Publications

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nanobiotechnology: putting cobalt on the menu. 200818654484
controlled cobalt doping of magnetosomes in vivo.magnetotactic bacteria biomineralize iron into magnetite (fe3o4) nanoparticles that are surrounded by lipid vesicles. these 'magnetosomes' have considerable potential for use in bio- and nanotechnological applications because of their narrow size and shape distribution and inherent biocompatibility. the ability to tailor the magnetic properties of magnetosomes by chemical doping would greatly expand these applications; however, the controlled doping of magnetosomes has so far not been achieved. ...200818654488
[magnetotactic bacteria's organella, magnetosome-localization, and cytoskeleton]. 200819044287
sinusoidal magnetic field stimulates magnetosome formation and affects mama, mms13, mms6, and maga expression in magnetospirillum magneticum amb-1.magnetic particles are currently one of the most important materials in the industrial sector, where they have been widely used for biotechnological and biomedical applications. to investigate the effects of the imposed magnetic field on biomineralization in magnetospirillum magneticum amb-1 and to suggest a new approach that enhances formation of magnetosomes, cultures inoculated with either magnetic or nonmagnetic precultures were incubated under a sinusoidal magnetic field or geomagnetic fiel ...200819096456
high-yield growth and magnetosome formation by magnetospirillum gryphiswaldense msr-1 in an oxygen-controlled fermentor supplied solely with air.magnetotactic bacteria are difficult to grow under defined conditions in culture, which has presented a major obstacle to commercial application of magnetosomes. we studied the relationships among the cell growth, magnetosome formation, dissolved oxygen concentration (do), and the ability to supply oxygen to the cells. mass culture of magnetospirillum gryphiswaldense msr-1 for the production of magnetosomes was established in a 42-l fermentor under the following conditions: (1) sterile air was t ...200818425510
in chlamydomonas, the loss of nd5 subunit prevents the assembly of whole mitochondrial complex i and leads to the formation of a low abundant 700 kda subcomplex.in the green alga chlamydomonas reinhardtii, a mutant deprived of complex i enzyme activity presents a 1t deletion in the mitochondrial nd5 gene. the loss of the nd5 subunit prevents the assembly of the 950 kda whole complex i. instead, a low abundant 700 kda subcomplex, loosely associated to the inner mitochondrial membrane, is assembled. the resolution of the subcomplex by sds-page gave rise to 19 individual spots, sixteen having been identified by mass spectrometry analysis. eleven, mainly as ...200818258177
development of a cell surface display system in a magnetotactic bacterium, "magnetospirillum magneticum" amb-1.bacterial cell surface display is a widely used technology for bioadsorption and for the development of a variety of screening systems. magnetotactic bacteria are unique species of bacteria due to the presence of magnetic nanoparticles within them. these intracellular, nanosized (50 to 100 nm) magnetic nanoparticles enable the cells to migrate and be manipulated by magnetic force. in this work, using this unique characteristic and based on whole-genomic and comprehensive proteomic analyses of th ...200818378651
mesaconyl-coenzyme a hydratase, a new enzyme of two central carbon metabolic pathways in bacteria.the coenzyme a (coa)-activated c5-dicarboxylic acids mesaconyl-coa and beta-methylmalyl-coa play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. first, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic co2 fixation in chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium. second, mesaconyl-coa and beta-methylmalyl-coa are intermediates in the ethylmalonyl-coa pathway for acetate assimilation in various bacte ...200818065535
expression of green fluorescent protein fused to magnetosome proteins in microaerophilic magnetotactic bacteria.the magnetosomes of magnetotactic bacteria are prokaryotic organelles consisting of a magnetite crystal bounded by a phospholipid bilayer that contains a distinct set of proteins with various functions. because of their unique magnetic and crystalline properties, magnetosome particles are potentially useful as magnetic nanoparticles in a number of applications, which in many cases requires the coupling of functional moieties to the magnetosome membrane. in this work, we studied the use of green ...200818539817
noncovalent immobilization of streptavidin on in vitro- and in vivo-biotinylated bacterial magnetic particles.biotinylated magnetic nanoparticles were constructed by displaying biotin acceptor peptide (bap) or biotin carboxyl carrier protein (bccp) on the surface of bacterial magnetic particles (bacmps) synthesized by magnetospirillum magneticum amb-1. bap-displaying bacmps (bap-bacmps) were extracted from bacterial cells and incubated with biotin and escherichia coli biotin ligase. then the in vitro biotinylation of bap-bacmps was confirmed using alkaline phosphatase-labeled antibiotin antibody. in con ...200818567691
disruption of a fur-like gene inhibits magnetosome formation in magnetospirillum gryphiswaldense msr-1.in this study, a genomic library of magnetospirillum gryphiswaldense msr-1 strain was constructed and a fur-like gene (encoding fur protein, ferric uptake regulator) was isolated and sequenced. this gene consisted of 420 bp and encoded 139 amino acid residues. to investigate the function of this gene in msr-1, a fur mutant was generated by double crossover with a kanamycin cassette inserted into its coding region. iron uptake and magnetosome formation were dramatically inhibited by disruption of ...200718205608
respiratory transformation of nitrous oxide (n2o) to dinitrogen by bacteria and archaea.n2o is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. it is an obligatory inorganic metabolite of denitrifying bacteria, and some production of n2o is also found in nitrifying and methanotrophic bacteria. we focus this review on the respiratory aspect of n2o transformation catalysed by the multicopper enzyme nitrous oxide reductase (n2or) that provides the bacterial cell with an electron sink for anaerobic growth. t ...200717027372
rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism.magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. thus, suggested formation mechanisms still need substantiating with data. here we report the examination of the magneto ...200718032611
