root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...200415066803
diversity and evolution of hydrogenase systems in rhizobia.uptake hydrogenases allow rhizobia to recycle the hydrogen generated in the nitrogen fixation process within the legume nodule. hydrogenase (hup) systems in bradyrhizobium japonicum and rhizobium leguminosarum bv. viciae show highly conserved sequence and gene organization, but important differences exist in regulation and in the presence of specific genes. we have undertaken the characterization of hup gene clusters from bradyrhizobium sp. (lupinus), bradyrhizobium sp. (vigna), and rhizobium tr ...200212324339
genetic and phenetic analyses of bradyrhizobium strains nodulating peanut (arachis hypogaea l.) roots.seventeen bradyrhizobium sp. strains and one azorhizobium strain were compared on the basis of five genetic and phenetic features: (i) partial sequence analyses of the 16s rrna gene (rdna), (ii) randomly amplified dna polymorphisms (rapd) using three oligonucleotide primers, (iii) total cellular protein profiles, (iv) utilization of 21 aliphatic and 22 aromatic substrates, and (v) intrinsic resistances to seven antibiotics. partial 16s rdna analysis revealed the presence of only two rdna homolog ...19957538280
photosynthetic bradyrhizobia are natural endophytes of the african wild rice oryza breviligulata.we investigated the presence of endophytic rhizobia within the roots of the wetland wild rice oryza breviligulata, which is the ancestor of the african cultivated rice oryza glaberrima. this primitive rice species grows in the same wetland sites as aeschynomene sensitiva, an aquatic stem-nodulated legume associated with photosynthetic strains of bradyrhizobium. twenty endophytic and aquatic isolates were obtained at three different sites in west africa (senegal and guinea) from nodal roots of o. ...200011097925
genotypic characterization of bradyrhizobium strains nodulating endemic woody legumes of the canary islands by pcr-restriction fragment length polymorphism analysis of genes encoding 16s rrna (16s rdna) and 16s-23s rdna intergenic spacers, repetitive extragenic palindromic pcr genomic fingerprinting, and partial 16s rdna sequencing.we present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (chamaecytisus proliferus) and other endemic woody legumes of the canary islands, spain. these and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16s ribosomal dna (rdna) pcr-restriction fragment length polymorphisms (pcr-rflps), 16s-23s rdna intergenic spacer (igs) rflps, and repetitiv ...19989603820
growth of fast- and slow-growing rhizobia on soybean rhizobia and bradyrhizobium spp. (lupine) have the ability to catabolize ethanol. of the 30 strains of rhizobia examined, only the fast- and slow-growing soybean rhizobia and the slow-growing bradyrhizobium sp. (lupine) were capable of using ethanol as a sole source of carbon and energy for growth. two strains from each of the other rhizobium species examined (r. meliloti, r. loti, and r. leguminosarum biovars phaseoli, trifolii, and viceae) failed to grow on ethanol. one rhi ...198616347190
bacterial growth rates and competition affect nodulation and root colonization by rhizobium meliloti.the addition of streptomycin to nonsterile soil suppressed the numbers of bacterial cells in the rhizosphere of alfalfa (medicago sativa l.) for several days, resulted in the enhanced growth of a streptomycin-resistant strain of rhizobium meliloti, and increased the numbers of nodules on the alfalfa roots. a bacterial mixture inoculated into sterile soil inhibited the colonization of alfalfa roots by r. meliloti, caused a diminution in the number of nodules, and reduced plant growth. enterobacte ...198616347173
novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic bradyrhizobium sp. strain hw13 isolated from a pristine environment.the tfd genes of ralstonia eutropha jmp134 are the only well-characterized set of genes responsible for 2,4-dichlorophenoxyacetic acid (2,4-d) degradation among 2,4-d-degrading bacteria. a new family of 2,4-d degradation genes, cadrabkc, was cloned and characterized from bradyrhizobium sp. strain hw13, a strain that was isolated from a buried hawaiian soil that has never experienced anthropogenic chemicals. the cadr gene was inferred to encode an arac/xyls type of transcriptional regulator from ...200211751829
identification of lotus rhizobia by direct dna hybridization of crushed root nodules.hybridization of crushed lotus pedunculatus root nodules with p-labeled total genomic dna probes was used to identify rhizobium loti and bradyrhizobium sp. (lotus rhizobia). probes always hybridized with homologous target dna and frequently with dnas of other strains from the same genus. intergeneric hybridization did not occur. results were comparable to those from colony hybridization.198716347400
analysis of bacteria contaminating ultrapure water in industrial systems.bacterial populations inhabiting ultrapure water (upw) systems were investigated. the analyzed upw systems included pilot scale, bench scale, and full size upw plants employed in the semiconductor and other industries. bacteria present in the polishing loop of the upw systems were enumerated by both plate counts and epifluorescence microscopy. assessment of bacterial presence in upw by epifluorescence microscopy (cyanotolyl tetrazolium chloride [ctc] and dapi [4',6'-diamidino-2-phenylindole] sta ...200211916667
symbiotic hydrogenase activity in bradyrhizobium sp. (vigna) increases nitrogen content in vigna unguiculata plants.bradyrhizobium sp. (lupinus) and bradyrhizobium sp. (vigna) mutants in which hydrogenase (hup) activity was affected were constructed and analyzed. vigna unguiculata plants inoculated with the bradyrhizobium sp. (vigna) hup mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield.200516269797
