Publications

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
the specific features of methionine biosynthesis and metabolism in plants.	plants, unlike other higher eukaryotes, possess all the necessary enzymatic equipment for de novo synthesis of methionine, an amino acid that supports additional roles than simply serving as a building block for protein synthesis. this is because methionine is the immediate precursor of s-adenosylmethionine (adomet), which plays numerous roles of being the major methyl-group donor in transmethylation reactions and an intermediate in the biosynthesis of polyamines and of the phytohormone ethylene ...	1998	9636232
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
identification and sequencing of a cytochrome p450 gene cluster from bradyrhizobium japonicum.	sequencing of a region from bradyrhizobium japonicum previously shown to encode for cytochromes p450 revealed a cluster of three complete p450 genes (cyp112, cyp114, and cyp117) plus a partial p450 gene fragment (cyp115p). present also are five additional open reading frames. the close positioning of the genes suggests that they comprise an operon. although the biochemical function of the gene products is uncertain, the similarities to other genes suggests an operon involved in terpenoid synthes ...	1998	9655913
differential regulation of rhizobium etli rpon2 gene expression during symbiosis and free-living growth.	the rhizobium etli rpon1 gene, encoding the alternative sigma factor sigma54 (rpon), was recently characterized and shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth (j. michiels, t. van soom, i. d'hooghe, b. dombrecht, t. benhassine, p. de wilde, and j. vanderleyden, j. bacteriol. 180:1729-1740, 1998). we identified a second rpon gene copy in r. etli, rpon2, encoding a 54.0-kda protein which displays 59% amino acid identity with th ...	1998	9658006
expression of the fixr-nifa operon in bradyrhizobium japonicum depends on a new response regulator, regr.	many nitrogen fixation-associated genes in the soybean symbiont bradyrhizobium japonicum are regulated by the transcriptional activator nifa, whose activity is inhibited by aerobiosis. nifa is encoded in the fixr-nifa operon, which is expressed at a low level under aerobic conditions and induced approximately fivefold under low-oxygen tension. this induction depends on a -24/-12-type promoter (fixrp1) that is recognized by the sigma54 rna polymerase and activated by nifa. low-level aerobic expre ...	1998	9683482
induced levels of heat shock proteins in a dnak mutant of lactococcus lactis.	the bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes and proteases, including the dnak-grpe-dnaj and the groels chaperone complexes. in order to investigate the importance of the dnak chaperone complex for growth and heat shock response regulation in lactococcus lactis, we have constructed two dnak mutants with c-terminal deletions in dnak. the minor deletion of 65 amino acids in the dnakdelta2 mutant resulted in a slight temperature-se ...	1998	9683484
cloning, characterization, and transcriptional analysis of a gene encoding an alpha-crystallin-related, small heat shock protein from the thermophilic cyanobacterium synechococcus vulcanus.	hspa, a gene encoding a 16-kda heat-induced protein from the thermophilic cyanobacterium synechococcus vulcanus, has been cloned and sequenced. the deduced amino acid sequence of the gene product showed significant homology to sequences of the family of alpha-crystallin-related, small heat shock proteins. a monocistronic mrna of hspa increased transiently in response to heat shock. the heat shock induction occurred at a vegetative promoter but without the circe (controlling inverted repeat of ch ...	1998	9683501
genetic diversity of nifh gene sequences in paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of pcr-amplified gene fragments.	the diversity of dinitrogenase reductase gene (nifh) fragments in paenibacillus azotofixans strains was investigated by using molecular methods. the partial nifh gene sequences of eight p. azotofixans strains, as well as one strain each of the close relatives paenibacillus durum, paenibacillus polymyxa, and paenibacillus macerans, were amplified by pcr by using degenerate primers and were characterized by dna sequencing. we found that there are two nifh sequence clusters, designated clusters i a ...	1998	9687429
acetoacetyl coenzyme a reductase and polyhydroxybutyrate synthesis in rhizobium (cicer) sp. strain cc 1192	biochemical controls that regulate the biosynthesis of poly-3-hydroxybutyrate (phb) were investigated in rhizobium (cicer) sp. strain cc 1192. this species is of interest for studying phb synthesis because the polymer accumulates to a large extent in free-living cells but not in bacteroids during nitrogen-fixing symbiosis with chickpea (cicer arietinum l.) plants. evidence is presented that indicates that cc 1192 cells retain the enzymic capacity to synthesize phb when they differentiate from th ...	1998	9687441
spatial and temporal deposition of hyphomonas strain vp-6 capsules involved in biofilm formation	hyphomonas strain vp-6 is a prosthecate bacterium isolated from the guayamas vent region and is a member of a genus of primary and common colonizers of marine surfaces. it adheres to solid substrata as a first step in biofilm formation. fine-structure microscopy and the use of specific stains and lectins reveal that it synthesizes two different extracellular polymeric substances (eps). one is a temporally synthesized, polar holdfast eps, and the other is a capsular eps that is present during the ...	1998	9687449
the requirement of rpon (sigma factor sigma54) in denitrification by pseudomonas stutzeri is indirect and restricted to the reduction of nitrite and nitric oxide.	the rpon region of pseudomonas stutzeri was cloned, and an rpon null mutant was constructed. rpon was not essential for denitrification in this bacterium but affected the expression levels and enzymatic activities of cytochrome cd1 nitrite reductase and nitric oxide reductase, whereas those of respiratory nitrate reductase and nitrous oxide reductase were comparable to wild-type levels. since the transcription of the structural genes nirs and norcb, coding for nitrite reductase and the nitric ox ...	1998	9687481
