Publications

cloning, purification, crystallization and preliminary crystallographic studies of bradyrhizobium fucosyltransferase nodz.	the alpha-1,6-fucosyltransferase nodz from bradyrhizobium sp. wm9 (lupinus), composed of 325 amino acids with a molecular weight of 37 kda, has been cloned, expressed and purified. protein crystals suitable for x-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. the crystals are hexagonal and belong to space group p6(1)22 or p6(5)22, with unit-cell parameters a = 125.5, c = 95.6 a, and contain 56.8% solvent and a single ...	2004	14747720
microbial characterization during the early habitation of the international space station.	an evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the international space station (iss) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. using 16s genetic sequencing and rep-pcr, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. of the bacterial strains that were isolated and fingerprinted, 19 displayed similar ...	2004	14749908
a dominant-negative fur mutation in bradyrhizobium japonicum.	in many bacteria, the ferric uptake regulator (fur) protein plays a central role in the regulation of iron uptake genes. because iron figures prominently in the agriculturally important symbiosis between soybean and its nitrogen-fixing endosymbiont bradyrhizobium japonicum, we wanted to assess the role of fur in the interaction. we identified a fur mutant by selecting for manganese resistance. manganese interacts with the fur protein and represses iron uptake genes. in the presence of high level ...	2004	14973020
use of the multipurpose transposon tn kpk2 for the mutational analysis of chromosomal regions upstream and downstream of the sipf gene in bradyrhizobium japonicum.	the dna regions upstream and downstream of the bradyrhizobium japonicum gene sipf were cloned by in vivo techniques and subsequently sequenced. in order to study the function of the predicted genes, a new transposon for in vitro mutagenesis, tn kpk2, was constructed. this mutagenesis system has a number of advantages over other transposons. tn kpk2 itself has no transposase gene, making transposition events stable. extremely short inverted repeats minimize the length of the transposable element ...	2004	14986109
insights into signal transduction involving pas domain oxygen-sensing heme proteins from the x-ray crystal structure of escherichia coli dos heme domain (ec dosh).	the x-ray crystal structure of the escherichia coli (ec) direct oxygen sensor heme domain (ec dosh) has been solved to 1.8 a using fe multiple-wavelength anomalous dispersion (mad), and the positions of met95 have been confirmed by selenomethionine ((se)met) mad. ec dosh is the sensing part of a larger two-domain sensing/signaling protein, in which the signaling domain has phosphodiesterase activity. the asymmetric unit of the crystal lattice contains a dimer comprised of two differently ligated ...	2004	15005609
polymerase chain reaction denaturing gradient gel electrophoresis analysis of the n2-fixing bacterial diversity in soil under acacia tortilis ssp. raddiana and balanites aegyptiaca in the dryland part of senegal.	denaturing gradient gel electrophoresis (dgge) of amplified nifh gene fragments was used to study the diazotrophic community of soil samples under acacia tortilis ssp. raddiana (legume tree) and balanites aegyptiaca (non-legume tree), two dominant plant species growing naturally in the dryland part of senegal. samples were taken along transects from the stem up to 10 m distance from it, at depths of 0-0.25 m and 0.25-0.50 m. sampling was done in the dry season (25 june 1999) and in the rainy sea ...	2004	15008817
phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the bradyrhizobium genus.	symbiotic nitrogen fixing bacteria-known as rhizobia-harbour a set of nodulation (nod) genes that control the synthesis of modified lipo-chitooligosaccharides, called nod factors that are required for legume nodulation. the noda gene, which is essential for symbiosis, is responsible for the attachment of the fatty acid group to the oligosaccharide backbone. the nodz, noll, and noei genes are involved in specific modifications of nod factors common to bradyrhizobia, i.e., the transfer of a fucosy ...	2004	15012950
soybean (glycine max. l.) and bacteroid glyoxylate cycle activities during nodular senescence.	soybean (glycine max. l.) nodular senescence results in the dismantling of the peribacteroid membrane (pbm) and in an increase of soybean isocitrate lyase (icl; ec 4.1.3.1) and malate synthase (ms; ec 4.1.3.2) mrna and protein levels. this suggests that in senescing soybean nodular cells, the specific glyoxylate cycle enzyme activities might be induced to reallocate carbon obtained from the pbm degradation. in order to evaluate as well the carbon metabolism of the nitrogen-fixing bradyrhizobium ...	2004	15022832
molecular characterization of nosrzdfylx genes coding for denitrifying nitrous oxide reductase of bradyrhizobium japonicum.	the nosrzdfylx gene cluster for the respiratory nitrous oxide reductase from bradyrhizobium japonicum strain usda110 has been cloned and sequenced. seven protein coding regions corresponding to nosr, nosz, the structural gene, nosd, nosf, nosy, nosl, and nosx were detected. the deduced amino acid sequence exhibited a high degree of similarity to other nitrous oxide reductases from various sources. the nosz protein included a signal peptide for protein export. mutant strains carrying either a nos ...	2004	15028871
phenotypic and genotypic analysis of rhizobia isolated from pasture legumes native of sardinia and asinara island.	thirty-five rhizobial strains were isolated from nodules of lotus edulis, l. ornithopodioides, l. cytisoides, hedysarum coronarium, ornithopus compressus and scorpiurus muricatus growing in sardinia and asinara island. basic characteristics applied to identification of rhizobia such as symbiotic properties, antibiotic- and salt-resistance, temperate-sensitivities, utilization of different sources of carbon and nitrogen were studied. the results from the 74 metabolic tests were used for cluster a ...	2004	15031655
expression of nir, nor and nos denitrification genes from bradyrhizobium japonicum in soybean root nodules.	expression of bradyrhizobium japonicum wild-type strain usda110 nirk, norc and nosz denitrification genes in soybean root nodules was studied by in situ histochemical detection of beta-galactosidase activity. similarly, p(nirk)-lacz, p(norc)-lacz, and p(nosz)-lacz fusions were also expressed in bacteroids isolated from root nodules. levels of beta-galactosidase activity were similar in both bacteroids and nodule sections from plants that were solely n(2)-dependent or grown in the presence of 4 m ...	2004	15032854
a novel symbiotic nitrogen-fixing member of the ochrobactrum clade isolated from root nodules of acacia mangium.	ten strains of root nodule bacteria were isolated from the nodules of acacia mangium grown in the philippines and thailand. partial sequences (approx. 300 bp) of the 16s rrna gene of each isolate were analyzed. the nucleotide sequences of strain dasa 35030 indicated high homology (>99%) with members of the genus ochrobactrum in brucellaceae, although the sequences of other isolates were homologous to those of two distinct genera bradyrhizobium and rhizobium. the strain dasa 35030 was strongly su ...	2004	15057707
