Publications

mutational and transcriptional analysis of the type iii secretion system of bradyrhizobium japonicum.	sequencing the symbiotic region of bradyrhizobium japonicum revealed a gene cluster (tts) encoding a type iii secretion system (ttss) that is similar to those found in mesorhizobium loti maff303099 and rhizobium strain ngr234. in addition to genes that are likely to encode structural core components of the ttss, the cluster contains several open reading frames that are found exclusively in rhizobia or that are specific to b. japonicum. depending on the host, mutations within this cluster affecte ...	2002	12481995
arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.	the beta-proteobacterial strain ulpas1, isolated from an arsenic-contaminated environment, is able to efficiently oxidize arsenite [as(iii)] to arsenate [as(v)]. mutagenesis with a lacz-based reporter transposon yielded two knockout derivatives deficient in arsenite oxidation. sequence analysis of the dna flanking the transposon insertions in the two mutants identified two adjacent open reading frames, named aoxa and aoxb, as well as a putative promoter upstream of the aoxa gene. reverse transcr ...	2003	12486049
biochemical and mutational characterization of the heme chaperone ccme reveals a heme binding site.	ccme is a heme chaperone that binds heme transiently in the periplasm of escherichia coli and delivers it to newly synthesized and exported c-type cytochromes. the chemical nature of the covalent bond between heme and h130 is not known. we have purified soluble histidine-tagged ccme and present its spectroscopic characteristics in the visible range. alanine scanning mutagenesis of conserved amino acids revealed that h130 is the only residue found to be strictly required for heme binding and deli ...	2003	12486054
evidence that carbon dioxide enrichment alleviates ureide-induced decline of nodule nitrogenase activity.	the hypothesis that elevated [co(2)] alleviates ureide inhibition of n(2)-fixation was tested. short-term responses of the acetylene reduction assay (ara), ureide accumulation and total non-structural carbohydrate (tnc) levels were measured following addition of ureide to the nutrient solution of hydroponically grown soybean. the plants were exposed to ambient (360 micromol mol(-1)) or elevated (700 micromol mol(-1)) [co(2)]. addition of 5 and 10 mm ureide to the nutrient solution inhibited n(2) ...	2003	12495923
characterization of rhizobia that nodulate legume species of the genus lespedeza and description of bradyrhizobium yuanmingense sp. nov.	legume species belonging to the genus lespedeza are annual or perennial herb or shrub plants that grow in the northern hemisphere. they are known for the formation of root nodules, but little information is available about their microsymbionts. in this study, 58 root-nodule isolates from lespedeza spp., obtained from china and the usa, were characterized using numerical taxonomic analysis of phenotypic features, sds-page analysis of whole-cell proteins, dna-dna hybridization, 16s rrna gene seque ...	2002	12508891
features of rhodobacter sphaeroides ccmfh.	in this study, the in vivo function and properties of two cytochrome c maturation proteins, ccmf and ccmh from rhodobacter sphaeroides, were analyzed. strains lacking ccmh or both ccmf and ccmh are unable to grow under anaerobic conditions where c-type cytochromes are required, demonstrating their critical role in the assembly of these electron carriers. consistent with this observation, strains lacking both ccmf and ccmh are deficient in c-type cytochromes when assayed under permissive growth c ...	2003	12511487
tmrna is required for correct timing of dna replication in caulobacter crescentus.	ssra, or tmrna, is a small rna that interacts with selected translating ribosomes to target the nascent polypeptides for degradation. here we report that ssra activity is required for normal timing of the g(1)-to-s transition in caulobacter crescentus. a deletion of the ssra gene, or of the gene encoding smpb, a protein required for ssra activity, results in a specific delay in the cell cycle during the g(1)-to-s transition. the ssra deletion phenotype is not due to accumulation of stalled ribos ...	2003	12511504
nodulation gene regulation in bradyrhizobium japonicum: a unique integration of global regulatory circuits.		2003	12513971
a host-specific bacteria-to-plant signal molecule (nod factor) enhances germination and early growth of diverse crop plants.	lipo-chitooligosaccharides (lcos), or nod factors, are host-specific bacteria-to-plant signal molecules essential for the establishment of a successful n(2)-fixing legume-rhizobia symbiosis. at submicromolar concentrations nod factors induce physiological changes in host and non-host plants. here we show that the nod factor nod bj v(c18:1,mefuc) of bradyrhizobium japonicum 532c enhances germination of a variety of economically important plants belonging to diverse botanical families: zea mays, o ...	2003	12520335
iscce1 and iscce2, two novel insertion sequences in clostridium cellulolyticum.	two new insertion sequences, iscce1 and iscce2, were found to be inserted into the cipc gene of spontaneous mutants of clostridium cellulolyticum. in these insertional mutants, the cipc gene was disrupted either by iscce1 alone or by both iscce1 and iscce2. iscce1 is 1,292 bp long and has one open reading frame. the open reading frame encodes a putative 348-amino-acid protein with significant levels of identity with putative proteins having unknown functions and with some transposases belonging ...	2003	12533447
characterization of helicobacter pylori nickel metabolism accessory proteins needed for maturation of both urease and hydrogenase.	previous studies demonstrated that two accessory proteins, hypa and hypb, play a role in nickel-dependent maturation of both hydrogenase and urease in helicobacter pylori. here, the two proteins were purified and characterized. hypa bound two ni(2+) ions per dimer with positive cooperativity (hill coefficient, approximately 2.0). the dissociation constants k(1) and k(2) for ni(2+) were 58 and 1.3 microm, respectively. studies on purified site-directed mutant proteins in each of the five histidin ...	2003	12533448
