1
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Yates MD, Mickol RL, Vignola A, Baldwin JW, Glaven SM, Tender LM. Performance of a combined electrotrophic and electrogenic biofilm operated under long-term, continuous cycling. Biotechnol Lett 2024; 46:213-221. [PMID: 38300444 DOI: 10.1007/s10529-023-03450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/14/2023] [Accepted: 11/04/2023] [Indexed: 02/02/2024]
Abstract
OBJECTIVES Evaluate electrochemically active biofilms as high energy density rechargeable microbial batteries toward providing persistent power in applications where traditional battery technology is limiting (, remote monitoring applications). RESULTS Here we demonstrated that an electrochemically active biofilm was able to store and release electrical charge for alternating charge/discharge cycles of up to 24 h periodicity (50% duty cycle) with no significant decrease in average current density (0.16 ± 0.04 A/m2) for over 600 days. However, operation at 24 h periodicity for > 50 days resulted in a sharp decrease in the current to nearly zero. This current crash was recoverable by decreasing the periodicity. Overall, the coulombic efficiency remained near unity within experimental error (102 ± 3%) for all of the tested cycling periods. Electrochemical characterization here suggests that electron transfer occurs through multiple routes, likely a mixture of direct and mediated mechanisms. CONCLUSIONS These results indicate that bidirectional electrogenic/electrotrophic biofilms are capable of efficient charge storage/release over a wide range of cycling frequency and may eventually enable development of sustainable, high energy density rechargeable batteries.
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Affiliation(s)
- Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, 20375, USA.
| | - Rebecca L Mickol
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, 20375, USA
| | - Amelia Vignola
- Acoustics Division, Naval Research Laboratory, Washington, DC, 20375, USA
| | - Jeffrey W Baldwin
- Acoustics Division, Naval Research Laboratory, Washington, DC, 20375, USA
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, 20375, USA
| | - Leonard M Tender
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, 20375, USA
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2
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Su Q, Bazylinski DA, Jensen MM. Effect of oxic and anoxic conditions on intracellular storage of polyhydroxyalkanoate and polyphosphate in Magnetospirillum magneticum strain AMB-1. Front Microbiol 2023; 14:1203805. [PMID: 37396362 PMCID: PMC10310966 DOI: 10.3389/fmicb.2023.1203805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms widely inhabiting the oxic-anoxic interface of aquatic environments. Beside biomineralizing magnetic nanocrystals, MTBs are able to sequester various chemical elements (e.g., carbon and phosphorus) for the biogenesis of intracellular granules, like polyhydroxyalkanoate (PHA) and polyphosphate (polyP), making them potentially important in biogeochemical cycling. Yet, the environmental controls of intracellular storage of carbon and phosphorus in MTB remain poorly understood. Here, we investigated the influence of oxic, anoxic and transient oxic-anoxic conditions on intracellular storage of PHA and polyP in Magnetospirillum magneticum strain AMB-1. In the incubations with oxygen, transmission electron microscopy revealed intercellular granules highly rich in carbon and phosphorus, which were further interpreted as PHA and polyP based on chemical and Energy-Dispersive X-ray spectroscopy analysis. Oxygen had a strong effect on PHA and polyP storage in AMB-1 cells, as PHA and polyP granules accounted for up to 47 ± 23% and 5.1 ± 1.7% of the cytoplasmic space, respectively, during continuous oxic conditions, while granules disappeared in anoxic incubations. Poly 3-hydroxybutyrate (PHB) and poly 3-hydroxyvalerate (PHV) accounted for 0.59 ± 0.66% and 0.0033 ± 0.0088% of dry cell weight, respectively, in anoxic incubations, while the values increased by a factor of 7 and 37 after oxygen was introduced. The results highlight a tight link between oxygen, carbon and phosphorus metabolisms in MTB, where favorable oxic growth conditions can lead to metabolic induction of polyP and PHA granule biogenesis.
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Affiliation(s)
- Qingxian Su
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Dennis A. Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, United States
| | - Marlene Mark Jensen
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
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3
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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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4
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Abstract
Magnetotactic bacteria (MTB) belong to several phyla. This class of microorganisms exhibits the ability of magneto-aerotaxis. MTB synthesize biominerals in organelle-like structures called magnetosomes, which contain single-domain crystals of magnetite (Fe3O4) or greigite (Fe3S4) characterized by a high degree of structural and compositional perfection. Magnetosomes from dead MTB could be preserved in sediments (called fossil magnetosomes or magnetofossils). Under certain conditions, magnetofossils are capable of retaining their remanence for millions of years. This accounts for the growing interest in MTB and magnetofossils in paleo- and rock magnetism and in a wider field of biogeoscience. At the same time, high biocompatibility of magnetosomes makes possible their potential use in biomedical applications, including magnetic resonance imaging, hyperthermia, magnetically guided drug delivery, and immunomagnetic analysis. In this review, we attempt to summarize the current state of the art in the field of MTB research and applications.
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5
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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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6
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Yates MD, Bird LJ, Eddie BJ, Onderko EL, Voigt CA, Glaven SM. Nanoliter scale electrochemistry of natural and engineered electroactive bacteria. Bioelectrochemistry 2020; 137:107644. [PMID: 32971484 DOI: 10.1016/j.bioelechem.2020.107644] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/09/2023]
Abstract
Bacterial extracellular electron transfer (EET) is envisioned for use in applied biotechnologies, necessitating electrochemical characterization of natural and engineered electroactive biofilms under conditions similar to the target application, including small-scale biosensing or biosynthesis platforms, which is often distinct from standard 100 mL-scale stirred-batch bioelectrochemical test platforms used in the laboratory. Here, we adapted an eight chamber, nanoliter volume (500 nL) electrochemical flow cell to grow biofilms of both natural (Biocathode MCL community, Marinobacter atlanticus, and Shewanella oneidensis MR1) or genetically modified (S. oneidensis ΔMtr and S. oneidensis ΔMtr + pLB2) electroactive bacteria on electrodes held at a constant potential. Maximum current density achieved by unmodified strains was similar between the nano- and milliliter-scale reactors. However, S. oneidensis biofilms engineered to activate EET upon exposure to 2,4-diacetylphloroglucinol (DAPG) produced current at wild-type levels in the stirred-batch reactor, but not in the nanoliter flow cell. We hypothesize this was due to differences in mass transport of DAPG, naturally-produced soluble redox mediators, and oxygen between the two reactor types. Results presented here demonstrate, for the first time, nanoliter scale chronoamperometry and cyclic voltammetry of a range of electroactive bacteria in a three-electrode reactor system towards development of miniaturized, and potentially high throughput, bioelectrochemical platforms.
