Publications

fingerprinting of cyanobacteria based on pcr with primers derived from short and long tandemly repeated repetitive sequences.	the presence of repeated dna (short tandemly repeated repetitive [strr] and long tandemly repeated repetitive [ltrr]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. primers corresponding to the strr and ltrr sequences were used in the pcr, resulting in a method which generate specific fingerprints for individual isolates. the method was useful both with purified dna and with intact cyanobacterial filaments or cells as te ...	1998	16349487
the vibrio fischeri-euprymna scolopes light organ association: current ecological paradigms.		1998	16349524
lipopolysaccharide profiles from nodules as markers of bradyrhizobium strains nodulating wild legumes.	to develop the use of electrophoretic lipopolysaccharide profiles for bradyrhizobium strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. the electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. to assess the reliability of using lip ...	1998	16349529
distribution of a population of rhizobium leguminosarum bv. trifolii among different size classes of soil aggregates.	a combination of the plant infection-soil dilution technique (most-probable-number [mpn] technique) and immunofluorescence direct count (ifdc) microscopy was used to examine the effects of three winter cover crop treatments on the distribution of a soil population of rhizobium leguminosarum bv. trifolii across different size classes of soil aggregates (<0.25, 0.25 to 0.5, 0.5 to 1.0, 1.0 to 2.0, and 2.0 to 5.0 mm). the aggregates were prepared from a willamette silt loam soil immediately after h ...	1998	16349531
spatial and temporal deposition of adhesive extracellular polysaccharide capsule and fimbriae by hyphomonas strain mhs-3.	hyphomonas strain mhs-3, a member of a genus of primary colonizers of surfaces immersed in marine water, synthesizes two structures that mediate adhesion to solid substrata, namely, capsular exopolysaccharide and fimbriae. specific stains, gold-labelled lectins, and monoclonal antibodies, along with transmission electron microscopy of synchronized populations, revealed that both structures are polarly and temporally expressed. the timed synthesis and placement of the fimbriae and capsule correla ...	1998	16349537
effects of ionic and osmotic strength on the glucosyltransferase of rhizobium meliloti responsible for cyclic beta-(1,2)-glucan biosynthesis.	the cyclic beta-(1,2)-glucans of rhizobium meliloti and agrobacterium tumefaciens play an important role during hypoosmotic adaptation, and the synthesis of these compounds is osmoregulated. glucosyltransferase, the enzyme responsible for cyclic beta-(1,2)-glucan biosynthesis, is present constitutively, suggesting that osmotic regulation of the biosynthesis of these glucans occurs through modulation of enzyme activity. in this study, we examined regulation of cyclic glucan biosynthesis in vitro ...	1998	16349538
characterization of mimivirus dna topoisomerase ib suggests horizontal gene transfer between eukaryal viruses and bacteria.	mimivirus, a parasite of acanthamoeba polyphaga, is the largest dna virus known; it encodes dozens of proteins with imputed functions in nucleic acid transactions. here we produced, purified, and characterized mimivirus dna topoisomerase ib (topib), which we find to be a structural and functional homolog of poxvirus topib and the poxvirus-like topoisomerases discovered recently in bacteria. arginine, histidine, and tyrosine side chains responsible for topib transesterification are conserved and ...	2006	16352556
role of the novel oprd family of porins in nutrient uptake in pseudomonas aeruginosa.	to circumvent the permeability barrier of its outer membrane, pseudomonas aeruginosa has evolved a series of specific porins. these channels have binding sites for related classes of molecules that facilitate uptake under nutrient-limited conditions. here, we report on the identification of a 19-member family of porins similar to the basic-amino-acid-specific porin oprd. the members of this family fell into one of two phylogenetically distinct clusters, one bearing high similarity to oprd and th ...	2006	16352820
comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of atp-binding cassette transporters.	the transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. we integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. for functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cob ...	2006	16352848
nod bj-v (c18:1, mefuc) production by bradyrhizobium japonicum (usda110, 532c) at suboptimal growth temperatures.	nod factors (lipo-chitooligosaccharides, or lcos) act as bacteria-to-plant signal molecules that modulate early events of the bradyrhizobium-soybean symbiosis. it is known that low root zone temperature inhibits the early stages of this symbiosis; however, the effect of low soil temperature on bacteria-to-plant signaling is largely uninvestigated. we evaluated the effect of low growth temperatures on the production kinetics of nod factor (lco) by b. japonicum. two strains of b. japonicum, 532c a ...	2006	16360810
effect of two amf life strategies on the tripartite symbiosis with bradyrhizobium japonicum and soybean.	this study is the first in assessing the effect of soil disturbance on the contribution of arbuscular mycorrhizal fungi (amf) with different life-history strategies to the tripartite symbiosis with soybeans and bradyrhizobium japonicum (kirchner) jordan. we hypothesized that gigaspora margarita becker and hall would be more affected by soil disturbance than glomus clarum nicol. and schenck, and consequently, the tripartite symbiosis would develop more rapidly and lead to greater n(2) fixation in ...	2006	16362418
evidence for an essential function of the n terminus of a small heat shock protein in vivo, independent of in vitro chaperone activity.	to investigate the mechanism of small heat shock protein (shsp) function, unbiased by current models of shsp chaperone activity, we performed a screen for mutations of synechocystis hsp16.6 that reduced the ability of the protein to provide thermotolerance in vivo. missense mutations at 17 positions throughout the protein and a c-terminal truncation of 5 aa were identified, representing the largest collection of shsp mutants impaired in function in vivo. ten mutant proteins were purified and tes ...	2005	16365319
odb: a database of operons accumulating known operons across multiple genomes.	operon structures play an important role in co-regulation in prokaryotes. although over 200 complete genome sequences are now available, databases providing genome-wide operon information have been limited to certain specific genomes. thus, we have developed an odb (operon database), which provides a data retrieval system of known operons among the many complete genomes. additionally, putative operons that are conserved in terms of known operons are also provided. the current version of our data ...	2005	16381886
