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Jing W, Guo R, Zhu X, Peng S, Li H, Xu D, Hu L, Mo H. Ferrous gluconate triggers ferroptosis in Escherichia coli: Implications of lipid peroxidation and DNA damage. Microbiol Res 2024; 284:127711. [PMID: 38636240 DOI: 10.1016/j.micres.2024.127711] [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: 03/13/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024]
Abstract
Microbial ferroptosis has been proved to combat drug-resistant pathogens, but whether this pattern can be applied to the prevention and control of Escherichia coli remains to be further explored. In this study, ferrous gluconate (FeGlu) showed remarkable efficacy in killing E. coli MG1655 with a mortality rate exceeding 99.9%, as well as enterotoxigenic E. coli H10407 (ETEC H10407) and enterohemorrhagic E. coli O157:H7 (EHEC O157:H7). Bacteria death was instigated by the infiltration of Fe2+, accompanied by a burst of intracellular reactive oxygen species (ROS) and lipid peroxidation. Notably, mitigating lipid peroxidation failed to alleviate death of E. coli. Further findings confirmed that FeGlu induced DNA damage, and ΔrecA mutant showed more sensitive, implicating that DNA damage was involved in the death of E. coli. The direct interaction of Fe2+ with DNA was demonstrated by fluorescent staining, gel electrophoresis, and circular dichroism (CD). Moreover, proteomic analysis unveiled 50 differentially expressed proteins (DEPs), including 18 significantly down-regulated proteins and 32 significantly up-regulated proteins. Among them, the down-regulation of SOS-responsive transcriptional suppressor LexA indicated DNA damage induced severely by FeGlu. Furthermore, FeGlu influenced pathways such as fatty acid metabolism (FadB, FadE), iron-sulfur cluster assembly (IscA, IscU, YadR), iron binding, and DNA-binding transcription, along with α-linolenic acid metabolism, fatty acid degradation, and pyruvate metabolism. These pathways were related to FeGlu stress, including lipid peroxidation and DNA damage. In summary, FeGlu facilitated ferroptosis in E. coli through mechanisms involving lipid peroxidation and DNA damage, which presents a new strategy for the development of innovative antimicrobial strategies targeting E. coli infections.
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Affiliation(s)
- Wenhui Jing
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Rongxian Guo
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
| | - Xiaolin Zhu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Shurui Peng
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Hongbo Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Dan Xu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Liangbin Hu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Haizhen Mo
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Wang F, Deng G, Liang N, Hu P, Liu K, Liu T, Li Y, Yuan M, Liu L, Xie J, Qiao L, Liu F, Zhang J. Serum ferritin level is an effective prognostic factor for lung cancer immunotherapy. Cancer Biol Ther 2023; 24:2285367. [PMID: 38031846 PMCID: PMC10783829 DOI: 10.1080/15384047.2023.2285367] [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: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Immunotherapy of lung cancer has achieved promising clinical results. However, it is urgent to develop predictive biomarkers for effective immunotherapy. While ferroptosis plays a critical role in immunotherapy efficacy, ferritin is an important regulatory factor. We, therefore, hypothesize that basal serum ferritin levels before immunotherapy and their corresponding changes during immunotherapy can be useful predictors of immunotherapy response in patients with lung cancer. We measured serum ferritin levels in 107 patients with lung cancer before and during immune checkpoint blockade treatments and studied the correlation between ferritin levels, response rate, and survival. Moreover, the correlation between basal ferritin and PD-L1 expression, tumor stages and pathological types was also analyzed. Patients with lower basal serum ferritin levels before immunotherapy had longer progression-free survival (PFS) (median 7 vs 4 months, P = .023) and higher disease control rate (DCR) (X2 = 4.837, P = .028), those with downregulated serum ferritin levels during immunotherapy correlated with longer PFS (median 9.5 vs 4 months, P < .001) and higher DCR (X2 = 6.475, P = .011). However, the "integrated factor", which was calculated as the combination of lower basal serum ferritin levels before immunotherapy and downregulated serum ferritin levels during immunotherapy, correlated with prolonged PFS (P < .001). Multivariate analyses revealed that the basal serum ferritin levels before immunotherapy and the corresponding changes during immunotherapy were both strong independent prognostic factors (hazard ratio (HR) = 1.60, P = .041; HR = 2.65, P = .001). These findings suggest that serum ferritin levels can be used as a prognostic biomarker for lung cancer in predicting immunotherapy efficacy.
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Affiliation(s)
- Fei Wang
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Department of Oncology, Zaozhuang Shizhong District People’s Hospital, Zaozhuang, China
| | - Guodong Deng
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Ning Liang
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Pingping Hu
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Kuo Liu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Tong Liu
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Yang Li
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Meng Yuan
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong Provincial Qianfoshan Hospital, Weifang Medical University, Jinan, China
| | - Li Liu
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Jian Xie
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Lili Qiao
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Fengjun Liu
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Jiandong Zhang
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Oncology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Department of Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
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3
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Norfolk WA, Shue C, Henderson WM, Glinski DA, Lipp EK. Vibrio alginolyticus growth kinetics and the metabolic effects of iron. Microbiol Spectr 2023; 11:e0268023. [PMID: 37966200 PMCID: PMC10714744 DOI: 10.1128/spectrum.02680-23] [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: 07/26/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Transmission of V. alginolyticus occurs opportunistically through direct seawater exposure and is a function of its abundance in the environment. Like other Vibrio spp., V. alginolyticus are considered conditionally rare taxa in marine waters, with populations capable of forming large, short-lived blooms under specific environmental conditions, which remain poorly defined. Prior research has established the importance of temperature and salinity as the major determinants of Vibrio geographical and temporal range. However, bloom formation can be strongly influenced by other factors that may be more episodic and localized, such as changes in iron availability. Here we confirm the broad temperature and salinity tolerance of V. alginolyticus and demonstrate the importance of iron supplementation as a key factor for growth in the absence of thermal or osmotic stress. The results of this research highlight the importance of episodic iron input as a crucial metric to consider for the assessment of V. alginolyticus risk.
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Affiliation(s)
- William A. Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - Charlyn Shue
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - W. Matthew Henderson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, Georgia, USA
| | - Donna A. Glinski
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, Georgia, USA
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
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4
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Pandey SS. The Role of Iron in Phytopathogenic Microbe-Plant Interactions: Insights into Virulence and Host Immune Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3173. [PMID: 37687419 PMCID: PMC10563075 DOI: 10.3390/plants12173173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Iron is an essential element required for the growth and survival of nearly all forms of life. It serves as a catalytic component in multiple enzymatic reactions, such as photosynthesis, respiration, and DNA replication. However, the excessive accumulation of iron can result in cellular toxicity due to the production of reactive oxygen species (ROS) through the Fenton reaction. Therefore, to maintain iron homeostasis, organisms have developed a complex regulatory network at the molecular level. Besides catalyzing cellular redox reactions, iron also regulates virulence-associated functions in several microbial pathogens. Hosts and pathogens have evolved sophisticated strategies to compete against each other over iron resources. Although the role of iron in microbial pathogenesis in animals has been extensively studied, mechanistic insights into phytopathogenic microbe-plant associations remain poorly understood. Recent intensive research has provided intriguing insights into the role of iron in several plant-pathogen interactions. This review aims to describe the recent advances in understanding the role of iron in the lifestyle and virulence of phytopathogenic microbes, focusing on bacteria and host immune responses.
