Publications

cloning and sequencing of the nitrogenase structural genes nifhdk of herbaspirillum seropedicae.	the nitrogenase structural genes (nifhdk) of the endophytic diazotroph herbaspirillum seropedicae were isolated from a genomic bank by plate hybridization. sequence analysis of the dna showed a consensus promoter region upstream for the nifh gene containing a -24/-12 type promoter together with nifa- and integration host factor (ihf)- binding sites. the derived protein sequences of nifh, nifd and nifk contained conserved cysteine residues for binding iron-sulfur clusters and the iron-molybdenum ...	1996	9222418
the bradyrhizobium japonicum coxwxyz gene cluster encodes a bb3-type ubiquinol oxidase.	bradyrhizobium japonicum, a symbiotic nitrogen-fixing bacterium, has a complex respiratory electron-transport chain, capable of functioning throughout a wide range of oxygen tensions. it does so by synthesizing a number of terminal oxidases, each appropriate for different environmental conditions. we have previously described the cloning of the large catalytic subunit, coxx, from one of the terminal oxidases from b. japonicum [surpin, m.a., moshiri, f., murphy, a.m. and maier, r.j. (1994) geneti ...	1996	8996107
total glutamine synthetase activity during soybean nodule development is controlled at the level of transcription and holoprotein turnover.	gln synthetase (gs) catalyzes the atp-dependent condensation of ammonia with glutamate to yield gln. in higher plants gs is an octameric enzyme and the subunits are encoded by members of a small multigene family. in soybeans (glycine max), following the onset of n2 fixation there is a dramatic increase in gs activity in the root nodules. gs activity staining of native polyacrylamide gels containing nodule and root extracts showed a common band of activity (gsrs). the nodules also contained a slo ...	1996	12226474
histidine 131, not histidine 43, of the bradyrhizobium japonicum fixn protein is exposed towards the periplasm and essential for the function of the cbb3-type cytochrome oxidase.	in subunit i (fixn) of the bradyrhizobium japonicum cbb3-type oxidase, only five instead of the normal six strictly conserved histidines (h) could be unambiguously assigned as the putative heme or copper ligands. the ambiguity concerned h43 or h131 as the presumptive n-terminal ligands of the low-spin heme b. we report here that a h43a replacement had a wild-type phenotype, whereas the h131a mutant was defective in oxidase function and subunit assembly or stability, suggesting that h131 serves a ...	1996	8830672
the hydrogenase gene cluster of rhizobium leguminosarum bv. viciae contains an additional gene (hypx), which encodes a protein with sequence similarity to the n10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity.	plasmid pal618 contains the genetic determinants for h2 uptake (hup) from rhizobium leguminosarum bv. viciae, including a cluster of 17 genes named hupslcdefghijk-hypabfcde. a 1.7-kb segment of insert dna located downstream of hype has now been sequenced, thus completing the sequence of the 20441-bp insert dna in plasmid pal618. an open reading frame (designated hypx) encoding a protein with a calculated m(r) of 62300 that exhibits extensive sequence similarity with hoxx from alcaligenes eutroph ...	1996	8842143
nodz of bradyrhizobium extends the nodulation host range of rhizobium by adding a fucosyl residue to nodulation signals.	the nodulation genes of rhizobia are involved in the production of the lipo-chitin oligosaccharides (lco), which are signal molecules required for nodule formation. a mutation in nodz of bradyrhizobium japonicum results in the synthesis of nodulation signals lacking the wild-type 2-o-methylfucose residue at the reducting-terminal n-acetylglucosamine. this phenotype is correlated with a defective nodulation of siratro (macroptilium atropurpureum). here we show that transfer of nodz to rhizobium l ...	1996	8858593
activity of nitrogen fixation and nitrogen assimilation enzymes in soybean plants inoculated with bradyrhizobium japonicum strains.	in studying the symbiotic associations of 8 bradyrhizobium japonicum strains with two soybean varieties (ns-10 and ns-21), we determined the activity of nitrogen fixing (nitrogenase, ng) and nitrogen assimilation (glutamine synthetase, gs) and glutamate dehydrogenase (gdh) enzymes and the content of soluble proteins. the number of nodules was not in correlation with dry matter mass and nitrogen content. dry matter mass and nitrogen content in the nodules of the soybean varieties in association w ...	1996	8876729
a cytochrome c biogenesis gene involved in pyoverdine production in pseudomonas fluorescens atcc 17400.	pseudomonas fluorescens atcc 17400 produces pyoverdine under iron-limiting conditions. a tn5 mutant, 2g11, produced lower amounts of different pyoverdine forms and was unable to grow under iron limitation caused by ethylenediamine-di(o-hydroxy-phenylacetic acid) (eddha) or zinc. this mutant was complemented by a 9.6 kb hindiii-bamhi dna fragment that contained eight contiguous open reading frames (orfs cyta to cyth). the proteins possibly encoded by this polycistronic gene cluster were all simil ...	1996	8878040
the bradyrhizobium japonicum aconitase gene (acna) is important for free-living growth but not for an effective root nodule symbiosis.	the bradyrhizobium japonicum acna gene encoding the tricarboxylic acid cycle enzyme aconitase was cloned and characterized. the gene was mapped immediately upstream of the cytochrome c biogenesis gene cycv and found to be transcribed in the opposite direction. the nucleotide sequence of acna was determined; the derived amino acid sequence shared a significant similarity with bacterial aconitases and with the human iron-responsive-element-binding protein. the level of expression of the acna gene ...	1996	8892815
genetic diversity among bradyrhizobium isolates that effectively nodulate peanut (arachis hypogaea).	symbiotic gene diversity and other measures of genetic diversity were examined in bradyrhizobium isolates that form an effective symbiosis with peanut (arachis hypogaea). initially, restriction fragment length polymorphism (rflp) analysis using a nitrogenase (nif) gene probe was performed on 33 isolates along with one bradyrhizobium elkanii and two bradyrhizobium japonicum strains. considerable diversity was observed among the rflp patterns of many of the isolates, especially those from south am ...	1996	8941988
the bradyrhizobium japonicum fega gene encodes an iron-regulated outer membrane protein with similarity to hydroxamate-type siderophore receptors.	iron is important in the symbiosis between soybean and its nitrogen-fixing endosymbiont bradyrhizobium japonicum, yet little is known about rhizobial iron acquisition strategies. analysis of outer membrane proteins (omps) from b. japonicum 61a152 identified three iron-regulated omps in the size range of several known receptors for fe(iii)-scavenging siderophores. one of the iron-regulated proteins, fega, was purified and microsequenced, and a reverse genetics approach was used to clone a fega-co ...	1996	8955412
three-dimensional structure of human electron transfer flavoprotein to 2.1-a resolution.	mammalian electron transfer flavoproteins (etf) are heterodimers containing a single equivalent of flavin adenine dinucleotide (fad). they function as electron shuttles between primary flavoprotein dehydrogenases involved in mitochondrial fatty acid and amino acid catabolism and the membrane-bound electron transfer flavoprotein ubiquinone oxidoreductase. the structure of human etf solved to 2.1-a resolution reveals that the etf molecule is comprised of three distinct domains: two domains are con ...	1996	8962055