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Affiliation(s)
- Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA.
| | - Lina J Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | | | - Christopher A Voigt
- Department of Biological Engineering and the Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA.
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7
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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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8
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Zhang WJ, Wu LF. Flagella and Swimming Behavior of Marine Magnetotactic Bacteria. Biomolecules 2020; 10:biom10030460. [PMID: 32188162 PMCID: PMC7175107 DOI: 10.3390/biom10030460] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 12/22/2022] Open
Abstract
Marine environments are generally characterized by low bulk concentrations of nutrients that are susceptible to steady or intermittent motion driven by currents and local turbulence. Marine bacteria have therefore developed strategies, such as very fast-swimming and the exploitation of multiple directional sensing–response systems in order to efficiently migrate towards favorable places in nutrient gradients. The magnetotactic bacteria (MTB) even utilize Earth’s magnetic field to facilitate downward swimming into the oxic–anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns. To ensure the desired flagella-propelled motility, marine MTBs have evolved an exquisite flagellar apparatus, and an extremely high number (tens of thousands) of flagella can be found on a single entity, displaying a complex polar, axial, bounce, and photosensitive magnetotactic behavior. In this review, we describe gene clusters, the flagellar apparatus architecture, and the swimming behavior of marine unicellular and multicellular magnetotactic bacteria. The physiological significance and mechanisms that govern these motions are discussed.
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Affiliation(s)
- Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, F-13402 CNRS-Marseille, France/CAS-Sanya 572000, China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, F-13402 CNRS-Marseille, France/CAS-Sanya 572000, China
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, CENTURI, F-13402 Marseille, France
- Correspondence: ; Tel.: +33-4-9116-4157
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9
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Abstract
Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular compartments that bear many hallmarks of eukaryotic organelles. One unique and elegant group of organisms is at the forefront of studies into the mechanisms of organelle formation and biomineralization. Magnetotactic bacteria (MTB) produce organelles called magnetosomes that contain nanocrystals of magnetic material, and understanding the molecular mechanisms behind magnetosome formation and biomineralization is a rich area of study. In this Review, we focus on the genetics behind the formation of magnetosomes and biomineralization. We cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB.
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Affiliation(s)
- Hayley C. McCausland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Arash Komeili
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
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10
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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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11
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Koziaeva VV, Rusakova SA, Slobodova NV, Uzun M, Kolganova TV, Skryabin KG, Grouzdev DS. Magnetospirillum kuznetsovii sp. nov., a novel magnetotactic bacterium isolated from a lake in the Moscow region. Int J Syst Evol Microbiol 2019; 69:1953-1959. [DOI: 10.1099/ijsem.0.003408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Veronika V. Koziaeva
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
| | - Svetlana A. Rusakova
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
| | - Natalia V. Slobodova
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
| | - Maria Uzun
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
- 2Faculty of Biology, Lomonosov Moscow State University, 119991, Leninskie Gory 1-12, Moscow, Russia
| | - Tatiana V. Kolganova
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
| | - Konstantin G. Skryabin
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
| | - Denis S. Grouzdev
- 1Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Leninsky Ave 33, bld. 2, Moscow, Russia
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12
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Wang Y, Casaburi G, Lin W, Li Y, Wang F, Pan Y. Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family. BMC Genomics 2019; 20:407. [PMID: 31117953 PMCID: PMC6532209 DOI: 10.1186/s12864-019-5751-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. RESULTS We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages. CONCLUSION Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Giorgio Casaburi
- Departments of Microbiology and Cell Science, Space Life Sciences Laboratory, University of Florida, Merritt Island, FL, 32953, USA
| | - Wei Lin
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Pan
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Detection of biogenic magnetic nanoparticles in ethmoid bones of migratory and non-migratory fishes. SN APPLIED SCIENCES 2018. [DOI: 10.1007/s42452-018-0072-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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14
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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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15
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Teng Z, Zhang Y, Zhang W, Pan H, Xu J, Huang H, Xiao T, Wu LF. Diversity and Characterization of Multicellular Magnetotactic Prokaryotes From Coral Reef Habitats of the Paracel Islands, South China Sea. Front Microbiol 2018; 9:2135. [PMID: 30271390 PMCID: PMC6142882 DOI: 10.3389/fmicb.2018.02135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 02/01/2023] Open
Abstract
While multicellular magnetotactic prokaryotes (MMPs) are ubiquitous in marine environments, the diversity of MMPs in sediments of coral reef ecosystems has rarely been reported. In this study, we made an investigation on the diversity and characteristics of MMPs in sediments at 11 stations in coral reef habitats of the Paracel Islands. The results showed that MMPs were present at nine stations, with spherical mulberry-like MMPs (s-MMPs) found at all stations and ellipsoidal pineapple-like MMPs (e-MMPs) found at seven stations. The maximum abundance of MMPs was 6 ind./cm3. Phylogenetic analysis revealed the presence of one e-MMP species and five s-MMP species including two species of a new genus. The results indicate that coral reef habitats of the Paracel Islands have a high diversity of MMPs that bio-mineralize multiple intracellular chains of iron crystals and play important role in iron cycling in such oligotrophic environment. These observations provide new perspective of the diversity of MMPs in general and expand knowledge of the occurrence of MMPs in coral reef habitats.
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Affiliation(s)
- Zhaojie Teng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuyang Zhang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Wenyan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Qingdao, China
| | - Hongmiao Pan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Qingdao, China
| | - Jianhong Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hui Huang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Tian Xiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Qingdao, China
| | - Long-Fei Wu
- Aix Marseille University, CNRS, LCB, Marseille, France.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Qingdao, China
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16
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Grishin DV, Zhdanov DD, Gladilina JA, Pokrovsky VS, Podobed OV, Pokrovskaya MV, Aleksandrova SS, Milyushkina AL, Vigovskiy MA, Sokolov NN. Construction and Characterization of a Recombinant Mutant Homolog of the CheW Protein from Thermotoga petrophila RKU-1. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818020051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Alves NJ, Moore M, Johnson BJ, Dean SN, Turner KB, Medintz IL, Walper SA. Environmental Decontamination of a Chemical Warfare Simulant Utilizing a Membrane Vesicle-Encapsulated Phosphotriesterase. ACS APPLIED MATERIALS & INTERFACES 2018; 10:15712-15719. [PMID: 29672020 DOI: 10.1021/acsami.8b02717] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
While technologies for the remediation of chemical contaminants continue to emerge, growing interest in green technologies has led researchers to explore natural catalytic mechanisms derived from microbial species. One such method, enzymatic degradation, offers an alternative to harsh chemical catalysts and resins. Recombinant enzymes, however, are often too labile or show limited activity when challenged with nonideal environmental conditions that may vary in salinity, pH, or other physical properties. Here, we demonstrate how phosphotriesterase encapsulated in a bacterial outer membrane vesicle can be used to degrade the organophosphate chemical warfare agent (CWA) simulant paraoxon in environmental water samples. We also carried out remediation assays on solid surfaces, including glass, painted metal, and fabric, that were selected as representative materials, which could potentially be contaminated with a CWA.