a silent abc transporter isolated from streptomyces rochei f20 induces multidrug resistance.	in the search for heterologous activators for actinorhodin production in streptomyces lividans, 3.4 kb of dna from streptomyces rochei f20 (a streptothricin producer) were characterized. subcloning experiments showed that the minimal dna fragment required for activation was 0.4 kb in size. the activation is mediated by increasing the levels of transcription of the actii-orf4 gene. sequencing of the minimal activating fragment did not reveal any clues about its mechanism; nevertheless, it was sho ...	1998	9696745
a redox-responsive pathway for aerobic regulation of photosynthesis gene expression in rhodobacter sphaeroides 2.4.1.	to further understand the proposed signal transduction pathway involving the presumed redox proteins rdxbh and cbb3 cytochrome oxidase in rhodobacter sphaeroides 2.4.1, a series of mutants lacking components of both the prr two-component activation system and the cbb3-type cytochrome oxidase or rdxbh were constructed. we report that under highly aerobic conditions, aberrant photosynthesis gene expression and spectral complex formation typical of cbb3- or rdxbh-deficient mutants were no longer ob ...	1998	9696749
the bacterial irr protein is required for coordination of heme biosynthesis with iron availability.	heme is a ubiquitous macromolecule that serves as the active group of proteins involved in many cellular processes. the multienzyme pathway for heme formation culminates with the insertion of iron into a protoporphyrin ring. the cytotoxicity of porphyrins suggests the need for coordination of its biosynthesis with iron availability. we isolated a mutant strain of the bacterium bradyrhizobium japonicum that, under iron limitation, accumulated protoporphyrin and showed aberrantly high expression o ...	1998	9705301
lotus corniculatus nodulation specificity is changed by the presence of a soybean lectin gene	plant lectins have been implicated as playing an important role in mediating recognition and specificity in the rhizobium-legume nitrogen-fixing symbiosis. to test this hypothesis, we introduced the soybean lectin gene le1 either behind its own promoter or behind the cauliflower mosaic virus 35s promoter into lotus corniculatus, which is nodulated by r. loti. we found that nodulelike outgrowths developed on transgenic l. corniculatus plant roots in response to bradyrhizobium japonicum, which nod ...	1998	9707526
isolation of sinorhizobium meliloti tn5 mutants with altered cytochrome terminal oxidase expression and improved symbiotic performance.	the relationship between whole-cell redox potential, cytochrome composition in free-living culture and symbiotic activity of sinorhizobium meliloti was studied. three tn5-induced mutants with increased cellular redox potential were generated. stationary cultures of mutants tb9 and tb16 in contrast to the parental strain produced the b-type terminal oxidase that may be similar to the symbiotically essential cytochrome oxidase cbb3 of bradyrhizobium japonicum. increase in the symbiotic effectivene ...	1998	9711854
cloning of conserved genes from zymomonas mobilis and bradyrhizobium japonicum that function in the biosynthesis of hopanoid lipids.	the squalene-hopene cyclase (shc) is the only enzyme involved in the biosynthesis of hopanoid lipids that has been characterized on the genetic level. to investigate if additional genes involved in hopanoid biosynthesis are clustered with the shc gene, we cloned and analyzed the nucleotide sequences located immediately upstream of the shc genes from zymomonas mobilis and bradyrhizobium japonicum. in z. mobilis, five open reading frames (orfs, designated as hpna-e) were detected in a close arrang ...	1998	9714766
three cdg operons control cellular turnover of cyclic di-gmp in acetobacter xylinum: genetic organization and occurrence of conserved domains in isoenzymes.	cyclic di-gmp (c-di-gmp) is the specific nucleotide regulator of beta-1,4-glucan (cellulose) synthase in acetobacter xylinum. the enzymes controlling turnover of c-di-gmp are diguanylate cyclase (dgc), which catalyzes its formation, and phosphodiesterase a (pdea), which catalyzes its degradation. following biochemical purification of dgc and pdea, genes encoding isoforms of these enzymes have been isolated and found to be located on three distinct yet highly homologous operons for cyclic diguany ...	1998	9721278
the pseudomonas aeruginosa rhlg gene encodes an nadph-dependent beta-ketoacyl reductase which is specifically involved in rhamnolipid synthesis.	a pseudomonas aeruginosa gene homologous to the fabg gene, which encodes the nadph-dependent beta-ketoacyl-acyl carrier protein (acp) reductase required for fatty acid synthesis, was identified. the insertional mutation of this fabg homolog (herein called rhlg) produced no apparent effect on the growth rate and total lipid content of p. aeruginosa cells, but the production of rhamnolipids was completely abrogated. these results suggest that the synthetic pathway for the fatty acid moiety of rham ...	1998	9721281
cloning and identification of conjugative transfer origins in the rhizobium meliloti genome.	a simple approach was used to identify rhizobium meliloti dna regions with the ability to convert a nontransmissible vector into a mobilizable plasmid, i.e., to contain origins of conjugative transfer (orit, mob). reca-defective r. meliloti merodiploid populations, where each individual contained a hybrid cosmid from an r. meliloti gr4 gene library, were used as donors en masse in conjugation with another r. meliloti recipient strain, selecting transconjugants for vector-encoded antibiotic resis ...	1998	9721299
sdek is required for early fruiting body development in myxococcus xanthus.	myxococcus xanthus cells carrying the omega4408 tn5lac insertion at the sde locus show defects in fruiting body development and sporulation. our analysis of sde expression patterns showed that this locus is induced early in the developmental program (0 to 2 h) and that expression increases approximately fivefold after 12 h of development. further studies showed that expression of sde is induced as growing cells enter stationary phase, suggesting that activation of the sde locus is not limited to ...	1998	9721305