a possible mitochondrial gene in the early-branching amitochondriate protist trichomonas vaginalis.	trichomonads are anaerobic flagellated protists that, based on analyses of ribosomal rna sequences, represent one of the earliest branching lineages among the eukaryotes. the absence of mitochondria in these organisms coupled with their deep phylogenetic position has prompted several authors to suggest that trichomonads, along with other deeply-branching amitochondriate protist groups, diverged from the main eukaryotic lineage prior to the endosymbiotic origin of mitochondria. in this report we ...	1996	8962102
the cytochrome bc1 complex but not cycm is necessary for symbiotic nitrogen fixation by rhizobium leguminosarum.	following tn5 mutagenesis of rhizobium leguminosarum biovar viciae, two mutants in one complementation group were identified as being unable to fix nitrogen in pea nodules. spectroscopic analysis revealed that the mutants had lowered levels of c-type cytochromes and cytochromes aa3, but increased levels of cytochrome d. cells of the mutants were greatly reduced in their ability to oxidize the artificial electron donor n,n,n',n'-tetramethyl-p-phenylenediamine but membranes prepared from them had ...	1996	9004501
cyclolaminarinose. a new biologically active beta-(1-->3) cyclic glucan.	a unique glucan has been isolated from a recombinant strain of a rhizobium meliloti ty7, a cyclic beta-(1-->2) glucan mutant carrying a locus specifying beta-(1-->3; 1-->6) glucan synthesis from bradyrhizobium japonicum usda110. this compound, which appears to have considerable hydrophobic affinity, was separated from a perchloric acid cell extract by adsorption to a c-18 silica column. unlike those cyclic glucans previously isolated from rhizobium meliloti or bradyrhizobium japonicum, this mole ...	1996	9008841
short communication: screening of native and foreign bradyrhizobium japonicum strains for high n2 fixation in soybean.	four local rhizobia isolates selected after two screening experiments and five usda bradyrhizobium japonicum strains were estimated for n2 fixation in soybean using the (15)n isotope dilution technique. strain usda 110 was superior to the local isolates in nodulation and n2 fixation when inoculated onto soybean cv tgx 1497-id in a nigerian soil and could therefore be used as an inoculant for enhanced n2 fixation in soybean in nigeria.	1996	24415429
characterization of the bradyrhizobium japonicum cycy protein, a membrane-anchored periplasmic thioredoxin that may play a role as a reductant in the biogenesis of c-type cytochromes.	a new member of membrane-anchored periplasmic thioredoxin-like proteins was identified in bradyrhizobium japonicum. it is the product of cycy, the last gene in a cluster of cytochrome c biogenesis genes. mutational analysis revealed that cycy is essential for the biosynthesis of all c-type cytochromes in this bacterium. the cycy protein was shown to be exported to the periplasm by its n-terminal signal sequence-like domain. results from western blot analyses of membrane and soluble fractions ind ...	1997	9020171
a bacterial basic region leucine zipper histidine kinase regulating toluene degradation.	the two-component signal transduction pathways in bacteria use a histidine-aspartate phosphorelay circuit to mediate cellular changes in response to environmental stimuli. here we describe a novel two-component todst system, which activates expression of the toluene degradation (tod) pathway in pseudomonas putida f1. the tods gene is predicted to encode a sensory hybrid kinase with two unique properties--a basic region leucine zipper dimerization motif at the n terminus and a duplicated histidin ...	1997	9037074
a hydrogen-sensing system in transcriptional regulation of hydrogenase gene expression in alcaligenes species.	heterologous complementation studies using alcaligenes eutrophus h16 as a recipient identified a hydrogenase-specific regulatory dna region on megaplasmid phg21-a of the related species alcaligenes hydrogenophilus. nucleotide sequence analysis revealed four open reading frames on the subcloned dna, designated hoxa, hoxb, hoxc, and hoxj. the product of hoxa is homologous to a transcriptional activator of the family of two-component regulatory systems present in a number of h2-oxidizing bacteria. ...	1997	9045826
identification of the lrp gene in bradyrhizobium japonicum and its role in regulation of delta-aminolevulinic acid uptake.	the heme precursor delta-aminolevulinic acid (ala) is taken up by the dipeptide permease (dpp) system in escherichia coli. in this study, we identified a bradyrhizobium japonicum genomic library clone that complemented both ala and dipeptide uptake activities in e. coli dpp mutants. the complementing b. japonicum dna encoded a product with 58% identity to the e. coli global transcriptional regulator lrp (leucine-responsive regulatory protein), implying the presence of dpp-independent ala uptake ...	1997	9045849
purification and characterization of the nadp-malic enzyme from bradyrhizobium japonicum a1017.	an nadp-malic enzyme [ec 1.1.1.40] was purified to homogeneity from bradyrhizobium japonicum a1017, and the molecular and physiological characteristics were surveyed. the molecular mass of one subunit of the purified enzyme was evaluated to be 77,600 da by sds-page, and the native enzyme was a tetramer in ph 7.0 and dimer in ph 8.0 conditions, showing complex oligomeric characteristics corresponding to ph value.	1997	9058984
the sequence of a symbiotically essential bradyrhizobium japonicum operon consisting of trpd, trpc and a moac-like gene.	the 2767 bp bamhi-hindiii fragment specifying the trpdc genes of b. japonicum i-110 was sequenced. the trpd and trpc genes each have three highly conserved 'crawford' consensus sequences and are part of an operon with three open reading frames (orfs). the third orf has a predicted product with 58% amino-acid sequence identity with the gene product of e. coli moac, a gene encoding an enzyme involved in biosynthesis of the molybdenum cofactor required for the activity of nitrate reductase and othe ...	1997	9061023
hoxa is a transcriptional regulator for expression of the hup structural genes in free-living bradyrhizobium japonicum.	a chromosomally integrated bradyrhizobium japonicum hoxa mutant is unable to oxidize hydrogen in free-living conditions. derepressing conditions that induce hydrogenase activity in free-living, wild-type b. japonicum cells cannot induce expression of the hydrogenase structural genes in the hoxa mutant. the dna-binding capacity of hoxa at the hup promoter region was studied by means of gel retardation. both heterotrophically growing cells and cells induced to express hydrogenase activity contain ...	1997	9076733
molecular studies on a new genetic locus linked to the common nodulation genes in bradyrhizobium japonicum.	orfa, an actively transcribed genetic locus linked to the common nodulation genes in bradyrhizobium japonicum usda110, was sequenced and analysed. the expression of orfa is neither dependent on the regulatory proteins nifa, ntrc, ntrb and nodd1 nor on either copy of sigma 54, rpon1 and rpon2. the transcriptional start site of orfa was determined and found to overlap the oppositely transcribed nodz gene by 224 nucleotides. an appropriately located -10 sequence identical to the consensus proposed ...	1997	9084141