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Affiliation(s)
- Nathan J Alves
- Department of Emergency Medicine , Indiana University School of Medicine , Indianapolis , Indiana 46202 , United States
| | - Martin Moore
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Brandy J Johnson
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Scott N Dean
- National Research Council Postdoctoral Fellow , Washington , District of Columbia 20001 , United States
| | - Kendrick B Turner
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Scott A Walper
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
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18
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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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19
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Felfoul O, Mohammadi M, Taherkhani S, de Lanauze D, Zhong Xu Y, Lafleur M, Gaboury L, Tabrizian M, Vuong T, Batist G, Beauchemin N, Radzioch D, Martel S. [Delivery in hypoxic tumor regions of a chemotherapeutic agent encapsulated in nanoliposomes carried by magnetoaerotactic bacteria]. Med Sci (Paris) 2018; 34:197-199. [PMID: 29547100 DOI: 10.1051/medsci/20183403002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ouajdi Felfoul
- Laboratoire de nanorobotique - département de génie informatique et génie logiciel, Institut de génie biomédical, Polytechnique Montréal, Montréal H3T 1J4, Canada
| | - Mahmood Mohammadi
- Laboratoire de nanorobotique - département de génie informatique et génie logiciel, Institut de génie biomédical, Polytechnique Montréal, Montréal H3T 1J4, Canada
| | - Samira Taherkhani
- Laboratoire de nanorobotique - département de génie informatique et génie logiciel, Institut de génie biomédical, Polytechnique Montréal, Montréal H3T 1J4, Canada - Département de Génie biomédical, université McGill, Montréal H3A 2B4, Canada
| | - Dominic de Lanauze
- Laboratoire de nanorobotique - département de génie informatique et génie logiciel, Institut de génie biomédical, Polytechnique Montréal, Montréal H3T 1J4, Canada
| | - Yong Zhong Xu
- Centre universitaire de santé McGill, Montréal H4A 3J1, Canada
| | - Michel Lafleur
- Département de chimie, université de Montréal, Montréal H3C 3J7, Canada
| | - Louis Gaboury
- Département de pathologie et de biologie cellulaire, Institut de recherche en immunologie et cancer (IRIC), université de Montréal, Montréal H3T 1J4, Canada
| | - Maryam Tabrizian
- Département de Génie biomédical, université McGill, Montréal H3A 2B4, Canada - Faculté de dentisterie, université McGill, Montréal H3A 1G1, Canada
| | - Té Vuong
- Département de pathologie et de biologie cellulaire, Institut de recherche en immunologie et cancer (IRIC), université de Montréal, Montréal H3T 1J4, Canada
| | - Gerald Batist
- Département d'oncologie, Centre du cancer Segal, hôpital général Juif, université McGill, Montréal H3T 1E2, Canada
| | - Nicole Beauchemin
- Départements de biochimie, médecine et oncologie, Centre de recherche sur le cancer Goodman, université McGill, 1160 avenue des Pins, Montréal H3A 1A3, Canada
| | - Danuta Radzioch
- Centre universitaire de santé McGill, Montréal H4A 3J1, Canada
| | - Sylvain Martel
- Laboratoire de nanorobotique - département de génie informatique et génie logiciel, Institut de génie biomédical, Polytechnique Montréal, Montréal H3T 1J4, Canada
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20
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Grishin DV, Zhdanov DD, Gladilina JA, Pokrovsky VS, Podobed OV, Pokrovskaya MV, Aleksandrova SS, Milyushkina AL, Vigovskiy MA, Sokolov NN. [Construction and characterization of a recombinant mutant homolog of the CheW protein from Thermotoga petrophila RKU-1]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:53-60. [PMID: 29460835 DOI: 10.18097/pbmc20186401053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the work a recombinant chemotaxis protein CheW from Thermotoga petrophila RKU-1 (TpeCheW) and its mutant homolog (TpeCheW-mut) were created. It was shown that, despite the low homology with CheW prototypes from intestinal bacteria, these proteins didn't cause metabolic overload and were well expressed by cells of E. coli laboratory strains. We have discovered a broad spectrum of industrial valuable properties of the TpeCheW-mut protein such as stability in a wide range of temperatures and pH, high expression level, solubility and possibility of the application of a simple low-stage purification methodology with the use of preliminary heat treatment. Possible directions of the scientific and industrial application of this protein were claimed.
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Affiliation(s)
- D V Grishin
- Institute of Biomedical Chemistry, Moscow, Russia
| | - D D Zhdanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - O V Podobed
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | | | - N N Sokolov
- Institute of Biomedical Chemistry, Moscow, Russia
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21
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Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China. GENOME ANNOUNCEMENTS 2017; 5:5/34/e00485-17. [PMID: 28839012 PMCID: PMC5571398 DOI: 10.1128/genomea.00485-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel spiral magnetotactic bacterium, Magnetospirillum sp. ME-1, was isolated from East Lake in China. Here we report the complete genome of ME-1, which contains a 4,551,873-bp circular chromosome and a 5,222-bp circular plasmid. The magnetosome biogenesis-specific genes are located in a 97,664-bp magnetosome genomic island.