molecular mechanisms of magnetosome formation.magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. this unique feat is accomplished with the help of magnetosomes, nanometer-sized magnetic crystals surrounded by a lipid bilayer membrane and organized into chains via a dedicated cytoskeleton within the cell. because of the special properties of these magnetic crystals, magnetotactic bacteria have been exploited for a variety of applications in diverse disciplines from g ...200717371202
comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.magnetotactic bacteria (mtb) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the earth's magnetic field. although a number of putative magnetotaxis genes were recently identified within a conserved genomic magne ...200717449609
molecular analysis of magnetotactic bacteria and development of functional bacterial magnetic particles for nano-biotechnology.biomineralization is an elaborate process that produces complex nano-structures consisting of organic and inorganic components of uniform size and highly ordered morphology that self-assemble into structures in a hierarchical manner. magnetotactic bacteria synthesize nano-sized magnetite crystals that are highly consistent in size and morphology within bacterial species; each particle is surrounded by a thin organic membrane, which facilitates their use for various biotechnological applications. ...200717306901
synthesis of magnetite nanoparticles for bio- and nanotechnology: genetic engineering and biomimetics of bacterial magnetosomes.magnetotactic bacteria (mtb) have the ability to navigate along the earth's magnetic field. this so-called magnetotaxis is a result of the presence of magnetosomes, organelles which comprise nanometer-sized intracellular crystals of magnetite (fe(3)o(4)) enveloped by a membrane. because of their unique characteristics, magnetosomes have a high potential for nano- and biotechnological applications, which require a specifically designed particle surface. the functionalization of magnetosomes is po ...200717295401
patch clamp and phenotypic analyses of a prokaryotic cyclic nucleotide-gated k+ channel using escherichia coli as a host.prokaryotic ion channels have been valuable in providing structural models for understanding ion filtration and channel-gating mechanisms. however, their functional examinations have remained rare and usually been carried out by incorporating purified channel protein into artificial lipid membranes. here we demonstrate the utilization of escherichia coli to host the functional analyses by examining a putative cyclic nucleotide-gated k+ channel cloned from magnetospirillum magnetotacticum, mmak. ...200717588940
purified and sterilized magnetosomes from magnetospirillum gryphiswaldense msr-1 were not toxic to mouse fibroblasts in vitro.to establish a criterion for measuring the purity of purified and sterilized magnetosomes from magnetospirillum gryphiswaldense and to evaluate their toxicity for mouse fibroblasts in vitro.200717594464
a simple and accurate method for quantification of magnetosomes in magnetotactic bacteria by common spectrophotometer.a simple apparatus for measuring the magnetism of magnetotactic bacteria was developed with a common laboratory spectrophotometer, which was based on measuring the change in light scattering resulting from cell alignment in a magnetic field. a multiple coils were built around the cuvette holder of the spectrophotometer to compensate geomagnetic field and to generate two mutually perpendicular magnetic fields. in addition, we defined a novel magnetism parameter, r(mag), by modifying the definitio ...200717030397
novel facultative anaerobic acidotolerant telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen.three facultative anaerobic acidotolerant gram-negative motile spirilla strains designated 26-4b1, 26-2 and k-1 were isolated from mesotrophic siberian fen as a component of methanogenic consortia. the isolates were found to grow chemoorganotrophically on several organic acids and glucose under anoxic and low oxygen pressure in the dark, tolerant up to 5kpa of oxygen. at low oxygen supply, faint autotrophic growth on the h(2):co(2) mixture was also observed. all three isolates were able to fix n ...200716876366
cytoplasmic atpase involved in ferrous ion uptake from magnetotactic bacterium magnetospirillum magneticum amb-1.a non-magnetic mutant of magnetospirillum magneticum amb-1 (nma61), harboring a defective gene located in orf4 (gene id: amb4111) was generated by transposon mutagenesis. biochemical characterization of the gene product of orf4 revealed that it was localized in the cytoplasm and displayed atpase activity. the ability of nma61 to take up iron was severely compromised. ferrous ion concentration in the medium decreased more with the wild-type than with nma61, while the iron content in the cytoplasm ...200717618623
isolation of the epsilon-caprolactam denitrifying bacteria from a wastewater treatment system manufactured with acrylonitrile-butadiene-styrene resin.epsilon-caprolactam has high cod and toxicity, so its discharge to natural water and soil systems may lead to an adverse environmental effect on water quality, endangering public health and welfare. this investigation attempts to isolate epsilon-caprolactam denitrifying bacteria from a wastewater treatment system manufactured with acrylonitrile-butadiene-styrene (abs) resin. the goal is to elucidate the effectiveness of isolated pure strain and abs mixed strains in treating epsilon-caprolactam f ...200717161908
deep-etching electron microscopy of cells of magnetospirillum magnetotacticum: evidence for filamentous structures connecting the magnetosome chain to the cell surface.magnetospirillum magnetotacticum are magnetotactic bacteria that form a single chain of magnetite magnetosomes within its cytoplasm. here, we studied the ultrastructure of m. magnetotacticum by freeze-fracture and deep-etching to understand the spatial correlation between the magnetosome chain and the cell envelope and its possible implications for magnetotaxis. magnetosomes were found mainly near the cell envelope, forming chains that were closely associated with the granular cytoplasmic materi ...200717171472
detection of epidermal growth factor receptor (egfr) mutations in non-small cell lung cancer (nsclc) using a fully automated system with a nano-scale engineered biomagnetite.a fully automated system using nano-scale engineered biomagnetite was developed to detect mutations in the epidermal growth factor receptor (egfr) gene in non-small cell lung cancer (nsclc). bacterial magnetic particles (bacmps) were isolated from the magnetic bacterium magnetospirillum magneticum amb-1 and conjugated to streptavidin. biotin-labeled target pcr products were then captured with the bacmps, hybridized with the detection probe and detected by fluorescence signaling. the process was ...200717187977
