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Fan L, Wu D, Goremykin V, Trost K, Knopp M, Zhang C, Martin WF, Zhu R. Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat Ecol Evol 2022; 6:1832-1835. [PMID: 36280779 DOI: 10.1038/s41559-022-01896-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Lu Fan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Dingfeng Wu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione E. Mach, San Michele all'Adige, Italy
| | - Katharina Trost
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Knopp
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany.
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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2
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Biosensors and Drug Delivery in Oncotheranostics Using Inorganic Synthetic and Biogenic Magnetic Nanoparticles. BIOSENSORS 2022; 12:bios12100789. [PMID: 36290927 PMCID: PMC9599632 DOI: 10.3390/bios12100789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
Abstract
Magnetic nanocarriers have attracted attention in translational oncology due to their ability to be employed both for tumor diagnostics and therapy. This review summarizes data on applications of synthetic and biogenic magnetic nanoparticles (MNPs) in oncological theranostics and related areas. The basics of both types of MNPs including synthesis approaches, structure, and physicochemical properties are discussed. The properties of synthetic MNPs and biogenic MNPs are compared with regard to their antitumor therapeutic efficiency, diagnostic potential, biocompatibility, and cellular toxicity. The comparative analysis demonstrates that both synthetic and biogenic MNPs could be efficiently used for cancer theranostics, including biosensorics and drug delivery. At the same time, reduced toxicity of biogenic particles was noted, which makes them advantageous for in vivo applications, such as drug delivery, or MRI imaging of tumors. Adaptability to surface modification based on natural biochemical processes is also noted, as well as good compatibility with tumor cells and proliferation in them. Advances in the bionanotechnology field should lead to the implementation of MNPs in clinical trials.
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3
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Genome Sequences of Two Pseudomonas Isolates That Can Use Metformin as the Sole Nitrogen Source. Microbiol Resour Announc 2022; 11:e0063922. [PMID: 35980179 PMCID: PMC9476953 DOI: 10.1128/mra.00639-22] [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] [Indexed: 11/20/2022] Open
Abstract
Metformin is a major water pollutant globally. We report the complete genome sequences of two pseudomonads,
Pseudomonas
sp. strain KHPS1 and
Pseudomonas hydrolytica
strain KHPS2, isolated from wastewater treatment plant sludge, which can grow on metformin as the nitrogen source. Both isolates contained ~80-kb plasmids that may contain metformin breakdown genes.
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4
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Zhao D, Yang J, Zhang G, Lu D, Zhang S, Wang W, Yan L. Potential and whole-genome sequence-based mechanism of elongated-prismatic magnetite magnetosome formation in Acidithiobacillus ferrooxidans BYM. World J Microbiol Biotechnol 2022; 38:121. [DOI: 10.1007/s11274-022-03308-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/13/2022] [Indexed: 01/15/2023]
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5
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Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y. Expanding magnetic organelle biogenesis in the domain Bacteria. MICROBIOME 2020; 8:152. [PMID: 33126926 PMCID: PMC7602337 DOI: 10.1186/s40168-020-00931-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. RESULTS Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. CONCLUSIONS These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle. Video Abstract.
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Affiliation(s)
- Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Greig A Paterson
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, L69 7ZE, Liverpool, UK
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Pekarsky A, Spadiut O. Intrinsically Magnetic Cells: A Review on Their Natural Occurrence and Synthetic Generation. Front Bioeng Biotechnol 2020; 8:573183. [PMID: 33195134 PMCID: PMC7604359 DOI: 10.3389/fbioe.2020.573183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
The magnetization of non-magnetic cells has great potential to aid various processes in medicine, but also in bioprocess engineering. Current approaches to magnetize cells with magnetic nanoparticles (MNPs) require cellular uptake or adsorption through in vitro manipulation of cells. A relatively new field of research is "magnetogenetics" which focuses on in vivo production and accumulation of magnetic material. Natural intrinsically magnetic cells (IMCs) produce intracellular, MNPs, and are called magnetotactic bacteria (MTB). In recent years, researchers have unraveled function and structure of numerous proteins from MTB. Furthermore, protein engineering studies on such MTB proteins and other potentially magnetic proteins, like ferritins, highlight that in vivo magnetization of non-magnetic hosts is a thriving field of research. This review summarizes current knowledge on recombinant IMC generation and highlights future steps that can be taken to succeed in transforming non-magnetic cells to IMCs.