expression of glnb and a glnb-like gene (glnk) in a ribulose bisphosphate carboxylase/oxygenase-deficient mutant of rhodobacter sphaeroides.	in a ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco)-deficient mutant of rhodobacter sphaeroides, strain 16phc, nitrogenase activity was derepressed in the presence of ammonia under photoheterotrophic growth conditions. previous studies also showed that reintroduction of a functional rubisco and calvin-benson-bassham (cbb) pathway suppressed the deregulation of nitrogenase synthesis in this strain. in this study, the derepression of nitrogenase synthesis in the presence of ammonia in s ...	1998	9721307
insertion sequences.	insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ...	1998	9729608
heterologous expression of the desulfovibrio gigas [nife] hydrogenase in desulfovibrio fructosovorans mr400.	the ability of desulfovibrio fructosovorans mr400 deltahynabc to express the heterologous cloned [nife] hydrogenase of desulfovibrio gigas was investigated. the [nife] hydrogenase operon from d. gigas, hynabcd, was cloned, sequenced, and introduced into d. fructosovorans mr400. a portion of the recombinant heterologous [nife] hydrogenase was totally matured, exhibiting catalytic and spectroscopic properties identical to those of the native d. gigas protein. a chimeric operon containing hynab fro ...	1998	9733707
exopolysaccharide (eps) synthesis in bradyrhizobium japonicum: sequence, operon structure and mutational analysis of an exo gene cluster.	the nucleotide sequence of a 8330-bp dna fragment from bradyrhizobium japonicum 110spc4 was determined. sequence analysis revealed that six orfs were present and the deduced amino acid sequences were homologous to enzymes involved in exopolysaccharide (eps) biosynthesis. the genes appear to be organized into at least four different operons. one gene was found to be homologous to exob, which encodes a udp-galactose 4'-epimerase. other orfs were homologous to udp-hexose transferases and one orf sh ...	1998	9747707
sucrose is a nonaccumulated osmoprotectant in sinorhizobium meliloti.	intracellular accumulation of sucrose in response to lowered water activity seems to occur only in photosynthetic organisms. here we demonstrate, for the first time, the potent ability of this common sugar, supplied exogenously, to reduce growth inhibition of sinorhizobium meliloti cells in media of inhibitory osmolarity. independently of the nature of the growth substrates and the osmotic agent, sucrose appears particularly efficient in promoting the recovery of cytoplasmic volume after plasmol ...	1998	9748435
poly-beta-hydroxybutyrate turnover in azorhizobium caulinodans is required for growth and affects nifa expression.	azorhizobium caulinodans is able to fix nitrogen in the free-living state and in symbiosis with the tropical legume sesbania rostrata. the bacteria accumulate poly-beta-hydroxybutyrate (phb) under both conditions. the structural gene for phb synthase, phbc, was inactivated by insertion of an interposon. the mutant strains obtained were devoid of phb, impaired in their growth properties, totally devoid of nitrogenase activity ex planta (nif-), and affected in nucleotide pools and induced fix- nod ...	1998	9748438
hrca, encoding the repressor of the groel genes in streptomyces albus g, is associated with a second dnaj gene.	expression of the principal chaperones of the heat shock stimulon of streptomyces albus g are under the negative control of different repressors. the dnak operon is regulated by hspr, the last gene of the operon (dnak-grpe-dnaj-hspr). hsp18, encoding a member of the small heat shock protein family, is regulated by orfy, which is in the opposite orientation upstream of hsp18. the groes-groel1 operon and the groel2 gene are regulated differently. they present tandem copies of the circe element fou ...	1998	9748446
bradyrhizobium japonicum fixk2, a crucial distributor in the fixlj-dependent regulatory cascade for control of genes inducible by low oxygen levels.	bradyrhizobium japonicum possesses a second fixk-like gene, fixk2, in addition to the previously identified fixk1 gene. the expression of both genes depends in a hierarchical fashion on the low-oxygen-responsive two-component regulatory system fixlj, whereby fixj first activates fixk2, whose product then activates fixk1. while the target genes for control by fixk1 are unknown, there is evidence for activation of the fixnoqp, fixghis, and rpon1 genes and some heme biosynthesis and nitrate respira ...	1998	9748464
alanine, not ammonia, is excreted from n2-fixing soybean nodule bacteroids.	symbiotic nitrogen fixation, the process whereby nitrogen-fixing bacteria enter into associations with plants, provides the major source of nitrogen for the biosphere. nitrogenase, a bacterial enzyme, catalyzes the reduction of atmospheric dinitrogen to ammonium. in rhizobia-leguminous plant symbioses, the current model of nitrogen transfer from the symbiotic form of the bacteria, called a bacteroid, to the plant is that nitrogenase-generated ammonia diffuses across the bacteroid membrane and is ...	1998	9751786
c-type cytochromes and manganese oxidation in pseudomonas putida mnb1.	pseudomonas putida mnb1 is an isolate from an mn oxide-encrusted pipeline that can oxidize mn(ii) to mn oxides. we used transposon mutagenesis to construct mutants of strain mnb1 that are unable to oxidize manganese, and we characterized some of these mutants. the mutants were divided into three groups: mutants defective in the biogenesis of c-type cytochromes, mutants defective in genes that encode key enzymes of the tricarboxylic acid cycle, and mutants defective in the biosynthesis of tryptop ...	1998	9758766
the cytochrome c maturation operon is involved in manganese oxidation in pseudomonas putida gb-1.	a pseudomonas putida strain, strain gb-1, oxidizes mn2+ to mn oxide in the early stationary growth phase. it also secretes a siderophore (identified as pyoverdine) when it is subjected to iron limitation. after transposon (tn5) mutagenesis several classes of mutants with differences in mn2+ oxidation and/or secretion of the mn2+-oxidizing activity were identified. preliminary analysis of the tn5 insertion site in one of the nonoxidizing mutants suggested that a multicopper oxidase-related enzyme ...	1998	9758767