expression level of heterologous tat genes is crucial for in vivo reconstitution of a functional tat translocase in escherichia coli.the tat system has the remarkable capacity of exporting proteins in folded conformation across the cytoplasmic membrane. the functional tat translocase from gram-negative bacteria consists of tata, tatb and tatc proteins. to gain information about the species specificity of the tat translocase, we cloned tat genes from gram-negative pathogens shigella flexneri 2a str. 301, vibrio cholerae el tor n16961, pseudomonas aeruginosa pao1, thermophilic sulfolobus solfataricus p2, thermus thermophilus hb ...200717336443
fluorescent bacterial magnetic nanoparticles as bimodal contrast agents.the purpose of this study was to assess whether fluorochrome-coupled bacterial magnetic nanoparticles can be used as bimodal contrast agent for both magnetic resonance imaging (mri) and near-infrared fluorescence optical (nirf) imaging of cultured macrophages.200717351430
controlled biomineralization by and applications of magnetotactic bacteria. 200717869601
intracellular magnetite biomineralization in bacteria proceeds by a distinct pathway involving membrane-bound ferritin and an iron(ii) species. 200717902080
polymerization of the actin-like protein mamk, which is associated with magnetosomes.the recombinant actin-like protein mamk was purified from escherichia coli and used as an antigen to generate the anti-mamk antibody. immunostaining studies showed a linear distribution of mamk in magnetospirillum magnetotacticum cells and of mamk in association with magnetosomes. moreover, we demonstrated that mamk polymerizes into filamentous bundles in vitro.200717905974
a novel ferric reductase purified from magnetospirillum gryphiswaldense msr-1.a ferric reductase was purified into an electrophoretically homologous state from magnetospirillum gryphiswaldense msr-1 strain. the enzyme was found within the cytoplasm and associated with the cytoplasmic membrane. the molecular weight of the purified enzyme was calculated as 16.1 kda using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and was almost identical to that calibrated using agarose gel filtration chromatography. it was nadh-dependent and required flavin mononucleotide a ...200717534559
isolation of magnetotactic bacterium wm-1 from freshwater sediment and phylogenetic characterization.the magnetotactic bacterium was isolated from freshwater sediment from north lake of wuhan. the isolate, designated wm-1, was gram-negative, helical shaped, and studied by means of electron microscopy. the strain wm-1 was 0.2-0.4 microm in diameter and 3-4 microm in length. the dna g + c content was found to be 65.7 mol%. phylogenetic analysis of the 16s rdna gene (accession number dq899734 in genebank) revealed that this isolate was a member ofalphasubdivision of the proteobacteria. strain wm-1 ...200717429614
cobalt ferrite nanocrystals: out-performing magnetotactic bacteria.magnetotactic bacteria produce exquisitely ordered chains of uniform magnetite (fe(3)o(4)) nanocrystals, and the use of the bacterial mms6 protein allows for the shape-selective synthesis of fe(3)o(4) nanocrystals. cobalt ferrite (cofe(2)o(4)) nanoparticles, on the other hand, are not known to occur in living organisms. here we report on the use of the recombinant mms6 protein in a templated synthesis of cofe(2)o(4) nanocrystals in vitro. we have covalently attached the full-length mms6 protein ...200719206653
dynamics of magnetotactic bacteria in a rotating magnetic field.the dynamics of the motile magnetotactic bacterium magnetospirillum gryphiswaldense in a rotating magnetic field is investigated experimentally and analyzed by a theoretical model. these elongated bacteria are propelled by single flagella at each bacterial end and contain a magnetic filament formed by a linear assembly of approximately 40 ferromagnetic nanoparticles. the movements of the bacteria in suspension are analyzed by consideration of the orientation of their magnetic dipoles in the fiel ...200717526564
evolutionary diversity of ketoacyl synthases in cellulolytic myxobacterium sorangium.the diversity of type i polyketide synthases (pkss) in cellulolytic myxobacterium sorangium was explored by assaying the ketoacyl synthases (kss) in 10 sorangium strains with two degenerate primer sets and 64 different ks fragments were obtained. for their deduced amino acid sequences, eight were identical to three known kss from sorangium and magnetospirillum, while the others showed 54-83% identities to the modular ks domains reported from various microorganisms. parts of the sorangium kss tig ...200716899349
the acidic repetitive domain of the magnetospirillum gryphiswaldense mamj protein displays hypervariability but is not required for magnetosome chain assembly.magnetotactic bacteria navigate along the earth's magnetic field using chains of magnetosomes, which are intracellular organelles comprising membrane-enclosed magnetite crystals. the assembly of highly ordered magnetosome chains is under genetic control and involves several specific proteins. based on genetic and cryo-electron tomography studies, a model was recently proposed in which the acidic mamj magnetosome protein attaches magnetosome vesicles to the actin-like cytoskeletal filament formed ...200717601786
bacterial magnetic particles (bmps)-pei as a novel and efficient non-viral gene delivery system.non-viral methods of gene delivery, especially using polyethylenimine (pei), have been widely used in gene therapy or dna vaccination. however, the pei system has its own drawbacks, which limits its applications.200717605136
controlled formation of magnetite crystal by partial oxidation of ferrous hydroxide in the presence of recombinant magnetotactic bacterial protein mms6.mms6 is a small acidic protein that is tightly associated with bacterial magnetite in magnetospirillum magneticum amb-1. this protein has previously shown iron binding activity, allowing it to generate uniform magnetic crystals by co-precipitation of ferrous and ferric ions. here, magnetite crystals were formed by the partial oxidation of ferrous hydroxide in the presence and absence of mms6. the crystals synthesised were systematically characterised according to their sizes and morphologies usi ...200717720242