odb: a database of operons accumulating known operons across multiple genomes.	operon structures play an important role in co-regulation in prokaryotes. although over 200 complete genome sequences are now available, databases providing genome-wide operon information have been limited to certain specific genomes. thus, we have developed an odb (operon database), which provides a data retrieval system of known operons among the many complete genomes. additionally, putative operons that are conserved in terms of known operons are also provided. the current version of our data ...	2005	16381886
metacyc: a multiorganism database of metabolic pathways and enzymes.	metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...	2005	16381923
metacyc: a multiorganism database of metabolic pathways and enzymes.	metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...	2005	16381923
the iron control element, acting in positive and negative control of iron-regulated bradyrhizobium japonicum genes, is a target for the irr protein.	bradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene cluster hmuvut-hmur-exbbd-tonb. transcription of the divergently oriented hmut and hmur genes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ice). here, we show by deletion analysis that the full-length ice is needed for this type of positive control. additional genes associated with ice-like motifs were identif ...	2006	16385063
functional characterization of the bradyrhizobium japonicum moda and modb genes involved in molybdenum transport.	a modabc gene cluster that encodes an abc-type, high-affinity molybdate transporter from bradyrhizobium japonicum has been isolated and characterized. b. japonicum moda and modb mutant strains were unable to grow aerobically or anaerobically with nitrate as nitrogen source or as respiratory substrate, respectively, and lacked nitrate reductase activity. the nitrogen-fixing ability of the mod mutants in symbiotic association with soybean plants grown in a mo-deficient mineral solution was severel ...	2006	16385130
cytochrome p450 alkane hydroxylases of the cyp153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases.	several strains that grow on medium-chain-length alkanes and catalyze interesting hydroxylation and epoxidation reactions do not possess integral membrane nonheme iron alkane hydroxylases. using pcr, we show that most of these strains possess enzymes related to cyp153a1 and cyp153a6, cytochrome p450 enzymes that were characterized as alkane hydroxylases. a vector for the polycistronic coexpression of individual cyp153 genes with a ferredoxin gene and a ferredoxin reductase gene was constructed. ...	2006	16391025
identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of methylosulfonomonas methylovora.	recently identified genes located downstream (3') of the msmef (transport encoding) gene cluster, msmgh, and located 5' of the structural genes for methanesulfonate monooxygenase (msamo) are described from methylosulfonomonas methylovora. sequence analysis of the derived polypeptide sequences encoded by these genes revealed a high degree of identity to abc-type transporters. msme showed similarity to a putative periplasmic substrate binding protein, msmf resembled an integral membrane-associated ...	2006	16391054
isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants.	the goal of this study was to initiate investigation of the genetics of bacterial poly-3-hydroxybutyrate (phb) metabolism at the community level. we constructed metagenome libraries from activated sludge and soil microbial communities in the broad-host-range incp cosmid prk7813. several unique clones were isolated from these libraries by functional heterologous complementation of a sinorhizobium meliloti bdha mutant, which is unable to grow on the phb cycle intermediate d-3-hydroxybutyrate due t ...	2006	16391068
rflp analysis of the rrna operon of a brazilian collection of bradyrhizobial strains from 33 legume species.	genetic diversity in tropical rhizobial species is still poorly known. with the aim of increasing this knowledge, three ribosomal regions of 119 strains belonging to the official brazilian culture collection of rhizobia and classified as bradyrhizobium based on morphological and physiological characteristics in vitro were analysed by rflp-pcr. the strains were isolated from 33 legume species, representing nine tribes and all three subfamilies; they all form very effective n2-fixing nodules and 4 ...	2006	16403890
identification of a ubiquinone-binding site that affects autophosphorylation of the sensor kinase regb.	rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. one of the key global redox regulators of the cell's metabolic physiology is the sensor kinase regb that controls the synthesis of numerous energy generation and utilization processes. in this study, we have succeeded in purifying full-length regb containing six transmembrane-spanning elements. exogenous addition of excess oxidized coenzyme q1 is capable of ...	2006	16407278
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.	recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...	2006	16407325
the bradyrhizobium japonicum napedabc genes are controlled by the fixlj-fixk(2)-nnrr regulatory cascade.	nitrate respiration by the n(2)-fixing symbiotic bacteria bradyrhizobium japonicum usda110 is mediated by a nap (periplasmic nitrate reductase) encoded by the napedabc genes. expression of a transcriptional fusion of the nap promoter region to the reporter gene lacz, p(nape)-lacz, was very low in aerobically grown cells of usda110, but expression was induced approx. 3-fold when the cells were cultured under microaerobic conditions, and 12-fold when nitrate was added to the microaerobic incubatio ...	2006	16417495
a multitude of crp/fnr-like transcription proteins in bradyrhizobium japonicum.	in bradyrhizobium japonicum, the nitrogen-fixing soya bean endosymbiont and facultative denitrifier, three crp (camp receptor protein)/fnr (fumarate and nitrate reductase regulatory protein)-type transcription factors [fixk(1), fixk(2) and nnrr (nitrite and nitric oxide reductase regulator)] have been studied previously in the context of the regulation of nitrogen fixation and denitrification. the gene expression of both fixk(1) and nnrr depends on fixk(2), which acts as a key distributor of the ...	2006	16417509