a new genetic locus in sinorhizobium meliloti is involved in stachydrine utilization	stachydrine, a betaine released by germinating alfalfa seeds, functions as an inducer of nodulation genes, a catabolite, and an osmoprotectant in sinorhizobium meliloti. two stachydrine-inducible genes were found in s. meliloti 1021 by mutation with a tn5-luxab promoter probe. both mutant strains (s10 and s11) formed effective alfalfa root nodules, but neither grew on stachydrine as the sole carbon and nitrogen source. when grown in the absence or presence of salt stress, s10 and s11 took up [14 ...	1998	9758825
molecular diversity of rhizobia occurring on native shrubby legumes in southeastern australia	the structure of rhizobial communities nodulating native shrubby legumes in open eucalypt forest of southeastern australia was investigated by a molecular approach. twenty-one genomic species were characterized by small-subunit ribosomal dna pcr-restriction fragment length polymorphism and phylogenetic analyses, among 745 rhizobial strains isolated from nodules sampled on 32 different legume host species at 12 sites. among these rhizobial genomic species, 16 belonged to the bradyrhizobium subgro ...	1998	9758831
purification and characterization of an nad-malic enzyme from bradyrhizobium japonicum a1017.	an nad-malic enzyme was purified to homogeneity from bradyrhizobium japonicum a1017, and its molecular characteristics were surveyed. the enzyme exhibited native and subunit molecular masses of 388 and 85 kda, respectively, suggesting that it exists as a homotetramer, and was activated by metabolic intermediates in glycolysis. the role of the enzyme in bacteroids' carbon metabolism is discussed.	1998	9758846
a novel multicomponent regulatory system mediates h2 sensing in alcaligenes eutrophus.	oxidation of molecular hydrogen catalyzed by [nife] hydrogenases is a widespread mechanism of energy generation among prokaryotes. biosynthesis of the h2-oxidizing enzymes is a complex process subject to positive control by h2 and negative control by organic energy sources. in this report we describe a novel signal transduction system regulating hydrogenase gene (hox) expression in the proteobacterium alcaligenes eutrophus. this multicomponent system consists of the proteins hoxb, hoxc, hoxj*, a ...	1998	9770510
overproduction of the bradyrhizobium japonicum c-type cytochrome subunits of the cbb3 oxidase in escherichia coli.	we report on a system to improve expression of mature c-type cytochromes in escherichia coli. it is based on the use of plasmid pec86 that expresses the e. coli cytochrome c maturation genes ccmabcdefgh constitutively, whereby the production of both endogenous and foreign c-type cytochromes was increased substantially. the periplasmic soluble domains of the c-type cytochrome subunits fixo and fixp of the bradyrhizobium japonicum cbb3 oxidase could be expressed in e. coli only when pec86 was prov ...	1998	9790980
a cytochrome cbb3 (cytochrome c) terminal oxidase in azospirillum brasilense sp7 supports microaerobic growth.	spectral analysis indicated the presence of a cytochrome cbb3 oxidase under microaerobic conditions in azospirillum brasilense sp7 cells. the corresponding genes (cytnoqp) were isolated by using pcr. these genes are organized in an operon, preceded by a putative anaerobox. the phenotype of an a. brasilense cytn mutant was analyzed. under aerobic conditions, the specific growth rate during exponential phase (mu(e)) of the a. brasilense cytn mutant was comparable to the wild-type specific growth r ...	1998	9791120
metal accumulation and vanadium-induced multidrug resistance by environmental isolates of escherichia hermannii and enterobacter cloacae.	contaminated soils from an oil refinery were screened for the presence of microorganisms capable of accumulating either nickel, vanadium, or both metals. three strains of bacteria that belonged to the family enterobacteriaceae were selected. two of them were escherichia hermannii strains, and outer membrane profile (omp) analysis showed that they were similar to a strain of clinical origin; the other one was an enterobacter cloacae strain that differed from clinical isolates. the selected bacter ...	1998	9797283
expression of alkane hydroxylase from acinetobacter sp. strain adp1 is induced by a broad range of n-alkanes and requires the transcriptional activator alkr.	in acinetobacter sp. strain adp1, alkane degradation depends on at least five essential genes. rubab and xcpr are constitutively transcribed. here we describe inducible transcription of alkm, which strictly depends on the presence of the transcriptional activator alkr. alkr itself is expressed at a low level, while a chromosomally located alkm::lacz fusion is inducible by middle-chain-length alkanes from heptane to undecane, which do not support growth of adp1, and by long-chain-length alkanes f ...	1998	9811637
three replicons of rhizobium sp. strain ngr234 harbor symbiotic gene sequences.	rhizobium sp. strain ngr234 contains three replicons: the symbiotic plasmid or pngr234a, a megaplasmid (pngr234b), and the chromosome. symbiotic gene sequences not present in pngr234a were analyzed by hybridization. dna sequences homologous to the genes fixljknopqghis were found on the chromosome, while sequences homologous to nodpq and exobdflk were found on pngr234b.	1998	9811668
detecting linkage disequilibrium in bacterial populations.	the distribution of the number of pairwise differences calculated from comparisons between n haploid genomes has frequently been used as a starting point for testing the hypothesis of linkage equilibrium. for this purpose the variance of the pairwise differences, vd, is used as a test statistic to evaluate the null hypothesis that all loci are in linkage equilibrium. the problem is to determine the critical value of the distribution of vd. this critical value can be estimated either by monte car ...	1998	9832514