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Affiliation(s)
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria
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7
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Liu P, Liu Y, Zhao X, Roberts AP, Zhang H, Zheng Y, Wang F, Wang L, Menguy N, Pan Y, Li J. Diverse phylogeny and morphology of magnetite biomineralized by magnetotactic cocci. Environ Microbiol 2020; 23:1115-1129. [PMID: 32985765 DOI: 10.1111/1462-2920.15254] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/20/2020] [Accepted: 09/24/2020] [Indexed: 01/29/2023]
Abstract
Magnetotactic bacteria (MTB) are diverse prokaryotes that produce magnetic nanocrystals within intracellular membranes (magnetosomes). Here, we present a large-scale analysis of diversity and magnetosome biomineralization in modern magnetotactic cocci, which are the most abundant MTB morphotypes in nature. Nineteen novel magnetotactic cocci species are identified phylogenetically and structurally at the single-cell level. Phylogenetic analysis demonstrates that the cocci cluster into an independent branch from other Alphaproteobacteria MTB, that is, within the Etaproteobacteria class in the Proteobacteria phylum. Statistical analysis reveals species-specific biomineralization of magnetosomal magnetite morphologies. This further confirms that magnetosome biomineralization is controlled strictly by the MTB cell and differs among species or strains. The post-mortem remains of MTB are often preserved as magnetofossils within sediments or sedimentary rocks, yet paleobiological and geological interpretation of their fossil record remains challenging. Our results indicate that magnetofossil morphology could be a promising proxy for retrieving paleobiological information about ancient MTB.
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Affiliation(s)
- Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Heng Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yue Zheng
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Fuxian Wang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, China
| | - Nicolas Menguy
- France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China.,IMPMC, CNRS UMR 7590, Sorbonne Universités, MNHN, UPMC, IRD UMR 206, Paris, France
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic MultiCellular Organisms, Chinese Academy of Sciences, Beijing, China
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8
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Uzun M, Alekseeva L, Krutkina M, Koziaeva V, Grouzdev D. Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases. Sci Data 2020; 7:252. [PMID: 32737307 PMCID: PMC7449369 DOI: 10.1038/s41597-020-00593-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
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Affiliation(s)
- Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Lolita Alekseeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Denis Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
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9
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Jacob JJ, Suthindhiran K. Diversity of Uncultured Magnetospirillum sp. from the Sediments of South Kerala Sedimentary Basin, India. Curr Microbiol 2020; 77:2456-2464. [PMID: 32591924 DOI: 10.1007/s00284-020-02098-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/18/2020] [Indexed: 11/26/2022]
Abstract
Studies on the geographic distribution of Magnetotactic bacteria (MTB) revealed their ubiquitous presence in diverse habitats on all continents. However, little is known about MTB inhabitation in the Indian coastal ecosystem. Here, we investigate the diversity of Magnetospirillum sp. from the iron mineral sediments deposit of the South Kerala sedimentary basin, India using culture-independent methods. The collected sediment samples were analysed for the presence of nitrate (zinc reduction), sulphide (cline method), Fe2+, total iron (ferrozine assay) and iron minerals (XRD analysis). Based on the geochemical measurements, the sediment possesses major factors such as nutrients, pH, temperature and chemical gradients in metabolic accessible form for MTB. The cubo-octahedral crystals of the magnetosome are also evident from the TEM micrographs of magnetically enriched sediment. CARD-FISH analysis showed the presence of Magnetospirillum in all the six samples analysed. Phylogenetic analysis based on 16S rRNA gene library showed that the clones belong to the class Alphaproteobacteria and are members of the genus Magnetospirillum. The results of the species-specific PCR study are consistent with CARD-FISH analysis and the identified uncultured Magnetospirillum were morphologically and phylogenetically similar to the isolates from diverse habitat. The identification of Magnetospirillum from Indian coast supports the hypothesis of wide geographic distribution of these bacteria.
