Publications

disaccharides as a new class of nonaccumulated osmoprotectants for sinorhizobium meliloti.	sucrose and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) are very unusual osmoprotectants for sinorhizobium meliloti because these compounds, unlike other bacterial osmoprotectants, do not accumulate as cytosolic osmolytes in salt-stressed s. meliloti cells. here, we show that, in fact, sucrose and ectoine belong to a new family of nonaccumulated sinorhizobial osmoprotectants which also comprises the following six disaccharides: trehalose, maltose, cellobiose, gentiobiose, ...	1999	10103242
pcr detection of genes encoding nitrite reductase in denitrifying bacteria.	using consensus regions in gene sequences encoding the two forms of nitrite reductase (nir), a key enzyme in the denitrification pathway, we designed two sets of pcr primers to amplify cd1- and cu-nir. the primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. sequence relationships of nir genes were also established. the cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in ...	1999	10103263
cuma, a gene encoding a multicopper oxidase, is involved in mn2+ oxidation in pseudomonas putida gb-1.	pseudomonas putida gb-1-002 catalyzes the oxidation of mn2+. nucleotide sequence analysis of the transposon insertion site of a nonoxidizing mutant revealed a gene (designated cuma) encoding a protein homologous to multicopper oxidases. addition of cu2+ increased the mn2+-oxidizing activity of the p. putida wild type by a factor of approximately 5. the growth rates of the wild type and the mutant were not affected by added cu2+. a second open reading frame (designated cumb) is located downstream ...	1999	10103278
a phosphotransferase that generates phosphatidylinositol 4-phosphate (ptdins-4-p) from phosphatidylinositol and lipid a in rhizobium leguminosarum. a membrane-bound enzyme linking lipid a and ptdins-4-p biosynthesis.	membranes of rhizobium leguminosarum contain a 3-deoxy-d-manno-octulosonic acid (kdo)-activated lipid a 4'-phosphatase required for generating the unusual phosphate-deficient lipid a found in this organism. the enzyme has been solubilized with triton x-100 and purified 80-fold. as shown by co-purification and thermal inactivation studies, the 4'-phosphatase catalyzes not only the hydrolysis of (kdo)2-[4'-32p]lipid iva but also the transfer the 4'-phosphate of kdo2-[4'-32p]lipid iva to the inosit ...	1999	10196199
azorhizobium caulinodans pii and glnk proteins control nitrogen fixation and ammonia assimilation.	we herein report that azorhizobium caulinodans pii and glnk are not necessary for glutamine synthetase (gs) adenylylation whereas both proteins are required for complete gs deadenylylation. the disruption of both glnb and glnk resulted in a high level of gs adenylylation under the condition of nitrogen fixation, leading to ammonium excretion in the free-living state. pii and glnk also controlled nif gene expression because nifa activated nifh transcription and nitrogenase activity was derepresse ...	1999	10198037
the membrane-attached electron carrier cytochrome cy from rhodobacter sphaeroides is functional in respiratory but not in photosynthetic electron transfer.	rhodobacter species are useful model organisms for studying the structure and function of c type cytochromes (cyt c), which are ubiquitous electron carriers with essential functions in cellular energy and signal transduction. among these species, rhodobacter capsulatus has a periplasmic cyt c2rc and a membrane-bound bipartite cyt cyrc. these electron carriers participate in both respiratory and photosynthetic electron-transfer chains. on the other hand, until recently, rhodobacter sphaeroides wa ...	1999	10200265
molecular and functional characterization of the rhodopseudomonas palustris no. 7 phosphoenolpyruvate carboxykinase gene.	the pcka gene, encoding the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (pepck), was cloned by pcr amplification from the purple nonsulfur bacterium rhodopseudomonas palustris no. 7. sequencing of a 2.5-kb chromosomal smai-psti fragment containing the structural gene revealed an open reading frame encoding 537 amino acids, homologous to known pcka genes. primer extension analysis identified a transcriptional start site 72 bp upstream of the pcka initiation codon and an upstream sequen ...	1999	10217755
the global nitrogen regulator ntca regulates transcription of the signal transducer pii (glnb) and influences its phosphorylation level in response to nitrogen and carbon supplies in the cyanobacterium synechococcus sp. strain pcc 7942.	the pii protein is encoded by a unique glnb gene in synechococcus sp. strain pcc 7942. its expression has been analyzed in the wild type and in ntca-null mutant cells grown under different conditions of nitrogen and carbon supply. rna-dna hybridization experiments revealed the presence of one transcript species 680 nucleotides long, whatever the nutrient conditions tested. a second transcript species, 620 nucleotides long, absent in the ntca null mutant, was observed in wild-type cells that were ...	1999	10217756
enhanced nitrogen fixation in a rhizobium etli ntrc mutant that overproduces the bradyrhizobium japonicum symbiotic terminal oxidase cbb3	the ntrc gene codes for a transcriptional activator protein that modulates gene expression in response to nitrogen. the cytochrome production pattern of a rhizobium etli ntrc mutant (cfn2012) was studied. co difference spectral analysis of membranes showed that cfn2012 produced a terminal oxidase similar to the symbiotic terminal oxidase of bacteroids in free-living cells under aerobic conditions, with a characteristic trough at 553 nm. cfn2012 produced two c-type cytochromes with molecular mass ...	1999	10223993
occurrence of choline and glycine betaine uptake and metabolism in the family rhizobiaceae and their roles in osmoprotection	the role of glycine betaine and choline in osmoprotection of various rhizobium, sinorhizobium, mesorhizobium, agrobacterium, and bradyrhizobium reference strains which display a large variation in salt tolerance was investigated. when externally provided, both compounds enhanced the growth of rhizobium tropici, sinorhizobium meliloti, sinorhizobium fredii, rhizobium galegae, agrobacterium tumefaciens, mesorhizobium loti, and mesorhizobium huakuii, demonstrating their utilization as osmoprotectan ...	1999	10224003
heme-based sensors in biological systems.	the past several years have been witness to a staggering rate of advancement in the understanding of how organisms respond to changes in the availability of diatomic molecules that are toxic and/or crucial to survival. heme-based sensors presently constitute the majority of the proteins known to sense no, o2 and co and to initiate the chemistry required to adapt to changes in their availabilities. knowledge of the three characterized members of this class, soluble guanylate cyclase, fixl and coo ...	1999	10226051
nodule-inducing activity of synthetic sinorhizobium meliloti nodulation factors and related lipo-chitooligosaccharides on alfalfa. importance of the acyl chain structure.	sinorhizobium meliloti nodulation factors (nfs) elicit a number of symbiotic responses in alfalfa (medicago sativa) roots. using a semiquantitative nodulation assay, we have shown that chemically synthesized nfs trigger nodule formation in the same range of concentrations (down to 10(-10) m) as natural nfs. the absence of o-sulfate or o-acetate substitutions resulted in a decrease in morphogenic activity of more than 100-fold and approximately 10-fold, respectively. to address the question of th ...	1999	10318686
