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Awal RP, Müller FD, Pfeiffer D, Monteil CL, Perrière G, Lefèvre CT, Schüler D. Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense. mBio 2023; 14:e0164923. [PMID: 37823629 PMCID: PMC10653835 DOI: 10.1128/mbio.01649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains, which are organized by the actin-like MamK protein. Although MamK is the most highly conserved magnetosome protein common to all MTB, its analysis has been confined to a small subgroup owing to the inaccessibility of most MTB. Our study takes advantage of a genetically tractable host where expression of diverse MamK orthologs together with a resurrected MamK LUCA and uncharacterized actin-like Mad28 proteins from deep-branching MTB resulted in gradual restoration of magnetosome chains in various mutants. Our results further indicate the existence of species-specific MamK interactors and shed light on the evolutionary relationships of one of the key proteins associated with bacterial magnetotaxis.
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Affiliation(s)
- Ram Prasad Awal
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Frank D. Müller
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Daniel Pfeiffer
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Caroline L. Monteil
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard-Lyon 1, Villeurbanne, France
| | - Christopher T. Lefèvre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Dirk Schüler
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
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2
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Awal RP, Lefevre CT, Schüler D. Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense. mBio 2023; 14:e0328222. [PMID: 37318230 PMCID: PMC10470508 DOI: 10.1128/mbio.03282-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/03/2023] [Indexed: 06/16/2023] Open
Abstract
Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.
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Affiliation(s)
- Ram Prasad Awal
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Christopher T. Lefevre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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3
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Dziuba MV, Paulus A, Schramm L, Awal RP, Pósfai M, Monteil CL, Fouteau S, Uebe R, Schüler D. Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium. THE ISME JOURNAL 2023; 17:326-339. [PMID: 36517527 PMCID: PMC9938234 DOI: 10.1038/s41396-022-01348-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]
Abstract
Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.
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Affiliation(s)
- M. V. Dziuba
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - A. Paulus
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany ,grid.7384.80000 0004 0467 6972Department of Microbial Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Bayreuth, Germany
| | - L. Schramm
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - R. P. Awal
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - M. Pósfai
- ELKH-PE Environmental Mineralogy Research Group, Veszprém, Hungary ,grid.7336.10000 0001 0203 5854Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary
| | - C. L. Monteil
- grid.5399.60000 0001 2176 4817Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - S. Fouteau
- grid.8390.20000 0001 2180 5818LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d’Evry, Universite Paris- Saclay, Evry, France
| | - R. Uebe
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany ,grid.7384.80000 0004 0467 6972Department of Microbial Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Bayreuth, Germany
| | - D. Schüler
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
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4
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Krawczyk-Bärsch E, Ramtke J, Drobot B, Müller K, Steudtner R, Kluge S, Hübner R, Raff J. Peptidoglycan as major binding motif for Uranium bioassociation on Magnetospirillum magneticum AMB-1 in contaminated waters. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129376. [PMID: 35897184 DOI: 10.1016/j.jhazmat.2022.129376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/30/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
The U(VI) bioassociation on Magnetospirillum magneticum AMB-1 cells was investigated using a multidisciplinary approach combining wet chemistry, microscopy, and spectroscopy methods to provide deeper insight into the interaction of U(VI) with bioligands of Gram-negative bacteria for a better molecular understanding. Our findings suggest that the cell wall plays a prominent role in the bioassociation of U(VI). In time-dependent bioassociation studies, up to 95 % of the initial U(VI) was removed from the suspension and probably bound on the cell wall within the first hours due to the high removal capacity of predominantly alive Magnetospirillum magneticum AMB-1 cells. PARAFAC analysis of TRLFS data highlights that peptidoglycan is the most important ligand involved, showing a stable immobilization of U(VI) over a wide pH range with the formation of three characteristic species. In addition, in-situ ATR FT-IR reveals the predominant strong binding to carboxylic functionalities. At higher pH polynuclear species seem to play an important role. This comprehensive molecular study may initiate in future new remediation strategies on effective immobilization of U(VI). In combination with the magnetic properties of the bacteria, a simple technical water purification process could be realized not only for U(VI), but probably also for other heavy metals.
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Affiliation(s)
- Evelyn Krawczyk-Bärsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Justus Ramtke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany; University of Applied Sciences Zittau/Görlitz, Faculty of Natural and Environmental Sciences, Theodor-Körner, Allee 8, 02763 Zittau, Germany
| | - Björn Drobot
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Katharina Müller
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Robin Steudtner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Sindy Kluge
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - René Hübner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Johannes Raff
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
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5
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Busigny V, Mathon FP, Jézéquel D, Bidaud CC, Viollier E, Bardoux G, Bourrand JJ, Benzerara K, Duprat E, Menguy N, Monteil CL, Lefevre CT. Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France. Environ Microbiol 2021; 24:721-736. [PMID: 33687779 DOI: 10.1111/1462-2920.15458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 01/16/2023]
Abstract
Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.
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Affiliation(s)
- Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Institut Universitaire de France, Paris, 75005, France
| | - François P Mathon
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, 74200, France
| | - Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Eric Viollier
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Gérard Bardoux
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Jean-Jacques Bourrand
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
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6
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Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y. Expanding magnetic organelle biogenesis in the domain Bacteria. MICROBIOME 2020; 8:152. [PMID: 33126926 PMCID: PMC7602337 DOI: 10.1186/s40168-020-00931-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. RESULTS Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. CONCLUSIONS These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle. Video Abstract.
