Publications

targeted mutagenesis of sigma54 activator proteins in myxococcus xanthus.	myxococcus xanthus dna segments related to the highly conserved central sequence of sigma54 activator proteins have been investigated. a genetic technique designed to inactivate a gene that encodes such an activator by inserting a plasmid-borne internal fragment of the putative gene has been tested. when the internal fragment inserted by homologous recombination into the corresponding chromosomal locus, the expected duplication of the gene was observed by southern hybridization. the single restr ...	1998	9811647
a chemotaxis cluster from agrobacterium tumefaciens.	we report the dna sequence of a 9.6-kb region of the agrobacterium tumefaciens chromosome containing a putative 8-kb chemotaxis operon. the putative operon begins with orf1, whose predicted protein product shows strong sequence identity to methyl-accepting chemotaxis proteins (mcps), followed by orf2, chey1, chea, cher, cheb, chey2, orf9, orf10. all of the identified homologues show a high degree of sequence conservation with their counterparts in the che operons from sinorhizobium meliloti and ...	1998	9767126
multiple transcriptional control of the lactococcus lactis trp operon.	the lactococcus lactis trpegdcfba operon is preceded by a noncoding leader region. transcriptional studies of the trp operon revealed three transcripts with respective sizes of 8 kb (encompassing the entire operon), 290 bases, and 160 bases (corresponding to parts of the leader region). these transcripts most likely result from initiation at the unique ptrp promoter, transcription termination at either t1 (upstream of the trp operon) or t2 (downstream of the trp operon), and/or processing. three ...	1998	9620968
expression and regulation of phosphate stress inducible genes in sinorhizobium meliloti.	sinorhizobium meliloti 104a14 was mutated with transposon tn5b22, which creates lacz transcriptional fusions when inserted in the correct orientation relative to the promoter. this promoter reporter allowed us to identify six phosphate stress inducible (psi) genes in s. meliloti that are up-regulated in response to inorganic phosphate (pi) starvation. the transposon and flanking dna were cloned from each psi::tn5b22 reporter mutant and the junction dna sequenced. high identity/similarity of the ...	1998	9805396
molecular genetic analysis of phosphite and hypophosphite oxidation by pseudomonas stutzeri wm88.	the first molecular and genetic characterization of a biochemical pathway for oxidation of the reduced phosphorus (p) compounds phosphite and hypophosphite is reported. the pathway was identified in pseudomonas stutzeri wm88, which was chosen for detailed studies from a group of organisms isolated based on their ability to oxidize hypophosphite (+1 valence) and phosphite (+3 valence) to phosphate (+5 valence). the genes required for oxidation of both compounds by p. stutzeri wm88 were cloned on ...	1998	9791102
an abc transporter plays a developmental aggregation role in myxococcus xanthus.	myxococcus xanthus is a gram-negative bacterium which has a complex life cycle. autochemotaxis, a process whereby cells release a self-generated signaling molecule, may be the principal mechanism facilitating directed motility in both the vegetative swarming and developmental aggregation stages of this life cycle. the process requires the frz signal transduction system, including frzz, a protein which is composed of two domains, both showing homology to the enteric chemotaxis response regulator ...	1998	9791121
gene organization and transcription analysis of the agrobacterium tumefaciens glycogen (glg) operon: two transcripts for the single phosphoglucomutase gene.	the gene organization and transcription of the agrobacterium glg operon differ from those in other bacteria. agrobacterium tumefaciens a348 contains a 9.1-kb gene cluster harboring genes for glycogen metabolism. the nucleotide sequence and gene organization of a region containing adp-glucose pyrophosphorylase (glgc), glycogen synthetase (glga), and phosphoglucomutase (pgm) genes have been previously described (a. uttaro and r. a. ugalde, gene 150:117-122, 1994). in this work we report that the g ...	1998	9851999
metabolic roles of a rhodobacter sphaeroides member of the sigma32 family.	we report the role of a gene (rpoh) from the facultative phototroph rhodobacter sphaeroides that encodes a protein (sigma37) similar to escherichia coli sigma32 and other members of the heat shock family of eubacterial sigma factors. r. sphaeroides sigma37 controls genes that function during environmental stress, since an r. sphaeroides deltarpoh mutant is approximately 30-fold more sensitive to the toxic oxyanion tellurite than wild-type cells. however, the deltarpoh mutant lacks several phenot ...	1998	9422586
mapping of 41 chemotaxis, flagellar and motility genes to a single region of the sinorhizobium meliloti chromosome.	three previously identified gene clusters that contain chemotaxis (che), flagellar (fla) and motility (mot) genes of sinorhizobium meliloti (formerly rhizobium meliloti) were mapped to a contiguous 45-kb region of the s. meliloti ru11/001 genome by pulsed-field gel electrophoresis (pfge) in combination with southern hybridization. the entire region was cloned and sequenced. the map combines 32 che, fla (flg, flh, fli) and mot genes and nine new open reading frames that probably encode taxis-rela ...	1998	9858749
characterization of genes involved in biosynthesis of a novel antibiotic from burkholderia cepacia bc11 and their role in biological control of rhizoctonia solani.	genetic manipulation of fluorescent pseudomonads has provided major insight into their production of antifungal molecules and their role in biological control of plant disease. burkholderia cepacia also produces antifungal activities, but its biological control activity is much less well characterized, in part due to difficulties in applying genetic tools. here we report genetic and biochemical characterization of a soil isolate of b. cepacia relating to its production of an unusual antibiotic t ...	1998	9758823