a nod factor binding lectin with apyrase activity from legume roots.	a lectin isolated from the roots of the legume, dolichos biflorus, binds to nod factors produced by rhizobial strains that nodulate this plant and has a deduced amino acid sequence with no significant homology to any lectin reported to date. this lectin also is an enzyme that catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside di- and triphosphates; the enzyme activity is increased in the presence of carbohydrate ligands. this lectin-nucleotide phosphohydrolase (lnp) has a substrate ...	1999	10318974
molecular characterization of a brucella species large dna fragment deleted in brucella abortus strains: evidence for a locus involved in the synthesis of a polysaccharide.	a brucella melitensis 16m dna fragment of 17,119 bp, which contains a large region deleted in b. abortus strains and dna flanking one side of the deletion, has been characterized. in addition to the previously identified omp31 gene, 14 hypothetical genes have been identified in the b. melitensis fragment, most of them showing homology to genes involved in the synthesis of a polysaccharide. considering that 10 of the 15 genes are missing in b. abortus and that all the polysaccharides described in ...	1999	10338472
heme transfer to the heme chaperone ccme during cytochrome c maturation requires the ccmc protein, which may function independently of the abc-transporter ccmab.	cytochrome c maturation in escherichia coli requires the ccm operon, which encodes eight membrane proteins (ccmabcdefgh). ccme is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of ccmf, ccmg, and ccmh. in this work we addressed the functions of the ccmabcd gene products with respect to holo-ccme formation and the subsequent ligation of heme to apocytochrome c. in the absence of the ccmabcd genes, heme is not bound to ccme. we report ...	1999	10339610
earthworm egg capsules as vectors for the environmental introduction of biodegradative bacteria.	earthworm egg capsules (cocoons) may acquire bacteria from the environment in which they are produced. we found that ralstonia eutropha (pjp4) can be recovered from eisenia fetida cocoons formed in soil inoculated with this bacterium. plasmid pjp4 contains the genes necessary for 2,4-dichlorophenoxyacetic acid (2,4-d) and 2, 4-dichlorophenol (2,4-dcp) degradation. in this study we determined that the presence of r. eutropha (pjp4) within the developing earthworm cocoon can influence the degradat ...	1999	10347016
high-efficiency transformation of rhizobium leguminosarum by electroporation.	electrotransformation of rhizobium leguminosarum was successfully carried out with a 15.1-kb plasmid, pmp154 (cmr), containing a nodabc-lacz fusion by electroporation. the maximum transformation efficiency, 10(8) transformants/microg of dna, was achieved at a field strength of 14 kv/cm with a pulse of 7.3 ms (186 omega). the number of transformants was found to increase with increasing cell density, with no sign of saturation. in relation to dna dosage, the maximum transformation efficiency (5.8 ...	1999	10347085
cd(ii)-responsive and constitutive mutants implicate a novel domain in merr.	expression of the tn21 mercury resistance (mer) operon is controlled by a metal-sensing repressor-activator, merr. when present, merr always binds to the same position on the dna (the operator mero), repressing transcription of the structural genes mertpcad in the absence of hg(ii) and inducing their transcription in the presence of hg(ii). although it has two potential binding sites, the purified merr homodimer binds only one hg(ii) ion, employing cys82 from one monomer and cys117 and cys126 fr ...	1999	10348859
the physiological contribution of acinetobacter pcak, a transport system that acts upon protocatechuate, can be masked by the overlapping specificity of vank.	vank is the fourth member of the ubiquitous major facilitator superfamily of transport proteins to be identified that, together with pcak, benk, and muck, contributes to aromatic catabolism in acinetobacter sp. strain adp1. vank and pcak have overlapping specificity for p-hydroxybenzoate and, most clearly, for protocatechuate: inactivation of both proteins severely impairs growth with protocatechuate, and the activity of either protein alone can mask the phenotype associated with inactivation of ...	1999	10348864
pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases.	coronatine, syringomycin, syringopeptin, tabtoxin, and phaseolotoxin are the most intensively studied phytotoxins of pseudomonas syringae, and each contributes significantly to bacterial virulence in plants. coronatine functions partly as a mimic of methyl jasmonate, a hormone synthesized by plants undergoing biological stress. syringomycin and syringopeptin form pores in plasma membranes, a process that leads to electrolyte leakage. tabtoxin and phaseolotoxin are strongly antimicrobial and func ...	1999	10357851
pas domains: internal sensors of oxygen, redox potential, and light.	pas domains are newly recognized signaling domains that are widely distributed in proteins from members of the archaea and bacteria and from fungi, plants, insects, and vertebrates. they function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. specificity in sensing arises, in part, from different cofactors that may be associated with the pas fold. transduction of redox signals may be a common mechanistic theme in many different pas domains. pas pr ...	1999	10357859
usefulness of fatty acid composition for differentiation of legionella species.	numerical analysis of fatty acid methyl ester (fame) profiles of 199 isolates and 76 reference strains, belonging to all validly described species of the genus legionella that can be cultured in laboratory media, was used to differentiate between the species of this genus. with the exception of the strains that autofluoresced red, it was possible to differentiate all the other legionella species. the strains of the species l. bozemanii, l. dumoffii, l. feeleii, l. gormanii, l. maceachernii, l. m ...	1999	10364593
the mdoc gene of escherichia coli encodes a membrane protein that is required for succinylation of osmoregulated periplasmic glucans.	osmoregulated periplasmic glucans (opgs) of escherichia coli are anionic oligosaccharides that accumulate in the periplasmic space in response to low osmolarity of the medium. their anionic character is provided by the substitution of the glucosidic backbone by phosphoglycerol originating from the membrane phospholipids and by succinyl residues from unknown origin. a phosphoglycerol-transferase-deficient mdob mutant was subjected to tn5 transposon mutagenesis, and putative mutant clones were scr ...	1999	10368134
identification of a putative p-transporter operon in the genome of a burkholderia strain living inside the arbuscular mycorrhizal fungus gigaspora margarita.	this article reports the identification of a putative p-transporter operon in the genome of a burkholderia sp. living in the cytoplasm of the arbuscular mycorrhizal fungus gigaspora margarita. its presence suggests that burkholderia sp. has the potential for p uptake from this environment. this finding raises new questions concerning the importance of intracellular bacteria for mycorrhizal symbiosis.	1999	10383982