specific detection of bradyrhizobium and rhizobium strains colonizing rice (oryza sativa) roots by 16s-23s ribosomal dna intergenic spacer-targeted addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities or occur as endophytes, e.g., in rice. two rhizobial strains which have been isolated from root nodules of the aquatic legumes aeschynomene fluminensis (irbg271) and sesbania aculeata (irbg74) were previously found to promote rice growth. in addition to analyzing their phylogenetic positions, we assessed the suitability of the 16s-23s ribosomal dna (rdna) intergenic spacer (igs) ...200111472944
isolation and characterization of canthaxanthin biosynthesis genes from the photosynthetic bacterium bradyrhizobium sp. strain ors278.a carotenoid biosynthesis gene cluster involved in canthaxanthin production was isolated from the photosynthetic bradyrhizobium sp. strain ors278. this cluster includes five genes identified as crte, crty, crti, crtb, and crtw that are organized in at least two operons. the functional assignment of each open reading frame was confirmed by complementation studies.200010851005
effect of bradyrhizobium photosynthesis on stem nodulation of aeschynomene sensitiva.some leguminous species of the genus aeschynomene are specifically stem-nodulated by photosynthetic bradyrhizobia. to study the effect of bacterial photosynthesis during symbiosis, we generated a photosynthesis-negative mutant of the bradyrhizobium sp. strain ors278 symbiont of aeschynomene sensitiva. the presence of a functional photosynthetic unit in bacteroids and the high expression of the photosynthetic genes observed in stem nodules demonstrate that the bacteria are photosynthetically acti ...200011114184
case of localized recombination in 23s rrna genes from divergent bradyrhizobium lineages associated with neotropical legumes.enzyme electrophoresis and rrna sequencing were used to analyze relationships of bradyrhizobium sp. nodule bacteria from four papilionoid legumes (clitoria javitensis, erythrina costaricensis, rhynchosia pyramidalis, and desmodium axillare) growing on barro colorado island (bci), panama. bacteria with identical multilocus allele profiles were commonly found in association with two or more legume genera. among the 16 multilocus genotypes (electrophoretic types [ets]) detected, six ets formed a cl ...200111319084
occurrence of lipid a variants with 27-hydroxyoctacosanoic acid in lipopolysaccharides from members of the family rhizobiaceae.lipopolysaccharides (lpss) isolated from several strains of rhizobium, bradyrhizobium, agrobacterium, and azorhizobium were screened for the presence of 27-hydroxyoctacosanoic acid. the lpss from all strains, with the exception of azorhizobium caulinodans, contained various amounts of this long-chain hydroxy fatty acid in the lipid a fractions. analysis of the lipid a sugars revealed three types of backbones: those containing glucosamine (as found in rhizobium meliloti and rhizobium fredii), tho ...19912007543
ecological indicators of native rhizobia in tropical soils.the relationship between environment and abundance of rhizobia was described by determining the populations of root nodule bacteria at 14 diverse sites on the island of maui. mean annual rainfall at the sites ranged from 320 to 1,875 mm, elevation from 37 to 1,650 m, and soil ph from 4.6 to 7.9. four different soil orders were represented in this study: inceptisols, mollisols, ultisols, and an oxisol. the rhizobial populations were determined by plant infection counts of five legumes (trifolium ...198816347624
bradyrhizobium sp. strains that nodulate the leguminous tree acacia albida produce fucosylated and partially sulfated nod factors.we determined the structures of nod factors produced by six different bradyrhizobium sp. strains nodulating the legume tree acacia albida (syn. faidherbia albida). compounds from all strains were found to be similar, i.e., o-carbamoylated and substituted by an often sulfated methyl fucose and different from compounds produced by rhizobium-mesorhizobium-sinorhizobium strains nodulating other species of the acaciae tribe.200011055966
identification and characterization of the rhizobium meliloti ntrc gene: r. meliloti has separate regulatory pathways for activation of nitrogen fixation genes in free-living and symbiotic cells.we show here that rhizobium meliloti, the nitrogen-fixing endosymbiont of alfalfa (medicago sativa), has a regulatory gene that is structurally homologous to previously characterized ntrc genes in enteric bacteria. dna sequence analysis showed that r. meliloti ntrc is homologous to previously sequenced ntrc genes from klebsiella pneumoniae and bradyrhizobium sp. (parasponia) and that an ntrb-like gene is situated directly upstream from r. meliloti ntrc. similar to its counterparts in k. pneumoni ...19872881918
cell surface carbohydrates of microaerobic, nitrogenase-active, continuous cultures of bradyrhizobium sp. strain 32h1.a continuous culture system was developed to examine the cell surface carbohydrates of bradyrhizobium sp. strain 32h1. when cultures were shifted from aerobic to microaerobic growth conditions, nitrogenase activity was induced and extracellular polysaccharide levels were greatly reduced; however, the levels of cell-associated cyclic beta-1,6 -1,3 glucans were found to be essentially unchanged.19921447152
general stress response signalling: unwrapping transcription complexes by dna relaxation via the sigma38 c-terminal domain.escherichia coli responds to stress by a combination of specific and general transcription signalling pathways. the general pathways typically require the master stress regulator sigma38 (rpos). here we show that the signalling from multiple stresses that relax dna is processed by a non-conserved eight-amino-acid tail of the sigma 38 c-terminal domain. by contrast, responses to two stresses that accumulate potassium glutamate do not rely on this short tail, but still require the overall c-termin ...200818761624