construction and preliminary analysis of a metagenomic library from a deep-sea sediment of east pacific nodule province.the pacific nodule province is a unique ocean area containing an abundance of polymetallic nodules. to explore more genetic information and discover potentially industrial useful genes of the microbial community from this particular area, a cosmid library with an average insert of about 35 kb was constructed from the deep-sea sediment. the bacteria in the cosmid library were composed mainly of proteobacteria including alphaproteobacteria, gammaproteobacteria and deltaproteobacteria. the end sequ ...200717850328
in vitro and in vivo antitumor effects of doxorubicin loaded with bacterial magnetosomes (dbms) on h22 cells: the magnetic bio-nanoparticles as drug carriers.hepatocellular carcinoma (hcc) is the most common form of cancer although effective therapeutic strategy especially targeted therapy is lacking. we recently employed bacterial magnetosomes (bms) as the magnetic-targeted drug carrier and found an antitumor effect of doxorubicin (dox)-loaded bms (dbms) in emt-6 and hl60 cell lines. the aim of this study was to evaluate the in vitro and in vivo anti-neoplastic effects of dbms on hepatic cancer. dbms, dox and bms displayed tumor suppression rates of ...200717920762
magnetic resonance imaging of fe3o4 nanoparticles embedded in living magnetotactic bacteria for potential use as carriers for in vivo applications.mc-1 magnetotactic bacteria (mtb) are studied for their potential use as bio-carriers for drug delivery. the exploitation of the flagella combined with nanoparticles magnetite or magnetosomes chain embedded in each bacterium and used to change the swimming direction of each mtb through magnetotaxis provide both propulsion and steering in small diameters blood vessels. but for guiding these mtb towards a target, being capable to image these living bacteria in vivo using an existing medical imagin ...200718002242
preliminary investigation of bio-carriers using magnetotactic bacteria.this paper proposes a novel micro-carrier based on magnetotactic bacteria (mtb). to confirm the feasibility of such carriers, the thrust force of the bacteria is evaluated. by measuring the swimming speed of mc-1 bacteria in an unbounded medium, a thrust of 4 pn generated by a single mc-1 bacterium is found. the effects on the mtb's swimming speed under the control of micro-electromagnets and influenced by the wall effects when each mtb is attached to a microbead are investigated.200617947027
origin of magnetosome membrane: proteomic analysis of magnetosome membrane and comparison with cytoplasmic membrane.prokaryotes are known to have evolved one or more unique organelles. although several hypotheses have been proposed concerning the biogenesis of these intracellular components, the majority of these proposals remains unclear. magnetotactic bacteria synthesize intracellular magnetosomes that are enclosed by lipid bilayer membranes. from the identification and characterization of several surface and transmembrane magnetosome proteins, we have postulated that magnetosomes are derived from the cytop ...200616955514
transcriptional organization and regulation of magnetosome operons in magnetospirillum gryphiswaldense.genes involved in magnetite biomineralization are clustered within the genomic magnetosome island of magnetospirillum gryphiswaldense. their transcriptional organization and regulation were studied by several approaches. cotranscription of genes within the mamab, mamdc, and mms clusters was demonstrated by reverse transcription-pcr (rt-pcr) of intergenic regions, indicating the presence of long polycistronic transcripts extending over more than 16 kb. the transcription start points of the mamab, ...200616957191
an acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria.magnetotactic bacteria are widespread aquatic microorganisms that use unique intracellular organelles to navigate along the earth's magnetic field. these organelles, called magnetosomes, consist of membrane-enclosed magnetite crystals that are thought to help to direct bacterial swimming towards growth-favouring microoxic zones at the bottom of natural waters. questions in the study of magnetosome formation include understanding the factors governing the size and redox-controlled synthesis of th ...200616299495
magnetosomes are cell membrane invaginations organized by the actin-like protein mamk.magnetosomes are membranous bacterial organelles sharing many features of eukaryotic organelles. using electron cryotomography, we found that magnetosomes are invaginations of the cell membrane flanked by a network of cytoskeletal filaments. the filaments appeared to be composed of mamk, a homolog of the bacterial actin-like protein mreb, which formed filaments in vivo. in a mamk deletion strain, the magnetosome-associated cytoskeleton was absent and individual magnetosomes were no longer organi ...200616373532
efficient and stable display of functional proteins on bacterial magnetic particles using mms13 as a novel anchor molecule.magnetic particles are increasingly used for various biomedical applications because they are easy to handle and separate from biological samples. in this work, a novel anchor molecule was used for targeted protein display onto magnetic nanoparticles. the magnetic bacterium magnetospirillum magneticum amb-1 synthesizes intracellular bacterial magnetic particles (bmps) covered with a lipid bilayer membrane. in our recent research, an integral bmp membrane protein, mms13, was isolated and used as ...200616391079
dynamic analysis of a genomic island in magnetospirillum sp. strain amb-1 reveals how magnetosome synthesis developed.the entire structure of a 98 kb genomic region that abounds in genes related to magnetosome synthesis was first described in the magnetospirillum sp. strain amb-1. the deletion of this 98 kb genomic region and the circular form after excision from the chromosome was detected by pcr amplification. this strongly suggests that the region has undergone a lateral gene transfer. the region has the characteristics of a genomic island: low gc content, location between two repetitive sequences, and the p ...200616423350
global gene expression analysis of iron-inducible genes in magnetospirillum magneticum amb-1.iron uptake systems were identified by global expression profiling of magnetospirillum magneticum amb-1. feo, tpd, and ftr, which encode ferrous iron transporters, were up-regulated under iron-rich conditions. the concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis.200616513757
