Publications

new mechanistic insights from structural studies of the oxygen-sensing domain of bradyrhizobium japonicum fixl.	the fixl heme domain serves as the dioxygen switch in the fixl/fixj two-component system of rhizobia. recent structural studies of the bradyrhizobium japonicum fixl heme domain (bjfixlh) have suggested an allosteric mechanism that is distinct from the classical hemoglobin model. to gain further insight into the fixl sensing mechanism, structures of bjfixlh bound to dioxygen, imidazole, and nitric oxide have been determined. these structures, particularly the structure of bjfixlh bound to its phy ...	2000	10747783
analysis of cellular fatty acids and phenotypic relationships of agrobacterium, bradyrhizobium, mesorhizobium, rhizobium and sinorhizobium species using the sherlock microbial identification system.	previous studies have demonstrated that cellular fatty acid analysis is a useful tool for identifying unknown strains of rhizobia and establishing taxonomic relationships between the species. in this study, the fatty acid profiles of over 600 strains belonging to the genera agrobacterium, bradyrhizobium, mesorhizobium, rhizobium and sinorhizobium were evaluated using the gaschromatography-based sherlock microbial identification system (mis). data collected with the mis showed that the three phyl ...	2000	10758890
identification of the novobiocin biosynthetic gene cluster of streptomyces spheroides ncib 11891.	the novobiocin biosynthetic gene cluster from streptomyces spheroides ncib 11891 was cloned by using homologous deoxynucleoside diphosphate (dndp)-glucose 4,6-dehydratase gene fragments as probes. double-stranded sequencing of 25.6 kb revealed the presence of 23 putative open reading frames (orfs), including the gene for novobiocin resistance, gyrb(r), and at least 11 further orfs to which a possible role in novobiocin biosynthesis could be assigned. an insertional inactivation experiment with a ...	2000	10770754
the h(2) sensor of ralstonia eutropha is a member of the subclass of regulatory [nife] hydrogenases.	two energy-generating hydrogenases enable the aerobic hydrogen bacterium ralstonia eutropha (formerly alcaligenes eutrophus) to use molecular hydrogen as the sole energy source. the complex synthesis of the nickel-iron-containing enzymes has to be efficiently regulated in response to h(2), which is available in low amounts in aerobic environments. h(2) sensing in r. eutropha is achieved by a hydrogenase-like protein which controls the hydrogenase gene expression in concert with a two-component r ...	2000	10781538
expression of uptake hydrogenase and molybdenum nitrogenase in rhodobacter capsulatus is coregulated by the regb-rega two-component regulatory system.	purple photosynthetic bacteria are capable of generating cellular energy from several sources, including photosynthesis, respiration, and h(2) oxidation. under nutrient-limiting conditions, cellular energy can be used to assimilate carbon and nitrogen. this study provides the first evidence of a molecular link for the coregulation of nitrogenase and hydrogenase biosynthesis in an anoxygenic photosynthetic bacterium. we demonstrated that molybdenum nitrogenase biosynthesis is under the control of ...	2000	10781552
catabolism of alpha-ketoglutarate by a suca mutant of bradyrhizobium japonicum: evidence for an alternative tricarboxylic acid cycle.	a complete tricarboxylic acid (tca) cycle is generally considered necessary for energy production from the dicarboxylic acid substrates malate, succinate, and fumarate. however, a bradyrhizobium japonicum suca mutant that is missing alpha-ketoglutarate dehydrogenase is able to grow on malate as its sole source of carbon. this mutant also fixes nitrogen in symbiosis with soybean, where dicarboxylic acids are its principal carbon substrate. using a flow chamber system to make direct measurements o ...	2000	10781553
carbon monoxide dehydrogenase activity in bradyrhizobium japonicum.	bradyrhizobium japonicum strain 110spc4 was capable of chemolithoautotrophic growth with carbon monoxide (co) as a sole energy and carbon source under aerobic conditions. the enzyme carbon monoxide dehydrogenase (codh; ec 1.2.99.2) has been purified 21-fold, with a yield of 16% and a specific activity of 58 nmol of co oxidized/min/mg of protein, by a procedure that involved differential ultracentrifugation, anion-exchange chromatography, hydrophobic interaction chromatography, and gel filtration ...	2000	10788353
horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis.	although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. in this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off tuckerton, n.j., at the rutgers university long-term ecosystem obse ...	2000	10788370
a lipochito-oligosaccharide, nod factor, induces transient calcium influx in soybean suspension-cultured cells.	lipochito-oligosaccharides (nod factors) produced by rhizobium or bradyrhizobium are the key signal molecules for eliciting nodulation in their corresponding host legumes. to elucidate the signal transduction events mediated by nod factors, we investigated the effects of nod factors on the cytosolic [ca2+] of protoplasts prepared from roots and suspension-cultured cells of soybean (glycine max and g. soja) using a fluorescent ca2+ indicator, fura-pe3. nodbj-v (c18:1, mefuc), which is a major com ...	2000	10792822
bradyrhizobium spp. (tgx) isolates nodulating the new soybean cultivars in africa are diverse and distinct from bradyrhizobia that nodulate north american soybeans.	the newly developed cultivars of soybean in africa, known as tropical glycine cross (tgx), are nodulated by bradyrhizobia indigenous to african soils, here designated bradyrhizobium spp. (tgx). isolates of bradyrhizobium spp. (tgx) obtained from nodules of tgx soybeans that were inoculated with soils from 65 locations in six african countries were characterized and grouped into 11 phylogenetic clusters on the basis of rflp of the 16s rrna gene. five restriction enzymes (rsai, hinfi, mspi, cfoi a ...	2000	10826808
differential effects of permeating and nonpermeating solutes on the fatty acid composition of pseudomonas putida.	we examined the effect of reduced water availability on the fatty acid composition of pseudomonas putida strain mt-2 grown in a defined medium in which the water potential was lowered with the permeating solutes nacl or polyethylene glycol (peg) with a molecular weight of 200 (peg 200) or the nonpermeating solute peg 8000. transmission electron microscopy showed that -1.0-mpa peg 8000-treated cells had convoluted outer membranes, whereas -1.0-mpa nacl-treated or control cells did not. at the ran ...	2000	10831419
use of repetitive dna sequences and the pcr to differentiate escherichia coli isolates from human and animal sources.	the rep-pcr dna fingerprint technique, which uses repetitive intergenic dna sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. box and rep primers were used to generate dna fingerprints from escherichia coli strains isolated from human and animal sources (geese, ducks, cows, pigs, chickens, and sheep). our initial studies revealed that the dna fingerprints obtained with the box primer were more effective for grouping e. coli strains than th ...	2000	10831440