requirements for cu(a) and cu-s center assembly of nitrous oxide reductase deduced from complete periplasmic enzyme maturation in the nondenitrifier pseudomonas putida.	bacterial nitrous oxide (n(2)o) reductase is the terminal oxidoreductase of a respiratory process that generates dinitrogen from n(2)o. to attain its functional state, the enzyme is subjected to a maturation process which involves the protein-driven synthesis of a unique copper-sulfur cluster and metallation of the binuclear cu(a) site in the periplasm. there are seven putative maturation factors, encoded by nosa, nosd, nosf, nosy, nosl, nosx, and sco. we wanted to determine the indispensable pr ...	2003	12533464
prediction and overview of the rpon-regulon in closely related species of the rhizobiales.	in the rhizobia, a group of symbiotic gram-negative soil bacteria, rpon (sigma54, sigman, ntra) is best known as the sigma factor enabling transcription of the nitrogen fixation genes. recent reports, however, demonstrate the involvement of rpon in other symbiotic functions, although no large-scale effort has yet been undertaken to unravel the rpon-regulon in rhizobia. we screened two complete rhizobial genomes (mesorhizobium loti, sinorhizobium meliloti) and four symbiotic regions (rhizobium et ...	2002	12537565
post-genomic insights into plant nodulation symbioses.	several legume genes involved in establishing nitrogen fixation have been discovered using functional genomics; when mutated, the genes affect symbioses, and all encode receptor kinases. this provides long-awaited insights into a complex plant-bacterium interaction and heralds the possibility of extending the range of plants susceptible to nitrogen-fixing nodulation.	2003	12540294
[study on the improvement of plasmid stability in soybean rhizobia].	by using luxab as the report genes, 3.2 kb parcba/de gene fragment from ptr102 was inserted into plafr3 which contained a 3.7 kb enhancing fragment and deleted its cos site. recombinant plasmids phn155 and phn156 were obtained. contrasted plasmids phn157 and phn158 which contained cos site were also constructed. these four plasmids were transferred into sinorhizobium fredii hn01 by tri-parental mating, and plasmid phn155 and phn158 were introduced into bradyrhizobium japonicum ta11 by two-parent ...	2000	12548995
characterization of the nodulation plasmid encoded chemoreceptor gene mcpg from rhizobium leguminosarum.	in general, chemotaxis in rhizobium has not been well characterized. methyl accepting chemotaxis proteins are sensory proteins important in chemotaxis of numerous bacteria, but their involvement in rhizobium chemotaxis is unclear and merits further investigation.	2003	12553885
[study on polyphasic taxonomy of rhizobia isolated from lespedeza species].	the diversity of rhizobia isolated from lespedeza spp. was determined on the basis of numerical analysis of phenotypic characteristics, sodium dodecyl sulfate-polyacrylarmide gel electrophoresis (sds-page) of proteins, dna-dna homology and restriction fragment length polymorphism (rflp) analysis of 16s-ribosomal dna genes. according to numerical analysis of 125 phenotypic characteristics, strains were divided into two groups at a similarity level of 67%. group i included all the fast-growing str ...	1999	12555566
characterization of ndvd, the third gene involved in the synthesis of cyclic beta-(1 --> 3),(1 --> 6)-d-glucans in bradyrhizobium japonicum.	previously, we identified two genes in bradyrhizobium japonicum (ndvb, ndvc) that are required for cyclic beta-(1 --> 3),(1 --> 6)-d-glucan synthesis and successful symbiotic interaction with soybean (glycine max). in this study, we report a new open reading frame (orf1) located in the intergenic region between ndvb and ndvc, which is essential for beta-glucan synthesis and effective nodulation of g. max. this new gene is designated ndvd (nodule development). the ndvd translation product has a p ...	2002	12556128
isolation and molecular characterization of pmg160, a mobilizable cryptic plasmid from rhodobacter blasticus.	a 3.4-kb cryptic plasmid was obtained from a new isolate of rhodobacter blasticus. this plasmid, designated pmg160, was mobilizable by the conjugative strain escherichia coli s17.1 into rhodobacter sphaeroides, rhodobacter capsulatus, and rhodopseudomonas palustris. it replicated in the latter strains but not in rhodospirillum rubrum, rhodocyclus gelatinosus, or bradyrhizobium species. plasmid pmg160 was stably maintained in r. sphaeroides for more than 100 generations in the absence of selectio ...	2003	12570988
comparative genetic diversity of the narg, nosz, and 16s rrna genes in fluorescent pseudomonads.	the diversity of the membrane-bound nitrate reductase (narg) and nitrous oxide reductase (nosz) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16s rrna gene by a pcr-restriction fragment length polymorphism assay. fragments of 1,008 bp and 1,433 bp were amplified via pcr with primers specific for the narg and nosz genes, respectively. the presence of the narg and nosz genes in the bacterial strains was confirmed by hy ...	2003	12571023
phenotypic and genotypic diversity of rhizobia nodulating pterocarpus erinaceus and p. lucens in senegal.	a total of fifty root nodules isolates of fast-growing and slow growing rhizobia from pterocarpus ennaceus and pterocarpus lucens respectively native of sudanean and sahelian regions of senegal were characterized. these isolates were compared to representative strains of known rhizobial species. twenty-two new isolates were slow growers and twenty-eight were fast growers. a polyphasic approach was performed including comparative total protein sodium dodecyl sulphate polyacrylamide gel (sds-page) ...	2002	12583718
hemin binding, functional expression, and complementation analysis of pap 31 from bartonella henselae.	growth of bartonella henselae is strongly heme dependent, and b. henselae is unable to synthesize heme itself. at least five outer membrane-associated proteins from b. henselae bind hemin, including the 31-kda protein designated pap31. the gene of this protein was heterologously expressed in escherichia coli m15(prep4) and detected with monoclonal antibodies in the outer membrane fraction. complementation of the hema-deficient mutant e. coli k-12 eb53 (arob tsx malt hema) with pap31 demonstrated ...	2003	12591895