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Affiliation(s)
- Jobin J Jacob
- Marine Biotechnology and Bioproducts Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - K Suthindhiran
- Marine Biotechnology and Bioproducts Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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10
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Amor M, Mathon FP, Monteil CL, Busigny V, Lefevre CT. Iron-biomineralizing organelle in magnetotactic bacteria: function, synthesis and preservation in ancient rock samples. Environ Microbiol 2020; 22:3611-3632. [PMID: 32452098 DOI: 10.1111/1462-2920.15098] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 12/22/2022]
Abstract
Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that incorporate iron from their environment to synthesize intracellular nanoparticles of magnetite (Fe3 O4 ) or greigite (Fe3 S4 ) in a genetically controlled manner. Magnetite and greigite magnetic phases allow MTB to swim towards redox transition zones where they thrive. MTB may represent some of the oldest microorganisms capable of synthesizing minerals on Earth and have been proposed to significantly impact the iron biogeochemical cycle by immobilizing soluble iron into crystals that subsequently fossilize in sedimentary rocks. In the present article, we describe the distribution of MTB in the environment and discuss the possible function of the magnetite and greigite nanoparticles. We then provide an overview of the chemical mechanisms leading to iron mineralization in MTB. Finally, we update the methods used for the detection of MTB crystals in sedimentary rocks and present their occurrences in the geological record.
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Affiliation(s)
- Matthieu Amor
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - François P Mathon
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France.,Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris, F-75005, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Vincent Busigny
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris, F-75005, France.,Institut Universitaire de France, Paris, 75005, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
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11
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Ke L, Chen Y, Liu P, Liu S, Wu D, Yuan Y, Wu Y, Gao M. Characteristics and optimised fermentation of a novel magnetotactic bacterium, Magnetospirillum sp. ME-1. FEMS Microbiol Lett 2019. [PMID: 29514248 DOI: 10.1093/femsle/fny052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Magnetotactic bacteria (MTB) can biosynthesise magnetosomes, which have great potential for commercial applications. A new MTB strain, Magnetospirillum sp. ME-1, was isolated and cultivated from freshwater sediments of East Lake (Wuhan, China) using the limiting dilution method. ME-1 had a chain of 17 ± 4 magnetosomes in the form of cubooctahedral crystals with a shape factor of 0.89. ME-1 was closest to Magnetospirillum sp. XM-1 according to 16S rRNA gene sequence similarity. Compared with XM-1, ME-1 possessed an additional copy of mamPA and a larger mamO in magnetosome-specific genes. ME-1 had an intact citric acid cycle, and complete pathway models of ammonium assimilation and dissimilatory nitrate reduction. Potential carbon and nitrogen sources in these pathways were confirmed to be used in ME-1. Adipate was determined to be used in the fermentation medium as a new kind of dicarboxylic acid. The optimised fermentation medium was determined by orthogonal tests. The large-scale production of magnetosomes was achieved and the magnetosome yield (wet weight) reached 120 mg L-1 by fed-batch cultivation of ME-1 at 49 h in a 10-L fermenter with the optimised fermentation medium. This study may provide insights into the isolation and cultivation of other new MTB strains and the production of magnetosomes.
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Affiliation(s)
- Linfeng Ke
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yajun Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Pengming Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Shan Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Dandan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Yihui Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
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12
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Koziaeva V, Dziuba M, Leão P, Uzun M, Krutkina M, Grouzdev D. Genome-Based Metabolic Reconstruction of a Novel Uncultivated Freshwater Magnetotactic coccus " Ca. Magnetaquicoccus inordinatus" UR-1, and Proposal of a Candidate Family " Ca. Magnetaquicoccaceae". Front Microbiol 2019; 10:2290. [PMID: 31632385 PMCID: PMC6783814 DOI: 10.3389/fmicb.2019.02290] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022] Open
Abstract
Magnetotactic bacteria are widely represented microorganisms that have the ability to synthesize magnetosomes. The magnetotactic cocci of the order Magnetococcales are the most frequently identified, but their classification remains unclear due to the low number of cultivated representatives. This paper reports the analysis of an uncultivated magnetotactic coccus UR-1 collected from the Uda River (in eastern Siberia). Genome analyses of this bacterium and comparison to the available Magnetococcales genomes identified a novel species called "Ca. Magnetaquicoccus inordinatus," and a delineated candidate family "Ca. Magnetaquicoccaceae" within the order Magnetococcales is proposed. We used average amino acid identity values <55-56% and <64-65% as thresholds for the separation of families and genera, respectively, within the order Magnetococcales. Analyses of the genome sequence of UR-1 revealed a potential ability for a chemolithoautotrophic lifestyle, with the oxidation of a reduced sulfur compound and carbon assimilation by rTCA. A nearly complete magnetosome genome island, containing a set of mam and mms genes, was also identified. Further comparative analyses of the magnetosome genes showed vertical inheritance as well as horizontal gene transfer as the evolutionary drivers of magnetosome biomineralization genes in strains of the order Magnetococcales.