rhizobitoxine production by bradyrhizobium elkanii enhances nodulation and competitiveness on macroptilium atropurpureum.	application of 1-aminoocyclopropane-1-carboxylic acid, an ethylene precursor, decreased nodulation of macroptilium atropurpureum by bradyrhizobium elkanii. b. elkanii produces rhizobitoxine, an ethylene synthesis inhibitor. elimination of rhizobitoxine production in b. elkanii increased ethylene evolution and decreased nodulation and competitiveness on m. atropurpureum. these results suggest that rhizobitoxine enhances nodulation and competitiveness of b. elkanii on m. atropurpureum.	2000	10831453
identification of sinorhizobium meliloti genes regulated during symbiosis.	rna fingerprinting by arbitrarily primed pcr was used to isolate sinorhizobium meliloti genes regulated during the symbiotic interaction with alfalfa (medicago sativa). sixteen partial cdnas were isolated whose corresponding genes were differentially expressed between symbiotic and free-living conditions. thirteen sequences corresponded to genes up-regulated during symbiosis, whereas three were instead repressed during establishment of the symbiotic interaction. seven cdnas corresponded to known ...	2000	10850975
inactivation of gltb abolishes expression of the assimilatory nitrate reductase gene (nasb) in pseudomonas putida kt2442.	by using mini-tn5 transposon mutagenesis, random transcriptional fusions of promoterless bacterial luciferase, luxab, to genes of pseudomonas putida kt2442 were generated. insertion mutants that responded to ammonium deficiency by induction of bioluminescence were selected. the mutant that responded most strongly was genetically analyzed and is demonstrated to bear the transposon within the assimilatory nitrate reductase gene (nasb) of p. putida kt2442. genetic evidence as well as sequence analy ...	2000	10852866
the hydrogenase cytochrome b heme ligands of azotobacter vinelandii are required for full h(2) oxidation capability.	the hydrogenase in azotobacter vinelandii, like other membrane-bound [nife] hydrogenases, consists of a catalytic heterodimer and an integral membrane cytochrome b. the histidines ligating the hemes in this cytochrome b were identified by h(2) oxidation properties of altered proteins produced by site-directed mutagenesis. four fully conserved and four partially conserved histidines in hoxz were substituted with alanine or tyrosine. the roles of these histidines in hoxz heme binding and hydrogena ...	2000	10852874
genetic and phenotypic analyses of the rdx locus of rhodobacter sphaeroides 2.4.1.	previously, we reported that rdxb, encoding a likely membrane-bound two [4fe-4s]-containing center, is involved in the aerobic regulation of photosystem gene expression in rhodobacter sphaeroides 2.4.1. to further investigate the role of rdxb as well as other genes of the rdxbhis operon on photosystem gene expression, we constructed a series of nonpolar, in-frame deletion mutations in each of the rdx genes. using both puc and puf operon lacz fusions to monitor photosystem gene expression, under ...	2000	10852880
virulence of the phytopathogen pseudomonas syringae pv. maculicola is rpon dependent.	we cloned the rpon (ntra and glnf) gene encoding sigma(54) from the phytopathogen pseudomonas syringae pv. maculicola strain es4326. the p. syringae es4326 rpon gene complemented pseudomonas aeruginosa, escherichia coli, and klebsiella aerogenes rpon mutants for a variety of rpon mutant phenotypes, including the inability to utilize nitrate as sole nitrogen source. dna sequence analysis of the p. syringae es4326 rpon gene revealed that the deduced amino acid sequence was most similar (86% identi ...	2000	10852883
the alternative sigma factor rpon is required for hrp activity in pseudomonas syringae pv. maculicola and acts at the level of hrpl transcription.	beta-glucuronidase (uida) reporter gene fusions were constructed for the hrpz, hrpl, and hrps genes from the phytopathogen pseudomonas syringae pv. maculicola strain es4326. these reporters, as well as an avrrpt2-uida fusion, were used to measure transcriptional activity in es4326 and a es4326 rpon mutant. rpon was required for the expression of avrrpt2, hrpz, and hrpl in vitro in minimal media and in vivo when infiltrated into arabidopsis thaliana leaves. in contrast, the expression of hrps was ...	2000	10852884
the role of pyruvate dehydrogenase and acetyl-coenzyme a synthetase in fatty acid synthesis in developing arabidopsis seeds.	acetyl-coenzyme a (acetyl-coa) formed within the plastid is the precursor for the biosynthesis of fatty acids and, through them, a range of important biomolecules. the source of acetyl-coa in the plastid is not known, but two enzymes are thought to be involved: acetyl-coa synthetase and plastidic pyruvate dehydrogenase. to determine the importance of these two enzymes in synthesizing acetyl-coa during lipid accumulation in developing arabidopsis seeds, we isolated cdna clones for acetyl-coa synt ...	2000	10859180
genome structure of the genus azospirillum.	azospirillum species are plant-associated diazotrophs of the alpha subclass of proteobacteria. the genomes of five of the six azospirillum species were analyzed by pulsed-field gel electrophoresis. all strains possessed several megareplicons, some probably linear, and 16s ribosomal dna hybridization indicated multiple chromosomes in genomes ranging in size from 4.8 to 9.7 mbp. the nifhdk operon was identified in the largest replicon.	2000	10869094
the role of region ii in the rna polymerase sigma factor sigma(n) (sigma(54)).	bacterial rna polymerase holoenzymes containing the sigma subunit sigma(n) (sigma(54)) can form a stable closed complex with promoter dna but only undergo transition to an open complex and transcription initiation when acted on by an activator protein. proteins of the sigma(n) family have a conserved n-terminal region of 50 amino acids (region i) that is separated from a conserved c-terminal region of around 360 amino acids (region iii) by a much more variable sequence of between 30 and 110 resi ...	2000	10871407
[the interaction of bradyrhizobium japonicum with clay minerals].	it is shown that such clay minerals as palygorskite and montmorillonite stimulate growth activity of bradyrhizobium japonicum. the bacteria come into contact with the above minerals. granulated preparations of rhizobia have been developed on the basis of the results obtained. these preparations are characterized by the high yield of viable cells and a possibility of long-term storage. the use of montmorillonite in production of granulated preparations provides the higher yield of viable bacteria ...	2000	10872286
characterization of an atrazine-degrading pseudaminobacter sp. isolated from canadian and french agricultural soils.	atrazine, a herbicide widely used in corn production, is a frequently detected groundwater contaminant. fourteen bacterial strains able to use this herbicide as a sole source of nitrogen were isolated from soils obtained from two farms in canada and two farms in france. these strains were indistinguishable from each other based on repetitive extragenic palindromic pcr genomic fingerprinting performed with primers eric1r, eric2, and boxa1r. based on 16s rrna sequence analysis of one representativ ...	2000	10877767