complete genomic sequence of nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum usda110.	the complete nucleotide sequence of the genome of a symbiotic bacterium bradyrhizobium japonicum usda110 was determined. the genome of b. japonicum was a single circular chromosome 9,105,828 bp in length with an average gc content of 64.1%. no plasmid was detected. the chromosome comprises 8317 potential protein-coding genes, one set of rrna genes and 50 trna genes. fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical gene ...	2002	12597275
complete genomic sequence of nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum usda110 (supplement).		2002	12597279
molecular analysis of the multiple groel proteins of chlamydiae.	genome sequencing revealed that all six chlamydiae genomes contain three groel-like genes (groel1, groel2, and groel3). phylogenetic analysis of groel1, groel2, and groel3 indicates that these genes are likely to have been present in chlamydiae since the beginning of the lineage. comparison of deduced amino acid sequences of the three groel genes with those of other organisms showed high homology only for groel1, although comparison of critical amino acid residues that are required for polypepti ...	2003	12618460
transcriptome analysis of sinorhizobium meliloti during symbiosis.	rhizobia induce the formation on specific legumes of new organs, the root nodules, as a result of an elaborated developmental program involving the two partners. in order to contribute to a more global view of the genetics underlying this plant-microbe symbiosis, we have mined the recently determined sinorhizobium meliloti genome sequence for genes potentially relevant to symbiosis. we describe here the construction and use of dedicated nylon macroarrays to study simultaneously the expression of ...	2003	12620125
fnr is involved in oxygen control of herbaspirillum seropedicae n-truncated nifa protein activity in escherichia coli.	herbaspirillum seropedicae is an endophytic diazotroph belonging to the beta-subclass of the class proteobacteria, which colonizes many members of the gramineae. the activity of the nifa protein, a transcriptional activator of nif genes in h. seropedicae, is controlled by ammonium ions through its n-terminal domain and by oxygen through mechanisms that are not well understood. here we report that the nifa protein of h. seropedicae is inactive and more susceptible to degradation in an fnr escheri ...	2003	12620839
two families of mechanosensitive channel proteins.	mechanosensitive (ms) channels that provide protection against hypoosmotic shock are found in the membranes of organisms from the three domains of life: bacteria, archaea, and eucarya. two families of ubiquitous ms channels are recognized, and these have been designated the mscl and mscs families. a high-resolution x-ray crystallographic structure is available for a member of the mscl family, and extensive molecular genetic, biophysical, and biochemical studies conducted in many laboratories hav ...	2003	12626684
dual intracellular localization and targeting of aminoimidazole ribonucleotide synthetase in cowpea.	de novo purine biosynthesis is localized to both mitochondria and plastids isolated from bradyrhizobium sp.-infected cells of cowpea (vigna unguiculata l. walp) nodules, but several of the pathway enzymes, including aminoimidazole ribonucleotide synthetase (airs [ec 6.3.3.1], encoded by vupur5), are encoded by single genes. immunolocalization confirmed the presence of airs protein in both organelles. enzymatically active airs was purified separately from nodule mitochondria and plastids. n-termi ...	2003	12644656
identification and characterization of a mandelamide hydrolase and an nad(p)+-dependent benzaldehyde dehydrogenase from pseudomonas putida atcc 12633.	the enzymes of the mandelate metabolic pathway permit pseudomonas putida atcc 12633 to utilize either or both enantiomers of mandelate as the sole carbon source. the genes encoding the mandelate pathway were found to lie on a single 10.5-kb restriction fragment. part of that fragment was shown to contain the genes coding for mandelate racemase, mandelate dehydrogenase, and benzoylformate decarboxylase arranged in an operon. here we report the sequencing of the remainder of the restriction fragme ...	2003	12670968
phosphorylation of soybean nodulin 26 on serine 262 enhances water permeability and is regulated developmentally and by osmotic signals.	soybean nodulin 26 is expressed and targeted to the symbiosome membrane of nitrogen-fixing nodules, where it forms an aquaporin channel with a modest water transport rate. in this study, we show that the phosphorylation of nodulin 26 on ser-262, which is catalyzed by a symbiosome membrane-associated calcium-dependent protein kinase, stimulates its intrinsic water transport rate. furthermore, using a phosphospecific antibody, we have elucidated the developmental appearance and regulation of nodul ...	2003	12671092
phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.	the examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. we developed a method for aseptically sampling a sediment-containing portion of a greenland ice core that had remained at -9 degrees c for over 100,000 years. epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. anaerobic enrichment cultures inoculated w ...	2003	12676695
the enigmatic mitochondrial orf ymf39 codes for atp synthase chain b.	ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. we speculated earlier, based on a weak sequence similarity between ymf39 from a green alga and the atpf gene product from bradyrhizobium, that ymf39 might code for subunit b of mitochondrial f(0)f(1)-atp synthase. to test this hypothesis, we have sequenced ymf39 from five protists with minimally derived mitochondrial genomes, the jakobids. in addition, we isolated the mitocho ...	2003	12711680
fur is not the global regulator of iron uptake genes in rhizobium leguminosarum.	rhizobium leguminosarum fur mutants were unaffected in fe-dependent regulation of several operons that specify different fe uptake systems, yet cloned r. leguminosarum fur partially corrected an escherichia coli fur mutant and r. leguminosarum fur protein bound to canonical fur boxes. the lack of a phenotype in fur mutants is not due to functional redundancy with irr, another member of the fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in fe-responsive re ...	2003	12724397
