1. |
Bertani LE,
Weko J,
Phillips KV,
Gray RF,
Kirschvink JL,
( 2001 ) Physical and genetic characterization of the genome of Magnetospirillum magnetotacticum, strain MS-1. PMID : 11250081 : DOI : 10.1016/s0378-1119(01)00331-6 Abstract >>
Pulsed-field gel analysis of Magnetospirillum magnetotacticum, strain MS-1, indicates that the genome is a single, circular structure of about 4.3 mb. A few genes, identified by sequence similarity, have been localized and arranged in a map with dnaA, indicating the presumed origin of replication. There are at least two rRNA operons. In addition, rRNA genes are found on a 40 kb, possibly extrachromosomal, structure. The genes thought to be involved in magnetite synthesis, bfr and magA, are located in the same 17% of the genome. A one base pair-overlap seen in the bfr genes of MS-1 is found also in the closely related magnetic strain AMB-1, but not in the non-magnetic relative A. itersonii.
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2. |
Gaidos EJ,
Bertani LE,
Beukes NJ,
Kirschvink JL,
( 2000 ) Paleoproterozoic snowball earth: extreme climatic and geochemical global change and its biological consequences. PMID : 10677473 : DOI : 10.1073/pnas.97.4.1400 PMC : PMC26445 Abstract >>
Geological, geophysical, and geochemical data support a theory that Earth experienced several intervals of intense, global glaciation ("snowball Earth" conditions) during Precambrian time. This snowball model predicts that postglacial, greenhouse-induced warming would lead to the deposition of banded iron formations and cap carbonates. Although global glaciation would have drastically curtailed biological productivity, melting of the oceanic ice would also have induced a cyanobacterial bloom, leading to an oxygen spike in the euphotic zone and to the oxidative precipitation of iron and manganese. A Paleoproterozoic snowball Earth at 2.4 Giga-annum before present (Ga) immediately precedes the Kalahari Manganese Field in southern Africa, suggesting that this rapid and massive change in global climate was responsible for its deposition. As large quantities of O(2) are needed to precipitate this Mn, photosystem II and oxygen radical protection mechanisms must have evolved before 2.4 Ga. This geochemical event may have triggered a compensatory evolutionary branching in the Fe/Mn superoxide dismutase enzyme, providing a Paleoproterozoic calibration point for studies of molecular evolution.
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3. |
Matsunaga T,
Sakaguchi T,
( 2000 ) Molecular mechanism of magnet formation in bacteria. PMID : 16232810 : Abstract >>
Magnetic bacteria have an ability to synthesize intracellular ferromagnetic crystalline particles consisting of magnetite (Fe3O4) or greigite (Fe3S4) which occur within a specific size range (50-100 nm). Bacterial magnetic particles (BMPs) can be distinguished by the regular morphology and the presence of an thin organic membrane enveloping crystals from abiologically formed magnetite. The particle is the smallest magnetic crystal that has a regular morphology within the single domain size. Therefore, BMPs have an unfathomable amount of potential value for various technological applications not only scientific interests. However, the molecular and genetic mechanism of magnetite biomineralization is hardly understood although iron oxide formation occurs widely in many higher animals as well as microorganisms. In order to elucidate the molecular and genetic mechanisms of magnetite biomineralization, a magnetic bacterium Magnetospirillum sp. AMB-1, for which gene transfer and transposon mutagenesis techniques had been recently developed, has been used as a model organism. Several findings and information on the BMPs formation process have been obtained within this decade by means of studies with this model organism and its related one. Biomineralization mechanism and potential availability in biotechnology of bacterial magnets have been elucidated through molecular and genetic approach.
