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Lucignano R, Sanità G, Esposito E, Russo Krauss I, D'Ursi AM, Buonocore M, Picone D. Human ferritin nanocarriers for drug-delivery: A molecular view of the disassembly process. Int J Biol Macromol 2024; 277:134373. [PMID: 39094874 DOI: 10.1016/j.ijbiomac.2024.134373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/20/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Ferritins are natural proteins which spontaneously self-assemble forming hollow nanocages physiologically deputed to iron storage and homeostasis. Thanks to their high stability and easy production in vitro, ferritins represent an intriguing system for nanobiotechnology. Here we investigated the mechanism of disassembly and reassembly of a human recombinant ferritin constituted by the heavy chain (hHFt) exploiting a new procedure which involves the use of minimal amounts of sodium dodecyl sulfate (SDS) and assessed its effectiveness in comparison with two commonly used protocols based on pH shift at highly acidic and alkaline values. The interest in this ferritin as drug nanocarrier is related to the strong affinity of the human H-chain for the transferrin receptor TfR-1, overexpressed in several tumoral cell lines. Using different techniques, like NMR, TEM and DLS, we demonstrated that the small concentrations of SDS can eliminate the nanocage architecture without detaching the monomers from each other, which instead remain strongly associated. Following this procedure, we encapsulated into the nanocage a small ruthenium complex with a remarkable improvement with respect to previous protocols in terms of yield, structural integrity of the recovered protein and encapsulation efficiency. In our opinion, the extensive network of interchain interactions preserved during the SDS-based disassembly procedure represents the key for a complete and correct hHFt reassembly.
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Affiliation(s)
- Rosanna Lucignano
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy
| | - Gennaro Sanità
- Institute of Applied Sciences and Intelligent Systems (ISASI), Naples Cryo Electron Microscopy Laboratory - EYE LAB, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Emanuela Esposito
- Institute of Applied Sciences and Intelligent Systems (ISASI), Naples Cryo Electron Microscopy Laboratory - EYE LAB, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy; CSGI (Consorzio per lo Sviluppo dei Sistemi a Grande Interfase), I-50019 Florence, Italy
| | - Anna Maria D'Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Michela Buonocore
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
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2
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Adak S, Ye N, Calderone LA, Duan M, Lubeck W, Schäfer RJB, Lukowski AL, Houk KN, Pandelia ME, Drennan CL, Moore BS. A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile. Nat Chem 2024:10.1038/s41557-024-01603-z. [PMID: 39285206 DOI: 10.1038/s41557-024-01603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 07/12/2024] [Indexed: 09/25/2024]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Meng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Wilson Lubeck
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rebecca J B Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | | | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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3
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Lucignano R, Ferraro G. Bioactive Molecules Delivery through Ferritin Nanoparticles: Sum Up of Current Loading Methods. Molecules 2024; 29:4045. [PMID: 39274893 PMCID: PMC11396501 DOI: 10.3390/molecules29174045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024] Open
Abstract
Ferritin (Ft) is a protein with a peculiar three-dimensional architecture. It is characterized by a hollow cage structure and is responsible for iron storage and detoxification in almost all living organisms. It has attracted the interest of the scientific community thanks to its appealing features, such as its nano size, thermal and pH stability, ease of functionalization, and low cost for large-scale production. Together with high storage capacity, these properties qualify Ft as a promising nanocarrier for the development of delivery systems for numerous types of biologically active molecules. In this paper, we introduce the basic structural and functional aspects of the protein, and summarize the methods employed to load bioactive molecules within the ferritin nanocage.
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Affiliation(s)
- Rosanna Lucignano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cinthia, 26, 80126 Naples, Italy
| | - Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cinthia, 26, 80126 Naples, Italy
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4
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Sultana F, Ghosh A. Exploring the evolutionary landscape and structural resonances of ferritin with insights into functional significance in plant. Biochimie 2024:S0300-9084(24)00173-1. [PMID: 39047810 DOI: 10.1016/j.biochi.2024.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/04/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The mineral iron plays a crucial role in facilitating the optimal functioning of numerous biological processes within the cellular environment. These processes involve the transportation of oxygen, energy production, immune system functioning, cognitive abilities, and muscle function. However, it is crucial to note that excessive levels of iron can result in oxidative damage within cells, primarily through Fenton reactions. Iron availability and toxicity present significant challenges that have been addressed through evolution. Ferritin is an essential protein that stores iron and is divided into different subfamilies, including DNA-binding proteins under starvation (Dps), bacterioferritin, and classical ferritin. Ferritin plays a critical role in maintaining cellular balance and protecting against oxidative damage. This study delves into ferritin's evolutionary dynamics across diverse taxa, emphasizing structural features and regulatory mechanisms. Insights into ferritin's evolution and functional diversity are gained through phylogenetic and structural analysis in bacterial Dps, bacterioferritin, and classical ferritin proteins. Additionally, the involvement of ferritin in plant stress responses and development is explored. Analysis of ferritin gene expression across various developmental stages and stress conditions provides insights into its regulatory roles. This comprehensive exploration enhances our understanding of ferritin's significance in plant biology, offering insights into its evolutionary history, structural diversity, and protective mechanisms against oxidative stress.
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Affiliation(s)
- Fahmida Sultana
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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5
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Pandey KK, Sahoo BR, Pattnaik AK. Protein Nanoparticles as Vaccine Platforms for Human and Zoonotic Viruses. Viruses 2024; 16:936. [PMID: 38932228 PMCID: PMC11209504 DOI: 10.3390/v16060936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Vaccines are one of the most effective medical interventions, playing a pivotal role in treating infectious diseases. Although traditional vaccines comprise killed, inactivated, or live-attenuated pathogens that have resulted in protective immune responses, the negative consequences of their administration have been well appreciated. Modern vaccines have evolved to contain purified antigenic subunits, epitopes, or antigen-encoding mRNAs, rendering them relatively safe. However, reduced humoral and cellular responses pose major challenges to these subunit vaccines. Protein nanoparticle (PNP)-based vaccines have garnered substantial interest in recent years for their ability to present a repetitive array of antigens for improving immunogenicity and enhancing protective responses. Discovery and characterisation of naturally occurring PNPs from various living organisms such as bacteria, archaea, viruses, insects, and eukaryotes, as well as computationally designed structures and approaches to link antigens to the PNPs, have paved the way for unprecedented advances in the field of vaccine technology. In this review, we focus on some of the widely used naturally occurring and optimally designed PNPs for their suitability as promising vaccine platforms for displaying native-like antigens from human viral pathogens for protective immune responses. Such platforms hold great promise in combating emerging and re-emerging infectious viral diseases and enhancing vaccine efficacy and safety.
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Affiliation(s)
- Kush K. Pandey
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bikash R. Sahoo
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Asit K. Pattnaik
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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6
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Eren E, Watts NR, Montecinos F, Wingfield PT. Encapsulated Ferritin-like Proteins: A Structural Perspective. Biomolecules 2024; 14:624. [PMID: 38927029 PMCID: PMC11202242 DOI: 10.3390/biom14060624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell's interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology.
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Affiliation(s)
| | | | | | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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8
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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9
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Zoller H, Tilg H. Ferritin-a promising biomarker in MASLD. Gut 2024; 73:720-721. [PMID: 38538068 DOI: 10.1136/gutjnl-2023-331848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Affiliation(s)
- Heinz Zoller
- Department of Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Tirol, Austria
- Christian Doppler Laboratory on Iron and Phosphate Biology, Christian Doppler Forschungsgesellschaft, Innsbruck, Tirol, Austria
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medizinische Universitat Innsbruck, Innsbruck, Tirol, Austria
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10
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Nithimethachoke T, Boonmak C, Morikawa M. A novel alkane monooxygenase evolved from a broken piece of ribonucleotide reductase in Geobacillus kaustophilus HTA426 isolated from Mariana Trench. Extremophiles 2024; 28:18. [PMID: 38353731 PMCID: PMC10867098 DOI: 10.1007/s00792-024-01332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/30/2023] [Indexed: 02/16/2024]
Abstract
We have accidentally found that a thermophilic Geobacillus kaustophilus HTA426 is capable of degrading alkanes although it has no alkane oxygenating enzyme genes. Our experimental results revealed that a putative ribonucleotide reductase small subunit GkR2loxI (GK2771) gene encodes a novel heterodinuclear Mn-Fe alkane monooxygenase/hydroxylase. GkR2loxI protein can perform two-electron oxidations similar to homonuclear diiron bacterial multicomponent soluble methane monooxygenases. This finding not only answers a long-standing question about the substrate of the R2lox protein clade, but also expands our understanding of the vast diversity and new evolutionary lineage of the bacterial alkane monooxygenase/hydroxylase family.