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Affiliation(s)
- Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Greig A Paterson
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, L69 7ZE, Liverpool, UK
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Arakaki A, Goto M, Maruyama M, Yoda T, Tanaka M, Yamagishi A, Yoshikuni Y, Matsunaga T. Restoration and Modification of Magnetosome Biosynthesis by Internal Gene Acquisition in a Magnetotactic Bacterium. Biotechnol J 2020; 15:e2000278. [DOI: 10.1002/biot.202000278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/02/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Atsushi Arakaki
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
| | - Mayu Goto
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
| | - Mina Maruyama
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
| | - Takuto Yoda
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering Tokyo Institute of Technology 2‐12‐1 O‐okayama Meguro‐ku Tokyo 152‐8550 Japan
| | - Ayana Yamagishi
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
| | - Yasuo Yoshikuni
- DNA Synthesis Science Program Lawrence Berkeley National Laboratory The U.S. Department of Energy Joint Genome Institute Berkeley CA 94720 USA
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science Institute of Engineering Tokyo University of Agriculture and Technology 2‐24‐16 Naka‐cho Koganei Tokyo 184‐8588 Japan
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) 2‐15, Natsushima‐cho Yokosuka Kanagawa 237‐0061 Japan
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8
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Uzun M, Alekseeva L, Krutkina M, Koziaeva V, Grouzdev D. Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases. Sci Data 2020; 7:252. [PMID: 32737307 PMCID: PMC7449369 DOI: 10.1038/s41597-020-00593-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
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Affiliation(s)
- Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Lolita Alekseeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Denis Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
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9
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Monteil CL, Grouzdev DS, Perrière G, Alonso B, Rouy Z, Cruveiller S, Ginet N, Pignol D, Lefevre CT. Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. THE ISME JOURNAL 2020; 14:1783-1794. [PMID: 32296121 PMCID: PMC7305187 DOI: 10.1038/s41396-020-0647-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/27/2022]
Abstract
Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.
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Affiliation(s)
- Caroline L Monteil
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
| | - Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Claude Bernard - Lyon 1, 69622, Villeurbanne, France
| | - Béatrice Alonso
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Zoé Rouy
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Stéphane Cruveiller
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Nicolas Ginet
- Aix Marseille University, CNRS, LCB, Marseille, France
| | - David Pignol
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Christopher T Lefevre
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
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10
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Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Jetten MSM, Schüler M, Becker S, Rohde C, Müller RW, Brümmer F, Rohde M, Engelhardt H, Jogler M, Jogler C. Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge. Syst Appl Microbiol 2019; 43:126022. [PMID: 31785948 DOI: 10.1016/j.syapm.2019.126022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 01/28/2023]
Abstract
The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1T from its next relative Planctopirus limnophila DSM 3776T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1T from Planctopirus limnophila DSM 3776T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.
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Affiliation(s)
- T Kohn
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - S Wiegand
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - C Boedeker
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - P Rast
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - A Heuer
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - M S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - M Schüler
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - S Becker
- University of Veterinary Medicine Hannover, Germany
| | - C Rohde
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - R-W Müller
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - F Brümmer
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - M Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Braunschweig, Germany
| | - H Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - M Jogler
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - C Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands; Department of Microbial Interactions, Friedrich Schiller Universität Jena, Germany.
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11
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Durak GM, Laumann M, Wolf SLP, Pawar A, Gebauer D, Böttcher T. Pseudo-Biomineralization: Complex Mineral Structures Shaped by Microbes. ACS Biomater Sci Eng 2019; 5:5088-5096. [DOI: 10.1021/acsbiomaterials.9b00387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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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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13
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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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14
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Monteil CL, Perrière G, Menguy N, Ginet N, Alonso B, Waisbord N, Cruveiller S, Pignol D, Lefèvre CT. Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis. Environ Microbiol 2018; 20:4415-4430. [PMID: 30043533 DOI: 10.1111/1462-2920.14364] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/19/2018] [Indexed: 01/06/2023]
Abstract
Ecological and evolutionary processes involved in magnetotactic bacteria (MTB) adaptation to their environment have been a matter of debate for many years. Ongoing efforts for their characterization are progressively contributing to understand these processes, including the genetic and molecular mechanisms responsible for biomineralization. Despite numerous culture-independent MTB characterizations, essentially within the Proteobacteria phylum, only few species have been isolated in culture because of their complex growth conditions. Here, we report a newly cultivated magnetotactic, microaerophilic and chemoorganoheterotrophic bacterium isolated from the Mediterranean Sea in Marseille, France: Candidatus Terasakiella magnetica strain PR-1 that belongs to an Alphaproteobacteria genus with no magnetotactic relative. By comparing the morphology and the whole genome shotgun sequence of this MTB with those of closer relatives, we brought further evidence that the apparent vertical ancestry of magnetosome genes suggested by previous studies within Alphaproteobacteria hides a more complex evolutionary history involving horizontal gene transfers and/or duplication events before and after the emergence of Magnetospirillum, Magnetovibrio and Magnetospira genera. A genome-scale comparative genomics analysis identified several additional candidate functions and genes that could be specifically associated to MTB lifestyle in this class of bacteria.