structural and functional defects caused by point mutations in the alpha-crystallin domain of a bacterial alpha-heat shock protein.	the diverse family of alpha-crystallin-type small heat shock proteins (alpha-hsps or shsps) is characterised by a central, moderately conserved alpha-crystallin domain. oligomerisation followed by dissociation of subparticles is thought to be a prerequisite for chaperone function. we demonstrate that hsph, a bacterial alpha-hsp from the soybean-symbiont bradyrhizobium japonicum, assembles into dynamic complexes freely exchanging subunits with homologous and heterologous complexes. the importance ...	2003	12729765
roses by other names: taxonomy of the rhizobiaceae.		2003	12730155
discordant phylogenies within the rrn loci of rhizobia.	it is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-proteobacteria by sequencing analysis of three loci within their rrn operons. tree topologies generated with 16s rrna gene sequences were ...	2003	12730157
the ftsh gene of the wine bacterium oenococcus oeni is involved in protection against environmental stress.	the wine bacterium oenococcus oeni has to cope with harsh environmental conditions, including an acidic ph, a high alcoholic content, nonoptimal growth temperatures, and growth-inhibitory compounds such as fatty acids, phenolic acids, and tannins. we describe the characterization and cloning of the o. oeni ftsh gene, encoding a protease belonging to the atp binding cassette protein superfamily. the o. oeni ftsh protein is closest in sequence similarity to the ftsh homologue of lactococcus lactis ...	2003	12732516
genetic characterization of escherichia coli populations from host sources of fecal pollution by using dna fingerprinting.	escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (rep) pcr fingerprinting. the genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. rep pcr fingerpr ...	2003	12732525
new nodw- or nifa-regulated bradyrhizobium japonicum genes.	a cluster of genes coding for putative plant cell-wall degrading enzymes (i.e., genes for two endoglucanases [guna and guna2], one pectinmethylesterase [pme], and one polygalacturonase [pgl]) was identified by sequence similarities in the symbiotic region of the bradyrhizobium japonicum chromosome. in addition, a systematic screen of the region revealed several genes potentially transcribed by the sigma(54)-rna polymerase and activated by the transcriptional regulator nifa (i.e., genes for prote ...	2003	12744463
nitric oxide reductase (norb) genes from pure cultures and environmental samples.	a pcr-based approach was developed to recover nitric oxide (no) reductase (norb) genes as a functional marker gene for denitrifying bacteria. norb database sequences grouped in two very distinct branches. one encodes the quinol-oxidizing single-subunit class (qnorb), while the other class is a cytochrome bc-type complex (cnorb). the latter oxidizes cytochrome c, and the gene is localized adjacent to norc. while both norb types occur in denitrifying strains, the qnorb type was also found in a var ...	2003	12788753
molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the pacific coast of mexico.	to understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the pacific coast of mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a pcr-based cloning approach. a total of 50 operational taxonomic units (otus) for nirk and 82 otus for nirs were obtained from all samples. forty-four of the nirs clones and 31 of the nirk clones were sequenced; the levels of similarity of the nirs clones were 52 t ...	2003	12788762
citrate synthase mutants of sinorhizobium fredii usda257 form ineffective nodules with aberrant ultrastructure.	the tricarboxylic acid (tca) cycle plays an important role in generating the energy required by bacteroids to fix atmospheric nitrogen. citrate synthase is the first enzyme that controls the entry of carbon into the tca cycle. we cloned and determined the nucleotide sequence of the glta gene that encodes citrate synthase in sinorhizobium fredii usda257, a symbiont of soybeans (glycine max [l.] merr.) and several other legumes. the deduced citrate synthase protein has a molecular weight of 48,198 ...	2003	12788763
on the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of atzd from pseudomonas sp. strain adp.	cyanuric acid hydrolase (atzd) from pseudomonas sp. strain adp was purified to homogeneity. of 22 cyclic amides and triazine compounds tested, only cyanuric acid and n-methylisocyanuric acid were substrates. other cyclic amidases were found not to hydrolyze cyanuric acid. ten bacteria that use cyanuric acid as a sole nitrogen source for growth were found to contain either atzd or trzd, but not both genes.	2003	12788776
phylogeny and characterization of three nifh-homologous genes from paenibacillus azotofixans.	in this paper, we report the cloning and characterization of three paenibacillus azotofixans dna regions containing genes involved in nitrogen fixation. sequencing analysis revealed the presence of nifb1h1d1k1 gene organization in the 4,607-bp saci dna fragment. this is the first report of linkage of a nifb open reading frame upstream of the structural nif genes. the second (nifb2h2) and third (nifh3) nif homologues are confined within the 6,350-bp hindiii and 2,840-bp ecori dna fragments, respe ...	2003	12788777
inactivation of the nod box distal half-site allows tetrameric nodd to activate noda transcription in an inducer-independent manner.	in rhizobium leguminosarum, nodd can activate noda transcription in response to inducer flavonoids. here, we show that the inducible noda promoter contains an intrinsic part through which nodd can activate noda transcription in an inducer-independent manner. evidence was provided that nodd binds to target dna through anchoring the two half-sites of the nod box as a tetramer. an imperfect inverted repeat at-n10-gat was found in each half-site and is critical for nodd binding. mutation of the inve ...	2003	12799442