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4. |
Kuo A,
Domene C,
Johnson LN,
Doyle DA,
Vénien-Bryan C,
( 2005 ) Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography. PMID : 16216578 : DOI : 10.1016/j.str.2005.07.011 Abstract >>
Potassium channels allow the selective flow of K(+) ions across membranes. In response to external gating signals, the potassium channel can move reversibly through a series of structural conformations from a closed to an open state. 2D crystals of the inwardly rectifying K(+) channel KirBac3.1 from Magnetospirillum magnetotacticum have been captured in two distinct conformations, providing "snap shots" of the gating process. Analysis by electron cryomicroscopy of these KirBac3.1 crystals has resulted in reconstructed images in projection at 9 A resolution. Kir channels are tetramers of four subunits arranged as dimers of dimers. Each subunit has two transmembrane helices (inner and outer). In one crystal form, the pore is blocked; in the other crystal form, the pore appears open. Modeling based on the KirBac1.1 (closed) crystal structure shows that opening of the ion conduction pathway could be achieved by bending of the inner helices and significant movements of the outer helices.
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5. |
Bazylinski DA,
Dean AJ,
Williams TJ,
Long LK,
Middleton SL,
Dubbels BL,
( 2004 ) Chemolithoautotrophy in the marine, magnetotactic bacterial strains MV-1 and MV-2. PMID : 15338111 : DOI : 10.1007/s00203-004-0716-y Abstract >>
Magnetite-producing magnetotactic bacteria collected from the oxic-anoxic transition zone of chemically stratified marine environments characterized by O2/H2S inverse double gradients, contained internal S-rich inclusions resembling elemental S globules, suggesting they oxidize reduced S compounds that could support autotrophy. Two strains of marine magnetotactic bacteria, MV-1 and MV-2, isolated from such sites grew in O2-gradient media with H2S or thiosulfate (S2O3(2-)) as electron sources and O2 as electron acceptor or anaerobically with S2O3(2-) and N2O as electron acceptor, with bicarbonate (HCO3-)/CO2 as sole C source. Cells grown with H2S contained S-rich inclusions. Cells oxidized S2O3(2-) to sulfate (SO4(2-)). Both strains grew microaerobically with formate. Neither grew microaerobically with tetrathionate (S4O6(2-)), methanol, or Fe2+ as FeS, or siderite (FeCO3). Growth with S2O3(2-) and radiolabeled 14C-HCO3- showed that cell C was derived from HCO3-/CO2. Cell-free extracts showed ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity. Southern blot analyses indicated the presence of a form II RubisCO (cbbM) but no form I (cbbL) in both strains. cbbM and cbbQ, a putative post-translational activator of RubisCO, were identified in MV-1. MV-1 and MV-2 are thus chemolithoautotrophs that use the Calvin-Benson-Bassham pathway. cbbM was also identified in Magnetospirillum magnetotacticum. Thus, magnetotactic bacteria at the oxic-anoxic transition zone of chemically stratified aquatic environments are important in C cycling and primary productivity.
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6. |
Spiridonova EM,
Berg IA,
Kolganova TV,
Ivanovskiĭ RN,
Kuznetsov BB,
Turova TP,
( N/A ) [An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups]. PMID : 15315232 : Abstract >>
Based on the analysis of GenBank nucleotide sequences of the cbbL and cbbM genes, coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC), the key enzyme of the Calvin cycle, a primer system was designed that allows about 800-bp-long fragments of these genes to be PCR-ampliflied in various photo- and chemotrophic bacteria. The efficiency of the designed primer system in detection of RuBPC genes was demonstrated in PCR with DNA of taxonomically diverse bacteria possessing RuBPC genes with a known primary structure. Nucleotide sequences of RuBPC gene fragments of bacteria belonging to the genera Acidithiobacillus. Ectothiorhodospira, Magnetospirillum, Methylocapsa, Thioalkalispira, Rhodobacter, and Rhodospirillum were determined to be deposited with GenBank and to be translated into amino acid sequences and subjected to phylogenetic analysis.
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7. |
Komeili A,
Vali H,
Beveridge TJ,
Newman DK,
( 2004 ) Magnetosome vesicles are present before magnetite formation, and MamA is required for their activation. PMID : 15004275 : DOI : 10.1073/pnas.0400391101 PMC : PMC374331 Abstract >>
Bacterial magnetosomes are intracellular compartments that house highly ordered magnetite crystals. By using Magnetospirillum sp. AMB-1 as a model system, we show that magnetosome vesicles exist in the absence of magnetite, biomineralization of magnetite proceeds simultaneously in multiple vesicles, and biomineralization proceeds from the same location in each vesicle. The magnetosome-associated protein, MamA, is required for the formation of functional magnetosome vesicles and displays a dynamic subcellular localization throughout the growth cycle of magnetotactic bacteria. Together, these results suggest that the magnetosome precisely coordinates magnetite biomineralization and can serve as a model system for the study of organelle biogenesis in noneukaryotic cells.