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Affiliation(s)
- Caroline L Monteil
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Claude Bernard - Lyon 1, 69622, Villeurbanne, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD - IMPMC, 4 place Jussieu, 75005, Paris, France
| | - Nicolas Ginet
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13402, Marseille, France
| | - Béatrice Alonso
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Nicolas Waisbord
- Department of Mechanical Engineering, Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Stéphane Cruveiller
- Commissariat à l'Energie Atomique et aux Energies Alternatives - Institut de Biologie François Jacob - Genoscope - Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, UMR - CNRS 8030 Génomique Métabolique, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - David Pignol
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Christopher T Lefèvre
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
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15
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Uebe R, Keren-Khadmy N, Zeytuni N, Katzmann E, Navon Y, Davidov G, Bitton R, Plitzko JM, Schüler D, Zarivach R. The dual role of MamB in magnetosome membrane assembly and magnetite biomineralization. Mol Microbiol 2018; 107:542-557. [PMID: 29243866 DOI: 10.1111/mmi.13899] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 11/30/2022]
Abstract
Magnetospirillum gryphiswaldense MSR-1 synthesizes membrane-enclosed magnetite (Fe3 O4 ) nanoparticles, magnetosomes, for magnetotaxis. Formation of these organelles involves a complex process comprising key steps which are governed by specific magnetosome-associated proteins. MamB, a cation diffusion facilitator (CDF) family member has been implicated in magnetosome-directed iron transport. However, deletion mutagenesis studies revealed that MamB is essential for the formation of magnetosome membrane vesicles, but its precise role remains elusive. In this study, we employed a multi-disciplinary approach to define the role of MamB during magnetosome formation. Using site-directed mutagenesis complemented by structural analyses, fluorescence microscopy and cryo-electron tomography, we show that MamB is most likely an active magnetosome-directed transporter serving two distinct, yet essential functions. First, MamB initiates magnetosome vesicle formation in a transport-independent process, probably by serving as a landmark protein. Second, MamB transport activity is required for magnetite nucleation. Furthermore, by determining the crystal structure of the MamB cytosolic C-terminal domain, we also provide mechanistic insight into transport regulation. Additionally, we present evidence that magnetosome vesicle growth and chain formation are independent of magnetite nucleation and magnetic interactions respectively. Together, our data provide novel insight into the role of the key bifunctional magnetosome protein MamB, and the early steps of magnetosome formation.
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Affiliation(s)
- René Uebe
- Department of Microbiology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Noa Keren-Khadmy
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
| | - Natalie Zeytuni
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
| | - Emanuel Katzmann
- Department of Molecular Structural Biology, Am Klopferspitz 18, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Yotam Navon
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
| | - Geula Davidov
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
| | - Ronit Bitton
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Am Klopferspitz 18, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel
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16
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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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17
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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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18
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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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A whole genome analysis reveals the presence of a plant PR1 sequence in the potato pathogen Streptomyces scabies and other Streptomyces species. Mol Phylogenet Evol 2016; 114:346-352. [PMID: 27530704 DOI: 10.1016/j.ympev.2016.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 08/01/2016] [Accepted: 08/11/2016] [Indexed: 11/23/2022]
Abstract
Streptomyces scabies is a common soil bacterium that causes scab symptoms in potatoes. Strong evidence indicates horizontal gene transfer (HGT) among bacteria has influenced the evolution of this plant pathogen and other Streptomyces spp. To extend the study of the HGT to the Streptomyces genus, we explored the effects of the inter-domain HGT in the S. scabies genome. We employed a semi-automatic pipeline based on BLASTp searches and phylogenetic reconstruction. The data show low impact of inter-domain HGT in the S. scabies genome; however, we found a putative plant pathogenesis related 1 (PR1) sequence in the genome of S. scabies and other species of the genus. It is possible that this gene could be used by S. scabies to out-compete other soil organisms.
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Jacob JJ, Suthindhiran K. Magnetotactic bacteria and magnetosomes - Scope and challenges. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 68:919-928. [PMID: 27524094 DOI: 10.1016/j.msec.2016.07.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/24/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
Geomagnetism aided navigation has been demonstrated by certain organisms which allows them to identify a particular location using magnetic field. This attractive technique to recognize the course was earlier exhibited in numerous animals, for example, birds, insects, reptiles, fishes and mammals. Magnetotactic bacteria (MTB) are one of the best examples for magnetoreception among microorganisms as the magnetic mineral functions as an internal magnet and aid the microbe to move towards the water columns in an oxic-anoxic interface (OAI). The ability of MTB to biomineralize the magnetic particles (magnetosomes) into uniform nano-sized, highly crystalline structure with uniform magnetic properties has made the bacteria an important topic of research. The superior properties of magnetosomes over chemically synthesized magnetic nanoparticles made it an attractive candidate for potential applications in microbiology, biophysics, biochemistry, nanotechnology and biomedicine. In this review article, the scope of MTB, magnetosomes and its challenges in research and industrial application have been discussed in brief. This article mainly focuses on the application based on the magnetotactic behaviour of MTB and magnetosomes in different areas of modern science.
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Affiliation(s)
- Jobin John Jacob
- Marine Biotechnology and Bioproducts Lab, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - K Suthindhiran
- Marine Biotechnology and Bioproducts Lab, School of Biosciences and Technology, VIT University, Vellore 632014, India.
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22
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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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23
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Lefèvre CT. Genomic insights into the early-diverging magnetotactic bacteria. Environ Microbiol 2015; 18:1-3. [PMID: 26286101 DOI: 10.1111/1462-2920.12989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 07/15/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher T Lefèvre
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de Biologie Environnementale et Biotechnologie, Laboratoire de Bioénergétique Cellulaire, Saint Paul lez Durance, France
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24
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Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D. Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes. Environ Microbiol 2015; 18:21-37. [PMID: 26060021 DOI: 10.1111/1462-2920.12907] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022]
Abstract
While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus 'Candidatus Magnetobacterium' homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep-branching MTB. Here we report the analysis of single-cell derived draft genomes of three deep-branching uncultivated MTB. Single-cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS-04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK-01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet-shaped magnetosomes and their arrangement in multiple bundles of chains.