root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...	2004	15066803
community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach.	the microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (mf) and reverse osmosis (ro) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16s rdna clone library and fluorescence in situ hybridization techniques. all methods showed that the alpha-proteobacteria was the largest microbial fraction in the samples, followed by the gamma-proteobacteria. this suggested that members of the ...	2004	12682791
intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes.	the functional and phylogenetic biodiversity of bacterial communities in a benzene, toluene, ethylbenzene and xylene (btex)-polluted groundwater was analysed. to evaluate the feasibility of using an air sparging treatment to enhance bacterial degradative capabilities, the presence of degrading microorganisms was monitored. the amplification of gene fragments corresponding to toluene monooxygenase (tmo), catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and toluene dioxygenase genes in dna extra ...	2004	14624316
bradyrhizobium elkanii rtxc gene is required for expression of symbiotic phenotypes in the final step of rhizobitoxine biosynthesis.	we disrupted the rtxc gene on the chromosome of bradyrhizobium elkanii usda94 by insertion of a nonpolar aph cartridge. the rtxc mutant, designated deltartxc, produced serinol and dihydrorhizobitoxine but no rhizobitoxine, both in culture and in planta. the introduction of cosmids harboring the rtxc gene into the deltartxc mutant complemented rhizobitoxine production, suggesting that rtxc is involved in the final step of rhizobitoxine biosynthesis in b. elkanii usda94. glycine max cv. lee inocul ...	2004	14711685
analysis of genetic relationship of sarothamnus scoparius microsymbionts and bradyrhizobium sp. by hybridization in microdilution wells.	dna-dna hybridization in microdilution wells was successfully used to determine the overall genomic similarity among sarothamnus scoparius microsymbionts isolated from poland and japan and representatives of bradyrhizobium species including bradyrhizobium sp. (lupinus) usda3045. geographically different s. scoparius rhizobia diverged into two genomospecies at the dna-dna similarity level of approximately 49%. polish isolates exhibited high dna similarity levels to the dna of bradyrhizobium japon ...	2004	16233609
isolation of novel bacteria and actinomycetes using soil-extract agar medium.	novel bacteria were discovered using an isolation technique consisting of (i) selection of microorganisms that grew on soil-extract agar medium, but not on conventional media, and (ii) detection of small microbial colonies with a microscope. three bacterial strains thus isolated were provisionally designated shinshu-th1, -th2, -th 3, and five actinomycete strains, shinshu-ms-01, -02, -03, -04, -05, respectively. sequence analysis of their 16s rdna showed that th1 had 95--96% homology with three ...	2005	16233821
[effect of plant growth regulators on physiological activity of bradyrhizobium japonicum ].	influence of plant growth regulators ivin, emistim c, eney and agrostimulin on the biomass production and exopolymers synthesis of soybean nodule bacteria, which have contrasting symbiotic properties, and glutamine synthetase activity of their cell-free extracts were studied. it was shown that the processes of the biomass and exopolymers accumulation had an opposite direction. of all preparations only ivin and agrostimulin intensificol growth activity of the microorganisms under study. the level ...	2005	16250234
global protein expression pattern of bradyrhizobium japonicum bacteroids: a prelude to functional proteomics.	as a prelude to using functional proteomics towards understanding the process of symbiotic nitrogen fixation between the legume soybean and the soil bacteria bradyrhizobium japonicum, we examined the total protein expression pattern of the nodule bacteria, often referred to as bacteroids. a partial proteome map was constructed by separating the total bacteroid proteins using high-resolution 2-de. of the several hundred protein spots analyzed using pmf, 180 spots were tentatively identified by se ...	2005	16254929
nitrogen-fixing nodules from rose wood legume trees (dalbergia spp.) endemic to madagascar host seven different genera belonging to alpha- and beta-proteobacteria.	although legume biodiversity is concentrated in tropical regions, the majority of studies on legume nodulating bacteria (lnb) are focused on cultivated leguminous plants from temperate regions. however, recent works on tropical regions tend to indicate that the actual diversity of lnb is largely underestimated. in this study, we report the isolation and characterization of 68 nitrogen-fixing root nodule bacteria collected from eight endemic tree species of dalbergia in madagascar. the isolates w ...	2005	16262864
european origin of bradyrhizobium populations infecting lupins and serradella in soils of western australia and south africa.	we applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin bradyrhizobium strains that persist in soils of western australia and south africa. the selected strains belonged to different randomly amplified polymorphic dna (rapd)-pcr clusters that were distinct from rapd clusters of applied inoculant strains. phylogenetic analyses were performed with nodulation genes (noda, nodz, noll, noei), housekeeping genes (dnak, reca, glnii, atpd), and 16s-23s rrna intergen ...	2005	16269740
novel dna sequences from natural strains of the nitrogen-fixing symbiotic bacterium sinorhizobium meliloti.	variation in genome size and content is common among bacterial strains. identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. in this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain rm1021 of the nitrogen-fixing bacterium sinorhizobium meliloti. using strain rm1021 as the driver and the type strain ...	2005	16269751
three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water.	soil contaminated with polychlorinated biphenyls (pcb) was used as an inoculum to grow a complex biofilm community on pcb oil (aroclor 1242) on a substratum (permanox). the biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (sscp), amplicons of the 16s rrna genes, and chemical analyses of the pcb congeners. sscp analysis of the young biofilm revealed a rather diverse microbial community with species of ...	2005	16269772
symbiotic hydrogenase activity in bradyrhizobium sp. (vigna) increases nitrogen content in vigna unguiculata plants.	bradyrhizobium sp. (lupinus) and bradyrhizobium sp. (vigna) mutants in which hydrogenase (hup) activity was affected were constructed and analyzed. vigna unguiculata plants inoculated with the bradyrhizobium sp. (vigna) hup mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield.	2005	16269797
nod factor induces soybean resistance to powdery mildew.	plants possess highly sensitive perception systems by which microbial signal molecules are recognized. in the bradyrhizobium-soybean (glycine max (l.) merr.) symbiosis, recognition is initiated through exchange of signal molecules, generally flavonoids from soybean and lipo-chitooligosaccharides (nod factors) from the microsymbiont. application of the nod factor nod bj-v (c18:1, mefuc) induced soybean resistance to powdery mildew caused by microsphaera diffusa. addition of nod factor (concentrat ...	2005	16310369
genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern ethiopia.	the genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern ethiopia was investigated by using pcr-rflp of the ribosomal operon [16s rrna gene, 23s rrna gene and the internal transcribed spacer (its) region between the 16s rrna and 23s rrna genes] and 16s rrna gene partial sequence (800 and 1350 bp) analyses. all of the isolates and the 28 reference strains could ...	2005	16014464
[study of chemotaxis of nodule bacteria of lupin to organic substances].	ability of different strains (359a, 400, 176, 365a) of nodule bacteria of lupin bradyrhizobium sp. (lupinus), which differ in symbiotic properties (competitiveness and nitrogen-fixing activity), to chemotaxis with respect to the organic substances revealed in root exudates of lupin (aminoacids, sugars, organic acids and their salts) has been investigated. it is shown, that alongside with the substances to which rhizobia of lupin, irrespective of their symbiotic properties, show the chemotaxic re ...	2005	16018202
iron-dependent cytochrome c1 expression is mediated by the status of heme in bradyrhizobium japonicum.	the heme prosthetic group of heme proteins contains iron, which can be a limiting nutrient. here, we show that cytochrome c1 protein from bradyrhizobium japonicum was strongly affected by the iron status, with low expression in cells grown under iron limitation. this control was not affected in mutants encoding the iron regulator irr or fur. furthermore, cytochrome c1 mrna was not influenced by the iron status, suggesting control at a posttranscriptional step. cytochrome c1 protein levels were v ...	2005	16030200
characterization of conformational changes coupled to ligand photodissociation from the heme binding domain of fixl.	using transient absorption spectroscopy and photoacoustic calorimetry (pac), we have characterized carbon monoxide photodissociation and rebinding to two forms of the heme domain of bradyrhizobium japonicum fixl. transient absorption results for the complete heme domain (fixl residues 140-270) and a truncated heme domain (missing 11 residues on the n-teminal end and 14 amino acid residues on the c-terminal end of the full length heme domain) show similar rates for ligand rebinding to the five-co ...	2005	16042379
comparative analyses of codon and amino acid usage in symbiotic island and core genome in nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum.	genes involved in the symbiotic interactions between the nitrogen-fixing endosymbiont bradyrhizobium japonicum, and its leguminous host are mostly clustered in a symbiotic island (si), acquired by the bacterium through a process of horizontal transfer. a comparative analysis of the codon and amino acid usage in core and si genes/proteins of b. japonicum has been carried out in the present study. the mutational bias, translational selection, and gene length are found to be the major sources of va ...	2005	16060695
two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, encode haloalkane dehalogenases with novel structures and substrate specificities.	haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, have open reading frames (orfs), mlr5434 and blr1087, respectively, that encode putative haloalkane dehalogenase homologues. the crude extracts of escherichia coli strains expressing mlr5434 and blr1087 showed the ability to dehalogenate 18 halogenated compounds, indicating that these orfs indeed encode haloal ...	2005	16085827
diverse rhizobia associated with woody legumes wisteria sinensis, cercis racemosa and amorpha fruticosa grown in the temperate zone of china.	fifty-nine bacterial isolates from root nodules of the woody legumes wisteria sinensis, cercis racemosa and amorpha fruticosa grown in the central and eastern regions of china were characterized with phenotypic analysis, pcr-based 16s and 23s rrna gene rflp, box pcr and 16s rrna gene sequencing. seven main phena were defined in numerical taxonomy, which corresponded to distinct groups within the genera agrobacterium, bradyrhizobium, mesorhizobium and rhizobium in 16s and 23s rrna gene pcr-rflp. ...	2005	16094873
compared tolerance to osmotic stress in various microorganisms: towards a survival prediction test.	the osmotic tolerance of microbial cells of different microorganisms was investigated as a function of glycerol concentration and temperatures. cells displayed specific sensitivity to dehydration in glycerol solutions. the viability of gram-negative strains (escherichia coli, bradyrhizobium japonicum), gram-positive strains (lactobacillus plantarum, l. bulgaricus), and yeasts (saccharomyces cerevisiae, candida utilis) decreased with increasing osmotic pressure. for each strain, a characteristic ...	2005	16116658
characterization of phages virulent for sarothamnus scoparius bradyrhizobia.	four virulent phages--phidl, phitl, phicyt21, and phios6, infective on sarothamnus scoparius rhizobia--were isolated from the soil and characterized for morphology, host range, rate of adsorption to bacterial cells, and genome size. new phages were separated into two morphological families: siphoviridae with long, noncontractile tails (phidl, phitl) and myoviridae with long, contractile tails (phicyt21, phios6). they were also classified into two groups by a host specificity. one of them include ...	2005	16132456
detection of homoserine lactone-like quorum sensing molecules in bradyrhizobium strains.	one hundred and forty-two bradyrhizobium strains were screened for their ability to produce n-acyl homoserine lactone-like molecules (ahls) by using an agrobacterium tumefaciens biosensor strain containing a trai-lacz fusion. approximately 22% (31 of 142) of the tested strains produced ahls that induced moderate to elevated beta-galactosidase activity levels in the biosensor strain. bradyrhizobium japonicum and bradyrhizobium elkanii strains were both shown to produce ahls. age of culture, and m ...	2005	16132457
an iron uptake operon required for proper nodule development in the bradyrhizobium japonicum-soybean symbiosis.	rhizobia live in the soil or enter into a nitrogen-fixing symbiosis with a suitable host plant. each environment presents different challenges with respect to iron acquisition. the soybean symbiont bradyrhizobium japonicum 61a152 can utilize a variety of siderophores (fe[iii]-specific ligands). purification of iron-regulated outer membrane proteins had previously allowed the cloning of a gene, fega, from b. japonicum 61a152, whose predicted protein shares significant amino acid similarity with k ...	2005	16167765
nh4+ currents across the peribacteroid membrane of soybean. macroscopic and microscopic properties, inhibition by mg2+, and temperature dependence indicate a subpicosiemens channel finely regulated by divalent cations.	the control of ammonium (nh(4)(+)) transport is critical in preventing futile cycles of nh(4)(+)/ammonia transport. an unusual nonselective cation channel with subpicosiemens single-channel conductance permeable to nh(4)(+) had previously been identified in the peribacteroid membrane (pbm) of symbiosomes from soybean (glycine max) nodules. here, we investigate the proposed channel mechanism and its control by luminal magnesium. currents carried by nh(4)(+) were measured in inside-out pbm patches ...	2005	16183839