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Affiliation(s)
- Tanasap Nithimethachoke
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan
| | - Chanita Boonmak
- Department of Microbiology, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd., Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan.
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Lu J, Xu X, Sun X, Du Y. Protein and peptide-based renal targeted drug delivery systems. J Control Release 2024; 366:65-84. [PMID: 38145662 DOI: 10.1016/j.jconrel.2023.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Renal diseases have become an increasingly concerned public health problem in the world. Kidney-targeted drug delivery has profound transformative potential on increasing renal efficacy and reducing extra-renal toxicity. Protein and peptide-based kidney targeted drug delivery systems have garnered more and more attention due to its controllable synthesis, high biocompatibility and low immunogenicity. At the same time, the targeting methods based on protein/peptide are also abundant, including passive renal targeting based on macromolecular protein and active targeting mediated by renal targeting peptide. Here, we review the application and the drug loading strategy of different proteins or peptides in targeted drug delivery, including the ferritin family, albumin, low molecular weight protein (LMWP), different peptide sequence and antibodies. In addition, we summarized the factors influencing passive and active targeting in drug delivery system, the main receptors related to active targeting in different kidney diseases, and a variety of nano forms of proteins based on the controllable synthesis of proteins.
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Affiliation(s)
- Jingyi Lu
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang 310014, China; College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Xiaoling Xu
- College of Medical Sciences, Zhejiang Shuren University, 8 Shuren Street, Hangzhou, Zhejiang 310015, China.
| | - Xuanrong Sun
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang 310014, China.
| | - Yongzhong Du
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang 310014, China; College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China; Innovation Center of Translational Pharmacy, Jinhua Institute of Zhejiang University, Jinhua 321299, China.
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12
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Ma L, Zheng JJ, Zhou N, Zhang R, Fang L, Yang Y, Gao X, Chen C, Yan X, Fan K. A natural biogenic nanozyme for scavenging superoxide radicals. Nat Commun 2024; 15:233. [PMID: 38172125 PMCID: PMC10764798 DOI: 10.1038/s41467-023-44463-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Biominerals, the inorganic minerals of organisms, are known mainly for their physical property-related functions in modern living organisms. Our recent discovery of the enzyme-like activities of nanomaterials, coined as nanozyme, inspires the hypothesis that nano-biominerals might function as enzyme-like catalyzers in cells. Here we report that the iron cores of biogenic ferritins act as natural nanozymes to scavenge superoxide radicals. Through analyzing eighteen representative ferritins from three living kingdoms, we find that the iron core of prokaryote ferritin possesses higher superoxide-diminishing activity than that of eukaryotes. Further investigation reveals that the differences in catalytic capability result from the iron/phosphate ratio changes in the iron core, which is mainly determined by the structures of ferritins. The phosphate in the iron core switches the iron core from single crystalline to amorphous iron phosphate-like structure, resulting in decreased affinity to the hydrogen proton of the ferrihydrite-like core that facilitates its reaction with superoxide in a manner different from that of ferric ions. Furthermore, overexpression of ferritins with high superoxide-diminishing activities in E. coli increases the resistance to superoxide, whereas bacterioferritin knockout or human ferritin knock-in diminishes free radical tolerance, highlighting the physiological antioxidant role of this type of nanozymes.
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Affiliation(s)
- Long Ma
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China
| | - Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Ning Zhou
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Long Fang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Yang
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology, Taizhou, Jiangsu, 225316, China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
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13
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Liu J, Li K, Li S, Yang G, Lin Z, Miao Z. Grape seed-derived procyanidin inhibits glyphosate-induced hepatocyte ferroptosis via enhancing crosstalk between Nrf2 and FGF12. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155278. [PMID: 38103315 DOI: 10.1016/j.phymed.2023.155278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/11/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Glyphosate (GLY) exposure induces hepatocyte ferroptosis through overproduction of reactive oxygen species, regarded as an important contributor to liver damage. Grape seed-derived procyanidin (GSDP) has been reported to be an effective antioxidant, but whether and, if any, how GSDP can attenuate GLY-induced liver injury via inhibiting ferroptosis is unclear. PURPOSE The current study aimed to investigate the hepato-protective effects and possible mechanisms of GSDP. METHODS GLY-induced liver damage mice model was established to explore the hepatoprotective roles of GSPE in vivo. Subsequently, bioinformatics methodology was used to predict the key pathways and factors related to the action targets of GSPE against hepatocyte ferroptosis. Finally, we explored the roles of nuclear factor E2 related factor 2 (Nrf2) and fibroblast growth factor 21 (FGF21) in blunting GLY-induced liver damage via suppressing ferroptosis in vitro. RESULTS GSDP exerts hepato-protective effects in vivo and in vitro through reduced oxidative stress and inhibited ferroptosis, which was related to the activation of Nrf2. Bioinformatics analysis showed an interaction between Nrf2 and FGF21. Furthermore, Nrf2 inhibition reduced FGF21 expression in the mRNA and protein levels. Fgf21 knockdown suppressed Nrf2 expression level, but recombinant FGF21 protein increased Nrf2 expression and promoted Nrf2 translocation into nucleus, suggesting a crosstalk between Nrf2 and FGF21. Intriguingly, the decreased levels of Nrf2 and FGF21 compromised the protective roles of GSDP against GLY-induced hepatocyte ferroptosis. CONCLUSION These findings suggest that GSDP attenuates GLY-caused hepatocyte ferroptosis via enhancing the interplay between Nrf2 and FGF21. Thus, GSDP may be a promising natural compound to antagonize ferroptosis-related damage.
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Affiliation(s)
- Jingbo Liu
- College of Biological and Brewing Engineering, Taishan University, No. 525 Dongyue Street, Tai'an, Shandong 271000, China.
| | - Kun Li
- Shanghai Pulmonary Hospital, No.507 Zhengmin Road, Yangpu District, Shanghai 200433, China
| | - Song Li
- College of Basic Medicine, Shandong First Medical University, No. 6699 Qingdao Road, Ji'nan 250024, China
| | - Guangcheng Yang
- College of Biological and Brewing Engineering, Taishan University, No. 525 Dongyue Street, Tai'an, Shandong 271000, China
| | - Zhenxian Lin
- College of Biological and Brewing Engineering, Taishan University, No. 525 Dongyue Street, Tai'an, Shandong 271000, China
| | - Zengmin Miao
- College of Life Sciences, Shandong First Medical University, No. 619 Changcheng Road, Tai'an 271016, China.
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14
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Zhang XD, Liu ZY, Wang MS, Guo YX, Wang XK, Luo K, Huang S, Li RF. Mechanisms and regulations of ferroptosis. Front Immunol 2023; 14:1269451. [PMID: 37868994 PMCID: PMC10587589 DOI: 10.3389/fimmu.2023.1269451] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Regulation of cell mortality for disease treatment has been the focus of research. Ferroptosis is an iron-dependent regulated cell death whose mechanism has been extensively studied since its discovery. A large number of studies have shown that regulation of ferroptosis brings new strategies for the treatment of various benign and malignant diseases. Iron excess and lipid peroxidation are its primary metabolic features. Therefore, genes involved in iron metabolism and lipid metabolism can regulate iron overload and lipid peroxidation through direct or indirect pathways, thereby regulating ferroptosis. In addition, glutathione (GSH) is the body's primary non-enzymatic antioxidants and plays a pivotal role in the struggle against lipid peroxidation. GSH functions as an auxiliary substance for glutathione peroxidase 4 (GPX4) to convert toxic lipid peroxides to their corresponding alcohols. Here, we reviewed the researches on the mechanism of ferroptosis in recent years, and comprehensively analyzed the mechanism and regulatory process of ferroptosis from iron metabolism and lipid metabolism, and then described in detail the metabolism of GPX4 and the main non-enzymatic antioxidant GSH in vivo.