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Affiliation(s)
- Sheo Shankar Pandey
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati 781035, India; ; Tel.: +91-361-2270095 (ext. 216)
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
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5
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Alrehaili J. Leprosy Classification, Clinical Features, Epidemiology, and Host Immunological Responses: Failure of Eradication in 2023. Cureus 2023; 15:e44767. [PMID: 37809252 PMCID: PMC10557090 DOI: 10.7759/cureus.44767] [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] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Leprosy is of big concern in the medical fraternity. Leprosy is also known as Hansen's disease. It is a curable communicable disease that remains prevalent in most countries all over the globe. It is a chronic granulomatous infection commonly caused by Mycobacterium leprae and Mycobacterium lepromatosis, which mainly show an effect on the skin and peripheral nerves. To control the disease and minimize the impact of the disease, much effort has been put into it for decades. Nearly 0.2 million fresh cases were documented in 2017 worldwide in spite of being declared "eradicated" by the WHO in the year 2000. However, impressive achievements have been made in several countries, including India; still, we are lagging behind the ultimate goal of the final disappearance of leprosy. Extensive migration is a crucial element that may transmit leprosy to unaffected areas. Additionally, there are several areas in the USA where person-to-person leprosy transmission has been reported without a prior history of exposure. Recently, WHO instigated a new Global Leprosy Strategy 2021-2030, termed "Towards Zero Leprosy." In this article, we review the clinical features, leprosy epidemiology, transmission, classification, host immunological response, and diagnostic challenges.
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6
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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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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [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] [Indexed: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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8
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Pereira MMR, de Oliveira FM, da Costa AC, Junqueira-Kipnis AP, Kipnis A. Ferritin from Mycobacterium abscessus is involved in resistance to antibiotics and oxidative stress. Appl Microbiol Biotechnol 2023; 107:2577-2595. [PMID: 36862179 DOI: 10.1007/s00253-023-12420-8] [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: 11/02/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 03/03/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) is a rapidly growing Mycobacterium belonging to the M. abscessus complex that is often associated with lung and soft tissue infection outbreaks. Mycma is resistant to many antimicrobials, including those used for treating tuberculosis. Therefore, Mycma infections are difficult to treat and may lead to high infectious complication rates. Iron is essential for bacterial growth and establishment of infection. During infection, the host reduces iron concentrations as a defense mechanism. To counteract the host-induced iron deficiency, Mycma produces siderophores to capture iron. Mycma has two ferritins (encoded by mycma_0076 and mycma_0077) modulated by different iron concentrations, which allow the survival of this pathogen during iron scarcity. In this study, we constructed knockout (Mycma 0076KO) and complemented (Mycma 0076KOc) gene strains for mycma_0076 to understand the function of 0076 ferritin. Deletion of mycma_0076 in Mycma led to the transition in colony morphology from smooth to rough, alteration of the glycopeptidolipids spectra, increased permeability of the envelope, reduction in biofilm formation, increased susceptibility to antimicrobials and hydrogen peroxide-induced oxidative stress, and decreased internalization by macrophages. This study shows that Mycma_0076 ferritin in Mycma is involved in resistance to oxidative stress and antimicrobials, and alteration of cell envelope architecture. KEY POINTS: • Deletion of the mycma_0076 gene altered colony morphology to rough; • Mycma 0076KO changed GPL profile; • Absence of Mycma_0076 ferritin results in increased susceptibility to antimicrobials and oxidative stress in Mycma. Legend: a In wild-type M. abscessus subsp. massiliense strain, iron is captured from the environment by carboxymycobactins and mycobactins (1). Iron-dependent regulator (IdeR) proteins bind to ferrous iron (Fe+2) in the bacterial cytoplasm leading to the activation of the IdeR-Fe+2 complex (2). The activated complex binds to the promoter regions of iron-dependent genes, called iron box, which in turn help in the recruitment of RNA polymerase to promote transcription of genes such as mycma_0076 and mycma_0077 ferritin genes (3). Mycma_0076 and Mycma_0077 ferritins bind to excess iron in the medium and promote Fe2+ oxidation into ferric iron (Fe3+) and store iron molecules to be released under iron scarcity conditions. (4) Genes related to biosynthesis and transport of glycopeptidolipids (GPL) are expressed normally and the cell envelope is composed of different GPL species (colored squares represented on the cell surface (GPLs). Consequently, WT Mycma present smooth colony phenotype (5). b In Mycma 0076KO strain, the lack of ferritin 0076 causes overexpression of mycma_0077 (6), but does not restore wild-type iron homeostasis and thus may result in free intracellular iron, even in the presence of miniferritins (MaDps). The excess iron potentiates oxidative stress (7) by generating hydroxyl radicals through Fenton Reaction. During this process, through an unknown mechanism, that could involve Lsr2 (8), the expression of GPL synthesis locus is regulated positively and/or negatively, resulting in alteration of GPL composition in the membrane (as represented by different colors of squares on the cell surface), resulting in a rough colony phenotype (9). The changes of GPL can increase cell wall permeability, contributing to antimicrobial susceptibility (10).
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Affiliation(s)
- Maria Micaella Rodrigues Pereira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
| | - Fábio Muniz de Oliveira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
- Indiana Center for Regenerative Medicine and Engineering, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | | | - André Kipnis
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil.
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9
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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10
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Oyster (Crassostrea gigas) ferritin should be a promising Fe2+ nanocarrier. Food Chem 2023; 404:134586. [DOI: 10.1016/j.foodchem.2022.134586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/26/2022] [Accepted: 10/09/2022] [Indexed: 11/22/2022]
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11
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Reutovich AA, Srivastava AK, Arosio P, Bou-Abdallah F. Ferritin nanocages as efficient nanocarriers and promising platforms for COVID-19 and other vaccines development. Biochim Biophys Acta Gen Subj 2023; 1867:130288. [PMID: 36470367 PMCID: PMC9721431 DOI: 10.1016/j.bbagen.2022.130288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The development of safe and effective vaccines against SARS-CoV-2 and other viruses with high antigenic drift is of crucial importance to public health. Ferritin is a well characterized and ubiquitous iron storage protein that has emerged not only as a useful nanoreactor and nanocarrier, but more recently as an efficient platform for vaccine development. SCOPE OF REVIEW This review discusses ferritin structure-function properties, self-assembly, and novel bioengineering strategies such as interior cavity and exterior surface modifications for cargo encapsulation and delivery. It also discusses the use of ferritin as a scaffold for biomedical applications, especially for vaccine development against influenza, Epstein-Barr, HIV, hepatitis-C, Lyme disease, and respiratory viruses such as SARS-CoV-2. The use of ferritin for the synthesis of mosaic vaccines to deliver a cocktail of antigens that elicit broad immune protection against different viral variants is also explored. MAJOR CONCLUSIONS The remarkable stability, biocompatibility, surface functionalization, and self-assembly properties of ferritin nanoparticles make them very attractive platforms for a wide range of biomedical applications, including the development of vaccines. Strong immune responses have been observed in pre-clinical studies against a wide range of pathogens and have led to the exploration of ferritin nanoparticles-based vaccines in multiple phase I clinical trials. GENERAL SIGNIFICANCE The broad protective antibody response of ferritin nanoparticles-based vaccines demonstrates the usefulness of ferritin as a highly promising and effective approaches for vaccine development.
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Affiliation(s)
| | - Ayush K Srivastava
- Department of Chemistry, State University of New York, Potsdam, NY 13676, USA
| | - Paolo Arosio
- Department of Molecular and Translational Medicine, University of Brescia, 25121 Brescia, Italy
| | - Fadi Bou-Abdallah
- Department of Chemistry, State University of New York, Potsdam, NY 13676, USA.
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12
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Celis AI, Relman DA, Huang KC. The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro. Cell Chem Biol 2023; 30:110-126.e3. [PMID: 36603582 PMCID: PMC9913275 DOI: 10.1016/j.chembiol.2022.12.001] [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: 12/07/2021] [Revised: 07/12/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023]
Abstract
Responses of the indigenous human gut commensal microbiota to iron are poorly understood because of an emphasis on in vitro studies of pathogen iron sensitivity. In a study of iron supplementation in healthy humans, we identified gradual microbiota shifts in some participants correlated with bacterial iron internalization. To identify direct effects due to taxon-specific iron sensitivity, we used participant stool samples to derive diverse in vitro communities. Iron supplementation of these communities caused small compositional shifts, mimicking those in vivo, whereas iron deprivation dramatically inhibited growth with irreversible, cumulative reduction in diversity and replacement of dominant species. Sensitivity of individual species to iron deprivation in axenic culture generally predicted iron dependency in a community. Finally, exogenous heme acted as a source of inorganic iron to prevent depletion of some species. Our results highlight the complementarity of in vivo and in vitro studies in understanding how environmental factors affect gut microbiotas.