capture and release of dna using aminosilane-modified bacterial magnetic particles for automated detection system of single nucleotide polymorphisms.bacterial magnetic particles (bmps) were modified with 3-[2-(2-aminoethylamino)-ethylamino]-propyltrimethoxysilane (aeea) to produce a dense amine surface. modification of bmps in a toluene solution resulted in an increased amine yield, and approximately 11.3 x 10(4) surface amines were detected on a single particle. the modified bmps were capable of efficient electrostatic capture of dna. the maximum amount of dna captured on 10 microg of aminosilane-modified bmps was 600 ng. a 10 mm phosphate ...200616523525
purification and characterization of benzoate-coa ligase from magnetospirillum sp. strain ts-6 capable of aerobic and anaerobic degradation of aromatic compounds.benzoate-coa ligase (ec 6.2.1.25), the initial enzyme of anaerobic benzoate degradation, was purified and characterized from magnetospirillum sp. strain ts-6 grown under both anaerobic and aerobic conditions. the enzyme purified from anaerobically grown cells was a homodimer with a relative molecular mass of 120 kda. the specific activity for benzoyl-coa synthesis was 13.4 micromol min(-1) mg(-1) protein. the enzyme purified from aerobically grown cells was concluded to be the same gene product ...200616553855
evaluation of gene expression analysis using rna-targeted partial genome arrays.highly parallel cdna targeting microarrays have been established over the last years as the quasi-standard for genome wide expression profiling in pro- and eukaryotes. protocols for the direct detection of rna or arna (amplified rna) are currently emerging. this allows to circumvent the bias introduced by enzymatic target molecule preparation. to systematically evaluate the extent of non-specific target binding on oligonucleotide microarrays designed for total rna expression profiling, a model s ...200616644169
signature proteins that are distinctive characteristics of actinobacteria and their subgroups.the actinobacteria constitute one of the main phyla of bacteria. presently, no morphological and very few molecular characteristics are known which can distinguish species of this highly diverse group. in this work, we have analyzed the genomes of four actinobacteria (viz. mycobacterium leprae tn, leifsonia xyli subsp. xyli str. ctcb07, bifidobacterium longum ncc2705 and thermobifida fusca yx) to search for proteins that are unique to actinobacteria. our analyses have identified 233 actinobacter ...200616670965
spatial localizations of mam22 and mam12 in the magnetosomes of magnetospirillum magnetotacticum.magnetospirillum magnetotacticum possesses intracellular magnetite particles with a chain-like structure, termed magnetosomes. the bacterium expresses 22-kda and 12-kda magnetosome-associated proteins, termed mam22 (mama) and mam12 (mamc), respectively. in this study, we investigated the structure of the purified magnetosomes with transmission electron microscopic techniques and found that the magnetosomes consisted of four compartments, i.e., magnetite crystal, magnetosomal membrane, interparti ...200616707673
quantifying the magnetic advantage in magnetotaxis.magnetotactic bacteria are characterized by the production of magnetosomes, nanoscale particles of lipid bilayer encapsulated magnetite, that act to orient the bacteria in magnetic fields. these magnetosomes allow magneto-aerotaxis, which is the motion of the bacteria along a magnetic field and toward preferred concentrations of oxygen. magneto-aerotaxis has been shown to direct the motion of these bacteria downward toward sediments and microaerobic environments favorable for growth. herein, we ...200616714352
catechol siderophore excretion by magnetotactic bacterium magnetospirillum magneticum amb-1.siderophore activity was detected in the culture supernatant of the magnetotactic bacterium magnetospirillum magneticum amb-1. here we report the first structural elucidation of a siderophore produced by a magnetotactic bacterium. the structure of the purified compound was 3,4-dihydroxybenzoic acid as determined by nuclear magnetic resonance (nmr) and electro-spray ionization mass spectroscopy (esi-ms).200616781476
how magnetotactic bacteria make magnetosomes queue up.magnetotactic bacteria contain chains of magnetosomes that comprise a permanent magnetic dipole in each cell. in two separate, recent papers, scheffel et al. and komeili et al. describe the roles of the proteins mamj and mamk in magnetosome chain formation. here, we describe the two studies and highlight questions that must be addressed in future investigations of how magnetotactic bacteria construct their magnetic compass needles.200616782341
bacterial cell biology: managing magnetosomes.sensing of magnetic fields by living organisms -- magnetosensing -- is best understood in magnetotactic bacteria. recently work has provided new insight into the biogenesis of bacterial magnetosomes, and links these organelles to a newly recognized prokaryotic cytoskeletal filament which organizes magnetosomes into a sensory structure capable of aligning cells with the geomagnetic field.200616713943
magnetic separation of cd14+ cells using antibody binding with protein a expressed on bacterial magnetic particles for generating dendritic cells.herein the potential of a highly efficient cell separation system using bacterial magnetic particles expressing protein a (protein a-bacmps) was demonstrated. protein a was expressed on bacmps using the transmembrane proteins mms13 and maga as anchor molecules. the evaluations of the numbers of bound antibody molecules and binding capabilities of the protein a-bacmps using mms13 indicated that the antibodies were efficiently introduced into protein a-bacmps using mms13 in comparison to maga. in ...200617045961
biogenesis of actin-like bacterial cytoskeletal filaments destined for positioning prokaryotic magnetic organelles.magnetosomes comprise a magnetic nanocrystal surrounded by a lipid bilayer membrane. these unique prokaryotic organelles align inside magnetotactic bacterial cells and serve as an intracellular compass allowing the bacteria to navigate along the geomagnetic field in aquatic environments. cryoelectron tomography of magnetospirillum strains has revealed that the magnetosome chain is surrounded by a network of filaments that may be composed of mamk given that the filaments are absent in the mamk mu ...200617085581
cloning and functional analysis of the sequences flanking mini-tn5 in the magnetosomes deleted mutant nm4 of magnetospirillum gryphiswaldense msr-1.a magnetosome deleted mutant nm4 of magnetospirillum gryphiswaldense msr-1 was generated by mini-tn5 transposon mutagenesis, and a 5045-bp fragment flanking mini-tn5 in nm4 was cloned by anchored pcr. sequencing analysis showed that this fragment involved six putative open reading frames (orfs); the mini-tn5 was inserted into orf4. functional complementary test indicated that the 5045-bp fragment was required for biosynthesis of magnetosomes in m. gryphiswaldense msr-1. the protein encoded by or ...200516483136
combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments.both magnetic collection and "race track" purification techniques were highly effective for selective enrichment of magnetotactic bacteria (mtb) from complex communities, as suggested by amplified ribosomal dna restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16s rrna genes. using these purification methods, the occurrence and diversity of mtb in microcosms from various marine and freshwater environments were assayed by using a combined microsco ...200515870364
evolution of different oligomeric glycyl-trna synthetases.there are two oligomeric types of glycyl-trna synthetases (glyrss) in genome, the alpha2beta2 tetramer and alpha2 dimer. here, we showed that the anticodon-binding domains (abds) of dimeric and tetrameric glyrss are non-homologous, although their catalytic central domains (ccds) are homologous. the dimeric glyrs_abd is fused to the c-terminal of ccd in alpha-subunit, but the tetrameric glyrs_abd is to the c-terminal in beta-subunit during evolution. generally, one species only contains one oligo ...200515733854
fabrication of optically enhanced zno nanorods and microrods using novel biocatalysts.we developed a straightforward method to produce hexagonal zno nanorods and microrods using a novel biocatalyst, magnetospirillum magnetotacticum. zno nanorods were synthesized homogeneously on growth substrates when the bacterial catalysts were deposited uniformly on substrates whereas zno microrods were formed when the catalysts were introduced to selective areas of growth substrates using microcontact printing. x-ray diffraction measurements reveal that these zno structures exhibit wurtzite s ...200516433431
complete genome sequence of the facultative anaerobic magnetotactic bacterium magnetospirillum sp. strain amb-1.magnetospirillum sp. strain amb-1 is a gram-negative alpha-proteobacterium that synthesizes nano-sized magnetites, referred to as magnetosomes, aligned intracellularly in a chain. the potential of this nano-sized material is growing and will be applicable to broad research areas. it has been expected that genome analysis would elucidate the mechanism of magnetosome formation by magnetic bacteria. here we describe the genome of magnetospirillum sp. amb-1 wild type, which consists of a single circ ...200516303747
the presumptive magnetosome protein mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in magnetospirillum gryphiswaldense.the mms16 protein has been previously found to be associated with isolated magnetosomes from two magnetospirillum strains. a function of this protein as a magnetosome-specific gtpase involved in the formation of intracellular magnetosome membrane vesicles was suggested. here we present a study of the mms16 protein from magnetospirillum gryphiswaldense to clarify its function. insertion-duplication mutagenesis of the mms16 gene did not affect the formation of magnetosome particles but resulted in ...200515774885
novel detection system for biomolecules using nano-sized bacterial magnetic particles and magnetic force microscopy.a system for streptavidin detection using biotin conjugated to nano-sized bacterial magnetic particles (bmps) has been developed. bmps, isolated from magnetic bacteria, were used as magnetic markers for magnetic force microscopy (mfm) imaging. the magnetic signal was obtained from a single particle using mfm without application of an external magnetic field. the number of biotin conjugated bmps (biotin-bmps) bound to streptavidin immobilized on the glass slides increased with streptavidin concen ...200516111780
anaerobic degradation of aromatic compounds by magnetospirillum strains: isolation and degradation genes.four magnetospirillum strains degrading toluene, phenol, benzoate, and other aromatic compounds under anaerobic conditions were isolated from denitrifying enrichment cultures. one of the isolates, toluene-degrading strain ts-6, contained genes that are homologous to those encoding benzylsuccinate synthase (bss) and benzoyl-coa reductase (bcr), two key enzymes of anaerobic toluene and benzoate degradation respectively in known denitrifying bacteria. transcription of the genes was confirmed. it wa ...200516116275
defluvicoccus vanus gen. nov., sp. nov., a novel gram-negative coccus/coccobacillus in the 'alphaproteobacteria' from activated sludge.a novel gram-negative coccus/coccobacillus, strain ben 114(t), growing in tetrads, clusters or aggregates, was isolated from activated sludge by micromanipulation. 16s rrna gene sequence analysis revealed that it belonged to the 'alphaproteobacteria', with no close relatives among cultured bacterial isolates. on the basis of phylogenetic data, this organism is considered to belong to a new genus, defluvicoccus, represented by the species defluvicoccus vanus sp. nov., a name chosen because of the ...200516166717
one channel: open and closed.structural information about the prokaryotic kirbac3.1 inward rectifier family k(+) channel from magnetospirillum magnetotacticum is reported. these results from two-dimensional electron cryomicroscopy (em) shed light on the gating mechanism of members of the kir channel family.200516216569
two different conformational states of the kirbac3.1 potassium channel revealed by electron crystallography.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 re ...200516216578
a hypervariable 130-kilobase genomic region of magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth.genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium magnetospirillum gryphiswaldense. we analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic "magnetosome island" (mai). in addition to all known magnetosome genes, the mai contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularl ...200516237001
development of efficient expression system for protein display on bacterial magnetic particles.bacterial magnetic particles (bmps) are utilized for various biomedical applications because they are easily manipulated by magnets, and functional proteins are easily displayed on bmps. to establish highly expressed protein display on bmps, strong promoters were identified using magnetospirillum magneticum amb-1 genome and proteome databases. initially, several proteins highly expressed in amb-1 were identified, and the upstream dna sequences of the open-reading frames were evaluated using a lu ...200516288989