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Affiliation(s)
- Xu-Dong Zhang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhong-Yuan Liu
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mao-Sen Wang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu-Xiang Guo
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiang-Kun Wang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kai Luo
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuai Huang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ren-Feng Li
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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15
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Liang A, Zhou W, Zhang H, Zhang J, Zhang XE, Fang T, Li F. Effects of Individual Amino Acids on the Blood Circulation of Biosynthetic Protein Nanocages: Toward Guidance on Surface Engineering. Adv Healthc Mater 2023; 12:e2300502. [PMID: 37067183 DOI: 10.1002/adhm.202300502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Protein nanocages (PNCs) hold great promise for developing multifunctional nanomedicines. Long blood circulation is a key requirement of PNCs for most in vivo application scenarios. In addition to the classical PEGylation strategy, short peptides with a specific sequence screened via phage display are also very effective in prolonging the blood half-life (t1/2 ) of PNCs. However, there is a lack of knowledge on how individual amino acids affect the circulation of PNCs. Here the effects of the 20 proteinogenic amino acids in the form of an X3 or X5 tag (X represents an amino acid) are explored on the pharmacokinetics of PNCs, which lead to the formation of a heatmap illustrating the extent of t1/2 prolongation by each proteinogenic amino acid. Significantly, oligo-lysine and oligo-arginine can effectively prolong the t1/2 of strongly negatively charged PNCs through charge neutralization, while oligo-cysteine can also do so, but via a different mechanism, mediating the covalent binding of PNCs with plasma albumin as a stealth material. These findings are extendible and offer guidance for surface-engineering biosynthetic PNCs and other nanoparticles.
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Affiliation(s)
- Ao Liang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Juan Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ti Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Rivera M. Mobilization of iron stored in bacterioferritin, a new target for perturbing iron homeostasis and developing antibacterial and antibiofilm molecules. J Inorg Biochem 2023; 247:112306. [PMID: 37451083 DOI: 10.1016/j.jinorgbio.2023.112306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Antibiotic resistance is a global public health threat. The care of chronic infections is complicated by bacterial biofilms. Biofilm embedded cells can be up to 1000-fold more tolerant to antibiotic treatment than planktonic cells. Antibiotic tolerance is a condition which does not involve mutation and enables bacteria to survive in the presence of antibiotics. The antibiotic tolerance of biofilm-cells often renders antibiotics ineffective, even against strains that do not carry resistance-impairing mutations. This review discusses bacterial iron homeostasis and the strategies being developed to target this bacterial vulnerability, with emphasis on a recently proposed approach which aims at targeting the iron storage protein bacterioferritin (Bfr) and its physiological partner, the ferredoxin Bfd. Bfr regulates cytosolic iron concentrations by oxidizing Fe2+ and storing Fe3+ in its internal cavity, and by forming a complex with Bfd to reduce Fe3+ in the internal cavity and release Fe2+ to the cytosol. Blocking the Bfr-Bfd complex in P. aeruginosa cells causes an irreversible accumulation of Fe3+ in BfrB and simultaneous cytosolic iron depletion, which leads to impaired biofilm maintenance and biofilm cell death. Recently discovered small molecule inhibitors of the Bfr-Bfd complex, which bind Bfr at the Bfd binding site, inhibit iron mobilization, and elicit biofilm cell death.
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Affiliation(s)
- Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA.
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17
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Williams SM, Chatterji D. Dps Functions as a Key Player in Bacterial Iron Homeostasis. ACS OMEGA 2023; 8:34299-34309. [PMID: 37779979 PMCID: PMC10536872 DOI: 10.1021/acsomega.3c03277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Iron plays a vital role in the maintenance of life, being central to various cellular processes, from respiration to gene regulation. It is essential for iron to be stored in a nontoxic and readily available form. DNA binding proteins under starvation (Dps) belong to the ferritin family of iron storage proteins and are adept at storing iron in their hollow protein shells. Existing solely in prokaryotes, these proteins have the additional functions of DNA binding and protection from oxidative stress. Iron storage proteins play a functional role in storage, release, and transfer of iron and therefore are central to the optimal functioning of iron homeostasis. Here we review the multifarious properties of Dps through relevant biochemical and structural studies with a focus on iron storage and ferroxidation. We also examine the role of Dps as a possible candidate as an iron donor to iron-sulfur (Fe-S) clusters, which are ubiquitous to many biological processes.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute
of Structural and Molecular Biology, Birkbeck,
University of London, Malet Street, London WC1E
7HX, United Kingdom
| | - Dipankar Chatterji
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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18
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Adak S, Ye N, Calderone LA, Schäfer RJB, Lukowski AL, Pandelia ME, Drennan CL, Moore BS. Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551874. [PMID: 37577561 PMCID: PMC10418191 DOI: 10.1101/2023.08.03.551874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes via the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third strategy of nitrile biosynthesis featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the 'eagle-killing' neurotoxin, aetokthonotoxin, AetD converts the alanyl side chain of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical, and biophysical techniques, we characterized AetD as a non-heme diiron enzyme that belongs to the emerging Heme Oxygenase-like Diiron Oxidase and Oxygenase (HDO) superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation that we propose proceeds via an aziridine intermediate. Our work presents a new paradigm for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other HDO enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Logan A. Calderone
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rebecca J. B. Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - April L. Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
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19
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Singh M, Penmatsa A, Nandi D. Functional Characterization of Salmonella Typhimurium Encoded YciF, a Domain of Unknown Function (DUF892) Family Protein, and Its Role in Protection during Bile and Oxidative Stress. J Bacteriol 2023; 205:e0005923. [PMID: 37367303 PMCID: PMC10367587 DOI: 10.1128/jb.00059-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
YciF (STM14_2092) is a member of the domain of unknown function (DUF892) family. It is an uncharacterized protein involved in stress responses in Salmonella Typhimurium. In this study, we investigated the significance of YciF and its DUF892 domain during bile and oxidative stress responses of S. Typhimurium. Purified wild-type YciF forms higher order oligomers, binds to iron, and displays ferroxidase activity. Studies on the site-specific mutants revealed that the ferroxidase activity of YciF is dependent on the two metal binding sites present within the DUF892 domain. Transcriptional analysis displayed that the ΔcspE strain, which has compromised expression of YciF, encounters iron toxicity due to dysregulation of iron homeostasis in the presence of bile. Utilizing this observation, we demonstrate that the bile mediated iron toxicity in ΔcspE causes lethality, primarily through the generation of reactive oxygen species (ROS). Expression of wild-type YciF, but not the three mutants of the DUF892 domain, in ΔcspE alleviate ROS in the presence of bile. Our results establish the role of YciF as a ferroxidase that can sequester excess iron in the cellular milieu to counter ROS-associated cell death. This is the first report of biochemical and functional characterization of a member of the DUF892 family. IMPORTANCE The DUF892 domain has a wide taxonomic distribution encompassing several bacterial pathogens. This domain belongs to the ferritin-like superfamily; however, it has not been biochemically and functionally characterized. This is the first report of characterization of a member of this family. In this study, we demonstrate that S. Typhimurium YciF is an iron binding protein with ferroxidase activity, which is dependent on the metal binding sites present within the DUF892 domain. YciF combats iron toxicity and oxidative damage caused due to exposure to bile. The functional characterization of YciF delineates the significance of the DUF892 domain in bacteria. In addition, our studies on S. Typhimurium bile stress response divulged the importance of comprehensive iron homeostasis and ROS in bacteria.