the dnakj operon belongs to the sigma32-dependent class of heat shock genes in bradyrhizobium japonicum.	the dnakj genes of bradyrhizobium japonicum were cloned and sequenced. they map adjacent to each other, as in other proteobacteria of the alpha and gamma subgroups. primer extension experiments identified two strongly heat-inducible transcripts starting 99 bp (t1) and 204 bp (t2) upstream of dnak. synthesis of the shorter transcript t1 in escherichia coli required the presence of a recently characterized sigma32 homologue (rpoh1) from b. japonicum. the -35 and -10 regions of the promoters associ ...	1997	9108282
bacterial nodulation protein nodz is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin.	the nodz gene, which is present in various soil bacteria such as bradyrhizobium japonicum, azorhizobium caulinodans, and rhizobium loti, is involved in the addition of a fucosyl residue to the reducing n-acetylglucosamine residue of lipochitin oligosaccharide (lco) signal molecules. using an escherichia coli strain that produces large quantities of the nodz protein of b. japonicum, we have purified the nodz protein to homogeneity. the purified nodz protein appears to be active in an in vitro tra ...	1997	9113990
replacement of pro109 by his in tlpa, a thioredoxin-like protein from bradyrhizobium japonicum, alters its redox properties but not its in vivo functions.	tlpa, the membrane-anchored, thioredoxin-like protein from bradyrhizobium japonicum, is essential for cytochrome aa3 biogenesis. the periplasmic domain of tlpa was previously shown to have protein thiol:disulfide oxidoreductase activity and reducing properties similar to those of cytoplasmic thioredoxins. here, we replaced the proline-109 in its active-site sequence c107 v108 p109 c110 by a histidine residue. the resulting active-site motif (cvhc) resembles that of oxidizing thiol:disulfide oxid ...	1997	9136895
nodv and nodw, a second flavonoid recognition system regulating nod gene expression in bradyrhizobium japonicum.	in bradyrhizobium japonicum, members of two global regulatory families, a lysr-type regulator, nodd1, and a two-component regulatory system, nodvw, positively regulate nod gene expression in response to plant-produced isoflavone signals. by analogy to other two-component systems, nodv and nodw are thought to activate transcription via a series of phosphorylation steps. these include the phosphorylation of nodv in response to the plant signal and the subsequent activation of nodw via the transfer ...	1997	9139921
three disparately regulated genes for sigma 32-like transcription factors in bradyrhizobium japonicum.	bradyrhizobium japonicum possesses a subclass of heat-shock genes whose members are transcribed from a sigma 32 consensus promoter. having identified previously one gene (rpoh1) encoding a sigma 32-like rna polymerase transcription factor, we report here the characterization of two additional rpoh-like genes (rpoh2 and rpoh3). b. japonicum thus represents the first example of an organism possessing an rpoh multigene family. all three rpoh genes encode functional proteins that are able to initiat ...	1997	9140968
the hypb protein from bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase.	the hypb protein from bradyrhizobium japonicum is a metal-binding gtpase required for hydrogenase expression. in-frame mutagenesis of hypb resulted in strains that were partially or completely deficient in hydrogenase expression, depending on the degree of disruption of the gene. complete deletion of the gene yielded a strain (jh delta eg) which lacked hydrogenase activity under all conditions tested, including the situation as bacteroids from soybean nodules. mutant strain jh delta 23h lacking ...	1997	9140970
roles of hoxx and hoxa in biosynthesis of hydrogenase in bradyrhizobium japonicum.	in-frame deletion mutagenesis was used to study the roles of two bradyrhizobium japonicum proteins, hoxx and hoxa, in hydrogenase biosynthesis; based on their sequences, these proteins were previously proposed to be sensor and regulator proteins, respectively, of a two-component regulatory system necessary for hydrogenase transcription. deletion of the hoxx gene resulted in a strain that expressed only 30 to 40% of wild-type hydrogenase activity. the inactive unprocessed form of the hydrogenase ...	1997	9171416
transcriptional regulation of delta-aminolevulinic acid dehydratase synthesis by oxygen in bradyrhizobium japonicum and evidence for developmental control of the hemb gene.	an increased demand for cytochromes is associated with symbiotic development and microaerobic metabolism in the bacterium bradyrhizobium japonicum, and evidence suggests that hemb, rather than hema, is the first essential bacterial heme synthesis gene in symbiosis with soybean. steady-state levels of mrna and protein encoded by hemb were strongly and rapidly induced by o2 deprivation as determined by rnase protection and immunoblot analyses, but hemh message was not induced. oxygen limitation re ...	1997	9171420
hydrogenase genes from rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein nifa.	rhizobium leguminosarum bv. viciae expresses an uptake hydrogenase in symbiosis with peas (pisum sativum) but, unlike all other characterized hydrogen-oxidizing bacteria, cannot express it in free-living conditions. the hydrogenase-specific transcriptional activator gene hoxa described in other species was shown to have been inactivated in r. leguminosarum by accumulation of frameshift and deletion mutations. symbiotic transcription of hydrogenase structural genes hupsl originates from a -24/-12 ...	1997	9177161
cloning and sequence analysis of a novel insertion element from plasmids harbored by the carbofuran-degrading bacterium, sphingomonas sp. cfo6.	sphingomonas sp. cfo6 (a member of the alpha group of proteobacteria) was isolated from a washington soil by enrichment on the insecticide carbofuran as a sole source of carbon and energy. this strain has been shown to harbor five plasmids, at least some of which are required for catabolism of carbofuran. rearrangements, deletions, and loss of individual plasmids resulting in the loss of the carbofuran-degrading phenotype were observed following treatment with heat or introduction of tn5. severa ...	1997	9200220
genetic evidence for 5-aminoimidazole-4-carboxamide ribonucleotide (aicar) as a negative effector of cytochrome terminal oxidase cbb3 production in rhizobium etli.	a rhizobium etli tn5mob-induced mutant (cfn035) exhibits an enhanced capacity to oxidize n,n,n',n', tetramethyl-p -phenylenediamine (tmpd), a presumptive indicator of elevated cytochrome c terminal oxidase activity. sequencing of the mutated gene in cfn035 revealed that it codes for the amidophosphoribosyl transferase enzyme (purf) that catalyzes the first step in the purine biosynthetic pathway. two c-type cytochromes with molecular weights of 32 and 27 kda were produced in strain cfn035, which ...	1997	9202382
bradyrhizobium japonicum does not require alpha-ketoglutarate dehydrogenase for growth on succinate or malate.	the suca gene, encoding the e1 component of alpha-ketoglutarate dehydrogenase, was cloned from bradyrhizobium japonicum usda110, and its nucleotide sequence was determined. the gene shows a codon usage bias typical of non-nif and non-fix genes from this bacterium, with 89.1% of the codons being g or c in the third position. a mutant strain of b. japonicum, lsg184, was constructed with the suca gene interrupted by a kanamycin resistance marker. lsg184 is devoid of alpha-ketoglutarate dehydrogenas ...	1997	8981998
a novel transporter involved in cobalt uptake.	cobalt is an essential component of a low molecular-mass nitrile hydratase (l-nhase) from rhodococcus rhodochrous j1. we have found a new gene, nhlf, in the dna region sandwiched between nhlba encoding l-nhase and amda encoding amidase, which are involved in the degradation of nitriles. the product of nhlf, nhlf, shows a significant sequence similarity with those of hoxn from alcaligenes eutrophus, hupn from bradyrhizobium japonicum, nixa from helicobacter pylori, and ureh from bacillus sp., whi ...	1997	8990157