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8. |
Gueneau de Novoa P,
Williams KP,
( 2004 ) The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. PMID : 14681369 : DOI : 10.1093/nar/gkh102 PMC : PMC308836 Abstract >>
tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.
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9. |
Zeytuni N,
Ozyamak E,
Ben-Harush K,
Davidov G,
Levin M,
Gat Y,
Moyal T,
Brik A,
Komeili A,
Zarivach R,
( 2011 ) Self-recognition mechanism of MamA, a magnetosome-associated TPR-containing protein, promotes complex assembly. PMID : 21784982 : DOI : 10.1073/pnas.1103367108 PMC : PMC3158213 Abstract >>
The magnetosome, a biomineralizing organelle within magnetotactic bacteria, allows their navigation along geomagnetic fields. Magnetosomes are membrane-bound compartments containing magnetic nanoparticles and organized into a chain within the cell, the assembly and biomineralization of magnetosomes are controlled by magnetosome-associated proteins. Here, we describe the crystal structures of the magnetosome-associated protein, MamA, from Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1. MamA folds as a sequential tetra-trico-peptide repeat (TPR) protein with a unique hook-like shape. Analysis of the MamA structures indicates two distinct domains that can undergo conformational changes. Furthermore, structural analysis of seven crystal forms verified that the core of MamA is not affected by crystallization conditions and identified three protein-protein interaction sites, namely a concave site, a convex site, and a putative TPR repeat. Additionally, relying on transmission electron microscopy and size exclusion chromatography, we show that highly stable complexes form upon MamA homooligomerization. Disruption of the MamA putative TPR motif or N-terminal domain led to protein mislocalization in vivo and prevented MamA oligomerization in vitro. We, therefore, propose that MamA self-assembles through its putative TPR motif and its concave site to create a large homooligomeric scaffold which can interact with other magnetosome-associated proteins via the MamA convex site. We discuss the structural basis for TPR homooligomerization that allows the proper function of a prokaryotic organelle.
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10. |
Berson AE,
Peters MR,
Waleh NS,
( 1990 ) Nucleotide sequence of recA gene of Aquaspirillum magnetotacticum. PMID : 2106674 : DOI : 10.1093/nar/18.3.675 PMC : PMC333497 Abstract >>
N/A
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11. |
Clarke OB,
Caputo AT,
Hill AP,
Vandenberg JI,
Smith BJ,
Gulbis JM,
( 2010 ) Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels. PMID : 20564790 : DOI : 10.1016/j.cell.2010.05.003 Abstract >>
Potassium channels embedded in cell membranes employ gates to regulate K+ current. While a specific constriction in the permeation pathway has historically been implicated in gating, recent reports suggest that the signature ion selectivity filter located in the outer membrane leaflet may be equally important. Inwardly rectifying K+ channels also control the directionality of flow, using intracellular polyamines to stem ion efflux by a valve-like action. This study presents crystallographic evidence of interdependent gates in the conduction pathway and reveals the mechanism of polyamine block. Reorientation of the intracellular domains, concomitant with activation, instigates polyamine release from intracellular binding sites to block the permeation pathway. Conformational adjustments of the slide helices, achieved by rotation of the cytoplasmic assembly relative to the pore, are directly correlated to the ion configuration in the selectivity filter. Ion redistribution occurs irrespective of the constriction, suggesting a more expansive role of the selectivity filter in gating than previously appreciated.