effect of canavanine from alfalfa seeds on the population biology of bacillus cereus	bacillus cereus uw85 suppresses diseases of alfalfa seedlings, although alfalfa seed exudate inhibits the growth of uw85 in culture (j. l. milner, s. j. raffel, b. j. lethbridge, and j. handelsman, appl. microbiol. biotechnol. 43:685-691, 1995). in this study, we determined the chemical basis for and biological role of the inhibitory activity. all of the alfalfa germ plasm tested included seeds that released inhibitory material. we purified the inhibitory material from one alfalfa cultivar and i ...	1998	9835549
sinorhizobium fredii and sinorhizobium meliloti produce structurally conserved lipopolysaccharides and strain-specific k antigens.	lipopolysaccharides (lps) and capsular polysaccharides (k antigens) may influence the interaction of rhizobia with their specific hosts; therefore, we conducted a comparative analysis of sinorhizobium fredii and sinorhizobium meliloti, which are genetically related, yet symbiotically distinct, nitrogen-fixing microsymbionts of legumes. we found that both species typically produce strain-specific k antigens that consist of 3-deoxy-d-manno-2-octulosonic acid (kdo), or other 1-carboxy-2-keto-3-deox ...	1998	9835585
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...	1998	9841665
tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from heliobacillus mobilis.	a dna sequence has been obtained for a 35.6-kb genomic segment from heliobacillus mobilis that contains a major cluster of photosynthesis genes. a total of 30 orfs were identified, 20 of which encode enzymes for bacteriochlorophyll and carotenoid biosynthesis, reaction-center (rc) apoprotein, and cytochromes for cyclic electron transport. donor side electron-transfer components to the rc include a putative rc-associated cytochrome c553 and a unique four-large-subunit cytochrome bc complex consis ...	1998	9843979
the yvyd gene of bacillus subtilis is under dual control of sigmab and sigmah.	during a search by computer-aided inspection of two-dimensional (2d) protein gels for sigmab-dependent general stress proteins exhibiting atypical induction profiles, a protein initially called hst23 was identified as a product of the yvyd gene of bacillus subtilis. in addition to the typical sigmab-dependent, stress- and starvation-inducible pattern, yvyd is also induced in response to amino acid depletion. by primer extension of rna isolated from the wild-type strain and appropriate mutants ca ...	1998	9852014
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
structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction.	the fixl proteins are biological oxygen sensors that restrict the expression of specific genes to hypoxic conditions. fixl's oxygen-detecting domain is a heme binding region that controls the activity of an attached histidine kinase. the fixl switch is regulated by binding of oxygen and other strong-field ligands. in the absence of bound ligand, the heme domain permits kinase activity. in the presence of bound ligand, this domain turns off kinase activity. comparison of the structures of two for ...	1998	9860942
multiple small heat shock proteins in rhizobia.	seven genes coding for small heat shock proteins (shsps) in bradyrhizobium japonicum have been identified. they are organized in five operons that are coordinately regulated by rose, a negatively cis-acting dna element. the deduced shsps can be divided into two separate classes: class a, consisting of proteins that show similarity to escherichia coli ibpa and ibpb, and class b, whose members display significant similarity to other shsps from prokaryotes and eukaryotes. two-dimensional gel electr ...	1999	9864316
regulation of the sol locus genes for butanol and acetone formation in clostridium acetobutylicum atcc 824 by a putative transcriptional repressor.	a gene (orf1, now designated solr) previously identified upstream of the aldehyde/alcohol dehydrogenase gene aad (r. v. nair, g. n. bennett, and e. t. papoutsakis, j. bacteriol. 176:871-885, 1994) was found to encode a repressor of the sol locus (aad, ctfa, ctfb and adc) genes for butanol and acetone formation in clostridium acetobutylicum atcc 824. primer extension analysis identified a transcriptional start site 35 bp upstream of the solr start codon. amino acid comparisons of solr identified ...	1999	9864345
a second gene for type i signal peptidase in bradyrhizobium japonicum, sipf, is located near genes involved in rna processing and cell division.	the tnphoa-induced bradyrhizobium japonicum mutant 184 shows slow growth and aberrant colonization of soybean nodules. using a dna fragment adjacent to the transposon insertion site as a probe, a 3.4-kb bglii fragment of b. japonicum 110spc4 dna was identified and cloned. sequence analysis indicated that two truncated orfs and three complete orfs were encoded on this fragment. a database search revealed homologies to several other prokaryotic proteins: pdxj (an enzyme involved in vitamin b6 bios ...	1998	9870699
thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community.	we used a culture-independent approach, namely, thermal gradient gel electrophoresis (tgge) analysis of ribosomal sequences amplified directly from community dna, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (gem) able t ...	1999	9872766
symbiotic deficiencies associated with a coxwxyz mutant of bradyrhizobium japonicum	the terminal oxidase complexes encoded by coxmnop and coxwxyz were studied by analysis of mutations in each of the two oxidases. carbon monoxide difference spectra obtained from membranes of coxmnop mutant bacteroids were like those obtained for the wild type, whereas bacteroid membranes of a coxwxyz mutant were deficient in co-reactive cytochrome b. experiments involving cyanide inhibition of oxidase activity were consistent with the conclusion that the coxx mutant is deficient in a membrane-as ...	1999	9872805
involvement of ureides in nitrogen fixation inhibition in soybean	the sensitivity of n2 fixation to drought stress in soybean (glycine max merr.) has been shown to be associated with high ureide accumulation in the shoots, which has led to the hypothesis that n2 fixation during drought is decreased by a feedback mechanism. the ureide feedback hypothesis was tested directly by measuring the effect of 10 mm ureide applied by stem infusion or in the nutrient solution of hydroponically grown plants on acetylene reduction activity (ara). an almost complete inhibiti ...	1999	9880371
