Publications

pathways for phosphatidylcholine biosynthesis in bacteria.	phosphatidylcholine (pc) is the major membrane-forming phospholipid in eukaryotes with important structural and signalling functions. although many prokaryotes lack pc, it can be found in significant amounts in membranes of rather diverse bacteria. two pathways for pc biosynthesis are known in bacteria, the methylation pathway and the phosphatidylcholine synthase (pcs) pathway. in the methylation pathway, phosphatidylethanolamine is methylated three times to yield pc, in reactions catalysed by o ...	2003	14663079
quorum sensing in nitrogen-fixing rhizobia.	members of the rhizobia are distinguished for their ability to establish a nitrogen-fixing symbiosis with leguminous plants. while many details of this relationship remain a mystery, much effort has gone into elucidating the mechanisms governing bacterium-host recognition and the events leading to symbiosis. several signal molecules, including plant-produced flavonoids and bacterially produced nodulation factors and exopolysaccharides, are known to function in the molecular conversation between ...	2003	14665677
genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate lupinus spp. and ornithopus spp.	the genetic diversity of 45 bradyrhizobial isolates that nodulate several lupinus and ornithopus species in different geographic locations was investigated by 16s rdna pcr-rflp and sequence analysis, 16s-23s rdna intergenic spacer (igs) pcr-rflp analysis, and eric-pcr genomic fingerprinting. reference strains of bradyrhizobium japonicum, b. liaoningense and b. elkanii and some canarian isolates from endemic woody legumes in the tribe genisteae were also included. the 16s rdna-rflp analysis resol ...	2003	14666990
a motility revertant of the ndvb mutant of bradyrhizobium japonicum.	a motility revertant of a bradyrhizobium japonicum ndvb mutant was isolated and characterized. the ndvb mutants of b. japonicum have been reported to be osmotically sensitive, as well as defective in motility, periplasmic cyclic beta-(1-->3), (1-->6)-d-glucan synthesis, and symbiosis with soybean. the motility revertant was restored for osmotic tolerance but not for cyclic beta-glucan production or effective symbiosis. these results support our hypothesis that cyclic beta-glucans have an importa ...	2003	14669923
metabolic reconstruction of sulfur assimilation in the extremophile acidithiobacillus ferrooxidans based on genome analysis.	acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at ph2 and obtains energy by the oxidation of sulfur and iron. it is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. nearly complete genome sequences of a. ferrooxidan ...	2003	14675496
multiple formate dehydrogenase enzymes in the facultative methylotroph methylobacterium extorquens am1 are dispensable for growth on methanol.	formate dehydrogenase has traditionally been assumed to play an essential role in energy generation during growth on c(1) compounds. however, this assumption has not yet been experimentally tested in methylotrophic bacteria. in this study, a whole-genome analysis approach was used to identify three different formate dehydrogenase systems in the facultative methylotroph methylobacterium extorquens am1 whose expression is affected by either molybdenum or tungsten. a complete set of single, double, ...	2004	14679220
null mutation of hvra compensates for loss of an essential rela/spot-like gene in rhodobacter capsulatus.	we report that a single rela/spot-like gene exists on the rhodobacter capsulatus chromosome, and its mutational loss is lethal. this gene could be mutated only under a mutational background of a null mutation in the nucleoid protein hvra. this result suggests that there may be a direct link between hvra-regulated promoters and the ppgpp-related stringent response.	2004	14679243
identification of fast and slow growing rhizobia nodulating soybean (glycine max [l.] merr) by a multiplex pcr reaction.	two dna fragments, a 730-bp and a 900-bp fragment, one homologous to host cultivar specificity genes nolbt of sinorhizobium fredii and the other one homologous to rsalpha, an insertion-like sequence present in bradyrhizobium japonicum, were generated by polymerase chain reaction (pcr) with two pairs of primers. the amount of each fragment generated by the multiplex pcr was proportional to the amount of template dna present. the amplification of the 900-bp rsalpha fragment was more sensitive, sin ...	2003	14680692
structure of hrcqb-c, a conserved component of the bacterial type iii secretion systems.	type iii secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. in addition, type iii secretion systems are also required for biogenesis of the bacterial flagellum. the hrcq(b) protein, a component of the secretion apparatus of pseudomonas ...	2004	14694203
structure of hrcqb-c, a conserved component of the bacterial type iii secretion systems.	type iii secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. in addition, type iii secretion systems are also required for biogenesis of the bacterial flagellum. the hrcq(b) protein, a component of the secretion apparatus of pseudomonas ...	2004	14694203
digging with experimental pick and computational shovel: a new addition to the histidine kinase superfamily.		2004	14702293
the hwe histidine kinases, a new family of bacterial two-component sensor kinases with potentially diverse roles in environmental signaling.	two-component signal transduction pathways play a major role in the response of bacteria to external cues. these pathways are initiated by large collection of histidine kinases (hks) containing a sensor domain that perceives the environmental signal followed by an hk domain that triggers a histidine-aspartate phosphorelay. previous phylogenetic analyses identified 11 major families of two-component hks by comparing signature motifs within the hk domain. here we describe a new family with homolog ...	2004	14702314
an evolutionary hot spot: the pngr234b replicon of rhizobium sp. strain ngr234.	rhizobium sp. strain ngr234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. since the overall organization of the ngr234 genome is strikingly similar to that of the narrow-host-range symbiont rhizobium meliloti strain 1021 (also known as sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? study of the early symbiotic genes of both bacteria (carried by the syma plasmids) did not provide obvious answers. yet, bo ...	2004	14702322