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12. |
Paynter JJ,
Andres-Enguix I,
Fowler PW,
Tottey S,
Cheng W,
Enkvetchakul D,
Bavro VN,
Kusakabe Y,
Sansom MS,
Robinson NJ,
Nichols CG,
Tucker SJ,
( 2010 ) Functional complementation and genetic deletion studies of KirBac channels: activatory mutations highlight gating-sensitive domains. PMID : 20876570 : DOI : 10.1074/jbc.M110.175687 PMC : PMC3003375 Abstract >>
The superfamily of prokaryotic inwardly rectifying (KirBac) potassium channels is homologous to mammalian Kir channels. However, relatively little is known about their regulation or about their physiological role in vivo. In this study, we have used random mutagenesis and genetic complementation in K(+)-auxotrophic Escherichia coli and Saccharomyces cerevisiae to identify activatory mutations in a range of different KirBac channels. We also show that the KirBac6.1 gene (slr5078) is necessary for normal growth of the cyanobacterium Synechocystis PCC6803. Functional analysis and molecular dynamics simulations of selected activatory mutations identified regions within the slide helix, transmembrane helices, and C terminus that function as important regulators of KirBac channel activity, as well as a region close to the selectivity filter of KirBac3.1 that may have an effect on gating. In particular, the mutations identified in TM2 favor a model of KirBac channel gating in which opening of the pore at the helix-bundle crossing plays a far more important role than has recently been proposed.
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13. |
Bavro VN,
De Zorzi R,
Schmidt MR,
Muniz JR,
Zubcevic L,
Sansom MS,
Vénien-Bryan C,
Tucker SJ,
( 2012 ) Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. PMID : 22231399 : DOI : 10.1038/nsmb.2208 PMC : PMC3272479 Abstract >>
KirBac channels are prokaryotic homologs of mammalian inwardly rectifying (Kir) potassium channels, and recent crystal structures of both Kir and KirBac channels have provided major insight into their unique structural architecture. However, all of the available structures are closed at the helix bundle crossing, and therefore the structural mechanisms that control opening of their primary activation gate remain unknown. In this study, we engineered the inner pore-lining helix (TM2) of KirBac3.1 to trap the bundle crossing in an apparently open conformation and determined the crystal structure of this mutant channel to 3.05 ? resolution. Contrary to previous speculation, this new structure suggests a mechanistic model in which rotational 'twist' of the cytoplasmic domain is coupled to opening of the bundle-crossing gate through a network of inter- and intrasubunit interactions that involve the TM2 C-linker, slide helix, G-loop and the CD loop.
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14. |
( 1996 ) Cloning and sequencing of a gene encoding a new member of the tetratricopeptide protein family from magnetosomes of Magnetospirillum magnetotacticum. PMID : 8675040 : DOI : 10.1016/0378-1119(95)00008-9 Abstract >>
A gene encoding the 22 kDa protein (MAM22) which was localized in the magnetosomes isolated from the magnetotactic bacterium, Magnetospirillum magnetotacticum, was cloned and sequenced. MAM22 was composed of 220 amino acids (aa) with a molecular weight of 24,186 Da. The deduced aa sequence exhibited significant homology with a number of proteins that belong to the tetratricopeptide repeat (TPR) protein family, including mitochondrial protein import receptors and peroxisomal protein import receptors. The presence of three repeats of a degenerate 34-aa consensus sequence, suggest that MAM22 localized in magnetosome membranes may interact with the cytoplasmic proteins containing similar TPR motifs.
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15. |
( 1997 ) Evidence for two types of subunits in the bacterioferritin of Magnetospirillum magnetotacticum. PMID : 9409768 : DOI : 10.1016/s0378-1119(97)00424-1 Abstract >>
In order to investigate the role of bacterioferritin (Bfr) in the biomineralization of magnetite by microorganisms, we have cloned and sequenced the bfr genes from M. magnetotacticum. The organism has two bfr genes that overlap by one nucleotide. Both encode putative protein products of 18 kDa, the expected size for Bfr subunits, and show a strong similarity to other Bfr subunit proteins. By scanning the DNA sequence databases, we found that a limited number of other organisms, including N. gonorrhea, P. aeruginosa, and Synechocystis PCC6803, also have two bfr genes. When the sequences of a number of microbial Bfrs are compared with each other, they fall into two distinct types with the organisms mentioned above having one of each type. Differences in heme- and metal-binding sites and ferroxidase activities of the two types of subunits are discussed.
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