lifestyles. We present evidence from genome minimization experiments to suggest that ROS defenses are obligately required for life. This review clarifies the variability in ROS defenses across Bacteria, including the novel diversity found in currently uncharacterized Candidate Phyla.
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Affiliation(s)
- Lisa A Johnson
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada.
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94
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Bennett BD, Gralnick JA. Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems. Free Radic Biol Med 2019; 140:167-171. [PMID: 31251977 DOI: 10.1016/j.freeradbiomed.2019.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/13/2019] [Accepted: 06/23/2019] [Indexed: 12/24/2022]
Abstract
Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe3+), and ferrous iron, the reduced state (Fe2+). Fe2+ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe2+ toxicity, focusing on molecular mechanistic studies in several model systems.
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Affiliation(s)
- B D Bennett
- Pacific Biosciences Research Center, University of Hawai‛i at Mānoa, Honolulu, HI, 96813, USA
| | - J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, 55108, USA.
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95
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Chakravarty D, Bihani SC, Banerjee M, Ballal A. Novel molecular insights into the anti-oxidative stress response and structure-function of a salt-inducible cyanobacterial Mn-catalase. PLANT, CELL & ENVIRONMENT 2019; 42:2508-2521. [PMID: 30993731 DOI: 10.1111/pce.13563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
KatB, a salt-inducible Mn-catalase, protects the cyanobacterium Anabaena from salinity/oxidative stress. In this report, we provide distinctive insights into the biological-biochemical function of KatB at the molecular level. Anabaena overexpressing the wild-type KatB protein (KatBWT) detoxified H2 O2 efficiently, showing reduced burden of reactive oxygen species compared with the strain overproducing KatBF2V (wherein F-2 is replaced by V). Correspondingly, the KatBWT protein also displayed several folds more activity than KatBF2V. Interestingly, the KatB variants with large hydrophobic amino acids (F/W/Y) were more compact, showed enhanced activity, and were resistant to thermal/chemical denaturation than variants with smaller residues (G/A/V) at the second position. X-ray crystallography-based analysis showed that F-2 was required for appropriate interactions between two subunits. These contacts provided stability to the hexamer, making it more compact. F-2, through its interaction with F-66 and W-43, formed the proper hydrophobic pocket that held the active site together. Consequently, only residues that supported activity (i.e., F/Y/W) were selected at the second position in Mn-catalases during evolution. This study (a) demonstrates that modification of nonactive site residues can alter the response of catalases to environmental stress and (b) has expanded the scope of amino acids that can be targeted for rational protein engineering in plants.
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Affiliation(s)
- Dhiman Chakravarty
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
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96
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Howe C, Moparthi VK, Ho FM, Persson K, Stensjö K. The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria. PLoS One 2019; 14:e0218300. [PMID: 31369577 PMCID: PMC6675082 DOI: 10.1371/journal.pone.0218300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 11/18/2022] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) have been found to detoxify H2O2. At their catalytic centers, the ferroxidase center (FOC), Dps proteins utilize Fe2+ to reduce H2O2 and therefore play an essential role in the protection against oxidative stress and maintaining iron homeostasis. Whereas most bacteria accommodate one or two Dps, there are five different Dps proteins in Nostoc punctiforme, a phototrophic and filamentous cyanobacterium. This uncommonly high number of Dps proteins implies a sophisticated machinery for maintaining complex iron homeostasis and for protection against oxidative stress. Functional analyses and structural information on cyanobacterial Dps proteins are rare, but essential for understanding the function of each of the NpDps proteins. In this study, we present the crystal structure of NpDps4 in its metal-free, iron- and zinc-bound forms. The FOC coordinates either two iron atoms or one zinc atom. Spectroscopic analyses revealed that NpDps4 could oxidize Fe2+ utilizing O2, but no evidence for its use of the oxidant H2O2 could be found. We identified Zn2+ to be an effective inhibitor of the O2-mediated Fe2+ oxidation in NpDps4. NpDps4 exhibits a FOC that is very different from canonical Dps, but structurally similar to the atypical one from DpsA of Thermosynechococcus elongatus. Sequence comparisons among Dps protein homologs to NpDps4 within the cyanobacterial phylum led us to classify a novel FOC class: the His-type FOC. The features of this special FOC have not been identified in Dps proteins from other bacterial phyla and it might be unique to cyanobacterial Dps proteins.