dimeric brucella abortus irr protein controls its own expression and binds haem.	brucella abortus needs to synthesize haem in order to replicate intracellularly and to produce virulence in mice. thus, to gain insight into the pathogenesis of the bacterium, regulatory proteins of the haem biosynthetic pathway were sought. an iron response regulator (irr) from bradyrhizobium japonicum, which is a close relative of brucella, was previously described as being involved in the coordination of haem biosynthesis and iron availability. the bru. abortus genome was searched for an irr ...	2005	16207924
alterations induced by glyphosate on lupin photosynthetic apparatus and nodule ultrastructure and some oxygen diffusion related proteins.	the effects of glyphosate on protein metabolism, mesophyll cell ultrastructure and nodule ultrastructure and functioning of lupinus albus cv. multolupa inoculated with bradyrhizobium sp. (lupinus) were investigated. young leaves and nodules were especially affected because these organs act as sinks of the herbicide. the alterations on nodular and chloroplast ultrastructure varied depending on herbicide concentration and time of exposure. after 3 days of 2.5 mm glyphosate application some toxic e ...	2005	16324849
characterization of a bifunctional puta homologue from bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor.	puta is a bifunctional flavoenzyme in bacteria that catalyzes the four-electron oxidation of proline to glutamate. in certain prokaryotes such as escherichia coli, puta is also a transcriptional repressor of the proline utilization (put) genes and thus is trifunctional. in this work, we have begun to assess differences between bifunctional and trifunctional puta enzymes by examining the puta protein from bradyrhizobium japonicum (bjputa). primary structure analysis of bjputa shows it lacks the d ...	2005	15966737
pyd genes of rhizobium sp. strain tal1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism.	rhizobium sp. strain tal1145 degrades the leucaena toxin mimosine and its degradation product 3-hydroxy-4-pyridone (hp). the aim of this investigation is to characterize the rhizobium genes for hp degradation and transport. these genes were localized by subcloning and mutagenesis on a previously isolated cosmid, puhr263, containing mid genes of tal1145 required for mimosine degradation. two structural genes, pyda and pydb, encoding a metacleavage dioxygenase and a hydrolase, respectively, are re ...	2005	15968058
phylogenetic analysis of the genera bradyrhizobium, mesorhizobium, rhizobium and sinorhizobium on the basis of 16s rrna gene and internally transcribed spacer region sequences.	a total of 128 strains was isolated from more than 23 legume hosts in korea. phylogenetic relationships between these korean isolates and reference strains of the genera bradyrhizobium, mesorhizobium, rhizobium and sinorhizobium were analysed using their 16s rrna gene and internally transcribed spacer (its) region sequences. among the bradyrhizobium strains, dendrograms based on both the 16s rrna gene and its region sequences produced two main groups. the its tree yielded at least two new cluste ...	2005	15653885
biodiversity of uptake hydrogenase systems from legume endosymbiotic bacteria.	uptake hydrogenases in legume endosymbiotic bacteria recycle hydrogen produced during the nitrogen fixation process in legume nodules. despite the described beneficial effect on plant productivity, the hydrogen oxidation capability is not widespread in the rhizobiaceae family. characterization of hydrogenase gene clusters in strains belonging to rhizobium, bradyrhizobium and azorhizobium reveals a similar overall genetic organization along with important differences in gene regulation. in additi ...	2005	15667257
molecular characterization of uptake hydrogenase in frankia.	a molecular characterization of uptake hydrogenase in frankia was performed by using two-dimensional gel electrophoresis, matrix-assisted laser-desorption ionization-time-of-flight mass spectrometry, pcr amplification and southern blotting. a polypeptide of approx. 60 kda was recognized in frankia ugl011102, avci1 and kb5 on the two-dimensional gel by blotting with ralstonia eutropha (hox g) antibody. further analysis by ms resulted in a peptide 'fingerprint', which was similar to the membrane-b ...	2005	15667266
molybdate-dependent expression of the periplasmic nitrate reductase in bradyrhizobium japonicum.	the napedabc genes of bradyrhizobium japonicum encode the periplasmic nitrate reductase, an mo-containing enzyme which catalyses the reduction of nitrate to nitrite when oxygen concentrations are limiting. in this bacterium, another set of genes, modabc, code for a high affinity abc-type mo transport system. a b. japonicum moda mutant has been obtained that is not capable of growing anaerobically with nitrate and lacks nitrate reductase activity. under nitrate respiring conditions, when mo conce ...	2005	15667283
the complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium bradyrhizobium japonicum.	denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. in bradyrhizobium japonicum, the n(2)-fixing microsymbiont of soya beans, denitrification depends on the napedabc, nirk, norcbqd, and nosrzdfylx gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. mutational analysis of the b. japoni ...	2005	15667287
simultaneous enumeration of different bacteria using reverse sample genome probing technique.	quantitative reverse sample genome probing (rsgp) with lambdadna as an internal standard was used to enumerate the total numbers of rhizobium sp. ccrc 13560, rhizobium meliloti ccrc 13516 and bradyrhizobium sp. ccrc 13585. k(lambda)/kx ratios varied between the three species but also in response to the amounts of lambdadna or genomic dna used in the labeling mixture or fixed upon the membrane. comparative enumerations of pure cultures revealed higher counts using genomic probing as compared with ...	2005	15676199
novel avidin-like protein from a root nodule symbiotic bacterium, bradyrhizobium japonicum.	bradyrhizobium japonicum is an important nitrogenfixing symbiotic bacterium, which can form root nodules on soybeans. these bacteria have a gene encoding a putative avidin- and streptavidin-like protein, which bears an amino acid sequence identity of only about 30% over the core regions with both of them. we produced this protein in escherichia coli both as the full-length wild type and as a c-terminally truncated core form and showed that it is indeed a high affinity biotin-binding protein that ...	2005	15695809
prevalence of burkholderia sp. nodule symbionts on four mimosoid legumes from barro colorado island, panama.	sequences of 16s rrna and partial 23s rrna genes and pcr assays with genotype-specific primers indicated that bacteria in the genus burkholderia were the predominant root nodule symbionts for four mimosoid legumes (mimosa pigra, m. casta, m. pudica, and abarema macradenia) on barro colorado island, panama. among 51 isolates from these and a fifth mimosoid host (pithecellobium hymenaeafolium), 44 were burkholderia strains while the rest were placed in rhizobium, mesorhizobium, or bradyrhizobium. ...	2005	15709366
role of arginine 220 in the oxygen sensor fixl from bradyrhizobium japonicum.	in the heme-based oxygen sensor protein fixl, conformational changes induced by oxygen binding to the heme sensor domain regulate the activity of a neighboring histidine kinase, eventually restricting expression of specific genes to hypoxic conditions. the conserved arginine 220 residue is suggested to play a key role in the signal transduction mechanism. to obtain detailed insights into the role of this residue, we replaced arg(220) by histidine (r220h), glutamine (r220q), glutamate (r220e), an ...	2005	15711013