purification and characterization of an alpha-glucosidase from rhizobium sp. (robinia pseudoacacia l.) strain usda 4280.	a novel alpha-glucosidase with an apparent subunit mass of 59 +/- 0. 5 kda was purified from protein extracts of rhizobium sp. strain usda 4280, a nodulating strain of black locust (robinia pseudoacacia l), and characterized. after purification to homogeneity (475-fold; yield, 18%) by ammonium sulfate precipitation, cation-exchange chromatography, hydrophobic chromatography, dye chromatography, and gel filtration, this enzyme had a pi of 4.75 +/- 0.05. the enzyme activity was optimal at ph 6.0 t ...	1999	10388682
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 ...	1999	10388707
a novel sinorhizobium meliloti operon encodes an alpha-glucosidase and a periplasmic-binding-protein-dependent transport system for alpha-glucosides.	the most abundant carbon source transported into legume root nodules is photosynthetically produced sucrose, yet the importance of its metabolism by rhizobia in planta is not yet known. to identify genes involved in sucrose uptake and hydrolysis, we screened a sinorhizobium meliloti genomic library and discovered a segment of s. meliloti dna which allows ralstonia eutropha to grow on the alpha-glucosides sucrose, maltose, and trehalose. tn5 mutagenesis localized the required genes to a 6.8-kb re ...	1999	10400573
structural and functional analyses of photosynthetic regulatory genes rega and regb from rhodovulum sulfidophilum, roseobacter denitrificans, and rhodobacter capsulatus.	genes coding for putative rega, regb, and senc homologues were identified and characterized in the purple nonsulfur photosynthetic bacteria rhodovulum sulfidophilum and roseobacter denitrificans, species that demonstrate weak or no oxygen repression of photosystem synthesis. this additional sequence information was then used to perform a comparative analysis with previously sequenced rega, regb, and senc homologues obtained from rhodobacter capsulatus and rhodobacter sphaeroides. these are photo ...	1999	10400577
the unique chaperone operon of thermotoga maritima: cloning and initial characterization of a functional hsp70 and small heat shock protein.	the hyperthermophilic eubacterium thermotoga maritima possesses an operon encoding an hsp70 molecular chaperone protein and a protein with meaningful homology to the small heat shock protein family of chaperones. this represents the first demonstrated co-operon organization for these two important classes of molecular chaperones. we have cloned and initially characterized these proteins as functional chaperones in vitro: the hsp70 is capable of atp hydrolysis and substrate binding, and the small ...	1999	10400580
the genes ruba and rubb for alkane degradation in acinetobacter sp. strain adp1 are in an operon with estb, encoding an esterase, and oxyr.	alkanes are oxidized in acinetobacter sp. strain adp1 by a three-component alkane monooxygenase, composed of alkane hydroxylase, rubredoxin, and rubredoxin reductase. ruba and rubb encode rubredoxin and a nad(p)h-dependent rubredoxin reductase. we demonstrate here that single base pair substitutions in ruba or rubb lead to defects in alkane degradation, showing that both genes are essential for alkane utilization. differences in the degradation capacity for hexadecane and dodecane in these mutan ...	1999	10400587
regulated expression of a highly conserved regulatory gene cluster is necessary for controlling photosynthesis gene expression in response to anaerobiosis in rhodobacter capsulatus.	we utilized primer extension analysis to demonstrate that the divergently transcribed regb and senc-rega-hvra transcripts contain stable 5' ends 43 nucleotides apart within the regb-senc intergenic region. dna sequence analysis indicates that this region contains two divergent promoters with overlapping sigma70 type -35 and -10 promoter recognition sequences. in vivo analysis of expression patterns of regb::lacz and senc-rega-hvra::lacz reporter gene fusions demonstrates that the regb and senc-r ...	1999	10400592
phosphorylation, dephosphorylation and dna-binding of the bradyrhizobium japonicum regsr two-component regulatory proteins.	under low oxygen conditions, induction of many genes required for nitrogen fixation in bradyrhizobium japonicum depends on the redox-responsive transcriptional activator nifa which is encoded in the fixr-nifa operon. basal expression of this operon depends on the response regulator regr and a dna element located around position -68 in the fixr-nifa promoter region. to investigate the functional properties of regr and the interaction with its putative cognate kinase, regs, we overproduced and aff ...	1999	10406954
characterization of an atypical superoxide dismutase from sinorhizobium meliloti.	sinorhizobium meliloti rm5000 is an aerobic bacterium that can live free in the soil or in symbiosis with the roots of leguminous plants. a single detectable superoxide dismutase (sod) was found in free-living growth conditions. the corresponding gene was isolated from a genomic library by using a sod fragment amplified by pcr from degenerate primers as a probe. the soda gene was located in the chromosome. it is transcribed monocistronically and encodes a 200-amino-acid protein with a theoretica ...	1999	10419947
ni(2+) transport and accumulation in rhodospirillum rubrum.	the cooctj gene products are coexpressed with co-dehydrogenase (codh) and facilitate in vivo nickel insertion into codh. a ni(2+) transport assay was used to monitor uptake and accumulation of (63)ni(2+) into r. rubrum and to observe the effect of mutations in the cooc, coot, and cooj genes on (63)ni(2+) transport and accumulation. cells grown either in the presence or absence of co transported ni(2+) with a k(m) of 19 +/- 4 microm and a v(max) of 310 +/- 22 pmol of ni/min/mg of total protein. i ...	1999	10419953
cloning, sequencing, and characterization of the cgmb gene of sinorhizobium meliloti involved in cyclic beta-glucan biosynthesis.	periplasmic cyclic beta-glucans of rhizobium species provide important functions during plant infection and hypo-osmotic adaptation. in sinorhizobium meliloti (also known as rhizobium meliloti), these molecules are highly modified with phosphoglycerol and succinyl substituents. we have previously identified an s. meliloti tn5 insertion mutant, s9, which is specifically impaired in its ability to transfer phosphoglycerol substituents to the cyclic beta-glucan backbone (m. w. breedveld, j. a. hadl ...	1999	10419956
succinate dehydrogenase (sdh) from bradyrhizobium japonicum is closely related to mitochondrial sdh.	the sdhcdab operon, encoding succinate dehydrogenase, was cloned from the soybean symbiont bradyrhizobium japonicum. sdh from b. japonicum is phylogenetically related to sdh from mitochondria. this is the first example of a mitochondrion-like sdh functionally expressed in escherichia coli.	1999	10419971
anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate.	the microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. quantitative growth experiments showed a complete mineralization of dimethylmalonate. according to phylogenetic analysis of the complete 16s rrna genes, two strains isolated from activated sewage sludge were related to the genus paracoccus within the alpha-proteobacteria ...	1999	10427013