comparative genomics of rickettsia prowazekii madrid e and breinl strains.	rickettsia prowazekii, the causative agent of epidemic typhus, has been responsible for millions of human deaths. madrid e is an attenuated strain of r. prowazekii, while breinl is a virulent strain. the genomic dna sequence of madrid e has recently been published. to study the genomic variations between madrid e (reference) and breinl (test) dnas, cohybridization experiments were performed on a dna microarray containing all 834 protein-coding genes of madrid e. of the 834 genes assessed, 24 gen ...	2004	14702324
nitrous oxide reductase (nosz) gene fragments differ between native and cultivated michigan soils.	the effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosz) fragments from denitrifying prokaryotes in native and cultivated soil was explored. thirty-six soil cores were composited from each of the two soil management conditions. nosz gene fragments were amplified from triplicate samples, and pcr products were cloned and screened by restriction fragment length polymorphism (rflp). the total nosz rflp profiles increased in similarity with soil sa ...	2004	14711656
bradyrhizobium elkanii rtxc gene is required for expression of symbiotic phenotypes in the final step of rhizobitoxine biosynthesis.	we disrupted the rtxc gene on the chromosome of bradyrhizobium elkanii usda94 by insertion of a nonpolar aph cartridge. the rtxc mutant, designated deltartxc, produced serinol and dihydrorhizobitoxine but no rhizobitoxine, both in culture and in planta. the introduction of cosmids harboring the rtxc gene into the deltartxc mutant complemented rhizobitoxine production, suggesting that rtxc is involved in the final step of rhizobitoxine biosynthesis in b. elkanii usda94. glycine max cv. lee inocul ...	2004	14711685
a functional cellulose synthase from ascidian epidermis.	among animals, urochordates (e.g., ascidians) are unique in their ability to biosynthesize cellulose. in ascidians cellulose is synthesized in the epidermis and incorporated into a protective coat know as the tunic. a putative cellulose synthase-like gene was first identified in the genome sequences of the ascidian ciona intestinalis. we describe here a cellulose synthase gene from the ascidian ciona savignyi that is expressed in the epidermis. the predicted c. savignyi cellulose synthase amino ...	2004	14722352
regulation of l-alanine dehydrogenase in rhizobium leguminosarum bv. viciae and its role in pea nodules.	alanine dehydrogenase (alda) is the principal enzyme with which pea bacteroids synthesize alanine de novo. in free-living culture, alda activity is induced by carboxylic acids (succinate, malate, and pyruvate), although the best inducer is alanine. measurement of the intracellular concentration of alanine showed that alda contributes to net alanine synthesis in laboratory cultures. divergently transcribed from alda is an asnc type regulator, aldr. mutation of aldr prevents induction of alda acti ...	2004	14729712
rhur, an extracytoplasmic function sigma factor activator, is essential for heme-dependent expression of the outer membrane heme and hemoprotein receptor of bordetella avium.	genes involved in iron (fe) acquisition often are regulated in response to the local availability of fe. in many bacteria, fe-dependent responsiveness is mediated by fur, a global fe-dependent transcriptional repressor. tighter regulatory control of fur-responsive genes is afforded by incorporating additional regulators into fur-dependent regulatory cascades. rhui, a fur-dependent extracytoplasmic function sigma factor of bordetella avium, in response to the dual stimulation of fe starvation and ...	2004	14742534
rare bacterium of new genus isolated with prolonged enrichment culture.	dynamic change in microbial flora was monitored with an oxygen electrode. the 1st phase microorganisms, which first grew well in lb medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. in a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existen ...	2004	14745160
the yersinia adhesin yada collagen-binding domain structure is a novel left-handed parallel beta-roll.	the crystal structure of the recombinant collagen-binding domain of yersinia adhesin yada from yersinia enterocolitica serotype o:3 was solved at 1.55 a resolution. the trimeric structure is composed of head and neck regions, and the collagen binding head region is a novel nine-coiled left-handed parallel beta-roll. before the beta-roll, the polypeptide loops from one monomer to the rest, and after the beta-roll the neck region does the same, making the transition from the globular head region t ...	2004	14765110
biochemical and proteomic analysis of the magnetosome membrane in magnetospirillum gryphiswaldense.	we analyzed the biochemical composition of the magnetosome membrane (mm) in magnetospirillum gryphiswaldense. isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. the binding characteristics of mm-associated proteins were studied by selective solubilization and limited proteolysis. the mm-associated proteins ...	2004	14766587
a dominant-negative fur mutation in bradyrhizobium japonicum.	in many bacteria, the ferric uptake regulator (fur) protein plays a central role in the regulation of iron uptake genes. because iron figures prominently in the agriculturally important symbiosis between soybean and its nitrogen-fixing endosymbiont bradyrhizobium japonicum, we wanted to assess the role of fur in the interaction. we identified a fur mutant by selecting for manganese resistance. manganese interacts with the fur protein and represses iron uptake genes. in the presence of high level ...	2004	14973020
transcriptional profiling of caulobacter crescentus during growth on complex and minimal media.	microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (pye) and minimal salts medium with glucose or xylose as the carbon source. nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. the differentially expressed genes included many encoding transport systems, most notably di ...	2004	14973021
teir, a luxr-type transcription factor required for testosterone degradation in comamonas testosteroni.	we have identified a new steroid-inducible gene (designated teir [testosterone-inducible regulator]) in comamonas testosteroni that is required for testosterone degradation. nucleotide sequence analysis of teir predicts a 391-amino-acid protein which shows homology between residues 327 and 380 (c-terminal domain) to the luxr helix-turn-helix dna binding domain and between residues 192 and 227 to the pas sensor domain. this domain distribution resembles that described for trar, a specific transcr ...	2004	14973025