the role of bradyrhizobium japonicum nitric oxide reductase in nitric oxide detoxification in soya bean root nodules.	the identification of nitric oxide-bound leghaemoglobin within soya bean nodules has led to the question of how bradyrhizobium japonicum bacteroids overcome the toxicity of this nitric oxide. it has previously been shown that one candidate for nitric oxide detoxification, the respiratory nitric oxide reductase, is expressed in soya bean nodules from plants supplied with nitrate. in this paper, the role of this enzyme in nitric oxide detoxification is assessed and discussion is provided on other ...	2006	16417520
potential for alternative intron-exon pairings in group ii intron rmint1 from sinorhizobium meliloti and its relatives.	ribozyme constructs derived from group ii intron rmint1 of sinorhizobium meliloti self-splice in vitro when incubated under permissive conditions, but exon ligation is unusually inefficient when the 5' exon is truncated close to the ibs2 intron-binding site. one plausible explanation for this observation is the presence of an alternative intron-exon pairing between an intron segment that overlaps with the ebs2 exon-binding site and a 5' exon site located just distal of ibs2 relative to the splic ...	2006	16431983
a reinforced merging methodology for mapping unique peptide motifs in members of protein families.	members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-d) structures. however, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. it is probable that each of their variable regions consists of a unique peptide motif (upm), which selectively interacts with other cellular proteins, rendering additional biological activities. ...	2006	16433931
blast screening of chlamydial genomes to identify signature proteins that are unique for the chlamydiales, chlamydiaceae, chlamydophila and chlamydia groups of species.	chlamydiae species are of much importance from a clinical viewpoint. their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. the obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. thus, it is of importance to develop additional means for their identification and characterization.	2006	16436211
effect of plant growth promoting rhizobacteria containing acc-deaminase on maize (zea mays l.) growth under axenic conditions and on nodulation in mung bean (vigna radiata l.).	this study was conducted to test the hypothesis that the bacterial strains possessing 1-aminocyclopropane-1-carboxylic acid (acc)-deaminase activity may also promote growth of inoculated plants and could increase nodulation in legumes upon co-inoculation with rhizobia.	2006	16441381
molecular phylogeny based on the 16s rrna gene of elite rhizobial strains used in brazilian commercial inoculants.	nitrogen is often a limiting nutrient, therefore the sustainability of food crops, forages and green manure legumes is mainly associated with their ability to establish symbiotic associations with stem and root-nodulating n2-fixing rhizobia. the selection, identification and maintenance of elite strains for each host are critical. decades of research in brazil resulted in a list of strains officially recommended for several legumes, but their genetic diversity is poorly known. this study aimed a ...	2006	16442259
oxygen reactivity of puta from helicobacter species and proline-linked oxidative stress.	proline is converted to glutamate in two successive steps by the proline utilization a (puta) flavoenzyme in gram-negative bacteria. puta contains a proline dehydrogenase domain that catalyzes the flavin adenine dinucleotide (fad)-dependent oxidation of proline to delta1-pyrroline-5-carboxylate (p5c) and a p5c dehydrogenase domain that catalyzes the nad+-dependent oxidation of p5c to glutamate. here, we characterize puta from helicobacter hepaticus (puta(hh)) and helicobacter pylori (puta(hp)) t ...	2006	16452403
pyruvate:quinone oxidoreductase in corynebacterium glutamicum: molecular analysis of the pqo gene, significance of the enzyme, and phylogenetic aspects.	corynebacterium glutamicum recently has been shown to possess pyruvate:quinone oxidoreductase (pqo), catalyzing the oxidative decarboxylation of pyruvate to acetate and co2 with a quinone as the electron acceptor. here, we analyze the expression of the c. glutamicum pqo gene, investigate the relevance of the pqo enzyme for growth and amino acid production, and perform phylogenetic studies. expression analyses revealed that transcription of pqo is initiated 45 bp upstream of the translational sta ...	2006	16452416
tetrapyrrole biosynthesis in rhodobacter capsulatus is transcriptionally regulated by the heme-binding regulatory protein, hbrl.	we demonstrate that the expression of hem genes in rhodobacter capsulatus is transcriptionally repressed in response to the exogenous addition of heme. a high-copy suppressor screen for regulators of hem gene expression resulted in the identification of an lysr-type transcriptional regulator, called hbrl, that regulates hem promoters in response to the availability of heme. hbrl is shown to activate the expression of hema and hemz in the absence of exogenous hemin and repress hemb expression in ...	2006	16452440
expression of nodule-specific uricase in soybean callus tissue is regulated by oxygen.	in soybean root nodules the enzyme uricase is expressed concomitantly with nodule development. the initial expression of this protein does not depend on active nitrogen fixation, as demonstrated by analysis of uricase activity in effective and ineffective root nodules. however, the maximal level of uricase activity is determined by the infecting rhizobium japonicum strain. sterile root cultures and callus tissue, devoid of the microsymbiont, were incubated at varying oxygen concentrations and an ...	1986	16453663
glutamine synthetase genes are regulated by ammonia provided externally or by symbiotic nitrogen fixation.	glutamine synthetase is the key enzyme in the assimilation by plants of reduced nitrogen provided from either the soil or fixed symbiotically in association with rhizobium. we have isolated a number of cdna clones for soybean glutamine synthetase (gs) from a nodule-cdna library, using rna from polysomes immunoprecipitated by gs antibodies. transcripts corresponding to two clones differing in their 3' non-translated sequences were present in both root and nodule tissue; however, the concentration ...	1987	16453762
expression and functional analysis of the rhizobium meliloti nifa gene.	the translational initiation point for rhizobium meliloti nifa, the specific activator for nitrogen fixation (nif) genes, was determined. when expressed in an escherichia coli linked transcriptional-translational system the dna coding for the r.meliloti nifa gene produced four polypeptide bands of 71 000, 67 000, 62 000 and 59 000 daltons. there are three in-frame atg codons at the n-terminus of the gene; by replacing the poor ribosome binding sites of the native dna with a synthetic consensus r ...	1988	16453824