conserved nodulation genes from the non-legume symbiont bradyrhizobium sp. (parasponia).a nodulation locus from the broad-host-range, non-legume symbiont bradyrhizobium sp. (parasponia) strain anu289, has been identified by hybridisation to cloned rhizobium trifolii nodulation (nod) genes. transfer of cloned anu289 nod genes to r.trifolii nodulation-deficient mutants showed that the locus contains a functional homologue of the r. trifolii nodd gene. dna sequence analysis revealed the presence of three additional genes noda, nodb and nodc clustered adjacent to nodd. the four genes f ...19863960737
protein domains and architectural innovation in plant-associated proteobacteria.evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...200515715905
photosynthetic bradyrhizobia from aeschynomene spp. are specific to stem-nodulated species and form a separate 16s ribosomal dna restriction fragment length polymorphism group.we obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated aeschynomene species a. elaphroxylon, a. uniflora, or a. schimperi and 69 root or stem nodule isolates from the stem-nodulated aeschynomene species a. afraspera, a. ciliata, a. indica, a. nilotica, a. sensitiva, and a. tambacoundensis from various places in senegal. these isolates, together with 45 previous isolates from various aeschynomene species, were studied for host-specific nodulation within the genu ...199910388707
sequence analysis of a non-classified, non-occluded dna virus that causes salivary gland hypertrophy of musca domestica, mdsghv.the genome of the virus that causes salivary gland hypertrophy in musca domestica (mdsghv) was sequenced. this non-classified, enveloped, double stranded, circular dna virus had a 124,279bp genome. the g + c content was 43.5% with 108 putative methionine-initiated open reading frames (orfs). thirty orfs had homology to database proteins: eleven to proteins coded by both baculoviruses and nudiviruses (p74, pif-1, pif-2, pif-3, odv-e66, rr1, rr2, iap, dutpase, mmp, and ac81-like), seven to nudivir ...200818495197
dual intracellular localization and targeting of aminoimidazole ribonucleotide synthetase in 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], 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 ...200312644656
isolation and characterization of symbiotic mutants of bradyrhizobium sp. (arachis) strain nc92: mutants with host-specific defects in nodulation and nitrogen fixation.random transposon tn5 mutagenesis of bradyrhizobium sp. (arachis) strain nc92, a member of the cowpea cross-inoculation group, was carried out, and kanamycin-resistant transconjugants were tested for their symbiotic phenotype on three host plants: groundnut, siratro, and pigeonpea. two nodulation (nod- phenotype) mutants were isolated. one is unable to nodulate all three hosts and appears to contain an insertion in one of the common nodulation genes (nodabcd); the other is a host-specific nodula ...19873032910
plasmids pjp4 and r68.45 can be transferred between populations of bradyrhizobia in nonsterile soil.incp plasmid r68.45, which carries several antibiotic resistance genes, and incp plasmid pjp4, which contains genes for mercury resistance and 2,4-dichlorophenoxyacetic acid degradation, were evaluated for their ability to transfer to soil populations of rhizobia. transfer of r68.45 was detected in nonsterile soil by using bradyrhizobium japonicum usda 123 as the plasmid donor and several bradyrhizobium sp. strains as recipients. plasmid transfer frequencies ranged up to 9.1 x 10 in soil amended ...199316348953
isolation and characterization of nodulation genes from bradyrhizobium sp. (vigna) strain irc 11.76-kilobase-pair (kb) segment of dna from bradyrhizobium sp. (vigna) strain irc 78 that hybridizes to nodulation genes of rhizobium meliloti strain 41 was isolated. hybridization of the 11.76-kb dna fragment to dna from other bradyrhizobium species revealed a high degree of sequence conservation in this region. transfer of the 11.76-kb segment to nodulation-defective (nod(-)) mutants of r. meliloti restored their ability to induce nodules on medicago sativa (alfalfa). mutants of strain irc ...198516593624
occurrence of h(2)-uptake hydrogenases in bradyrhizobium sp. (lupinus) and their expression in nodules of lupinus spp. and ornithopus compressus.fifty-four strains of bradyrhizobium sp. (lupinus) from worldwide collections were screened by a colony hybridization method for the presence of dna sequences homologous to the structural genes of the bradyrhizobium japonicum hydrogenase. twelve strains exhibited strong colony hybridization signals, and subsequent southern blot hybridization experiments showed that they fell into two different groups on the basis of the pattern of ecori fragments containing the homology to the hup probe. all str ...198916666550
cell-associated oligosaccharides of bradyrhizobium spp.we report the initial characterization of the cell-associated oligosaccharides produced by four bradyrhizobium strains: bradyrhizobium japonicum usda 110, usda 94, and atcc 10324 and bradyrhizobium sp. strain 32h1. the cell-associated oligosaccharides of these strains were found to be composed solely of glucose and were predominantly smaller than the cyclic beta-1,2-glucans produced by agrobacterium and rhizobium species. linkage studies and nuclear magnetic resonance analyses demonstrated that ...19902294083
effects of k+ on the proton motive force of bradyrhizobium sp. strain previous studies, respiring bradyrhizobium sp. strain 32h1 cells grown under 0.2% o2, conditions that derepress n2 fixation, were found to have a low proton motive force of less than -121 mv, because of a low membrane potential (delta psi). in contrast, cells grown under 21% o2, which do not fix n2, had high proton motive force values of -175 mv or more, which are typical of respiring bacteria, because of high delta psi values. in the present study, we found that a delta psi of 0 mv in respir ...19863009414