cloning of the malic enzyme gene from corynebacterium glutamicum and role of the enzyme in lactate metabolism.	malic enzyme is one of at least five enzymes, known to be present in corynebacterium glutamicum, capable of carboxylation and decarboxylation reactions coupling glycolysis and the tricarboxylic acid cycle. to date, no information is available concerning the physiological role of the malic enzyme in this bacterium. the male gene from c. glutamicum has been cloned and sequenced. the protein encoded by this gene has been purified to homogeneity, and the biochemical properties have been established. ...	2000	10877795
fluorescent whole-cell hybridization with 16s rrna-targeted oligonucleotide probes to identify brucella spp. by flow cytometry.	a whole-cell hybridization assay with fluorescent oligonucleotide probes derived from the 16s rrna sequence of brucella abortus in combination with flow cytometry has been developed. with the three fluorescent probes selected, a positive signal was observed with all the representative strains of the species and biovars of brucella and with a total of nine different brucella clinical isolates. using the b9 probe in the hybridization assay, it was possible to discriminate between brucella suis bio ...	2000	10878084
aflp fingerprint analysis of bradyrhizobium strains isolated from faidherbia albida and aeschynomene species.	the diversity of bradyrhizobium isolates from faidherbia albida and aeschynomenee species was assessed using aflp analysis, a high-resolution genomic fingerprinting technique. reference strains from bradyrhizobium japonicum, bradyrhizobium elkanii and bradyrhizobium liaoningense were included for comparison. at a similarity level of 50%, a total of 34 different groups were obtained by cluster analysis of the genomic fingerprints. four of these clusters correspond to the three reference species, ...	2000	10879988
identification of active-site residues in bradyrhizobium japonicum malonamidase e2.	malonamidase (ma) e2 was previously purified and characterized from bradyrhizobium japonicum usda 110. the gene encoding this enzyme has been cloned, sequenced and expressed in escherichia coli. the recombinant mae2 was purified to homogeneity from the transformed e. coli. the biochemical properties of the recombinant enzyme are essentially identical to those from wild-type b. japonicum. a database search showed that the mae2 protein has a high sequence similarity with the common signature seque ...	2000	10880349
tmrnas that encode proteolysis-inducing tags are found in all known bacterial genomes: a two-piece tmrna functions in caulobacter.	a general mechanism in bacteria to rescue stalled ribosomes and to clear the cell of incomplete polypeptides involves an rna species, tmrna (ssra), which functions as both a trna and an mrna. this rna encodes a peptide tag that is incorporated at the end of the aberrant polypeptide and targets it for proteolysis. we have identified a circularly permuted version of the tmrna gene in alpha-proteobacteria as well as in a lineage of cyanobacteria. the genes in these two groups seem to have arisen fr ...	2000	10884408
the bacterial enhancer-dependent sigma(54) (sigma(n)) transcription factor.		2000	10894718
new substrates for the dicarboxylate transport system of sinorhizobium meliloti.	the dicarboxylate transport (dct) system of sinorhizobium meliloti, which is essential for a functional nitrogen-fixing symbiosis, has been thought to transport only dicarboxylic acids. we show here that the permease component of the dct system, dcta, can transport orotate, a monocarboxylic acid, with an apparent k(m) of 1.7 mm and a v(max) of 163 nmol min(-1) per mg of protein in induced cells. dcta was not induced by the presence of orotate. the transport of orotate was inhibited by several co ...	2000	10894729
alfalfa root nodule invasion efficiency is dependent on sinorhizobium meliloti polysaccharides.	the soil bacterium sinorhizobium meliloti is capable of entering into a nitrogen-fixing symbiosis with medicago sativa (alfalfa). particular low-molecular-weight forms of certain polysaccharides produced by s. meliloti are crucial for establishing this symbiosis. alfalfa nodule invasion by s. meliloti can be mediated by any one of three symbiotically important polysaccharides: succinoglycan, eps ii, or k antigen (also referred to as kps). using green fluorescent protein-labeled s. meliloti cells ...	2000	10894742
prolonged stationary-phase incubation selects for lrp mutations in escherichia coli k-12.	evolution by natural selection occurs in cultures of escherichia coli maintained under carbon starvation stress. mutants of increased fitness express a growth advantage in stationary phase (gasp) phenotype, enabling them to grow and displace the parent as the majority population. the first gasp mutation was identified as a loss-of-function allele of rpos, encoding the stationary-phase global regulator, sigma(s) (m. m. zambrano, d. a. siegele, m. a. almirón, a. tormo, and r. kolter, science 259:1 ...	2000	10894750
differential degradation of escherichia coli sigma32 and bradyrhizobium japonicum rpoh factors by the ftsh protease.	the escherichia coli heat shock sigma factor sigma32 (rpoh) is rapidly degraded under non-stress conditions. the integrity of the dnak chaperone machinery and the atp-dependent ftsh protease are required for sigma32 proteolysis in vivo. bradyrhizobium japonicum expresses three sigma32-type transcription factors, rpoh1, rpoh2, and rpoh3, which are functional in e. coli. we compared the stability of these sigma factors with e. coli sigma32 stability. in e. coli c600 (wild-type), the half-lives of ...	2000	10903518
in rhizobium leguminosarum, nodd represses its own transcription by competing with rna polymerase for binding sites.	we isolated rna polymerase (rnap) from rhizobium leguminosarum, the nitrogen-fixing symbiont of peas and vicia: its 91 kda subunit, which is homologous to sigma(70) of escherichia coli rnap, is necessary for transcription of the regulatory nodd gene, which in the presence of certain flavonoids induces transcription of other nod genes that are needed for the early steps of infection. we also show that negative autoregulation of nodd was achieved through competition between rnap and nodd for their ...	2000	10908336
stimulation of adhesiveness, infectivity, and competitiveness for nodulation of bradyrhizobium japonicum by its pretreatment with soybean seed lectin.	soybean seed lectin stimulates adsorption of bradyrhizobium japonicum to its host roots. pretreatment of the rhizobia with soybean seed lectin for at least 6-12 h previous to their interaction with the plants was required to detect the stimulatory effect. this activity could be observed with as few as 1000 soybean seed lectin molecules per bacterium, and required specific carbohydrate binding. infectivity and competitiveness for nodulation were also stimulated by preincubation of the rhizobia ei ...	2000	10913702
enhanced attachment of bradyrhizobium japonicum to soybean through reduced root colonization of internally seedborne microorganisms.	internally seedborne microorganisms are those surviving common surface sterilization procedures. such microbes often colonize the radicle surface of a germinating soybean (glycine max) seed, introducing an undefined parameter into studies on attachment and infection by bradyrhizobium japonicum. bacterial isolates from surface-sterilized soybean seed, cv. williams 82 and cv. maverick, used in our studies, were identified as agrobacterium radiobacter, aeromonas sp., bacillus spp., chryseomonas lut ...	2000	10932352