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Affiliation(s)
- Arianna I Celis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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13
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Obozina AS, Komedchikova EN, Kolesnikova OA, Iureva AM, Kovalenko VL, Zavalko FA, Rozhnikova TV, Tereshina ED, Mochalova EN, Shipunova VO. Genetically Encoded Self-Assembling Protein Nanoparticles for the Targeted Delivery In Vitro and In Vivo. Pharmaceutics 2023; 15:pharmaceutics15010231. [PMID: 36678860 PMCID: PMC9861179 DOI: 10.3390/pharmaceutics15010231] [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: 11/25/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Targeted nanoparticles of different origins are considered as new-generation diagnostic and therapeutic tools. However, there are no targeted drug formulations within the composition of nanoparticles approved by the FDA for use in the clinic, which is associated with the insufficient effectiveness of the developed candidates, the difficulties of their biotechnological production, and inadequate batch-to-batch reproducibility. Targeted protein self-assembling nanoparticles circumvent this problem since proteins are encoded in DNA and the final protein product is produced in only one possible way. We believe that the combination of the endless biomedical potential of protein carriers as nanoparticles and the standardized protein purification protocols will make significant progress in "magic bullet" creation possible, bringing modern biomedicine to a new level. In this review, we are focused on the currently existing platforms for targeted self-assembling protein nanoparticles based on transferrin, lactoferrin, casein, lumazine synthase, albumin, ferritin, and encapsulin proteins, as well as on proteins from magnetosomes and virus-like particles. The applications of these self-assembling proteins for targeted delivery in vitro and in vivo are thoroughly discussed, including bioimaging applications and different therapeutic approaches, such as chemotherapy, gene delivery, and photodynamic and photothermal therapy. A critical assessment of these protein platforms' efficacy in biomedicine is provided and possible problems associated with their further development are described.
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Affiliation(s)
| | | | | | - Anna M. Iureva
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Vera L. Kovalenko
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Fedor A. Zavalko
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | | | | | - Elizaveta N. Mochalova
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Nanobiomedicine Division, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Victoria O. Shipunova
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Nanobiomedicine Division, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence:
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14
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Sudarev VV, Dolotova SM, Bukhalovich SM, Bazhenov SV, Ryzhykau YL, Uversky VN, Bondarev NA, Osipov SD, Mikhailov AE, Kuklina DD, Murugova TN, Manukhov IV, Rogachev AV, Gordeliy VI, Gushchin IY, Kuklin AI, Vlasov AV. Ferritin self-assembly, structure, function, and biotechnological applications. Int J Biol Macromol 2022; 224:319-343. [DOI: 10.1016/j.ijbiomac.2022.10.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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15
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Keller-Costa T, Kozma L, Silva SG, Toscan R, Gonçalves J, Lago-Lestón A, Kyrpides NC, Nunes da Rocha U, Costa R. Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. MICROBIOME 2022; 10:151. [PMID: 36138466 PMCID: PMC9502895 DOI: 10.1186/s40168-022-01343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. RESULTS Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. CONCLUSION This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.
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Affiliation(s)
- Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Lydia Kozma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- École Polytechnique Fédérale de Lausanne, Écublens, Switzerland
| | - Sandra G. Silva
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Rodolfo Toscan
- Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jorge Gonçalves
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica Y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
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16
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Fokt H, Cleto S, Oliveira H, Araújo D, Castro J, Cerca N, Vieira MJ, Almeida C. Bacteriocin Production by Escherichia coli during Biofilm Development. Foods 2022; 11:foods11172652. [PMID: 36076837 PMCID: PMC9455227 DOI: 10.3390/foods11172652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli is a highly versatile bacterium ranging from commensal to intestinal pathogen, and is an important foodborne pathogen. E. coli species are able to prosper in multispecies biofilms and secrete bacteriocins that are only toxic to species/strains closely related to the producer strain. In this study, 20 distinct E. coli strains were characterized for several properties that confer competitive advantages against closer microorganisms by assessing the biofilm-forming capacity, the production of antimicrobial molecules, and the production of siderophores. Furthermore, primer sets for E. coli bacteriocins–colicins were designed and genes were amplified, allowing us to observe that colicins were widely distributed among the pathogenic E. coli strains. Their production in the planktonic phase or single-species biofilms was uncommon. Only two E. coli strains out of nine biofilm-forming were able to inhibit the growth of other E. coli strains. There is evidence of larger amounts of colicin being produced in the late stages of E. coli biofilm growth. The decrease in bacterial biomass after 12 h of incubation indicates active type I colicin production, whose release normally requires E. coli cell lysis. Almost all E. coli strains were siderophore-producing, which may be related to the resistance to colicin as these two molecules may use the same transporter system. Moreover, E. coli CECT 504 was able to coexist with Salmonella enterica in dual-species biofilms, but Shigella dysenteriae was selectively excluded, correlating with high expression levels of colicin (E, B, and M) genes observed by real-time PCR.
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Affiliation(s)
- Hanna Fokt
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Sara Cleto
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Hugo Oliveira
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS–Associate Laboratory, 4710-057 Braga, Portugal
| | - Daniela Araújo
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, 4485-655 Vila do Conde, Portugal
| | - Joana Castro
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, 4485-655 Vila do Conde, Portugal
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS–Associate Laboratory, 4710-057 Braga, Portugal
| | - Maria João Vieira
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS–Associate Laboratory, 4710-057 Braga, Portugal
| | - Carina Almeida
- Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS–Associate Laboratory, 4710-057 Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, 4485-655 Vila do Conde, Portugal
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- Correspondence: ; Tel.: +351-252-660-600
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17
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Gilbert NE, LeCleir GR, Strzepek RF, Ellwood MJ, Twining BS, Roux S, Pennacchio C, Boyd PW, Wilhelm SW. Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities. ISME COMMUNICATIONS 2022; 2:54. [PMID: 37938659 PMCID: PMC9723758 DOI: 10.1038/s43705-022-00132-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 06/09/2022] [Indexed: 04/18/2023]
Abstract
The trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.
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Affiliation(s)
- Naomi E Gilbert
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Gary R LeCleir
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert F Strzepek
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Michael J Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | | | - S Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C Pennacchio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA.
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18
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Codolo G, Coletta S, D’Elios MM, de Bernard M. HP-NAP of Helicobacter pylori: The Power of the Immunomodulation. Front Immunol 2022; 13:944139. [PMID: 35844568 PMCID: PMC9277015 DOI: 10.3389/fimmu.2022.944139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
The miniferritin HP-NAP of Helicobacter pylori was originally described as a neutrophil-activating protein because of the capacity to activate neutrophils to generate oxygen radicals and adhere to endothelia. Currently, the main feature for which HP-NAP is known is the ability to promote Th1 responses and revert the immune suppressive profile of macrophages. In this review, we discuss the immune modulating properties of the protein regarding the H. pylori infection and the evidence that support the potential clinical application of HP-NAP in allergy and cancer immunotherapy.