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22
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Lin W, Pan Y, Bazylinski DA. Diversity and ecology of and biomineralization by magnetotactic bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:345-356. [PMID: 28557300 DOI: 10.1111/1758-2229.12550] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/20/2017] [Accepted: 05/21/2017] [Indexed: 06/07/2023]
Abstract
Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-bounded crystals of magnetite (Fe3 O4 ) and/or greigite (Fe3 S4 ) called magnetosomes. MTB play important roles in the geochemical cycling of iron, sulfur, nitrogen and carbon. Significantly, they also represent an intriguing model system not just for the study of microbial biomineralization but also for magnetoreception, prokaryotic organelle formation and microbial biogeography. Here we review current knowledge on the ecology of and biomineralization by MTB, with an emphasis on more recent reports of unexpected ecological and phylogenetic findings regarding MTB. In this study, we conducted a search of public metagenomic databases and identified six novel magnetosome gene cluster-containing genomic fragments affiliated with the Deltaproteobacteria and Gammaproteobacteria classes of the Proteobacteria phylum, the Nitrospirae phylum and the Planctomycetes phylum from the deep subseafloor, marine oxygen minimum zone, groundwater biofilm and estuary sediment, thereby extending our knowledge on the diversity and distribution of MTB as well deriving important information as to their ecophysiology. We point out that the increasing availability of sequence data will facilitate researchers to systematically explore the ecology and biomineralization of MTB even further.
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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
- France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
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23
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Gorobets O, Gorobets S, Koralewski M. Physiological origin of biogenic magnetic nanoparticles in health and disease: from bacteria to humans. Int J Nanomedicine 2017; 12:4371-4395. [PMID: 28652739 PMCID: PMC5476634 DOI: 10.2147/ijn.s130565] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The discovery of biogenic magnetic nanoparticles (BMNPs) in the human brain gives a strong impulse to study and understand their origin. Although knowledge of the subject is increasing continuously, much remains to be done for further development to help our society fight a number of pathologies related to BMNPs. This review provides an insight into the puzzle of the physiological origin of BMNPs in organisms of all three domains of life: prokaryotes, archaea, and eukaryotes, including humans. Predictions based on comparative genomic studies are presented along with experimental data obtained by physical methods. State-of-the-art understanding of the genetic control of biomineralization of BMNPs and their properties are discussed in detail. We present data on the differences in BMNP levels in health and disease (cancer, neurodegenerative disorders, and atherosclerosis), and discuss the existing hypotheses on the biological functions of BMNPs, with special attention paid to the role of the ferritin core and apoferritin.
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Affiliation(s)
- Oksana Gorobets
- National Technical University of Ukraine (Igor Sikorsky Kyiv Polytechnic Institute)
- Institute of Magnetism, National Academy of Sciences, Kiev, Ukraine
| | - Svitlana Gorobets
- National Technical University of Ukraine (Igor Sikorsky Kyiv Polytechnic Institute)
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24
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Origin of microbial biomineralization and magnetotaxis during the Archean. Proc Natl Acad Sci U S A 2017; 114:2171-2176. [PMID: 28193877 DOI: 10.1073/pnas.1614654114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.
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25
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Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF. The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of P
roteobacteria. Environ Microbiol 2017; 19:1103-1119. [DOI: 10.1111/1462-2920.13637] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Boyang Ji
- Aix Marseille Univ, CNRS, LCB; Marseille France
| | - Sheng-Da Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Wei-Jia Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Zoe Rouy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | - François Alberto
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Claire-Lise Santini
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | | | - Nathalie Pradel
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- Aix Marseille Univ, Univ Toulon, CNRS, IRD; Marseille France
| | | | | | - Ying Li
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Claudine Médigue
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | | | | | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
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26
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Felfoul O, Mohammadi M, Taherkhani S, de Lanauze D, Xu YZ, Loghin D, Essa S, Jancik S, Houle D, Lafleur M, Gaboury L, Tabrizian M, Kaou N, Atkin M, Vuong T, Batist G, Beauchemin N, Radzioch D, Martel S. Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions. NATURE NANOTECHNOLOGY 2016; 11:941-947. [PMID: 27525475 PMCID: PMC6094936 DOI: 10.1038/nnano.2016.137] [Citation(s) in RCA: 552] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 06/24/2016] [Indexed: 05/06/2023]
Abstract
Oxygen-depleted hypoxic regions in the tumour are generally resistant to therapies. Although nanocarriers have been used to deliver drugs, the targeting ratios have been very low. Here, we show that the magneto-aerotactic migration behaviour of magnetotactic bacteria, Magnetococcus marinus strain MC-1 (ref. 4), can be used to transport drug-loaded nanoliposomes into hypoxic regions of the tumour. In their natural environment, MC-1 cells, each containing a chain of magnetic iron-oxide nanocrystals, tend to swim along local magnetic field lines and towards low oxygen concentrations based on a two-state aerotactic sensing system. We show that when MC-1 cells bearing covalently bound drug-containing nanoliposomes were injected near the tumour in severe combined immunodeficient beige mice and magnetically guided, up to 55% of MC-1 cells penetrated into hypoxic regions of HCT116 colorectal xenografts. Approximately 70 drug-loaded nanoliposomes were attached to each MC-1 cell. Our results suggest that harnessing swarms of microorganisms exhibiting magneto-aerotactic behaviour can significantly improve the therapeutic index of various nanocarriers in tumour hypoxic regions.
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Affiliation(s)
- Ouajdi Felfoul
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | - Mahmood Mohammadi
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | - Samira Taherkhani
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
- Dept. of Biomedical Eng., McGill University, Montréal, Canada
| | - Dominic de Lanauze
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | | | - Dumitru Loghin
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | - Sherief Essa
- Dept. of Chemistry, University of Montréal (UdM), Montréal, Canada
- Dept. of Biomedical Eng., McGill University, Montréal, Canada
| | | | - Daniel Houle
- McGill University Health Centre, Montréal, Canada
| | - Michel Lafleur
- Dept. of Chemistry, University of Montréal (UdM), Montréal, Canada
| | - Louis Gaboury
- Institute for Research in Immunology and Cancer (IRIC), Dept. of Pathology and Cell Biology, University of Montréal, Montréal, Canada
| | - Maryam Tabrizian
- Dept. of Biomedical Eng., McGill University, Montréal, Canada
- Faculty of Dentistry, McGill University, Montréal, Canada
| | - Neila Kaou
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | - Michael Atkin
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
| | - Té Vuong
- Segal Cancer Centre, Jewish General Hospital, Dept. of Oncology, McGill University, Montréal, Canada
| | - Gerald Batist
- Segal Cancer Centre, Jewish General Hospital, Dept. of Oncology, McGill University, Montréal, Canada
| | - Nicole Beauchemin
- Rosalind and Morris Goodman Cancer Research Centre, Dept. of Biochemistry, Medicine and Oncology, McGill University, Montréal, Canada
| | | | - Sylvain Martel
- NanoRobotics Laboratory, Dept. of Computer and Software Eng., Inst. of Biomedical Eng., Polytechnique Montréal, Montréal, Canada
- Corresponding author ()
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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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Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals. J Bacteriol 2016; 198:2794-802. [PMID: 27481925 DOI: 10.1128/jb.00280-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/16/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-length linear, long-length linear, cell membrane, and intracellular dispersing), which were related to the protein functions. Mms6, which regulates magnetite crystal growth, localized along magnetosome chain structures under magnetite-forming (microaerobic) conditions but was dispersed in the cell under nonforming (aerobic) conditions. Correlative fluorescence and electron microscopy analyses revealed that Mms6 preferentially localized to magnetosomes enclosing magnetite crystals. We suggest that a highly organized spatial regulation mechanism controls magnetosome protein localization during magnetosome formation in magnetotactic bacteria. IMPORTANCE Magnetotactic bacteria synthesize magnetite (Fe3O4) nanocrystals in a prokaryotic organelle called the magnetosome. This organelle is formed using various magnetosome proteins in multiple steps, including vesicle formation, magnetosome alignment, and magnetite crystal formation, to provide compartmentalized nanospaces for the regulation of iron concentrations and redox conditions, enabling the synthesis of a morphologically controlled magnetite crystal. Thus, to rationalize the complex organelle development, the localization of magnetosome proteins is considered to be highly regulated; however, the mechanisms remain largely unknown. Here, we performed comparative localization analysis of magnetosome proteins that revealed the presence of a spatial regulation mechanism within the linear structure of magnetosomes. This discovery provides evidence of a highly regulated protein localization mechanism for this bacterial organelle development.