the naphthalene catabolic (nag) genes of polaromonas naphthalenivorans cj2: evolutionary implications for two gene clusters and novel regulatory control.	polaromonas naphthalenivorans cj2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (c.-o. jeon et al., proc. natl. acad. sci. usa 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. beginning from a 484-bp nagac-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. we found that the naph ...	2006	16461653
catabolism of 1,5-anhydro-d-fructose in sinorhizobium morelense s-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-d-fructose reductase and its application in sugar analysis and rare sugar synthesis.	the bacterium sinorhizobium morelense s-30.7.5 was isolated by a microbial screening using the sugar 1,5-anhydro-d-fructose (af) as the sole carbon source. this strain metabolized af by a novel pathway involving its reduction to 1,5-anhydro-d-mannitol (am) and the further conversion of am to d-mannose by c-1 oxygenation. growth studies showed that the af metabolizing capability is not confined to s. morelense s-30.7.5 but is a more common feature among the rhizobiaceae. the af reducing enzyme wa ...	2006	16461673
expression cloning and periplasmic orientation of the francisella novicida lipid a 4'-phosphatase lpxf.	francisella tularensis and related intracellular pathogens synthesize lipid a molecules that differ from their escherichia coli counterparts. although a functional orthologue of lpxk, the gene encoding the lipid a 4'-kinase, is present in francisella, no 4'-phosphate moiety is attached to francisella lipid a. we now demonstrate that a membrane-bound phosphatase present in francisella novicida u112 selectively removes the 4'-phosphate residue from tetra- and pentaacylated lipid a molecules. a clo ...	2006	16467300
tfam detects co-evolution of trna identity rules with lateral transfer of histidyl-trna synthetase.	we present tfam, an automated, statistical method to classify the identity of trnas. tfam, currently optimized for bacteria, classifies initiator trnas and predicts the charging identity of both typical and atypical trnas such as suppressors with high confidence. we show statistical evidence for extensive variation in trna identity determinants among bacterial genomes due to variation in overall tdna base content. with tfam we have detected the first case of eukaryotic-like trna identity rules i ...	2006	16473847
functional implications of the propionate 7-arginine 220 interaction in the fixlh oxygen sensor from bradyrhizobium japonicum.	bjfixl from bradyrhizobium japonicum is a heme-based oxygen sensor implicated in the signaling cascade that enables the bacterium to adapt to fluctuating oxygen levels. signal transduction is initiated by the binding of o(2) to the heme domain of bjfixl, resulting in protein conformational changes that are transmitted to a histidine kinase domain. we report structural changes of the heme and its binding pocket in the fe(ii) deoxy and fe(iii) met states of the wild-type bjfixlh oxygen sensor doma ...	2006	16475796
rhizobial exopolysaccharides: genetic control and symbiotic functions.	specific complex interactions between soil bacteria belonging to rhizobium, sinorhizobium, mesorhizobium, phylorhizobium, bradyrhizobium and azorhizobium commonly known as rhizobia, and their host leguminous plants result in development of root nodules. nodules are new organs that consist mainly of plant cells infected with bacteroids that provide the host plant with fixed nitrogen. proper nodule development requires the synthesis and perception of signal molecules such as lipochitooligosacchari ...	2006	16483356
brucella abortus synthesizes phosphatidylcholine from choline provided by the host.	the brucella cell envelope is characterized by the presence of phosphatidylcholine (pc), a common phospholipid in eukaryotes that is rare in prokaryotes. studies on the composition of brucella abortus 2308 phospholipids revealed that the synthesis of pc depends on the presence of choline in the culture medium, suggesting that the methylation biosynthetic pathway is not functional. phospholipid composition of pmta and pcs mutants indicated that in brucella, pc synthesis occurs exclusively via the ...	2006	16484204
isolation and characterization of type i signal peptidase of different malaria parasites.	type i signal peptidases are important membrane-bound serine proteases responsible for the cleavage of the signal peptide of the proteins. these enzymes are unique serine proteases that carry out catalysis using a serine/lysine catalytic dyad. in the present study, we report the isolation of type i signal peptidase from the malaria parasites plasmodium falciparum, plasmodium knowlesi, and plasmodium yoelii and some characterization of type i signal peptidase of plasmodium falciparum. we show tha ...	2005	16489263
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
ameba-associated microorganisms and diagnosis of nosocomial pneumonia.	to elucidate the role of ameba-associated microorganisms (aams) as etiologic agents of pneumonia, we screened for legionella spp., parachlamydia acanthamoeba, afipia sp., bosea spp., bradyrhizobium spp., mesorhizobium amorphae, rasbo bacterium, azorhizobium caulinodans, acanthamoeba polyphaga mimivirus, and conventional microorganisms in 210 pneumonia patients in intensive-care units by using culture, polymerase chain reaction, and serologic testing. these resulted in 59 diagnoses in 40 patients ...	2006	16494750
the pea nodule environment restores the ability of a rhizobium leguminosarum lipopolysaccharide acpxl mutant to add 27-hydroxyoctacosanoic acid to its lipid a.	members of the rhizobiaceae contain 27-hydroxyoctacosanoic acid (27ohc(28:0)) in their lipid a. a rhizobium leguminosarum 3841 acpxl mutant (named here rlv22) lacking a functional specialized acyl carrier lacked 27ohc(28:0) in its lipid a, had altered growth and physiological properties (e.g., it was unable to grow in the presence of an elevated salt concentration [0.5% nacl]), and formed irregularly shaped bacteroids, and the synchronous division of this mutant and the host plant-derived symbio ...	2006	16513742
function of the n-terminal cap of the pas domain in signaling by the aerotaxis receptor aer.	aer, the escherichia coli receptor for behavioral responses to oxygen (aerotaxis), energy, and redox potential, contains a pas sensory-input domain. within the pas superfamily, the n-terminal segment (n-cap) is poorly conserved and its role is not well understood. we investigated the role of the n-cap (residues 1 to 19) in the aer pas domain by missense and truncation mutagenesis. aer-pas n-cap truncations and an aer-m21p substitution resulted in low cellular levels of the mutant proteins, sugge ...	2006	16513745