is1631 occurrence in bradyrhizobium japonicum highly reiterated sequence-possessing strains with high copy numbers of repeated sequences rsalpha and rsbeta.	from bradyrhizobium japonicum highly reiterated sequence-possessing (hrs) strains indigenous to niigata and tokachi in japan with high copy numbers of the repeated sequences rsalpha and rsbeta (k. minamisawa, t. isawa, y. nakatsuka, and n. ichikawa, appl. environ. microbiol. 64:1845-1851, 1998), several insertion sequence (is)-like elements were isolated by using the formation of dna duplexes by denaturation and renaturation of total dna, followed by treatment with s1 nuclease. most of these seq ...	1999	10427040
a chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes.	we provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (mt) and many primitive amitochondrial (a-mt) eukaryotes was a fusion microbe composed of a clostridium-like eubacterium and a sulfolobus-like archaebacterium. the analysis is based on several observations: (i) the genome signatures (dinucleotide relative abundance values) of clostridium and sulfolobus are compatible (sufficiently similar) and each has significantly more similarity in genome signature ...	1999	10430918
a highly conserved sequence is a novel gene involved in de novo vitamin b6 biosynthesis.	the cercospora nicotianae sor1 (singlet oxygen resistance) gene was identified previously as a gene involved in resistance of this fungus to singlet-oxygen-generating phototoxins. although homologues to sor1 occur in organisms in four kingdoms and encode one of the most highly conserved proteins yet identified, the precise function of this protein has, until now, remained unknown. we show that sor1 is essential in pyridoxine (vitamin b6) synthesis in c. nicotianae and aspergillus flavus, althoug ...	1999	10430950
sequence analysis, characterization and co-specific transcription of the cox gene cluster on the megaplasmid phcg3 of oligotropha carboxidovorans.	sequence, transcriptional, mutational and physiological analyses indicate that the carbon monoxide (co) dehydrogenase of oligotropha carboxidovorans is an integral and unique part of an elaborate co oxidizing system. it is encoded by the 14.5kb gene cluster coxbcmsldefghik residing on the 128kb megaplasmid phcg3. the co dehydrogenase structural genes coxmsl are flanked by nine accessory genes arranged as the cox gene cluster. the cox genes are specifically and coordinately transcribed under chem ...	1999	10433972
iron coordination structures of oxygen sensor fixl characterized by fe k-edge extended x-ray absorption fine structure and resonance raman spectroscopy.	fixl is a heme-based o(2) sensor protein involved in a two-component system of a symbiotic bacterium. in the present study, the iron coordination structure in the heme domain of rhizobium meliloti fixlt (rmfixlt, a soluble truncated fixl) was examined using fe k-edge extended x-ray absorption fine structure (exafs) and resonance raman spectroscopic techniques. in the exafs analyses, the interatomic distances and angles of the fe-ligand bond and the iron displacement from the heme plane were obta ...	1999	10438488
identification and characterization of hupt, a gene involved in negative regulation of hydrogen oxidation in bradyrhizobium japonicum.	the bradyrhizobium japonicum hupt gene was sequenced, and its gene product was found to be homologous to ntrb-like histidine kinases. a hupt mutant expresses higher levels of hydrogenase activity than the wild-type strain under hydrogenase-inducing conditions (i.e., microaerobiosis plus hydrogen, or symbiosis), whereas in noninduced hupt cells, hupsl expression is derepressed but does not lead to hydrogenase activity. we conclude that hupt is involved in the repression of hupsl synthesis at the ...	1999	10438783
evolution and horizontal transfer of dutpase-encoding genes in viruses and their hosts.	dutpase is a ubiquitous and essential enzyme responsible for regulating cellular levels of dutp. the dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. crystallized single-copy dutpases have been shown to assemble as homotrimers. dutpase is encoded as an auxiliary gene in a number of virus genomes. the origin of viral dut genes has remained unresolved since their initial discovery. a comprehensive analysis of dutpase amino acid sequence relationships was performed t ...	1999	10438861
proteome analysis of heat shock protein expression in bradyrhizobium japonicum.	a set of 19 heat shock proteins (hsp) was observed - by subtractive two-dimensional gel electrophoresis - to be induced when bradyrhizobium japonicum, the nitrogen-fixing root-nodule symbiont of soybean, was temperature up-shifted from 28 degrees c to 43 degrees c. up-regulated protein spots were excised from multiple two-dimensional gels. the proteins were concentrated using a funnel-gel device before being blotted onto poly(vinylidene difluoride) membranes for digestion with trypsin before ms ...	1999	10447671
cold shock response of bacillus subtilis: isoleucine-dependent switch in the fatty acid branching pattern for membrane adaptation to low temperatures.	bacillus subtilis has developed sophisticated mechanisms to withstand fluctuations in temperature. membrane fatty acids are the major determinants for a sufficiently fluid membrane state to ensure the membrane's function at all temperatures. the fatty acid profile of b. subtilis is characterized by a high content of branched fatty acids irrespective of the growth medium. here, we report on the importance of isoleucine for b. subtilis to survive cold shock from 37 to 15 degrees c. cold shock expe ...	1999	10464205
identification of nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase.	immunoblot analyses performed with three monoclonal antibodies (mabs) that recognized the nitrite oxidoreductase (nor) of the genus nitrobacter were used for taxonomic investigations of nitrite oxidizers. we found that these mabs were able to detect the nitrite-oxidizing systems (nos) of the genera nitrospira, nitrococcus, and nitrospina. the mab designated hyb 153-2, which recognized the alpha subunit of the nor (alpha-nor), was specific for species belonging to the genus nitrobacter. in contra ...	1999	10473425
helicobacter pylori physiology predicted from genomic comparison of two strains.	helicobacter pylori is a gram-negative bacteria which colonizes the gastric mucosa of humans and is implicated in a wide range of gastroduodenal diseases. this paper reviews the physiology of this bacterium as predicted from the sequenced genomes of two unrelated strains and reconciles these predictions with the literature. in general, the predicted capabilities are in good agreement with reported experimental observations. h. pylori is limited in carbohydrate utilization and will use amino acid ...	1999	10477312
identification of a plasmid-borne locus in rhizobium etli kim5s involved in lipopolysaccharide o-chain biosynthesis and nodulation of phaseolus vulgaris.	screening of derivatives of rhizobium etli kim5s randomly mutagenized with mtn5ssgusa30 resulted in the identification of strain kim-g1. its rough colony appearance, flocculation in liquid culture, and ndv(-) fix(-) phenotype were indicative of a lipopolysaccharide (lps) defect. electrophoretic analysis of cell-associated polysaccharides showed that kim-g1 produces only rough lps. composition analysis of purified lps oligosaccharides from kim-g1 indicated that it produces an intact lps core tris ...	1999	10482500