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Affiliation(s)
- Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Marina Dziuba
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Denis Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
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13
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Leão P, Le Nagard L, Yuan H, Cypriano J, Da Silva-Neto I, Bazylinski DA, Acosta-Avalos D, de Barros HL, Hitchcock AP, Lins U, Abreu F. Magnetosome magnetite biomineralization in a flagellated protist: evidence for an early evolutionary origin for magnetoreception in eukaryotes. Environ Microbiol 2019; 22:1495-1506. [PMID: 31188524 DOI: 10.1111/1462-2920.14711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 11/30/2022]
Abstract
The most well-recognized magnetoreception behaviour is that of the magnetotactic bacteria (MTB), which synthesize membrane-bounded magnetic nanocrystals called magnetosomes via a biologically controlled process. The magnetic minerals identified in prokaryotic magnetosomes are magnetite (Fe3 O4 ) and greigite (Fe3 S4 ). Magnetosome crystals, regardless of composition, have consistent, species-specific morphologies and single-domain size range. Because of these features, magnetosome magnetite crystals possess specific properties in comparison to abiotic, chemically synthesized magnetite. Despite numerous discoveries regarding MTB phylogeny over the last decades, this diversity is still considered underestimated. Characterization of magnetotactic microorganisms is important as it might provide insights into the origin and establishment of magnetoreception in general, including eukaryotes. Here, we describe the magnetotactic behaviour and characterize the magnetosomes from a flagellated protist using culture-independent methods. Results strongly suggest that, unlike previously described magnetotactic protists, this flagellate is capable of biomineralizing its own anisotropic magnetite magnetosomes, which are aligned in complex aggregations of multiple chains within the cell. This organism has a similar response to magnetic field inversions as MTB. Therefore, this eukaryotic species might represent an early origin of magnetoreception based on magnetite biomineralization. It should add to the definition of parameters and criteria to classify biogenic magnetite in the fossil record.
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Affiliation(s)
- Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Le Nagard
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Hao Yuan
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Inácio Da Silva-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, USA
| | | | | | - Adam P Hitchcock
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Dieudonné A, Pignol D, Prévéral S. Magnetosomes: biogenic iron nanoparticles produced by environmental bacteria. Appl Microbiol Biotechnol 2019; 103:3637-3649. [PMID: 30903215 DOI: 10.1007/s00253-019-09728-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 01/10/2023]
Abstract
The scientific community's interest in magnetotactic bacteria has increased substantially in recent decades. These prokaryotes have the particularity of synthesizing nanomagnets, called magnetosomes. The majority of research is based on several scientific questions. Where do magnetotactic bacteria live, what are their characteristics, and why are they magnetic? What are the molecular phenomena of magnetosome biomineralization and what are the physical characteristics of magnetosomes? In addition to scientific curiosity to better understand these stunning organisms, there are biotechnological opportunities to consider. Magnetotactic bacteria, as well as magnetosomes, are used in medical applications, for example cancer treatment, or in environmental ones, for example bioremediation. In this mini-review, we investigated all the aspects mentioned above and summarized the currently available knowledge.
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Affiliation(s)
- Anissa Dieudonné
- UMR 7265, Aix Marseille Univ, CEA, CNRS, BIAM, LBC, Saint Paul-Lez-Durance, France
| | - David Pignol
- UMR 7265, Aix Marseille Univ, CEA, CNRS, BIAM, LBC, Saint Paul-Lez-Durance, France
| | - Sandra Prévéral
- UMR 7265, Aix Marseille Univ, CEA, CNRS, BIAM, LBC, Saint Paul-Lez-Durance, France.