transcriptional and functional analysis of oxalyl-coenzyme a (coa) decarboxylase and formyl-coa transferase genes from lactobacillus acidophilus.	oxalic acid is found in dietary sources (such as coffee, tea, and chocolate) or is produced by the intestinal microflora from metabolic precursors, like ascorbic acid. in the human intestine, oxalate may combine with calcium, sodium, magnesium, or potassium to form less soluble salts, which can cause pathological disorders such as hyperoxaluria, urolithiasis, and renal failure in humans. in this study, an operon containing genes homologous to a formyl coenzyme a transferase gene (frc) and an oxa ...	2006	16517636
genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium nitrobacter winogradskyi nb-255.	the alphaproteobacterium nitrobacter winogradskyi (atcc 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. there were extensive similarities to genes in two alphaproteobacteria, bradyrhizobium japonicum usda110 (1,300 genes) and rhodopseudomonas palustris cga009 cg (815 genes). genes encoding p ...	2006	16517654
the atu and liu clusters are involved in the catabolic pathways for acyclic monoterpenes and leucine in pseudomonas aeruginosa.	evidence suggests that the pseudomonas aeruginosa pao1 gnyrdbhal cluster, which is involved in acyclic isoprenoid degradation (a. l. díaz-pérez, n. a. zavala-hernández, c. cervantes, and j. campos-garcía, appl. environ. microbiol. 70:5102-5110, 2004), corresponds to the liurabcde cluster (b. hoschle, v. gnau, and d. jendrossek, microbiology 151:3649-3656, 2005). a liu (leucine and isovalerate utilization) homolog cluster was found in the pao1 genome and is related to the catabolism of acyclic mo ...	2006	16517656
transformation of rhizobia with broad-host-range plasmids by using a freeze-thaw method.	several species of rhizobia were successfully transformed with broad-host-range plasmids of different replicons by using a modified freeze-thaw method. a generic binary vector (ppzp211) was maintained in mesorhizobium loti without selection and stably inherited during nodulation. the method could extend the potential of rhizobia as a vehicle for plant transformation.	2006	16517691
making ends meet: repairing breaks in bacterial dna by non-homologous end-joining.	dna double-strand breaks (dsbs) are one of the most dangerous forms of dna lesion that can result in genomic instability and cell death. therefore cells have developed elaborate dsb-repair pathways to maintain the integrity of genomic dna. there are two major pathways for the repair of dsbs in eukaryotes: homologous recombination and non-homologous end-joining (nhej). until very recently, the nhej pathway had been thought to be restricted to the eukarya. however, an evolutionarily related nhej a ...	2006	16518468
an empirical test of partner choice mechanisms in a wild legume-rhizobium interaction.	mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. trade between partners with conflicting interests requires mechanisms to prevent exploitation. partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. here, we test this theory in a wild legumerhizobium symbiosis. rhizobial bacteria inhabit legume root nodules and convert atmospheric ...	2006	16519238
an empirical test of partner choice mechanisms in a wild legume-rhizobium interaction.	mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. trade between partners with conflicting interests requires mechanisms to prevent exploitation. partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. here, we test this theory in a wild legumerhizobium symbiosis. rhizobial bacteria inhabit legume root nodules and convert atmospheric ...	2006	16519238
sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria.	the cell wall envelopes of gram-positive bacteria represent a surface organelle that not only functions as a cytoskeletal element but also promotes interactions between bacteria and their environment. cell wall peptidoglycan is covalently and noncovalently decorated with teichoic acids, polysaccharides, and proteins. the sum of these molecular decorations provides bacterial envelopes with species- and strain-specific properties that are ultimately responsible for bacterial virulence, interaction ...	2006	16524923
the rhizobium etli sigma70 (siga) factor recognizes a lax consensus promoter.	a collection of rhizobium etli promoters was isolated from a genomic dna library constructed in the promoter-trap vector pbbmcs53, by their ability to drive the expression of a gusa reporter gene. thirty-seven clones were selected, and their transcriptional start-sites were determined. the upstream sequence of these 37 start-sites, and the sequences of seven previously identified promoters were compared. on the basis of sequence conservation and mutational analysis, a consensus sequence cttgacn1 ...	2006	16528104
adenylate-coupled ion movement. a mechanism for the control of nodule permeability to o2 diffusion.	in response to changes in phloem supply, adenylate demand, and oxygen status, legume nodules are known to exercise rapid (seconds to hours) physiological control over their permeability to oxygen diffusion. diffusion models have attributed this permeability control to the reversible flow of water into or out of intercellular spaces. to test hypotheses on the mechanism of diffusion barrier control, nodulated soybean (glycine max l. merr.) plants were exposed to a range of treatments known to alte ...	2006	16531483
restriction of nodulation by bradyrhizobium japonicum is mediated by factors present in the roots of glycine max.	reciprocal grafting experiments done using soybean plant introduction genotypes indicated that restriction of nodulation by bradyrhizobium japonicum is determined by the genotype of the root and is dependent on plant growth temperature. microscopic analyses indicated that the soybean plant introduction genotypes restrict nodulation of b. japonicum at symbiotic stages which occur both before and after the formation of nodule primordia.	1995	16534946
diversity among field populations of bradyrhizobium japonicum in poland.	genetic structure in field populations of bradyrhizobium japonicum isolated in poland was determined by using several complementary techniques. of the 10 field sites examined, only 4 contained populations of indigenous b. japonicum strains. the polish bradyrhizobia were divided into at least two major groups on the basis of protein profiles on polyacrylamide gels, serological reaction with polyclonal antisera, repetitive extragenic palindromic pcr fingerprints of genomic dna, and southern hybrid ...	1995	16534985
host-controlled restriction of nodulation by bradyrhizobium japonicum strains in serogroup 110.	we previously reported the identification of a soybean plant introduction (pi) genotype, pi 417566, which restricts nodulation by bradyrhizobium japonicum mn1-1c (usda 430), strains in serogroup 129, and usda 110 (p. b. cregan, h. h. keyser, and m. j. sadowsky, appl. environ. microbiol. 55:2532-2536, 1989, and crop sci. 29:307-312, 1989). in this study, we further characterized nodulation restriction by pi 417566. twenty-four serogroup 110 isolates were tested for restricted nodulation on pi 417 ...	1995	16535054