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Affiliation(s)
- Gaia Codolo
- Department of Biology, University of Padova, Padova, Italy
| | - Sara Coletta
- Department of Biology, University of Padova, Padova, Italy
| | - Mario Milco D’Elios
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
- *Correspondence: Marina de Bernard, ; Mario Milco D’Elios,
| | - Marina de Bernard
- Department of Biology, University of Padova, Padova, Italy
- *Correspondence: Marina de Bernard, ; Mario Milco D’Elios,
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19
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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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20
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Shtykova EV, Petoukhov MV, Mozhaev AA. Formation of Iron Oxide Nanoparticles in the Internal Cavity of Ferritin-Like Dps Protein: Studies by Anomalous X-Ray Scattering. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:511-523. [PMID: 35790408 DOI: 10.1134/s0006297922060037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
DNA-binding protein from starved cells (Dps) takes a special place among dodecamer mini-ferritins. Its most important function is protection of bacterial genome from various types of destructive external factors via in cellulo Dps-DNA co-crystallization. This protective response results in the emergence of bacterial resistance to antibiotics and other drugs. The protective properties of Dps have attracted a significant attention of researchers. However, Dps has another equally important functional role. Being a ferritin-like protein, Dps acts as an iron depot and protects bacterial cells from the oxidative damage initiated by the excess of iron. Here we investigated formation of iron oxide nanoparticles in the internal cavity of the Dps dodecamer. We used anomalous small-angle X-ray scattering as the main research technique, which allows to examine the structure of metal-containing biological macromolecules and to analyze the size distribution of metal nanoparticles formed in them. The contributions of protein and metal components to total scattering were distinguished by varying the energy of the incident X-ray radiation near the edge of the metal atom absorption band (the K-band for iron). We examined Dps specimens containing 50, 500, and 2000 iron atoms per protein dodecamer. Analysis of the particle size distribution showed that, depending on the iron content in the solution, the size of the nanoparticles formed inside the protein molecule was 2 to 4 nm and the growth of metal nanoparticles was limited by the size of the protein inner cavity. We also found some amount of iron ions in the Dps surface layer. This layer is very important for the protein to perform its protective functions, since the surface-located N-terminal domains determine the nature of interactions between Dps and DNA. In general, the results obtained in this work can be useful for the next step in studying the Dps phenomenon, as well as in creating biocompatible and solution-stabilized metal nanoparticles.
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Affiliation(s)
- Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia.
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Centre, Russian Academy of Sciences, Moscow, 119333, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
- National Research University Higher School of Economics, Moscow, 101000, Russia
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21
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Rajasekaran MB, Hussain R, Siligardi G, Andrews SC, Watson KA. Crystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system. Biometals 2022; 35:573-589. [PMID: 35348940 PMCID: PMC9174327 DOI: 10.1007/s10534-022-00389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022]
Abstract
EfeUOB/M has been characterised in Pseudomonas syringae pathovar. syringae as a novel type of ferrous-iron transporter, consisting of an inner-membrane protein (EfeUPsy) and three periplasmic proteins (EfeOPsy, EfeMPsy and EfeBPsy). The role of an iron permease and peroxidase function has been identified for the EfeU and EfeB proteins, respectively, but the role of EfeO/M remains unclear. EfeMPsy is an 'M75-only' EfeO-like protein with a C-terminal peptidase-M75 domain (EfeOII/EfeM family). Herein, we report the 1.6 Å resolution crystal structure of EfeMPsy, the first structural report for an EfeM component of P. syringae pv. syringae. The structure possesses the bi-lobate architecture found in other bacterial periplasmic substrate/solute binding proteins. Metal binding studies, using SRCD and ICP-OES, reveal a preference of EfeMPsy for copper, iron and zinc. This work provides detailed knowledge of the structural scaffold, the metal site geometry, and the divalent metal binding potential of EfeM. This work provides crucial underpinning for a more detailed understanding of the role of EfeM/EfeO proteins and the peptidase-M75 domains in EfeUOB/M iron uptake systems in bacteria.
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Affiliation(s)
- Mohan B Rajasekaran
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN19QJ, UK
| | - Rohanah Hussain
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Giuliano Siligardi
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Simon C Andrews
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK
| | - Kimberly A Watson
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK.
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22
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Xu X, Tian K, Lou X, Du Y. Potential of Ferritin-Based Platforms for Tumor Immunotherapy. Molecules 2022; 27:molecules27092716. [PMID: 35566065 PMCID: PMC9104857 DOI: 10.3390/molecules27092716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
Ferritin is an iron storage protein that plays a key role in iron homeostasis and cellular antioxidant activity. Ferritin has many advantages as a tumor immunotherapy platform, including a small particle size that allows for penetration into tumor-draining lymph nodes or tumor tissue, a unique structure consisting of 24 self-assembled subunits, cavities that can encapsulate drugs, natural targeting functions, and a modifiable outer surface. In this review, we summarize related research applying ferritin as a tumor immune vaccine or a nanocarrier for immunomodulator drugs based on different targeting mechanisms (including dendritic cells, tumor-associated macrophages, tumor-associated fibroblasts, and tumor cells). In addition, a ferritin-based tumor vaccine expected to protect against a wide range of coronaviruses by targeting multiple variants of SARS-CoV-2 has entered phase I clinical trials, and its efficacy is described in this review. Although ferritin is already on the road to transformation, there are still many difficulties to overcome. Therefore, three barriers (drug loading, modification sites, and animal models) are also discussed in this paper. Notwithstanding, the ferritin-based nanoplatform has great potential for tumor immunotherapy, with greater possibility of clinical transformation.
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Affiliation(s)
- Xiaoling Xu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (X.X.); (K.T.)
| | - Kewei Tian
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (X.X.); (K.T.)
| | - Xuefang Lou
- School of Medicine, Zhejiang University City College, Hangzhou 310015, China
- Correspondence: (X.L.); (Y.D.); Tel.: +86-571-88208435 (Y.D.); Fax: +86-571-88208435 (Y.D.)
| | - Yongzhong Du
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: (X.L.); (Y.D.); Tel.: +86-571-88208435 (Y.D.); Fax: +86-571-88208435 (Y.D.)
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Peng MW, Qi J, Yan P, Guan Y, Liu YY, Sun ZH, Zhang LJ, Weng X, Shen Y, Fang F, Guo JS, Chen YP. Insight into the structure and metabolic function of iron-rich nanoparticles in anammox bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150879. [PMID: 34627893 DOI: 10.1016/j.scitotenv.2021.150879] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are iron abundant and depend heavily on iron-binding proteins. The iron demand of anammox bacteria is relatively large. However, it still remains some doubts where these large quantities of available iron come from and how they are regulated in anammox bacteria. Herein, iron-rich nanoparticles in anammoxosomes were detected by synchrotron soft X-ray tomography coupled with scanning transmission X-ray microscopy (STXM). The iron-rich nanoparticles were identified as ferric oxide (α-Fe2O3) mineral cores, and the local atomic structure of iron-rich nanoparticles was obtained by X-ray absorption fine-structure (XAFS) spectra. The bacterioferritin of Q1Q315 and Q1Q5F8 were detected by proteomics analysis. On this basis, the metabolic pathway centered on iron-rich nanoparticles was proposed.
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Affiliation(s)
- Meng-Wen Peng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China; China Three Gorges Corporation, Beijing 100038, China
| | - Jing Qi
- 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
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science & Technology of China, Hefei 230026, China
| | - Ying-Ying Liu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zhi-Hu Sun
- National Synchrotron Radiation Laboratory, University of Science & Technology of China, Hefei 230026, China
| | - Li-Juan Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xun Weng
- 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
| | - 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
| | - 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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Zurita C, Tsushima S, Solari PL, Jeanson A, Creff G, Den Auwer C. Interaction of Th(IV), Pu(IV) and Fe(III) with ferritin protein: how similar? JOURNAL OF SYNCHROTRON RADIATION 2022; 29:45-52. [PMID: 34985422 PMCID: PMC8733997 DOI: 10.1107/s1600577521012340] [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] [Accepted: 11/21/2021] [Indexed: 05/28/2023]
Abstract
Ferritin is the main protein of Fe storage in eukaryote and prokaryote cells. It is a large multifunctional, multi-subunit protein consisting of heavy H and light L subunits. In the field of nuclear toxicology, it has been suggested that some actinide elements, such as thorium and plutonium at oxidation state +IV, have a comparable `biochemistry' to iron at oxidation state +III owing to their very high tendency for hydrolysis and somewhat comparable ionic radii. Therefore, the possible mechanisms of interaction of such actinide elements with the Fe storage protein is a fundamental question of bio-actinidic chemistry. We recently described the complexation of Pu(IV) and Th(IV) with horse spleen ferritin (composed mainly of L subunits). In this article, we bring another viewpoint to this question by further combining modeling with our previous EXAFS data for Pu(IV) and Th(IV). As a result, the interaction between the L subunits and both actinides appears to be non-specific but driven only by the density of the presence of Asp and Glu residues on the protein shell. The formation of an oxyhydroxide Th or Pu core has not been observed under the experimental conditions here, nor the interaction of Th or Pu with the ferric oxyhydroxide core.