trends between gene content and genome size in prokaryotic species with larger genomes.	although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. we have compared 115 completed prokaryotic genomes by using the clusters of orthologous groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategie ...	2004	14973198
the bacillus subtilis heat shock stimulon.	all organisms respond to a sudden increase in temperature by the so-called heat shock response. this response results in the induction of a subset of genes, designated heat shock genes coding for heat shock proteins, which allow the cell to cope with the stress regimen. research carried out during the last 10 years with eubacteria has revealed that the heat shock genes of a given species fall into different classes (regulons), where each class is regulated by a different transcriptional regulato ...	2003	14984053
use of the multipurpose transposon tn kpk2 for the mutational analysis of chromosomal regions upstream and downstream of the sipf gene in bradyrhizobium japonicum.	the dna regions upstream and downstream of the bradyrhizobium japonicum gene sipf were cloned by in vivo techniques and subsequently sequenced. in order to study the function of the predicted genes, a new transposon for in vitro mutagenesis, tn kpk2, was constructed. this mutagenesis system has a number of advantages over other transposons. tn kpk2 itself has no transposase gene, making transposition events stable. extremely short inverted repeats minimize the length of the transposable element ...	2004	14986109
phosphatidylethanolamine is not essential for growth of sinorhizobium meliloti on complex culture media.	in addition to phosphatidylglycerol (pg), cardiolipin (cl), and phosphatidylethanolamine (pe), sinorhizobium meliloti also possesses phosphatidylcholine (pc) as a major membrane lipid. the biosynthesis of pc in s. meliloti can occur via two different routes, either via the phospholipid n-methylation pathway, in which pe is methylated three times in order to obtain pc, or via the phosphatidylcholine synthase (pcs) pathway, in which choline is condensed with cdp-diacylglycerol to obtain pc directl ...	2004	14996797
visualization of the phylogenetic content of five genomes using dekapentagonal maps.	the methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. if the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. analyses of genomes representing five photosynthetic ...	2004	15003123
regulatory role of rhizobium etli cnpaf512 fnrn during symbiosis.	the rhizobium etli cnpaf512 fnrn gene was identified in the fixabcx rpon(2) region. the corresponding protein contains the hallmark residues characteristic of proteins belonging to the class ib group of fnr-related proteins. the expression of r. etli fnrn is highly induced under free-living microaerobic conditions and during symbiosis. this microaerobic and symbiotic induction of fnrn is not controlled by the sigma factor rpon and the symbiotic regulator nifa or fixlj, but it is due to positive ...	2004	15006745
soybean (glycine max. l.) and bacteroid glyoxylate cycle activities during nodular senescence.	soybean (glycine max. l.) nodular senescence results in the dismantling of the peribacteroid membrane (pbm) and in an increase of soybean isocitrate lyase (icl; ec 4.1.3.1) and malate synthase (ms; ec 4.1.3.2) mrna and protein levels. this suggests that in senescing soybean nodular cells, the specific glyoxylate cycle enzyme activities might be induced to reallocate carbon obtained from the pbm degradation. in order to evaluate as well the carbon metabolism of the nitrogen-fixing bradyrhizobium ...	2004	15022832
dna sequence duplication in rhodobacter sphaeroides 2.4.1: evidence of an ancient partnership between chromosomes i and ii.	the complex genome of rhodobacter sphaeroides 2.4.1, composed of chromosomes i (ci) and ii (cii), has been sequenced and assembled. we present data demonstrating that the r. sphaeroides genome possesses an extensive amount of exact dna sequence duplication, 111 kb or approximately 2.7% of the total chromosomal dna. the chromosomal dna sequence duplications were aligned to each other by using mummer. frequency and size distribution analyses of the exact dna duplications revealed that the interchr ...	2004	15028685
the fixabcx genes in rhodospirillum rubrum encode a putative membrane complex participating in electron transfer to nitrogenase.	in our efforts to identify the components participating in electron transport to nitrogenase in rhodospirillum rubrum, we used mini-tn5 mutagenesis followed by metronidazole selection. one of the mutants isolated, snt-1, exhibited a decreased growth rate and about 25% of the in vivo nitrogenase activity compared to the wild-type values. the in vitro nitrogenase activity was essentially wild type, indicating that the mutation affects electron transport to nitrogenase. sequencing showed that the t ...	2004	15028689
molecular characterization of nosrzdfylx genes coding for denitrifying nitrous oxide reductase of bradyrhizobium japonicum.	the nosrzdfylx gene cluster for the respiratory nitrous oxide reductase from bradyrhizobium japonicum strain usda110 has been cloned and sequenced. seven protein coding regions corresponding to nosr, nosz, the structural gene, nosd, nosf, nosy, nosl, and nosx were detected. the deduced amino acid sequence exhibited a high degree of similarity to other nitrous oxide reductases from various sources. the nosz protein included a signal peptide for protein export. mutant strains carrying either a nos ...	2004	15028871
phenotypic and genotypic analysis of rhizobia isolated from pasture legumes native of sardinia and asinara island.	thirty-five rhizobial strains were isolated from nodules of lotus edulis, l. ornithopodioides, l. cytisoides, hedysarum coronarium, ornithopus compressus and scorpiurus muricatus growing in sardinia and asinara island. basic characteristics applied to identification of rhizobia such as symbiotic properties, antibiotic- and salt-resistance, temperate-sensitivities, utilization of different sources of carbon and nitrogen were studied. the results from the 74 metabolic tests were used for cluster a ...	2004	15031655
expression of nir, nor and nos denitrification genes from bradyrhizobium japonicum in soybean root nodules.	expression of bradyrhizobium japonicum wild-type strain usda110 nirk, norc and nosz denitrification genes in soybean root nodules was studied by in situ histochemical detection of beta-galactosidase activity. similarly, p(nirk)-lacz, p(norc)-lacz, and p(nosz)-lacz fusions were also expressed in bacteroids isolated from root nodules. levels of beta-galactosidase activity were similar in both bacteroids and nodule sections from plants that were solely n(2)-dependent or grown in the presence of 4 m ...	2004	15032854