positive transcriptional feedback controls hydrogenase expression in alcaligenes eutrophus h16.	the protein hoxa is the central regulator of the alcaligenes eutrophus h16 hox regulon, which encodes two hydrogenases, a nickel permease and several accessory proteins required for hydrogenase biosynthesis. expression of the regulatory gene hoxa was analyzed. screening of an 8-kb region upstream of hoxa with a promoter probe vector localized four promoter activities. one of these was found in the region immediately 5' of hoxa; the others were correlated with the nickel metabolism genes hypa1, h ...	1999	10482509
identification of a functional fur gene in bradyrhizobium japonicum.	the recent identification of the iron response regulator (irr) in bradyrhizobium japonicum raised the question of whether the global regulator fur is present in that organism. a fur gene homolog was isolated by the functional complementation of an escherichia coli fur mutant. the b. japonicum fur bound to a fur box dna element in vitro, and a fur mutant grown in iron-replete medium was derepressed for iron uptake activity. thus, b. japonicum expresses at least two regulators of iron metabolism.	1999	10482529
aberrant nodulation response of vigna umbellata to a bradyrhizobium japonicum nodz mutant and nodulation signals.	the (brady)rhizobium nodulation gene products synthesize lipo-chitin oligosaccharide (lco) signal molecules that induce nodule primordia on legume roots. in spot inoculation assays with roots of vigna umbellata, bradyrhizobium elkanii lco and chemically synthesized lco induced aberrant nodule structures, similar to the activity of these lcos on glycine soja (soybean). lcos containing a pentameric chitin backbone and a reducing-end 2-o-methyl fucosyl moiety were active on v. umbellata. in contras ...	1999	10494629
opening the iron box: transcriptional metalloregulation by the fur protein.		1999	10515908
expression of p(ii) and glutamine synthetase is regulated by p(ii), the ntrbc products, and processing of the glnba mrna in rhodospirillum rubrum.	we have studied the transcription of the glnb and glna genes in rhodospirillum rubrum with firefly luciferase as a reporter enzyme. under nh(4)(+) and n(2) conditions, glnba was cotranscribed from a weak and a strong promoter. in nitrogen-fixing cultures, activity of the latter was highly enhanced by ntrc, but transcription from both promoters occurred under both conditions. there is no promoter controlling transcription of glna alone, supporting our proposal that the glna mrna is produced by pr ...	1999	10515946
phylogenetic analyses of bradyrhizobium strains nodulating soybean (glycine max) in thailand with reference to the usda strains of bradyrhizobium.	to elucidate the phylogenetic relationships between thai soybean bradyrhizobia and usda strains of bradyrhizobium, restriction fragment length polymorphism (rflp) analysis using the nifdk gene probe and sequencing of the partial 16s rrna gene were performed. in our previous work, thai isolates of bradyrhizobium sp. (glycine max) were separated clearly from bradyrhizobium japonicum and bradyrhizobium elkanii based on the rflp analysis using the noddyabc gene probe. rflp analysis using the nifdk g ...	1999	10528395
biosynthesis of trehalose from maltooligosaccharides in rhizobia.	previously, the enzymes for trehalose synthesis that are present in escherichia coli were demonstrated in bradyrhizobium japonicum and b. elkanii. an alternative mechanism recently reported for the synthesis of trehalose from maltooligosaccharides was considered based on the fact that high concentrations of sugars in liquid culture stimulated the accumulation of trehalose. an assay for the synthesis of trehalose from maltooligosaccharides using crude, gel-filtered protein preparations was develo ...	1999	10528404
a protein residing at the subunit interface of the bacterial ribosome.	surface labeling of escherichia coli ribosomes with the use of the tritium bombardment technique has revealed a minor unidentified ribosome-bound protein (spot y) that is hidden in the 70s ribosome and becomes highly labeled on dissociation of the 70s ribosome into subunits. in the present work, the n-terminal sequence of the protein y was determined and its gene was identified as yfia, an orf located upstream the phe operon of e. coli. this 12.7-kda protein was isolated and characterized. an af ...	1999	10535924
loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of azospirillum lipoferum.	laccase, a p-diphenol oxidase typical of plants and fungi, has been found recently in a proteobacterium, azospirillum lipoferum. laccase activity was detected in both a natural isolate and an in vitro-obtained phase variant that originated from the laccase-negative wild type. in this study, the electron transport systems of the laccase-positive variant and its parental laccase-negative forms were compared. during exponential (but not stationary) growth under fully aerobic (but not under microaer ...	1999	10542175
characterization of an operon encoding two c-type cytochromes, an aa(3)-type cytochrome oxidase, and rusticyanin in thiobacillus ferrooxidans atcc 33020.	despite the importance of thiobacillus ferrooxidans in bioremediation and bioleaching, little is known about the genes encoding electron transfer proteins implicated in its energetic metabolism. this paper reports the sequences of the four cox genes encoding the subunits of an aa(3)-type cytochrome c oxidase. these genes are in a locus containing four other genes: cyc2, which encodes a high-molecular-weight cytochrome c; cyc1, which encodes a c(4)-type cytochrome (c(552)); open reading frame 1, ...	1999	10543786
relationships of bradyrhizobia from the legumes apios americana and desmodium glutinosum.	multilocus enzyme electrophoresis, partial 23s rrna sequences, and nearly full-length 16s rrna sequences all indicated high genetic similarity among root-nodule bacteria associated with apios americana, desmodium glutinosum, and amphicarpaea bracteata, three common herbaceous legumes whose native geographic ranges in eastern north america overlap extensively. a total of 19 distinct multilocus genotypes (electrophoretic types [ets]) were found among the 35 a. americana and 33 d. glutinosum isolat ...	1999	10543803
glyphosate effects on phenolic metabolism of nodulated soybean (glycine max l. merr.).	glyphosate is a herbicide that blocks the shikimic acid pathway. three bradyrhizobium japonicum strains with different sensitivities to glyphosate were used to test the effect of this herbicide on the phenolic metabolism of nodulated soybeans and on the bacteroid nitrogenase activity. glyphosate caused an inhibition in the bacteroid nitrogenase activity that was related with the sensitivity of the nodule-forming strains. both leaves and nodules accumulated huge amounts of shikimate and phenolic ...	1999	10552587
glutathione and homoglutathione synthesis in legume root nodules.	high-performance liquid chromatography (hplc) with fluorescence detection was used to study thiol metabolism in legume nodules. glutathione (gsh) was the major non-protein thiol in all indeterminate nodules examined, as well as in the determinate nodules of cowpea (vigna unguiculata), whereas homoglutathione (hgsh) predominated in soybean (glycine max), bean (phaseolus vulgaris), and mungbean (vigna radiata) nodules. all nodules had greater thiol concentrations than the leaves and roots of the s ...	1999	10557236