the active-site cysteines of the periplasmic thioredoxin-like protein ccmg of escherichia coli are important but not essential for cytochrome c maturation in vivo.	a new member of the family of periplasmic protein thiol:disulfide oxidoreductases, ccmg (also called dsbe), was characterized with regard to its role in cytochrome c maturation in escherichia coli. the ccmg protein was shown to be membrane bound, facing the periplasm with its c-terminal, hydrophilic domain. a chromosomal, nonpolar in-frame deletion in ccmg resulted in the complete absence of all c-type cytochromes. replacement of either one or both of the two cysteine residues of the predicted a ...	1998	9537397
evidence for a regulatory link of nitrogen fixation and photosynthesis in rhodobacter capsulatus via hvra.	a rhodobacter capsulatus reporter strain, carrying a constitutively expressed nifa gene and a nifh-lacz gene fusion, was used for random transposon tn5 mutagenesis to search for genes required for the ntrc-independent ammonium repression of nifa activity. a mutation in hvra, which is known to be involved in low-light activation of the photosynthetic apparatus, released both ammonium and oxygen control of nifh expression in this reporter strain, demonstrating a regulatory link of nitrogen fixatio ...	1998	9537402
characterization of the bvgr locus of bordetella pertussis.	bordetella pertussis, the causative agent of whooping cough, produces a wide array of factors that are associated with its ability to cause disease. the expression and regulation of these virulence factors is dependent upon the bvg locus (originally designated the vir locus), which encodes two proteins: bvga, a 23-kda cytoplasmic protein, and bvgs, a 135-kda transmembrane protein. it is proposed that bvgs responds to environmental signals and interacts with bvga, a transcriptional regulator whic ...	1998	9537363
characterization of rhizobium leguminosarum exopolysaccharide glycanases that are secreted via a type i exporter and have a novel heptapeptide repeat motif.	the prsde genes encode a type i protein secretion system required for the secretion of the nodulation protein nodo and at least three other proteins from rhizobium leguminosarum bv. viciae. at least one of these proteins was predicted to be a glycanase involved in processing of bacterial exopolysaccharide (eps). two strongly homologous genes (plya and plyb) were identified as encoding secreted proteins with polysaccharide degradation activity. both plya and plyb degrade eps and carboxymethyl cel ...	1998	9537364
the rhizobium etli rpon locus: dna sequence analysis and phenotypical characterization of rpon, ptsn, and ptsa mutants.	the rpon region of rhizobium etli was isolated by using the bradyrhizobium japonicum rpon1 gene as a probe. nucleotide sequence analysis of a 5,600-bp dna fragment of this region revealed the presence of four complete open reading frames (orfs), orf258, rpon, orf191, and ptsn, coding for proteins of 258, 520, 191, and 154 amino acids, respectively. the gene product of orf258 is homologous to members of the atp-binding cassette-type permeases. orf191 and ptsn are homologous to conserved orfs foun ...	1998	9537369
xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence.	xanthan is an industrially important exopolysaccharide produced by the phytopathogenic, gram-negative bacterium xanthomonas campestris pv. campestris. it is composed of polymerized pentasaccharide repeating units which are assembled by the sequential addition of glucose-1-phosphate, glucose, mannose, glucuronic acid, and mannose on a polyprenol phosphate carrier (l. ielpi, r. o. couso, and m. a. dankert, j. bacteriol. 175:2490-2500, 1993). a cluster of 12 genes in a region designated xpsi or gum ...	1998	9537354
the sinorhizobium meliloti mucr protein, which is essential for the production of high-molecular-weight succinoglycan exopolysaccharide, binds to short dna regions upstream of exoh and exoy.	sinorhizobium meliloti (rhizobium meliloti) is able to produce two different exopolysaccharides, succinoglycan and galactoglucan. mutations in the mucr gene of s. meliloti result in the stimulation of galactoglucan synthesis, while the type of succinoglycan produced is modified. in culture supernatants of a mucr mutant, low-molecular-weight succinoglycan is present, whereas no high-molecular-weight succinoglycan could be detected. the biosynthesis of succinoglycan is directed by the products of ...	1998	9529524
exopolysaccharide ii production is regulated by salt in the halotolerant strain rhizobium meliloti efb1.	the halotolerant strain rhizobium meliloti efb1 modifies the production of extracellular polysaccharides in response to salt. efb1 colonies grown in the presence of 0.3 m nacl show a decrease in mucoidy, and in salt-supplemented liquid medium this organism produces 40% less exopolysaccharides. we isolated transposon-induced mutant that, when grown in the absence of salt, had a colony morphology (nonmucoid) similar to the colony morphology of the wild type grown in the presence of salt. calcofluo ...	1998	9501442
isrm4-1 and isrm9, two novel insertion sequences from sinorhizobium meliloti.	two novel insertion sequences, isrm4-1 and isrm9 have been identified in sinorhizobium meliloti. isrm4-1 is 936-bp in length, flanked by 17-bp putative terminal inverted repeats and a putative target duplication of 3-bp. isrm4-1 is a member of the is5 family of insertion sequences, closely related to isrm4. isrm9 is 2797-bp in length and carries 25-bp inverted repeats with target duplication of 7-bp: isrm9 belongs to the is21 family of insertion elements. on the non-psym plasmid prmegr4b from s. ...	1998	9511748
isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere.	a set of self-transmissible plasmids with incq plasmid-mobilizing capacity was isolated by triparental exogenous isolation from the wheat rhizosphere with an escherichia coli incq plasmid host and a ralstonia eutropha recipient. three plasmids of 38 to 45 kb, denoted pipo1, pipo2, and pipo3, were selected for further study. no selectable traits (antibiotic or heavy-metal resistance) were identified in these plasmids. the plasmids were characterized by replicon typing via pcr and hybridization wi ...	1998	9501428
rearrangement of actin microfilaments in plant root hairs responding to rhizobium etli nodulation signals	the response of the actin cytoskeleton to nodulation (nod) factors secreted by rhizobium etli has been studied in living root hairs of bean (phaseolus vulgaris) that were microinjected with fluorescein isothiocyanate-phalloidin. in untreated control cells or cells treated with the inactive chitin oligomer, the actin cytoskeleton was organized into long bundles that were oriented parallel to the long axis of the root hair and extended into the apical zone. upon exposure to r. etli nod factors, th ...	1998	9501120
a cell cycle-regulated adenine dna methyltransferase from caulobacter crescentus processively methylates gantc sites on hemimethylated dna.	the kinetic properties of an adenine dna methyltransferase involved in cell cycle regulation of caulobacter crescentus have been elucidated by using defined unmethylated or hemimethylated dna (dnahm) substrates. catalytic efficiency is significantly enhanced with a dnahm substrate. biphasic kinetic behavior during methyl incorporation is observed when unmethylated or dnahm substrates are used, indicating that a step after chemistry limits enzyme turnover and is most likely the release of enzyme ...	1998	9501183
use of green fluorescent protein to assess urease gene expression by uropathogenic proteus mirabilis during experimental ascending urinary tract infection.	proteus mirabilis, a cause of complicated urinary tract infection, expresses urease when exposed to urea. while it is recognized that the positive transcriptional activator urer induces gene expression, the levels of expression of the enzyme during experimental infection are not known. to investigate in vivo expression of p. mirabilis urease, the gene encoding green fluorescent protein (gfp) was used to construct reporter fusions. translational fusions of urease accessory gene ured, which is pre ...	1998	9423875
spatial and temporal deposition of adhesive extracellular polysaccharide capsule and fimbriae by hyphomonas strain mhs-3.	hyphomonas strain mhs-3, a member of a genus of primary colonizers of surfaces immersed in marine water, synthesizes two structures that mediate adhesion to solid substrata, namely, capsular exopolysaccharide and fimbriae. specific stains, gold-labelled lectins, and monoclonal antibodies, along with transmission electron microscopy of synchronized populations, revealed that both structures are polarly and temporally expressed. the timed synthesis and placement of the fimbriae and capsule correla ...	1998	16349537
fingerprinting of cyanobacteria based on pcr with primers derived from short and long tandemly repeated repetitive sequences.	the presence of repeated dna (short tandemly repeated repetitive [strr] and long tandemly repeated repetitive [ltrr]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. primers corresponding to the strr and ltrr sequences were used in the pcr, resulting in a method which generate specific fingerprints for individual isolates. the method was useful both with purified dna and with intact cyanobacterial filaments or cells as te ...	1998	16349487
lipopolysaccharide profiles from nodules as markers of bradyrhizobium strains nodulating wild legumes.	to develop the use of electrophoretic lipopolysaccharide profiles for bradyrhizobium strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. the electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. to assess the reliability of using lip ...	1998	16349529
effects of ionic and osmotic strength on the glucosyltransferase of rhizobium meliloti responsible for cyclic beta-(1,2)-glucan biosynthesis.	the cyclic beta-(1,2)-glucans of rhizobium meliloti and agrobacterium tumefaciens play an important role during hypoosmotic adaptation, and the synthesis of these compounds is osmoregulated. glucosyltransferase, the enzyme responsible for cyclic beta-(1,2)-glucan biosynthesis, is present constitutively, suggesting that osmotic regulation of the biosynthesis of these glucans occurs through modulation of enzyme activity. in this study, we examined regulation of cyclic glucan biosynthesis in vitro ...	1998	16349538
differential effects of dimethylsulfoniopropionate, dimethylsulfonioacetate, and other s-methylated compounds on the growth of sinorhizobium meliloti at low and high osmolarities.	an extract from the marine alga ulva lactuca was highly osmoprotective in salt-stressed cultures of sinorhizobium meliloti 102f34. this beneficial activity was due to algal 3-dimethylsulfoniopropionate (dmsp), which was accumulated as a dominant compatible solute and strongly reduced the accumulation of endogenous osmolytes in stressed cells. synthetic dmsp also acted as a powerful osmoprotectant and was accumulated as a nonmetabolizable cytosolic osmolyte (up to a concentration of 1,400 nmol/mg ...	1998	16349544
[cloning, sequencing and expression of sinorhizobium meliloti strain 042b gene nodd].	s. meliloti strain 042b is a rhizobium strain which can form nodules both on alfalfa and on soybean. in this study, nodd gene of 042b was cloned into pbbr1mcs-5. by functional analysis in the system of r. leguminosarum bv. viciae lpr5045 (psym-, pmp154), it was found that the nodd has responses both to luteolin and to genistein. this result showed that the 042b nodd gene is probably a specific nodulation determinant which determined its capability of nodulation on both alfalfa and soybean. the n ...	1999	12555522