dissection of the transcription machinery for housekeeping genes of bradyrhizobium japonicum.	by using a pcr approach, the bradyrhizobium japonicum siga gene, which encodes the primary rna polymerase sigma factor, sigma80, was cloned and its nucleotide sequence was established. the deduced protein is highly homologous to the siga protein of rhizobium meliloti (72% amino acid sequence identity) but less so to rpod of escherichia coli (51% identity). well conserved is the c-terminal end of the protein, which is probably involved in promoter recognition and binding of the rna polymerase cor ...	1997	8990287
the formation of nitrogen-fixing bacteroids is delayed but not abolished in soybean infected by an [alpha]-ketoglutarate dehydrogenase-deficient mutant of bradyrhizobium japonicum.	a mutant strain of bradyrhizobium japonicum usda 110 devoid of [alpha]-ketoglutarate dehydrogenase activity (lsg184) was used to test whether this tricarboxylic acid cycle enzyme is necessary to support nitrogen fixation during symbiosis with soybean (glycine max). lsg184 formed nodules about 5 d later than the wild-type strain, and the nodules, although otherwise normal in structure, contained many fewer infected host cells than is typical. at 19 d after inoculation cells infected with the muta ...	1997	12223774
the rhizobium meliloti puta gene: its role in the establishment of the symbiotic interaction with alfalfa.	little is known about the energy sources used by rhizobia during colonization, invasion and root nodule formation on leguminous plants. we have recently reported that an impaired proline metabolism in rhizobium meliloti leads to a reduced nodulation efficiency and competitiveness on alfalfa roots. in the present study we have characterized the r. meliloti proline dehydrogenase gene (puta) and addressed the question of its role in symbiosis. this rhizobial gene encodes a 1224-amino-acid-long poly ...	1997	9004223
expression of early nodulin genes in alfalfa mycorrhizae indicates that signal transduction pathways used in forming arbuscular mycorrhizae and rhizobium-induced nodules may be conserved.	transcripts for two genes expressed early in alfalfa nodule development (msenod40 and msenod2) are found in mycorrhizal roots, but not in noncolonized roots or in roots infected with the fungal pathogen rhizoctonia solani. these same two early nodulin genes are expressed in uninoculated roots upon application of the cytokinin 6-benzylaminopurine. correlated with the expression of the two early nodulin genes, we found that mycorrhizal roots contain higher levels of trans-zeatin riboside than nonm ...	1997	11038545
an important developmental role for oligosaccharides during early embryogenesis of cyprinid fish.	derivatives of chitin oligosaccharides have been shown to play a role in plant organogenesis at nanomolar concentrations. here we present data which indicate that chitin oligosaccharides are important for embryogenesis in vertebrates. we characterize chitin oligosaccharides synthesized in vitro by zebrafish and carp embryos in the late gastrulation stage by incorporation of radiolabeled n-acetyl-d-[u14c]glucosamine and by hplc in combination with enzymatic conversion using the bradyrhizobium nod ...	1997	9223299
heme c incorporation into the c-type cytochromes fixo and fixp is essential for assembly of the bradyrhizobium japonicum cbb3-type oxidase.	the monoheme and diheme c-type cytochromes fixo and fixp are two of the subunits of the respiratory cbb3-type oxidase of bradyrhizobium japonicum. the cysteines of the respective heme c binding motifs cxxch were changed to serines by site-directed mutagenesis, which led to inactive oxidases in all mutants. western blot analyses showed that an intact heme binding site in the fixo polypeptide is a prerequisite not only for the synthesis of holo-fixo protein but also for the formation of the entire ...	1997	9257693
metals control activity and expression of the heme biosynthesis enzyme delta-aminolevulinic acid dehydratase in bradyrhizobium japonicum.	the heme biosynthesis enzyme delta-aminolevulinic acid dehydratase (alad) requires magnesium or zinc for activity, depending on the organism, and the heme moiety contains iron. thus, metals are important for heme formation in at least two different ways. bradyrhizobium japonicum alad* is an engineered derivative of wild-type alad that requires zn2+ for activity rather than mg2+ (s. chauhan and m. r. o'brian, j. biol. chem. 270:19823-19827, 1995). the ph optimum for alad* activity was over 3.5 un ...	1997	9287008
biodiversity of bradyrhizobia nodulating lupinus spp.	the genetic structure of bradyrhizobium isolates recovered from three lupinus species (lupinus campestris, lupinus montanus, and lupinus exaltatus) grown in mexico was examined. among 41 bradyrhizobium isolates, 18 electrophoretic types (ets) were distinguished by multilocus enzyme electrophoresis of five metabolic enzymes. the mean genetic diversity, 0.64, indicated that there was great genetic diversity in the population sampled. most isolates (63%) fell into two closely related clusters (clus ...	1997	9336911
magnetic resonance studies on the active site and metal centers of bradyrhizobium japonicum porphobilinogen synthase.	porphobilinogen synthase (pbgs) is a metalloenzyme which catalyzes the asymmetric condensation of two molecules of 5-aminolevulinic acid (ala) to form porphobilinogen. there are at least four types of pbgs, categorized according to metal ion usage. the pbgs from bradyrhizobium japonicum requires mg(ii) in catalytic metal site a, has an allosteric mg(ii) in metal site c, and also contains an activating monovalent cation binding site [petrovich et al. (1996) j. biol. chem. 271, 8692-8699]. 13c nmr ...	1997	9341235
identification of active sites in amidase: evolutionary relationship between amide bond- and peptide bond-cleaving enzymes.	mainly based on various inhibitor studies previously performed, amidases came to be regarded as sulfhydryl enzymes. not completely satisfied with this generally accepted interpretation, we performed a series of site-directed mutagenesis studies on one particular amidase of rhodococcus rhodochrous j1 that was involved in its nitrile metabolism. for these experiments, the recombinant amidase was produced as the inclusion body in escherichia coli to greatly facilitate its recovery and subsequent pu ...	1997	9342349
cloning and characterization of the flavobacterium johnsoniae (cytophaga johnsonae) gliding motility gene, glda.	the mechanism of bacterial gliding motility (active movement over surfaces without the aid of flagella) is not known. a large number of nonmotile mutants of the gliding bacterium flavobacterium johnsoniae (cytophaga johnsonae) have been previously isolated, and genetic techniques to analyze these mutants have recently been developed. we complemented a nonmotile mutant of f. johnsoniae (uw102-09) with a library of wild-type dna by using the shuttle cosmid pcp17. the complementing plasmid (pcp100) ...	1997	9342376
the sequences of hypf, hypc and hypd complete the hyp gene cluster required for hydrogenase activity in bradyrhizobium japonicum.	a region of dna 6 kb downstream of the hydrogenase (h2ase) structural genes and directly downstream of the hypb gene of bradyrhizobium japonicum was shown by mutational analysis to be necessary for h2ase synthesis. sequencing of this region revealed two complete open reading frames, and the 5' fragment of a third orf. they encode proteins with homologies to the hypf, hypc and the n-terminus of hypd from other h2ase-containing organisms. the hypf of b. japonicum encodes a 753-aa protein with a pr ...	1997	9358044