closely related form i ribulose bisphosphate carboxylase/oxygenase molecules that possess different co2/o2 substrate specificities.	the deduced primary sequence (cbbl and cbbs) of form i ribulose 1, 5-bisphosphate carboxylase/oxygenase (rubisco) from bradyrhizobium japonicum places this enzyme within the type ic subgroup of red-like rubisco enzymes. in addition, b. japonicum appears to organize most of the structural genes of the calvin-benson-bassham (cbb) pathway in at least one major operon. functional expression and characterization of the b. japonicum and xanthobacter flavus enzymes from this group revealed that these m ...	1999	9882445
discontinuous occurrence of the hsp70 (dnak) gene among archaea and sequence features of hsp70 suggest a novel outlook on phylogenies inferred from this protein.	occurrence of the hsp70 (dnak) gene was investigated in various members of the domain archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria aquifex pyrophilus and thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16s rrna sequences. the gene was not detected in 8 of 10 archaea examined but was found in a. pyrophilus and t. maritima, from which it was cloned and sequenced. comparative analyses of the hsp70 amino aci ...	1999	9882656
control of herbaspirillum seropedicae nifa activity by ammonium ions and oxygen.	the activity of a truncated form of herbaspirillum seropedicae nifa in different genetic backgrounds showed that its regulatory domain is involved in nitrogen control but not in o2 sensitivity or fe dependence. the model for nitrogen control involving pii could thus apply to the proteobacteria at large. nifa may have a role in controlling adp-ribosylation of nitrogenase in azospirillum brasilense.	1999	9882688
genes involved in the formation and assembly of rhizobial cytochromes and their role in symbiotic nitrogen fixation.	rhizobia fix nitrogen in a symbiotic association with leguminous plants and this occurs in nodules. a low-oxygen environment is needed for nitrogen fixation, which paradoxically has a requirement for rapid respiration to produce atp. these conflicting demands are met by control of oxygen flux and production of leghaemoglobin (an oxygen carrier) by the plant, coupled with the expression of a high-affinity oxidase by the nodule bacteria (bacteroids). many of the bacterial genes encoding cytochrome ...	1998	9889979
purification and functional reconstitution of soybean nodulin 26. an aquaporin with water and glycerol transport properties.	infection of soybean roots by nitrogen-fixing bradyrhizobium japonicum leads to expression of plant nodule-specific genes known as nodulins. nodulin 26, a member of the major intrinsic protein/aquaporin (aqp) channel family, is a major component of the soybean symbiosome membrane (sm) that encloses the rhizobium bacteroid. to investigate the water and solute transport characteristics of nodulin 26, we purified the protein from sms and reconstituted it into carboxyfluorescein-loaded liposomes for ...	1999	9890916
characterization of the escherichia coli ccmh protein reveals new insights into the redox pathway required for cytochrome c maturation.	the ccmh protein of escherichia coli is encoded by the last gene of the ccm gene cluster required for cytochrome c maturation. a mutant in which the entire ccmh gene was deleted failed to synthesize both indigenous and foreign c-type cytochromes. however, deletion of the c-terminal hydrophilic domain homologous to cych of other gram-negative bacteria affected neither the biogenesis of indigenous c-type cytochromes nor that of the bradyrhizobium japonicum cytochrome c550. this confirmed that only ...	1999	9914305
poly-3-hydroxybutyrate degradation in rhizobium (sinorhizobium) meliloti: isolation and characterization of a gene encoding 3-hydroxybutyrate dehydrogenase.	we have cloned and sequenced the 3-hydroxybutyrate dehydrogenase-encoding gene (bdha) from rhizobium (sinorhizobium) meliloti. the gene has an open reading frame of 777 bp that encodes a polypeptide of 258 amino acid residues (molecular weight 27,177, pi 6.07). the r. meliloti bdh protein exhibits features common to members of the short-chain alcohol dehydrogenase superfamily. bdha is the first gene transcribed in an operon that also includes xdha, encoding xanthine oxidase/dehydrogenase. transc ...	1999	9922248
noll of rhizobium sp. strain ngr234 is required for o-acetyltransferase activity.	following (iso)flavonoid induction, nodulation genes of the symbiotic nitrogen-fixing bacterium rhizobium sp. strain ngr234 elaborate a large family of lipooligosaccharidic nod factors (nodngr factors). when secreted into the rhizosphere of compatible legumes, these signal molecules initiate root hair deformation and nodule development. the nonreducing glucosamine residue of nodngr factors are n acylated, n methylated, and mono- or biscarbamoylated, while position c-6 of the reducing extremity i ...	1999	9922261
characterization of is1547, a new member of the is900 family in the mycobacterium tuberculosis complex, and its association with is6110.	unlike classically defined insertion sequence (is) elements, which are delimited by their inverted terminal repeats, some is elements do not have inverted terminal repeats. among this group of atypical is elements, is116, is900, is901, and is1110 have been proposed as members of the is900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. in this study, we repor ...	1999	9922269
sporadic distribution of trna(arg)ccu introns among alpha-purple bacteria: evidence for horizontal transmission and transposition of a group i intron.	a group i intron interrupts the trna(arg)ccu gene of the alpha-purple bacterium agrobacterium tumefaciens (b. reinhold-hurek and d. a. shub, nature [london] 357:173-176, 1992). in this study, we assess the distribution of the corresponding intron among 12 additional species of alpha-purple bacteria. of 10 newly identified trna(arg)ccu genes, we found only two that contained an intron homologous to that of the agrobacterium intron. this restricted and scattered distribution of the trna(arg)ccug i ...	1999	9922276