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15
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Degli Esposti M. A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria. Genome Biol Evol 2018; 9:3039-3053. [PMID: 29106540 PMCID: PMC5714133 DOI: 10.1093/gbe/evx225] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 12/15/2022] Open
Abstract
Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochondria and bacteria. Nonorthologous proteins can also contribute to some biochemical steps as originally uncovered in Escherichia coli, which is the best studied organism for Q biosynthesis in prokaryotes. However, the origin of the biosynthetic pathway of Q has remained obscure. Here, I show by genome analysis that Q biosynthesis originated in cyanobacteria and then diversified in anaerobic alpha proteobacteria which have extant relatives in members of the Rhodospirillaceae family. Two distinct biochemical pathways diverged when ambient oxygen reached current levels on earth, one leading to the well-known series of Ubi genes found in E. coli, and the other containing CoQ proteins originally found in eukaryotes. Extant alpha proteobacteria show Q biosynthesis pathways that are more similar to that present in mitochondria than to that of E. coli. Hence, this work clarifies not only the origin but also the evolution of Q biosynthesis from bacteria to mitochondria.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genoa, Italy.,Center for Genomic Sciences, Universidad National Autonoma de Mexico Campus of Cuernavaca, Cuernavaca, Morelos, Mexico
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16
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Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y. Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution. ISME JOURNAL 2018; 12:1508-1519. [PMID: 29581530 PMCID: PMC5955933 DOI: 10.1038/s41396-018-0098-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022]
Abstract
The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and "Candidatus Lambdaproteobacteria" classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.
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Affiliation(s)
- Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Greig A Paterson
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZE, UK
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China. .,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Werckmann J, Cypriano J, Lefèvre CT, Dembelé K, Ersen O, Bazylinski DA, Lins U, Farina M. Localized iron accumulation precedes nucleation and growth of magnetite crystals in magnetotactic bacteria. Sci Rep 2017; 7:8291. [PMID: 28811607 PMCID: PMC5557804 DOI: 10.1038/s41598-017-08994-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/14/2017] [Indexed: 12/16/2022] Open
Abstract
Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles that originate from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here we address the question: can iron transported inside MTB for the production of magnetite crystals be spatially mapped using electron microscopy? Cultured and uncultured MTB from brackish and freshwater lagoons were studied using analytical transmission electron microscopy in an attempt to answer this question. Scanning transmission electron microscopy was used at sub-nanometric resolution to determine the distribution of elements by implementing high sensitivity energy dispersive X-ray (EDS) mapping and electron energy loss spectroscopy (EELS). EDS mapping showed that magnetosomes are enmeshed in a magnetosomal matrix in which iron accumulates close to the magnetosome forming a continuous layer visually appearing as a corona. EELS, obtained at high spatial resolution, confirmed that iron was present close to and inside the lipid bilayer magnetosome membrane. This study provides important clues to magnetite formation in MTB through the discovery of a mechanism where iron ions accumulate prior to magnetite biomineralization.
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Affiliation(s)
- Jacques Werckmann
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.
| | - Jefferson Cypriano
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Christopher T Lefèvre
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108, Saint Paul lez Durance, France
| | - Kassiogé Dembelé
- Institut de physique et chimie des matériaux de Strasbourg (IPCMS) UMR 7504 CNRS 23 rue du Lœss, BP 43 67034, Strasbourg Cedex 2, France
| | - Ovidiu Ersen
- Institut de physique et chimie des matériaux de Strasbourg (IPCMS) UMR 7504 CNRS 23 rue du Lœss, BP 43 67034, Strasbourg Cedex 2, France
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, Nevada, 89154-4004, USA
| | - Ulysses Lins
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Marcos Farina
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
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18
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Yan L, Da H, Zhang S, López VM, Wang W. Bacterial magnetosome and its potential application. Microbiol Res 2017; 203:19-28. [PMID: 28754204 DOI: 10.1016/j.micres.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/08/2017] [Accepted: 06/17/2017] [Indexed: 01/01/2023]
Abstract
Bacterial magnetosome, synthetized by magnetosome-producing microorganisms including magnetotactic bacteria (MTB) and some non-magnetotactic bacteria (Non-MTB), is a new type of material comprising magnetic nanocrystals surrounded by a phospholipid bilayer. Because of the special properties such as single magnetic domain, excellent biocompatibility and surface modification, bacterial magnetosome has become an increasingly attractive for researchers in biology, medicine, paleomagnetism, geology and environmental science. This review briefly describes the general feature of magnetosome-producing microorganisms. This article also highlights recent advances in the understanding of the biochemical and magnetic characteristics of bacterial magnetosome, as well as the magnetosome formation mechanism including iron ions uptake, magnetosome membrane formation, biomineralization and magnetosome chain assembly. Finally, this review presents the potential applications of bacterial magnetosome in biomedicine, wastewater treatment, and the significance of mineralization of magnetosome in biology and geology.