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Affiliation(s)
- Madhulika Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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20
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Guerra JPL, Penas D, Tavares P, Pereira AS. Influence of Cupric (Cu 2+) Ions on the Iron Oxidation Mechanism by DNA-Binding Protein from Starved Cells (Dps) from Marinobacter nauticus. Int J Mol Sci 2023; 24:10256. [PMID: 37373403 DOI: 10.3390/ijms241210256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by oxidizing and storing ferrous ions within their cavity, using either hydrogen peroxide or molecular oxygen as the co-substrate, thus reducing the toxic effects of Fenton reactions. Interestingly, the interaction between Dps and transition metals (other than iron) is a known but relatively uncharacterized phenomenon. The impact of non-iron metals on the structure and function of Dps proteins is a current topic of research. This work focuses on the interaction between the Dps from Marinobacter nauticus (a marine facultative anaerobe bacterium capable of degrading petroleum hydrocarbons) and the cupric ion (Cu2+), one of the transition metals of greater biological relevance. Results obtained using electron paramagnetic resonance (EPR), Mössbauer and UV/Visible spectroscopies revealed that Cu2+ ions bind to specific binding sites in Dps, exerting a rate-enhancing effect on the ferroxidation reaction in the presence of molecular oxygen and directly oxidizing ferrous ions when no other co-substrate is present, in a yet uncharacterized redox reaction. This prompts additional research on the catalytic properties of Dps proteins.
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Affiliation(s)
- João P L Guerra
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Daniela Penas
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro Tavares
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alice S Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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21
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Guo J, Lyu S, Qi Y, Chen X, Yang L, Zhao C, Wang H. Molecular evolution and gene expression of ferritin family involved in immune defense of lampreys. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 146:104729. [PMID: 37187445 DOI: 10.1016/j.dci.2023.104729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/06/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
Ferritin, one of the key regulators of iron homeostasis, is widely present throughout almost all species. The vertebrate ferritin family, which originates from a single gene in the ancestral invertebrates, contains the widest variety of ferritin subtypes among all animal species. However, the evolutionary history of the vertebrate ferritin family remains to be further clarified. In this study, genome-wide identification of the ferritin homologs is performed in lampreys, which are the extant representatives of jawless vertebrates that diverged from the future jawed vertebrates more than 500 million years ago. Molecular evolutionary analyses show that four members of the lamprey ferritin family, L-FT1-4, are derived from a common ancestor with jawed vertebrate ferritins prior to the divergence of the jawed vertebrate ferritin subtypes. The lamprey ferritin family shares evolutionarily conserved characteristics of the ferritin H subunit with higher vertebrates, but certain members such as L-FT1 additionally accumulate some features of the M or L subunits. Expression profiling reveals that lamprey ferritins are highly expressed in the liver. The transcription of L-FT1 is significantly induced in the liver and heart during lipopolysaccharide stimulation, indicating that L-FTs may play a role in the innate immune response to bacterial infection in lampreys. Furthermore, the transcriptional expression of L-FT1 in quiescent and LPS-activated leukocytes is up- and down-regulated by the lamprey TGF-β2, an essential regulator of the inflammatory response, respectively. Our results provide new insights into the origin and evolution of the vertebrate ferritin family and reveal that lamprey ferritins may be involved in immune regulation as target genes of the TGF-β signaling pathway.
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Affiliation(s)
- Junfu Guo
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116081, China
| | - Shuangyu Lyu
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116081, China
| | - Yanchen Qi
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
| | - Xuanyi Chen
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116081, China
| | - Lu Yang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116081, China
| | - Chunhui Zhao
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China.
| | - Hao Wang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116081, China.
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22
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Wang J, Wang Q, Tang YJ, Fu HM, Fang F, Guo JS, Yan P, Chen YP. Unraveling the structure and function of bacterioferritin in Candidatus Kuenenia stuttgartiensis: Iron storage sites maintain cellular iron homeostasis. WATER RESEARCH 2023; 238:120016. [PMID: 37146397 DOI: 10.1016/j.watres.2023.120016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 04/03/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Anammox bacteria rely heavily on iron and have many iron storage sites. However, the biological significance of these iron storage sites has not been clearly defined. In this study, we explored the properties and location of iron storage sites to better understand their cellular function. To do this, the Candidatus Kuenenia stuttgartiensis iron storage protein, bacterioferritin (K.S Bfr), was successfully expressed and purified. In vitro, correctly assembled globulins were observed by transmission electron microscopy. The self-assembled K.S Bfr has active redox and can bind Fe2+ and mineralize it in the protein cavity. In vivo, engineered bacteria with K.S Bfr showed good adaptability to Fe2+, with a survival rate of 78.9% when exposed to 5 mM Fe2+, compared with only 66.0% for wild-type bacteria lacking K.S Bfr. A potential iron regulatory strategy similar to that of Anammox was identified in transcriptomic analysis of engineered bacteria. This system may be controlled by the iron uptake regulator Furto transport Fe2+ via FeoB and store excess Fe2+ in K.S Bfr to maintain cellular homeostasis. K.S Bfr has superior iron storage capacity both intracellularly and in vitro. The discovery of K.S Bfr reveals the storage location of iron-rich nanoparticles, increases our understanding of the adaptability of iron-dependent bacteria to Fe2+, and suggests possible iron regulation strategies in Anammox bacteria.
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Affiliation(s)
- Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Yu-Jiao Tang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
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23
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Cruz-López R, Carrano CJ. Iron uptake, transport and storage in marine brown algae. Biometals 2023; 36:371-383. [PMID: 36930341 DOI: 10.1007/s10534-023-00489-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/10/2023] [Indexed: 03/18/2023]
Abstract
Iron is a vital although biologically inaccessible trace nutrient for nearly all forms of life but "free" iron can be deleterious to cells and thus iron uptake and storage must be carefully controlled. The marine environment is particularly iron poor making mechanisms for its uptake and storage even more imperative. In this brief review we explore the known and potential iron uptake and storage pathways for the biologically and economically important marine brown macroalgae (seaweeds/kelps).
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Affiliation(s)
- Ricardo Cruz-López
- Instituto de Investigaciones Oceanológicas (IIO), Universidad Autónoma de Baja California (UABC), Ensenada, Baja California, México.
| | - Carl J Carrano
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182-1030, USA
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Liu J, Yang G, Zhang H. Glyphosate-triggered hepatocyte ferroptosis via suppressing Nrf2/GSH/GPX4 axis exacerbates hepatotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160839. [PMID: 36521597 DOI: 10.1016/j.scitotenv.2022.160839] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Glyphosate (GLY) exposure has been reported to damage organs in animals, in particular the liver, due to increased reactive oxygen species (ROS). Ferroptosis is defined as a new type of cell death that is characterized by the increase of ROS. The purpose of this study was to elucidate whether the relationship between ferroptosis and GLY-induced hepatotoxicity is of significance to enlarge the knowledge about GLY toxicity and consequences for human and animal health. To this end, in this study, we investigated the role of ferroptosis in GLY-induced hepatotoxicity both in vivo and in vitro. The results showed that GLY exposure triggered ferroptosis in L02 cells, but pretreatment with ferroptosis inhibitor ferrostatin (Fer-1) rescued ferroptosis-induced injury, thereby indicating that ferroptosis plays a key role in GLY-induced hepatotoxicity. Moreover, N-acetylcysteine, a glutathione (GSH) synthesis precursor, reversed GLY-triggered ferroptosis damage, thus indicating that GSH exhaustion may be a prerequisite for GLY-triggered hepatotoxicity. Mechanistically, GLY inhibited GSH biosynthesis via blocking the phosphorylation and nuclear translocation of Nrf2, which resulted in GSH depletion-induced hepatocyte ferroptosis. In a mouse model, GLY exposure triggered ferroptosis-induced liver damage, which can be rescued by pretreatment with Fer-1 or tBHQ (a specific agonist of Nrf2). To our knowledge, this is the first study to reveal that GLY-triggered hepatocyte ferroptosis via suppressing Nrf2/GSH/GPX4 axis exacerbates hepatotoxicity, which expands our knowledge about GLY toxicity in animal and human health.