new assay for rhizobitoxine based on inhibition of 1-aminocyclopropane-1-carboxylate synthase.	rhizobitoxine is synthesized by the legume symbiont bradyrhizobium elkanii and the plant pathogen burkholderia andropogonis. rhizobitoxine competitively inhibited 1-aminocyclopropane-1-carboxylate (acc) synthase ble-acs2 from the tomato, a key enzyme in the pathway of ethylene biosynthesis. based on this inhibition of acc synthase, we have developed a new assay for rhizobitoxine.	1999	9925628
the site of oxygen limitation in soybean nodules	in legume nodules the [o2] in the infected cells limits respiration and nitrogenase activity, becoming more severe if nodules are exposed to subambient o2 levels. to identify the site of o2 limitation, adenylate pools were measured in soybean (glycine max) nodules that were frozen in liquid n2 before being ground, lyophilized, sonicated, and separated on density gradients of nonaqueous solvents (heptane/tetrachloroethylene) to yield fractions enriched in bacteroid or plant components. in nodules ...	1999	9952434
purification of the trehalase gmtre1 from soybean nodules and cloning of its cdna. gmtre1 is expressed at a low level in multiple tissues.	trehalose (alpha-d-glucopyranosyl-1,1-alpha-d-glucopyranoside), a disaccharide widespread among microbes and lower invertebrates, is generally believed to be nonexistent in higher plants. however, the recent discovery of arabidopsis genes whose products are involved in trehalose synthesis has renewed interest in the possibility of a function of trehalose in higher plants. we previously showed that trehalase, the enzyme that degrades trehalose, is present in nodules of soybean (glycine max [l.] m ...	1999	9952444
expression of a soybean gene encoding the tetrapyrrole-synthesis enzyme glutamyl-trna reductase in symbiotic root nodules.	heme and chlorophyll accumulate to high levels in legume root nodules and in photosynthetic tissues, respectively, and they are both derived from the universal tetrapyrrole precursor delta-aminolevulinic acid (ala). the first committed step in ala and tetrapyrrole synthesis is catalyzed by glutamyl-trna reductase (gtr) in plants. a soybean (glycine max) root-nodule cdna encoding gtr was isolated by complementation of an escherichia coli gtr-defective mutant for restoration of ala prototrophy. gt ...	1999	9952455
cell cycle control of a holdfast attachment gene in caulobacter crescentus.	attachment to surfaces by the prosthecate bacterium caulobacter crescentus is mediated by an adhesive organelle, the holdfast, found at the tip of the stalk. indirect evidence suggested that the holdfast first appears at the swarmer pole of the predivisional cell. we used fluorescently labeled lectin and transmission electron microscopy to detect the holdfast in different cell types. while the holdfast was readily detectable in stalked cells and at the stalked poles of predivisional cells, we we ...	1999	9973336
molecular characterization of the nitrite-reducing system of staphylococcus carnosus.	characterization of a nitrite reductase-negative staphylococcus carnosus tn917 mutant led to the identification of the nir operon, which encodes nirbd, the dissimilatory nadh-dependent nitrite reductase; sira, the putative oxidase and chelatase, and sirb, the uroporphyrinogen iii methylase, both of which are necessary for biosynthesis of the siroheme prosthetic group; and nirr, which revealed no convincing similarity to proteins with known functions. we suggest that nirr is essential for nir pro ...	1999	10049379
the bradyrhizobium japonicum nola gene encodes three functionally distinct proteins.	examination of nola revealed that nola can be uniquely translated from three atg start codons. translation from the first atg (atg1) predicts a protein (nola1) having an n-terminal, helix-turn-helix dna-binding motif similar to the dna-binding domains of the merr-type regulatory proteins. translation from atg2 and atg3 would give the n-terminally truncated proteins nola2 and nola3, respectively, lacking the dna-binding domain. consistent with this, immunoblot analyses of bradyrhizobium japonicum ...	1999	10049387
complete sequence of a 184-kilobase catabolic plasmid from sphingomonas aromaticivorans f199.	the complete 184,457-bp sequence of the aromatic catabolic plasmid, pnl1, from sphingomonas aromaticivorans f199 has been determined. a total of 186 open reading frames (orfs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. the unusual coclustering of gene ...	1999	10049392
tn5-induced and spontaneous switching of sinorhizobium meliloti to faster-swarming behavior.	tn5 mutants of sinorhizobium meliloti rmb7201 which swarmed 1.5 to 2. 5 times faster than the parental strain in semisolid agar, moist sand, and viscous liquid were identified. these faster-swarming (fs) mutants outgrew the wild type 30- to 40-fold within 2 days in mixed swarm colonies. the fs mutants survived and grew as well as or better than the wild type under all of the circumstances tested, except in a soil matrix subjected to air drying. exopolysaccharide (eps) synthesis was reduced in ea ...	1999	10049888
glycine betaine: reserve form of choline in penicillium fellutanum in low-sulfate medium.	in spite of choline's importance in fungal metabolism, its sources in cytoplasm have not been fully established. 13c nuclear magnetic resonance analysis of mycelial extracts from day-5 penicillium fellutanum cultures showed that, as well as choline-o-sulfate, intracellular glycine betaine is another reserve form of choline, depending on the availability of sulfate in the culture medium. these observations are discussed relative to the multiple roles of choline and its precursors in p. fellutanum ...	1999	10049905
a novel 53-kda nodulin of the symbiosome membrane of soybean nodules, controlled by bradyrhizobium japonicum.	a nodule-specific 53-kda protein (gmnod53b) of the symbiosome membrane from soybean was isolated and its lysc digestion products were microsequenced. cdna clones of this novel nodulin, obtained from cdna library screening with an rt-pcr (reverse-transcriptase polymerase chain reaction)-generated hybridization probe exhibited no homology to proteins identified so far. the expression of gmnod53b coincides with the onset of nitrogen fixation. therefore, it is a late nodulin. among other changes, th ...	1999	10065559