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Affiliation(s)
- Sebastian Kolinko
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Michael Richter
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Frank-Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany.,Department of Life Sciences & Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Andreas Brachmann
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Dirk Schüler
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany.,Department of Microbiology, University Bayreuth, Bayreuth, Germany
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25
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Lin W, Pan Y. A putative greigite-type magnetosome gene cluster from the candidate phylum Latescibacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:237-242. [PMID: 25382584 DOI: 10.1111/1758-2229.12234] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
The intracellular biomineralization of magnetite and/or greigite magnetosomes in magnetotactic bacteria (MTB) is strictly controlled by a group of conserved genes, termed magnetosome genes, which are organized as clusters (or islands) in MTB genomes. So far, all reported MTB are affiliated within the Proteobacteria phylum, the Nitrospirae phylum and the candidate division OP3. Here, we report the discovery of a putative magnetosome gene cluster structure from the draft genome of an uncultivated bacterium belonging to the candidate phylum Latescibacteria (formerly candidate division WS3) recently recovered by Rinke and colleagues, which contains 10 genes with homology to magnetosome mam genes of magnetotactic Proteobacteria and Nitrospirae. Moreover, these genes are phylogenetically closely related to greigite-type magnetosome genes that were only found from the Deltaproteobacteria MTB before, suggesting that the greigite genes may originate earlier than previously imagined. These findings indicate that some members of Latescibacteria may be capable of forming greigite magnetosomes, and thus may play previously unrecognized roles in environmental iron and sulfur cycles. The conserved genomic structure of magnetosome gene cluster in Latescibacteria phylum supports the hypothesis of horizontal transfer of these genes among distantly related bacterial groups in nature.
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Affiliation(s)
- Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences, Beijing, 100029, China
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26
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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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27
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Interplay between two bacterial actin homologs, MamK and MamK-Like, is required for the alignment of magnetosome organelles in Magnetospirillum magneticum AMB-1. J Bacteriol 2014; 196:3111-21. [PMID: 24957623 DOI: 10.1128/jb.01674-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many bacterial species contain multiple actin-like proteins tasked with the execution of crucial cell biological functions. MamK, an actin-like protein found in magnetotactic bacteria, is important in organizing magnetosome organelles into chains that are used for navigation along geomagnetic fields. MamK and numerous other magnetosome formation factors are encoded by a genetic island termed the magnetosome island. Unlike most magnetotactic bacteria, Magnetospirillum magneticum AMB-1 (AMB-1) contains a second island of magnetosome-related genes that was named the magnetosome islet. A homologous copy of mamK, mamK-like, resides within this islet and encodes a protein capable of filament formation in vitro. Previous work had shown that mamK-like is expressed in vivo, but its function, if any, had remained unknown. Though MamK-like is highly similar to MamK, it contains a mutation that in MamK and other actins blocks ATPase activity in vitro and filament dynamics in vivo. Here, using genetic analysis, we demonstrate that mamK-like has an in vivo role in assisting organelle alignment. In addition, MamK-like forms filaments in vivo in a manner that is dependent on the presence of MamK and the two proteins interact in a yeast two-hybrid assay. Surprisingly, despite the ATPase active-site mutation, MamK-like is capable of ATP hydrolysis in vitro and promotes MamK filament turnover in vivo. Taken together, these experiments suggest that direct interactions between MamK and MamK-like contribute to magnetosome alignment in AMB-1.
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28
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Dufour SC, Laurich JR, Batstone RT, McCuaig B, Elliott A, Poduska KM. Magnetosome-containing bacteria living as symbionts of bivalves. ISME JOURNAL 2014; 8:2453-62. [PMID: 24914799 DOI: 10.1038/ismej.2014.93] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 11/10/2022]
Abstract
Bacteria containing magnetosomes (protein-bound nanoparticles of magnetite or greigite) are common to many sedimentary habitats, but have never been found before to live within another organism. Here, we show that octahedral inclusions in the extracellular symbionts of the marine bivalve Thyasira cf. gouldi contain iron, can exhibit magnetic contrast and are most likely magnetosomes. Based on 16S rRNA sequence analysis, T. cf. gouldi symbionts group with symbiotic and free-living sulfur-oxidizing, chemolithoautotrophic gammaproteobacteria, including the symbionts of other thyasirids. T. cf. gouldi symbionts occur both among the microvilli of gill epithelial cells and in sediments surrounding the bivalves, and are therefore facultative. We propose that free-living T. cf. gouldi symbionts use magnetotaxis as a means of locating the oxic-anoxic interface, an optimal microhabitat for chemolithoautotrophy. T. cf. gouldi could acquire their symbionts from near-burrow sediments (where oxic-anoxic interfaces likely develop due to the host's bioirrigating behavior) using their superextensile feet, which could transfer symbionts to gill surfaces upon retraction into the mantle cavity. Once associated with their host, however, symbionts need not maintain structures for magnetotaxis as the host makes oxygen and reduced sulfur available via bioirrigation and sulfur-mining behaviors. Indeed, we show that within the host, symbionts lose the integrity of their magnetosome chain (and possibly their flagellum). Symbionts are eventually endocytosed and digested in host epithelial cells, and magnetosomes accumulate in host cytoplasm. Both host and symbiont behaviors appear important to symbiosis establishment in thyasirids.
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Affiliation(s)
- Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Jason R Laurich
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Rebecca T Batstone
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Bonita McCuaig
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Alexander Elliott
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Kristin M Poduska
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X7, Canada
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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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Grouzdev DS, Dziuba MV, Sukhacheva MS, Mardanov AV, Beletskiy AV, Kuznetsov BB, Skryabin KG. Draft Genome Sequence of Magnetospirillum sp. Strain SO-1, a Freshwater Magnetotactic Bacterium Isolated from the Ol'khovka River, Russia. GENOME ANNOUNCEMENTS 2014; 2:e00235-14. [PMID: 24723706 PMCID: PMC3983295 DOI: 10.1128/genomea.00235-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/26/2014] [Indexed: 11/25/2022]
Abstract
Here, we present the draft genome sequence of Magnetospirillum sp. strain SO-1, a freshwater magnetotactic spirillum isolated from the sediments of the Ol'khovka River, Russia.