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Affiliation(s)
- Cyril Zurita
- Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Satoru Tsushima
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany
- World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | | | | | - Gaëlle Creff
- Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
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25
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Islas S, Cuéllar-Cruz M. Silica-Carbonate of Ba(II) and Fe 2+/Fe 3+ Complex as Study Models to Understand Prebiotic Chemistry. ACS OMEGA 2021; 6:35629-35640. [PMID: 34984294 PMCID: PMC8717530 DOI: 10.1021/acsomega.1c05415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
The Precambrian era is called the first stage of the Earth history and is considered the longest stage in the geological time scale. Despite its duration, several of its environmental and chemical characteristics are still being studied. It is an era of special relevance not only for its duration but also because it is when a set of conditions gave rise to the first organism. This pioneer organism has been proposed to have been formed by a mineral and an organic part. A chemical element suggested to have been part of the structure of this cell is iron. However, what special characteristic does iron have with respect to other chemical elements to be proposed as part of this first cell? To answer this and other questions, it is indispensable to have a model that will allow extrapolating the first chemical structures of the pioneer organism formed in the Precambrian. In this context, for several decades, in vitro structures chemically formed by silica-carbonates have been synthetized, called biomorphs, because they could emulate living organisms and might resemble primitive organisms. It has been inferred that because biomorphs form structures with characteristic morphologies, they could resemble the microfossils found in the cherts of the Precambrian. Aiming at providing some insight on how iron contributed to the formation of the chemical structures of the primitive organism, we evaluated how iron contributes to the morphology and chemical-crystalline structure during the synthesis of these compounds under different conditions found in the primitive atmosphere. Experimentally, synthesis of biomorphs was performed at four different atmospheric conditions including UV light, nonionizing microwave radiation (NIR-mw), water steam (WS), and CO2 in the presence of Fe2+, Fe3+, and Fe2+/Fe3+, obtaining 48 different conditions. The produced biomorphs were observed under scanning electron microscopy (SEM). Afterward, their chemical composition and crystalline structure were analyzed through Raman and IR spectroscopy.
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Affiliation(s)
- Selene
R. Islas
- Instituto
de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Ciudad de México 04510, México
| | - Mayra Cuéllar-Cruz
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, C.P. 36050 Guanajuato, Guanajuato, México
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26
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Almeida AV, Carvalho AJ, Pereira AS. Encapsulin nanocages: Protein encapsulation and iron sequestration. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Casar CP, Momper LM, Kruger BR, Osburn MR. Iron-Fueled Life in the Continental Subsurface: Deep Mine Microbial Observatory, South Dakota, USA. Appl Environ Microbiol 2021; 87:e0083221. [PMID: 34378953 PMCID: PMC8478452 DOI: 10.1128/aem.00832-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/29/2021] [Indexed: 11/20/2022] Open
Abstract
Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.
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Affiliation(s)
- C. P. Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - L. M. Momper
- Earth and Environmental Sciences Practice, Exponent, Inc., Pasadena, California, USA
| | - B. R. Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, Nevada, USA
| | - M. R. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
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29
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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30
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Li H, Xia X, Tan X, Zang J, Wang Z, Ei-Seedi HR, Du M. Advancements of nature nanocage protein: preparation, identification and multiple applications of ferritins. Crit Rev Food Sci Nutr 2021; 62:7117-7128. [PMID: 33860692 DOI: 10.1080/10408398.2021.1911925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Ferritin is an important iron storage protein, which is widely existed in all forms of life. Ferritin can regulate iron homeostasis when iron ions are lacking or enriched in the body, so as to avoid iron deficiency diseases and iron poisoning. Ferritin presents a hollow nanocage, which can store ions or other small molecular substances in the cavity. Therefore, ferritin shows its potential as a functional nanomaterial that can deliver nutrients or drugs in a targeted manner to improve bioavailability. Due to the special structure, the research on ferritin has attracted more and more attention in recent years. In this paper, the structural characteristics of ferritin were introduced, and the natural purification and prokaryotic expression methods of ferritin from different sources were described. At the same time, ferritin can bind to small molecules, so that it has the activity of small molecules, to construct a new type of ferritin. As a result, ferritin plays an important role as a nutrient substance, in targeted transport, and disease monitoring, etc. In conclusion, the yield of ferritin can be improved by means of molecular biology. Meanwhile, molecular modification can be used to make ferritin have unique activity and function, which lays a foundation for subsequent research. HighlightsThe molecular and structural properties of ferritins were clearly described.Isolation and purification technologies of ferritin were compared.Characterization, functions and molecular modifications mechanism of ferritin were reviewed.The applications of ferritin in pharmaceutical and food industry were prospected.
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Affiliation(s)
- Han Li
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xiaoyu Xia
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhenyu Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Hesham R Ei-Seedi
- Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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31
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Cunrath O, Palmer JD. An overview of Salmonella enterica metal homeostasis pathways during infection. ACTA ACUST UNITED AC 2021; 2:uqab001. [PMID: 34250489 PMCID: PMC8264917 DOI: 10.1093/femsml/uqab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022]
Abstract
Nutritional immunity is a powerful strategy at the core of the battlefield between host survival and pathogen proliferation. A host can prevent pathogens from accessing biological metals such as Mg, Fe, Zn, Mn, Cu, Co or Ni, or actively intoxicate them with metal overload. While the importance of metal homeostasis for the enteric pathogen Salmonella enterica Typhimurium was demonstrated many decades ago, inconsistent results across various mouse models, diverse Salmonella genotypes, and differing infection routes challenge aspects of our understanding of this phenomenon. With expanding access to CRISPR-Cas9 for host genome manipulation, it is now pertinent to re-visit past results in the context of specific mouse models, identify gaps and incongruities in current knowledge landscape of Salmonella homeostasis, and recommend a straight path forward towards a more universal understanding of this historic host-microbe relationship.
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Affiliation(s)
- Olivier Cunrath
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
| | - Jacob D Palmer
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
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32
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Legros J, Jan S, Bonnassie S, Gautier M, Croguennec T, Pezennec S, Cochet MF, Nau F, Andrews SC, Baron F. The Role of Ovotransferrin in Egg-White Antimicrobial Activity: A Review. Foods 2021; 10:823. [PMID: 33920211 PMCID: PMC8070150 DOI: 10.3390/foods10040823] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Eggs are a whole food which affordably support human nutritional requirements worldwide. Eggs strongly resist bacterial infection due to an arsenal of defensive systems, many of which reside in the egg white. However, despite improved control of egg production and distribution, eggs remain a vehicle for foodborne transmission of Salmonella enterica serovar Enteritidis, which continues to represent a major public health challenge. It is generally accepted that iron deficiency, mediated by the iron-chelating properties of the egg-white protein ovotransferrin, has a key role in inhibiting infection of eggs by Salmonella. Ovotransferrin has an additional antibacterial activity beyond iron-chelation, which appears to depend on direct interaction with the bacterial cell surface, resulting in membrane perturbation. Current understanding of the antibacterial role of ovotransferrin is limited by a failure to fully consider its activity within the natural context of the egg white, where a series relevant environmental factors (such as alkalinity, high viscosity, ionic composition, and egg white protein interactions) may exert significant influence on ovotransferrin activity. This review provides an overview of what is known and what remains to be determined regarding the antimicrobial activity of ovotransferrin in egg white, and thus enhances understanding of egg safety through improved insight of this key antimicrobial component of eggs.