[cloning of dna fragment related to salt tolerance in sinorhizobium meliloti 042b].	total dna partially digested by ecor i was prepared for s. meliloti 042b, in which 15-25 kb dna fragments were collected. vector plafr i was purified and digested by ecor i, and then the various dna fragments of 042b were ligated with plafr i by t4dna ligase. gene library of s. meliloti 042b was constructed with plafr i using e. coli s17-1 as recipient. the number of bacterial recombinants obtained was about 8,000 and 95% of them contained foreign dna fragments. using ntg, 042b was mutated on fy ...	1999	12555552
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
function and regulation of glna in the methanogenic archaeon methanococcus maripaludis.	the glna gene in the domains bacteria and archaea encodes glutamine synthetase, a universally distributed enzyme that functions in ammonia assimilation and glutamine synthesis. we investigated the regulation and function of glna in the methanogenic archaeon methanococcus maripaludis. the deduced amino acid sequence of the gene demonstrated its membership in class gsi-alpha of glutamine synthetases. the gene appeared to be expressed as a monocistronic operon. glna mrna levels and specific activit ...	1999	9864338
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
exopolysaccharide biosynthesis in lactococcus lactis nizo b40: functional analysis of the glycosyltransferase genes involved in synthesis of the polysaccharide backbone.	we used homologous and heterologous expression of the glycosyltransferase genes of the lactococcus lactis nizo b40 eps gene cluster to determine the activity and substrate specificities of the encoded enzymes and established the order of assembly of the trisaccharide backbone of the exopolysaccharide repeating unit. epsd links glucose-1-phosphate from udp-glucose to a lipid carrier, epse and epsf link glucose from udp-glucose to lipid-linked glucose, and epsg links galactose from udp-galactose t ...	1999	9864348
characterization of a facultatively psychrophilic bacterium, vibrio rumoiensis sp. nov., that exhibits high catalase activity	a novel facultatively psychrophilic bacterium, strain s-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses h2o2 as a bleaching and microbicidal agent. the catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of corynebacterium glutamicum, staphylococcus aureus, pseudomonas fluorescens, and five other species tested in this study. the strain seemed to possess only one kind of catalase, ...	1999	9872761
identification and characterization of is2404 and is2606: two distinct repeated sequences for detection of mycobacterium ulcerans by pcr.	molecular analysis of mycobacterium ulcerans has revealed two new insertion sequences (iss), is2404 and is2606. is2404 was identified by complete sequencing of a previously described repetitive dna segment from m. ulcerans. this element is 1,274 bp long, contains 12-bp inverted repeats and a single open reading frame (orf) potentially encoding a protein of 327 amino acids (aa), and apparently generates 7-bp direct repeats upon transposition. amino acid similarity was found between the putative t ...	1999	10074520
the sinorhizobium meliloti insertion sequence (is) elements isrm102f34-1/isrm7 and isrm220-13-5 belong to a new family of insertion sequence elements.	the sinorhizobium meliloti insertion sequence (is) elements isrm102f34-1 and isrm220-13-5 are 1481 and 1550 base pairs (bp) in size, respectively. isrm102f34-1 is bordered by 15 bp imperfect terminal inverted repeat sequences (two mismatches), whereas the terminal inverted repeat of isrm220-13-5 has a length of 16 bp (two mismatches). both insertion sequence elements generate a 6-bp target duplication upon transposition. the putative transposase enzymes of isrm102f34-1 and isrm220-13-5 consist o ...	1999	10079521
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
high-affinity transport of choline-o-sulfate and its use as a compatible solute in bacillus subtilis.	we report here that the naturally occurring choline ester choline-o-sulfate serves as an effective compatible solute for bacillus subtilis, and we have identified a high-affinity atp-binding cassette (abc) transport system responsible for its uptake. the osmoprotective effect of this trimethylammonium compound closely matches that of the potent and widely employed osmoprotectant glycine betaine. growth experiments with a set of b. subtilis strains carrying defined mutations in the glycine betain ...	1999	9925583
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
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
osmosensing by bacteria: signals and membrane-based sensors.	bacteria can survive dramatic osmotic shifts. osmoregulatory responses mitigate the passive adjustments in cell structure and the growth inhibition that may ensue. the levels of certain cytoplasmic solutes rise and fall in response to increases and decreases, respectively, in extracellular osmolality. certain organic compounds are favored over ions as osmoregulatory solutes, although k+ fluxes are intrinsic to the osmoregulatory response for at least some organisms. osmosensors must undergo tran ...	1999	10066837
toxicity and osmoprotective activities of analogues of glycine betaine obtained by solid phase organic synthesis towards sinorhizobium meliloti.	seven analogues of the bacterial osmoprotectant glycine betaine (gb, trimethylammonioacetate), in which the methyl groups of the me3n+ moiety are replaced by various substituents, were obtained by spos using wang resin. their biological activities (osmoprotection vs toxicity), appeared closely related to their uptake efficiency and their catabolism in the betaine-demethylating model bacterium sinorhizobium meliloti.	1999	9990455
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