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Affiliation(s)
- Jingbo Liu
- College of Biological and Brewing Engineering, Taishan University, No. 525 Dongyue Street, 271000 Tai'an City, Shandong Province, China.
| | - Guangcheng Yang
- College of Biological and Brewing Engineering, Taishan University, No. 525 Dongyue Street, 271000 Tai'an City, Shandong Province, China
| | - Hongna Zhang
- College of Bioscience and Engineering, Hebei University of Economics and Business, No. 47 Xuefu Road, 050061 Shijiazhuang City, Hebei Province, China.
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25
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Estêvão J, Osorio H, Costas B, Cruz A, Fernández-Boo S. Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108566. [PMID: 36736640 DOI: 10.1016/j.fsi.2023.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The grooved carpet shell (Ruditapes decussatus) is a clam species with high economic and social importance in several European and Mediterranean countries. Production of this species suffered a decline caused by biotic (parasite infection) and abiotic factors (environmental factors, stress, poor management methods and intensive culture of the introduced species Ruditapes philippinarum). The protozoan parasite Perkinsus olseni is also responsible for the decline of production, being nowadays one of the major issues for clam culture. Molecular biomarkers that might represent tolerance of R. decussatus to P. olseni have already been uncovered, shedding light in a possible production improvement by selecting those clams with a strongest immune response. In the present study, new tolerance biomarkers to P. olseni infection in R. decussatus were identified. The haemolymph proteomic profiles of naturally non/low-infected (tolerant) and highly-infected (susceptible) clams by the parasite across several heavy affected areas of Europe were characterized through a shotgun proteomics approach. Also, the mechanisms that might be involved in the responses against the disease in chronic infections were explored. Proteins related to energy restoration and balance, metabolic regulation, energy accumulation, ROS production, lysosomal activity, amino acid synthesis, proteolytic activity, iron regulation, iron withholding, and immune response modulation were significantly regulated in susceptible clams. In the tolerant group, proteins related to phagocytosis regulation, control of cell growth and proliferation, gonadal maturation, regulation of apoptosis, growth modulation, response to oxidative stress, iron regulation, shell development and metabolic regulation were significantly expressed. In summary, the protein expression profile of tolerant individuals suggests that an efficient pathogen elimination mechanism coupled to a better metabolic regulation leads to a tolerance to the parasite infection by limiting the spread through the tissues.
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Affiliation(s)
- João Estêvão
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Hugo Osorio
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - Benjamin Costas
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Andreia Cruz
- Oceano Fresco S.A, Porto de Abrigo, 2450-075, Nazaré, Portugal
| | - Sergio Fernández-Boo
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal.
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26
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Bihani SC, Nagar V, Kumar M. Mechanistic and evolutionary insights into alkaline phosphatase superfamily through structure-function studies on Sphingomonas alkaline phosphatase. Arch Biochem Biophys 2023; 736:109524. [PMID: 36716801 DOI: 10.1016/j.abb.2023.109524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/20/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Alkaline phosphatases (APs), represented by E. coli AP (ECAP), employ an arginine residue to stabilize the phosphoryl group in the active site; whereas, AP from Sphingomonas (SPAP) shows a unique combination of substrate-binding residues; Thr89, Asn110, Lys171, and Arg173. Although such combination has been observed only in SPAP, these residues are present separately in different members of the AP superfamily. Here, we establish the presence of two distinct classes of APs; ECAP-type and SPAP-type. Bioinformatic analyses show that SPAP-type of APs are widely distributed in the bacterial kingdom. The role of active site residues in the catalytic mechanism has been delineated through a set of crystal structures reported here. These structures, representing different stages of the reaction pathway provide wealth of information for the catalytic mechanism. Despite critical differences in the substrate binding residues, SPAP follows a mechanism similar to that of ECAP-type of APs. Structure-based phylogenetic analysis suggests that SPAP and ECAP may have diverged very early during the evolution from a common ancestor. Moreover, it is proposed that the SPAP-type of APs are fundamental members of the AP superfamily and are more closely related to other members of the superfamily as compared to the ECAP-type of APs.
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Affiliation(s)
- Subhash C Bihani
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Vandan Nagar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India; Food Microbiology Group, Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
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27
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Sánchez-Jiménez A, Marcos-Torres FJ, Llamas MA. Mechanisms of iron homeostasis in Pseudomonas aeruginosa and emerging therapeutics directed to disrupt this vital process. Microb Biotechnol 2023. [PMID: 36857468 DOI: 10.1111/1751-7915.14241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen able to infect any human tissue. One of the reasons for its high adaptability and colonization of host tissues is its capacity of maintaining iron homeostasis through a wide array of iron acquisition and removal mechanisms. Due to their ability to cause life-threatening acute and chronic infections, especially among cystic fibrosis and immunocompromised patients, and their propensity to acquire resistance to many antibiotics, the World Health Organization (WHO) has encouraged the scientific community to find new strategies to eradicate this pathogen. Several recent strategies to battle P. aeruginosa focus on targeting iron homeostasis mechanisms, turning its greatest advantage into an exploitable weak point. In this review, we discuss the different mechanisms used by P. aeruginosa to maintain iron homeostasis and the strategies being developed to fight this pathogen by blocking these mechanisms. Among others, the use of iron chelators and mimics, as well as disruption of siderophore production and uptake, have shown promising results in reducing viability and/or virulence of this pathogen. The so-called 'Trojan-horse' strategy taking advantage of the siderophore uptake systems is emerging as an efficient method to improve delivery of antibiotics into the bacterial cells. Moreover, siderophore transporters are considered promising targets for the developing of P. aeruginosa vaccines.
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Affiliation(s)
- Ana Sánchez-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Francisco J Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María A Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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28
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Wang W, Wang Y, Xi H, Song Z, Zhang W, Xie L, Ma D, Qin N, Wang H. Extension Peptide of Plant Ferritin from Setaria italica Presents a Novel Fold. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:934-943. [PMID: 36576327 DOI: 10.1021/acs.jafc.2c07595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The extension peptide (EP) is the most distinctive feature of mature plant ferritin. Some EPs have exhibited serine-like protease activity, which is associated with iron uptake and release. EP forms a helix and a long loop, followed by a conserved core helical bundle. However, whether the EP adopts a stable or uniform folding pattern in all plants remains unclear. To clarify this, we investigated the crystal structure of ferritin-1 from Setaria italica (SiFer1), a type of monocotyledon. In our structure of SiFer1, the EP is different from other EPs in other solved structures of plant ferritins and consisted of a pair of β-sheets, a shorter helix, and two loops, which masks two hydrophobic pockets on the outer surface of every subunit. Furthermore, sequence analysis and structure comparison suggest that the EPs in ferritins from monocotyledons may adopt a novel fold pattern, and the conformations of EPs in ferritins are alterable among different plant species. Furthermore, additional eight iron atoms were first founded binding in the fourfold channels, demonstrating the vital function of fourfold channels in iron diffusion. In all, our structure provides new clues for understanding plant ferritins and the functions of the EP.
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Affiliation(s)
- Wenming Wang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Yuan Wang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Hongfang Xi
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Zidan Song
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Wenlong Zhang
- College of Chinese Medicine and Food Engineering, Experimental Management Center, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Leilei Xie
- College of Chinese Medicine and Food Engineering, Experimental Management Center, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Danyang Ma
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Nan Qin
- College of Chinese Medicine and Food Engineering, Experimental Management Center, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Hongfei Wang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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29
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Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis. Int J Mol Sci 2022; 24:ijms24010469. [PMID: 36613913 PMCID: PMC9820295 DOI: 10.3390/ijms24010469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H2O2 treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.
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30
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Manicki M, Aydin H, Abriata LA, Overmyer KA, Guerra RM, Coon JJ, Dal Peraro M, Frost A, Pagliarini DJ. Structure and functionality of a multimeric human COQ7:COQ9 complex. Mol Cell 2022; 82:4307-4323.e10. [PMID: 36306796 PMCID: PMC10058641 DOI: 10.1016/j.molcel.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/01/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.
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Affiliation(s)
- Mateusz Manicki
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Halil Aydin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53506, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub and Altos Labs Bay Area Institute of Science, San Francisco, CA, USA.