digalactosyl diacylglycerols, plant glycolipids rarely found in bacteria, are major membrane components of bacteroid forms of bradyrhizobium japonicum.	the membrane lipids of free living and bacteroid forms of bradyrhizobium japonicum, obtained from nodules occupied by both typed and untyped bacteria, were isolated and characterized by a combination of nmr spectroscopy, mass spectrometry, and other chemical and physical methods. these studies indicated that both the free living and bacteroid forms of this organism contain glycolipids almost exclusively of the type found in plant cells. in the bacteroid forms, there was a dramatic shift towards ...	1997	9363436
genetic diversity of rhizobial symbionts isolated from legume species within the genera astragalus, oxytropis, and onobrychis.	the genetic diversity of 44 rhizobial isolates from astragalus, oxytropis, and onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (mrsp) analysis of 16s rrna genes and by pcr dna fingerprinting with repetitive sequences (rep-pcr). a comparison of tree topologies of reference strains constructed with data obtained by mrsp and by 16s rrna gene sequence analyses showed that the topologies were in good agreement, indicating that the ...	1997	9406393
metabolic roles of a rhodobacter sphaeroides member of the sigma32 family.	we report the role of a gene (rpoh) from the facultative phototroph rhodobacter sphaeroides that encodes a protein (sigma37) similar to escherichia coli sigma32 and other members of the heat shock family of eubacterial sigma factors. r. sphaeroides sigma37 controls genes that function during environmental stress, since an r. sphaeroides deltarpoh mutant is approximately 30-fold more sensitive to the toxic oxyanion tellurite than wild-type cells. however, the deltarpoh mutant lacks several phenot ...	1998	9422586
identification of the bradyrhizobium japonicum degp gene as part of an operon containing small heat-shock protein genes.	a degp (htra)-like gene of bradyrhizobium japonicum was identified immediately downstream of two genes (hspb and hspc) coding for small heat-shock proteins. all three genes are oriented in the same direction and are separated by only 85 and 72 bp, and a heat-inducible transcript covering hspb, hspc, and degp was detected by rt-pcr. these results show that the genes are organized in an operon. two mutants, a degp insertion mutant and a deltahspbcdegp mutant, were constructed by marker replacement ...	1998	9446679
in vivo genomic footprinting analysis reveals that the complex bradyrhizobium japonicum fixrnifa promoter region is differently occupied by two distinct rna polymerase holoenzymes.	the bradyrhizobium japonicum fixrnifa operon is transcribed from two promoters: fixrp1, a -24/-12 promoter recognized by the sigma54-holoenzyme form of the rna polymerase, and fixrp2, a -35/-10 promoter that is transcribed by a second, unidentified, form of rna polymerase holoenzyme. the fixrp1 promoter is autoregulated during microaerobiosis by nifa, whereas fixrp2 is also activated, but by a different regulatory protein. the main transcription start sites for these promoters are just two nucle ...	1998	9448277
three phylogenetic groups of noda and nifh genes in sinorhizobium and mesorhizobium isolates from leguminous trees growing in africa and latin america.	the diversity and phylogeny of noda and nifh genes were studied by using 52 rhizobial isolates from acacia senegal, prosopis chilensis, and related leguminous trees growing in africa and latin america. all of the strains had similar host ranges and belonged to the genera sinorhizobium and mesorhizobium, as previously determined by 16s rrna gene sequence analysis. the restriction patterns and a sequence analysis of the noda and nifh genes divided the strains into the following three distinct grou ...	1998	9464375
characterization of marine temperate phage-host systems isolated from mamala bay, oahu, hawaii.	to understand the ecological and genetic role of viruses in the marine environment, it is critical to know the infectivity of viruses and the types of interactions that occur between marine viruses and their hosts. we isolated four marine phages from turbid plaques by using four indigenous bacterial hosts obtained from concentrated water samples from mamala bay, oahu, hawaii. two of the rod-shaped bacterial hosts were identified as sphingomonas paucimobilis and flavobacterium sp. all of the phag ...	1998	9464390
isolation and characterization of rhodobacter capsulatus mutants affected in cytochrome cbb3 oxidase activity.	the facultative phototrophic bacterium rhodobacter capsulatus contains only one form of cytochrome (cyt) c oxidase, which has recently been identified as a cbb3-type cyt c oxidase. this is unlike other related species, such as rhodobacter sphaeroides and paracoccus denitrificans, which contain an additional mitochondrial-like aa3-type cyt c oxidase. an extensive search for mutants affected in cyt c oxidase activity in r. capsulatus led to the isolation of at least five classes of mutants. plasmi ...	1998	9473054
genetic and functional analysis of the styrene catabolic cluster of pseudomonas sp. strain y2.	the chromosomal region of pseudomonas sp. strain y2 involved in the conversion of styrene to phenylacetate (upper catabolic pathway) has been cloned and sequenced. four catabolic genes, styabcd, and two regulatory genes, stysr, were identified. this gene cluster when transferred to escherichia coli w confers to this phenylacetate-degrading host the ability to grow on styrene as the sole carbon and energy source. genes styabcd are homologous to those encoding the styrene upper catabolic pathway i ...	1998	9495743
characterization of a protocatechuate catabolic gene cluster from rhodococcus opacus 1cp: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity.	the catechol and protocatechuate branches of the 3-oxoadipate pathway, which are important for the bacterial degradation of aromatic compounds, converge at the common intermediate 3-oxoadipate enol-lactone. a 3-oxoadipate enol-lactone-hydrolyzing enzyme, purified from benzoate-grown cells of rhodococcus opacus (erythropolis) 1cp, was found to have a larger molecular mass under denaturing conditions than the corresponding enzymes previously purified from gamma-proteobacteria. sequencing of the n ...	1998	9495744
how replacements of the 12 conserved histidines of subunit i affect assembly, cofactor binding, and enzymatic activity of the bradyrhizobium japonicum cbb3-type oxidase.	alignments of the amino acid sequences of subunit i (fixn or ccon) of the cbb3-type oxidases show 12 conserved histidines. six of them are diagnostic of heme-copper oxidases and are thought to bind the following cofactors: the low spin heme b and the binuclear high spin heme b-cub center. the other six are fixn(ccon)-specific and their function is unknown. to analyze the contribution of these 12 invariant histidines of fixn in cofactor binding and function of the bradyrhizobium japonicum cbb3-ty ...	1998	9497378
rearrangement of actin microfilaments in plant root hairs responding to rhizobium etli nodulation signals	the response of the actin cytoskeleton to nodulation (nod) factors secreted by rhizobium etli has been studied in living root hairs of bean (phaseolus vulgaris) that were microinjected with fluorescein isothiocyanate-phalloidin. in untreated control cells or cells treated with the inactive chitin oligomer, the actin cytoskeleton was organized into long bundles that were oriented parallel to the long axis of the root hair and extended into the apical zone. upon exposure to r. etli nod factors, th ...	1998	9501120