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29
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Peigneux A, Valverde-Tercedor C, López-Moreno R, Pérez-González T, Fernández-Vivas MA, Jiménez-López C. Learning from magnetotactic bacteria: A review on the synthesis of biomimetic nanoparticles mediated by magnetosome-associated proteins. J Struct Biol 2016; 196:75-84. [PMID: 27378728 DOI: 10.1016/j.jsb.2016.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 11/16/2022]
Abstract
Much interest has gained the biomineralization process carried out by magnetotactic bacteria. These bacteria are ubiquitous in natural environments and share the ability to passively align along the magnetic field lines and actively swim along them. This ability is due to their magnetosome chain, each magnetosome consisting on a magnetic crystal enveloped by a lipid bilayer membrane to which very unique proteins are associated. Magnetotactic bacteria exquisitely control magnetosome formation, making the magnetosomes the ideal magnetic nanoparticle of potential use in many technological applications. The difficulty to scale up magnetosome production has triggered the research on the in vitro production of biomimetic (magnetosome-like) magnetite nanoparticles. In this context, magnetosome proteins are being used to mediate such in vitro magnetite precipitation experiments. The present work reviews the knowledgement on the magnetosome proteins thought to have a role on the in vivo formation of magnetite crystals in the magnetosome, and the recombinant magnetosome proteins used in vitro to form biomimetic magnetite. It also summarizes the data provided in the literature on the biomimetic magnetite nanoparticles obtained from those in vitro experiments.
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Affiliation(s)
- Ana Peigneux
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain
| | - Carmen Valverde-Tercedor
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain
| | - Rafael López-Moreno
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain
| | - Teresa Pérez-González
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain
| | - M A Fernández-Vivas
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain
| | - Concepción Jiménez-López
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, s/n, 18071 Granada, Spain.
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30
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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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Hershey DM, Ren X, Melnyk RA, Browne PJ, Ozyamak E, Jones SR, Chang MCY, Hurley JH, Komeili A. MamO Is a Repurposed Serine Protease that Promotes Magnetite Biomineralization through Direct Transition Metal Binding in Magnetotactic Bacteria. PLoS Biol 2016; 14:e1002402. [PMID: 26981620 PMCID: PMC4794232 DOI: 10.1371/journal.pbio.1002402] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/10/2016] [Indexed: 11/19/2022] Open
Abstract
Many living organisms transform inorganic atoms into highly ordered crystalline materials. An elegant example of such biomineralization processes is the production of nano-scale magnetic crystals in magnetotactic bacteria. Previous studies implicated the involvement of two putative serine proteases, MamE and MamO, during the early stages of magnetite formation in Magnetospirillum magneticum AMB-1. Here, using genetic analysis and X-ray crystallography, we show that MamO has a degenerate active site, rendering it incapable of protease activity. Instead, MamO promotes magnetosome formation through two genetically distinct, noncatalytic activities: activation of MamE-dependent proteolysis of biomineralization factors and direct binding to transition metal ions. By solving the structure of the protease domain bound to a metal ion, we identify a surface-exposed di-histidine motif in MamO that contributes to metal binding and show that it is required to initiate biomineralization in vivo. Finally, we find that pseudoproteases are widespread in magnetotactic bacteria and that they have evolved independently in three separate taxa. Our results highlight the versatility of protein scaffolds in accommodating new biochemical activities and provide unprecedented insight into the earliest stages of biomineralization.
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Affiliation(s)
- David M. Hershey
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Xuefeng Ren
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Ryan A. Melnyk
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Patrick J. Browne
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Ertan Ozyamak
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Stephanie R. Jones
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Michelle C. Y. Chang
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - James H. Hurley
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- * E-mail:
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32
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Nudelman H, Valverde-Tercedor C, Kolusheva S, Perez Gonzalez T, Widdrat M, Grimberg N, Levi H, Nelkenbaum O, Davidov G, Faivre D, Jimenez-Lopez C, Zarivach R. Structure-function studies of the magnetite-biomineralizing magnetosome-associated protein MamC. J Struct Biol 2016; 194:244-52. [PMID: 26970040 DOI: 10.1016/j.jsb.2016.03.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/17/2016] [Accepted: 03/01/2016] [Indexed: 11/18/2022]
Abstract
Magnetotactic bacteria are Gram-negative bacteria that navigate along geomagnetic fields using the magnetosome, an organelle that consists of a membrane-enveloped magnetic nanoparticle. Magnetite formation and its properties are controlled by a specific set of proteins. MamC is a small magnetosome-membrane protein that is known to be active in iron biomineralization but its mechanism has yet to be clarified. Here, we studied the relationship between the MamC magnetite-interaction loop (MIL) structure and its magnetite interaction using an inert biomineralization protein-MamC chimera. Our determined structure shows an alpha-helical fold for MamC-MIL with highly charged surfaces. Additionally, the MamC-MIL induces the formation of larger magnetite crystals compared to protein-free and inert biomineralization protein control experiments. We suggest that the connection between the MamC-MIL structure and the protein's charged surfaces is crucial for magnetite binding and thus for the size control of the magnetite nanoparticles.