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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31
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Bacterioferritin nanocage: Structure, biological function, catalytic mechanism, self-assembly and potential applications. Biotechnol Adv 2022; 61:108057. [DOI: 10.1016/j.biotechadv.2022.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022]
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32
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Leister D, Marino G, Minagawa J, Dann M. An ancient function of PGR5 in iron delivery? TRENDS IN PLANT SCIENCE 2022; 27:971-980. [PMID: 35618596 DOI: 10.1016/j.tplants.2022.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
In all phototrophic organisms, the photosynthetic apparatus must be protected from light-induced damage. One important mechanism that mitigates photodamage in plants is antimycin A (AA)-sensitive cyclic electron flow (CEF), the evolution of which remains largely obscure. Here we show that proton gradient regulation 5 (PGR5), a key protein involved in AA-sensitive CEF, displays intriguing commonalities - including sequence and structural features - with a group of ferritin-like proteins. We therefore propose that PGR5 may originally have been involved in prokaryotic iron mobilization and delivery, which facilitated a primordial type of CEF as a side effect. The abandonment of the bacterioferritin system during the transformation of cyanobacterial endosymbionts into chloroplasts might have allowed PGR5 to functionally specialize in CEF.
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Affiliation(s)
- Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - Giada Marino
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Marcel Dann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany; Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan.
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33
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Bradley JM, Gray E, Richardson J, Moore GR, Le Brun NE. Protein encapsulation within the internal cavity of a bacterioferritin. NANOSCALE 2022; 14:12322-12331. [PMID: 35969005 PMCID: PMC9439638 DOI: 10.1039/d2nr01780f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The thermal and chemical stability of 24mer ferritins has led to attempts to exploit their naturally occurring nanoscale (8 nm) internal cavities for biotechnological applications. An area of increasing interest is the encapsulation of molecules either for medical or biocatalysis applications. Encapsulation requires ferritin dissociation, typically induced using high temperature or acidic conditions (pH ≥ 2), which generally precludes the inclusion of fragile cargo such as proteins or peptide fragments. Here we demonstrate that minimizing salt concentration combined with adjusting the pH to ≤8.5 (i.e. low proton/metal ion concentration) reversibly shifts the naturally occurring equilibrium between dimeric and 24meric assemblies of Escherichia coli bacterioferritin (Bfr) in favour of the disassembled form. Interconversion between the different oligomeric forms of Bfr is sufficiently slow under these conditions to allow the use of size exclusion chromatography to obtain wild type protein in the purely dimeric and 24meric forms. This control over association state was exploited to bind heme at natural sites that are not accessible in the assembled protein. The potential for biotechnological applications was demonstrated by the encapsulation of a small, acidic [3Fe-4S] cluster-containing ferredoxin within the Bfr internal cavity. The capture of ∼4-6 negatively charged ferredoxin molecules per cage indicates that charge complementarity with the inner protein surface is not an essential determinant of successful encapsulation.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Elizabeth Gray
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Jake Richardson
- Bioimaging Facility, John Innes Centre, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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34
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Toboz P, Amiri M, Tabatabaei N, Dufour CR, Kim SH, Fillebeen C, Ayemoba CE, Khoutorsky A, Nairz M, Shao L, Pajcini KV, Kim KW, Giguère V, Oliveira RL, Constante M, Santos MM, Morales CR, Pantopoulos K, Sonenberg N, Pinho S, Tahmasebi S. The amino acid sensor GCN2 controls red blood cell clearance and iron metabolism through regulation of liver macrophages. Proc Natl Acad Sci U S A 2022; 119:e2121251119. [PMID: 35994670 PMCID: PMC9436309 DOI: 10.1073/pnas.2121251119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
GCN2 (general control nonderepressible 2) is a serine/threonine-protein kinase that controls messenger RNA translation in response to amino acid availability and ribosome stalling. Here, we show that GCN2 controls erythrocyte clearance and iron recycling during stress. Our data highlight the importance of liver macrophages as the primary cell type mediating these effects. During different stress conditions, such as hemolysis, amino acid deficiency or hypoxia, GCN2 knockout (GCN2-/-) mice displayed resistance to anemia compared with wild-type (GCN2+/+) mice. GCN2-/- liver macrophages exhibited defective erythrophagocytosis and lysosome maturation. Molecular analysis of GCN2-/- cells demonstrated that the ATF4-NRF2 pathway is a critical downstream mediator of GCN2 in regulating red blood cell clearance and iron recycling.
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Affiliation(s)
- Phoenix Toboz
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal, QC, H3A 1A3, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Catherine R. Dufour
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Seung Hyeon Kim
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Carine Fillebeen
- Lady Davis Institute for Medical Research, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Charles E. Ayemoba
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Arkady Khoutorsky
- Department of Anesthesia and Faculty of Dentistry, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Manfred Nairz
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Lijian Shao
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Kostandin V. Pajcini
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Ki-Wook Kim
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Vincent Giguère
- Department of Biochemistry, McGill University, Montreal, QC, H3A 1A3, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Regiana L. Oliveira
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Marco Constante
- Nutrition and Microbiome Laboratory, Centre de recherche du CHUM and Department of Medicine, Université de Montréal, Montréal, QC, H3X 0A9, Canada
| | - Manuela M. Santos
- Nutrition and Microbiome Laboratory, Centre de recherche du CHUM and Department of Medicine, Université de Montréal, Montréal, QC, H3X 0A9, Canada
| | - Carlos R. Morales
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC, H3A 1A3, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Sandra Pinho
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, 60612
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Wang Q, Zhou YM, Xing CY, Li WC, Shen Y, Yan P, Guo JS, Fang F, Chen YP. Encapsulins from Ca. Brocadia fulgida: An effective tool to enhance the tolerance of engineered bacteria (pET-28a-cEnc) to Zn 2. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128954. [PMID: 35462189 DOI: 10.1016/j.jhazmat.2022.128954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Zn2+ is largely discharged from many industries and poses a severe threat to the environment, making its remediation crucial. Encapsulins, proteinaceous nano-compartments, may protect cells against environmental stresses by sequestering toxic substances. To determine whether hemerythrin-containing encapsulins (cEnc) from anammox bacteria Ca. Brocadia fulgida can help cells deal with toxic substances such as Zn2+, we transferred cEnc into E.coli by molecular biology technologies for massive expression and then cultured them in media with increasing Zn2+ levels. The engineered bacteria (with cEnc) grew better and entered the apoptosis phase later, while wild bacteria showed poor survival. Furthermore, tandem mass tag-based quantitative proteomic analysis was used to reveal the underlying regulatory mechanism by which the genetically-engineered bacteria (with cEnc) adapted to Zn2+ stress. When Zn2+ was sequestered in cEnc as a transition, the engineered bacteria presented a complex network of regulatory systems against Zn2+-induced cytotoxicity, including functions related to ribosomes, sulfur metabolism, flagellar assembly, DNA repair, protein synthesis, and Zn2+ efflux. Our findings offer an effective and promising stress control strategy to enhance the Zn2+ tolerance of bacteria for Zn2+ remediation and provide a new application for encapsulins.
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Affiliation(s)
- Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yue-Ming Zhou
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Chong-Yang Xing
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wen-Chao Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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Kim HJ, Ishida K, Ishida‐Ito M, Hertweck C. Sequential Allylic Alcohol Formation by a Multifunctional Cytochrome P450 Monooxygenase with Rare Redox Partners. Angew Chem Int Ed Engl 2022; 61:e202203264. [PMID: 35416382 PMCID: PMC9322674 DOI: 10.1002/anie.202203264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/21/2022]
Abstract
Caryoynencin is a toxic and antifungal fatty acid derivative produced by a number of plant-pathogenic and insect-protective bacteria (Trinickia caryophylli and Burkholderia spp.). In addition to the reactive tetrayne unit, the presence of an allylic alcohol moiety is critical for antimicrobial activities. By a combination of mutational analyses, heterologous expression and in vitro reconstitution experiments we show that the cytochrome P450 monooxygenase CayG catalyzes the complex transformation of a saturated carbon backbone into an allylic alcohol. Unexpectedly, CayG employs a ferritin-like protein (CayK) or a rubredoxin (CayL) component for electron transport. A desaturation-hydroxylation sequence was deduced from a time-course study and in vitro biotransformations with pathway intermediates, substrate analogues, protegencin congeners from Pseudomonas protegens Pf-5, and synthetic derivatives. This unusual multifunctional oxygenase may inspire future biocatalytic applications.