protein synthesis by bradyrhizobium japonicum bacteroids declines as a function of nodule age.	isolated bacteroids of bradyrhizobium japonicum accumulated exogenously supplied [(sup35)s]methionine or [(sup3)h]leucine and incorporated them into cytosolic proteins. the accumulation of these labeled amino acids was inhibited by azide. only 3 to 6% of these accumulated amino acids were incorporated into protein. protein synthesis was not stimulated by incubation of bacteroids in the presence of potassium salts, malate, or amino acids, but azide, chloramphenicol, and acridine did inhibit the p ...	1996	16535424
enzymes of poly-(beta)-hydroxybutyrate metabolism in soybean and chickpea bacteroids.	the enzymatic capacity for metabolism of poly-(beta)-hydroxybutyrate (phb) has been examined in nitrogen-fixing symbioses of soybean (glycine max l.) plants, which may accumulate substantial amounts of phb, and chickpea (cicer arietinum l.) plants, which contain little or no phb. in the free-living state, both bradyrhizobium japonicum cb 1809 and rhizobium sp. (cicer) cc 1192, which form nodules on soybean and chickpea plants, respectively, produced substantial amounts of phb. to obtain informat ...	1996	16535445
variation in the nod gene rflps, nucleotide sequences of 16s rrna genes, nod factors, and nodulation abilities of bradyrhizobium strains isolated from thai vigna plants.	the analysis of nod genes and 16s rrna gene regions, nod factors, and nodulation abilities of brady rhizobium strains isolated from tropical thai vigna species is reported. a total of 55 bradyrhizobium strains isolated from two cultivated and six wild vigna species growing in central and northern thailand were evaluated. thai vigna spp. bradyrhizobium strains showed higher levels of nod gene rflp diversity compared with thai soybean brady rhizobium strains or temperate strains of bradyrhizobium ...	2006	16541157
gem system: automatic prototyping of cell-wide metabolic pathway models from genomes.	successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. however, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology.	2006	16553966
a monovalent streptavidin with a single femtomolar biotin binding site.	streptavidin and avidin are used ubiquitously because of the remarkable affinity of their biotin binding, but they are tetramers, which disrupts many of their applications. making either protein monomeric reduces affinity by at least 10(4)-fold because part of the binding site comes from a neighboring subunit. here we engineered a streptavidin tetramer with only one functional biotin binding subunit that retained the affinity, off rate and thermostability of wild-type streptavidin. in denaturant ...	2006	16554831
oxidative stress promotes degradation of the irr protein to regulate haem biosynthesis in bradyrhizobium japonicum.	the haem proteins catalase and peroxidase are stress response proteins that detoxify reactive oxygen species. in the bacterium bradyrhizobium japonicum, expression of the gene encoding the haem biosynthesis enzyme delta-aminolevulinic acid dehydratase (alad) is normally repressed by the irr protein in iron-limited cells. irr degrades in the presence of iron, which requires haem binding to the protein. here, we found that alad levels were elevated in iron-limited cells of a catalase-deficient mut ...	2006	16556232
bradyrhizobium japonicum senses iron through the status of haem to regulate iron homeostasis and metabolism.	the irr protein from the bacterium bradyrhizobium japonicum is expressed under iron limitation to mediate iron control of haem biosynthesis. the regulatory input to irr is the status of haem and its precursors iron and protoporphyrin at the site of haem synthesis. here, we show that irr controls the expression of iron transport genes and many other iron-regulated genes not directly involved in haem synthesis. irr is both a positive and negative effector of gene expression, and in at least some c ...	2006	16573691
nickel: a micronutrient element for hydrogen-dependent growth of rhizobium japonicum and for expression of urease activity in soybean leaves.	soybean plants and rhizobium japonicum 122 des, a hydrogen uptake-positive strain, were cultured in media purified to remove ni. supplemental ni had no significant effect on the dry matter or total n content of plants. however, the addition of ni to both nitrate-grown and symbiotically grown plants resulted in a 7- to 10-fold increase in urease activity (urea amidohydrolase, ec 3.5.1.5) in leaves and significantly increased the hydrogenase activity (ec 1.18.3.1) in isolated nodule bacteroids. wh ...	1983	16578770
intra- and interspecies transfer and expression of rhizobium japonicum hydrogen uptake genes and autotrophic growth capability.	cosmids containing hydrogen uptake genes have previously been isolated in this laboratory. four new cosmids that contain additional hup gene(s) have now been identified by conjugal transfer of a rhizobium japonicum 122des gene bank into a tn5-generated hup(-) mutant and screening for the acquisition of hup activity. the newly isolated cosmids, phu50-phu53, contain part of the previously isolated phu1 but extend as far as 20 kilobases beyond its border. phu52 complements five of six hup(-) mutant ...	1985	16578786
[chemotaxis and growth of bradyrhizobium japonicum in the presence of fine-dispersed silica].	the chemotactic properties of the soybean nodule bacterium bradyrhizobium japonicum were studied in the presence of synthetic fine-dispersed materials. it was shown that fine-dispersed silica (fds) and its variety modified with aluminum oxide (mfds) reduce bacterial chemotaxis to glucose. in addition, fds increases the irregular motility of b. japonicum, and mfds decreases it. this is in agreement with the effect of the materials on the rate of nodule bacterium growth.	2006	16579445
[genetic diversity and phylogeny of soybean bradyrhizobia isolated from south and north region of china].	studies on genetic diversity and phylogeny of soybean bradyrhizobia isolated from south and north region of china were investigated through 16s rrna gene pcr rflp, 16s rrna gene sequencing and 16s-23s rrna igs pcr rflp assays. results of 16s rrna gene pcr rflp and 16s rrna gene sequencing analysis reveal that strains tested are ascribed into bradyrhizobium japonicum and b. elkanii species. b. japonicum is the dominant species and accounts for 91% of strains tested, but b. elkanii just up to 9%, ...	2006	16579479
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