comparative genomics of gene-family size in closely related bacteria.	the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.	2004	15059260
expression islands clustered on the symbiosis island of the mesorhizobium loti genome.	rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. the establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. we developed a macroarray for mesorhizobium loti maff303099, a microsymbiont of the model legume lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. global transcriptional ...	2004	15060047
fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy.	a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ...	2004	15060178
adenylate gradients and ar:o2 effects on legume nodules. ii. changes in the subcellular adenylate pools.	central infected zone tissue of soybean (glycine max l. merr.) nodules was fractionated into separate subcellular compartments using density gradient centrifugation in nonaqueous solvents to better understand how exposure to ar:o(2) (80:20%, v/v) atmosphere affects c and n metabolism, and to explore a potential role for adenylates in regulating o(2) diffusion. when nodules were switched from air to ar:o(2), adenylate energy charge (aec) in the plant cytosol rose from 0.63 +/- 0.02 to 0.73 +/- 0. ...	2004	15064369
occurrence and phylogenetic diversity of sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons.	bacterial strains of the genus sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (pah) as the sole source of carbon and energy. the direct detection of sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. in this study, a culture-independent pcr-based detection method using specific primers targeting the sphingomonas 16s rrna gene combined with denaturing ...	2004	15066784
root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...	2004	15066803
analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.	a 492- to 495-bp fragment of the gene coding for the large subunit of the form i ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) (rbcl) was amplified by pcr from facultatively lithotrophic aerobic co-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic dna extracts from tephra and ash deposits from kilauea volcano, for which atmospheric co and hydrogen have been previously documented as important substrates. pcr products from the mats and volcanic site ...	2004	15066819
microorganisms resistant to free-living amoebae.	free-living amoebae feed on bacteria, fungi, and algae. however, some microorganisms have evolved to become resistant to these protists. these amoeba-resistant microorganisms include established pathogens, such as cryptococcus neoformans, legionella spp., chlamydophila pneumoniae, mycobacterium avium, listeria monocytogenes, pseudomonas aeruginosa, and francisella tularensis, and emerging pathogens, such as bosea spp., simkania negevensis, parachlamydia acanthamoebae, and legionella-like amoebal ...	2004	15084508
gurke and pasticcino3 mutants affected in embryo development are impaired in acetyl-coa carboxylase.	normal embryo development is required for correct seedling formation. the arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. we have recently identified lethal acc1 mutants affected in acetyl-coa carboxylase 1 (accase 1) that display a similar embryo phenotype. a series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct seque ...	2004	15088065
hybf, a zinc-containing protein involved in nife hydrogenase maturation.	hypa and hypb are maturation proteins required for incorporation of nickel into the hydrogenase large subunit. to examine the functions of these proteins in nickel insertion, the hybf gene, which is a homolog of hypa essential for maturation of hydrogenases 1 and 2 from escherichia coli, was overexpressed, and the product was purified. this protein behaves like a monomer in gel filtration and contains stoichiometric amounts of zinc but insignificant or undetectable amounts of nickel and iron. in ...	2004	15090500
divergence and redundancy of 16s rrna sequences in genomes with multiple rrn operons.	the level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16s rrna-based methods. furthermore, the occurrence of widespread horizontal gene transfer (hgt) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. for this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16s rrna sequences were evaluated. bacterial genomes display up to 15 operons ...	2004	15090503
conserved glycines in the c terminus of minc proteins are implicated in their functionality as cell division inhibitors.	alignment of 36 minc sequences revealed four completely conserved c-terminal glycines. as minc inhibits cytokinesis in neisseria gonorrhoeae and escherichia coli, the functional importance of these glycines in n. gonorrhoeae minc (minc(ng)) and e. coli minc (minc(ec)) was investigated through amino acid substitution by using site-directed mutagenesis. each mutant was evaluated for its ability to arrest cell division and to interact with itself and mind. in contrast to overexpression of wild-type ...	2004	15090526
ancestral hemoglobins in archaea.	hemoglobins are ubiquitous in eukarya and bacteria but, until now, have not been found in archaea. a phylogenetic analysis of the recently revealed microbial family of globin-coupled heme-based sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (pgb). here, we report the discovery and characterization of two pgbs from the archaea: appgb from the obligately aerobic hyperthermophile aeropyrum pernix, and mapgb from the strictly anaerobic methanog ...	2004	15096613
a comparative genome analysis identifies distinct sorting pathways in gram-positive bacteria.	surface proteins in gram-positive bacteria are frequently required for virulence, and many are attached to the cell wall by sortase enzymes. bacteria frequently encode more than one sortase enzyme and an even larger number of potential sortase substrates that possess an lpxtg-type cell wall sorting signal. in order to elucidate the sorting pathways present in gram-positive bacteria, we performed a comparative analysis of 72 sequenced microbial genomes. we show that sortase enzymes can be partiti ...	2004	15102780
casuarina cunninghamiana tissue extracts stimulate the growth of frankia and differentially alter the growth of other soil microorganisms.	aqueous extracts of host plant casuarina cunninghamiana tissue altered the in vitro growth of its diazotrophic microsymbiont frankia and a selection of other soil microorganisms. the growth of actinomycetous frankia strains, 55005. avci1, cesi5, cji82 001, and cj was stimulated by aqueous extracts of c. cunninghamiana tissue. green cladodes (photosynthetic branches), unsuberized roots, and suberized roots were more stimulatory than dry cladodes and seed tissue. aqueous extracts of green cladodes ...	2004	15112734