the mosaic structure of the symbiotic plasmid of rhizobium etli cfn42 and its relation to other symbiotic genome compartments.	symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. in rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. to understand the structure and evolution of the symbiotic genome compartments (sgcs), it is necessary to analyze their common genetic content and organization as well as to study their differences. to date, five sgcs belonging to distinct spec ...	2003	12801410
identification and characterization of transposable elements of paracoccus pantotrophus.	we studied diversity and distribution of transposable elements residing in different strains (dsm 11072, dsm 11073, dsm 65, and lmd 82.5) of a soil bacterium paracoccus pantotrophus (alpha-proteobacteria). with application of a shuttle entrapment vector pmec1, several novel insertion sequences (iss) and transposons (tns) have been identified. they were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, termin ...	2003	12813068
the c-terminal flexible domain of the heme chaperone ccme is important but not essential for its function.	ccme is a heme chaperone active in the cytochrome c maturation pathway of escherichia coli. it first binds heme covalently to strictly conserved histidine h130 and subsequently delivers it to apo-cytochrome c. the recently solved structure of soluble ccme revealed a compact core consisting of a beta-barrel and a flexible c-terminal domain with a short alpha-helical turn. in order to elucidate the function of this poorly conserved domain, ccme was truncated stepwise from the c terminus. removal o ...	2003	12813076
bradyrhizobium japonicum nnrr, a denitrification regulator, expands the fixlj-fixk2 regulatory cascade.	in bradyrhizobium japonicum, a gene named nnrr was identified which encodes a protein with high similarity to fnr/crp-type transcriptional regulators. mutant strains carrying an nnrr null mutation were unable to grow anaerobically in the presence of nitrate or nitrite, and they lacked both nitrate and nitrite reductase activities. anaerobic activation of an nnrr'-'lacz fusion required fixlj and fixk(2). in turn, n oxide-mediated induction of nir and nor genes encoding nitrite and nitric oxide re ...	2003	12813094
a distal arginine in oxygen-sensing heme-pas domains is essential to ligand binding, signal transduction, and structure.	to evaluate the contributions of the g(beta)-2 arginine to signal transduction in oxygen-sensing heme-pas domains, we replaced this residue with alanine in bradyrhizobium japonicum fixl and examined the results on heme-domain structure, ligand binding, and kinase regulation. in the isolated r220a bjfixl heme-pas domain, the iron-histidine bond was increased in length by 0.31 a, the heme flattened even without a ligand, and the interaction of a presumed regulatory loop (the fg loop) with the heli ...	2003	12820879
molecular and functional analysis of the lepb gene, encoding a type i signal peptidase from rickettsia rickettsii and rickettsia typhi.	the type i signal peptidase lepb genes from rickettsia rickettsii and rickettsia typhi, the etiologic agents of rocky mountain spotted fever and murine typhus, respectively, were cloned and characterized. sequence analysis of the cloned lepb genes from r. rickettsii and r. typhi shows open reading frames of 801 and 795 nucleotides, respectively. alignment analysis of the deduced amino acid sequences reveals the presence of highly conserved motifs that are important for the catalytic activity of ...	2003	12867468
expression cloning and biochemical characterization of a rhizobium leguminosarum lipid a 1-phosphatase.	lipid a of rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, displays several significant structural differences when compared with escherichia coli. an especially striking feature of r. leguminosarum lipid a is that it lacks both the 1- and 4'-phosphate groups. distinct lipid a phosphatases that attack either the 1 or the 4' positions have previously been identified in extracts of r. leguminosarum and rhizobium etli but not sinorhizobium meliloti or e. coli. here we describe the id ...	2003	12869541
a novel dna-binding site for the ferric uptake regulator (fur) protein from bradyrhizobium japonicum.	the fur protein is a global regulator of iron metabolism and other processes in many bacterial species. a key feature of the model of fur function is the recognition of a dna element within target promoters with similarity to a 19-bp at-rich palindromic sequence called a fur box. the irr gene from bradyrhizobium japonicum is under the control of fur. here, we provide evidence that b. japonicum fur (bjfur) binds to the irr gene promoter with high affinity despite the absence of dna sequence simil ...	2003	12881516
comparative analysis of the bradyrhizobium japonicum suca region.	to study the adjustments made to the tricarboxylic acid cycle during symbiosis of nitrogen-fixing rhizobia with their host legumes, we have characterized the genes encoding the alpha-ketoglutarate dehydrogenase enzyme complex in bradyrhizobium japonicum. the genes were arranged in the order suca-sucb-scda-lpda, where scdarepresents a short-chain dehydrogenase gene (genbank accession no. ay049030). all four genes appeared to be co-transcribed, an arrangement that is so far unique to b. japonicum. ...	2003	12897832
rhizobium leguminosarum biovar viciae 1-aminocyclopropane-1-carboxylate deaminase promotes nodulation of pea plants.	ethylene inhibits nodulation in various legumes. in order to investigate strategies employed by rhizobium to regulate nodulation, the 1-aminocyclopropane-1-carboxylate (acc) deaminase gene was isolated and characterized from one of the acc deaminase-producing rhizobia, rhizobium leguminosarum bv. viciae 128c53k. acc deaminase degrades acc, the immediate precursor of ethylene in higher plants. through the action of this enzyme, acc deaminase-containing bacteria can reduce ethylene biosynthesis in ...	2003	12902221
a cytochrome c from a lupanine-transforming pseudomonas putida strain is expressed in escherichia coli during aerobic cultivation and efficiently exported and assembled in the periplasm.	we have cloned, sequenced, and heterologously expressed a periplasmic cytochrome c from a lupanine-utilizing pseudomonas putida strain. aerobic batch cultivation of escherichia coli tb1 harboring the cytochrome c gene placed downstream of the lac promoter in puc9 vector resulted in significant production of the holo-cytochrome c in the periplasm ( approximately 4 mg of hemoprotein/liter of culture). the recombinant cytochrome c was purified to homogeneity and was found to be functional in accept ...	2003	12902264