active efflux and diffusion are involved in transport of pseudomonas aeruginosa cell-to-cell signals.	many gram-negative bacteria communicate by n-acyl homoserine lactone signals called autoinducers (ais). in pseudomonas aeruginosa, cell-to-cell signaling controls expression of extracellular virulence factors, the type ii secretion apparatus, a stationary-phase sigma factor (sigmas), and biofilm differentiation. the fact that a similar signal, n-(3-oxohexanoyl) homoserine lactone, freely diffuses through vibrio fischeri and escherichia coli cells has led to the assumption that all ais are freely ...	1999	9973347
characterization of insertions of is476 and two newly identified insertion sequences, is1478 and is1479, in xanthomonas campestris pv. campestris.	thirty-two plasmid insertion mutants were independently isolated from two strains of xanthomonas campestris pv. campestris in taiwan. of the 32 mutants, 14 (44%), 8 (25%), and 4 (12%) mutants resulted from separate insertions of an is3 family member, is476, and two new insertion sequences (is), is1478 and is1479. while is1478 does not have significant sequence homology with any is elements in the embl/genbank/ddbj database, is1479 demonstrated 73% sequence homology with is1051 in x. campestris p ...	1999	9973349
identification and characterization of a two-component sensor-kinase and response-regulator system (dcus-dcur) controlling gene expression in response to c4-dicarboxylates in escherichia coli.	the dcub gene of escherichia coli encodes an anaerobic c4-dicarboxylate transporter that is induced anaerobically by fnr, activated by the cyclic amp receptor protein, and repressed in the presence of nitrate by narl. in addition, dcub expression is strongly induced by c4-dicarboxylates, suggesting the presence of a novel c4-dicarboxylate-responsive regulator in e. coli. this paper describes the isolation of a tn10 mutant in which the 160-fold induction of dcub expression by c4-dicarboxylates is ...	1999	9973351
sequence and function of luxu: a two-component phosphorelay protein that regulates quorum sensing in vibrio harveyi.	vibrio harveyi regulates the expression of bioluminescence (lux) in response to cell density, a phenomenon known as quorum sensing. in v. harveyi, two independent quorum-sensing systems exist, and each produces, detects, and responds to a specific cell density-dependent autoinducer signal. the autoinducers are recognized by two-component hybrid sensor kinases called luxn and luxq, and sensory information from both systems is transduced by a phosphorelay mechanism to the response regulator protei ...	1999	9922254
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
new mobilizable vectors suitable for gene replacement in gram-negative bacteria and their use in mapping of the 3' end of the xanthomonas campestris pv. campestris gum operon.	we describe useful vectors to select double-crossover events directly in site-directed marker exchange mutagenesis in gram-negative bacteria. these vectors contain the gusa marker gene, providing colorimetric screens to identify bacteria harboring those sequences. the applicability of these vectors was shown by mapping the 3' end of the xanthomonas campestris gum operon, involved in biosynthesis of xanthan.	1999	9872790
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
rhizobium (sinorhizobium) meliloti phn genes: characterization and identification of their protein products.	in escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. the c-p (carbon-phosphorus) lyase enzyme encoded by this operon which catalyzes the cleavage of c-p bonds in phosphonates has been recalcitrant to biochemical characterization. to advance the understanding of this enzyme, we have cloned dna from rhizobium (sinorhizobium) meliloti that contains homologues of the e. coli phng, -h, -i, -j, and -k genes. we demonstrated by insertional mutag ...	1999	9882650
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
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
ligand specificity of a high-affinity binding site for lipo-chitooligosaccharidic nod factors in medicago cell suspension cultures.	rhizobial lipo-chitooligosaccharides (lcos) are signaling molecules involved in host-range recognition for the establishment of the symbiosis with leguminous plants. the major lco of rhizobium meliloti, the symbiont of medicago plants contains four or five n-acetylglucosamines, o-acetylated and n-acylated with a c16:2 fatty acid on the terminal nonreducing sugar and o-sulfated on the reducing sugar. in this paper, the ligand specificity of a high-affinity binding site (nod factor binding site 2 ...	1999	10200326
the phn genes of burkholderia sp. strain rp007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism.	cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (pah) catabolic genes by emphasizing classical nah-like (nah, ndo, pah, and dox) sequences. here we report the description of a divergent set of pah catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. this phn locus, which contains nine open reading frames (orfs), was isolated on an 11.5-kb hindiii fragment from phenanthre ...	1999	9882667
azospirillum irakense produces a novel type of pectate lyase.	the pela gene from the n2-fixing plant-associated bacterium azospirillum irakense, encoding a pectate lyase, was isolated by heterologous expression in escherichia coli. nucleotide sequence analysis of the region containing pela indicated an open reading frame of 1,296 bp, coding for a preprotein of 432 amino acids with a typical amino-terminal signal peptide of 24 amino acids. n-terminal amino acid sequencing confirmed the processing of the protein in e. coli at the signal peptidase cleavage si ...	1999	10198006