a hybrid clustering approach to recognition of protein families in 114 microbial genomes.	grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses (e.g., homology-based prediction of structure or function). standard clustering methods such as single-linkage clustering capture a history of cluster topologies as a function of threshold, but in practice their usefulness is limited because unrelated sequences join clusters before biologically meaningful families are fully constituted, e.g. as the result of matches to so-called promiscuous domain ...	2004	15115543
new method of denitrification analysis of bradyrhizobium field isolates by gas chromatographic determination of (15)n-labeled n(2).	to evaluate the denitrification abilities of many bradyrhizobium field isolates, we developed a new (15)n-labeled n(2) detection methodology, which is free from interference from atmospheric n(2) contamination. (30)n(2) ((15)n(15)n) and (29)n(2) ((15)n(14)n) were detected as an apparent peak by a gas chromatograph equipped with a thermal conductivity detector with n(2) gas having natural abundance of (15)n (0.366 atom%) as a carrier gas. the detection limit was 0.04% (30)n(2), and the linearity ...	2004	15128547
national science foundation-sponsored workshop report. draft plan for soybean genomics.	recent efforts to coordinate and define a research strategy for soybean (glycine max) genomics began with the establishment of a soybean genetics executive committee, which will serve as a communication focal point between the soybean research community and granting agencies. secondly, a workshop was held to define a strategy to incorporate existing tools into a framework for advancing soybean genomics research. this workshop identified and ranked research priorities essential to making more inf ...	2004	15141067
genome-wide comparison of the his-to-asp phosphorelay signaling components of three symbiotic genera of rhizobia.	histidine-to-aspartate (his-asp) phosphorelay (or two-component) systems are very common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli. the his-asp phosphorelay components include "sensor histidine kinase (hk)", "phosphotransfer intermediate (hpt)", and "response regulator (rr)". with special reference to three bacterial species (mesorhizobium loti, bradyrhizobium japonicum, sinorhizobium meliloti), each of which belongs to a ...	2004	15141946
bacterial signal transduction network in a genomic perspective.	bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. the complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. comparative studies revealed certain general trends in the organization of diverse signalling systems. these include (i) modular structure of signalling proteins; (ii) comm ...	2004	15142243
the ferric uptake regulator (fur) protein from bradyrhizobium japonicum is an iron-responsive transcriptional repressor in vitro.	the fur protein represses transcription of iron-responsive genes in bacteria. the discovery that fur is a zinc metalloprotein and the use of surrogate metals for fe(2+) for in vitro studies question whether fur is a direct iron sensor. in the present study, we show that the affinity of fur from bradyrhizobium japonicum (bjfur) for its target dna increases 30-fold in the presence of metal, with a k(d) value of about 2 nm. dnase i footprinting experiments showed that bjfur protected its binding si ...	2004	15148310
the sinorhizobium meliloti fur gene regulates, with dependence on mn(ii), transcription of the sitabcd operon, encoding a metal-type transporter.	sinorhizobium meliloti is an alpha-proteobacterium able to induce nitrogen-fixing nodules on roots of specific legumes. in order to propagate in the soil and for successful symbiotic interaction the bacterium needs to sequester metals like iron and manganese from its environment. the metal uptake has to be in turn tightly regulated to avoid toxic effects. in this report we describe the characterization of a chromosomal region of s. meliloti encoding the sitabcd operon and the putative regulatory ...	2004	15150249
reduction of dark chilling stress in n-fixing soybean by nitrate as indicated by chlorophyll a fluorescence kinetics.	sub-optimal night temperatures below 15 degrees c (dark chilling) frequently reduce soybean [glycine max (l.) merrill] production. nitrate application is known to alleviate some of the negative effects of low root zone temperatures, probably by counteracting the inhibition caused by decreased symbiotic nitrogen fixation (snf). under field conditions, however, dark chilling is frequently not accompanied by low root zone temperatures. the possibility that nitrate might increase dark-chilling toler ...	2004	15153191
identification and characterization of the dna-binding domain of the multifunctional puta flavoenzyme.	the puta flavoprotein from escherichia coli is a transcriptional repressor and a bifunctional enzyme that regulates and catalyzes proline oxidation. puta represses transcription of genes puta and putp by binding to the control dna region of the put regulon. the objective of this study is to define and characterize the dna binding domain of puta. the dna binding activity of puta, a 1320 amino acid polypeptide, has been localized to n-terminal residues 1-261. after exploring a potential dna-bindin ...	2004	15155740
genomic diversity of burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a burkholderia mallei-specific prophage in b. pseudomallei 1026b.	burkholderia pseudomallei is the etiologic agent of the disease melioidosis and is a category b biological threat agent. the genomic sequence of b. pseudomallei k96243 was recently determined, but little is known about the overall genetic diversity of this species. suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of b. pseudomallei, 1026b and k96243. numerous mobile genetic elements, including a temperate bacteriophage de ...	2004	15175308
the acidic nature of the ccmg redox-active center is important for cytochrome c maturation in escherichia coli.	cytochrome c biogenesis in escherichia coli is a complex process requiring at least eight genes (ccmabcdefgh). one of these genes, ccmg, encodes a thioredoxin-like protein with unusually specific redox activity. here, we investigate the basis for ccmg function and demonstrate the importance of acidic residues surrounding the redox-active center.	2004	15175318