insights into the domains required for dimerization and assembly of human alphab crystallin.	protein pin array technology was used to identify subunit-subunit interaction sites in the small heat shock protein (shsp) alphab crystallin. subunit-subunit interaction sites were defined as consensus sequences that interacted with both human alphaa crystallin and alphab crystallin. the human alphab crystallin protein pin array consisted of contiguous and overlapping peptides, eight amino acids in length, immobilized on pins that were in a 96-well elisa plate format. the interaction of alphab c ...	2005	15722445
snp identification and snap marker development for a gmnark gene controlling supernodulation in soybean.	supernodulation in soybean (glycine max l. merr.) is an important source of nitrogen supply to subterranean ecological systems. single nucleotide-amplified polymorphism (snap) markers for supernodulation should allow rapid screening of the trait in early growth stages, without the need for inoculation and phenotyping. the gene gmnark (glycine max nodule autoregulation receptor kinase), controlling autoregulation of nodulation, was found to have a single nucleotide polymorphism (snp) between the ...	2005	15731930
occurrence of nodulation in unexplored leguminous trees native to the west african tropical rainforest and inoculation response of native species useful in reforestation.	despite the abundance and diversity of timber tree legumes in the west african rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. in the first part of this study the occurrence of nodulation was determined in 156 leguminous species growing in six natural forest areas in guinea, mostly mature trees. in the second part, an in situ experiment of rhizobial inoculation was performed on eight sele ...	2005	15760366
bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (papilionoideae: genisteae) from the canary islands, along with bradyrhizobium japonicum bv. genistearum, bradyrhizobium genospecies alpha and bradyrhizobium genospecies beta.	highly diverse bradyrhizobium strains nodulate genistoid legumes (brooms) in the canary islands, morocco, spain and the americas. phylogenetic analyses of its, atpd, glnii and reca sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely bradyrhizobium japonicum and three unnamed genospecies. dna-dna hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name bradyrhizobium canarien ...	2005	15774626
crystal structures of deoxy and co-bound bjfixlh reveal details of ligand recognition and signaling.	rhizobia directly regulate the expression of genes required for symbiotic nitrogen fixation in response to oxygen concentration via the sensor protein fixl. the n-terminal pas domain of fixl contains a histidine-coordinated heme and regulates the activity of its effector domain, a c-terminal histidine kinase, in response to binding of oxygen and other ligands at the heme. to further investigate ligand-induced inhibition of fixl, we have determined the crystal structures of the heme domain in bot ...	2005	15779889
insights into heme-based o2 sensing from structure-function relationships in the fixl proteins.	fixl proteins are bacterial heme-containing signal transduction proteins responsible for sensing the o(2) concentration in the organism's environment. in sinorhizobium meliloti fixl is a protein histidine kinase that, together with its response regulator fixj, constitute an oxygen-sensitive switch for regulation of the organism's nitrogen fixation and microaerobic respiration genes. the o(2) sensitivity of the switch is such that it transitions during the process of symbiosis in alfalfa roots. b ...	2005	15811514
genetic diversity of benzoyl coenzyme a reductase genes detected in denitrifying isolates and estuarine sediment communities.	benzoyl coenzyme a (benzoyl-coa) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-coa) in the metabolism of many aromatic compounds. the diversity of benzoyl-coa reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the arthur kill in new jersey and the chesapeake bay in maryland was investigated. degenerate primers were developed from t ...	2005	15812036
transcription activation in vitro by the bradyrhizobium japonicum regulatory protein fixk2.	in bradyrhizobium japonicum, the n2-fixing root nodule endosymbiont of soybean, a group of genes required for microaerobic, anaerobic, or symbiotic growth is controlled by fixk2, a key regulator that is part of the fixlj-fixk2 cascade. fixk2 belongs to the family of cyclic amp receptor protein/fumarate and nitrate reductase (crp/fnr) transcription factors that recognize a palindromic dna motif (crp/fnr box) associated with the regulated promoters. here, we report on a biochemical analysis of fix ...	2005	15866917
soybean genotypic difference in growth, nutrient accumulation and ultrastructure in response to manganese and iron supply in solution culture.	*	2005	15897206
diverse bacteria isolated from root nodules of phaseolus vulgaris and species within the genera campylotropis and cassia grown in china.	eighty bacterial isolates from root nodules of the leguminous plants phaseolus vulgaris, campylotropis spp. and cassia spp. grown in china were classified into five groups by phenotypic analyses, sds-page of whole-cell proteins, pcr-based 16s rrna gene restriction-fragment-length-polymorphism and sequencing. thirty-three isolates from the three plant genera were identified as agrobacterium tumefaciens because they are closely related to the type strain of a. tumefaciens. fourteen isolates from p ...	2005	15900972
evaluation of the role of genes encoding for dehydrin proteins (lea d-11) during drought stress in arbuscular mycorrhizal glycine max and lactuca sativa plants.	in this study, it has been determined whether the arbuscular mycorrhizal (am) symbiosis is able to alter the pattern of dehydrin (lea d-11 group) transcript accumulation under drought stress, and whether such a possible alteration functions in the protection of the host plants against drought. two dehydrin-encoding genes have been cloned from glycine max (gmlea 8 and gmlea 10) and one from lactuca sativa (lslea 1) and they have been analysed for their contribution to the response against drought ...	2005	15911559
proteomic analysis of soybean root hairs after infection by bradyrhizobium japonicum.	infection of soybean root hairs by bradyrhizobium japonicum is the first of several complex events leading to nodulation. in the current proteomic study, soybean root hairs after inoculation with b. japonicum were separated from roots. total proteins were analyzed by two-dimensional (2-d) polyacrylamide gel electrophoresis. in one experiment, 96 protein spots were analyzed by matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry (ms) to compare protein profiles ...	2005	15915644
effect of chlorimuron-ethyl on bradyrhizobium japonicum and its symbiosis with soybean.	possible side-effects of the acetolactate synthase (als)-inhibiting herbicide chlorimuron-ethyl on bradyrhizobium japonicum (kirchner & jordan) in pure culture and on inoculated soybean plants growing under controlled conditions were investigated. growth of b japonicum strain e109 was not affected by this herbicide even when exposed to concentrations 150 times higher than recommended field doses. however, nodulation of soybean plants treated 5 days after emergence with chlorimuron-ethyl at stand ...	2005	15920784