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Affiliation(s)
- Hila Nudelman
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Carmen Valverde-Tercedor
- Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain; Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Teresa Perez Gonzalez
- Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain
| | - Marc Widdrat
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Noam Grimberg
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Hilla Levi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Or Nelkenbaum
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Geula Davidov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Damien Faivre
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Concepcion Jimenez-Lopez
- Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain.
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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Degli Esposti M. Genome Analysis of Structure-Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme. Genome Biol Evol 2015; 8:126-47. [PMID: 26615219 PMCID: PMC4758237 DOI: 10.1093/gbe/evv239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure-function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genova, Italy Center for Genomic Sciences, UNAM, Cuernavaca, Mexico
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34
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Valverde-Tercedor C, Montalbán-López M, Perez-Gonzalez T, Sanchez-Quesada MS, Prozorov T, Pineda-Molina E, Fernandez-Vivas MA, Rodriguez-Navarro AB, Trubitsyn D, Bazylinski DA, Jimenez-Lopez C. Size control of in vitro synthesized magnetite crystals by the MamC protein of Magnetococcus marinus strain MC-1. Appl Microbiol Biotechnol 2015; 99:5109-21. [PMID: 25874532 DOI: 10.1007/s00253-014-6326-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 12/09/2014] [Accepted: 12/14/2014] [Indexed: 11/27/2022]
Abstract
Magnetotactic bacteria are a diverse group of prokaryotes that share the unique ability of biomineralizing magnetosomes, which are intracellular, membrane-bounded crystals of either magnetite (Fe3O4) or greigite (Fe3S4). Magnetosome biomineralization is mediated by a number of specific proteins, many of which are localized in the magnetosome membrane, and thus is under strict genetic control. Several studies have partially elucidated the effects of a number of these magnetosome-associated proteins in the control of the size of magnetosome magnetite crystals. However, the effect of MamC, one of the most abundant proteins in the magnetosome membrane, remains unclear. In this present study, magnetite nanoparticles were synthesized inorganically in free-drift experiments at 25 °C in the presence of different concentrations of the iron-binding recombinant proteins MamC and MamCnts (MamC without its first transmembrane segment) from the marine, magnetotactic bacterium Magnetococcus marinus strain MC-1 and three commercial proteins [α-lactalbumin (α-Lac), myoglobin (Myo), and lysozyme (Lyz)]. While no effect was observed on the size of magnetite crystals formed in the presence of the commercial proteins, biomimetic synthesis in the presence of MamC and MamCnts at concentrations of 10-60 μg/mL resulted in the production of larger and more well-developed magnetite crystals (~30-40 nm) compared to those of the control (~20-30 nm; magnetite crystals grown protein-free). Our results demonstrate that MamC plays an important role in the control of the size of magnetite crystals and could be utilized in biomimetic synthesis of magnetite nanocrystals.
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Affiliation(s)
- C Valverde-Tercedor
- Departamento de Microbiologia, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain,
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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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Abstract
Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.
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Kashyap S, Woehl TJ, Liu X, Mallapragada SK, Prozorov T. Nucleation of iron oxide nanoparticles mediated by Mms6 protein in situ. ACS NANO 2014; 8:9097-9106. [PMID: 25162493 DOI: 10.1021/nn502551y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomineralization proteins are widely used as templating agents in biomimetic synthesis of a variety of organic-inorganic nanostructures. However, the role of the protein in controlling the nucleation and growth of biomimetic particles is not well understood, because the mechanism of the bioinspired reaction is often deduced from ex situ analysis of the resultant nanoscale mineral phase. Here we report the direct visualization of biomimetic iron oxide nanoparticle nucleation mediated by an acidic bacterial recombinant protein, Mms6, during an in situ reaction induced by the controlled addition of sodium hydroxide to solution-phase Mms6 protein micelles incubated with ferric chloride. Using in situ liquid cell scanning transmission electron microscopy we observe the liquid iron prenucleation phase and nascent amorphous nanoparticles forming preferentially on the surface of protein micelles. Our results provide insight into the early steps of protein-mediated biomimetic nucleation of iron oxide and point to the importance of an extended protein surface during nanoparticle formation.
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Affiliation(s)
- Sanjay Kashyap
- Ames Laboratory, U.S. Department of Energy , Ames, Iowa 50011, United States
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38
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Arakaki A, Yamagishi A, Fukuyo A, Tanaka M, Matsunaga T. Co-ordinated functions of Mms proteins define the surface structure of cubo-octahedral magnetite crystals in magnetotactic bacteria. Mol Microbiol 2014; 93:554-67. [DOI: 10.1111/mmi.12683] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Atsushi Arakaki
- Division of Biotechnology and Life Science; Institute of Engineering; Tokyo University of Agriculture and Technology; Koganei Tokyo Japan
| | - Ayana Yamagishi
- Division of Biotechnology and Life Science; Institute of Engineering; Tokyo University of Agriculture and Technology; Koganei Tokyo Japan
| | - Ayumi Fukuyo
- Division of Biotechnology and Life Science; Institute of Engineering; Tokyo University of Agriculture and Technology; Koganei Tokyo Japan
| | - Masayoshi Tanaka
- Division of Biotechnology and Life Science; Institute of Engineering; Tokyo University of Agriculture and Technology; Koganei Tokyo Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science; Institute of Engineering; Tokyo University of Agriculture and Technology; Koganei Tokyo Japan
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Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae. ISME JOURNAL 2014; 8:2463-77. [PMID: 24914800 DOI: 10.1038/ismej.2014.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/27/2014] [Accepted: 05/08/2014] [Indexed: 11/09/2022]
Abstract
Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.