magnetic cell separation using antibody binding with protein a expressed on bacterial magnetic particles.bacterial magnetic particles (bacmps) are efficient platforms of proteins for surface display systems. in this study, mononuclear cells from peripheral blood were separated using bacmps expressing protein a on the bacmp membrane surface (protein a-bacmps), which were complexed with the fc fragment of anti-mouse igg antibody. the procedure of positive selection involves incubation of mononuclear cells and mouse monoclonal antibodies against different cell surface antigens (cd8, cd14, cd19, cd20) ...200415516111
siderophore production of a periplasmic transport binding protein kinase gene defective mutant of magnetospirillum magneticum amb-1.a non-magnetic mutant, nma61, of the magnetic bacterium magnetospirillum magneticum amb-1 was generated by transposon mutagenesis to identify genes involved in magnetosome synthesis. the genomic region of nma61 interrupted by a mini-tn5 transposon was analyzed. the transposon was inserted in an open reading frame (orf) coding for a periplasmic transport binding protein kinase gene homologue. three adjacent orfs and a promoter were identified upstream, indicating that the sequences comprised an o ...200415381078
molecular analysis of a subcellular compartment: the magnetosome membrane in magnetospirillum gryphiswaldense.the ability of magnetotactic bacteria (mtb) to orient and migrate along magnetic field lines is based on magnetosomes, which are membrane-enclosed intracellular crystals of a magnetic iron mineral. magnetosome biomineralization is achieved by a process involving control over the accumulation of iron and deposition of the magnetic particle, which has a specific morphology, within a vesicle provided by the magnetosome membrane. in magnetospirillum gryphiswaldense, the magnetosome membrane has a di ...200414668979
biochemical and proteomic analysis of the magnetosome membrane in magnetospirillum gryphiswaldense.we analyzed the biochemical composition of the magnetosome membrane (mm) in magnetospirillum gryphiswaldense. isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. the binding characteristics of mm-associated proteins were studied by selective solubilization and limited proteolysis. the mm-associated proteins ...200414766587
magnetosome vesicles are present before magnetite formation, and mama is required for their activation.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 dynami ...200415004275
rescue of protein splicing activity from a magnetospirillum magnetotacticum intein-like element.the self-catalytic protein splicing mechanism is mediated by the intein plus the first amino acid following the intein c-terminus (termed the +1 residue). although polymorphisms of conserved residues elsewhere in inteins have been widely reported, no splicing-competent intein has been observed without a ser, thr or cys in this functionally essential +1 position. this residue is the nucleophile in two steps of the protein splicing pathway: ligation of the extein fragments during transesterificati ...200415046582
unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin).efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ...200415060050
magnetosome formation in prokaryotes. 200415083157
assembly of g protein-coupled receptors onto nanosized bacterial magnetic particles using mms16 as an anchor molecule.g protein-coupled receptors (gpcrs) play a central role in a wide range of biological processes and are prime targets for drug discovery. gpcrs have large hydrophobic domains, and therefore purification of gpcrs from cells is frequently time-consuming and typically results in loss of native conformation. in this work, gpcrs have been successfully assembled into the lipid membrane of nanosized bacterial magnetic particles (bmps) produced by the magnetic bacterium magnetospirillum magneticum amb-1 ...200415128546
rapid and sensitive detection of 17beta-estradiol in environmental water using automated immunoassay system with bacterial magnetic particles.a fully automated immunoassay of 17beta-estradiol (e2) was performed using anti-e2 monoclonal antibody immobilized on bacterial magnetic particles (antie2-bmps) and alkaline phosphatase-conjugated e2 (alp-e2). e2 concentration in environmental water samples was evaluated by decrease in luminescence based on competitive reaction. a linear correlation between the luminescence intensity and e2 concentration was obtained between 0.5 and 5 ppb. the minimum detectable concentration of e2 was 20 ppt. a ...200415129724
inactivation of the flagellin gene flaa in magnetospirillum gryphiswaldense results in nonmagnetotactic mutants lacking flagellar filaments.magnetotactic bacteria synthesize magnetosomes, which cause them to orient and migrate along magnetic field lines. the analysis of magnetotaxis and magnetosome biomineralization at the molecular level has been hindered by the unavailability of genetic methods, namely the lack of a means to introduce directed gene-specific mutations. here we report a method for knockout mutagenesis by homologous recombination in magnetospirillum gryphiswaldense. multiple flagellin genes, which are unlinked in the ...200415184166
bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?invasive bacteria are known to have captured and adapted eukaryotic host genes. they also readily acquire colonizing genes from other bacteria by horizontal gene transfer. closely related species such as helicobacter pylori and helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. the protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for suc ...200415186489
genetic clues on the evolution of anaerobic catabolism of aromatic compounds. 200415256545
[an oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups].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 pos ...200415315232
single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (aldh2) gene using bacterial magnetic particles based on dissociation curve analysis.single nucleotide polymorphism (snp) detection for aldehyde dehydrogenase 2 (aldh2) gene based on dna thermal dissociation curve analysis was successfully demonstrated using an automated system with bacterial magnetic particles (bmps) by developing a new method for avoiding light scattering caused by nanometer-size particles when using commercially available fluorescent dyes such as fitc, cy3, and cy5 as labeling chromophores. biotin-labeled pcr products in aldh2, two allele-specific probes (cy3 ...200415329927
chemolithoautotrophy in the marine, magnetotactic bacterial strains mv-1 and mv-2.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 ...200415338111