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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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Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, Müller R, Zhang Y, Schüler D. Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters. NATURE NANOTECHNOLOGY 2014; 9:193-197. [PMID: 24561353 DOI: 10.1038/nnano.2014.13] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
The synthetic production of monodisperse single magnetic domain nanoparticles at ambient temperature is challenging. In nature, magnetosomes--membrane-bound magnetic nanocrystals with unprecedented magnetic properties--can be biomineralized by magnetotactic bacteria. However, these microbes are difficult to handle. Expression of the underlying biosynthetic pathway from these fastidious microorganisms within other organisms could therefore greatly expand their nanotechnological and biomedical applications. So far, this has been hindered by the structural and genetic complexity of the magnetosome organelle and insufficient knowledge of the biosynthetic functions involved. Here, we show that the ability to biomineralize highly ordered magnetic nanostructures can be transferred to a foreign recipient. Expression of a minimal set of genes from the magnetotactic bacterium Magnetospirillum gryphiswaldense resulted in magnetosome biosynthesis within the photosynthetic model organism Rhodospirillum rubrum. Our findings will enable the sustainable production of tailored magnetic nanostructures in biotechnologically relevant hosts and represent a step towards the endogenous magnetization of various organisms by synthetic biology.
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Affiliation(s)
- Isabel Kolinko
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Anna Lohße
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Sarah Borg
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Oliver Raschdorf
- 1] Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany [2] Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Jogler
- 1] Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany [2]
| | - Qiang Tu
- 1] Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany [2] Shandong University - Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, Jinan 250100, China
| | - Mihály Pósfai
- University of Pannonia, Department of Earth and Environmental Sciences, Veszprém, H-8200 Hungary
| | - Eva Tompa
- University of Pannonia, Department of Earth and Environmental Sciences, Veszprém, H-8200 Hungary
| | - Jürgen M Plitzko
- 1] Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany [2] Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Andreas Brachmann
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Gerhard Wanner
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University - Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, Jinan 250100, China
| | - Dirk Schüler
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
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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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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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36
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Abreu F, Morillo V, Nascimento FF, Werneck C, Cantão ME, Ciapina LP, de Almeida LGP, Lefèvre CT, Bazylinski DA, de Vasconcelos ATR, Lins U. Deciphering unusual uncultured magnetotactic multicellular prokaryotes through genomics. ISME JOURNAL 2013; 8:1055-68. [PMID: 24196322 DOI: 10.1038/ismej.2013.203] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 09/20/2013] [Accepted: 10/09/2013] [Indexed: 11/09/2022]
Abstract
Candidatus Magnetoglobus multicellularis (Ca. M. multicellularis) is a member of a group of uncultured magnetotactic prokaryotes that possesses a unique multicellular morphology. To better understand this organism's physiology, we used a genomic approach through pyrosequencing. Genomic data analysis corroborates previous structural studies and reveals the proteins that are likely involved in multicellular morphogenesis of this microorganism. Interestingly, some detected protein sequences that might be involved in cell adhesion are homologues to phylogenetically unrelated filamentous multicellular bacteria proteins, suggesting their contribution in the early development of multicellular organization in Bacteria. Genes related to the behavior of Ca. M. multicellularis (chemo-, photo- and magnetotaxis) and its metabolic capabilities were analyzed. On the basis of the genomic-physiologic information, enrichment media were tested. One medium supported chemoorganoheterotrophic growth of Ca. M. multicellularis and allowed the microorganisms to maintain their multicellular morphology and cell cycle, confirming for the first time that the entire life cycle of the MMP occurs in a multicellular form. Because Ca. M. multicellularis has a unique multicellular life style, its cultivation is an important achievement for further studies regarding the multicellular evolution in prokaryotes.
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Affiliation(s)
- Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviana Morillo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabrícia F Nascimento
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa Werneck
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauricio Egidio Cantão
- 1] Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil [2] Embrapa Suínos e Aves, Santa Catarina, Brazil
| | - Luciane Prioli Ciapina
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Christopher T Lefèvre
- Laboratoire de Bioénergétique Cellulaire, CEA Cadarache/CNRS/Aix-Marseille Université, UMR7265 Biologie Végétale et Microbiologie Environnementales, Saint Paul lez Durance, France
| | - 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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MamX encoded by the mamXY operon is involved in control of magnetosome maturation in Magnetospirillum gryphiswaldense MSR-1. BMC Microbiol 2013; 13:203. [PMID: 24020498 PMCID: PMC3847676 DOI: 10.1186/1471-2180-13-203] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022] Open
Abstract
Background Magnetotactic bacteria produce membrane-enveloped magnetite crystals (magnetosomes) whose formation is controlled primarily by a gene island termed the magnetosome island (MAI). Characterization of single gene and operon function in MAI has elucidated in part the genetic basis of magnetosome formation. The mamX gene, located in the mamXY operon, is highly conserved in the MAI of all Magnetospirillum strains studied to date. Little is known regarding the function of mamX in the process of biomineralization. Results A mamX deletion mutant (∆mamX) and its complemented strain (CmamX) by conjugation in M. gryphiswaldense strain MSR-1 were constructed. There were no striking differences in cell growth among ∆mamX, CmamX, and wild-type strain (WT). ∆mamX displayed a much weaker magnetic response than WT. Transmission electron microscopy revealed the presence of irregular, superparamagnetic magnetite particles in ∆mamX, in contrast to regular, single-domain particles in WT and CmamX. The phenotype of ∆mamX was similar to that of an ftsZ-like deleted mutant and mamXY operon deleted mutant reported previously. Quantitative real-time RT-PCR (qPCR) results indicated that the deletion of mamX had differential effects on the transcription levels of the other three genes in the operon. Conclusions The MamX protein plays an important role in controlling magnetosome size, maturation, and crystal form. The four MamXY proteins appear to have redundant functions involved in magnetosome formation. Our findings provide new insights into the coordinated function of MAI genes and operons in magnetosome formation.