functional bradyrhizobium japonicum nifa expression under a hybrid nptii-nifh promoter in e. coli and acetobacter diazotrophicus srt4.	a hybrid promoter consisting of the in tandem fusion of the tn5 nptii and the klebsiella pneumoniae nifh promoters was constructed to study the functionality of the nif genes transcriptional activator nifa from bradyrhizobium japonicum in two different host bacteria. beta-galactosidase experiments in e. coli revealed that the hybrid nptii-nifh promoter can behave as a constitutive or a nifa-inducible promoter depending on the aeration conditions. expression of the b. japonicum nifa from the hybr ...	1998	10932742
rnase iii processing of intervening sequences found in helix 9 of 23s rrna in the alpha subclass of proteobacteria.	we provide experimental evidence for rnase iii-dependent processing in helix 9 of the 23s rrna as a general feature of many species in the alpha subclass of proteobacteria (alpha-proteobacteria). we investigated 12 rhodobacter, rhizobium, sinorhizobium, rhodopseudomonas, and bartonella strains. the processed region is characterized by the presence of intervening sequences (ivss). the 23s rdna sequences between positions 109 and 205 (escherichia coli numbering) were determined, and potential seco ...	2000	10940010
redox signaling: globalization of gene expression.	here we show that the extent of electron flow through the cbb(3) oxidase of rhodobacter sphaeroides is inversely related to the expression levels of those photosynthesis genes that are under control of the prrba two-component activation system: the greater the electron flow, the stronger the inhibitory signal generated by the cbb(3) oxidase to repress photosynthesis gene expression. using site-directed mutagenesis, we show that intramolecular electron transfer within the cbb(3) oxidase is involv ...	2000	10944106
altered exopolysaccharides of bradyrhizobium japonicum mutants correlate with impaired soybean lectin binding, but not with effective nodule formation.	the exact mechanism(s) of infection and symbiotic development between rhizobia and legumes is not yet known, but changes in rhizobial exopolysaccharides (epss) affect both infection and nodule development of the legume host. early events in the symbiotic process between bradyrhizobium japonicum and soybean (glycine max [l.] merr.) were studied using two mutants, defective in soybean lectin (sbl) binding, which had been generated from b. japonicum 2143 (usda 3i-1b-143 derivative) by tn5 mutagenes ...	2000	10945216
altered cell surface hydrophobicity of lipopolysaccharide-deficient mutant of bradyrhizobium japonicum.	the authors previously isolated a lipopolysaccharide (lps) deficient tn5-mutant of bradyrhizobium japonicum, and subsequently isolated the lps gene region. in this study the lps deficiency of b. japonicum was studied in terms of its cell surface characteristics. by monitoring the kinetics of the partition with hexadecane the lps-mutant was found to be far more hydrophobic than the wild type strain; the partition coefficients were 3.19 min(-1) for the mutant, as compared with only 1.40 min(-1) fo ...	2000	10958967
the nosx and nirx proteins of paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase.	the nos (nitrous oxide reductase) operon of paracoccus denitrificans contains a nosx gene homologous to those found in the nos operons of other denitrifiers. nosx is also homologous to nirx, which is so far unique to p. denitrificans. single mutations of these genes did not result in any apparent phenotype, but a double nosx nirx mutant was unable to reduce nitrous oxide. promoter-lacz assays and immunoblotting against nitrous oxide reductase showed that the defect was not due to failure of expr ...	2000	10960107
genetic footprinting with mariner-based transposition in pseudomonas aeruginosa.	the complete dna sequence of pseudomonas aeruginosa provides an opportunity to apply functional genomics to a major human pathogen. a comparative genomics approach combined with genetic footprinting was used as a strategy to identify genes required for viability in p. aeruginosa. use of a highly efficient in vivo mariner transposition system in p. aeruginosa facilitated the analysis of candidate genes of this class. we have developed a rapid and efficient allelic exchange system by using the i-s ...	2000	10963681
molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, spartina alterniflora.	n(2) fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. however, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. denaturing gradient gel electrophoresis (dgge) of pcr-amplified nifh sequence segments was used in previous studies to examine the stability and dynamics of the spartina rhizosphere diazotroph assemblages in the north ...	2000	10966395
genotypic characterization of bradyrhizobium strains nodulating small senegalese legumes by 16s-23s rrna intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses.	we examined the genotypic diversity of 64 bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in senegal (west africa) belonging to the genera abrus, alysicarpus, bryaspis, chamaecrista, cassia, crotalaria, desmodium, eriosema, indigofera, moghania, rhynchosia, sesbania, tephrosia, and zornia, which play an ecological role and have agronomic potential in arid regions. the strains were characterized by intergenic spacer (between 16s and 23s rrna genes) pcr and res ...	2000	10966419
role of respiratory nitrate reductase in ability of pseudomonas fluorescens yt101 to colonize the rhizosphere of maize.	selection of the denitrifying community by plant roots (i.e., increase in the denitrifier/total heterotroph ratio in the rhizosphere) has been reported by several authors. however, very few studies to evaluate the role of the denitrifying function itself in the selection of microorganisms in the rhizosphere have been performed. in the present study, we compared the rhizosphere survival of the denitrifying pseudomonas fluorescens yt101 strain with that of its isogenic mutant deficient in the abil ...	2000	10966422
changes in the physiological and agricultural characteristics of peat-based bradyrhizobium japonicum inoculants after long-term storage.	commercial soybean inoculants processed with sterilised peat and stored at 20 degrees c for 1-8 years were used as experimental materials to assess the changes in the physiological activity of bradyrhizobium japonicum after storage. viable counts decreased and physiological characteristics of the bacterium changed during storage, with an increase in the time taken for colony appearance on a medium without yeast extract, an increase in the lag time for nodule appearance on soybean grown in glass ...	2000	10968634
signal peptide-dependent protein transport in bacillus subtilis: a genome-based survey of the secretome.	one of the most salient features of bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. this has led to the commercial exploitation of bacilli as major "cell factories" for secreted enzymes. the recent sequencing of the genome of b. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. most importantly, the genome sequen ...	2000	10974125
chaperone activity and homo- and hetero-oligomer formation of bacterial small heat shock proteins.	rhizobia are the only bacteria known to induce a multitude of small heat shock proteins (shsps) upon temperature upshift. the shsps of bradyrhizobium japonicum fall into two different classes, class a and class b. here, we studied the chaperone activity and oligomeric features of two representative members of each class. the purified shsps were efficient chaperones, as demonstrated by their ability to prevent thermally induced aggregation of citrate synthase in vitro. homo-oligomer formation of ...	2000	10978322