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Affiliation(s)
- Hak Joong Kim
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Keishi Ishida
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Mie Ishida‐Ito
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Christian Hertweck
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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Abstract
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
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Affiliation(s)
- Tobias W. Giessen
- Departments of Biomedical Engineering and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Sequence, Expression, and Anti-GCRV Function of the Ferritin from the Grass Carp, Ctenopharyngodon idellus. Int J Mol Sci 2022; 23:ijms23126835. [PMID: 35743279 PMCID: PMC9224801 DOI: 10.3390/ijms23126835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Ferritin possesses an immune function to defend against pathogen infection. To elucidate the immunity-protecting roles of ferritin from Ctenopharyngodon idellus (Ciferritin) against virus infection, the cDNA and promoter sequences of Ciferritin were determined, and the correlations between Ciferrtin expressions and promoter methylation levels were analyzed. In addition, the functional role of Ciferrtin on GCRV (grass carp reovirus) infection was assessed. The full-length cDNA of Ciferritin is 1053 bp, consists of a 531 bp open-reading frame, and encodes 176 amino acids. Ciferritin showed the highest sequence identity with the ferritin middle subunit of Mylopharyngodon piceus (93.56%), followed by the subunits of Megalobrama amblycephala and Sinocyclocheilus rhinocerous. Ciferritin contains a conserved ferritin domain (interval: 10−94 aa), and the caspase recruitment domain (CARD) and Rubrerythrin domain were also predicted. In the spleen and kidney, significantly higher Ciferritin expressions were observed at 6, 12, 24, or 168 h post GCRV infection than those in the PBS injection group (p < 0.05). The Ciferrtin expression level in the progeny of maternal-immunized grass carp was significantly higher than that in the progeny of common grass carp (p < 0.05). Ciferritin promoter methylation level in the progeny from common grass carp was 1.27 ± 0.15, and in the progeny of the maternal-immunized group was 1.00 ± 0.14. In addition, methylation levels of “CpG9” and “CpG10” loci were significantly lower in the progeny of maternal-immunized fish than those in the common group. Except for the “CpG5”, methylation levels of all other detected “CpG” loci negatively correlated with Ciferritin expression levels. Furthermore, the total methylation level of “CpG1−10” negatively correlated with the Ciferritin expressions. The Ciferritin expression level was significantly up-regulated, and the VP7 protein levels were significantly reduced, at 24 h post GCRV infection in the Ciferritin over-expression cells (p < 0.05). The results from the present study provide sequence, epigenetic modification and expression, and anti-GCRV functional information of Ciferritin, which provide a basis for achieving resistance to GCRV in grass carp breeding.
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Grant CR, Amor M, Trujillo HA, Krishnapura S, Iavarone AT, Komeili A. Distinct gene clusters drive formation of ferrosome organelles in bacteria. Nature 2022; 606:160-164. [PMID: 35585231 PMCID: PMC10906721 DOI: 10.1038/s41586-022-04741-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/07/2022] [Indexed: 12/20/2022]
Abstract
Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification1-3. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins4,5. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown6,7. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus6. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.
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Affiliation(s)
- Carly R Grant
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Matthieu Amor
- Aix-Marseille Université, CEA, CNRS, BIAM, Saint-Paul-lez-Durance, France
| | - Hector A Trujillo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sunaya Krishnapura
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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Transcriptomic Analysis of the Molecular Response Mechanism of Microcystis aeruginosa to Iron Limitation Stress. WATER 2022. [DOI: 10.3390/w14111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Iron is an essential micronutrient for cyanobacteria. It is involved in physiological activities such as photosynthesis, respiration, and the synthesis of pigments. The impact of iron limitation on planktonic algae growth occurs in surface oceans globally, as well as in freshwater ecosystems. However, the molecular and physiological effects and response mechanism of cyanobacteria under iron-limited conditions have not been reported in detail. In this study, the effects of iron limitation on the cell density, chlorophyll content, and photosynthetic activity of Microcystis aeruginosa were determined, and transcriptome sequencing was undertaken. In a severely iron-deficient environment, the cell density and chlorophyll-a content of M. aeruginosa were significantly lower than in the iron-rich group (a 55.42% and 83.51% reduction, respectively). Similarly, the photosynthetic efficiency of M. aeruginosa was also inhibited by iron deficiency, and the maximum photochemical efficiency (Fv/Fm) of the severe iron deficiency group was only 66.72% of the control group. The transcriptome results showed that to cope with the iron-deficient environment, most genes involved in iron absorption and transport in M. aeruginosa were up-regulated. In particular, the fur and perR genes that regulate the iron uptake regulatory protein (Fur) were both up-regulated. Due to the high demand for iron in the photosynthetic electron transport chain of M. aeruginosa, most photosynthesis-related genes were down-regulated, for example, petJ, which regulates iron-containing cytochrome c6. In contrast, most of the genes related to glycolysis and respiration were up-regulated. These changes in gene expression may be a survival strategy for M. aeruginosa to cope with a long-term iron-deficient environment. This study provides insights into the molecular response mechanism of M. aeruginosa under iron limitation stress.
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Xu Y, Li Y, Li J, Chen W. Ethyl carbamate triggers ferroptosis in liver through inhibiting GSH synthesis and suppressing Nrf2 activation. Redox Biol 2022; 53:102349. [PMID: 35623314 PMCID: PMC9142717 DOI: 10.1016/j.redox.2022.102349] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 12/20/2022] Open
Abstract
Humans are inevitably exposed to ethyl carbamate (EC) via consumption of fermented food and beverages. EC, known as an environmental toxin, can cause oxidative stress-mediated severe toxicity, but the underlying mechanisms remain unveiled. Ferroptosis is a newly identified ROS-mediated non-apoptotic cell death characterized by iron accumulation and excessive lipid oxidation. In this study, we first found that EC triggered ferroptosis in liver cells by detection of decreased cell viability, GSH, GPX4 and Ferritin levels, as well as increased iron and MDA contents. Ferroptosis inhibitor ferrostatin-1 (Fer-1) pretreatment rescued ferroptotic damage, indicating that ferroptosis was critical for EC-caused cell death. Furthermore, GSH synthesis precursor N-acetylcysteine displayed significant anti-ferroptotic properties and we suggested that GSH depletion might be the main cause of ferroptosis under EC exposure. EC-triggered GSH depletion mainly depended on suppressed GSH synthesis via inhibition of SLC7A11 and GCLC expressions. Notably, EC blocked Nrf2 activation by repression of phosphorylation modification and nuclear translocation, which further resulted in ferroptosis occurrence. We also observed EC-induced liver dysfunction and inflammation, accompanied with oxidative stress, ferroptosis and downregulated Nrf2 signaling in Balb/c mice, which could be effectively reversed by Fer-1 and tBHQ pretreatment. Together, our study indicated that ferroptosis is a new mechanism for EC-caused toxicity, which was attributed to Nrf2 inactivation and GSH depletion. Ethyl carbamate (EC) caused ferroptosis in L02 cells and liver tissues. GSH depletion was critical for EC-induced ferroptotic cell death. EC exposure blocked GSH synthesis-related pathways. Inactivation of Nrf2 signaling was involved in EC-triggered ferroptosis.
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Affiliation(s)
- Yang Xu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yuting Li
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxin Li
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Wei Chen
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China.