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Affiliation(s)
- Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China.
| | - Huiyun Da
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
| | - Viviana Morillo López
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV 89154, USA
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
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19
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Zhang H, Menguy N, Wang F, Benzerara K, Leroy E, Liu P, Liu W, Wang C, Pan Y, Chen Z, Li J. Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes. Front Microbiol 2017; 8:969. [PMID: 28611762 PMCID: PMC5447723 DOI: 10.3389/fmicb.2017.00969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are morphologically and phylogenetically diverse prokaryotes. They can form intracellular chain-assembled magnetite (Fe3O4) or greigite (Fe3S4) nanocrystals each enveloped by a lipid bilayer membrane called a magnetosome. Magnetotactic cocci have been found to be the most abundant morphotypes of MTB in various aquatic environments. However, knowledge on magnetosome biomineralization within magnetotactic cocci remains elusive due to small number of strains that have been cultured. By using a coordinated fluorescence and scanning electron microscopy method, we discovered a unique magnetotactic coccus strain (tentatively named SHHC-1) in brackish sediments collected from the estuary of Shihe River in Qinhuangdao city, eastern China. It phylogenetically belongs to the Alphaproteobacteria class. Transmission electron microscopy analyses reveal that SHHC-1 cells formed many magnetite-type magnetosomes organized as two bundles in each cell. Each bundle contains two parallel chains with smaller magnetosomes generally located at the ends of each chain. Unlike most magnetotactic alphaproteobacteria that generally form magnetosomes with uniform crystal morphologies, SHHC-1 magnetosomes display a more diverse variety of crystal morphology even within a single cell. Most particles have rectangular and rhomboidal projections, whilst others are triangular, or irregular. High resolution transmission electron microscopy observations coupled with morphological modeling indicate an idealized model-elongated octahedral crystals, a form composed of eight {111} faces. Furthermore, twins, multiple twins and stack dislocations are frequently observed in the SHHC-1 magnetosomes. This suggests that biomineralization of strain SHHC-1 magnetosome might be less biologically controlled than other magnetotactic alphaproteobacteria. Alternatively, SHHC-1 is more sensitive to the unfavorable environments under which it lives, or a combination of both factors may have controlled the magnetosome biomineralization process within this unique MTB.
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Affiliation(s)
- Heng Zhang
- Department of Life Science and Technology, Heilongjiang Bayi Agricultural UniversityDaqing, China.,Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
| | - Nicolas Menguy
- France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China.,IMPMC, Centre National de la Recherche Scientifique, UMR 7590, Sorbonne Universités, MNHN, UPMC, IRD UMR 206Paris, France
| | - Fuxian Wang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
| | - Karim Benzerara
- IMPMC, Centre National de la Recherche Scientifique, UMR 7590, Sorbonne Universités, MNHN, UPMC, IRD UMR 206Paris, France
| | - Eric Leroy
- France Chimie Me'tallurgique des Terres Rares, ICMPE, UMR 7182, Centre National de la Recherche ScientifiqueThiais, France
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
| | - Wenqi Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
| | - Chunli Wang
- Department of Life Science and Technology, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
| | - Zhibao Chen
- Department of Life Science and Technology, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of SciencesBeijing, China
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20
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Barber-Zucker S, Zarivach R. A Look into the Biochemistry of Magnetosome Biosynthesis in Magnetotactic Bacteria. ACS Chem Biol 2017; 12:13-22. [PMID: 27930882 DOI: 10.1021/acschembio.6b01000] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Magnetosomes are protein-rich membrane organelles that encapsulate magnetite or greigite and whose chain alignment enables magnetotactic bacteria (MTB) to sense the geomagnetic field. As these bacteria synthesize uniform magnetic particles, their biomineralization mechanism is of great interest among researchers from different fields, from material engineering to medicine. Both magnetosome formation and magnetic particle synthesis are highly controlled processes that can be divided into several crucial steps: membrane invagination from the inner-cell membrane, protein sorting, the magnetosomes' arrangement into chains, iron transport, chemical environment regulation of the magnetosome lumen, magnetic particle nucleation, and finally crystal growth, size, and morphology control. This complex system involves an ensemble of unique proteins that participate in different stages during magnetosome formation, some of which were extensively studied in recent years. Here, we present the current knowledge on magnetosome biosynthesis with a focus on the different proteins and the main biochemical pathways along this process.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Life
Sciences,
the National Institute for Biotechnology in the Negev and Ilse Katz
Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Raz Zarivach
- Department of Life
Sciences,
the National Institute for Biotechnology in the Negev and Ilse Katz
Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
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21
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Araujo ACV, Morillo V, Cypriano J, Teixeira LCRS, Leão P, Lyra S, Almeida LGD, Bazylinski DA, Ribeiro de Vasconcelos AT, Abreu F, Lins U. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment. BMC Genomics 2016; 17:726. [PMID: 27801294 PMCID: PMC5088516 DOI: 10.1186/s12864-016-3064-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Magnetotactic bacteria (MTB) are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. RESULTS Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4) magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s-1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. CONCLUSION Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively large number of genes encoding transporters as well as chemotaxis receptors in the genome of Mf. australis strain IT-1 combined with its rapid swimming velocities, indicate that cells respond rapidly to environmental changes.