metabolic engineering of poly(3-hydroxyalkanoates): from dna to plastic.	poly(3-hydroxyalkanoates) (phas) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. a wealth of biological diversity in pha formation exists, with at least 100 different pha constituents and at least five different dedicated pha biosynthetic pathways. this diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic eng ...	1999	10066830
isolation of ethylene-insensitive soybean mutants that are altered in pathogen susceptibility and gene-for-gene disease resistance	plants commonly respond to pathogen infection by increasing ethylene production, but it is not clear if this ethylene does more to promote disease susceptibility or disease resistance. ethylene production and/or responsiveness can be altered by genetic manipulation. the present study used mutagenesis to identify soybean (glycine max l. merr.) lines with reduced sensitivity to ethylene. two new genetic loci were identified, etr1 and etr2. mutants were compared with isogenic wild-type parents for ...	1999	10069832
regulation of soybean nodulation independent of ethylene signaling	leguminous plants regulate the number of bradyrhizobium- or rhizobium-infected sites that develop into nitrogen-fixing root nodules. ethylene has been implicated in the regulation of nodule formation in some species, but this role has remained in question for soybean (glycine max). the present study used soybean mutants with decreased responsiveness to ethylene, soybean mutants with defective regulation of nodule number, and ag+ inhibition of ethylene perception to examine the role of ethylene i ...	1999	10069833
further studies of the role of cyclic beta-glucans in symbiosis. an ndvc mutant of bradyrhizobium japonicum synthesizes cyclodecakis-(1-->3)-beta-glucosyl.	the cyclic beta-(1-->3),beta-(1-->6)-d-glucan synthesis locus of bradyrhizobium japonicum is composed of at least two genes, ndvb and ndvc. mutation in either gene affects glucan synthesis, as well as the ability of the bacterium to establish a successful symbiotic interaction with the legume host soybean (glycine max). b. japonicum strain ab-14 (ndvb::tn5) does not synthesize beta-glucans, and strain ab-1 (ndvc::tn5) synthesizes a cyclic beta-glucan lacking beta-(1-->6)-glycosidic bonds. we det ...	1999	10069844
characterization of the pyoluteorin biosynthetic gene cluster of pseudomonas fluorescens pf-5.	ten genes (plt) required for the biosynthesis of pyoluteorin, an antifungal compound composed of a bichlorinated pyrrole linked to a resorcinol moiety, were identified within a 24-kb genomic region of pseudomonas fluorescens pf-5. the deduced amino acid sequences of eight plt genes were similar to the amino acid sequences of genes with known biosynthetic functions, including type i polyketide synthases (pltb, pltc), an acyl coenzyme a (acyl-coa) dehydrogenase (plte), an acyl-coa synthetase (pltf ...	1999	10094695
genes coding for phosphotransacetylase and acetate kinase in sinorhizobium meliloti are in an operon that is inducible by phosphate stress and controlled by phob.	recent work in this laboratory has shown that the gene coding for acetate kinase (acka) in sinorhizobium meliloti is up-regulated in response to phosphate limitation. characterization of the region surrounding acka revealed that it is adjacent to pta, which codes for phosphotransacetylase, and that these two genes are part of an operon composed of at least two additional genes in the following order: an open reading frame (orfa), pta, acka, and the partial sequence of a gene with an inferred pep ...	1999	10094701
isolation and characterization of alfalfa-nodulating rhizobia present in acidic soils of central argentina and uruguay	we describe the isolation and characterization of alfalfa-nodulating rhizobia from acid soils of different locations in central argentina and uruguay. a collection of 465 isolates was assembled, and the rhizobia were characterized for acid tolerance. growth tests revealed the existence of 15 acid-tolerant (at) isolates which were able to grow at ph 5.0 and formed nodules in alfalfa with a low rate of nitrogen fixation. analysis of those isolates, including partial sequencing of the genes encodin ...	1999	10103231
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
diversity of nitrous oxide reductase (nosz) genes in continental shelf sediments.	diversity of the nitrous oxide reductase (nosz) gene was examined in sediments obtained from the atlantic ocean and pacific ocean continental shelves. approximately 1,100 bp of the nosz gene were amplified via pcr, using nosz gene-specific primers. thirty-seven unique copies of the nosz gene from these marine environments were characterized, increasing the nosz sequence database fourfold. the average dna similarity for comparisons between all 49 variants of the nosz gene was 64% +/- 10%. alignme ...	1999	10103268
molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures.	bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16s ribosomal dna (rdna) sequence analysis of dnas extracted from triplicate soil plots. pcr products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in repli ...	1999	10103273
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
proline accumulation in maize (zea mays l.) primary roots at low water potentials. ii. metabolic source of increased proline deposition in the elongation zone	the proline (pro) concentration increases greatly in the growing region of maize (zea mays l.) primary roots at low water potentials (psiw), largely as a result of an increased net rate of pro deposition. labeled glutamate (glu), ornithine (orn), or pro was supplied specifically to the root tip of intact seedlings in solution culture at high and low psiw to assess the relative importance of pro synthesis, catabolism, utilization, and transport in root-tip pro deposition. labeling with [3h]glu in ...	1999	10198094