biotechnological applications of bioluminescence and chemiluminescence.recent progress in molecular biology has made available several biotechnological tools that take advantage of the high detectability and rapidity of bioluminescence and chemiluminescence spectroscopy. these developments provide inroads to in vitro and in vivo continuous monitoring of biological processes (e.g. gene expression, protein-protein interaction and disease progression), with clinical, diagnostic and drug discovery applications. furthermore, combining luminescent enzymes or photoprotein ...200415158059
new insights into the evolutionary history of type 1 rhodopsins.type 1 (archaeal) rhodopsins and related rhodopsin-like proteins had been described in a few halophile archaea, gamma-proteobacteria, a single cyanobacteria, some fungi, and a green alga. in exhaustive database searches, we detected rhodopsin-related sequences derived not only from additional fungal species but also from organisms belonging to three groups in which opsins had hitherto not been described: the alpha-proteobacterium magnetospirillum magnetotacticum, the cryptomonad alga guillardia ...200415045490
membrane vesicles in magnetotactic bacteria.magnetotactic bacteria are microorganisms that respond to magnetic fields. we have studied the surface ultrastructure of magnetospirillum magnetotacticum and uncultured magnetotactic bacteria from a marine environment using transmission electron microscopy and freeze-etching. numerous membrane vesicles were observed on the surface of magnetospirillum magnetotacticum bacteria. all uncultured magnetotactic bacteria presented membrane vesicles on their surface in addition to an extensive capsular m ...200314717452
single nucleotide mismatch analysis using oligonucleotide probes synthesized on bacterial magnetic particle.an approach to analyze mismatches using short and specific oligonucleotide probes directly synthesized on bacterial magnetic particles (bmps) by phosphoramidite methods was exploited. approximately 126 molecules of 4-mer oligonucleotides/particle were synthesized on bmps with high reaction efficiencies. hybridization between fitc-labeled oligonucleotides and chemically synthesized oligonucleotides on bmps was performed. perfect matched and mismatched hybridizations were successfully discriminate ...200312919813
exposure of magnetic bacteria to simulated mobile phone-type rf radiation has no impact on mortality.the interaction of mobile phone rf emissions with biogenic magnetite in the human brain has been proposed as a potential mechanism for mobile phone bioeffects. this is of particular interest in light of the discovery of magnetite in human brain tissue. previous experiments using magnetite-containing bacteria exposed directly to emissions from a mobile phone have indicated that these emissions might be causing greater levels of cell death in these bacterial populations when compared to sham expos ...200315376948
development of a genetic system for magnetospirillum gryphiswaldense.genetic analysis of bacterial magnetosome biomineralization has been hindered by the lack of an appropriate methodology for cultivation and genetic manipulation of most magnetotactic bacteria. in this report, a genetic system for magnetospirillum gryphiswaldense is described. the system includes a plating technique that allows the screening of magnetic vs non-magnetic colonies, and a protocol for the transfer of foreign dna by electroporation and high-frequency conjugation. various broad-host-ra ...200312560986
siderophore production by the magnetic bacterium magnetospirillum magneticum amb-1.siderophore production by the magnetic bacterium magnetospirillum magneticum amb-1 is elicited by sufficient iron rather than by iron starvation. in order to clarify this unusual pattern, siderophore production was monitored in parallel to iron assimilation using the chrome azurol sulfonate assay and the ferrozine method respectively. iron concentration lowered approximately five times less than its initial concentration only within 4 h post-inoculation, rendering the medium iron deficient. a co ...200312586419
a comprehensive view on proteasomal sequences: implications for the evolution of the proteasome.proteasomes are large multimeric self-compartmentizing proteases, which play a crucial role in the clearance of misfolded proteins, breakdown of regulatory proteins, processing of proteins by specific partial proteolysis, cell cycle control as well as preparation of peptides for immune presentation. two main types can be distinguished by their different tertiary structure: the 20s proteasome and the proteasome-like heat shock protein encoded by heat shock locus v, hslv. usually, each biological ...200312595256
dna extraction using bacterial magnetic particles modified with hyperbranched polyamidoamine dendrimer.a cascading hyperbranched polyamidoamine dendrimer was synthesized on the surface of bacterial magnetite from magnetospirillum magneticum amb-1 to allow enhanced extraction of dna from fluid suspensions. characterization of the synthesis revealed linear doubling of the surface amine charge from generations one through five starting with an amino silane initiator. furthermore, transmission electron microscopy revealed clear dispersion of the single domain magnetite in aqueous solution. the dendri ...200312615391
characterization of aldehyde ferredoxin oxidoreductase gene defective mutant in magnetospirillum magneticum amb-1.a non-magnetic mutant of magnetospirillum magneticum amb-1, designated as nma21, was generated by mini-tn5 transposon mutagenesis to identify genes involved in bacterial magnetic particle (bmp) synthesis. alignment of the dna sequences flanking the transposon allowed the isolation of an open reading frame (orf2) within an operon consisting of five genes. the amino acid sequence of orf2 showed homology with tungsten-containing aldehyde ferredoxin oxidoreductase (aor) from pyrococcus furiosus (48% ...200312646191
single nucleotide polymorphism genotyping of aldehyde dehydrogenase 2 gene using a single bacterial magnetic particle.a single nucleotide polymorphism (snp) genotyping for aldehyde dehydrogenase 2 gene (aldh2) has been developed by using a nano-sized magnetic particle, which was synthesized intracellularly by magnetic bacteria. streptavidin-immobilized on bacterial magnetic particles (bmps) were prepared using biotin labeled cross-linkers reacting with the amine group on bmps. aldh2 fragments from genomic dna were amplified using a tritc labeled primer and biotin labeled primer pair, and conjugated onto bmp sur ...200312706576
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