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Affiliation(s)
- Ana Carolina Vieira Araujo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.,Current institution: Departamento de Biologia, Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil
| | - Viviana Morillo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.,School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | | | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Sidcley Lyra
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Luiz Gonzaga de Almeida
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, 25651-070, Petrópolis, RJ, Brazil
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Ana Tereza Ribeiro de Vasconcelos
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, 25651-070, Petrópolis, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.
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22
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North-Seeking Magnetotactic Gammaproteobacteria in the Southern Hemisphere. Appl Environ Microbiol 2016; 82:5595-602. [PMID: 27401974 DOI: 10.1128/aem.01545-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 06/29/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Magnetotactic bacteria (MTB) comprise a phylogenetically diverse group of prokaryotes capable of orienting and navigating along magnetic field lines. Under oxic conditions, MTB in natural environments in the Northern Hemisphere generally display north-seeking (NS) polarity, swimming parallel to the Earth's magnetic field lines, while those in the Southern Hemisphere generally swim antiparallel to magnetic field lines (south-seeking [SS] polarity). Here, we report a population of an uncultured, monotrichously flagellated, and vibrioid MTB collected from a brackish lagoon in Brazil in the Southern Hemisphere that consistently exhibits NS polarity. Cells of this organism were mainly located below the oxic-anoxic interface (OAI), suggesting it is capable of some type of anaerobic metabolism. Magnetosome crystalline habit and composition were consistent with elongated prismatic magnetite (Fe3O4) particles. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this organism belongs to a distinct clade of the Gammaproteobacteria class. The presence of NS MTB in the Southern Hemisphere and the previously reported finding of SS MTB in the Northern Hemisphere reinforce the idea that magnetotaxis is more complex than we currently understand and may be modulated by factors other than O2 concentration and redox gradients in sediments and water columns. IMPORTANCE Magnetotaxis is a navigational mechanism used by magnetotactic bacteria to move along geomagnetic field lines and find an optimal position in chemically stratified sediments. For that, magnetotactic bacteria swim parallel to the geomagnetic field lines under oxic conditions in the Northern Hemisphere, whereas those in the Southern Hemisphere swim antiparallel to magnetic field lines. A population of uncultured vibrioid magnetotactic bacteria was discovered in a brackish lagoon in the Southern Hemisphere that consistently swim northward, i.e., the opposite of the overwhelming majority of other Southern Hemisphere magnetotactic bacteria. This finding supports the idea that magnetotaxis is more complex than previously thought.