new evidence for bacterial diversity in the ascoma of the ectomycorrhizal fungus tuber borchii vittad.	the microbial community associated with ascocarps of the ectomycorrhizal fungus tuber borchii vittad. was studied by both cultivation and direct extraction of bacterial 16s rrna gene (rdna) sequence approaches. the inner part of six t. borchii ascoma collected in north-central italy was used to establish a bacterial culture collection and to extract the total genomic dna to obtain a library of 16s rdnas representative of the truffle bacterial community. most of the isolates were affiliated to th ...	2005	15927744
recombinant pas-heme domains of oxygen sensing proteins: high level production and physical characterization.	details of a high-level recombinant production method for the heme-pas domains of heme oxygen sensing proteins from sinorhizobium meliloti (sm) (formerly rhizobium meliloti, rm), bradyrhizobium japonicum (bj), and escherichia coli (ec) are described. using a newly proposed, concise, and unambiguous naming system (also described here) these proteins are: smfixlh(128-264), bjfixlh(140-270), and ecdosh(1-147). in addition, high-level production of bjfixl(140-505), the soluble full-length protein co ...	2005	15939306
ppsr: a multifaceted regulator of photosynthesis gene expression in purple bacteria.	purple bacteria control the level of expression and the composition of their photosystem according to light and redox conditions. this control involves several regulatory systems that have been now well characterized. among them, the ppsr regulator plays a central role, because it directly or indirectly controls the synthesis of all of the different components of the photosystem. in this review, we report our knowledge of the ppsr protein, highlighting the diversity of its mode of action and foc ...	2005	15948946
population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in bradyrhizobium species cohesion and delineation.	a combination of population genetics and phylogenetic inference methods was used to delineate bradyrhizobium species and to uncover the evolutionary forces acting at the population-species interface of this bacterial genus. maximum-likelihood gene trees for atpd, glnii, reca, and nifh loci were estimated for diverse strains from all but one of the named bradyrhizobium species, and three unnamed "genospecies," including photosynthetic isolates. topological congruence and split decomposition analy ...	2005	15579380
the manganese-responsive repressor mur of rhizobium leguminosarum is a member of the fur-superfamily that recognizes an unusual operator sequence.	the manganese uptake regulator mur of rhizobium leguminosarum is a close homologue of the global iron regulatory protein fur. mur represses the sitabcd operon, which encodes a mn2+ transport system, specifically in response to mn2+ but not fe2+. in previous work the authors mapped the 5' ends of two sit operon transcripts, termed ts1 and ts2, which were co-ordinately regulated by mn2+-mur, but this paper now shows that only ts1 is a primary transcript. dnase i protection analyses showed that pur ...	2005	16339952
[evolution and phylogeny of rhizobia].	nitrogen fixation an ancient process that may is have originated in the archaean eon under the primitive atmosphere anoxygenic conditions. diazotrophy is an exclusive process of prokaryotes, only euryarchaeota and 6 of 54 bacteria phyla have diazotrophs lineages. some of them coevolved with flowering plants for the establishment of molecular bases of a mutualistic symbiosis relationship. in rhizobia, the nitrogen fixation occurs inside the nodules, special structures on the roots or stems of leg ...	2005	17061545
arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase e2.	malonamidase e2 (mae2) from bradyrhizobium japonicum is an enzyme that hydrolyzes malonamate to malonate and has a ser-cis-ser-lys catalytic triad at the active site. the crystal structures of wild type and mutant mae2 exhibited that the guanido group of arg-158 could be involved in the binding of malonamate in which the negative charge of the carboxyl group could destabilize a negatively charged transition-state oxyanion in the enzymatic reaction. in an attempt to elucidate the specific roles o ...	2006	17077089
glutamate is involved in acid stress response in bradyrhizobium sp. semia 6144 (arachis hypogaea l.) microsymbiont.	in the present study, the effect of acid stress on ammonium assimilation in bradyrhizobium sp. semia 6144 (arachis hypogaea l.) microsymbiont was analyzed. the bacterial growth rate was decreased by 50%, and a significant increase in intracellular glutamate concentration was detected when the strain grew at acid ph (5.5). assays of the enzymes involved in glutamate synthesis showed increased activities of glutamine synthetase (gs) and glutamate synthase (nadph-gogat) under acid stress condition. ...	2006	17091217
nod factor enhances calcium uptake by soybean.	inoculation with rhizobia or application of nod factors (lipo-chitooligosaccharides, lcos) causes transient increases in cytosolic calcium concentration in root hairs of legume plants. we conducted experiments to evaluate whether application of lco and inoculation with rhizobia improved (45)cacl(2) uptake into soybean (glycine max [l.] merr.) leaves. roots of soybean seedlings with one developing trifoliolate were immersed in murashige and skoog (ms) basal liquid medium containing treatment solu ...	2006	17092733
isolation of a novel nodulin: a molecular marker of osmotic stress in glycine max/bradyrhizobium japonicum nodule.	symbiotic n(2) fixation of legume crops is highly sensitive to drought, which results in a dramatic drop of n accumulation and yield. the symbiosis between soybean (glycine max) and bradyrhizobium japonicum, because of its extreme sensitivity to drought, was chosen as a model to analyse the response to drought stress at a molecular level. the mrna differential display technique was performed to isolate cdna markers differentially expressed in well-watered [100% of n(2) fixation capacity (nfc)] a ...	2006	16913873
role of glutathione in the growth of bradyrhizobium sp. (peanut microsymbiont) under different environmental stresses and in symbiosis with the host plant.	glutathione (gsh) plays an important role in the defence of microorganisms and plants against different environmental stresses. to determine the role of gsh under different stresses, such as acid ph, saline shock, and oxidative shock, a gsh-deficient mutant (bradyrhizobium sp. 6144-s7z) was obtained by disruption of the gsha gene, which encodes the enzyme gamma-glutamylcysteine synthetase. growth of the mutant strain was significantly reduced in liquid minimal saline medium, and the gsh content ...	2006	16917515
isocitrate dehydrogenase of bradyrhizobium japonicum is not required for symbiotic nitrogen fixation with soybean.	a mutant strain of bradyrhizobium japonicum usda110 lacking isocitrate dehydrogenase activity was created to determine whether this enzyme was required for symbiotic nitrogen fixation with soybean (glycine max cv. williams 82). the isocitrate dehydrogenase mutant, strain 5051, was constructed by insertion of a streptomycin resistance gene cassette. the mutant was devoid of isocitrate dehydrogenase activity and of immunologically detectable protein, indicating there is only one copy in the genome ...	2006	16936027