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42
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Kim HJ, Ishida K, Ishida-Ito M, Hertweck C. Sequential Allylic Alcohol Formation by a Multifunctional Cytochrome P450 Monooxygenase with Rare Redox Partners. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hak Joong Kim
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Mie Ishida-Ito
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Department of Biomolecular Chemistry Beutenbergstr. 11a 07745 Jena GERMANY
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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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44
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Distinct structural characteristics define a new subfamily of Mycoplasma ferritin. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability. Biomolecules 2022; 12:biom12030366. [PMID: 35327558 PMCID: PMC8945002 DOI: 10.3390/biom12030366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 12/14/2022] Open
Abstract
Ferritins are iron storage proteins assembled from 24 subunits into a spherical and hollow structure. The genomes of many bacteria harbor genes encoding two types of ferritin-like proteins, the bacterial ferritins (Ftn) and the bacterioferritins (Bfr), which bind heme. The genome of P. aeruginosa PAO1 (like the genomes of many bacteria) contains genes coding for two different types of ferritin-like molecules, ftnA (PA4235) and bfrB (PA3531). The reasons for requiring the presence of two distinct types of iron storage protein in bacterial cells have remained largely unexplained. Attempts to understand this issue in P. aeruginosa through the recombinant expression of the ftnA and bfrB genes in E. coli host cells, coupled to the biochemical and structural characterization of the recombinant 24-mer FtnA and 24-mer BfrB molecules, have shown that each of the recombinant molecules can form an Fe3+-mineral core. These observations led to the suggestion that 24-mer FtnA and 24-mer BfrB molecules coexist in P. aeruginosa cells where they share iron storage responsibilities. Herein, we demonstrate that P. aeruginosa utilizes a single heterooligomeric 24-mer Bfr assembled from FtnA and BfrB subunits. The relative content of the FtnA and BfrB subunits in Bfr depends on the O2 availability during cell culture, such that Bfr isolated from aerobically cultured P. aeruginosa is assembled from a majority of BfrB subunits. In contrast, when the cells are cultured in O2-limiting conditions, the proportion of FtnA subunits in the isolated Bfr increases significantly and can become the most abundant subunit. Despite the variability in the subunit composition of Bfr, the 24-mer assembly is consistently arranged from FtnA subunit dimers devoid of heme and BfrB subunit dimers each containing a heme molecule.
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46
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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47
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Malych R, Füssy Z, Ženíšková K, Arbon D, Hampl V, Hrdý I, Sutak R. The response of Naegleria gruberi to oxidative stress. Metallomics 2022; 14:6527579. [PMID: 35150262 DOI: 10.1093/mtomcs/mfac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/06/2022] [Indexed: 11/14/2022]
Abstract
Aerobic organisms require oxygen for respiration but must simultaneously cope with oxidative damages inherently linked with this molecule. Unicellular amoeboflagellates of the genus Naegleria, containing both free-living species and opportunistic parasite, thrive in aerobic environments. However, they are also known to maintain typical features of anaerobic organisms. Here, we describe the mechanisms of oxidative damage mitigation in Naegleria gruberi and focus on the molecular characteristics of three noncanonical proteins interacting with oxygen and its derived reactive forms. We show that this protist expresses hemerythrin, protoglobin and an aerobic-type rubrerythrin, with spectral properties characteristic of the cofactors they bind. We provide evidence that protoglobin and hemerythrin interact with oxygen in vitro and confirm the mitochondrial localization of rubrerythrin by immunolabeling. Our proteomic analysis and immunoblotting following heavy metal treatment revealed upregulation of hemerythrin, while rotenone treatment resulted in an increase in rubrerythrin protein levels together with vast upregulation of alternative oxidase. Our study provided new insights into the mechanisms employed by N. gruberi to cope with different types of oxidative stress and allowed us to propose specific roles for three unique and understudied proteins: hemerythrin, protoglobin and rubrerythrin.
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Affiliation(s)
- Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kateřina Ženíšková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Dominik Arbon
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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48
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Chakravarty D, Bihani SC, Banerjee M, Kalwani P, Ballal A. Unique functional insights into the antioxidant response of the cyanobacterial Mn-catalase (KatB). Free Radic Biol Med 2022; 179:266-276. [PMID: 34793931 DOI: 10.1016/j.freeradbiomed.2021.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/12/2021] [Indexed: 01/06/2023]
Abstract
KatB, a hexameric Mn-catalase, plays a vital role in overcoming oxidative and salinity stress in the ecologically important, N2-fixing cyanobacterium, Anabaena. The 5 N-terminal residues of KatB, which show a high degree of conservation in cyanobacteria, form an antiparallel β-strand at the subunit interface of the KatB hexamer. In this study, the contribution of these N-terminal non-active site residues, towards the maintenance of the structure, biochemical properties, and redox balance was evaluated. Each N-terminal amino acid residue from the 2nd to the 7th position of KatB was individually mutated to Ala (to express KatBF2A/KatBF3A/KatBH4A/KatBK5E/KatBK6A/KatBE7A) or this entire 6 amino acid stretch was deleted (to yield KatBTrunc). All the above-mentioned KatB variants, along with the wild-type KatB protein (KatBWT), were overproduced in E. coli and purified. In comparison to KatBWT, the KatBF2A/KatBH4A/KatBTrunc proteins were less compact, more prone to chemical/thermal denaturation, and were unexpectedly inactive. KatBF3A/KatBK5E/KatBK6A showed biophysical/biochemical properties that were in between that of KatBWT and KatBF2A/KatBH4A/KatBTrunc. Surprisingly, KatBE7A was more thermostable with higher activity than KatBWT. On exposure to H2O2, E. coli expressing KatBWT/KatBE7A showed considerably reduced formation of ROS and increased survival than the other KatB variants. Utilizing the KatB structure, the molecular basis responsible for the altered stability/activity of the KatB mutants was delineated. This study demonstrates the physiological importance of the N-terminal β-strand of Mn-catalases in combating H2O2 stress and shows that the non-active site residues can be used for rational protein engineering to develop Mn-catalases with improved characteristics.
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Affiliation(s)
- Dhiman Chakravarty
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Radiation Biology & Health Sciences Division, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Prakash Kalwani
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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49
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Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, Zarazúa-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, Baslé A, Clarke DJ, Marles-Wright J. Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment. SCIENCE ADVANCES 2022; 8:eabj4461. [PMID: 35080974 PMCID: PMC8791618 DOI: 10.1126/sciadv.abj4461] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zak McIver
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas Lambert
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jasmine Emma Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Kelly J. Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Faye L. Cruickshank
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Patrick James
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Louise E. Horsfall
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kevin J. Waldron
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marcus D. Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Jon Marles-Wright
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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50
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Quilapi AM, Vargas-Lagos C, Martínez D, Muñoz JL, Spies J, Esperguel I, Tapia J, Oyarzún-Salazar R, Vargas-Chacoff L. Brain immunity response of fish Eleginops maclovinus to infection with Francisella noatunensis. FISH & SHELLFISH IMMUNOLOGY 2022; 120:695-705. [PMID: 34808359 DOI: 10.1016/j.fsi.2021.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
The brain's immune system is selective and hermetic in most species, including fish, favoring immune responses mediated by soluble immunomodulatory factors such as serotonin and the availability of nutrients against infectious processes. Francisella noatunensis coexist with fish such as Eleginops maclovinus, which raises questions about the susceptibility and immune response of the brain of E. maclovinus against Francisella. In this study, we inoculated fish with different doses of Francisella and took samples for 28 days. We detected bacteria in the brain of fish injected with a high concentration of Francisella at all time points. qPCR analysis of immune genes indicated a response mainly in the medium-dose and early expression of genes involved in iron metabolism. Finally, brain serotonin levels were higher than in uninfected fish in all conditions, suggesting possible immunomodulatory participation in an infectious process.
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Affiliation(s)
- Ana María Quilapi
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Universidad Santo Tomás, Osorno, Chile; Magister en Ciencias Mención Microbiología, Universidad Austral de Chile, Valdivia, Chile.
| | - Carolina Vargas-Lagos
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Danixa Martínez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Jose Luis Muñoz
- Centro de Investigación y Desarrollo i ∼ mar, Universidad de los Lagos, Casilla 557, Puerto Montt, Chile
| | - Johana Spies
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Ivan Esperguel
- Magister en Ciencias Mención Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Jaime Tapia
- Institute of Chemistry and Natural Resources, Universidad de Talca, Chile
| | | | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile.
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