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Genetic dissection of the mamAB and mms6 operons reveals a gene set essential for magnetosome biogenesis in Magnetospirillum gryphiswaldense. J Bacteriol 2014; 196:2658-69. [PMID: 24816605 DOI: 10.1128/jb.01716-14] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biosynthesis of bacterial magnetosomes, which are intracellular membrane-enclosed, nanosized magnetic crystals, is controlled by a set of >30 specific genes. In Magnetospirillum gryphiswaldense, these are clustered mostly within a large conserved genomic magnetosome island (MAI) comprising the mms6, mamGFDC, mamAB, and mamXY operons. Here, we demonstrate that the five previously uncharacterized genes of the mms6 operon have crucial functions in the regulation of magnetosome biomineralization that partially overlap MamF and other proteins encoded by the adjacent mamGFDC operon. While all other deletions resulted in size reduction, elimination of either mms36 or mms48 caused the synthesis of magnetite crystals larger than those in the wild type (WT). Whereas the mms6 operon encodes accessory factors for crystal maturation, the large mamAB operon contains several essential and nonessential genes involved in various other steps of magnetosome biosynthesis, as shown by single deletions of all mamAB genes. While single deletions of mamL, -P, -Q, -R, -B, -S, -T, and -U showed phenotypes similar to those of their orthologs in a previous study in the related M. magneticum, we found mamI and mamN to be not required for at least rudimentary iron biomineralization in M. gryphiswaldense. Thus, only mamE, -L, -M, -O, -Q, and -B were essential for formation of magnetite, whereas a mamI mutant still biomineralized tiny particles which, however, consisted of the nonmagnetic iron oxide hematite, as shown by high-resolution transmission electron microscopy (HRTEM) and the X-ray absorption near-edge structure (XANES). Based on this and previous studies, we propose an extended model for magnetosome biosynthesis in M. gryphiswaldense.
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41
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Degli Esposti M, Chouaia B, Comandatore F, Crotti E, Sassera D, Lievens PMJ, Daffonchio D, Bandi C. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 2014; 9:e96566. [PMID: 24804722 PMCID: PMC4013037 DOI: 10.1371/journal.pone.0096566] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.
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Affiliation(s)
| | - Bessem Chouaia
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Francesco Comandatore
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | - Elena Crotti
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Davide Sassera
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Claudio Bandi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
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Valverde-Tercedor C, Abadía-Molina F, Martinez-Bueno M, Pineda-Molina E, Chen L, Oestreicher Z, Lower BH, Lower SK, Bazylinski DA, Jimenez-Lopez C. Subcellular localization of the magnetosome protein MamC in the marine magnetotactic bacterium Magnetococcus marinus strain MC-1 using immunoelectron microscopy. Arch Microbiol 2014; 196:481-8. [PMID: 24760293 DOI: 10.1007/s00203-014-0984-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 02/07/2023]
Abstract
Magnetotactic bacteria are a diverse group of prokaryotes that biomineralize intracellular magnetosomes, composed of magnetic (Fe3O4) crystals each enveloped by a lipid bilayer membrane that contains proteins not found in other parts of the cell. Although partial roles of some of these magnetosome proteins have been determined, the roles of most have not been completely elucidated, particularly in how they regulate the biomineralization process. While studies on the localization of these proteins have been focused solely on Magnetospirillum species, the goal of the present study was to determine, for the first time, the localization of the most abundant putative magnetosome membrane protein, MamC, in Magnetococcus marinus strain MC-1. MamC was expressed in Escherichia coli and purified. Monoclonal antibodies were produced against MamC and immunogold labeling TEM was used to localize MamC in thin sections of cells of M. marinus. Results show that MamC is located only in the magnetosome membrane of Mc. marinus. Based on our findings and the abundance of this protein, it seems likely that it is important in magnetosome biomineralization and might be used in controlling the characteristics of synthetic nanomagnetite.
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Affiliation(s)
- C Valverde-Tercedor
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
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Abstract
Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.
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Arnoux P, Siponen MI, Lefèvre CT, Ginet N, Pignol D. Structure and evolution of the magnetochrome domains: no longer alone. Front Microbiol 2014; 5:117. [PMID: 24723915 PMCID: PMC3971196 DOI: 10.3389/fmicb.2014.00117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/08/2014] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) can swim along Earth's magnetic field lines, thanks to the alignment of dedicated cytoplasmic organelles. These organelles, termed magnetosomes, are proteolipidic vesicles filled by a 35–120 nm crystal of either magnetite or greigite. The formation and alignment of magnetosomes are mediated by a group of specific genes, the mam genes, encoding the magnetosome-associated proteins. The whole process of magnetosome biogenesis can be divided into four sequential steps; (i) cytoplasmic membrane invagination, (ii) magnetosomes alignment, (iii) iron crystal nucleation and (iv) species-dependent mineral size and shape control. Since both magnetite and greigite are a mix of iron (III) and iron (II), iron redox state management within the magnetosome vesicle is a key issue. Recently, studies have started pointing out the importance of a MTB-specific c-type cytochrome domain found in several magnetosome-associated proteins (MamE, P, T, and X). This magnetochrome (MCR) domain is almost always found in tandem, and this tandem is either found alone (MamT), in combination with a PDZ domain (MamP), a domain of unknown function (MamX) or with a trypsin combined to one or two PDZ domains (MamE). By taking advantage of new genomic data available on MTB and a recent structural study of MamP, which helped define the MCR domain boundaries, we attempt to retrace the evolutionary history within and between the different MCR-containing proteins. We propose that the observed tandem repeat of MCR is the result of a convergent evolution and attempt to explain why this domain is rarely found alone.
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Affiliation(s)
- Pascal Arnoux
- Commissariat à l'énergie Atomique, DSV, IBEB, Lab Bioenerget Cellulaire Saint-Paul-lez-Durance, France ; Centre National de la Recherche Scientifique, UMR Biol Veget and Microbiol Environ Saint-Paul-lez-Durance, France ; Aix-Marseille Université Saint-Paul-lez-Durance, France
| | - Marina I Siponen
- Commissariat à l'énergie Atomique, DSV, IBEB, Lab Bioenerget Cellulaire Saint-Paul-lez-Durance, France ; Centre National de la Recherche Scientifique, UMR Biol Veget and Microbiol Environ Saint-Paul-lez-Durance, France ; Aix-Marseille Université Saint-Paul-lez-Durance, France
| | - Christopher T Lefèvre
- Commissariat à l'énergie Atomique, DSV, IBEB, Lab Bioenerget Cellulaire Saint-Paul-lez-Durance, France ; Centre National de la Recherche Scientifique, UMR Biol Veget and Microbiol Environ Saint-Paul-lez-Durance, France ; Aix-Marseille Université Saint-Paul-lez-Durance, France
| | - Nicolas Ginet
- Commissariat à l'énergie Atomique, DSV, IBEB, Lab Bioenerget Cellulaire Saint-Paul-lez-Durance, France ; Centre National de la Recherche Scientifique, UMR Biol Veget and Microbiol Environ Saint-Paul-lez-Durance, France ; Aix-Marseille Université Saint-Paul-lez-Durance, France
| | - David Pignol
- Commissariat à l'énergie Atomique, DSV, IBEB, Lab Bioenerget Cellulaire Saint-Paul-lez-Durance, France ; Centre National de la Recherche Scientifique, UMR Biol Veget and Microbiol Environ Saint-Paul-lez-Durance, France ; Aix-Marseille Université Saint-Paul-lez-Durance, France
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45
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Abstract
We report the complete genomic sequence of Magnetospirillum gryphiswaldense MSR-1 (DSM 6361), a type strain of the genus Magnetospirillum belonging to the Alphaproteobacteria. Compared to the reported draft sequence, extensive rearrangements and differences were found, indicating high genomic flexibility and "domestication" by accelerated evolution of the strain upon repeated passaging.