characterization of activity and expression of isocitrate lyase in mycobacterium avium and mycobacterium tuberculosis.	analysis by two-dimensional gel electrophoresis revealed that mycobacterium avium expresses several proteins unique to an intracellular infection. one abundant protein with an apparent molecular mass of 50 kda was isolated, and the n-terminal sequence was determined. it matches a sequence in the m. tuberculosis database (sanger) with similarity to the enzyme isocitrate lyase of both corynebacterium glutamicum and rhodococcus fascians. only marginal similarity was observed between this open readi ...	1999	10572116
negative regulation of the gene for fe-containing superoxide dismutase by an ni-responsive factor in streptomyces coelicolor.	in streptomyces coelicolor, transcription of the sodf genes, encoding fe-containing superoxide dismutases, is negatively regulated by nickel. gel mobility shift assays with sodf1 promoter fragments and cell extracts from the a3(2) strain indicate the presence of a nickel-responsive dna-binding protein, most likely a transcriptional repressor. the boundary for the ni-responsive cis-acting region was identified both in vitro and vivo. ni does not regulate the level of the putative repressor but on ...	1999	10572144
characterization of the bradyrhizobium japonicum ftsh gene and its product.	the bradyrhizobium japonicum ftsh gene was cloned by using a set of widely applicable degenerated oligonucleotides. western blot experiments indicated that the ftsh protein was produced under standard growth conditions and that it was not heat inducible. attempts to delete the ftsh gene in b. japonicum failed, suggesting a pivotal cellular function of this gene. the expression of b. japonicum ftsh in an ftsh-negative escherichia coli strain significantly enhanced the fitness of this mutant and r ...	1999	10572147
stress genes and proteins in the archaea.	the field covered in this review is new; the first sequence of a gene encoding the molecular chaperone hsp70 and the first description of a chaperonin in the archaea were reported in 1991. these findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular ...	1999	10585970
rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate.	biological n(2) fixation represents the major source of n input in agricultural soils including those in arid regions. the major n(2)-fixing systems are the symbiotic systems, which can play a significant role in improving the fertility and productivity of low-n soils. the rhizobium-legume symbioses have received most attention and have been examined extensively. the behavior of some n(2)-fixing systems under severe environmental conditions such as salt stress, drought stress, acidity, alkalinit ...	1999	10585971
differential and independent roles of a sigma(32) homolog (rpoh) and an hrca repressor in the heat shock response of agrobacterium tumefaciens.	the heat shock response in alpha proteobacteria is unique in that a combination of two regulators is involved: a positive regulator, rpoh (sigma(32) homolog), found in the alpha, beta, and gamma proteobacteria, and a negative regulator, hrca, widely distributed in eubacteria but not in the gamma proteobacteria. to assess the differential roles of the two regulators in these bacteria, we cloned the hrca-grpe operon of agrobacterium tumefaciens, analyzed its transcription, and constructed deletion ...	1999	10601208
citrate synthase mutants of sinorhizobium meliloti are ineffective and have altered cell surface polysaccharides.	the glta gene, encoding sinorhizobium meliloti 104a14 citrate synthase, was isolated by complementing an escherichia coli glta mutant. the s. meliloti glta gene was mutated by inserting a kanamycin resistance gene and then using homologous recombination to replace the wild-type glta with the glta::kan allele. the resulting strain, csdx1, was a glutamate auxotroph, and enzyme assays confirmed the absence of a requirement for glutamate. csdx1 did not grow on succinate, malate, aspartate, pyruvate, ...	1999	10601220
classifying symbiotic proteins from bradyrhizobium japonicum into functional groups by proteome analysis of altered gene expression levels.	the advent of whole genome sequences has brought with it a vast number of new potential proteins whose function is unknown. we describe an approach to sorting proteins into functional groups by comparative two-dimensional (2-d) gel mapping of cells grown under different physiological conditions. computerized image analysis selects the proteins whose expression levels change significantly for subsequent identification by mass spectrometry. the protein groupings are further subdivided by directed ...	1999	10612277
typing of listeria monocytogenes strains by repetitive element sequence-based pcr.	listeria monocytogenes strains possess short repetitive extragenic palindromic (rep) elements and enterobacterial repetitive intergenic consensus (eric) sequences. we used repetitive element sequence-based pcr (rep-pcr) to evaluate the potential of rep and eric elements for typing l. monocytogenes strains isolated from humans, animals, and foods. on the basis of rep-pcr fingerprints, l. monocytogenes strains were divided into four major clusters matching origin of isolation. rep-pcr fingerprints ...	1999	9854072
role of hrca and circe in the heat shock regulatory network of bradyrhizobium japonicum.	a large number of bacteria regulate chaperone gene expression by the circe-hrca system in which a dna element called circe serves as binding site for the repressor protein hrca under non-heat-shock conditions. we have cloned the two consecutive genes hrca and grpe of bradyrhizobium japonicum by using a complementation approach that screened for grpe function. in vivo and in vitro transcript mapping demonstrated that both genes are transcribed separately from rpoh (sigma(32))-dependent promoters. ...	2000	10613857
proline catabolism by pseudomonas putida: cloning, characterization, and expression of the put genes in the presence of root exudates.	pseudomonas putida kt2442 is a root-colonizing strain which can use proline, one of the major components in root exudates, as its sole carbon and nitrogen source. a p. putida mutant unable to grow with proline as the sole carbon and nitrogen source was isolated after random mini-tn5-km mutagenesis. the mini-tn5 insertion was located at the puta gene, which is adjacent to and divergent from the putp gene. the puta gene codes for a protein of 1,315 amino acid residues which is homologous to the pu ...	2000	10613867
hbar, a 4-hydroxybenzoate sensor and fnr-crp superfamily member, regulates anaerobic 4-hydroxybenzoate degradation by rhodopseudomonas palustris.	under anaerobic conditions, structurally diverse aromatic compounds are catabolized by bacteria to form benzoyl-coenzyme a (benzoyl-coa), the starting compound for a central reductive pathway for aromatic ring degradation. the structural genes required for the conversion of 4-hydroxybenzoate (4-hba) to benzoyl-coa by rhodopseudomonas palustris have been identified. here we describe a regulatory gene, hbar, that is part of the 4-hba degradation gene cluster. an hbar mutant that was constructed wa ...	2000	10613868
sequence analysis of the cryptic plasmid pmg101 from rhodopseudomonas palustris and construction of stable cloning vectors.	a 15-kb cryptic plasmid was obtained from a natural isolate of rhodopseudomonas palustris. the plasmid, designated pmg101, was able to replicate in r. palustris and in closely related strains of bradyrhizobium japonicum and phototrophic bradyrhizobium species. however, it was unable to replicate in the purple nonsulfur bacterium rhodobacter sphaeroides and in rhizobium species. the replication region of pmg101 was localized to a 3.0-kb sali-xhoi fragment, and this fragment was stably maintained ...	2000	10618203