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.	this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...	1998	9501433
unusual organization of the genes coding for hydsl, the stable [nife]hydrogenase in the photosynthetic bacterium thiocapsa roseopersicina bbs.	the characterization of a hyd gene cluster encoding the stable, bidirectional [nife]hydrogenase 1 enzyme in thiocapsa roseopersicina bbs, a purple sulfur photosynthetic bacterium belonging to the family chromatiaceae, is presented. the heterodimeric hydrogenase 1 had been purified to homogeneity and thoroughly characterized (k. l. kovacs et al., j. biol. chem. 266:947-951, 1991; c. bagyinka et al., j. am. chem. soc. 115:3567-3585, 1993). as an unusual feature, a 1,979-bp intergenic sequence (is) ...	1998	9515914
rhizobium etli cychjkl gene locus involved in c-type cytochrome biogenesis: sequence analysis and characterization of two cych mutants.	the cychjkl gene locus was cloned from rhizobium etli by the rescue of a tn5mob insertion of a mutant (ifc01) which was affected in the production of c-type cytochromes. the cych, cycj, cyck and cycl genes are proposed to code for different subunits of a haem lyase complex involved in the attachment of haem to cytochrome c apoproteins. cych of 365 aa shared 27, 36, 47 and 63% identity with cych from paracoccus denitrificans, bradyrhizobium japonicum, r. meliloti, and r. leguminosarum, respective ...	1998	9524269
the circe element and its putative repressor control cell cycle expression of the caulobacter crescentus groesl operon.	the groesl operon is under complex regulation in caulobacter crescentus. in addition to strong induction after exposure to heat shock, under physiological growth conditions, its expression is subject to cell cycle control. transcription and translation of the groe genes occur primarily in predivisional cells, with very low levels of expression in stalked cells. the regulatory region of groesl contains both a sigma32-like promoter and a circe element. overexpression of c. crescentus sigma32 gives ...	1998	9537357
the rhizobium etli rpon locus: dna sequence analysis and phenotypical characterization of rpon, ptsn, and ptsa mutants.	the rpon region of rhizobium etli was isolated by using the bradyrhizobium japonicum rpon1 gene as a probe. nucleotide sequence analysis of a 5,600-bp dna fragment of this region revealed the presence of four complete open reading frames (orfs), orf258, rpon, orf191, and ptsn, coding for proteins of 258, 520, 191, and 154 amino acids, respectively. the gene product of orf258 is homologous to members of the atp-binding cassette-type permeases. orf191 and ptsn are homologous to conserved orfs foun ...	1998	9537369
thioredoxin is an essential protein induced by multiple stresses in bacillus subtilis.	thioredoxin, a small, ubiquitous protein which participates in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, is an essential protein in bacillus subtilis. a variety of stresses, including heat or salt stress or ethanol treatment, strongly enhanced the synthesis of thioredoxin in b. subtilis. the stress induction of the monocistronic trxa gene encoding thioredoxin occurs at two promoters. the general stress sigma factor, sigmab, was required for the ...	1998	9537387
the active-site cysteines of the periplasmic thioredoxin-like protein ccmg of escherichia coli are important but not essential for cytochrome c maturation in vivo.	a new member of the family of periplasmic protein thiol:disulfide oxidoreductases, ccmg (also called dsbe), was characterized with regard to its role in cytochrome c maturation in escherichia coli. the ccmg protein was shown to be membrane bound, facing the periplasm with its c-terminal, hydrophilic domain. a chromosomal, nonpolar in-frame deletion in ccmg resulted in the complete absence of all c-type cytochromes. replacement of either one or both of the two cysteine residues of the predicted a ...	1998	9537397
the atrazine catabolism genes atzabc are widespread and highly conserved.	pseudomonas strain adp metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genes atzabc, to yield cyanuric acid, a nitrogen source for many bacteria. here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous to atza, -b, and -c. the sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. this differs from bacterial genes involved in the catabolism of othe ...	1998	9537398
roles of the bradyrhizobium japonicum terminal oxidase complexes in microaerobic h2-dependent growth	spectral, inhibitor, and o2-consumption studies on membranes from free-living and bacteroid forms of bradyrhizobium japonicum have revealed the existence of a number of terminal oxidases, and four terminal oxidase gene clusters within the heme-copper cytochrome family have been cloned. here the complexes encoded by coxmnop and coxwxyz, genes with homology to cua-containing cytochrome c oxidases and b-type ubiquinol oxidases respectively, are studied by analysis of mutants in each of the two oxid ...	1998	9554944
expression and regulation of the sodf gene encoding iron- and zinc-containing superoxide dismutase in streptomyces coelicolor müller.	streptomyces coelicolor müller contains two superoxide dismutases (sods), nickel-containing (nisod) and iron- and zinc-containing sod (feznsod). the sodf gene encoding feznsod was isolated by using pcr primers corresponding to the n-terminal peptide sequence of the purified feznsod and a c-terminal region conserved among known fesods and mnsods. the deduced amino acid sequence exhibited highest similarity to mn- and fesods from propionibacterium shermanii and mycobacterium spp. the transcription ...	1998	9555880
availability of o2 as a substrate in the cytoplasm of bacteria under aerobic and microaerobic conditions.	the growth rates of pseudomonas putida kt2442 and mt-2 on benzoate, 4-hydroxybenzoate, or 4-methylbenzoate showed an exponential decrease with decreasing oxygen tensions (partial o2 tension [po2] values). the oxygen tensions resulting in half-maximal growth rates were in the range of 7 to 8 mbar of o2 (corresponding to 7 to 8 microm o2) (1 bar = 10(5) pa) for aromatic compounds, compared to 1 to 2 mbar for nonaromatic compounds like glucose or succinate. the decrease in the growth rates coincide ...	1998	9555896
the rhizobium meliloti exok and exsh glycanases specifically depolymerize nascent succinoglycan chains.	the rhizobium meliloti exok and exsh glycanases have been proposed to contribute to production of low molecular weight (lmw) succinoglycan by depolymerizing high molecular weight succinoglycan chains in r. meliloti cultures. we expressed and purified exok and exsh and determined that neither enzyme can extensively cleave succinoglycan prepared from r. meliloti cultures, although neutral/heat treatment and acid/heat treatment convert succinoglycan to forms that can be cleaved efficiently by both ...	1998	9560202
transmembrane heme delivery systems.	heme proteins play pivotal roles in a wealth of biological processes. despite this, the molecular mechanisms by which heme traverses bilayer membranes for use in biosynthetic reactions are unknown. the biosynthesis of c-type cytochromes requires that heme is transported to the bacterial periplasm or mitochondrial intermembrane space where it is covalently ligated to two reduced cysteinyl residues of the apocytochrome. results herein suggest that a family of integral membrane proteins in prokaryo ...	1998	9560218