regb/rega, a highly conserved redox-responding global two-component regulatory system.	the reg regulon from rhodobacter capsulatus and rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. the redox signal that is detected by the membrane-bound sensor kinase, regb, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c o ...	2004	15187184
use of tn kpk2 for sequencing a 10.6-kb psti dna fragment of bradyrhizobium japonicum and for the construction of aspa and ndva mutants.	transposon tn kpk2 was used to saturate a randomly cloned bradyrhizobium japonicum psti fragment and the insertions were used as starting points for the sequence determination. the first gene of the 10.6-kb dna insert encodes a homologue to ndva, the product of which is known to be involved in the formation of periplasmic cyclic glucans. selected tn kpk2 insertions were introduced into the b. japonicum wild-type strain. the resulting mutants were subsequently tested for their symbiotic interacti ...	2004	15188087
mutational analysis and biochemical characterization of the burkholderia thailandensis dw503 quorum-sensing network.	numerous gram-negative bacteria communicate and regulate gene expression through a cell density-responsive mechanism termed quorum sensing (qs), which involves the synthesis and perception of diffusible n-acyl-homoserine lactones (ahl). in this study we genetically and physiologically characterized the burkholderia thailandensis dw503 qs network. in silico analysis of the b. thailandensis genome revealed the presence of at least three ahl synthases (ahs) and five transcriptional regulators belon ...	2004	15205437
computational inference of scenarios for alpha-proteobacterial genome evolution.	the alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches sep ...	2004	15210995
identification of burkholderia cenocepacia genes required for bacterial survival in vivo.	burkholderia cenocepacia (formerly burkholderia cepacia complex genomovar iii) causes chronic lung infections in patients with cystic fibrosis. in this work, we used a modified signature-tagged mutagenesis (stm) strategy for the isolation of b. cenocepacia mutants that cannot survive in vivo. thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 b. cenocepacia transposon mutants, arranged in pools of ...	2004	15213146
inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.	the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ...	2004	15214963
impact of glyphosate on the bradyrhizobium japonicum symbiosis with glyphosate-resistant transgenic soybean: a minireview.	glyphosate-resistant (gr) soybean [glycine max (l.) merr.] expressing an insensitive 5-enolpyruvylshikimic acid-3-phosphate synthase (epsps) gene has revolutionized weed control in soybean production. the soybean nitrogen fixing symbiont, bradyrhizobium japonicum, possesses a glyphosate-sensitive enzyme and upon exposure to glyphosate accumulates shikimic acid and hydroxybenzoic acids such as protocatechuic acid (pca), accompanied with b. japonicum growth inhibition and death at high concentrati ...	2004	15224916
biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life.		2004	15231774
two c-p lyase operons in pseudomonas stutzeri and their roles in the oxidation of phosphonates, phosphite, and hypophosphite.	dna sequencing and analysis of two distinct c-p lyase operons in pseudomonas stutzeri wm88 were completed. the htxabcdefghijklmn operon encodes a hypophosphite-2-oxoglutarate dioxygenase (htxa), whereas the predicted amino acid sequences of htxb to htxn are each homologous to the components of the escherichia coli phn operon, which encodes c-p lyase, although homologs of e. coli phnf and phno are absent. the genes in the htx operon are cotranscribed based on gene organization, and the presence o ...	2004	15231805
characterization of nopp, a type iii secreted effector of rhizobium sp. strain ngr234.	the type three secretion system (ttss) encoded by pngr234a, the symbiotic plasmid of rhizobium sp. strain ngr234, is responsible for the flavonoid- and nodd1-dependent secretion of nodulation outer proteins (nops). abolition of secretion of all or specific nops significantly alters the nodulation ability of ngr234 on many of its hosts. in the closely related strain rhizobium fredii usda257, inactivation of the ttss modifies the host range of the mutant so that it includes the improved glycine ma ...	2004	15231809
global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns.	oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. in this paper we analyzed oligonucleotide usage (ou) biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages.	2004	15239845
chloromethane-dependent expression of the cmu gene cluster of hyphomicrobium chloromethanicum.	the methylotrophic bacterium hyphomicrobium chloromethanicum cm2 can utilize chloromethane (ch(3)cl) as the sole carbon and energy source. previously genes cmub, cmuc, cmua, and fold were shown to be essential for the growth of methylobacterium chloromethanicum on ch(3)cl. these ch(3)cl-specific genes were subsequently detected in h. chloromethanicum. transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for ch(3)cl metabolism in h. chloromethanicum. ...	2004	15240299
molecular analysis of carbon monoxide-oxidizing bacteria associated with recent hawaiian volcanic deposits.	genomic dna extracts from four sites at kilauea volcano were used as templates for pcr amplification of the large subunit (coxl) of aerobic carbon monoxide dehydrogenase. the sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. pcr primers amplified coxl sequences from the omp clade of co oxidizers, which includes isolates such as oligotropha carboxidovorans, mycobacterium tuber ...	2004	15240307
fur is involved in manganese-dependent regulation of mnta (sita) expression in sinorhizobium meliloti.	fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. in this work we analyzed the phenotype of a fur mutant in sinorhizobium meliloti, an alpha-proteobacterium that fixes n(2) in association with host plants. we demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a fur-independent manner. however, manganese-dependent expressi ...	2004	15240318
regulation of expression of symbiotic genes in rhizobium sp. ngr234.	research in the field of rhizobium-legume symbiosis faces a new challenge: integrate the wealth of information generated by genomic projects. the goal: apprehend the complexity of the molecular mechanisms involved in symbiotic associations. at the time of writing, the genomes of three micro-symbionts (bradyrhizobium japonicum, mesorhizobium loti and sinorhizobium meliloti) have been sequenced, and two more (those of rhizobium leguminosarum and rhizobium etli) will be completed in the near future ...	2003	15242276