the hmuq and hmud genes from bradyrhizobium japonicum encode heme-degrading enzymes.	utilization of heme by bacteria as a nutritional iron source involves the transport of exogenous heme, followed by cleavage of the heme macrocycle to release iron. bradyrhizobium japonicum can use heme as an iron source, but no heme-degrading oxygenase has been described. here, bioinformatics analyses of the b. japonicum genome identified two paralogous genes renamed hmuq (bll7075) and hmud (bll7423) that encode proteins with weak similarity to the heme-degrading monooxygenase isdg from staphylo ...	2006	16952937
unexpected stereorecognition in nitrilase-catalyzed hydrolysis of beta-hydroxy nitriles.	biocatalytic enantioselective hydrolysis of beta-hydroxy nitriles to corresponding (s)-enriched beta-hydroxy carboxylic acids has been achieved for the first time by an isolated nitrilase bll6402 from bradyrhizobium japonicum usda110. this offers a new "green" approach to optically pure beta-hydroxy nitriles and beta-hydroxy carboxylic acids. the observed remote stereorecognition is surprising because this nitrilase shows no enantioselectivity for the hydrolysis of alpha-hydroxy nitriles such as ...	2006	16986917
plant growth promoting potential of free-living diazotrophs and other rhizobacteria isolated from northern indian soil.	the viable count of free-living diazotrophic bacteria in different crop rhizospheres varied from 1.11 x 10(4) to 8.5 x 10(5) cfu/g of soil. the majority of the diazotrophs phenotypically belong to either azotobacter chroococcum, non-a. chroococcum type and to a heterogenous group tentatively named putative nitrogen-fixing (pnf) bacteria. in this study, 25 isolates of the pnf group were screened for their multiple plant growth-promoting (pgp) traits and grouped into 5 pgp types. an isolate, pnf(1 ...	2006	17004301
endogenous isoflavones are essential for the establishment of symbiosis between soybean and bradyrhizobium japonicum.	legume iso/flavonoids have been implicated in the nodulation process, but questions remain as to their specific role(s), and no unequivocal evidence exists showing that these compounds are essential for nodulation. two hypotheses suggest that the primary role of iso/flavonoids is their ability to induce rhizobial nod gene expression and/or their ability to modulate internal root auxin concentrations. the present work provides direct, genetic evidence that isoflavones are essential for nodulation ...	2006	17018035
the bradyrhizobium japonicum fur protein is an iron-responsive regulator in vivo.	the fur protein is a global regulator of iron metabolism in many bacterial species. however, fur homologs from some rhizobia appear not to mediate iron-dependent gene expression in vivo. here, transcriptional profiling analysis showed that more than one-fourth of the genes within the iron stimulon of bradyrhizobium japonicum were aberrantly controlled by iron in a fur mutant. however, fur has only a modest role in regulating iron transport genes. quantitative real time reverse transcriptase pcr ...	2006	17039378
variation in the nod gene rflps, nucleotide sequences of 16s rrna genes, nod factors, and nodulation abilities of bradyrhizobium strains isolated from thai vigna plants.	the analysis of nod genes and 16s rrna gene regions, nod factors, and nodulation abilities of brady rhizobium strains isolated from tropical thai vigna species is reported. a total of 55 bradyrhizobium strains isolated from two cultivated and six wild vigna species growing in central and northern thailand were evaluated. thai vigna spp. bradyrhizobium strains showed higher levels of nod gene rflp diversity compared with thai soybean brady rhizobium strains or temperate strains of bradyrhizobium ...	2006	16541157
nitrate-dependent anaerobic carbon monoxide oxidation by aerobic co-oxidizing bacteria.	two dissimilatory nitrate-reducing (burkholderia xenovorans lb400 and xanthobacter sp. str. cox) and two denitrifying isolates (stappia aggregata iam 12614 and bradyrhizobium sp. str. cpp), previously characterized as aerobic co oxidizers, consumed co at ecologically relevant levels (<100 ppm) under anaerobic conditions in the presence, but not absence, of nitrate. none of the isolates were able to grow anaerobically with co as a carbon or energy source, however, and nitrate-dependent anaerobic ...	2006	16542399
oxidative stress promotes degradation of the irr protein to regulate haem biosynthesis in bradyrhizobium japonicum.	the haem proteins catalase and peroxidase are stress response proteins that detoxify reactive oxygen species. in the bacterium bradyrhizobium japonicum, expression of the gene encoding the haem biosynthesis enzyme delta-aminolevulinic acid dehydratase (alad) is normally repressed by the irr protein in iron-limited cells. irr degrades in the presence of iron, which requires haem binding to the protein. here, we found that alad levels were elevated in iron-limited cells of a catalase-deficient mut ...	2006	16556232
proposal for combining bradyrhizobium spp. (aeschynomene indica) with blastobacter denitrificans and to transfer blastobacter denitrificans (hirsch and muller, 1985) to the genus bradyrhizobium as bradyrhizobium denitrificans (comb. nov.).	the symbiotic bradyrhizobia of aeschynomene indica and the aquatic budding bacterium blastobacter denitrificans have much in common and this study broadens the characters that are shared between the two. the 23s rrna gene sequences of the bradyrhizobial isolates were most similar to each other and to the sequence of bl. denitrificans. evidence for the presence of photosynthetic genes in the genome of bl. denitrificans was obtained by pcr using primers to the conserved m subunit (pufm) of the pho ...	2006	16564957
molecular diversity of native bradyrhizobia isolated from lima bean (phaseolus lunatus l.) in peru.	the diversity of a collection of 21 bradyrhizobial isolates from lima bean (phaseolus lunatus l.) was assayed by molecular methods. moderately high to high genetic diversity was revealed by multilocus enzyme electrophoresis (mlee) analysis of seven enzyme loci and genomic fingerprints with eric and box primers. two groups with differences in growth rate were found among the isolates and their differentiation as two divergent bradyrhizobial lineages was supported by pcr-rflp of the rpob gene and ...	2006	16564961
bradyrhizobium japonicum senses iron through the status of haem to regulate iron homeostasis and metabolism.	the irr protein from the bacterium bradyrhizobium japonicum is expressed under iron limitation to mediate iron control of haem biosynthesis. the regulatory input to irr is the status of haem and its precursors iron and protoporphyrin at the site of haem synthesis. here, we show that irr controls the expression of iron transport genes and many other iron-regulated genes not directly involved in haem synthesis. irr is both a positive and negative effector of gene expression, and in at least some c ...	2006	16573691