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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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39
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Ji B, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian J, Yang J, Zhang L, Zhang W, Pan H, Henrissat B, Coutinho PM, Li Y, Xiao T, Médigue C, Barbe V, Pignol D, Talla E, Wu LF. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain. Environ Microbiol 2013; 16:525-44. [PMID: 23841906 DOI: 10.1111/1462-2920.12180] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/17/2013] [Accepted: 06/02/2013] [Indexed: 11/30/2022]
Abstract
Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.
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Affiliation(s)
- Boyang Ji
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F-13402, Marseille Cedex 20, France
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Magnetochrome: a c-type cytochrome domain specific to magnetotatic bacteria. Biochem Soc Trans 2013; 40:1319-23. [PMID: 23176475 DOI: 10.1042/bst20120104] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Magnetotactic bacteria consist of a group of taxonomically, physiologically and morphologically diverse prokaryotes, with the singular ability to align with geomagnetic field lines, a phenomenon referred to as magnetotaxis. This magnetotactic property is due to the presence of iron-rich crystals embedded in lipidic vesicles forming an organelle called the magnetosome. Magnetosomes are composed of single-magnetic-domain nanocrystals of magnetite (Fe(3)O(4)) or greigite (Fe(3)S(4)) embedded in biological membranes, thereby forming a prokaryotic organelle. Four specific steps are described in this organelle formation: (i) membrane specialization, (ii) iron acquisition, (iii) magnetite (or greigite) biocrystallization, and (iv) magnetosome alignment. The formation of these magnetic crystals is a genetically controlled process, which is governed by enzyme-catalysed processes. On the basis of protein sequence analysis of genes known to be involved in magnetosome formation in Magnetospirillum magneticum AMB-1, we have identified a subset of three membrane-associated or periplasmic proteins containing a double cytochrome c signature motif CXXCH: MamE, MamP and MamT. The presence of these proteins suggests the existence of an electron-transport chain inside the magnetosome, contributing to the process of biocrystallization. We have performed heterologous expression in E. coli of the cytochrome c motif-containing domains of MamE, MamP and MamT. Initial biophysical characterization has confirmed that MamE, MamP and MamT are indeed c-type cytochromes. Furthermore, determination of redox potentials for this new family of c-type cytochromes reveals midpoint potentials of -76 and -32 mV for MamP and MamE respectively.
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41
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Lefèvre CT, Trubitsyn D, Abreu F, Kolinko S, Jogler C, de Almeida LGP, de Vasconcelos ATR, Kube M, Reinhardt R, Lins U, Pignol D, Schüler D, Bazylinski DA, Ginet N. Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis. Environ Microbiol 2013; 15:2712-35. [PMID: 23607663 DOI: 10.1111/1462-2920.12128] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 03/20/2013] [Indexed: 01/20/2023]
Abstract
Magnetotactic bacteria (MTB) represent a group of diverse motile prokaryotes that biomineralize magnetosomes, the organelles responsible for magnetotaxis. Magnetosomes consist of intracellular, membrane-bounded, tens-of-nanometre-sized crystals of the magnetic minerals magnetite (Fe3O4) or greigite (Fe3S4) and are usually organized as a chain within the cell acting like a compass needle. Most information regarding the biomineralization processes involved in magnetosome formation comes from studies involving Alphaproteobacteria species which biomineralize cuboctahedral and elongated prismatic crystals of magnetite. Many magnetosome genes, the mam genes, identified in these organisms are conserved in all known MTB. Here we present a comparative genomic analysis of magnetotactic Deltaproteobacteria that synthesize bullet-shaped crystals of magnetite and/or greigite. We show that in addition to mam genes, there is a conserved set of genes, designated mad genes, specific to the magnetotactic Deltaproteobacteria, some also being present in Candidatus Magnetobacterium bavaricum of the Nitrospirae phylum, but absent in the magnetotactic Alphaproteobacteria. Our results suggest that the number of genes associated with magnetotaxis in magnetotactic Deltaproteobacteria is larger than previously thought. We also demonstrate that the minimum set of mam genes necessary for magnetosome formation in Magnetospirillum is also conserved in magnetite-producing, magnetotactic Deltaproteobacteria. Some putative novel functions of mad genes are discussed.
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Affiliation(s)
- Christopher T Lefèvre
- CEA Cadarache/CNRS/Aix-Marseille Université, UMR7265 Service de Biologie Végétale et de Microbiologie Environnementale, Laboratoire de Bioénergétique Cellulaire, 13108, Saint Paul lez Durance, France
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Lefèvre CT, Trubitsyn D, Abreu F, Kolinko S, de Almeida LGP, de Vasconcelos ATR, Lins U, Schüler D, Ginet N, Pignol D, Bazylinski DA. Monophyletic origin of magnetotaxis and the first magnetosomes. Environ Microbiol 2013; 15:2267-74. [PMID: 23438345 DOI: 10.1111/1462-2920.12097] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 01/14/2013] [Indexed: 11/26/2022]
Abstract
Horizontal gene transfer (HGT), the transfer of genetic material other than by descent, is thought to have played significant roles in the evolution and distribution of genes in prokaryotes. These include those responsible for the ability of motile, aquatic magnetotactic bacteria (MTB) to align and swim along magnetic field lines and the biomineralization of magnetosomes that are responsible for this behaviour. There is some genomic evidence that HGT might be responsible for the distribution of magnetosome genes in different phylogenetic groups of bacteria. For example, in the genomes of a number of MTB, magnetosome genes are present as clusters within a larger structure known as the magnetosome genomic island surrounded by mobile elements such as insertion sequences and transposases as well as tRNA genes. Despite this, there is no strong direct proof of HGT between these organisms. Here we show that a phylogenetic tree based on magnetosome protein amino acid sequences from a number of MTB was congruent with the tree based on the organisms' 16S rRNA gene sequences. This shows that evolution and divergence of these proteins and the 16S rRNA gene occurred similarly. This suggests that magnetotaxis originated monophyletically in the Proteobacteria phylum and implies that the common ancestor of all Proteobacteria was magnetotactic.