the nitrogen-fixing gene (nifh) of rhodopseudomonas palustris: a case of lateral gene transfer?	nitrogen fixation is catalysed by some photosynthetic bacteria. this paper presents a phylogenetic comparison of a nitrogen fixation gene (nifh) with the aim of elucidating the processes underlying the evolutionary history of rhodopseudomonas palustris. in the nifh phylogeny, strains of rps. palustris were placed in close association with rhodobacter spp. and other phototrophic purple non-sulfur bacteria belonging to the alpha-proteobacteria, separated from its close relatives bradyrhizobium jap ...	2004	15256566
a novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101.	p-nitrophenol (4-np) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. to date, several 4-np-degrading bacteria have been isolated; however, the genetic information remains very limited. in this study, a novel 4-np degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101, was identified and characterized. the deduced amino acid sequences of npcb, npca, and npcc showed identity with phenol 2-hydroxylase compon ...	2004	15262926
the homogentisate pathway: a central catabolic pathway involved in the degradation of l-phenylalanine, l-tyrosine, and 3-hydroxyphenylacetate in pseudomonas putida.	pseudomonas putida metabolizes phe and tyr through a peripheral pathway involving hydroxylation of phe to tyr (phhab), conversion of tyr into 4-hydroxyphenylpyruvate (tyrb), and formation of homogentisate (hpd) as the central intermediate. homogentisate is then catabolized by a central catabolic pathway that involves three enzymes, homogentisate dioxygenase (hmga), fumarylacetoacetate hydrolase (hmgb), and maleylacetoacetate isomerase (hmgc), finally yielding fumarate and acetoacetate. whereas t ...	2004	15262943
bradyrhizobium betae sp. nov., isolated from roots of beta vulgaris affected by tumour-like deformations.	some varieties of sugar beet, beta vulgaris, cultivated in northern spain have large deformations that resemble the tumours produced by agrobacterium species. in an attempt to isolate the agent responsible for these deformations, several endophytic slow-growing bacterial strains were isolated, the macroscopic morphology of which resembled that of bradyrhizobium species. these strains were not able to produce tumours in nicotiana tabacum plants and, based on phylogenetic analysis of their 16s rrn ...	2004	15280302
pod set related to photosynthetic rate and endogenous aba in soybeans subjected to different water regimes and exogenous aba and ba at early reproductive stages.	the physiological reasons for reduced pod set in soybean (glycine max) caused by drought during anthesis are not established. the objective of this study was to investigate the involvement of photosynthetic rate (a), pod endogenous abscisic acid (aba) and exogenously applied aba and 6-benzylaminopurine (ba) in regulating pod set in soybean during drought.	2004	15286011
cpndb: a chaperonin sequence database.	type i chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. sequences of cpn60 genes, encoding 60-kda chaperonin protein subunits (cpn60, also known as groel or hsp60), are useful for phylogenetic studies and as targets for detection and identification of organisms. conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal pcr primers. here, we introduce cpndb, a curated collectio ...	2004	15289485
indole-3-acetic acid biosynthesis is deficient in gluconacetobacter diazotrophicus strains with mutations in cytochrome c biogenesis genes.	gluconacetobacter diazotrophicus is an endophyte of sugarcane frequently found in plants grown in agricultural areas where nitrogen fertilizer input is low. recent results from this laboratory, using mutant strains of g. diazotrophicus unable to fix nitrogen, suggested that there are two beneficial effects of g. diazotrophicus on sugarcane growth: one dependent and one not dependent on nitrogen fixation. a plant growth-promoting substance, such as indole-3-acetic acid (iaa), known to be produced ...	2004	15292139
polyhydroxyalkanoate (pha) accumulation in sulfate-reducing bacteria and identification of a class iii pha synthase (phaec) in desulfococcus multivorans.	seven strains of sulfate-reducing bacteria (srb) were tested for the accumulation of polyhydroxyalkanoates (phas). during growth with benzoate desulfonema magnum accumulated large amounts of poly(3-hydroxybutyrate) [poly(3hb)]. desulfosarcina variabilis (during growth with benzoate), desulfobotulus sapovorans (during growth with caproate), and desulfobacterium autotrophicum (during growth with caproate) accumulated poly(3hb) that accounted for 20 to 43% of cell dry matter. desulfobotulus sapovor ...	2004	15294771
roots, cycles and leaves. expression of the phosphoenolpyruvate carboxylase kinase gene family in soybean.	phosphorylation of phosphoenolpyruvate carboxylase (pepc; ec 4.1.1.31) plays an important role in the control of central metabolism of higher plants. this phosphorylation is controlled largely at the level of expression of pepc kinase (ppck) genes. we have analyzed the expression of both ppck genes and the pepc genes that encode pepc in soybean (glycine max). soybean contains at least four ppck genes. we report the genomic and cdna sequences of these genes and demonstrate the function of the gen ...	2004	15299132
[the chemotactic properties of bradyrhizobium japonicum in the presence of natural fine-grained minerals].	the natural argillaceous minerals montmorillonite and palygorskite were found to enhance the motility of bradyrhizobium japonicum cells and to slow down their chemotactic motion to glucose. the latter effect of the minerals is probably due to the adsorption of mineral particles on the cell surface and the blockade of the receptors that are responsible for the chemotactic behavior of the bacterium.	2004	15315230
cloning and expression of afpa, a gene encoding an antifreeze protein from the arctic plant growth-promoting rhizobacterium pseudomonas putida gr12-2.	the arctic plant growth-promoting rhizobacterium pseudomonas putida gr12-2 secretes an antifreeze protein (afp) that promotes survival at subzero temperatures. the afp is unusual in that it also exhibits a low level of ice nucleation activity. a dna fragment with an open reading frame encoding 473 amino acids was cloned by pcr and inverse pcr using primers designed from partial amino acid sequences of the isolated afp. the predicted gene product, afpa, had a molecular mass of 47.3 kda, a pi of 3 ...	2004	15317770