genomic and proteomic analysis of phieco32, a novel escherichia coli bacteriophage.a novel bacteriophage infecting escherichia coli was isolated during a large-scale screen for bacteriophages that may be used for therapy of mastitis in cattle. the 77,554-bp genome of the bacteriophage, named phieco32, was sequenced and annotated, and its virions were characterized by electron microscopy and proteomics. two phieco32-encoded proteins that interact with host rna polymerase were identified. one of them is an ecf family sigma factor that may be responsible for transcription of some ...200818294652
putative porin of bradyrhizobium sp. (lupinus) bacteroids induced by glyphosate.application of glyphosate (n-[phosphonomethyl] glycine) to bradyrhizobium sp. (lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. the most significant change was the presence of a 44-kda polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mm). the polypeptide has been characterized by the amino acid sequencing of its n terminus and the isolation and nucleic acid sequencing of its encoding gene. it is putativ ...200717557843
analysis of babesia bovis infection-induced gene expression changes in larvae from the cattle tick, rhipicephalus (boophilus) microplus.cattle babesiosis is a tick-borne disease of cattle that has severe economic impact on cattle producers throughout the world's tropical and subtropical countries. the most severe form of the disease is caused by the apicomplexan, babesia bovis, and transmitted to cattle through the bite of infected cattle ticks of the genus rhipicephalus, with the most prevalent species being rhipicephalus (boophilus) microplus. we studied the reaction of the r. microplus larval transcriptome in response to infe ...201222871314
two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrb and ntrc.we report that the ntrb and ntrc proteins of bradyrhizobium sp. [parasponia] strain rp501 share homology with other regulatory proteins. there is extensive conservation of c-terminal regions between products of rp501 ntrb; klebsiella pneumoniae ntrb; escherichia coli envz, cpxa, and phor; agrobacterium tumefaciens vira; and, to a lesser extent, e. coli chea. there is also extensive conservation of n-terminal regions between products of rp501 ntrc; k. pneumoniae ntrc; e. coli ompr, sfra, phob, ch ...19863020561
phylogenomics and signature proteins for the alpha proteobacteria and its main groups.alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.200718045498
glutaredoxins: roles in iron homeostasis.glutaredoxins, proteins traditionally involved in redox reactions, are also required for iron-sulfur cluster assembly and haem biosynthesis. these new roles are probably related to the ability of some glutaredoxins to bind labile [2fe-2s] clusters and to transfer them rapidly and efficiently to acceptor proteins. recent results point to putative roles for glutaredoxins in the sensing of cellular iron and in iron-sulfur cluster biogenesis, either as scaffold proteins for the de novo synthesis of ...201019811920
identification of bacterial carotenoid cleavage dioxygenase homologues that cleave the interphenyl alpha,beta double bond of stilbene derivatives via a monooxygenase reaction.carotenoid cleavage oxygenases (ccos), which are also referred to as carotenoid cleavage dioxygenases (ccds) are a new class of nonheme iron-type enzymes that oxidatively cleave double bonds in the conjugated carbon chain of carotenoids. the oxidative cleavage mechanism of these enzymes is not clear, and both monooxygenase and dioxygenase mechanisms have been proposed for different carotenoid cleavage enzymes. ccos have been described from plants, animals, fungi, and cyanobacteria, but little is ...200818478524
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...200616859499
metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium rhodospirillum centenum.rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic n2-fixing environment. it is emerging as a genetically amenable model organism for molecular genetic analysis of cyst formation, photosynthesis, phototaxis, and cellular development. here, we present an analysis of the genome of this bacterium.201020500872
glutaredoxins: roles in iron homeostasis.glutaredoxins, proteins traditionally involved in redox reactions, are also required for iron-sulfur cluster assembly and haem biosynthesis. these new roles are probably related to the ability of some glutaredoxins to bind labile [2fe-2s] clusters and to transfer them rapidly and efficiently to acceptor proteins. recent results point to putative roles for glutaredoxins in the sensing of cellular iron and in iron-sulfur cluster biogenesis, either as scaffold proteins for the de novo synthesis of ...201019811920
the vaginal bacterial communities of japanese women resemble those of women in other racial determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
mutl homologs in restriction-modification systems and the origin of eukaryotic morc atpases.the provenance and biochemical roles of eukaryotic morc proteins have remained poorly understood since the discovery of their prototype morc1, which is required for meiotic nuclear division in animals. the morc family contains a combination of a gyrase, histidine kinase, and mutl (ghkl) and s5 domains that together constitute a catalytically active atpase module. we identify the prokaryotic morcs and establish that the morc family belongs to a larger radiation of several families of ghkl protein ...200818346280
the vaginal bacterial communities of japanese women resemble those of women in other racial determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
biodegradation of 5-nitroanthranilic acid by bradyrhizobium sp. strain js329.biodegradation of synthetic compounds has been studied extensively, but the metabolic diversity required for catabolism of many natural compounds has not been addressed. 5-nitroanthranilic acid (5naa), produced in soil by streptomyces scabies, is also the starting material for synthetic dyes and other nitroaromatic compounds. bradyrhizobium js329 was isolated from soil by selective enrichment with 5naa. when grown on 5naa, the isolate released stoichiometric amounts of nitrite and half of the st ...201020081004