ralstonia eutropha tf93 is blocked in tat-mediated protein export.	ralstonia eutropha (formerly alcaligenes eutrophus) tf93 is pleiotropically affected in the translocation of redox enzymes synthesized with an n-terminal signal peptide bearing a twin arginine (s/t-r-r-x-f-l-k) motif. immunoblot analyses showed that the catalytic subunits of the membrane-bound [nife] hydrogenase (mbh) and the molybdenum cofactor-binding periplasmic nitrate reductase (nap) are mislocalized to the cytoplasm and to the inner membrane, respectively. moreover, physiological studies s ...	2000	10633089
discovery of a nonclassical siderophore, legiobactin, produced by strains of legionella pneumophila.	the mechanisms by which legionella pneumophila, a facultative intracellular parasite and the agent of legionnaires' disease, acquires iron are largely unexplained. several earlier studies indicated that l. pneumophila does not elaborate siderophores. however, we now present evidence that supernatants from l. pneumophila cultures can contain a nonproteinaceous, high-affinity iron chelator. more specifically, when aerobically grown in a low-iron, chemically defined medium (cdm), l. pneumophila sec ...	2000	10633110
mutagenesis and functional characterization of the glnb, glna, and nifa genes from the photosynthetic bacterium rhodospirillum rubrum.	nitrogen fixation is tightly regulated in rhodospirillum rubrum at two different levels: transcriptional regulation of nif expression and posttranslational regulation of dinitrogenase reductase by reversible adp-ribosylation catalyzed by the drat-drag (dinitrogenase reductase adp-ribosyltransferase-dinitrogenase reductase-activating glycohydrolase) system. we report here the characterization of glnb, glna, and nifa mutants and studies of their relationship to the regulation of nitrogen fixation. ...	2000	10648524
high-resolution physical map of the sinorhizobium meliloti 1021 psyma megaplasmid.	to facilitate sequencing of the sinorhizobium meliloti 1021 psyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. the 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.	2000	10648551
characterization of an azospirillum brasilense tn5 mutant with enhanced n(2) fixation: the effect of orf280 on nifh expression.	disruption of an open reading frame (orf) of 840 bp (280 amino acids; orf280) in an azospirillum brasilense tn5 mutant resulted in a pleiotrophic phenotype. besides an enhanced n(2)-fixing capacity and altered expression pattern of a nifh-gusa fusion, growth on the charged polar amino acids glutamate and arginine was severely affected. orf280, similar to previously identified orfs present in bradyrhizobium japonicum (orf277), paracoccus denitrificans (orf278) and rhodobacter capsulatus (orf277), ...	2000	10650197
extracellular glycanases of rhizobium leguminosarum are activated on the cell surface by an exopolysaccharide-related component.	rhizobium leguminosarum secretes two extracellular glycanases, plya and plyb, that can degrade exopolysaccharide (eps) and carboxymethyl cellulose (cmc), which is used as a model substrate of plant cell wall cellulose polymers. when grown on agar medium, cmc degradation occurred only directly below colonies of r. leguminosarum, suggesting that the enzymes remain attached to the bacteria. unexpectedly, when a plya-plyb-secreting colony was grown in close proximity to mutants unable to produce or ...	2000	10671451
two genes encoding a putative multidrug efflux pump of the rnd/mfp family are cotranscribed with an rpoh gene in bradyrhizobium japonicum.	the rpoh3 gene of bradyrhizobium japonicum codes for one of three sigma32-type transcription factors in this organism and is flanked by rag (rpoh3-associated) genes comprising the chromosomal arrangement ragabrpoh3ragcd. the first genes in this cluster code for a classical two-component regulatory system with an unknown function (narberhaus et al., 1997. mol. microbiol. 24, 93-104). the deduced proteins of the last two genes display a high sequence similarity to heavy metal or multidrug efflux p ...	2000	10675036
three new nifa-regulated genes in the bradyrhizobium japonicum symbiotic gene region discovered by competitive dna-rna hybridization.	the so-called symbiotic region of the bradyrhizobium japonicum chromosome (c. kündig, h. hennecke, and m. göttfert, j. bacteriol. 175:613-622, 1993) was screened for the presence of genes controlled by the nitrogen fixation regulatory protein nifa. southern blots of restriction enzyme-digested cosmids that represent an ordered, overlapping library of the symbiotic region were competitively hybridized with in vitro-labeled rna from anaerobically grown wild-type cells and an excess of rna isolated ...	2000	10692350
transcriptional and mutational analysis of the uptake hydrogenase of the filamentous cyanobacterium anabaena variabilis atcc 29413.	a 10-kb dna region of the cyanobacterium anabaena variabilis atcc 29413 containing the structural genes of the uptake hydrogenase (hupsl) was cloned and sequenced. in contrast to the hupl gene of anabaena sp. strain pcc 7120, which is interrupted by a 10.5-kb dna fragment in vegetative cells, there is no programmed rearrangement within the hupl gene during the heterocyst differentiation of a. variabilis. the hupsl genes were transcribed as a 2.7-kb operon and were induced only under nitrogen-fix ...	2000	10692368
dual roles of bradyrhizobium japonicum nickelin protein in nickel storage and gtp-dependent ni mobilization.	the hydrogenase accessory protein hypb, or nickelin, has two functions in the n(2)-fixing, h(2)-oxidizing bacterium bradyrhizobium japonicum. one function of hypb involves the mobilization of nickel into hydrogenase. hypb also carries out a nickel storage/sequestering function in b. japonicum, binding nine nickel ions per monomer. here we report that the two roles (nickel mobilization and storage) of hypb can be separated in vitro and in vivo using molecular and biochemical approaches. the role ...	2000	10692376
identification of genes in the rosr regulon of rhizobium etli.	rosr is a determinant of nodulation competitiveness and cell surface characteristics of rhizobium etli and has sequence similarity to a family of transcriptional repressors. to understand how rosr affects these phenotypes, we mutagenized a rosr mutant derivative of r. etli strain ce3 with a mini-tn5 that contains a promoterless gusa gene at one end, which acts as a transcriptional reporter. using a mass-mating technique, we introduced rosr into each mutant in trans and screened for mutants that ...	2000	10692377
membrane topology of the nixa nickel transporter of helicobacter pylori: two nickel transport-specific motifs within transmembrane helices ii and iii.	nixa, the high-affinity cytoplasmic membrane nickel transport protein of helicobacter pylori, imports ni(2+) into the cell for insertion into the active site of the urease metalloenzyme, which is required for gastric colonization. nixa fractionates with the cytoplasmic membrane, and protein cross-linking studies suggest that nixa functions as a monomer. a preliminary topological model of nixa with seven transmembrane domains was previously proposed based on hydropathy, charge dispersion, and hom ...	2000	10692379