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Abreu F, Carolina A, Araujo V, Leão P, Silva KT, Carvalho FMD, Cunha ODL, Almeida LG, Geurink C, Farina M, Rodelli D, Jovane L, Pellizari VH, Vasconcelos ATD, Bazylinski DA, Lins U. Culture‐independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments. Environ Microbiol 2016; 18:4426-4441. [DOI: 10.1111/1462-2920.13388] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
| | | | - V. Araujo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
| | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
| | - Karen Tavares Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
| | | | - Oberdan de Lima Cunha
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica25651‐070Petrópolis RJ Brazil
| | - Luiz Gonzaga Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica25651‐070Petrópolis RJ Brazil
| | - Corey Geurink
- School of Life SciencesUniversity of Nevada at Las VegasLas Vegas NV89154‐4004 USA
| | - Marcos Farina
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
| | - Daniel Rodelli
- Instituto Oceanográfico, Universidade de São Paulo05508‐900São Paulo SP Brazil
| | - Luigi Jovane
- Instituto Oceanográfico, Universidade de São Paulo05508‐900São Paulo SP Brazil
| | - Vivian H. Pellizari
- Instituto Oceanográfico, Universidade de São Paulo05508‐900São Paulo SP Brazil
| | - Ana Tereza de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica25651‐070Petrópolis RJ Brazil
| | - Dennis A. Bazylinski
- School of Life SciencesUniversity of Nevada at Las VegasLas Vegas NV89154‐4004 USA
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro21941‐902Rio de Janeiro RJ Brazil
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Barber-Zucker S, Keren-Khadmy N, Zarivach R. From invagination to navigation: The story of magnetosome-associated proteins in magnetotactic bacteria. Protein Sci 2015; 25:338-51. [PMID: 26457474 DOI: 10.1002/pro.2827] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/07/2015] [Indexed: 11/11/2022]
Abstract
Magnetotactic bacteria (MTB) are a group of Gram-negative microorganisms that are able to sense and change their orientation in accordance with the geomagnetic field. This unique capability is due to the presence of a special suborganelle called the magnetosome, composed of either a magnetite or gregite crystal surrounded by a lipid membrane. MTB were first detected in 1975 and since then numerous efforts have been made to clarify the special mechanism of magnetosome formation at the molecular level. Magnetosome formation can be divided into several steps, beginning with vesicle invagination from the cell membrane, through protein sorting, followed by the combined steps of iron transportation, biomineralization, and the alignment of magnetosomes into a chain. The magnetosome-chain enables the sensing of the magnetic field, and thus, allows the MTB to navigate. It is known that magnetosome formation is tightly controlled by a distinctive set of magnetosome-associated proteins that are encoded mainly in a genomically conserved region within MTB called the magnetosome island (MAI). Most of these proteins were shown to have an impact on the magnetism of MTB. Here, we describe the process in which the magnetosome is formed with an emphasis on the different proteins that participate in each stage of the magnetosome formation scheme.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Noa Keren-Khadmy
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
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Magnetotactic bacteria as potential sources of bioproducts. Mar Drugs 2015; 13:389-430. [PMID: 25603340 PMCID: PMC4306944 DOI: 10.3390/md13010389] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/17/2014] [Indexed: 11/16/2022] Open
Abstract
Magnetotactic bacteria (MTB) produce intracellular organelles called magnetosomes which are magnetic nanoparticles composed of magnetite (Fe3O4) or greigite (Fe3S4) enveloped by a lipid bilayer. The synthesis of a magnetosome is through a genetically controlled process in which the bacterium has control over the composition, direction of crystal growth, and the size and shape of the mineral crystal. As a result of this control, magnetosomes have narrow and uniform size ranges, relatively specific magnetic and crystalline properties, and an enveloping biological membrane. These features are not observed in magnetic particles produced abiotically and thus magnetosomes are of great interest in biotechnology. Most currently described MTB have been isolated from saline or brackish environments and the availability of their genomes has contributed to a better understanding and culturing of these fastidious microorganisms. Moreover, genome sequences have allowed researchers to study genes related to magnetosome production for the synthesis of magnetic particles for use in future commercial and medical applications. Here, we review the current information on the biology of MTB and apply, for the first time, a genome mining strategy on these microorganisms to search for secondary metabolite synthesis genes. More specifically, we discovered that the genome of the cultured MTB Magnetovibrio blakemorei, among other MTB, contains several metabolic pathways for the synthesis of secondary metabolites and other compounds, thereby raising the possibility of the co-production of new bioactive molecules along with magnetosomes by this species.
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Lin W, Benzerara K, Faivre D, Pan Y. Intracellular biomineralization in bacteria. Front Microbiol 2014; 5:293. [PMID: 24971081 PMCID: PMC4053769 DOI: 10.3389/fmicb.2014.00293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/28/2014] [Indexed: 12/18/2022] Open
Affiliation(s)
- Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Sorbonne Universités, CNRS UMR 7590, Muséum National d'Histoire Naturelle, IRD UMR 206 Paris, France
| | - Damien Faivre
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces Potsdam, Germany
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
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