differential regulation of two divergent sinorhizobium meliloti genes for hpii-like catalases during free-living growth and protective role of both catalases during symbiosis.	two catalases, kata and katb, have been detected in sinorhizobium meliloti growing on rich medium. here we characterize a new catalase gene encoding a third catalase (katc). katc activity was detectable only at the end of the stationary phase in s. meliloti growing in minimum medium, whereas kata activity was found during the exponential phase. analysis with a katc-lacz fusion demonstrated that katc expression is mainly regulated at the transcription level. an increase of catalase activity corre ...	1999	10198032
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
a deacylase in rhizobium leguminosarum membranes that cleaves the 3-o-linked beta-hydroxymyristoyl moiety of lipid a precursors.	lipid a from the nitrogen-fixing bacterium rhizobium leguminosarum displays many structural differences compared with lipid a of escherichia coli. r. leguminosarum lipid a lacks the usual 1- and 4'-phosphate groups but is derivatized with a galacturonic acid substituent at position 4'. r. leguminosarum lipid a often contains an aminogluconic acid moiety in place of the proximal glucosamine 1-phosphate unit. striking differences also exist in the secondary acyl chains attached to e. coli versus r ...	1999	10196200
transcription of two sigma 70 homologue genes, siga and sigb, in stationary-phase mycobacterium tuberculosis.	the siga and sigb genes of mycobacterium tuberculosis encode two sigma 70-like sigma factors of rna polymerase. while transcription of the siga gene is growth rate independent, sigb transcription is increased during entry into stationary phase. the siga gene transcription is unresponsive to environmental stress but that of sigb is very responsive, more so in stationary-phase growth than in log-phase cultures. these data suggest that siga is a primary sigma factor which, like sigma70, controls th ...	1999	9882660
strength and regulation of the different promoters for chromosomal beta-lactamases of klebsiella oxytoca.	the two groups of chromosomal beta-lactamases from klebsiella oxytoca (oxy-1 and oxy-2) can be overproduced 73- to 223-fold, due to point mutations in the consensus sequences of their promoters. the different versions of promoters from blaoxy-1 and blaoxy-2 were cloned upstream of the chloramphenicol acetyltransferase (cat) gene of pkk232-8, and their relative strengths were determined in escherichia coli and in k. oxytoca. the three different mutations in the oxy beta-lactamase promoters result ...	1999	10103190
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
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
the choline-converting pathway in staphylococcus xylosus c2a: genetic and physiological characterization.	a staphylococcus xylosus c2a gene cluster, which encodes enzymes in the pathway for choline uptake and dehydrogenation (cud), to form the osmoprotectant glycine betaine, was identified. the cud locus comprises four genes, three of which encode proteins with significant similarities to those known to be involved in choline transport and conversion in other organisms. the physiological role of the gene products was confirmed by analysis of cud deletion mutants. the fourth gene possibly codes for a ...	1999	10094709
the eff-482 locus of sinorhizobium meliloti cxm1-105 that influences symbiotic effectiveness consists of three genes encoding an endoglycanase, a transcriptional regulator and an adenylate cyclase.	the mutant t482 of sinorhizobium meliloti cxm1-105, which carries a tn5 insertion on megaplasmid 1, exhibits an enhanced symbiotic efficiency phenotype. three genes, eglc, cya3 and syrb2, were identified in the eff-482 region tagged by the tn5 insertion in t482. the eglc gene encodes an endoglycanase which contributes to the depolymerization of the exo-polysaccharide succinoglycan. the n-terminal region of the predicted cya3 gene product was similar to eukaryotic-type adenylate cyclases from bre ...	1999	10485295
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
bios, a biotin-induced, stationary-phase, and possible lysr-type regulator in sinorhizobium meliloti.	sinorhizobium meliloti 1021 produces biotin required for growth, but it also responds to external biotin signals from alfalfa plants through the bios regulatory locus. mutation of bios increases biotin uptake, extends stationary phase in the presence of biotin, and impairs competitive growth in the presence of biotin. new data supporting the relevance of this gene to plant-microbe interactions show that a bios-gusa reporter fusion is expressed by bacteria on plant roots, by bacteria in alfalfa r ...	1999	10494632
the sinorhizobium meliloti insertion sequence (is) element isrm14 is related to a previously unrecognized is element located adjacent to the escherichia coli locus of enterocyte effacement (lee) pathogenicity island.	isrm14 is 2695 basepairs (bp) in size and bordered by 22 bp imperfect inverted repeats (irs). a 9-bp target sequence is duplicated upon isrm14 transposition. the dna strand that putatively encodes the transposase enzyme carries three open reading frames (orfs) designated orfs1 to 3, which specify putative proteins of 15. 9 kda, 13.1 kda, and 61.1 kda, respectively. according to its structural characteristics, isrm14 belongs to the recently proposed is66 family of is elements. the orfs1 to 3 enco ...	1999	10489437
nitrite and nitrous oxide reductase regulation by nitrogen oxides in rhodobacter sphaeroides f. sp. denitrificans il106.	we have cloned the nap locus encoding the periplasmic nitrate reductase in rhodobacter sphaeroides f. sp. denitrificans il106. a mutant with this enzyme deleted is unable to grow under denitrifying conditions. biochemical analysis of this mutant shows that in contrast to the wild-type strain, the level of synthesis of the nitrite and n(2)o reductases is not increased by the addition of nitrate. growth under denitrifying conditions and induction of n oxide reductase synthesis are both restored by ...	1999	10498715