molecular characterization of a gene region involved in lipopolysaccharide biosynthesis in bradyrhizobium japonicum: cloning, sequencing and expression of rfaf gene.	a 3.0-kb region involved in lipopolysaccharide biosynthesis in bradyrhizobium japonicum was sequenced. one complete open reading frame was identified which encodes a polypeptide of 354 amino acid residues with a predicted molecular mass of 38 209 da. expression of the protein using a t7 gene expression system revealed a band of similar molecular mass after sodium dodecyl sulfate polyacrylamide gel electrophoresis. a database search against known gene sequences revealed a significant sequence sim ...	2000	10981699
varying the abundance of o antigen in rhizobium etli and its effect on symbiosis with phaseolus vulgaris.	judged by migration of its lipopolysaccharide (lps) in gel electrophoresis, the o antigen of rhizobium etli mutant strain ce166 was apparently of normal size. however, its lps sugar composition and staining of the lps bands after electrophoresis indicated that the proportion of its lps molecules that possessed o antigen was only 40% of the wild-type value. its lps also differed from the wild type by lacking quinovosamine (2-amino-2,6-dideoxyglucose). both of these defects were due to a single ge ...	2000	10986232
keys to symbiotic harmony.		2000	11004160
the toryz (yeck bisz) operon encodes a third respiratory trimethylamine n-oxide reductase in escherichia coli.	the bisz gene of escherichia coli was previously described as encoding a minor biotin sulfoxide (bso) reductase in addition to the main cytoplasmic bso reductase, bisc. in this study, bisz has been renamed torz based on the findings that (i) the torz gene product, torz, is able to reduce trimethylamine n-oxide (tmao) more efficiently than bso; (ii) although torz is more homologous to bisc than to the tmao reductase tora (63 and 42% identity, respectively), it is located mainly in the periplasm a ...	2000	11004177
transcriptional control of the sulfur-regulated cysh operon, containing genes involved in l-cysteine biosynthesis in bacillus subtilis.	the molecular mechanisms of regulation of the genes involved in the biosynthesis of cysteine are poorly characterized in bacillus subtilis and other gram-positive bacteria. in this study we describe the expression pattern of the b. subtilis cysh operon in response to sulfur starvation. a 6.1-kb polycistronic transcript which includes the cysh, cysp, ylnb, ylnc, ylnd, ylne, and ylnf genes was identified. its synthesis was induced by sulfur limitation and strongly repressed by cysteine. the cysh o ...	2000	11004190
erratum to: "stimulation of adhesiveness, infectivity, and competitiveness for nodulation of bradyrhizobium japonicum by its pretreatment with soybean seed lectin".		2000	11004414
genetic manipulation of isoflavone 7-o-methyltransferase enhances biosynthesis of 4'-o-methylated isoflavonoid phytoalexins and disease resistance in alfalfa.	4'-o-methylation of an isoflavonoid intermediate is a key reaction in the biosynthesis of the phytoalexin medicarpin in legumes. however, isoflavone o-methyltransferase (iomt) from alfalfa converts the isoflavone daidzein to 7-o-methyl daidzein (isoformononetin) in vitro as well as in vivo in unchallenged leaves of transgenic alfalfa ectopically expressing iomt. in contrast, elicitation of iomt-overexpressing plants with cucl(2) or infecting these plants with phoma medicaginis leads to greater a ...	2000	11006341
characterization, seasonal occurrence, and diel fluctuation of poly(hydroxyalkanoate) in photosynthetic microbial mats.	in situ poly(hydroxyalkanoate) (pha) levels and repeating-unit compositions were examined in stratified photosynthetic microbial mats from great sippewissett salt marsh, mass., and ebro delta, spain. unlike what has been observed in pure cultures of phototrophic bacteria, the prevalence of hydroxyvalerate (hv) repeating units relative to hydroxybutyrate (hb) repeating units was striking. in the cyanobacteria-dominated green material of sippewissett mats, the mole percent ratio of repeating units ...	2000	11010871
generation of new hydrogen-recycling rhizobiaceae strains by introduction of a novel hup minitransposon.	hydrogen evolution by nitrogenase is a source of inefficiency for the nitrogen fixation process by the rhizobium-legume symbiosis. to develop a strategy to generate rhizobial strains with h(2)-recycling ability, we have constructed a tn5 derivative minitransposon (tnhb100) that contains the ca. 18-kb h(2) uptake (hup) gene cluster from rhizobium leguminosarum bv. viciae upm791. bacteroids from tnhb100-containing strains of r. leguminosarum bv. viciae pre, bradyrhizobium japonicum, r. etli, and m ...	2000	11010872
identification and analysis of the polyhydroxyalkanoate-specific beta-ketothiolase and acetoacetyl coenzyme a reductase genes in the cyanobacterium synechocystis sp. strain pcc6803.	synechocystis sp. strain pcc6803 possesses a polyhydroxyalkanoate (pha)-specific beta-ketothiolase encoded by phaa(syn) and an acetoacetyl-coenzyme a (coa) reductase encoded by phab(syn). a similarity search of the entire synechocystis genome sequence identified a cluster of two putative open reading frames (orfs) for these genes, slr1993 and slr1994. sequence analysis showed that the orfs encode proteins having 409 and 240 amino acids, respectively. the two orfs are colinear and most probably c ...	2000	11010896
heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution.	heat shock proteins 60 (groel) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles. these chaperone proteins have been advanced as propitious marker sequences for tracing the evolution of mitochondrial (mt) genomes. similarities among hsp60 sequences based on significant segment pair alignment calculations are used to deduce associations of sequences taking into account groel functional/structural domain differences and to relate hsp60 duplications pervasi ...	2000	11027334
nod factors and chitooligomers elicit an increase in cytosolic calcium in aequorin-expressing soybean cells.	rhizobial nod factors (nfs) function as nodulation signals that trigger symbiotic responses of leguminous host plants. nfs consist of a chitin oligomer backbone carrying a fatty acid at the non-reducing end. depending on the rhizobial strain, nfs carry additional substituents, which may determine host specificity. transgenic suspension-cultured soybean (glycine max [l.] merr.) cells expressing aequorin have been used to record cytosolic [ca(2+)] changes upon treatment with purified nfs and chiti ...	2000	11027722
characterization of the hydrogen-deuterium exchange activities of the energy-transducing hupsl hydrogenase and h(2)-signaling hupuv hydrogenase in rhodobacter capsulatus.	rhodobacter capsulatus synthesizes two homologous protein complexes capable of activating molecular h(2), a membrane-bound [nife] hydrogenase (hupsl) linked to the respiratory chain, and an h(2) sensor encoded by the hupuv genes. the activities of hydrogen-deuterium (h-d) exchange catalyzed by the hupsl-encoded and the hupuv-encoded enzymes in the presence of d(2) and h(2)o were studied comparatively. whereas hupsl is in the membranes, hupuv activity was localized in the soluble cytoplasmic frac ...	2000	11029418