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Affiliation(s)
- Julie Legros
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Reading RG6 6AX, UK;
| | - Sophie Jan
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Sylvie Bonnassie
- UFR Sciences de la vie et de L’environnement, Université de Rennes 1, 35000 Rennes, France;
| | - Michel Gautier
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Thomas Croguennec
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Stéphane Pezennec
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Marie-Françoise Cochet
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Françoise Nau
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
| | - Simon C. Andrews
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Reading RG6 6AX, UK;
| | - Florence Baron
- STLO, INRAE, Institut Agro, 35042 Rennes, France; (J.L.); (S.J.); (M.G.); (T.C.); (S.P.); (M.-F.C.); (F.N.)
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Picard L, Paris C, Dhalleine T, Morin E, Oger P, Turpault MP, Uroz S. The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system. Environ Microbiol 2021; 24:784-802. [PMID: 33817942 DOI: 10.1111/1462-2920.15508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/23/2021] [Accepted: 04/03/2021] [Indexed: 11/27/2022]
Abstract
Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.
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Affiliation(s)
- Laura Picard
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 « Laboratoire d'Ingénierie des Biomolécules », Ecole Nationale Supérieure d'Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, F-54505, France.,Plateau d'Analyse Structurale et Métabolomique (PASM) - SF4242 EFABA, Vandœuvre-lès-Nancy, F-54505, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS UMR 5240 « Microbiologie, Adaptation et Pathogénie », Villeurbanne, F-69621, France
| | - Marie-Pierre Turpault
- INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
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Cleto S, Haslinger K, Prather KLJ, Lu TK. Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica. BMC Biol 2021; 19:46. [PMID: 33722216 PMCID: PMC7962358 DOI: 10.1186/s12915-021-00971-z] [Citation(s) in RCA: 6] [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: 10/14/2020] [Accepted: 01/31/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Iron is essential for bacterial survival. Bacterial siderophores are small molecules with unmatched capacity to scavenge iron from proteins and the extracellular milieu, where it mostly occurs as insoluble Fe3+. Siderophores chelate Fe3+ for uptake into the cell, where it is reduced to soluble Fe2+. Siderophores are key molecules in low soluble iron conditions. The ability of bacteria to synthesize proprietary siderophores may have increased bacterial evolutionary fitness; one way that bacteria diversify siderophore structure is by incorporating different polyamine backbones while maintaining the catechol moieties. RESULTS We report that Serratia plymuthica V4 produces a variety of siderophores, which we term the siderome, and which are assembled by the concerted action of enzymes encoded in two independent gene clusters. Besides assembling serratiochelin A and B with diaminopropane, S. plymuthica utilizes putrescine and the same set of enzymes to assemble photobactin, a siderophore found in the bacterium Photorhabdus luminescens. The enzymes encoded by one of the gene clusters can independently assemble enterobactin. A third, independent operon is responsible for biosynthesis of the hydroxamate siderophore aerobactin, initially described in Enterobacter aerogenes. Mutant strains not synthesizing polyamine-siderophores significantly increased enterobactin production levels, though lack of enterobactin did not impact the production of serratiochelins. Knocking out SchF0, an enzyme involved in the assembly of enterobactin alone, significantly reduced bacterial fitness. CONCLUSIONS This study shows the natural occurrence of serratiochelins, photobactin, enterobactin, and aerobactin in a single bacterial species and illuminates the interplay between siderophore biosynthetic pathways and polyamine production, indicating routes of molecular diversification. Given its natural yields of diaminopropane (97.75 μmol/g DW) and putrescine (30.83 μmol/g DW), S. plymuthica can be exploited for the industrial production of these compounds.
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Affiliation(s)
- Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristina Haslinger
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Kristala L J Prather
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Tan Z, Lu P, Adewole D, Diarra M, Gong J, Yang C. Iron requirement in the infection of Salmonella and its relevance to poultry health. J APPL POULTRY RES 2021. [DOI: 10.1016/j.japr.2020.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Sushko T, Kavaleuski A, Grabovec I, Kavaleuskaya A, Vakhrameev D, Bukhdruker S, Marin E, Kuzikov A, Masamrekh R, Shumyantseva V, Tsumoto K, Borshchevskiy V, Gilep A, Strushkevich N. A new twist of rubredoxin function in M. tuberculosis. Bioorg Chem 2021; 109:104721. [PMID: 33618255 DOI: 10.1016/j.bioorg.2021.104721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Electron transfer mediated by metalloproteins drives many biological processes. Rubredoxins are a ubiquitous [1Fe-0S] class of electron carriers that play an important role in bacterial adaptation to changing environmental conditions. In Mycobacterium tuberculosis, oxidative and acidic stresses as well as iron starvation induce rubredoxins expression. However, their functions during M. tuberculosis infection are unknown. In the present work, we show that rubredoxin B (RubB) is able to efficiently shuttle electrons from cognate reductases, FprA and FdR to support catalytic activity of cytochrome P450s, CYP124, CYP125, and CYP142, which are important for bacterial viability and pathogenicity. We solved the crystal structure of RubB and characterized the interaction between RubB and CYPs using site-directed mutagenesis. Mutations that not only neutralize single charge but also change the specific residues on the surface of RubB did not dramatically decrease activity of studied CYPs. Together with isothermal calorimetry (ITC) experiments, the obtained results suggest that interactions are transient and not highly specific. The redox potential of RubB is -264 mV vs. Ag/AgCl and the measured extinction coefficients are 9931 M-1cm-1 and 8371 M-1cm-1 at 380 nm and 490 nm, respectively. Characteristic parameters of RubB along with the discovered function might be useful for biotechnological applications. Our findings suggest that a switch from ferredoxins to rubredoxins might be crucial for M. tuberculosis to support CYPs activity during the infection.
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Affiliation(s)
- Tatsiana Sushko
- The Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Anna Kavaleuskaya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Daniil Vakhrameev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; ESRF - The European Synchrotron, 38000 Grenoble, France
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Alexey Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Rami Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Victoria Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Kouhei Tsumoto
- The Institute of Medical Science, the University of Tokyo, Tokyo, Japan; Department of Bioengineering, School of Engineering, the University of Tokyo, Tokyo, Japan
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus; Institute of Biomedical Chemistry, Moscow, Russia
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Thomas MD, Ewunkem AJ, Boyd S, Williams DK, Moore A, Rhinehardt KL, Van Beveren E, Yang B, Tapia A, Han J, Harrison SH, Graves JL. Too much of a good thing: Adaption to iron (II) intoxication in Escherichia coli. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:53-67. [PMID: 33717488 PMCID: PMC7937436 DOI: 10.1093/emph/eoaa051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022]
Abstract
Background There has been an increased usage of metallic antimicrobial materials to control pathogenic and multi-drug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. Methodology Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. Results After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-h optical densities compared to controls. Furthermore, these populations showed increased resistance toward other metals [iron (III) and gallium (III)] and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. Conclusions and implications Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern. Lay summary: The evolution of iron resistance in E. coli leads to multi-drug and general metal resistance through the acquisition of mutations in three genes (fecA, ptsP and ilvG) while also initiating cellular defenses as part of their normal growth process.
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Affiliation(s)
- Misty D Thomas
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- BEACON, Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Sada Boyd
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Danielle K Williams
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Adiya Moore
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Kristen L Rhinehardt
- Computational Data Science and Engineering, North Carolina Agricultural and Technical State University, 1601 E. Market Street, Greensboro, NC 27411, USA
| | - Emma Van Beveren
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Bobi Yang
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Anna Tapia
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Jian Han
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Scott H Harrison
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
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Li H, Tan X, Xia X, Zang J, El-Seedi H, Wang Z, Du M. Improvement of thermal stability of oyster (Crassostrea gigas) ferritin by point mutation. Food Chem 2020; 346:128879. [PMID: 33406454 DOI: 10.1016/j.foodchem.2020.128879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 11/17/2020] [Accepted: 12/13/2020] [Indexed: 11/26/2022]
Abstract
Ferritin can be widely used as functional nanomaterial. But the physiological activity of ferritin can be damaged under excessive temperatures, which affect the self-assembly property. In this study, point mutation was produced in Asp120 to Gly120 of ferritin amino acid sequence and the heat resistance was improved significantly. The thermal denaturation temperature of mutated ferritin is 89.17 °C and has increased by 13 °C more than the wild-type oyster ferritin. The effect of thermal treatment on the denaturation, aggregation state, particle size and the structure of ferritin was not changed before 90 °C. The computational modeling and analysis indicated that mutated ferritin promotes the overall structural stability assembly via decreasing the interaction energies of 62 percent energies in 3-fold interface. Improving the thermal stability of oyster ferritin by point mutation enhances its applications as a food ingredient.