cyclic organization of the carbohydrate metabolism in sinorhizobium meliloti.	the pathways of polysaccharide biosynthesis were investigated in cells of sinorhizobium meliloti (strain su47) using a stable isotope approach. the isotopic labeling of the periplasmic beta-1,2-glucans synthesized from glucose labeled at various positions evidenced the involvement of catabolic pathways, namely the pentose-phosphate and entner-doudoroff pathways, into the early steps of polysaccharide synthesis. the exopolysaccharides produced at the same time had a labeling pattern similar to th ...	1999	10491206
flbt couples flagellum assembly to gene expression in caulobacter crescentus.	the biogenesis of the polar flagellum of caulobacter crescentus is regulated by the cell cycle as well as by a trans-acting regulatory hierarchy that functions to couple flagellum assembly to gene expression. the assembly of early flagellar structures (ms ring, switch, and flagellum-specific secretory system) is required for the transcription of class iii genes, which encode the remainder of the basal body and the external hook structure. similarly, the assembly of class iii gene-encoded structu ...	1999	10498731
regulation of divergent transcription from the uvra-ssb promoters in sinorhizobium meliloti.	the sinorhizobium meliloti uvra gene was isolated by complementation of a rhodobacter sphaeroides uvra- mutant. dna sequencing of the region upstream of the s. meliloti uvra gene reveals the presence of the ssb gene in the opposite transcriptional orientation. pcr-mediated mutagenesis demonstrated that expression of these two genes is inducible by dna damage, and depends, in both cases, on the direct repeat gttcn7gttc (cited according to the direction of uvra transcription). comparison of the se ...	1999	10503543
unraveling the function of glycosyltransferases in streptococcus thermophilus sfi6.	streptococcus thermophilus sfi6 produces a texturizing exopolysaccharide (eps) consisting of a -->3)[alpha-d-galp-(1-->6)]-beta-d-glcp-(1-->3)-alpha-d-galpnac-(1--> 3)-beta-d-galp-(1--> repeating unit. we previously identified and analyzed a 14.5-kb gene cluster from s. thermophilus sfi6 consisting of 13 genes responsible for its eps production. within this gene cluster, we found a central region of genes (epse, epsf, epsg, and epsi) that showed similarity to glycosyltransferases. in this study, ...	1999	10515925
influence of fermentation conditions and microfiltration processes on membrane fouling during recovery of glucuronane polysaccharides from fermentation broths.	we have investigated the recovery of exopolysaccharides produced by sinorhizobium meliloti m5n1 cs bacteria from fermentation broths using different membrane filtration processes: cross-flow filtration with a 7 mm i.d. tubular ceramic membrane of 0.5-microm pores under fixed transmembrane pressure or fixed permeate flux and dynamic filtration with a 0.2 microm nylon membrane using a 16-cm rotating disc filter. with the tubular membrane, the polysaccharide mass flux was mainly limited by polymer ...	1999	10516575
combined genetic and physical map of the complex genome of agrobacterium tumefaciens.	a combined genetic and physical map of the agrobacterium tumefaciens a348 (derivative of c58) genome was constructed to address the discrepancy between initial single-chromosome genetic maps and more recent physical mapping data supporting the presence of two nonhomologous chromosomes. the combined map confirms the two-chromosome genomic structure and the correspondence of the initial genetic maps to the circular chromosome. the linear chromosome is almost devoid of auxotrophic markers, which pr ...	1999	10464183
the cpxra signal transduction system of escherichia coli: growth-related autoactivation and control of unanticipated target operons.	in escherichia coli, the cpxra two-component signal transduction system senses and responds to aggregated and misfolded proteins in the bacterial envelope. we show that cpxr-p (the phosphorylated form of the cognate response regulator) activates cpxra expression in conjunction with rpos, suggesting an involvement of the cpx system in stationary-phase survival. engagement of the cpxra system in functions beyond protein management is indicated by several putative targets identified after a genomic ...	1999	10542180
fate of plasmid-bearing, luciferase marker gene tagged bacteria after feeding to the soil microarthropod onychiurus fimatus (collembola).	in order to study the potential impact of the soil microarthropod onychiurus fimatus (collembola) on the microbial community, we analysed the fate of luciferase marker gene tagged bacterial strains fed to young adult specimens in petri dish microcosm experiments. in faeces collected from o. fimatus, escherichia coli s17-1/prp4luc and sinorhizobium meliloti l33 were only detectable for 2 days after feeding whereas strain hr2/prp4luc, a close relative of stenotrophomonas maltophilia, isolated from ...	1999	10508937
alteration of enod40 expression modifies medicago truncatula root nodule development induced by sinorhizobium meliloti	molecular mechanisms involved in the control of root nodule organogenesis in the plant host are poorly understood. one of the nodulin genes associated with the earliest phases of this developmental program is enod40. we show here that transgenic medicago truncatula plants overexpressing enod40 exhibit accelerated nodulation induced by sinorhizobium meliloti. this resulted from increased initiation of primordia, which was accompanied by a proliferation response of the region close to the root tip ...	1999	10521525
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
identification of lumichrome as a sinorhizobium enhancer of alfalfa root respiration and shoot growth.	sinorhizobium meliloti bacteria produce a signal molecule that enhances root respiration in alfalfa (medicago sativa l.) and also triggers a compensatory increase in whole-plant net carbon assimilation. nuclear magnetic resonance, mass spectrometry, and ultraviolet-visible absorption identify the enhancer as lumichrome, a common breakdown product of riboflavin. treating alfalfa roots with 3 nm lumichrome increased root respiration 21% (p < 0.05) within 48 h. a closely linked increase in net carb ...	1999	10535912