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Affiliation(s)
- Christoph Howe
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Vamsi K. Moparthi
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Felix M. Ho
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karina Persson
- Department of Chemistry, Umeå University, Umeå, Sweden
- * E-mail: (KS); (KP)
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail: (KS); (KP)
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97
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Giessen TW, Orlando BJ, Verdegaal AA, Chambers MG, Gardener J, Bell DC, Birrane G, Liao M, Silver PA. Large protein organelles form a new iron sequestration system with high storage capacity. eLife 2019; 8:46070. [PMID: 31282860 PMCID: PMC6668986 DOI: 10.7554/elife.46070] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/06/2019] [Indexed: 12/21/2022] Open
Abstract
Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from Quasibacillus thermotolerans. Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin. People often think of the cell as the basic unit of life. Despite this, individual cells are also subdivided into many compartments, called ‘organelles’ because they act like the internal organs of the cell. For example, organelles can break down nutrients, store information in the form of DNA, or help remove waste. Even bacterial cells, despite being smaller and simpler than most other cell types, contain organelle-like structures. These are tiny compartments, termed protein organelles, which are enclosed by ‘shells’ made from self-assembling proteins within the cell. Cells need iron to carry out the chemical reactions necessary for life. Iron is therefore an essential nutrient, but it can also be toxic if not stored properly inside the cell. Cells often solve this problem by locking iron away inside small, specialised protein cages called ferritins until it can be used. Most organisms, from humans to bacteria, have ferritins, but some do not, and the way these organisms store iron remains largely unknown. The bacterium Quasibacillus thermotolerans is an example of an organism that lacks ferritins. However, it does contain a recently discovered type of protein organelle, called an encapsulin. Giessen et al. wanted to find out more about the structure of this protein organelle, and to determine if it helped these bacteria store iron. Q. thermotolerans’ encapsulin turned out to be the largest of its kind discovered to date. Detailed imaging experiments, using a combination of electron microscopy and X-ray- based techniques, revealed that the protein shell of the encapsulin had an overall structure resembling chain mail and contained multiple pores. These pores were negatively charged, meaning that they could efficiently attract iron (which has a positive charge) and funnel it into the interior of the compartment. The compartment itself was able to store at least 20 times more iron than ferritins, making this encapsulin one of the most efficient methods of iron storage in any cell. These findings will help us better understand how bacteria that lack ferritins cope with the problem of iron storage. In the future, encapsulins could also be used as a target for new therapies to fight bacterial infections, or even as the building blocks for microscopic chemical reactors or ‘storage facilities’ in industrial applications.
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Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States
| | - Benjamin J Orlando
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Andrew A Verdegaal
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jules Gardener
- Center for Nanoscale Systems, Harvard University, Cambridge, United States
| | - David C Bell
- Center for Nanoscale Systems, Harvard University, Cambridge, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Gabriel Birrane
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Maofu Liao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, United States
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98
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Bacterioferritin of Magnetospirillum gryphiswaldense Is a Heterotetraeicosameric Complex Composed of Functionally Distinct Subunits but Is Not Involved in Magnetite Biomineralization. mBio 2019; 10:mBio.02795-18. [PMID: 31113903 PMCID: PMC6529640 DOI: 10.1128/mbio.02795-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The biomineralization pathway of magnetite in magnetotactic bacteria is still poorly understood and a matter of intense debates. In particular, the existence, nature, and location of possible mineral precursors of magnetite are not clear. One possible precursor has been suggested to be ferritin-bound ferrihydrite. To clarify its role for magnetite biomineralization, we analyzed and characterized ferritin-like proteins from the magnetotactic alphaproteobacterium Magnetospirillum gryphiswaldense MSR-1, employing genetic, biochemical, and spectroscopic techniques. Transmission Mössbauer spectroscopy of the wild type (WT) and a bacterioferritin (bfr) deletion strain uncovered that the presence of ferrihydrite in cells is coupled to the presence of Bfr. However, bfr and dps deletion mutants, encoding another ferritin-like protein, or even mutants with their codeletion had no impact on magnetite formation in MSR-1. Thus, ferritin-like proteins are not involved in magnetite biomineralization and Bfr-bound ferrihydrite is not a precursor of magnetite biosynthesis. Using transmission electron microscopy and bacterial two-hybrid and electrophoretic methods, we also show that MSR-1 Bfr is an atypical representative of the Bfr subfamily, as it forms tetraeicosameric complexes from two distinct subunits. Furthermore, our analyses revealed that these subunits are functionally divergent, with Bfr1 harboring a ferroxidase activity while only Bfr2 contributes to heme binding. Because of this functional differentiation and the poor formation of homooligomeric Bfr1 complexes, only heterooligomeric Bfr protects cells from oxidative stress in vivo. In summary, our results not only provide novel insights into the biomineralization of magnetite but also reveal the unique properties of so-far-uncharacterized heterooligomeric bacterioferritins.IMPORTANCE Magnetotactic bacteria like Magnetospirillum gryphiswaldense are able to orient along magnetic field lines due to the intracellular formation of magnetite nanoparticles. Biomineralization of magnetite has been suggested to require a yet-unknown ferritin-like ferrihydrite component. Here, we report the identification of a bacterioferritin as the source of ferrihydrite in M. gryphiswaldense and show that, contrary to previous reports, bacterioferritin is not involved in magnetite biomineralization but required for oxidative stress resistance. Additionally, we show that bacterioferritin of M. gryphiswaldense is an unusual member of the bacterioferritin subfamily as it is composed of two functionally distinct subunits. Thus, our findings extend our understanding of the bacterioferritin subfamily and also solve a longstanding question about the magnetite biomineralization pathway.
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99
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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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100
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Kuwata T, Okada Y, Yamamoto T, Sato D, Fujiwara K, Fukumura T, Ikeguchi M. Structure, Function, Folding, and Aggregation of a Neuroferritinopathy-Related Ferritin Variant. Biochemistry 2019; 58:2318-2325. [DOI: 10.1021/acs.biochem.8b01068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Takumi Kuwata
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Yuta Okada
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Tomoki Yamamoto
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Daisuke Sato
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kazuo Fujiwara
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Takuma Fukumura
- EM Research and Development Department, JEOL Ltd., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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