role of hsfa gene on host-specificity by bradyrhizobium japonicum in a broad range of tropical legumes.	bradyrhizobium japonicum mutant strain nad163, containing a 30-kb deletion mutant encompassing the hsfa gene, was inoculated onto a broad range of legume species to test host-specificity. most legume species formed ineffective nodules except vigna angularis var. chibopat and glycine max var. pureunkong. a hsfa insertion mutant, bjjc211, gave similar results to strain nad163, implying that many legume species require hsfa for host-specific nitrogen fixation. to determine whether other genes in th ...	2000	10696474
nickel availability and hupsl activation by heterologous regulators limit symbiotic expression of the rhizobium leguminosarum bv. viciae hydrogenase system in hup(-) rhizobia.	a limited number of rhizobium and bradyrhizobium strains possess a hydrogen uptake (hup) system that recycles the hydrogen released from the nitrogen fixation process in legume nodules. to extend this ability to rhizobia that nodulate agronomically important crops, we investigated factors that affect the expression of a cosmid-borne hup system from rhizobium leguminosarum bv. viciae upm791 in r. leguminosarum bv. viciae, rhizobium etli, mesorhizobium loti, and sinorhizobium meliloti hup(-) strai ...	2000	10698755
quantification of hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16s rrna analysis.	the bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rrna analysis. 16s ribosomal dna (rdna) libraries were created from three sludge samples taken on different dates. partial rrna gene sequences were obtained for 46 rdna clones, and nearly complete 16s rrna sequences were obtained for 18 clones. seventeen of these clones were members of the beta subdivision, and their sequences showed high homology t ...	2000	10698787
molecular basis of symbiotic promiscuity.	eukaryotes often form symbioses with microorganisms. among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. of these, symbioses between legumes and rhizobia (azorhizobium, bradyrhizobium, mesorhizobium, and rhizobium) are the most important from an agricultural perspective. nitrogen- ...	2000	10704479
sinorhizobium meliloti puta gene regulation: a new model within the family rhizobiaceae.	proline dehydrogenase (puta) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. in sinorhizobium meliloti, as in other microorganisms, the puta gene is transcriptionally activated in response to proline. in rhodobacter capsulatus, agrobacterium, and most probably in bradyrhizobium, this activation is dependent on an lrp-like protein encoded by the putr gene, located immediately upstream of puta. interestingly, sequence and genetic analysis of the region upstream of th ...	2000	10715000
reciprocal domain evolution within a transactivator in a restricted sequence space.	offhough the concept of domain merging and shuffling as a major force in protein evolution is well established, it has been difficult to demonstrate how domains coadapt. here we show evidence of coevolution of the sinorhizobium meliloti nifa (smnifa) domains. we found that, because of the lack of a conserved glycine in its dna-binding domain, this transactivator protein interacts weakly with the enhancers. this defect, however, was compensated by evolving a highly efficient activation domain tha ...	2000	10716734
the symbiotically essential cbb(3)-type oxidase of bradyrhizobium japonicum is a proton pump.	purified cbb(3)-type oxidase of bradyrhizobium japonicum was reconstituted into phospholipid vesicles. tight vesicles were obtained as shown by the disturbance of deltaph with cccp and the membrane potential with valinomycin, which led to a six-fold increase in cytochrome c oxidase activity. the vesicles were thus suitable for proton translocation experiments. in the presence of valinomycin, a pulse with reduced cytochrome c caused an acidification with a subsequent alkalinization, whereas the s ...	2000	10722835
bradyrhizobium japonicum isocitrate dehydrogenase exhibits calcium-dependent hysteresis.	bradyrhizobium japonicum nadp(+)-dependent isocitrate dehydrogenase was purified both from cultured cells and from the symbiotic form of the bacteria and was found to be identical in terms of n-terminal amino acid sequence, kinetics, and physicochemical properties. magnesium and glycerol were absolute requirements for maintaining enzyme activity. the n-terminal amino acid sequence of the enzyme was more similar to the sequences from soybean and yeast than to other bacterial sequences. there was ...	2000	10729195
cloning and sequence analysis of the mercury resistance operon of streptomyces sp. strain chr28 reveals a novel putative second regulatory gene.	a dna library of prj28, a large linear plasmid encoding mercury resistance, was constructed, and the mercury resistance genes were cloned. the 5,921-bp sequence was analyzed and showed a high degree of similarity to the streptomyces lividans 1326 mercury resistance operon. genes merr, mert, merp, and orfiv were found in a similar order and in a single transcription unit. mera and merb were found to be transcribed in the opposite direction to genes merr, mert, merp, and orfiv, as in s. lividans 1 ...	2000	10735885
identification of an operon required for ferrichrome iron utilization in vibrio cholerae.	mutagenesis of vibrio cholerae with tnphoa, followed by screening for fusions that were activated under low-iron conditions, led to the identification of seven independent fusion strains, each of which was deficient in the ability to utilize ferrichrome as a sole iron source for growth in a plate bioassay and had an insertion in genes encoding products homologous to escherichia coli fhua or fhud. expression of the gene fusions was independent of irgb but regulated by fur. we report here a map of ...	2000	10735886
characterization of the protocatechuic acid catabolic gene cluster from streptomyces sp. strain 2065.	protocatechuate 3,4-dioxygenase (ec 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the beta-ketoadipate pathway. a protocatechuate 3,4-dioxygenase was purified from streptomyces sp. strain 2065 grown in p-hydroxybenzoate, and the n-terminal sequences of the beta- and alpha-subunits were obtained. pcr amplification was used for the cloning of the corresponding genes, and dna sequencing of the flanking regions showed that t ...	2000	10742233
fur-independent regulation of iron metabolism by irr in bradyrhizobium japonicum.	bradyrhizobium japonicum expresses both fur and irr, proteins that mediate iron-dependent regulation of gene expression. control of irr mrna accumulation by iron was aberrant in a fur mutant strain, and fur repressed an irr::lacz promoter fusion in the presence of iron. furthermore, metal-dependent binding of fur to an irr gene promoter was demonstrated in a region with no significant similarity to the fur-binding consensus dna element. these data suggest that the modest control of irr transcrip ...	2000	10746770
new mechanistic insights from structural studies of the oxygen-sensing domain of bradyrhizobium japonicum fixl.	the fixl heme domain serves as the dioxygen switch in the fixl/fixj two-component system of rhizobia. recent structural studies of the bradyrhizobium japonicum fixl heme domain (bjfixlh) have suggested an allosteric mechanism that is distinct from the classical hemoglobin model. to gain further insight into the fixl sensing mechanism, structures of bjfixlh bound to dioxygen, imidazole, and nitric oxide have been determined. these structures, particularly the structure of bjfixlh bound to its phy ...	2000	10747783