transcription regulation of the nir gene cluster encoding nitrite reductase of paracoccus denitrificans involves nnr and niri, a novel type of membrane protein.	the nirix gene cluster of paracoccus denitrificans is located between the nir and nor gene clusters encoding nitrite and nitric oxide reductases respectively. the niri sequence corresponds to that of a membrane-bound protein with six transmembrane helices, a large periplasmic domain and cysteine-rich cytoplasmic domains that resemble the binding sites of [4fe-4s] clusters in many ferredoxin-like proteins. nirx is soluble and apparently located in the periplasm, as judged by the predicted signal ...	1999	10540283
on the origin of branches in escherichia coli.	some escherichia coli strains with impaired cell division form branched cells at high frequencies during certain growth conditions. here, we show that neither ftsi nor ftsz activity is required for the development of branches. buds did not form at specific positions along the cell surface during high-branching conditions. antibiotics affecting cell wall synthesis had a positive effect on branch formation in the case of ampicillin, cephalexin, and penicillin g, whereas mecillinam and d-cycloserin ...	1999	10542160
inhibition of the fixl sensor kinase by the fixt protein in sinorhizobium meliloti.	nitrogen fixation in symbiotic rhizobia is subject to multiple levels of gene regulation. in sinorhizobium meliloti, the alfalfa symbiont, the fixlj two-component regulatory system plays a major role in inducing nitrogen fixation and respiration gene expression in response to the low ambient o(2) concentration of the nodule. here we report on the mode of action of the fixt protein, a recently identified repressor of nitrogen fixation gene expression in s. meliloti. first, we provide evidence tha ...	1999	10542296
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
structural transitions in the fixj receiver domain.	two-component signal transduction pathways are sophisticated phosphorelay cascades widespread in prokaryotes and also found in fungi, molds and plants. fixl/fixj is a prototypical system responsible for the regulation of nitrogen fixation in the symbiotic bacterium sinorhizobium meliloti. in microaerobic conditions the membrane-bound kinase fixl uses atp to transphosphorylate a histidine residue, and the response regulator fixj transfers the phosphoryl group from the phosphohistidine to one of i ...	1999	10647182
methylmalonyl-coa mutase encoding gene of sinorhizobium meliloti.	a cluster of genes on megaplasmid prmesu47b, bhba-d, is required for growth on the polyhydroxyalkanoate degradation pathway intermediates 3-hydroxybutyrate and acetoacetate as sole carbon source. dna sequence analysis of the bhba gene indicated that it encoded a protein of 712 amino acids (aa) (78kda) which appeared to be a homodimeric methylmalonyl-coa mutase enzyme (ec 5.4.99.2). cell-free extract of a bhba::tn5 mutant was devoid of methylmalonyl-coa mutase activity, thus confirming the identi ...	1999	9889346
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
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
analysis of nifh gene pool complexity in soil and litter at a douglas fir forest site in the oregon cascade mountain range.	nitrogen-fixing microbial populations in a douglas fir forest on the western slope of the oregon cascade mountain range were analyzed. the complexity of the nifh gene pool (nifh is the marker gene which encodes nitrogenase reductase) was assessed by performing nested pcr with bulk dna extracted from plant litter and soil. the restriction fragment length polymorphisms (rflps) of pcr products obtained from litter were reproducibly different than the rflps of pcr products obtained from the underlyi ...	1999	9925556
activation and inactivation of pseudomonas stutzeri methylbenzene catabolism pathways mediated by a transposable element.	the arrangement of the genes involved in o-xylene, m-xylene, and p-xylene catabolism was investigated in three pseudomonas stutzeri strains: the wild-type strain ox1, which is able to grow on o-xylene but not on the meta and para isomers; the mutant m1, which grows on m-xylene and p-xylene but is unable to utilize the ortho isomer; and the revertant r1, which can utilize all the three isomers of xylene. a 3-kb insertion sequence (is) termed isps1, which inactivates the m-xylene and p-xylene cata ...	1999	10223973
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
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
mycoplasma pneumoniae protein p30 is required for cytadherence and associated with proper cell development.	the attachment organelle of mycoplasma pneumoniae is a polar, tapered cell extension containing an intracytoplasmic, electron-dense core. this terminal structure is the leading end in gliding motility, and its duplication is thought to precede cell division, raising the possibility that mutations affecting cytadherence also confer a defect in motility or cell development. mycoplasma surface protein p30 is associated with the attachment organelle, and p30 mutants ii-3 and ii-7 do not cytadhere. i ...	1999	9973332
identification of genetic determinants for the hemolytic activity of streptococcus agalactiae by iss1 transposition.	streptococcus agalactiae is a poorly transformable bacterium and studies of molecular mechanisms are difficult due to the limitations of genetic tools. employing the novel pgh9:iss1 transposition vector we generated plasmid-based mutant libraries of s. agalactiae strains o90r and ac475 by random chromosomal integration. a screen for mutants with a nonhemolytic phenotype on sheep blood agar led to the identification of a genetic locus harboring several genes that are essential for the hemolytic f ...	1999	10322024