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...201124710297
insights into an unusual nonribosomal peptide synthetase biosynthesis: identification and characterization of the ge81112 biosynthetic gene cluster.the ge81112 tetrapeptides (1-3) represent a structurally unique class of antibiotics, acting as specific inhibitors of prokaryotic protein synthesis. here we report the cloning and sequencing of the ge81112 biosynthetic gene cluster from streptomyces sp. l-49973 and the development of a genetic manipulation system for streptomyces sp. l-49973. the biosynthetic gene cluster for the tetrapeptide antibiotic ge81112 (geta-n) was identified within a 61.7-kb region comprising 29 open reading frames (o ...201020710026
regulation of nodulation in the soybean-rhizobium symbiosis : strain and cultivar variability.double inoculation (15 h apart) of the soybean cultivar williams with bradyrhizobium japonicum i-110ars reveals a rapid regulatory plant response that inhibits nodulation of distal portions of the primary root (m pierce, wd bauer 1984 plant physiol 73: 286-290). only living, homologous rhizobia elicit the response. we conducted similar double inoculation experiments to test the hypothesis that this is a universal phenomenon in soybean symbioses. we investigated interactions of the cultivar mccal ...198716665616
Evolutionary instability of symbiotic function in Bradyrhizobium japonicum.Bacterial mutualists are often acquired from the environment by eukaryotic hosts. However, both theory and empirical work suggest that this bacterial lifestyle is evolutionarily unstable. Bacterial evolution outside of the host is predicted to favor traits that promote an independent lifestyle in the environment at a cost to symbiotic function. Consistent with these predictions, environmentally-acquired bacterial mutualists often lose symbiotic function over evolutionary time. Here, we investiga ...201122073160
paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms.while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ...200616529662
two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions.genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ...201324260360
detection of novel integrons in the metagenome of human saliva.integrons are genetic elements capable of capturing and expressing open reading frames (orfs) embedded within gene cassettes. they are involved in the dissemination of antibiotic resistance genes (args) in clinically important pathogens. although the args are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. in this work, a pcr-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral m ...201627304457
partner choice in medicago truncatula-sinorhizobium nitrogen-fixing symbiosis, plant sanctions against ineffective bacteria have been demonstrated in previous studies performed on soybean and yellow bush lupin, both developing determinate nodules with bradyrhizobium sp. strains. in this study, we focused on the widely studied symbiotic association medicago truncatula-sinorhizobium meliloti, which forms indeterminate nodules. using two strains isolated from the same soil and displaying different nitrogen fixation phenotypes on the same fixed pl ...201020200033
comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids.symbiotic rhizobia differentiate physiologically and morphologically into nitrogen-fixing bacteroids inside legume host nodules. the differentiation is apparently terminal in some legume species, such as peas (pisum sativum) and peanuts (arachis hypogaea), likely due to extreme cell swelling induced by the host. in other legume species, such as beans (phaseolus vulgaris) and cowpeas (vigna unguiculata), differentiation into bacteroids, which are similar in size and shape to free-living rhizobia, ...201020837702
molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in bradyrhizobium sp. strain js329.biodegradation pathways of synthetic nitroaromatic compounds and anilines are well documented, but little is known about those of nitroanilines. we previously reported that the initial step in 5-nitroanthranilic acid (5naa) degradation by bradyrhizobium sp. strain js329 is a hydrolytic deamination to form 5-nitrosalicylic acid (5nsa), followed by ring fission catalyzed by 5nsa dioxygenase. the mechanism of release of the nitro group was unknown. in this study, we subcloned, sequenced, and expres ...201121498645
complete genome and comparative analysis of the chemolithoautotrophic bacterium oligotropha carboxidovorans om5.oligotropha carboxidovorans om5 t. (dsm 1227, atcc 49405) is a chemolithoautotrophic bacterium capable of utilizing co (carbon monoxide) and fixing co2 (carbon dioxide). we previously published the draft genome of this organism and recently submitted the complete genome sequence to genbank.201020863402
variable nitrogen fixation in wild populus.the microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. in legumes and actinorhizal plants, a portion of essential nitrogen (n) is obtained through symbiosis with nodule-inhabiting, n2-fixing microorganisms. however, a variety of non-nodulating plant species can also thrive in natural, low-n settings. some of these species may rely on endophytes, microorganisms that live within plants, to fix n2 gas into usable forms. here we repor ...201627196608
physiological and evolutionary studies of nap systems in shewanella piezotolerans wp3.most of the shewanella species contain two periplasmic nitrate reductases (nap-α and nap-β), which is a unique feature of this genus. in the present study, the physiological function and evolutionary relationship of the two nap systems were studied in the deep-sea bacterium shewanella piezotolerans wp3. both of the wp3 nap gene clusters: nap-α (napd1a1b1c) and nap-β (napd2a2b2) were shown to be involved in nitrate respiration. phylogenetic analyses suggest that nap-β originated earlier than nap- ...201021124486