high-level production of porphyrins in metabolically engineered escherichia coli: systematic extension of a pathway assembled from overexpressed genes involved in heme biosynthesis.	due to their spectroscopic properties porphyrins are of special interest for a variety of applications, ranging from drug development or targeting to material sciences and chemical and biological sensors. since chemical syntheses are limited in terms of regio- and stereoselective functionalization of porphyrins, a biosynthetic approach with tailored enzyme catalysts offers a promising alternative. in this paper, we describe assembly of the entire heme biosynthetic pathway in a three-plasmid syst ...	2003	12902282
the ti plasmid of agrobacterium tumefaciens harbors an attm-paralogous gene, aiib, also encoding n-acyl homoserine lactonase activity.	the agrobacterium tumefaciens c58 genome contains three putative n-acyl homoserine lactone (acyl-hsl) hydrolases, which are closely related to the lactonase aiia of bacillus. when expressed in escherichia coli, two of the putative acyl-hsl hydrolases, attm and aiib, conferred the ability to degrade acyl-hsls on the host. in erwinia strain 6276, the lactonases reduced the endogenous acyl-hsl level and the bacterial virulence in planta.	2003	12902298
identification of extracytoplasmic proteins in bradyrhizobium japonicum using phage display.	a novel gene bank of bradyrhizobium japonicum usda110spc4 was constructed using pg3dss, a phagemid vector designed for detecting genes encoding secreted proteins. in this phagemid, the phage protein iii lacks its indigenous signal peptide required for protein secretion, thus recombinant fusion proteins are displayed on the phage surface only if a functional signal peptide is provided by an inserted dna fragment. in addition, the n-terminal half of protein iii has been replaced by a short linker ...	2003	12906117
effect of trehalose on survival of bradyrhizobium japonicum during desiccation.	a major reason for the ineffectiveness of legume inoculants in the field is the rapid death of rhizobia because of desiccation. the major purpose of this study was to identify conditions under which alpha,alpha-trehalose would improve survival of bradyrhizobium japonicum during desiccation.	2003	12911696
application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.	a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes.	2003	12914674
regulation of the vitamin b12 metabolism and transport in bacteria by a conserved rna structural element.	cobalamin in the form of adenosylcobalamin (ado-cbl) is known to repress expression of genes for vitamin b(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of ado-cbl to 5'untranslated gene regions (5'utr). using comparative analysis of genes and regulatory regions, we identified a highly conserved rna structure, the b12-element, which is widely distributed in 5'utrs of vitamin b(12)-related genes in eubacteria. multiple alignment o ...	2003	12923257
disparate oxygen responsiveness of two regulatory cascades that control expression of symbiotic genes in bradyrhizobium japonicum.	two oxygen-responsive regulatory systems controlling numerous symbiotic genes in bradyrhizobium japonicum were assayed in free-living cultures for their capacity to activate target genes under different oxygen conditions. nifa- and fixlj-controlled target genes showed disparate relative expression patterns. induction of nifa-dependent genes was observed only at oxygen concentrations below 2% in the gas phase, whereas that of fixlj-controlled targets progressively increased when the oxygen concen ...	2003	12949117
ancient origin of the tryptophan operon and the dynamics of evolutionary change.	the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ...	2003	12966138
an improved probability mapping approach to assess genome mosaicism.	maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. however, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. here we extend the probability mapping approach by improving taxon sampling o ...	2003	12974984
bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.	a strictly aerobic, mesophilic bacterium, strain amx 51(t), was isolated from anaerobic digester sludge. cells were gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum. the isolate had phenotypic traits of the genus bosea, including cellular fatty acid and substrate utilization profiles. physiological characteristics and antibiotic susceptibility were determined. phylogenetic analysis revealed that strain amx 51(t) was a member of the alpha-proteobacteria, mo ...	2003	13130002
[polysaccharides produced by rhizobium strains; oligosaccharides produced by acid hydrolysis of rhizobium japonicum polysaccharides].		1958	13537427
the effect of cobalt on the growth of rhizobium japonicum.		1960	13763818
growth inhibition by biotin in a strain of rhizobium japonicum.		1963	14066493
quick serological method of classifying strains of rhizobium japonicum in nodules.	means, ura m. (u.s. department of agriculture, beltsville, md.), herbert w. johnson, and r. a. date. quick serological method of classifying strains of rhizobium japonicum in nodules. j. bacteriol. 87:547-553. 1964.-a new method of classifying strains of rhizobium japonicum serologically by utilizing the contents of nodules as antigens is described. the method differs from standard procedures only in the preparation of antigens, but it is less time-consuming. agglutination reactions of culture a ...	1964	14127569
preparation and some properties of a soluble nitrate reductase from rhizobium japonicum.		1964	14194853
influence of gamma radiation on the nitrogen fixation activity of rhizobium japonicum in symbiosis with two varieties of soy-beans.		1964	14211345
the enzymatic synthesis of a (beta-i,2-)-linked glucan by an extract of rhizobium japonicum.		1964	14220709
minimal antigenic constitution of 28 strains of rhizobium japonicum.		1965	14290956