positive selection for mutations affecting bioconversion of aromatic compounds in agrobacterium tumefaciens: analysis of spontaneous mutations in the protocatechuate 3,4-dioxygenase gene.	a positive selection method for mutations affecting bioconversion of aromatic compounds was applied to a mutant strain of agrobacterium tumefaciens a348. the nucleotide sequence of the a348 pcahgb genes, which encode protocatechuate 3,4-dioxygenase (pcahg) and beta-carboxy-cis,cis-muconate cycloisomerase (pcab) for the first two steps in catabolism of the diphenolic protocatechuate, was determined. an omega element was introduced into the pcab gene of a348, creating strain ado2077. in the presen ...	2000	11029436
characterization of the dna- and metal-binding properties of vibrio anguillarum fur reveals conservation of a structural zn(2+) ion.	the ferric uptake regulator, fur, represses iron uptake and siderophore biosynthetic genes under iron-replete conditions. here we report in vitro solution studies on vibrio anguillarum fur binding to the consensus 19-bp escherichia coli iron box in the presence of several divalent metals. we found that v. anguillarum fur binds the iron box in the presence of mn(2+), co(2+), cd(2+), and to a lesser extent ni(2+) but, unlike e. coli fur, not in the presence of zn(2+). we also found that v. anguill ...	2000	11029454
expression of early nodulin genes in alfalfa mycorrhizae indicates that signal transduction pathways used in forming arbuscular mycorrhizae and rhizobium-induced nodules may be conserved.	transcripts for two genes expressed early in alfalfa nodule development (msenod40 and msenod2) are found in mycorrhizal roots, but not in noncolonized roots or in roots infected with the fungal pathogen rhizoctonia solani. these same two early nodulin genes are expressed in uninoculated roots upon application of the cytokinin 6-benzylaminopurine. correlated with the expression of the two early nodulin genes, we found that mycorrhizal roots contain higher levels of trans-zeatin riboside than nonm ...	1997	11038545
differential expression of two soybean apyrases, one of which is an early nodulin.	two cdna clones were isolated from soybean (glycine soja) by polymerase chain reaction with primers designed to conserved motifs found in apyrases (nucleotide phosphohydrolase). the two cdnas are predicted to encode for two, distinct, apyrase proteins of approximately 50 kda (i.e., gs50) and 52 kda (i.e., gs52). phylogenetic analysis indicated that gs52 is orthologous to a family of apyrases recently suggested to play a role in legume nodulation. gs50 is paralogous to this family and, therefore, ...	2000	11043467
[improvement of nitrogen fixation efficiency and plasmid stability in bradyrhizobium japonicum by the introduction of dctabd and parcba/de genes].	a recombinant plasmid phn207 containing c4-dicarboxylic acid transport genes (dctabd) from sinorhizobium meliloti, parcba/de genes from ptr102 and reporter genes luxab from pdb30 was constructed by using plafr3 as the vector. the phn207 was then introduced into the bradyrhizobium japonicum ta11 and cb1809 by bi-parental mating. it was confirmed that parcba/de genes could increase the stability of plafr3 in the transconjugants under both free-living and symbiotic condition. the results of plant p ...	2000	11055128
key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine roseobacter lineage.	aromatic compound degradation in six bacteria representing an ecologically important marine taxon of the alpha-proteobacteria was investigated. initial screens suggested that isolates in the roseobacter lineage can degrade aromatic compounds via the beta-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. six roseobacter isolates were screened for the presence of protocatechuate 3,4-dioxygenase, a key enzyme in the beta-ketoadipate pathway. all six isolates ...	2000	11055908
bradyrhizobium sp. strains that nodulate the leguminous tree acacia albida produce fucosylated and partially sulfated nod factors.	we determined the structures of nod factors produced by six different bradyrhizobium sp. strains nodulating the legume tree acacia albida (syn. faidherbia albida). compounds from all strains were found to be similar, i.e., o-carbamoylated and substituted by an often sulfated methyl fucose and different from compounds produced by rhizobium-mesorhizobium-sinorhizobium strains nodulating other species of the acaciae tribe.	2000	11055966
genetic characterization of soybean rhizobia in paraguay.	the soybean is an exotic plant introduced in paraguay in this century; commercial cropping expanded after the 1970s. inoculation is practiced in just 15 to 20% of the cropping areas, but root nodulation occurs in most sites where soybeans grow. little is known about rhizobial diversity in south america, and no study has been performed in paraguay until this time. therefore, in this study, the molecular characterization of 78 rhizobial isolates from soybean root nodules, collected under field con ...	2000	11055970
an imperfect inverted repeat is critical for dna binding of the response regulator regr of bradyrhizobium japonicum.	regr is the response regulator of the regsr two-component regulatory system in bradyrhizobium japonicum. the only target known so far is the fixr-nifa operon, encoding the redox-responsive transcription factor nifa, which activates many genes required for symbiotic nitrogen fixation in soybean nodules. in previous in vivo studies, we identified a 32 bp upstream activating sequence located around position -68, which is essential for regr-dependent expression of the fixr-nifa operon. here, we used ...	2000	11058113
terminal oxidases of bacillus subtilis strain 168: one quinol oxidase, cytochrome aa(3) or cytochrome bd, is required for aerobic growth.	the gram-positive endospore-forming bacterium bacillus subtilis has, under aerobic conditions, a branched respiratory system comprising one quinol oxidase branch and one cytochrome oxidase branch. the system terminates in one of four alternative terminal oxidases. cytochrome caa(3) is a cytochrome c oxidase, whereas cytochrome bd and cytochrome aa(3) are quinol oxidases. a fourth terminal oxidase, ythab, is a putative quinol oxidase predicted from dna sequence analysis. none of the terminal oxid ...	2000	11073895
interspecies complementation of escherichia coli ccm mutants: ccme (cycj) from bradyrhizobium japonicum acts as a heme chaperone during cytochrome c maturation.	biogenesis of c-type cytochromes in alpha- and gamma-proteobacteria requires the function of a set of orthologous genes (ccm genes) that encode specific maturation factors. the escherichia coli ccme protein is a periplasmic heme chaperone. the membrane protein ccmc is required for loading ccme with heme. by expressing ccme (cycj) from bradyrhizobium japonicum in e. coli we demonstrated that heme is bound covalently to this protein at a strictly conserved histidine residue. the b. japonicum homol ...	2000	11073932
aluminum-induced 1-->3-beta-d-glucan inhibits cell-to-cell trafficking of molecules through plasmodesmata. a new mechanism of aluminum toxicity in plants.	symplastic intercellular transport in plants is achieved by plasmodesmata (pd). these cytoplasmic channels are well known to interconnect plant cells to facilitate intercellular movement of water, nutrients, and signaling molecules including hormones. however, it is not known whether al may affect this cell-to-cell transport process, which is a critical feature for roots as organs of nutrient/water uptake. we have microinjected the dye lucifer yellow carbohydrazide into peripheral root cells of ...	2000	11080277