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Affiliation(s)
- Han Li
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyu Xia
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hesham El-Seedi
- Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Zhenyu Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China.
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Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Baslé A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem 2020; 295:15511-15526. [PMID: 32878987 DOI: 10.1074/jbc.ra120.014502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/24/2020] [Indexed: 11/06/2022] Open
Abstract
Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.
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Affiliation(s)
- Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Didi He
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Kelly J Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Will A Stanley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laurène Adam
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin J Waldron
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland.
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Guo L, Wang J, Gou Y, Tan L, Liu H, Pan Y, Zhao Y. Comparative proteomics reveals stress responses of Vibrio parahaemolyticus biofilm on different surfaces: Internal adaptation and external adjustment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:138386. [PMID: 32417469 DOI: 10.1016/j.scitotenv.2020.138386] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Vibrio parahaemolyticus is a kind of gram-negative marine pathogen, which usually adheres to stainless steel (SS), glass (GS) and other abiotic surfaces in aquaculture and food processing in the form of biofilm and causes the spread of gastrointestinal illness. However, the deeply survival adaptation mechanism of V. parahaemolyticus biofilm cells on these contact surface remained unclear. Here, proteomics was used to investigated the physiological response of the V. parahaemolyticus biofilms cells to different abiotic surfaces (SS, GS and polystyrene (PS)). In addition, the effect of contact materials on the physical-chemical properties of biofilms are also characterized. Results showed that the expression of proteins of biofilm cells established on the SS surface were mainly related to the alleviation of metal ion stress and toxicity. The up-regulated proteins in the biofilm cells formed on the GS surface were mainly involved in the biological processes of sugar uptake, protein synthesis and bacterial chemotaxis. Meanwhile, the significantly expressed proteins in the biofilm cells formed on the PS surface were mainly involved in the cellular physiological activity of aromatic compound metabolism, osmotic stress and nutrient transport. All functional proteins mentioned above were closely related to the interaction characteristics of the contact surface and biofilm. This study provided an in-depth comparison of V. parahaemolyticus biofilm formation on these three abiotic surfaces, and presented a model in first time for the adaptation behavior of biofilm cells on different surfaces as affected by metal ion stress, nutrition, osmotic stress, and sugar utilization, which could facilitate an efficient control strategy for biofilm formation in industrial field.
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Affiliation(s)
- Linxia Guo
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jingjing Wang
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Department of Food Science, Foshan University, Foshan, 528000, China
| | - Yi Gou
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Ling Tan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China.
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Gabashvili AN, Chmelyuk NS, Efremova MV, Malinovskaya JA, Semkina AS, Abakumov MA. Encapsulins-Bacterial Protein Nanocompartments: Structure, Properties, and Application. Biomolecules 2020; 10:biom10060966. [PMID: 32604934 PMCID: PMC7355545 DOI: 10.3390/biom10060966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, a new class of prokaryotic compartments, collectively called encapsulins or protein nanocompartments, has been discovered. The shell proteins of these structures self-organize to form icosahedral compartments with a diameter of 25-42 nm, while one or more cargo proteins with various functions can be encapsulated in the nanocompartment. Non-native cargo proteins can be loaded into nanocompartments and the surface of the shells can be further functionalized, which allows for developing targeted drug delivery systems or using encapsulins as contrast agents for magnetic resonance imaging. Since the genes encoding encapsulins can be integrated into the cell genome, encapsulins are attractive for investigation in various scientific fields, including biomedicine and nanotechnology.
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Affiliation(s)
- Anna N. Gabashvili
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Nelly S. Chmelyuk
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
| | - Maria V. Efremova
- Department of Nuclear Medicine, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Institute of Biological and Medical Imaging and Institute of Developmental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Alevtina S. Semkina
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Maxim A. Abakumov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
- Correspondence: ; Tel.: +7-903-586-4777
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Li H, Tan X, Xia X, Zang J, Wang Z, Du M. Thermal treatment modified the physicochemical properties of recombinant oyster (Crassostrea gigas) ferritin. Food Chem 2020; 314:126210. [DOI: 10.1016/j.foodchem.2020.126210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/19/2019] [Accepted: 01/11/2020] [Indexed: 12/13/2022]
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Chen S, Johnson BK, Yu T, Nelson BN, Walker ED. Elizabethkingia anophelis: Physiologic and Transcriptomic Responses to Iron Stress. Front Microbiol 2020; 11:804. [PMID: 32457715 PMCID: PMC7221216 DOI: 10.3389/fmicb.2020.00804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we investigated the global gene expression responses of Elizabethkingia anophelis to iron fluxes in the midgut of female Anopheles stephensi mosquitoes fed sucrose or blood, and in iron-poor or iron-rich culture conditions. Of 3,686 transcripts revealed by RNAseq technology, 218 were upregulated while 112 were down-regulated under iron-poor conditions. Hemolysin gene expression was significantly repressed when cells were grown under iron-rich or high temperature (37°C) conditions. Furthermore, hemolysin gene expression was down-regulated after a blood meal, indicating that E. anophelis cells responded to excess iron and its associated physiological stress by limiting iron loading. By contrast, genes encoding respiratory chain proteins were up-regulated under iron-rich conditions, allowing these iron-containing proteins to chelate intracellular free iron. In vivo studies showed that growth of E. anophelis cells increased 3-fold in blood-fed mosquitoes over those in sucrose-fed ones. Deletion of siderophore synthesis genes led to impaired cell growth in both iron-rich and iron-poor media. Mutants showed more susceptibility to H2O2 toxicity and less biofilm formation than did wild-type cells. Mosquitoes with E. anophelis experimentally colonized in their guts produced more eggs than did those treated with erythromycin or left unmanipulated, as controls. Results reveal that E. anophelis bacteria respond to varying iron concentration in the mosquito gut, harvest iron while fending off iron-associated stress, contribute to lysis of red blood cells, and positively influence mosquito host fecundity.
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Affiliation(s)
- Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Benjamin K. Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Brooke N. Nelson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
- Department of Entomology, Michigan State University, East Lansing, MI, United States
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de Alcântara NR, de Oliveira FM, Garcia W, Dos Santos OAL, Junqueira-Kipnis AP, Kipnis A. Dps protein is related to resistance of Mycobacterium abscessus subsp. massiliense against stressful conditions. Appl Microbiol Biotechnol 2020; 104:5065-5080. [PMID: 32253472 DOI: 10.1007/s00253-020-10586-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) belongs to the Mycobacterium abscessus complex and is a rapidly growing non-tuberculous mycobacterium. The chronic pulmonary, skin, and soft tissue infections that it causes may be difficult to treat due to its intrinsic resistance to the commonly used antimicrobial drugs, making it a serious world public health problem. Iron is an essential nutrient for the growth of microorganisms; nonetheless, it can be toxic when in excess. Thus, bacteria require an iron homeostasis mechanism to succeed in different environments. DNA-binding proteins from starved cells (Dps) are miniferritins with the property to act as additional iron storage proteins but also can bind to DNA, protecting it against hydroxyl radical. Annotation of the Mycma genome revealed the gene mycma_03135 with 79% sequential identity when compared to MSMEG_3242 gene from M. smegmatis mc2 155, which codifies for a known Dps. Recombinant Dps from M. abscessus (rMaDps) was produced in Escherichia coli, purified in soluble form and shown to form high mass oligomers in solution with ferroxidase activity, DNA binding, and protection against damage. The expression of the mycma_03135 gene was induced during Mycma growth in the presence of hydrogen peroxide (H2O2). Additionally, the expression of rMaDps by E. coli conferred greater resistance to H2O2. Thus, this study is the first to identify and characterize a Dps from M. abscessus. KEY POINTS: Mycobacterium abscessus subsp. massiliense express a miniferritin protein (Dps). Mycma Dps binds to DNA and protects against oxidative stress.