[chemotaxis and growth of bradyrhizobium japonicum in the presence of fine-dispersed silica].	the chemotactic properties of the soybean nodule bacterium bradyrhizobium japonicum were studied in the presence of synthetic fine-dispersed materials. it was shown that fine-dispersed silica (fds) and its variety modified with aluminum oxide (mfds) reduce bacterial chemotaxis to glucose. in addition, fds increases the irregular motility of b. japonicum, and mfds decreases it. this is in agreement with the effect of the materials on the rate of nodule bacterium growth.	2006	16579445
[genetic diversity and phylogeny of soybean bradyrhizobia isolated from south and north region of china].	studies on genetic diversity and phylogeny of soybean bradyrhizobia isolated from south and north region of china were investigated through 16s rrna gene pcr rflp, 16s rrna gene sequencing and 16s-23s rrna igs pcr rflp assays. results of 16s rrna gene pcr rflp and 16s rrna gene sequencing analysis reveal that strains tested are ascribed into bradyrhizobium japonicum and b. elkanii species. b. japonicum is the dominant species and accounts for 91% of strains tested, but b. elkanii just up to 9%, ...	2006	16579479
biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network.	free-living amoebae (fla) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. in addition to their own pathogenicity, fla can also act as trojan horses and be naturally infected with amoeba-resisting bacteria (arb) that may be involved in human infections, such as pneumonia. we investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. using amoebal enrichment on nonnutrient ...	2006	16597941
symbiotic bradyrhizobium japonicum reduces n2o surrounding the soybean root system via nitrous oxide reductase.	n(2)o reductase activity in soybean nodules formed with bradyrhizobium japonicum was evaluated from n(2)o uptake and conversion of (15)n-n(2)o into (15)n-n(2). free-living cells of usda110 showed n(2)o reductase activity, whereas a nosz mutant did not. complementation of the nosz mutant with two cosmids containing the nosrzdfylx genes of b. japonicum usda110 restored the n(2)o reductase activity. when detached soybean nodules formed with usda110 were fed with (15)n-n(2)o, they rapidly emitted (1 ...	2006	16597953
effect of organic n source on bacterial growth, lipo-chitooligosaccharide production, and early soybean nodulation by bradyrhizobium japonicum.	production of bradyrhizobium japonicum inoculants is problematic because high inoculation rates are necessary but expensive, while production of rhizobial nod factors (lipo-chitooligosaccharides (lcos)), key signal molecules in the establishment of legume-rhizobia symbioses, may be inhibited at high culture cell densities. we conducted experiments to determine the effects of growth medium n source on b. japonicum growth, lco production, and early nodulation of soybean. we found that 1.57 mmol am ...	2006	16604119
the rhizobium leguminosarum regulator irra affects the transcription of a wide range of genes in response to fe availability.	we show that an unusual transcriptional regulator, called irra, regulates many genes in the symbiotic n2-fixing bacterium rhizobium leguminosarum in response to iron availability. several operons in r. leguminosarum are expressed at lower levels in cells grown in fe-depleted compared to fe-replete medium. these include hema1, which encodes the haem biosynthesis enzyme amino-levulinic acid synthase; sufs2bcds1xa, which specify enzymes for fes cluster synthesis; rira, a global, fe-responsive trans ...	2006	16625355
bradyrhizobia isolated from root nodules of parasponia (ulmaceae) do not constitute a separate coherent lineage.	rhizobial bacteria almost exclusively nodulate members of the families fabaceae, mimosaceae and caesalpiniaceae, but are found on a single non-legume taxon, parasponia (ulmaceae). based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. this hypothesis was investigated by focusing on four isolates that are representat ...	2006	16627647
[glutamate dehydrogenase activity of bradyrhizobium japonicum in the presence of phytoregulators].	influence of plant growth regulators ivin and emistim c, and flavonoids daidzein and quercetin on the glutamate dehydrogenase activity of soybean nodule bacteria, with contrasting symbiotic properties, were studied. it was shown that all used phytoregulators stimulated glutamate dehydrogenase activity of bradyrhizobium japonicum 71t (the strain with highly efficient symbiotic properties) 1.2-4.9 times. bradyrhizobium japonicum 21110 (the strain with inefficient symbiotic properties) diminished t ...	2006	17100324
jasmonates induce nod factor production by bradyrhizobium japonicum.	jasmonates are signaling molecules involved in induced systemic resistance, wounding and stress responses of plants. we have previously demonstrated that jasmonates can induce nod genes of bradyrhizobium japonicum when measured by beta-galactosidase activity. in order to test whether jasmonates can effectively induce the production and secretion of nod factors (lipo-chitooligosaccharides, lcos) from b. japonicum, we induced two b. japonicum strains, 532c and usda3, with jasmonic acid (ja), methy ...	2006	17107814
genotypic characteristics of the rrn operon and genome of indigenous soybean bradyrhizobia in cropping zones of china.	four genetic assays, 16s rrna restriction fragment length polymorphism (rflp), 16s rrna sequencing, 16s-23s rrna intergenetic spacer (igs) rflp, and amplified fragment length polymorphism (aflp), were conducted to determine the genotypic characteristics of 44 indigenous strains of bradyrhizobium from soybean (glycine max l.) cropping zones of china. the results generated from different assays showed that soybean bradyrhizobial isolates comprised four genomic groups. group i was composed of strai ...	2006	17110965
bacterial diversity in aortic aneurysms determined by 16s ribosomal rna gene analysis.	aortic aneurysms are common vascular conditions that cause considerable morbidity and mortality. understanding of the mechanisms involved in the pathogenesis of the condition remains limited. recently, infection has been suggested as possible contributor in the development of the disease. the aim of the present study was to examine aortic aneurysms for the presence of bacterial dna using polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequenci ...	2006	17098542
evolution of enzymatic activities in the enolase superfamily: d-tartrate dehydratase from bradyrhizobium japonicum.	we focus on the assignment of function to and elucidation of structure-function relationships for a member of the mechanistically diverse enolase superfamily encoded by the bradyrhizobium japonicum genome (bll6730; gi:27381841). as suggested by sequence alignments, the active site contains the same functional groups found in the active site of mandelate racemase (mr) that catalyzes a 1,1-proton transfer reaction: two acid/base catalysts, lys 184 at the end of the second beta-strand, and a his 32 ...	2006	17144653
diversity and relationships of bradyrhizobia from legumes native to eastern north america.	dna sequencing and polymerase chain reaction (pcr) assays with lineage-specific primers were used to analyze the diversity of 276 isolates of bradyrhizobium sp. nodule bacteria associated with 13 native legumes species in the northeastern united states, representing eight genera in six legume tribes. a pcr screen with two primer pairs in the rrna region indicated that seven of the legume species were exclusively associated with strains having markers resembling bradyrhizobium elkanii, while the ...	2006	17473884