[study of the polysaccharides produced by strains of rhizobium. structure of 2 trisaccharide from rhizobium japonicum].		1960	14415498
2-oxoglutarate:nadp(+) oxidoreductase in azoarcus evansii: properties and function in electron transfer reactions in aromatic ring reduction.	the conversion of [(14)c]benzoyl-coenzyme a (coa) to nonaromatic products in the denitrifying beta-proteobacterium azoarcus evansii grown anaerobically on benzoate was investigated. with cell extracts and 2-oxoglutarate as the electron donor, benzoyl-coa reduction occurred at a rate of 10 to 15 nmol min(-1) mg(-1). 2-oxoglutarate could be replaced by dithionite (200% rate) and by nadph ( approximately 10% rate); in contrast nadh did not serve as an electron donor. anaerobic growth on aromatic co ...	2003	14526024
community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils.	we investigated communities of denitrifying bacteria from adjacent meadow and forest soils. our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosz, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. denit ...	2003	14532052
low sequence similarity and gene content of symbiotic clusters of bradyrhizobium sp. wm9 (lupinus) indicate early divergence of "lupin" lineage in the genus bradyrhizobium.	two sequenced nodulation regions of lupin bradyrhizobium sp. wm9 carried the majority of genes involved in the nod factor production. the nod region i harbored: nola, nodd, noda, nodb, nodc, nods, nodi, nodj, nolo, nodz, fixr, nifa, fixa, nodm, nolk and noel. this gene arrangement resembled that found in the nodulation region of bradyrhizobium japonicum usda110, however strain wm9 harbored only one nodd gene copy, while the nodm, nolk and noel genes had no counterparts in the 410 kb symbiotic re ...	2003	14533715
the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons.	is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ...	2003	14563872
shotgun phage display - selection for bacterial receptins or other exported proteins.	shotgun phage display cloning involves construction of libraries from randomly fragmented bacterial chromosomal dna, cloned genes, or eukaryotic cdnas, into a phagemid vector. the library obtained consists of phages expressing polypeptides corresponding to all genes encoded by the organism, or overlapping peptides derived from the cloned gene. from such a library, polypeptides with affinity for another molecule can be isolated by affinity selection, panning. the technique can be used to identify ...	2003	14569614
prediction of reduction potential changes in rubredoxin: a molecular mechanics approach.	predicting the effects of mutation on the reduction potential of proteins is crucial in understanding how reduction potentials are modulated by the protein environment. previously, we proposed that an alanine vs. a valine at residue 44 leads to a 50-mv difference in reduction potential found in homologous rubredoxins because of a shift in the polar backbone relative to the iron site due to the different side-chain sizes. here, the aim is to determine the effects of mutations to glycine, isoleuci ...	2003	14581187
usefulness of rpob gene sequencing for identification of afipia and bosea species, including a strategy for choosing discriminative partial sequences.	bacteria belonging to the genera afipia and bosea are amoeba-resisting bacteria that have been recently reported to colonize hospital water supplies and are suspected of being responsible for intensive care unit-acquired pneumonia. identification of these bacteria is now based on determination of the 16s ribosomal dna sequence. however, the 16s rrna gene is not polymorphic enough to ensure discrimination of species defined by dna-dna relatedness. the complete rpob sequences of 20 strains were fi ...	2003	14602635
development and application of a dapb-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium pseudomonas stutzeri a15.	pseudomonas stutzeri a15 is a nitrogen-fixing bacterium isolated from paddy rice. strain a15 is able to colonize and infect rice roots. this strain may provide rice plants with fixed nitrogen and hence promote plant growth. in this article, we describe the use of dapb-based in vivo expression technology to identify p. stutzeri a15 genes that are specifically induced during colonization and infection (cii). we focused on the identification of p. stutzeri a15 genes that are switched on during rice ...	2003	14602651
identification and use of actinomycetes for enhanced nodulation of soybean co-inoculated with bradyrhizobium japonicum.	the utilization of actinomycetes as potential soybean (glycine max (l.)) co-inoculants was evaluated. soil samples from carbondale and belleville, ill., were used to inoculate pre-germinated soybean plants to determine antibiotic sensitivity in the native bradyrhizobium japonicum population. sensitivity was in the order kanamycin > tetracycline > oxytetracycline > rifampicin > neomycin. antagonism by five actinomycete cultures toward seven test strains of b. japonicum was also assessed. the rank ...	2003	14608383
acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics.	acidobacteria have been established as a novel phylum of bacteria that is consistently detected in many different habitats around the globe by 16s rdna-based molecular surveys. the phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important ecological role and extensive metabolic versatility. however, the genetic and physiological information about acidobacteria is scarce. in order to gain insight into genome structure, evolution and diversit ...	2003	14617179
identification and characterization of the nickel uptake system for urease biogenesis in streptococcus salivarius 57.i.	ureases are multisubunit enzymes requiring ni(2+) for activity. the low ph-inducible urease gene cluster in streptococcus salivarius 57.i is organized as an operon, beginning with urei, followed by ureabc (structural genes), and ureefgd (accessory genes). urease biogenesis also requires a high-affinity ni(2+) uptake system. by searching the partial genome sequence of a closely related organism, streptococcus thermophilus lmg18311, three open reading frame (orfs) homologous to those encoding prot ...	2003	14617641