isocitrate dehydrogenase and glyoxylate cycle enzyme activities in bradyrhizobium japonicum under various growth conditions.	bradyrhizobium japonicum, the nitrogen-fixing symbiotic partner of soybean, was grown on various carbon substrates and assayed for the presence of the glyoxylate cycle enzymes, isocitrate lyase and malate synthase. the highest levels of isocitrate lyase [165-170 nmol min-1 (mg protein)-1] were found in cells grown on acetate or beta-hydroxybutyrate, intermediate activity was found after growth on pyruvate or galactose, and very little activity was found in cells grown on arabinose, malate, or gl ...	1998	9560426
the bradyrhizobium japonicum phob gene is required for phosphate-limited growth but not for symbiotic nitrogen fixation.	we identified by cloning and dna sequence analysis the phosphate regulatory gene phob of bradyrhizobium japonicum. the deduced gene product displayed pronounced similarity to the phob protein of sinorhizobium meliloti (71.4% identical amino acids). escherichia coli (50.2%) and other bacterial species. insertion of a kanamycin resistance cassette into phob led to impaired growth of the b. japonicum mutant in media containing approximately 25 microm phosphate or less. a standard plant infection te ...	1998	9561731
the rhizobium etli fixl protein differs in structure from other known fixl proteins.	the central heme-binding domain in the fixl proteins of sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium leguminosarum biovar viciae and azorhizobium caulinodans, is highly conserved. the similarity with the corresponding domain in the rhizobium etli fixl protein is considerably less. this observation prompted us to analyze the heme-binding capacities of the r. etli fixl protein. the r. etli fixl gene was overexpressed in escherichia coli. in the presence of s. meliloti fixj, the over ...	1998	9563844
a transposable partitioning locus used to stabilize plasmid-borne hydrogen oxidation and trifolitoxin production genes in a sinorhizobium strain.	improved nitrogen-fixing inoculum strains for leguminous crops must be able to effectively compete with indigenous strains for nodulation, enhance legume productivity compared to the productivity obtained with indigenous strains, and maintain stable expression of any added genes in the absence of selection pressure. we constructed a transposable element containing the tfx region for expression of increased nodulation competitiveness and the par locus for plasmid stability. the transposon was ins ...	1998	9572932
biodegradation of aliphatic-aromatic copolyesters by thermomonospora fusca and other thermophilic compost isolates.	random aliphatic-aromatic copolyesters synthesized from 1,4-butanediol, adipic acid, and terephthalic acid (bta) have excellent thermal and mechanical properties and are biodegradable by mixed cultures (e.g., in compost). over 20 bta-degrading strains were isolated by using compost as a microbial source. among these microorganisms, thermophilic actinomycetes obviously play an outstanding role and appear to dominate the initial degradation step. two actinomycete strains exhibited about 20-fold hi ...	1998	9572944
new bradyrhizobium japonicum strains that possess high copy numbers of the repeated sequence rs alpha.	in a survey of dna fingerprints of indigenous bradyrhizobium japonicum with the species-specific repeated sequences rs alpha and rs beta, 21 isolates from three field sites showed numerous rs-specific hybridization bands. the isolates were designated highly reiterated sequence-possessing (hrs) isolates, and their dna hybridization profiles were easily distinguished from the normal patterns. some hrs isolates from two field sites possessed extremely high numbers of rs alpha copies, ranging from 8 ...	1998	9572961
regulation of lipid synthesis in bradyrhizobium japonicum: low oxygen concentrations trigger phosphatidylinositol biosynthesis.	lowering oxygen tension in free-living bradyrhizobium japonicum resulted in a dramatic switch of membrane chemistry in which phosphatidylcholine, the predominant lipid in aerated cultures, was no longer synthesized and phosphatidylethanolamine became the major lipid. besides this change, phosphatidylinositol, a typical plant lipid rarely found in bacteria, was also synthesized.	1998	9572982
regulation of the carnitine pathway in escherichia coli: investigation of the cai-fix divergent promoter region.	the divergent structural operons caitabcde and fixabcx of escherichia coli are required for anaerobic carnitine metabolism. transcriptional monocopy lacz fusion studies showed that both operons are coexpressed during anaerobic growth in the presence of carnitine, respond to common environmental stimuli (like glucose and nitrate), and are modulated positively by the same general regulators, crp and fnr, and negatively by h-ns. overproduction of the caif specific regulatory protein mediating the c ...	1998	9573142
(methyl)ammonium transport in the nitrogen-fixing bacterium azospirillum brasilense.	an ammonium transporter of azospirillum brasilense was characterized. in contrast to most previously reported putative prokaryotic nh4+ transporter genes, a. brasilense amtb is not part of an operon with glnb or glnz which, in a. brasilense, encode nitrogen regulatory proteins pii and pz, respectively. sequence analysis predicts the presence of 12 transmembrane domains in the deduced amtb protein and classifies amtb as an integral membrane protein. nitrogen regulates the transcription of the amt ...	1998	9573149
unconventional genomic organization in the alpha subgroup of the proteobacteria.	pulsed-field gel electrophoresis was used to analyze the genomic organization of 16 bacteria belonging or related to the family rhizobiaceae of the alpha subgroup of the class proteobacteria. the number and sizes of replicons were determined by separating nondigested dna. hybridization of an rrn gene probe was used to distinguish between chromosomes and plasmids. members of the genus agrobacterium all possess two chromosomes, and each biovar has a specific genome size. as previously demonstrated ...	1998	9573163
promoter selectivity of the bradyrhizobium japonicum rpoh transcription factors in vivo and in vitro.	expression of the dnakj and groesl1 heat shock operons of bradyrhizobium japonicum depends on a sigma32-like transcription factor. three such factors (rpoh1, rpoh2, and rpoh3) have previously been identified in this organism. we report here that they direct transcription from some but not all sigma32-type promoters when the respective rpoh genes are expressed in escherichia coli. all three rpoh factors were purified as soluble c-terminally histidine-tagged proteins, although the bulk of overprod ...	1998	9573191
regulatory conservation and divergence of sigma32 homologs from gram-negative bacteria: serratia marcescens, proteus mirabilis, pseudomonas aeruginosa, and agrobacterium tumefaciens.	the heat shock response in escherichia coli is mediated primarily by the rpoh gene, encoding sigma32, which is specifically required for transcription of heat shock genes. a number of sigma32 homologs have recently been cloned from gram-negative bacteria that belong to the gamma or alpha subdivisions of the proteobacteria. we report here some of the regulatory features of several such homologs (rpoh) expressed in e. coli as well as in respective cognate bacteria. when expressed in an e. coli del ...	1998	9573192
characterization of bradyrhizobium japonicum pcabdc genes involved in 4-hydroxybenzoate degradation.	the pca structural genes encode enzymes that participate in the conversion of protocatechuate to succinate and acetylcoenzyme a. a 3. 05-kb region of the bradyrhizobium japonicum strain usda110 genome has been characterized, which contains the pcab, pcad and pcac genes. the predicted protein sequences of the three genes have extensive homologies with beta-carboxy-cis,cis-muconate cycloisomerase (pcab), beta-ketodiapate enol-lactone hydrolase (pcad), and gamma-carboxymuconolactone decarboxylase ( ...	1998	9582432