occurrence of an unusual hopanoid-containing lipid a among lipopolysaccharides from bradyrhizobium species.the chemical structures of the unusual hopanoid-containing lipid a samples of the lipopolysaccharides (lps) from three strains of bradyrhizobium (slow-growing rhizobia) have been established. they differed considerably from other gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. ...201425371196
genes and pathways for co2 fixation in the obligate, chemolithoautotrophic acidophile, acidithiobacillus ferrooxidans, carbon fixation in a. ferrooxidans.acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low ph (ph 1-2). although a substantial amount of information is available regarding co2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study.201020799944
genome-wide discovery of putative srnas in paracoccus denitrificans expressed under nitrous oxide emitting conditions.nitrous oxide (n2o) is a stable, ozone depleting greenhouse gas. emissions of n2o into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. it is clear more effective mitigation strategies are required to reduce emissions. one way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume n2o. with this ultimate aim in mi ...201627895629
physiological and evolutionary studies of nap systems in shewanella piezotolerans wp3.most of the shewanella species contain two periplasmic nitrate reductases (nap-α and nap-β), which is a unique feature of this genus. in the present study, the physiological function and evolutionary relationship of the two nap systems were studied in the deep-sea bacterium shewanella piezotolerans wp3. both of the wp3 nap gene clusters: nap-α (napd1a1b1c) and nap-β (napd2a2b2) were shown to be involved in nitrate respiration. phylogenetic analyses suggest that nap-β originated earlier than nap- ...201021124486
symmetric and asymmetric mitotic segregation patterns influence wolbachia distribution in host somatic tissue.wolbachia are maternally inherited bacterial endosymbionts that occupy many but not all tissues of adult insects. during the initial mitotic divisions in drosophila embryogenesis, wolbachia exhibit a symmetric pattern of segregation. wolbachia undergo microtubule-dependent and cell-cycle-regulated movement between centrosomes. symmetric segregation occurs during late anaphase when wolbachia cluster around duplicated and separating centrosomes. this centrosome association is microtubule-dependent ...200919934219
distribution analysis of hydrogenases in surface waters of marine and freshwater environments.surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. in some marine habitats, h(2) evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. until now the only known biological process involved in h(2) metabolism in marine environments is nitrogen fixation.201021079771
calpain chronicle--an enzyme family under multidisciplinary characterization.calpain is an intracellular ca2+-dependent cysteine protease (ec; clan ca, family c02) discovered in 1964. it was also called canp (ca2+-activated neutral protease) as well as casf, cdp, kaf, etc. until 1990. calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." in the huma ...201121670566
sinorhizobium fredii usda257 and s. fredii usda191, cultivar-specific and non-specific symbionts of soybean, produce distinct cell surface appendages.sinorhizobium fredii usda257 and s. fredii usda191 are fast-growing rhizobia that form nitrogen-fixing nodules on soybean roots. in contrast to usda191, usda257 exhibits cultivar specificity and can form nodules only on primitive soybean cultivars. in response to flavonoids released from soybean roots these two rhizobia secrete nodulation outer proteins (nop) to the extracellular milieu through a type iii secretion system. in spite of the fact that nop proteins are known to regulate legume nodul ...201121764962
parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.bacteria confined to intracellular environments experience extensive genome reduction. in extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. to understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid pachypsylla venusta, a sap-feeding insect that harbors an ancient endosym ...201424398322
emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism.all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ...201121823229
the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria.mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ...201122014084
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with "auxin-like" morphological changes, cell envelope remodeling and upregulation of central metabolic pathways.there is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d), as one of the most widely applied pesticides in the world, is one such example. this herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unkno ...201525919284
evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme.isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii).201324004839
reactive oxygen species-inducible ecf σ factors of bradyrhizobium japonicum.extracytoplasmic function (ecf) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. the genome of bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ecf σ factors belonging to nine different ecf σ factor families. the genes for two of them, ecfq (bll1028) and ecff (blr3038), are highly induced in response to the reactive oxyge ...201222916258
phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. the p content in average soil is about 0.05% (w/w) but only 0.1% of the total p is available to plant because of poor solubility and its fixation in soil (illmer and schinner, soil biol biochem 27:257-263, 1995). an adequate supply of p ...201325674415