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Affiliation(s)
| | - Fábio Muniz de Oliveira
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | | | | | - André Kipnis
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil.
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Kamnev AA, Tugarova AV, Shchelochkov AG, Kovács K, Kuzmann E. Diffuse reflectance infrared Fourier transform (DRIFT) and Mössbauer spectroscopic study of Azospirillum brasilense Sp7: Evidence for intracellular iron(II) oxidation in bacterial biomass upon lyophilisation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117970. [PMID: 31887674 DOI: 10.1016/j.saa.2019.117970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Microbial cells are well known to be capable of remaining viable when desiccated, and a variety of beneficial microorganisms can thus be preserved for storage. For the ubiquitous widely studied soil bacterium Azospirillum brasilense (wild-type strain Sp7), which has a significant agrobiotechnological potential owing to its plant-growth-promoting capabilities perspective for its use in biofertilisers, Fourier transform infrared (FTIR) spectroscopy (in the diffuse reflectance mode, DRIFT) was used to control the state of biomass, together with 57Fe transmission Mössbauer spectroscopy to monitor intracellular iron speciation in live rapidly frozen cell suspension and in the lyophilised biomass (both measured at T = 80 K). It has been shown for the first time that a relatively large part of ferrous iron in live cells (22% of the whole cellular iron pool, represented by two high-spin Fe(II) forms, in the 18-h culture grown on 57Fe(III) complex with nitrilotriacetic acid as the sole source of iron) gets largely oxidised upon lyophilisation. The remaining part of iron(II) in the resulting dry biomass was found to be ca. 3% only. The major part of ferric iron in the dry biomass was shown to be comprised of ferritin-like ferric species (giving a typical magnetically split sextet at T = 5 K), while the iron(III) formed from cellular iron(II) by oxidation in air in the course of drying remained in a paramagnetic state even at T = 5 K. The possibility of intracellular iron(II) oxidation to iron(III) upon desiccation may be a specific natural strategy to avoid cell damage caused by Fenton-type reactions in dormant (frozen, dried) cells. The results obtained may have important implications related to iron speciation and redox transformations in dried bacterial preparations intended for long-term storage.
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Affiliation(s)
- Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prosp. Entuziastov, 13, Saratov 410049, Russia.
| | - Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prosp. Entuziastov, 13, Saratov 410049, Russia
| | - Alexei G Shchelochkov
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prosp. Entuziastov, 13, Saratov 410049, Russia
| | - Krisztina Kovács
- Laboratory of Nuclear Chemistry, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, Budapest 1512, Hungary
| | - Ernő Kuzmann
- Laboratory of Nuclear Chemistry, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, Budapest 1512, Hungary
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Oliveira FM, Marinho FV, Oliveira SC, Resende DP, Junqueira-Kipnis AP, Kipnis A. Mycobacterium abscessus subsp. massiliense expressing bacterioferritin have improved resistance to stressful conditions. J Appl Microbiol 2020; 128:1802-1813. [PMID: 31975455 DOI: 10.1111/jam.14585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/08/2019] [Accepted: 01/15/2020] [Indexed: 01/01/2023]
Abstract
AIMS The importance of bacterioferritin in the virulence and pathogenicity of the genus Mycobacterium is still unclear. The aim of this study was to analyse if the expression of a recombinant bacterioferritin from M. tuberculosis (Mtb) by Mycma could improve the capacity of this bacillus to resist the host defence mechanisms. METHODS AND RESULTS Recombinant Mycma, expressing bacterioferritin (Rv1876) from Mtb, was developed by transformation with pMIP12_Rv1876. To determine bacterioferritin influence on Mycma physiology and virulence, the mycobacteria growth was analysed in vitro and in vivo. It was observed that the expression of bacterioferritin improved the growth rate of recombinant Mycma_BfrA under iron excess and oxidative stress, as compared to the wild type. Furthermore, in the murine model of infection, it was observed that Mycma_BfrA-infected mice had higher bacillary load and a more pronounced lesion in the lungs when compared with the wild type. CONCLUSION This study showed that bacterioferritin confers additional resistance to stress conditions, resulting in increased pathogenicity of Mycma during mice infection. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides new insights about the importance of bacterioferritin in the virulence and pathogenicity of the Mycobacterium genus.
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Affiliation(s)
- F M Oliveira
- Department of Biosciences and Technology, Tropical Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
| | - F V Marinho
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - S C Oliveira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D P Resende
- Department of Biosciences and Technology, Tropical Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
| | - A P Junqueira-Kipnis
- Department of Biosciences and Technology, Tropical Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
| | - A Kipnis
- Department of Biosciences and Technology, Tropical Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
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Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
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Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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48
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Ibekwe AM, Murinda SE. Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects. Microorganisms 2019; 7:microorganisms7120660. [PMID: 31817873 PMCID: PMC6955928 DOI: 10.3390/microorganisms7120660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.
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Affiliation(s)
- Abasiofiok Mark Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
- Correspondence: ; Tel.: +951-369-4828
| | - Shelton E. Murinda
- Animal and Veterinary Sciences Department, Center for Antimicrobial Research and Food Safety, California State Polytechnic University, Pomona, CA 91768, USA;
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49
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Hussain S, Min Z, Xiuxiu Z, Khan MH, Lifeng L, Hui C. Significance of Fe(II) and environmental factors on carbon-fixing bacterial community in two paddy soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109456. [PMID: 31398779 DOI: 10.1016/j.ecoenv.2019.109456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
The seasonal flooding and drainage process affect the paddy soils, the existence of the iron state either Fe(III) or Fe(II) is the main redox system of paddy soil. Its morphological transformation affects the redox nature of paddy soils, which also affects the distribution of bacterial community diversity. This study based on molecular biological methods (qPCR, Illumina MiSeq sequencing technique) to investigate the effect of Fe(II) and environmental factors on cbbM genes containing carbon fixing microbes. Both Eh5 and pH were reduced with Fe(II) concentrations. The Fe(II) addition significantly affects the cbbM gene copy number in both texture soils. In loamy soil, cbbM gene copy number increased with high addition of Fe(II), while both low and high concentrations significantly reduced the cbbM gene copy number in sandy soil. Chemotrophic bacterial abundance significantly increased by 79.7% and 54.8% with high and low Fe(II) addition in loamy soil while in sandy soil its abundance decreased by 53% and 54% with the low and high Fe(II) accumulation. The phototrophic microbial community increased by 37.8% with low Fe(II) concentration and decreased by 16.2% with a high concentration in loamy soil, while in sandy soil increased by 21% and 14.3% in sandy soil with low and high Fe(II) addition. Chemoheterotrophic carbon fixing bacterial abundance decreased with the Fe(II) accumulation in both soil textures in loamy soil its abundance decreased by 5.8% and 24.8%, while in sand soil 15.7% and 12.8% with low and high Fe(II) concentrations. The Fe(II) concentration and soil textures maybe two of the major factors to shape the bacterial community structure in paddy soils. These results provide a scientific basis for management of paddy soil fertility and it can be beneficial to take measures to ease the greenhouse gases effect.
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Affiliation(s)
- Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Min
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhu Xiuxiu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Lifeng
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cao Hui
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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50
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Bennett BD, Gralnick JA. Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems. Free Radic Biol Med 2019; 140:167-171. [PMID: 31251977 DOI: 10.1016/j.freeradbiomed.2019.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/13/2019] [Accepted: 06/23/2019] [Indexed: 12/24/2022]
Abstract
Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe3+), and ferrous iron, the reduced state (Fe2+). Fe2+ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe2+ toxicity, focusing on molecular mechanistic studies in several model systems.
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Affiliation(s)
- B D Bennett
- Pacific Biosciences Research Center, University of Hawai‛i at Mānoa, Honolulu, HI, 96813, USA
| | - J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, 55108, USA.
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