linear beta-1,3 glucans are elicitors of defense responses in tobacco.	laminarin, a linear beta-1,3 glucan (mean degree of polymerization of 33) was extracted and purified from the brown alga laminaria digitata. its elicitor activity on tobacco (nicotiana tabacum) was compared to that of oligogalacturonides with a mean degree of polymerization of 10. the two oligosaccharides were perceived by suspension-cultured cells as distinct chemical stimuli but triggered a similar and broad spectrum of defense responses. a dose of 200 microg ml(-1) laminarin or oligogalacturo ...	2000	11080280
localization of a nod factor-binding protein in legume roots and factors influencing its distribution and expression.	the roots of the legume dolichos biflorus contain a lectin/nucleotide phosphohydrolase (db-lnp) that binds to the nod factor signals produced by rhizobia that nodulate this plant. in this study we show that db-lnp is differentially distributed along the surface of the root axis in a pattern that correlates with the zone of nodulation of the root. db-lnp is present on the surface of young and emerging root hairs and redistributes to the tips of the root hairs in response to treatment of the roots ...	2000	11080281
glutathione and homoglutathione synthetases of legume nodules. cloning, expression, and subcellular localization.	the thiol tripeptides glutathione (gsh) and homoglutathione (hgsh) are very abundant in legume root nodules and their synthesis is catalyzed by the enzymes gamma-glutamylcysteine synthetase (gammaecs), gsh synthetase (gshs), and hgsh synthetase (hgshs). as an essential step to elucidate the role of thiols in n(2) fixation we have isolated cdnas encoding the three enzymes and have quantified the transcripts in nodules. assay of enzyme activities in highly purified nodule organelles revealed that ...	2000	11080313
characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, acetobacter diazotrophicus.	a major 30.5-kb cluster of nif and associated genes of acetobacter diazotrophicus (syn. gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. this cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. the overall arrangement of genes is most ...	2000	11092875
divergent mechanisms of 5' 23s rrna ivs processing in the alpha-proteobacteria.	widespread occurrence of a separate small rna derived from the 5'-end of 23s rrna and of an intervening sequence (ivs) which separates this domain from the main segment of 23s rrna in the alpha-proteobacteria implies that processing reactions which act to excise the ivs are also maintained in this group. we previously characterized the first example of processing of this ivs in rhodopseudomonas palustris, which is classified with the bradyrhizobia in this case, ivs excision occurs by a multistep ...	2000	11095671
photosynthetic bradyrhizobia are natural endophytes of the african wild rice oryza breviligulata.	we investigated the presence of endophytic rhizobia within the roots of the wetland wild rice oryza breviligulata, which is the ancestor of the african cultivated rice oryza glaberrima. this primitive rice species grows in the same wetland sites as aeschynomene sensitiva, an aquatic stem-nodulated legume associated with photosynthetic strains of bradyrhizobium. twenty endophytic and aquatic isolates were obtained at three different sites in west africa (senegal and guinea) from nodal roots of o. ...	2000	11097925
the bradyrhizobium japonicum proline biosynthesis gene proc is essential for symbiosis.	plant host-derived proline is proposed to serve as an energy source for rhizobia in the rhizosphere and in symbiotic root nodules. the bradyrhizobium japonicum proc gene was isolated, and a proc mutant strain that behaved as a strict proline auxotroph in culture was constructed. the proc strain elicited undeveloped nodules on soybeans that lacked nitrogen fixation activity and plant hemoglobin. we conclude that the proc gene is essential for symbiosis and suggest that the mutant does not obtain ...	2000	11097929
origin and evolution of the mitochondrial proteome.	the endosymbiotic theory for the origin of mitochondria requires substantial modification. the three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha-proteobacteria. random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mito ...	2000	11104819
restriction fragment length polymorphism analysis of 16s rdna and low molecular weight rna profiling of rhizobial isolates from shrubby legumes endemic to the canary islands.	thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the canary islands were characterised by 16s rdna pcr-rflp analyses (ardra) and lmw rna profiling, and compared with reference strains representing bradyrhizobium japonicum, b. elkanii, b. liaoningense, and two unclassified bradyrhizobium sp. (lupinus) strains. both techniques showed similar results, indicating the existence of three genotypes among the canarian isolates. analysis of the combined r ...	2000	11108022
effect of bradyrhizobium photosynthesis on stem nodulation of aeschynomene sensitiva.	some leguminous species of the genus aeschynomene are specifically stem-nodulated by photosynthetic bradyrhizobia. to study the effect of bacterial photosynthesis during symbiosis, we generated a photosynthesis-negative mutant of the bradyrhizobium sp. strain ors278 symbiont of aeschynomene sensitiva. the presence of a functional photosynthetic unit in bacteroids and the high expression of the photosynthetic genes observed in stem nodules demonstrate that the bacteria are photosynthetically acti ...	2000	11114184
identification of residues involved in catalytic activity of the inverting glycosyl transferase wbbe from salmonella enterica serovar borreze.	synthesis of the o:54 o antigen of salmonella enterica is initiated by the nonprocessive glycosyl transferase wbbe, assigned to family 2 of the glycosyl transferase enzymes (gt2). gt2 enzymes possess a characteristic n-terminal domain, domain a. based on structural data from the gt2 representative spsa (s. j. charnock and g. j. davies, biochemistry 38:6380-6385, 1999), this domain is responsible for nucleotide binding. it possesses two invariant asp residues, the first forming a hydrogen bond to ...	2001	11114903
renaturation of bacillus thermoglucosidasius hrca repressor by dna and thermostability of the hrca-dna complex in vitro.	hrca, a negative control repressor for chaperone expression from the obligate thermophile bacillus thermoglucosidasius kp1006, was purified in a his-tagged form in the presence of 6 m urea but hardly renatured to an intact state due to extreme insolubility. renaturation trials revealed that the addition of dna to purified b. thermoglucosidasius hrca can result in solubilization of hrca free from the denaturing agent urea. results from band shift and light scattering assays provided three new fin ...	2001	11114912
methylotrophic methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.	rhizobia described so far belong to three distinct phylogenetic branches within the alpha-2 subclass of proteobacteria. here we report the discovery of a fourth rhizobial branch involving bacteria of the methylobacterium genus. rhizobia isolated from crotalaria legumes were assigned to a new species, "methylobacterium nodulans," within the methylobacterium genus on the basis of 16s ribosomal dna analyses. we demonstrated that these rhizobia facultatively grow on methanol, which is a characterist ...	2001	11114919