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46
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Morillo V, Abreu F, Araujo AC, de Almeida LGP, Enrich-Prast A, Farina M, de Vasconcelos ATR, Bazylinski DA, Lins U. Isolation, cultivation and genomic analysis of magnetosome biomineralization genes of a new genus of South-seeking magnetotactic cocci within the Alphaproteobacteria. Front Microbiol 2014; 5:72. [PMID: 24616719 PMCID: PMC3934378 DOI: 10.3389/fmicb.2014.00072] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022] Open
Abstract
Although magnetotactic bacteria (MTB) are ubiquitous in aquatic habitats, they are still considered fastidious microorganisms with regard to growth and cultivation with only a relatively low number of axenic cultures available to date. Here, we report the first axenic culture of an MTB isolated in the Southern Hemisphere (Itaipu Lagoon in Rio de Janeiro, Brazil). Cells of this new isolate are coccoid to ovoid in morphology and grow microaerophilically in semi-solid medium containing an oxygen concentration ([O2]) gradient either under chemoorganoheterotrophic or chemolithoautotrophic conditions. Each cell contains a single chain of approximately 10 elongated cuboctahedral magnetite (Fe3O4) magnetosomes. Phylogenetic analysis based on the 16S rRNA gene sequence shows that the coccoid MTB isolated in this study represents a new genus in the Alphaproteobacteria; the name Magnetofaba australis strain IT-1 is proposed. Preliminary genomic data obtained by pyrosequencing shows that M. australis strain IT-1 contains a genomic region with genes involved in biomineralization similar to those found in the most closely related magnetotactic cocci Magnetococcus marinus strain MC-1. However, organization of the magnetosome genes differs from M. marinus.
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Affiliation(s)
- Viviana Morillo
- 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
| | - Ana C Araujo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Luiz G P de Almeida
- Laboratório Nacional de Computação Científica, Departamento de Matemática Aplicada e Computacional Petrópolis, Brazil
| | - Alex Enrich-Prast
- Instituto de Biologia, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Marcos Farina
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Ana T R de Vasconcelos
- Laboratório Nacional de Computação Científica, Departamento de Matemática Aplicada e Computacional Petrópolis, Brazil
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas Las Vegas, NV, USA
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
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47
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Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS One 2013; 8:e83383. [PMID: 24349502 PMCID: PMC3859672 DOI: 10.1371/journal.pone.0083383] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
Bacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes, as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of topologies and comparative results from Approximately Unbiased tests provide support for positioning the Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the Rickettsidae, and the Magnetococcidae.
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Affiliation(s)
- Matteo P. Ferla
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J. Cameron Thrash
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Stephen J. Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Wayne M. Patrick
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- * E-mail:
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48
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Pósfai M, Lefèvre CT, Trubitsyn D, Bazylinski DA, Frankel RB. Phylogenetic significance of composition and crystal morphology of magnetosome minerals. Front Microbiol 2013; 4:344. [PMID: 24324461 PMCID: PMC3840360 DOI: 10.3389/fmicb.2013.00344] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/30/2013] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria (MTB) biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic perspectives to review the correlations between magnetosome mineral habits and the phylogenetic affiliations of MTB, and show that these correlations have important implications for the evolution of magnetosome synthesis, and thus magnetotaxis.
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Affiliation(s)
- Mihály Pósfai
- Department of Earth and Environmental Sciences, University of Pannonia Veszprém, Hungary
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49
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Lefèvre CT, Wu LF. Evolution of the bacterial organelle responsible for magnetotaxis. Trends Microbiol 2013; 21:534-43. [PMID: 23948365 DOI: 10.1016/j.tim.2013.07.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/13/2013] [Accepted: 07/18/2013] [Indexed: 02/05/2023]
Abstract
There are few examples of protein- and lipid-bounded organelles in bacteria that are encoded by conserved gene clusters and lead to a specific function. The magnetosome chain represents one of these rare examples and is responsible for magnetotaxis in magnetotactic bacteria (MTB), a behavior thought to aid in finding their optimal growth conditions. The origin and evolution of the magnetotaxis is still a matter of debate. Recent breakthroughs in isolation, cultivation, single-cell separation, and whole-genome sequencing have generated abundant data that give new insights into the biodiversity and evolution of MTB.
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Affiliation(s)
- Christopher T Lefèvre
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)/Centre National de la Recherche Scientifique (CNRS)/Aix-Marseille Université, Unité Mixte de Recherche (UMR) 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire de Bioénergétique Cellulaire, 13108, Saint-Paul-lès-Durance, France.
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50
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Cytochrome cd1 nitrite reductase NirS is involved in anaerobic magnetite biomineralization in Magnetospirillum gryphiswaldense and requires NirN for proper d1 heme assembly. J Bacteriol 2013; 195:4297-309. [PMID: 23893106 DOI: 10.1128/jb.00686-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The alphaproteobacterium Magnetospirillum gryphiswaldense synthesizes magnetosomes, which are membrane-enveloped crystals of magnetite. Here we show that nitrite reduction is involved in redox control during anaerobic biomineralization of the mixed-valence iron oxide magnetite. The cytochrome cd1-type nitrite reductase NirS shares conspicuous sequence similarity with NirN, which is also encoded within a larger nir cluster. Deletion of any one of these two nir genes resulted in impaired growth and smaller, fewer, and aberrantly shaped magnetite crystals during nitrate reduction. However, whereas nitrite reduction was completely abolished in the ΔnirS mutant, attenuated but significant nitrite reduction occurred in the ΔnirN mutant, indicating that only NirS is a nitrite reductase in M. gryphiswaldense. However, the ΔnirN mutant produced a different form of periplasmic d(1) heme that was not noncovalently bound to NirS, indicating that NirN is required for full reductase activity by maintaining a proper form of d1 heme for holo-cytochrome cd(1) assembly. In conclusion, we assign for the first time a physiological function to NirN and demonstrate that effective nitrite reduction is required for biomineralization of wild-type crystals, probably by contributing to oxidation of ferrous iron under oxygen-limited conditions.
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