reductive evolution and the loss of pdc/pas domains from the genus staphylococcus.the per-arnt-sim (pas) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. although pas domains and the subclass of phoq-dcus-cita (pdc) domains have a common structure, there is limited amino acid sequence similarity. to gain greater insight into the evolution of pdc/pas domains present in the bacterial kingdom and staphylococci in specific, the pdc/pas domains from the genomic sequences of 4 ...201323902280
bacterial rubisco is required for efficient bradyrhizobium/aeschynomene symbiosis.rhizobia and legume plants establish symbiotic associations resulting in the formation of organs specialized in nitrogen fixation. in such organs, termed nodules, bacteria differentiate into bacteroids which convert atmospheric nitrogen and supply the plant with organic nitrogen. as a counterpart, bacteroids receive carbon substrates from the plant. this rather simple model of metabolite exchange underlies symbiosis but does not describe the complexity of bacteroids' central metabolism. a previo ...201121750740
genome sequence of the lupin-nodulating bradyrhizobium sp. strain wsm1417.bradyrhizobium sp. strain wsm1417 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (n2) fixing root nodule of lupinus sp. collected in papudo, chile, in 1995. however, this microsymbiont is a poorly effective n2 fixer with the legume host lupinus angustifolius l.; a lupin species of considerable economic importance in both chile and australia. the symbiosis formed with l. angustifolius produces less than half of the dry matter achieved by t ...201324976884
co-inoculation with rhizobia and amf inhibited soybean red crown rot: from field study to plant defense-related gene expression analysis.soybean red crown rot is a major soil-borne disease all over the world, which severely affects soybean production. efficient and sustainable methods are strongly desired to control the soil-borne diseases.201222442737
the yarhg domain: an extracellular domain in search of a function.we have identified a new bacterial protein domain that we hypothesise binds to peptidoglycan. this domain is called the yarhg domain after the most highly conserved sequence-segment. the domain is found in the extracellular space and is likely to be composed of four alpha-helices. the domain is found associated with protein kinase domains, suggesting it is associated with signalling in some bacteria. the domain is also found associated with three different families of peptidases. the large numbe ...201222615736
rhizobium pongamiae sp. nov. from root nodules of pongamia pinnata.pongamia pinnata has an added advantage of n2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. it harbours "rhizobia" as an endophytic bacterial community on its root nodules. a gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain vklr-01(t) was isolated from root nodules of pongamia that grew optimal at 28°c, ph 7.0 in presence of 2% nacl. isolate vklr-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt st ...201324078904
gtag- and cgtc-tagged palindromic dna repeats in prokaryotes.reps (repetitive extragenic palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in dna supercoiling, transcription termination, mrna stabilization.201323902135
common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.unbiased high-throughput sequencing of whole metagenome shotgun dna libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. to assess the extent and diversity of sequence contaminants, we aligned 57 "1000 genomes project" sequencing runs from six centers ...201424837716
symbiotic effectiveness of inoculation with bradyrhizobium isolates on soybean [glycine max (l.) merrill] genotypes with different maturities.the influence of soybean genotypes with different maturity groups on the symbiotic effectiveness of bradyrhizobium spp under high native soil n is not well known. therefore, the objective of this work was to evaluate the influence of maturity time of soybean genotypes on the symbiotic effectiveness of bradyrhizobium spp. at higher soil n. three isolates of bradyrhizobium spp. (uk-isolate, tal-379 isolate and local-isolate) and six soybean genotypes, three late maturing (wogayen, tgx-1336424 and ...201426034703
genome sequence of the ornithopus/lupinus-nodulating bradyrhizobium sp. strain wsm471.bradyrhizobium sp. strain wsm471 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (n2) fixing root nodule formed on the annual legume ornithopus pinnatus (miller) druce growing at oyster harbour, albany district, western australia in 1982. this strain is in commercial production as an inoculant for lupinus and ornithopus. here we describe the features of bradyrhizobium sp. strain wsm471, together with genome sequence information and annota ...201324976882
evaluation of 3 dental unit waterline contamination testing methods.previous studies have found inconsistent results from testing methods used to measure heterotrophic plate count (hpc) bacteria in dental unit waterline (duwl) samples. this study used 63 samples to compare the results obtained from an in-office chairside method and 2 currently used commercial laboratory hpc methods (standard methods 9215c and 9215e). the results suggest that the standard method 9215e is not suitable for application to duwl quality monitoring, due to the detection of limited numb ...201525574718
housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in rhizobium etli and rhizobium leguminosarum.a traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. the genome sequence of r. etli cfn42 predicts the presence of panc and panb genes clustered together on the ...201121463532
pyruvic oxime dioxygenase from heterotrophic nitrifier alcaligenes faecalis is a nonheme fe((ii))-dependent enzyme homologous to class ii aldolase.pyruvic oxime dioxygenase (pod), a key enzyme in heterotrophic nitrification, was purified from alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. pod was purified as the homotetramer of the subunit whose molecular weight was 30,000. the deduced amino acid sequence of pod was homologous with a class ii aldolase that has been regarded as the zn((ii))-dependent enzyme catalyzing aldol reactions. the recombinant protein showed weak pod activity, and was activated ...201728059164