aerobic benzoyl-coenzyme a (coa) catabolic pathway in azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-coa semialdehyde dehydrogenase.	benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. the intermediates of this pathway are coenzyme a (coa) thioesters throughout, and ring cleavage is nonoxygenolytic. the fate of the ring cleavage product 3,4-dehydroadipyl-coa semialdehyde was studied in the beta-proteobacterium azoarcus evansii. cell extracts contained a benzoate-induced, nadp(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. a pos ...	2006	16585753
expression of hydrogenase activity in free-living rhizobium japonicum.	a medium is described on which selected rhizobium japonicum strains express hydrogenase (h(2) uptake) activity under free-living conditions. low concentrations of carbon substrates, decreased oxygen tension, and the quantity of combined nitrogen in the medium were major factors influencing hydrogenase expression. hydrogenase activity was dependent upon a preincubation period in the presence of h(2) under conditions such that the cells did not exhibit nitrogenase activity. h(2) uptake rates were ...	1978	16592544
construction of a rhizobium japonicum gene bank and use in isolation of a hydrogen uptake gene.	a gene bank of rhizobium japonicum dna was constructed by using the broad host range conjugative cosmid plafr1. eighty-three percent of the clones in the bank contained cosmids with insert dna averaging 22.6 kilobase pairs in length. a series of cosmids containing a hydrogen uptake (hup) gene was identified by transferring the gene bank into a h(2) uptake-negative (hup(-)) r. japonicum point mutant (pj17nal) and screening tetracycline-resistant colonies for the ability to grow chemolithotrophica ...	1983	16593268
expression of beta-galactosidase controlled by a nitrogenase promoter in stem nodules of aeschynomene scabra.	a 365-base-pair (bp) dna fragment, containing the promoter region of the nitrogenase reductase (nifh) gene from stem rhizobium btai1, has been isolated and sequenced. the transcription initiation sites were localized at positions 152 (major initiation) and 114 (minor initiation) nucleotides upstream of the translation initiation codon. the 200-bp nucleotide sequence upstream of the nifh structural gene shows substantial homology to the corresponding nifh regions of cowpea rhizobium (100%), paras ...	1984	16593514
cloned avirulence gene of pseudomonas syringae pv. glycinea determines race-specific incompatibility on glycine max (l.) merr.	a genomic library of pseudomonas syringae pv. glycinea race 6 dna was constructed in the mobilizable cosmid vector plafr1 and maintained in escherichia coli hb101. completeness of the library was estimated by assaying clones for the expression of ice-nucleating activity in e. coli. ice-nucleation activity was represented approximately once in every 600 clones. six hundred eighty random race 6 cosmid clones were mobilized from e. coli by plasmid prk2013 in individual conjugations to a race 5 stra ...	1984	16593517
choline kinase ii is present only in nodules that synthesize stable peribacteroid membranes.	host-cell cytoplasm from soybean plants infected with the peribacteroid membrane (pbm)-building rhizobium japonicum strain 61-a-101 (effective, n(2)-fixing) had much higher choline kinase activity than cytoplasm from either uninfected tissue or tissue infected with the non-pbm-building (ineffective, non-n(2)-fixing) strain 61-a-24. ion-exchange chromatography showed that both types of nodule and root tissue possessed constitutive choline kinase i activity that had a k(m) for choline of approxima ...	1986	16593653
bacterial delta-aminolevulinic acid synthase activity is not essential for leghemoglobin formation in the soybean/bradyrhizobium japonicum symbiosis.	previous studies of legume nodules have indicated that formation of the heme moiety of leghemoglobin is a function of the bacterial symbiont. we now show that a hema mutant of bradyrhizobium japonicum that cannot carry out the first step in heme biosynthesis forms fully effective nodules on soybeans. the bacterial mutant strain was constructed by first isolating the wild-type hema gene encoding delta-aminolevulinic acid synthase (ec 2.3.1.37) from a cosmid library, using a fragment of the rhizob ...	1986	16593670
bioluminescence in soybean root nodules: demonstration of a general approach to assay gene expression in vivo by using bacterial luciferase.	two plasmid vectors pfit001 and ppale001, containing luxab genes encoding bacterial luciferase [alkanal, reduced-fmn:oxygen oxidoreductase (1-hydroxylating, luminescing), ec 1.14.14.3] from vibrio harveyi, have been constructed. escherichia coli carrying derivatives of pfit001 with dna inserts in the unique ecori site located in luxb form "dark" colonies that can be readily distinguished from the bioluminescent or "bright" colonies. in contrast, promoterless ppale001 is used as a promoter-search ...	1986	16593783
isolation of a cytochrome aa(3) gene from bradyrhizobium japonicum.	bradyhizobium japonicum strain lo501 is a tn5-induced mutant that does not express the terminal oxidase cytochrome aa(3) (cytochrome-c oxidase, ec 1.9.3.1). two and one-half kilobase pairs of lo501 genomic dna that flanks the transposon was isolated and used as a hybridization probe to obtain the wild-type gene from a cosmid library. two subcloned fragments from two of the isolated cosmids were ligated into broad host range vectors, and restriction maps of these fragments were generated. the res ...	1987	16593835
k regulates bacteroid-associated functions of bradyrhizobium.	cowpea bradyrhizobium 32h1 cells, when grown under 0.2% o(2), synthesize nitrogenase, as well as a methylammonium (ammonium) transport system and an electrogenic k(+)/h(+) antiporter. this effect was seen in growth medium containing 8-12 mm k(+) but not with 50 mum k(+). addition of k(+) to cells growing under low o(2) tensions in low-k(+) medium led to various phenotypic properties associated with bacteroids, including the ability to reduce acetylene, induction of an ammonium transport carrier ...	1987	16593858
induction of bradyrhizobium japonicum common nod genes by isoflavones isolated from glycine max.	the early events in legume nodulation by rhizobium spp. involve a conserved gene cluster known as the common nod region. a broad-host-range plasmid (pea2-21) containing a bradyrhizobium japonicum noddabc-lacz translational fusion was constructed and used to monitor nod gene expression in response to soybean root extract. two inducing compounds were isolated and identified. analysis using ultraviolet absorption spectra, proton nuclear magnetic resonance, and mass spectrometry showed that the two ...	1987	16593884