[survival of bradyrhizobium japonicum strain 646a introduced into soil of the soybean, common bean and maize rhizosphere].	the number dynamics of bradyrhizobium japonicum strain 646a introduced into soil in the soybean, common bean and maize rhizosphere and its dependence on inoculum doses have been studied in greenhouse experiments. it was shown that b. japonicum number in the maize, common bean and soybean rhizosphere depends on the inoculum doses (r = 0.79-0.95). it was less than 0.1% of total saprophytic bacteria number and it had no essential effect on this plant productivity. the soybean symbiosis with nodule ...	2003	14618780
solution structure and dna binding of the effector domain from the global regulator prra (rega) from rhodobacter sphaeroides: insights into dna binding specificity.	prr/rega response regulator is a global transcription regulator in purple bacteria rhodobacter sphaeroides and rhodobacter capsulatus, and is essential in controlling the metabolic changes between aerobic and anaerobic environments. we report here the structure determination by nmr of the c-terminal effector domain of prra, prrac. it forms a three-helix bundle containing a helix-turn-helix dna binding motif. the fold is similar to fis protein, but the domain architecture is different from previo ...	2003	14627811
a dna element recognised by the molybdenum-responsive transcription factor mode is conserved in proteobacteria, green sulphur bacteria and archaea.	the transition metal molybdenum is essential for life. escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an abc transport system. in e. coli and other proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor mode.	2003	14641908
interaction between the h2 sensor hupuv and the histidine kinase hupt controls hupsl hydrogenase synthesis in rhodobacter capsulatus.	the photosynthetic bacterium rhodobacter capsulatus contains two [nife]hydrogenases: an energy-generating hydrogenase, hupsl, and a regulatory hydrogenase, hupuv. the synthesis of hupsl is specifically activated by h(2) through a signal transduction cascade comprising three proteins: the h(2)-sensing hupuv protein, the histidine kinase hupt, and the transcriptional regulator hupr. whereas a phosphotransfer between hupt and hupr was previously demonstrated, interaction between hupuv and hupt was ...	2003	14645270
molecular and cell biology of a family of voltage-dependent anion channel porins in lotus japonicus.	voltage-dependent anion channels (vdacs) are generally considered as the main pathway for metabolite transport across the mitochondrial outer membrane. recent proteomic studies on isolated symbiosome membranes from legume nodules indicated that vdacs might also be involved in transport of nutrients between plants and rhizobia. in an attempt to substantiate this, we carried out a detailed molecular and cellular characterization of vdacs in lotus japonicus and soybean (glycine max). database searc ...	2004	14657408
new connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated rna decay system.	several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. recent findings suggest that chromosomally encoded copies of toxins and antitoxins of post-segregational cell killing systems - such as the rele system - might function as regulatory switches under stress conditions. the rele toxin cleaves ribosome-associated transcripts, whereas another post-segregational cell killing toxin, pare, functions as a gyrase inhibitor.	2003	14659018
identification and distribution of insertion sequences of paracoccus solventivorans.	three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ...	2003	14660342
biochemical, genetic, and zoosporicidal properties of cyclic lipopeptide surfactants produced by pseudomonas fluorescens.	zoospores play an important role in the infection of plant and animal hosts by oomycetes and other zoosporic fungi. in this study, six fluorescent pseudomonas isolates with zoosporicidal activities were obtained from the wheat rhizosphere. zoospores of multiple oomycetes, including pythium species, albugo candida, and phytophthora infestans, were rendered immotile within 30 s of exposure to cell suspensions or cell culture supernatants of the six isolates, and subsequent lysis occurred within 60 ...	2003	14660362
laboratory cultivation of widespread and previously uncultured soil bacteria.	most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. we cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. these isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative analysis of their 16s rrna genes. ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. they ...	2003	14660368
molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity.	isolates belonging to six genera not previously known to oxidize co were obtained from enrichments with aquatic and terrestrial plants. dna from these and other isolates was used in pcr assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxl). coxl and putative coxl fragments were amplified from known co oxidizers (e.g., oligotropha carboxidovorans and bradyrhizobium japonicum), from novel co-oxidizing isolates (e.g., aminobacter sp. strain cox, burkholderia sp. strain lu ...	2003	14660374
metagenome survey of biofilms in drinking-water networks.	most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. first, a sequence analysis of 650 16s rrna clones indicated a high diversity within the biofilm communities, with the ma ...	2003	14660379
phylogenetic and biochemical evidence for sterol synthesis in the bacterium gemmata obscuriglobus.	sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. in this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryo ...	2003	14660793
the bradyrhizobium japonicum napedabc genes encoding the periplasmic nitrate reductase are essential for nitrate respiration.	the napedabc gene cluster that encodes the periplasmic nitrate reductase from bradyrhizobium japonicum usda110 has been isolated and characterized. napa encodes the catalytic subunit, and the napb and napc gene products are predicted to be a soluble dihaem c and a membrane-anchored tetrahaem c-type cytochrome, respectively. nape encodes a transmembrane protein of unknown function, and the napd gene product is a soluble protein which is assumed to play a role in the maturation of napa. western bl ...	2003	14663073