ethanolamine utilization in vibrio alginolyticus.ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ...201223234435
identification of the major proteins of an immune modulating fraction from adult fasciola hepatica released by nonidet p40.fasciola hepatica np-40 released protein extract (fhnpe) exhibits potent th1 immunosuppressive properties in vitro and in vivo. however, the protein composition of this active fraction, responsible for th1 immune modulatory activity, has yet to be resolved. therefore, fhnpe, a nonidet p-40 extract, was subjected to a proteomic analysis in order to identify individual protein components. this was performed using an in house f. hepatica est database following 2d electrophoresis combined with de no ...201223021260
mapk machinery in plants: recognition and response to different stresses through multiple signal transduction pathways.the mitogen-activated protein kinase (mapk) cascades play diverse roles in intra- and extra-cellular signaling in plants. map kinases are the component of kinase modules which transfer information from sensors to responses in eukaryotes including plants. they play a pivotal role in transduction of diverse extracellular stimuli such as biotic and abiotic stresses as well as a range of developmental responses including differentiation, proliferation and death. several cascades are induced by diffe ...201020980831
short clones or long clones? a simulation study on the use of paired reads in metagenomics.metagenomics is the study of environmental samples using sequencing. rapid advances in sequencing technology are fueling a vast increase in the number and scope of metagenomics projects. most metagenome sequencing projects so far have been based on sanger or roche-454 sequencing, as only these technologies provide long enough reads, while illumina sequencing has not been considered suitable for metagenomic studies due to a short read length of only 35 bp. however, now that reads of length 75 bp ...201020122183
identification of the major proteins of an immune modulating fraction from adult fasciola hepatica released by nonidet p40.fasciola hepatica np-40 released protein extract (fhnpe) exhibits potent th1 immunosuppressive properties in vitro and in vivo. however, the protein composition of this active fraction, responsible for th1 immune modulatory activity, has yet to be resolved. therefore, fhnpe, a nonidet p-40 extract, was subjected to a proteomic analysis in order to identify individual protein components. this was performed using an in house f. hepatica est database following 2d electrophoresis combined with de no ...201223021260
clustering metagenomic sequences with interpolated markov models.sequencing of environmental dna (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a high ...201021044341
how genome complexity can explain the difficulty of aligning reads to genomes.although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship.201526678826
molecular characterization of tb, a new approach for an ancient brucellaphage.tb (tbilisi), the reference brucellaphage strain, was classified as a member of the podoviridae family with icosahedral capsids (57 +/- 2 nm diameter) and short tails (32 +/- 3 nm long). brucellaphage dna was double stranded and unmethylated; its molecular size was 34.5 kilobase pairs. some sequences were found through rapd analysis, ta cloning technology, and structural proteins were observed by using sds-page. thus, the results have laid the foundation for the wider use of brucellaphage's basi ...200919742121
application of representational difference analysis to identify genomic differences between bradyrhizobium elkanii and b. japonicum species.bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with b. japonicum, it fully supplies the plant nitrogen demands. despite the similarity between b. japonicum and b. elkanii species, several works demonstrated genetic and physiological differences between them. in this work representational difference analysis (rda) was used for genomic comparison between b. elkanii semia 587, a crop inoculant strain, and b. japonicum usda 110, a reference stra ...201024031597
feature-by-feature--evaluating de novo sequence assembly.the whole-genome sequence assembly (wgsa) problem is among one of the most studied problems in computational biology. despite the availability of a plethora of tools (i.e., assemblers), all claiming to have solved the wgsa problem, little has been done to systematically compare their accuracy and power. traditional methods rely on standard metrics and read simulation: while on the one hand, metrics like n50 and number of contigs focus only on size without proportionately emphasizing the informat ...201222319599
isolation of novel afipia septicemium and identification of previously unknown bacteria bradyrhizobium sp. ohsu_iii from blood of patients with poorly defined illnesses.cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. we re-initiated a set of 3 cultures for analysis of the "uncultivable" or poorly-grown microbes using ngs technology. broth of cultures from 3 blood samples, submitted from ohsu between 2000 and 2004, were inoculated in ...201324155888
distinct responses of soil microbial communities to elevated co2 and o3 in a soybean agro-ecosystem.the concentrations of atmospheric carbon dioxide (co2) and tropospheric ozone (o3) have been rising due to human activities. however, little is known about how such increases influence soil microbial communities. we hypothesized that elevated co2 (eco2) and elevated o3 (eo3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. to test the ...201324108327
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