isolation of genes involved in nodulation competitiveness from rhizobium leguminosarum bv. trifolii t24.	rhizobium leguminosarum bv. trifolii t24 produces a potent anti-rhizobial compound, trifolitoxin, and exclusively nodulates clover roots when in mixed inoculum with trifolitoxin-sensitive strains of r. leguminosarum bv. trifolii [schwinghamer, e. a. & belkengren r. p. (1968) arch. mikrobiol. 64, 130-145]. in the present study, the isolation of trifolitoxin production and resistance genes is described. a cosmid genomic library of t24 was prepared in plafr3. no trifolitoxin expression was observed ...	1988	16593933
biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network.	free-living amoebae (fla) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. in addition to their own pathogenicity, fla can also act as trojan horses and be naturally infected with amoeba-resisting bacteria (arb) that may be involved in human infections, such as pneumonia. we investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. using amoebal enrichment on nonnutrient ...	2006	16597941
purification and characterization of trzf: biuret hydrolysis by allophanate hydrolase supports growth.	trzf, the allophanate hydrolase from enterobacter cloacae strain 99, was cloned, overexpressed in the presence of a chaperone protein, and purified to homogeneity. native trzf had a subunit molecular weight of 65,401 and a subunit stoichiometry of alpha(2) and did not contain significant levels of metals. trzf showed time-dependent inhibition by phenyl phosphorodiamidate and is a member of the amidase signature protein family. trzf was highly active in the hydrolysis of allophanate but was not a ...	2006	16597948
symbiotic bradyrhizobium japonicum reduces n2o surrounding the soybean root system via nitrous oxide reductase.	n(2)o reductase activity in soybean nodules formed with bradyrhizobium japonicum was evaluated from n(2)o uptake and conversion of (15)n-n(2)o into (15)n-n(2). free-living cells of usda110 showed n(2)o reductase activity, whereas a nosz mutant did not. complementation of the nosz mutant with two cosmids containing the nosrzdfylx genes of b. japonicum usda110 restored the n(2)o reductase activity. when detached soybean nodules formed with usda110 were fed with (15)n-n(2)o, they rapidly emitted (1 ...	2006	16597953
pseudomonad cyclopentadecanone monooxygenase displaying an uncommon spectrum of baeyer-villiger oxidations of cyclic ketones.	baeyer-villiger monooxygenases (bvmos) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. in this study, we have cloned, sequenced, and overexpressed in escherichia coli a new bvmo, cyclopentadecanone monooxygenase (cpdb or cpdmo), originally derived from pseudomonas sp. strain hi-70. the 601-residue primary structure of cpdb revealed only 29% to 50% sequence identity to those of known ...	2006	16597975
effect of organic n source on bacterial growth, lipo-chitooligosaccharide production, and early soybean nodulation by bradyrhizobium japonicum.	production of bradyrhizobium japonicum inoculants is problematic because high inoculation rates are necessary but expensive, while production of rhizobial nod factors (lipo-chitooligosaccharides (lcos)), key signal molecules in the establishment of legume-rhizobia symbioses, may be inhibited at high culture cell densities. we conducted experiments to determine the effects of growth medium n source on b. japonicum growth, lco production, and early nodulation of soybean. we found that 1.57 mmol am ...	2006	16604119
mekhla, a novel domain with similarity to pas domains, is fused to plant homeodomain-leucine zipper iii proteins.	homeodomain (hd) proteins play important roles in the development of plants, fungi, and animals. here we identify a novel domain, mekhla, in the c terminus of hd-leu zipper (hd-zip) iii plant hd proteins that shares similarity with a group of bacterial proteins and a protein from the green alga chlamydomonas reinhardtii. the group of bacterial mekhla proteins is found in cyanobacteria and other bacteria often found associated with plants. phylogenetic analysis suggests that a mekhla protein tran ...	2006	16607028
selenium is involved in regulation of periplasmic hydrogenase gene expression in desulfovibrio vulgaris hildenborough.	desulfovibrio vulgaris hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. the d. vulgaris hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [fefe], [feni]1, and [fenise] hydrogenases, are usually detected. in this work, we studied t ...	2006	16621815
bradyrhizobia isolated from root nodules of parasponia (ulmaceae) do not constitute a separate coherent lineage.	rhizobial bacteria almost exclusively nodulate members of the families fabaceae, mimosaceae and caesalpiniaceae, but are found on a single non-legume taxon, parasponia (ulmaceae). based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. this hypothesis was investigated by focusing on four isolates that are representat ...	2006	16627647
the hysteresis effect in carpal kinematics.	carpal bones show hysteresis that is dependent on the direction of wrist motion during a continuous active loading protocol. we describe an accurate methodology for analyzing the hysteresis effect and we apply this model to analyze the effect of sequential ligament sectioning on scapholunate instability.	2006	16632053
the genome of rhizobium leguminosarum has recognizable core and accessory components.	rhizobium leguminosarum is an alpha-proteobacterial n2-fixing symbiont of legumes that has been the subject of more than a thousand publications. genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. we have sequenced the genome of r. leguminosarum biovar viciae strain 3841.	2006	16640791
labeling of carbon pools in bradyrhizobium japonicum and rhizobium leguminosarum bv viciae bacteroids following incubation of intact nodules with co(2).	the aim of the work reported here was to ascertain that the patterns of labeling seen in isolated bacteroids also occurred in bacteroids in intact nodules and to observe early metabolic events following exposure of intact nodules to (14)co(2). intact nodules of soybean (glycine max l. merr. cv ripley) inoculated with bradyrhizobium japonicum usda 110 and pea (pisum sativum l. cv progress 9) inoculated with rhizobium leguminosarum bv viciae isolate 128c53 were detached and immediately fed (14)co( ...	1992	16653034
p relaxation responses associated with n(2)/o(2) diffusion in soybean nodule cortical cells and excised cortical tissue.	n(2)-fixing bradyrhizobium japonicum nodules and cortical tissue derived from these nodules were examined in vivo by (31)p nuclear magnetic resonance (nmr) spectroscopy. perfusion of the viable nodules and excised cortical tissue with o(2) followed by n(2) or ar caused a loss of orthophosphate (pi) resonance magnetization associated with the major portion of acidic pi (delta 0.9 ppm, ph 5.5) residing in the cortical cells. resumption of o(2) perfusion restored approximately 80% of the intensity ...	1992	16653184
production of the soybean-chlorosis toxin by rhizobium japonicum in pure culture.		1965	16656177