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Affiliation(s)
- Christopher T Lefèvre
- CEA Cadarache/CNRS/Aix-Marseille Université, UMR7265 Service de Biologie Végétale et de Microbiologie Environnementale, Laboratoire de Bioénergétique Cellulaire, 13108, Saint Paul lez Durance, France.
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Abstract
Cells compartmentalize their biochemical functions in a variety of ways, notably by creating physical barriers that separate a compartment via membranes or proteins. Eukaryotes have a wide diversity of membrane-based compartments, many that are lineage- or tissue-specific. In recent years, it has become increasingly evident that membrane-based compartmentalization of the cytosolic space is observed in multiple prokaryotic lineages, giving rise to several types of distinct prokaryotic organelles. Endosymbionts, previously believed to be a hallmark of eukaryotes, have been described in several bacteria. Protein-based compartments, frequent in bacteria, are also found in eukaryotes. In the present review, we focus on selected intracellular compartments from each of these three categories, membrane-based, endosymbiotic and protein-based, in both prokaryotes and eukaryotes. We review their diversity and the current theories and controversies regarding the evolutionary origins. Furthermore, we discuss the evolutionary processes acting on the genetic basis of intracellular compartments and how those differ across the domains of life. We conclude that the distinction between eukaryotes and prokaryotes no longer lies in the existence of a compartmentalized cell plan, but rather in its complexity.
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44
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Abreu F, Sousa AA, Aronova MA, Kim Y, Cox D, Leapman RD, Andrade LR, Kachar B, Bazylinski DA, Lins U. Cryo-electron tomography of the magnetotactic vibrio Magnetovibrio blakemorei: insights into the biomineralization of prismatic magnetosomes. J Struct Biol 2012; 181:162-8. [PMID: 23246783 DOI: 10.1016/j.jsb.2012.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/10/2012] [Accepted: 12/05/2012] [Indexed: 11/28/2022]
Abstract
We examined the structure and biomineralization of prismatic magnetosomes in the magnetotactic marine vibrio Magnetovibrio blakemorei strain MV-1 and a non-magnetotactic mutant derived from it, using a combination of cryo-electron tomography and freeze-fracture. The vesicles enveloping the Magnetovibrio magnetosomes were elongated and detached from the cell membrane. Magnetosome crystal formation appeared to be initiated at a nucleation site on the membrane inner surface. Interestingly, while scattered filaments were observed in the surrounding cytoplasm, their association with the magnetosome chains could not be unequivocally established. Our data suggest fundamental differences between prismatic and octahedral magnetosomes in their mechanisms of nucleation and crystal growth as well as in their structural relationships with the cytoplasm and plasma membrane.
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Affiliation(s)
- Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, CCS, Bloco I, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
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45
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Zeytuni N, Baran D, Davidov G, Zarivach R. Inter-phylum structural conservation of the magnetosome-associated TPR-containing protein, MamA. J Struct Biol 2012; 180:479-87. [PMID: 22917855 DOI: 10.1016/j.jsb.2012.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
Abstract
Magnetotactic bacteria enclose the magnetosome, a unique prokaryotic sub-cellular organelle that allows the biomineralization of magnetic nano-crystals. Membrane-coated magnetosomes are arranged into a linear chain that permits magnetotactic bacteria to navigate geomagnetic fields. Magnetosome assembly and biomineralization are controlled by conserved magnetosome-associated proteins, including MamA, a tetra-trico-peptide repeat (TPR)-containing protein that was shown to coat the magnetosome membrane. In this study, two MamA structures from Candidatus Magnetobacterium bavaricum (Mbav) were determined via X-ray crystallography. These structures confirm that Mbav MamA folds as a sequential TPR protein and shares a high degree of structural similarity with homologous MamA proteins from Magnetospirillum species. Furthermore, the two TPR-containing domains of MamA are separated by an interphylum-conserved region containing a flexible hinge that is involved in ligand binding and recognition. Finally, substantial differences were found in the local stabilization of the MamA N-terminal domain as a result of the loss of an evolutionary conserved salt bridge.
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Affiliation(s)
- Natalie Zeytuni
- Department of Life Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
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Insight into the evolution of magnetotaxis in Magnetospirillum spp., based on mam gene phylogeny. Appl Environ Microbiol 2012; 78:7238-48. [PMID: 22865076 DOI: 10.1128/aem.01951-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrioid- to helical-shaped magnetotactic bacteria phylogenetically related to the genus Magnetospirillum were isolated in axenic cultures from a number of freshwater and brackish environments located in the southwestern United States. Based on 16S rRNA gene sequences, most of the new isolates represent new Magnetospirillum species or new strains of known Magnetospirillum species, while one isolate appears to represent a new genus basal to Magnetospirillum. Partial sequences of conserved mam genes, genes reported to be involved in the magnetosome and magnetosome chain formation, and form II of the ribulose-1,5-bisphosphate carboxylase/oxygenase gene (cbbM) were determined in the new isolates and compared. The cbbM gene was chosen for comparison because it is not involved in magnetosome synthesis; it is highly conserved and is present in all but possibly one of the genomes of the magnetospirilla and the new isolates. Phylogenies based on 16S rRNA, cbbM, and mam gene sequences were reasonably congruent, indicating that the genes involved in magnetotaxis were acquired by a common ancestor of the Magnetospirillum clade. However, in one case, magnetosome genes might have been acquired through horizontal gene transfer. Our results also extend the known diversity of the Magnetospirillum group and show that they are widespread in freshwater environments.