in vivo studies on the positive control function of nifa: a conserved hydrophobic amino acid patch at the central domain involved in transcriptional activation.	the eubacterial enhancer-binding proteins activate transcription by binding to distant sites and, simultaneously, contacting the rna polymerase r54 promoter complex (esigma54). the positive control function is located at the central domain of these proteins, but it is not know which specific region has the determinants for the interaction with esigma54. here, we present genetic evidence that a small region of hydrophobic amino acids, previously denominated c3, at the central domain of bradyrhizo ...	1998	9593296
localization of the wilson's disease protein product to mitochondria.	wilson's disease (wnd) is an inherited disorder of copper homeostasis characterized by abnormal accumulation of copper in several tissues, particularly in the liver, brain, and kidney. the disease-associated gene encodes a copper-transporting p-type atpase, the wnd protein, the subcellular location of which could be regulated by copper. we demonstrate that the wnd protein is present in cells in two forms, the 160-kda and the 140-kda products. the 160-kda product was earlier shown to be targeted ...	1998	9600907
towards a biocatalyst for (s)-styrene oxide production: characterization of the styrene degradation pathway of pseudomonas sp. strain vlb120.	in order to design a biocatalyst for the production of optically pure styrene oxide, an important building block in organic synthesis, the metabolic pathway and molecular biology of styrene degradation in pseudomonas sp. strain vlb120 was investigated. a 5.7-kb xhoi fragment, which contained on the same strand of dna six genes involved in styrene degradation, was isolated from a gene library of this organism in escherichia coli by screening for indigo formation. t7 rna polymerase expression expe ...	1998	9603811
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 ...	1998	9603820
the atzabc genes encoding atrazine catabolism are located on a self-transmissible plasmid in pseudomonas sp. strain adp.	pseudomonas sp. strain adp initiates atrazine catabolism via three enzymatic steps, encoded by atza, -b, and -c, which yield cyanuric acid, a nitrogen source for many bacteria. in-well lysis, southern hybridization, and plasmid transfer studies indicated that the atza, -b, and -c genes are localized on a 96-kb self-transmissible plasmid, padp-1, in pseudomonas sp. strain adp. high-performance liquid chromatography analyses showed that cyanuric acid degradation was not encoded by padp-1. padp-1 w ...	1998	9603862
characterization of chemotactic responses and flagella of hyphomicrobium strain w1-1b.	motile swarmer cells of hyphomicrobium strain w1-1b displayed positive chemotactic responses toward methylamine, dimethylamine, and trimethylamine but did not display significant chemotactic responses towards methanol and arginine. electron micrographs of negatively stained intact flagellar filaments indicated a novel striated surface pattern. the flagella were composed of two proteins of 39 and 41 kda. neither protein was a glycoprotein as determined by schiff's staining and by enzyme immunoass ...	1998	9603896
the bradyrhizobium japonicum noed gene: a negatively acting, genotype-specific nodulation gene for soybean.	bradyrhizobium japonicum strain usda 110 is restricted for nodulation by soybean genotype pi 417566. we previously reported the identification of a usda 110 tn5 mutant, strain d4.2-5, that had the ability to overcome nodulation restriction conditioned by pi 417566 (s. m. lohrke, j. h. orf, e. martínez-romero, and m. j. sadowsky, appl. environ. microbiol. 61:2378-2383, 1995). in this study, we report the cloning and characterization of the negatively acting dna region mutated in strain d4.2-5 tha ...	1998	9612946
characterization of the hcnabc gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by anr in the strictly aerobic biocontrol agent pseudomonas fluorescens cha0.	the secondary metabolite hydrogen cyanide (hcn) is produced by pseudomonas fluorescens from glycine, essentially under microaerophilic conditions. the genetic basis of hcn synthesis in p. fluorescens cha0 was investigated. the contiguous structural genes hcnabc encoding hcn synthase were expressed from the t7 promoter in escherichia coli, resulting in hcn production in this bacterium. analysis of the nucleotide sequence of the hcnabc genes showed that each hcn synthase subunit was similar to kno ...	1998	9620970
transcriptional regulation of alcaligenes eutrophus hydrogenase genes.	alcaligenes eutrophus h16 produces a soluble hydrogenase (sh) and a membrane-bound hydrogenase (mbh) which catalyze the oxidation of h2, supplying the organism with energy for autotrophic growth. the promoters of the structural genes for the sh and the mbh, psh and pmbh, respectively, were identified by means of the primer extension technique. both promoters were active in vivo under hydrogenase-derepressing conditions but directed only low levels of transcription under condition which repressed ...	1998	9620971
the fixk2 protein is involved in regulation of symbiotic hydrogenase expression in bradyrhizobium japonicum.	the roles of the nitrogen fixation regulatory proteins nifa, fixk1, and fixk2 in the symbiotic regulation of hydrogenase structural gene expression in bradyrhizobium japonicum have been investigated. bacteroids from fixj and fixk2 mutants have little or no hydrogenase activity, and extracts from these mutant bacteroids contain no hydrogenase protein. bacteroids from a fixk1 mutant exhibit wild-type levels of hydrogenase activity. in beta-galactosidase transcriptional assays with nifa and fixk2 e ...	1998	9620982
a novel dna element that controls bacterial heat shock gene expression.	the hsparpoh1 and hspbcdegp heat shock operons of bradyrhizobium japonicum are preceded by a novel, conserved dna element of approximately 100 bp, which is responsible for the temperature-regulated transcription of their sigma70-type promoters. we designated this motif rose for repression of heat shock gene expression and found additional rose elements upstream of two newly identified heat shock operons. a critical core region in the hspa-associated rose1 was defined by introducing insertions or ...	1998	9622356
release of flavonoids by the soybean cultivars mccall and peking and their perception as signals by the nitrogen-fixing symbiont sinorhizobium fredii	sinorhizobium fredii strain usda191 forms n-fixing nodules on the soybean (glycine max l. merr.) cultivars (cvs) mccall and peking, but s. fredii strain usda257 nodulates only cv peking. we wondered whether specificity in this system is conditioned by the release of unique flavonoid signals from one of the cultivars or by differential perception of signals by the strains. we isolated flavonoids and used nodc and nolx, which are nod-box-dependent and -independent nod genes, respectively, to deter ...	1998	9625713
trifolitoxin production increases nodulation competitiveness of rhizobium etli ce3 under agricultural conditions.	a major barrier to the use of nitrogen-fixing inoculum strains for the enhancement of legume productivity is the inability of commercially available strains to compete with indigenous rhizobia for nodule formation. despite extensive research on nodulation competitiveness, there are no examples of field efficacy studies of strains that have been genetically improved for nodulation competitiveness. we have shown previously that production of the peptide antibiotic trifolitoxin (tfx) by rhizobium e ...	1998	9647840