tmrdb (tmrna database).	the tmrna database (tmrdb) is maintained at the university of texas health science center at tyler, texas, and accessible on the world wide web at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.++ +html. mirror sites are located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the institute of biological sciences, aarhus, denmark (http://www.bioinf.au. dk/tmrdb/). the tmrdb provides information and citation links about tmrna, a molecule that combines functions ...	2001	11125081
evidence for a functional similarity between the two-component regulatory systems regsr, actsr, and regba (prrba) in alpha-proteobacteria.	the symbiotic bacteria bradyrhizobium japonicum and sinorhizobium meliloti, and the purple photosynthetic bacteria rhodobacter capsulatus, rhodovulum sulfidophilum, roseobacter denitrificans and rhodobacter sphaeroides possess homologous two-component regulatory systems, namely regsr, actsr, regba and prrba. the respective response regulators of these bacteria control expression of different regulons that are involved in n2 fixation, co2 fixation, photosynthesis or acid tolerance. we therefore a ...	2000	11131020
small-subunit rrna genotyping of rhizobia nodulating australian acacia spp.	the structure of rhizobial communities nodulating acacia in southeastern australia from south queensland to tasmania was investigated by a molecular approach. a total of 118 isolates from nodule samples from 13 different acacia species collected at 44 sites were characterized by small-subunit (ssu) ribosomal dna (rdna) pcr-restriction fragment length polymorphism analysis. nine rhizobial genomospecies were identified, and these taxa corresponded to previously described genomospecies (b. lafay an ...	2001	11133471
identification of the nik gene cluster of brucella suis: regulation and contribution to urease activity.	analysis of a brucella suis 1330 gene fused to a gfp reporter, and identified as being induced in j774 murine macrophage-like cells, allowed the isolation of a gene homologous to nika, the first gene of the escherichia coli operon encoding the specific transport system for nickel. dna sequence analysis of the corresponding b. suis nik locus showed that it was highly similar to that of e. coli except for localization of the nikr regulatory gene, which lies upstream from the structural nikabcde ge ...	2001	11133934
differential response of soybean (glycine max (l.) merr.) genotypes to lipo-chito-oligosaccharide nod bj v (c(18:1) mefuc).	lipo-chito-oligosaccharides (lcos) are bacteria-to-plant signal molecules essential for the establishment of rhizobia-legume symbioses. lcos invoke a number of physiological changes in the host plants, such as root hair deformation, cortical cell division and ontogeny of complete nodule structures. the responses of five soybean cultivars to nod bj: v (c(18:1) mefuc) isolated from bradyrhizobium japonicum strain 532c were studied with a new technique. two distinct types of root hair deformation w ...	2000	11141178
influence of tomato genotype on growth of inoculated and indigenous bacteria in the spermosphere.	we previously demonstrated a genetic basis in tomato for support of the growth of a biological control agent, bacillus cereus uw85, in the spermosphere after seed inoculation (k. p. smith, j. handelsman, and r. m. goodman, proc. natl. acad. sci. usa 96:4786-4790, 1999). here we report results of studies examining the host effect on the support of growth of bacillus and pseudomonas strains, both inoculated on seeds and recruited from soil, using selected inbred tomato lines from the recombinant i ...	2001	11157211
nitrogen fixation genes in an endosymbiotic burkholderia strain.	in this paper we report the identification and characterization of a dna region containing putative nif genes and belonging to a burkholderia endosymbiont of the arbuscular mycorrhizal fungus gigaspora margarita. a genomic library of total dna extracted from the fungal spores was also representative of the bacterial genome and was used to investigate the prokaryotic genome. screening of the library with azospirillum brasilense nifhdk genes as the prokaryotic probes led to the identification of a ...	2001	11157237
synthesis of a low-molecular-weight form of exopolysaccharide by bradyrhizobium japonicum usda 110.	a novel extracellular low-molecular-weight polysaccharide was detected as a contaminant within extracellular cyclic beta-1,6-beta-1,3-glucan preparations from bradyrhizobium japonicum usda 110 cultures. compositional analysis, methylation analysis, and nuclear magnetic resonance analysis revealed that this low-molecular-weight polysaccharide was composed of the same pentasaccharide repeating unit previously described for the high-molecular-weight form of the exopolysaccharide (eps) synthesized b ...	2001	11157281
genetic characterization of a sinorhizobium meliloti chromosomal region in lipopolysaccharide biosynthesis.	the genetic characterization of a 5.5-kb chromosomal region of sinorhizobium meliloti 2011 that contains lpsb, a gene required for the normal development of symbiosis with medicago spp., is presented. the nucleotide sequence of this dna fragment revealed the presence of six genes: grea and lpsb, transcribed in the forward direction; and lpse, lpsd, lpsc, and lrp, transcribed in the reverse direction. except for lpsb, none of the lps genes were relevant for nodulation and nitrogen fixation. analy ...	2001	11157937
one of two hemn genes in bradyrhizobium japonicum is functional during anaerobic growth and in symbiosis.	previously, we screened the symbiotic gene region of the bradyrhizobium japonicum chromosome for new nifa-dependent genes by competitive dna-rna hybridization (a. nienaber, a. huber, m. göttfert, h. hennecke, and h. m. fischer, j. bacteriol. 182:1472-1480, 2000). here we report more details on one of the genes identified, a hemn-like gene (now called hemn(1)) whose product exhibits significant similarity to oxygen-independent coproporphyrinogen iii dehydrogenases involved in heme biosynthesis in ...	2001	11157943
potential symbiosis-specific genes uncovered by sequencing a 410-kilobase dna region of the bradyrhizobium japonicum chromosome.	the physical and genetic map of the bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. therefore, we determined the nucleotide sequence of a 410-kb region. the overall g+c nucleotide content was 59.1%. using a minimum gene length of 150 nucleotid ...	2001	11157954
bacterial rna polymerase subunit omega and eukaryotic rna polymerase subunit rpb6 are sequence, structural, and functional homologs and promote rna polymerase assembly.	bacterial dna-dependent rna polymerase (rnap) has subunit composition beta'betaalpha(i)alpha(ii)omega. the role of omega has been unclear. we show that omega is homologous in sequence and structure to rpb6, an essential subunit shared in eukaryotic rnap i, ii, and iii. in escherichia coli, overproduction of omega suppresses the assembly defect caused by substitution of residue 1362 of the largest subunit of rnap, beta'. in yeast, overproduction of rpb6 suppresses the assembly defect caused by th ...	2001	11158566