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Zeytuni N, Offer T, Davidov G, Zarivach R. Crystallization and preliminary crystallographic analysis of the C-terminal domain of MamM, a magnetosome-associated protein from Magnetospirillum gryphiswaldense MSR-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:927-30. [PMID: 22869124 PMCID: PMC3412775 DOI: 10.1107/s1744309112025638] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/05/2012] [Indexed: 11/10/2022]
Abstract
MamM is a unique magnetosome-associated protein that shares substantial homology with cation diffusion facilitator (CDF) proteins, a group of heavy-metal-ion efflux transporters that participate in metal-ion homeostasis in all domains of life. Magnetotactic bacteria utilize CDF proteins in iron-oxide biomineralization and in magnetosome formation. Here, the crystallization and preliminary X-ray analysis of recombinant Magnetospirillum gryphiswaldense MamM is reported. The C-terminal domain of MamM was crystallized in the orthorhombic space group C222(1), with unit-cell parameters a = 37.1, b = 94.0, c = 53.3 Å. X-ray diffraction data were collected to a resolution of 2.0 Å.
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Affiliation(s)
- Natalie Zeytuni
- Department of Life Sciences and National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, PO Box 653, Beer-Sheva 84105, Israel
| | - Tal Offer
- Department of Life Sciences and National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, PO Box 653, Beer-Sheva 84105, Israel
| | - Geula Davidov
- Department of Life Sciences and National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, PO Box 653, Beer-Sheva 84105, Israel
| | - Raz Zarivach
- Department of Life Sciences and National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, PO Box 653, Beer-Sheva 84105, Israel
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Compromised DNA damage repair promotes genetic instability of the genomic magnetosome island in Magnetospirillum magneticum AMB-1. Curr Microbiol 2012; 65:98-107. [PMID: 22538470 DOI: 10.1007/s00284-012-0131-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
Magnetotactic bacteria (MTB) are capable of synthesizing nano-sized, intracellular membrane-bound magnetosomes. To learn more about the genetic factors involved in magnetosome formation, transposon mutagenesis was carried out by conjugation using a hyperactive mariner transposon to obtain nonmagnetic mutants of Magnetospirillum magneticum AMB-1. A mutant with defect in uvrA gene encoding the DNA binding subunit of the UvrABC complex responsible for the process of nucleotide excision repair, was obtained. Growth, magnetosome formation and maintenance of magnetosome island (MAI) were further analyzed in the absence of UvrA. Interruption of uvrA led to decreased capacity to form magnetosome when cultured in the presence of oxygen. The deficiency in UvrA also resulted in an accelerated loss of the MAI under aerobic conditions indicating that the nucleotide excision repair system guards against the instability of the MAI. The incapacity of MTB to efficiently initiate recombination mediated by RecA rescued the instability of MAI observed in uvrA mutant. Elevated recombination activity resulting from the accumulation of unrepaired mutations may thus account for the instability of MAI in the absence of UvrA.
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Klumpp S, Faivre D. Interplay of magnetic interactions and active movements in the formation of magnetosome chains. PLoS One 2012; 7:e33562. [PMID: 22442698 PMCID: PMC3307741 DOI: 10.1371/journal.pone.0033562] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/16/2012] [Indexed: 11/19/2022] Open
Abstract
Magnetotactic bacteria assemble chains of magnetosomes, organelles that contain magnetic nano-crystals. A number of genetic factors involved in the controlled biomineralization of these crystals and the assembly of magnetosome chains have been identified in recent years, but how the specific biological regulation is coordinated with general physical processes such as diffusion and magnetic interactions remains unresolved. Here, these questions are addressed by simulations of different scenarios for magnetosome chain formation, in which various physical processes and interactions are either switched on or off. The simulation results indicate that purely physical processes of magnetosome diffusion, guided by their magnetic interactions, are not sufficient for the robust chain formation observed experimentally and suggest that biologically encoded active movements of magnetosomes may be required. Not surprisingly, the chain pattern is most resembling experimental results when both magnetic interactions and active movement are coordinated. We estimate that the force such active transport has to generate is compatible with forces generated by the polymerization or depolymerization of cytoskeletal filaments. The simulations suggest that the pleiotropic phenotypes of mamK deletion strains may be due to a defect in active motility of magnetosomes and that crystal formation in magneteosome vesicles is coupled to the activation of their active motility in M. gryphiswaldense, but not in M. magneticum.
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Affiliation(s)
- Stefan Klumpp
- Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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Uebe R, Henn V, Schüler D. The MagA protein of Magnetospirilla is not involved in bacterial magnetite biomineralization. J Bacteriol 2012; 194:1018-23. [PMID: 22194451 PMCID: PMC3294778 DOI: 10.1128/jb.06356-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria have the ability to orient along geomagnetic field lines based on the formation of magnetosomes, which are intracellular nanometer-sized, membrane-enclosed magnetic iron minerals. The formation of these unique bacterial organelles involves several processes, such as cytoplasmic membrane invagination and magnetosome vesicle formation, the accumulation of iron in the vesicles, and the crystallization of magnetite. Previous studies suggested that the magA gene encodes a magnetosome-directed ferrous iron transporter with a supposedly essential function for magnetosome formation in Magnetospirillum magneticum AMB-1 that may cause magnetite biomineralization if expressed in mammalian cells. However, more recent studies failed to detect the MagA protein among polypeptides associated with the magnetosome membrane and did not identify magA within the magnetosome island, a conserved genomic region that is essential for magnetosome formation in magnetotactic bacteria. This raised increasing doubts about the presumptive role of magA in bacterial magnetosome formation, which prompted us to reassess MagA function by targeted deletion in Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1. Contrary to previous reports, magA mutants of both strains still were able to form wild-type-like magnetosomes and had no obvious growth defects. This unambiguously shows that magA is not involved in magnetosome formation in magnetotactic bacteria.
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Affiliation(s)
- René Uebe
- Ludwig Maximillian University Munich, Department of Biology I, Großhaderner Str. 2, D-82152 Martinsried, Germany
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