expression of the rnd-type efflux pump adeabc in acinetobacter baumannii is regulated by the aders two-component system.	the adeabc pump of acinetobacter baumannii bm4454, which confers resistance to various antibiotic classes including aminoglycosides, is composed of the adea, adeb, and adec proteins; adeb is a member of the rnd superfamily. the adea, adeb, and adec genes are contiguous and adjacent to ades and ader, which are transcribed in the opposite direction and which specify proteins homologous to sensors and regulators of two-component systems, respectively (s. magnet, p. courvalin, and t. lambert, antimi ...	2004	15328088
biosynthesis of artificial microperoxidases by exploiting the secretion and cytochrome c maturation apparatuses of escherichia coli.	microperoxidases were initially isolated as peptide fragments containing covalently bound heme and are derived from naturally occurring c-type cytochromes. they are not only used as model compounds but also have potential applications as biosensors, electron carriers, photoreceptors, microzymes, and drugs. in a systematic attempt to define the minimal requirements for covalent attachment of hemes to c-type cytochromes, we have succeeded to produce artificial microperoxidases with peptide sequenc ...	2004	15328415
new protein-protein interactions identified for the regulatory and structural components and substrates of the type iii secretion system of the phytopathogen xanthomonas axonopodis pathovar citri.	we have initiated a project to identify protein-protein interactions involved in the pathogenicity of the bacterial plant pathogen xanthomonas axonopodis pv. citri. using a yeast two-hybrid system based on gal4 dna-binding and activation domains, we have focused on identifying interactions involving subunits, regulators, and substrates of the type iii secretion system coded by the hrp (for hypersensitive response and pathogenicity), hrc (for hrp conserved), and hpa (for hrp associated) genes. we ...	2004	15342589
transcriptional repressor copr: use of selex to study the copr operator indicates that evolution was directed at maximal binding affinity.	copr is one of the two copy number control elements of the streptococcal plasmid pip501. it represses transcription of the repr mrna encoding the essential replication initiator protein about 10- to 20-fold by binding to its operator region upstream of the repr promoter pii. copr binds at two consecutive sites in the major groove of the dna that share the consensus motif 5'-cgtg. previously, the minimal operator was narrowed down to 17 bp, and equilibrium dissociation constants for dna binding a ...	2004	15342596
stability of the heme environment of the nitric oxide synthase from staphylococcus aureus in the absence of pterin cofactor.	we have used resonance raman spectroscopy to probe the heme environment of a recently discovered nos from the pathogenic bacterium staphylococcus aureus, named sanos. we detect two forms of the co complex in the absence of l-arginine, with nu(fe-co) at 482 and 497 cm(-1) and nu(c-o) at 1949 and 1930 cm(-1), respectively. similarly to mammalian nos, the binding of l-arginine to sanos caused the formation of a single co complex with nu(fe-co) and nu(c-o) frequencies at 504 and 1,917 cm(-1), respec ...	2004	15345570
co-sensing mechanisms.	carbon monoxide (co) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for co. this article reviews the current evidence for a variety of proteins with demonstrated or potential co-sensing ability. particular emphasis is placed on the molecular description of cooa, a heme-containing co sensor from rhodospirillum rubrum, since its biological role as a c ...	2004	15353565
the promoters of two isoflavone synthase genes respond differentially to nodulation and defense signals in transgenic soybean roots.	isoflavonoids are a group of secondary metabolites common to leguminous plants that play roles in nodulation and defense responses. isoflavone synthase (ifs) catalyzes the key entry point step of isoflavone biosynthesis from the general phenylpropanoid pathway. we have cloned the 5' upstream regions of the genes encoding the two isoflavone synthase isoforms from soybean. we characterized the tissue-specific expression patterns of ifs1 and ifs2 genes of soybean by quantitative rt-pcr. isoflavone ...	2004	15356384
analysis of the root nodule-enhanced transcriptome in soybean.	for high throughput screening of root nodule-enhanced genes, cdna libraries specific for three different developmental stages of soybean root nodules were constructed after inoculation with bradyrhizobium japonicum usda110. 5,469 cdna clones were sequenced and grouped into 2,511 non-redundant (nr) ests consisting of 769 contigs and 1,742 singletons. using similarity searches against several public databases we constructed a functional classification of the ests into root nodule-specific nodulin ...	2004	15359124
perception of bradyrhizobium japonicum nod factor by soybean [glycine max (l.) merr.] root hairs under abiotic stress conditions.	suboptimal growth conditions, such as low rhizosphere temperature, high salinity, and low ph can negatively affect the rhizobia-legume symbioses, resulting in poor nodulation and lower amounts of nitrogen fixed. early stages of the bradyrhizobium japonicum-soybean [glycine max (l.) merr.] symbiosis, such as excretion of genistein (the plant-to-bacteria signal) and infection initiation can be inhibited by abiotic stresses; however, the effect on early events modulated by nod factors (bacteria-to- ...	2004	15361528
symbiotic autoregulation of nifa expression in rhizobium leguminosarum bv. viciae.	nifa is the general transcriptional activator of nitrogen fixation genes in diazotrophic bacteria. in rhizobium leguminosarum bv. viciae upm791, the nifa gene is part of a gene cluster (orf71 orf79 fixw orf5 fixabcx nifab) separated by 896 bp from an upstream and divergent truncated duplication of nifh (deltanifh). symbiotic expression analysis of genomic nifa::lacz fusions revealed that in strain upm791 nifa is expressed mainly from a sigma54-dependent promoter (p(nifa1)) located upstream of or ...	2004	15375140
an energy taxis transducer promotes root colonization by azospirillum brasilense.	motility responses triggered by changes in the electron transport system are collectively known as energy taxis. in azospirillum brasilense, energy taxis was shown to be the principal form of locomotor control. in the present study, we have identified a novel chemoreceptor-like protein, named tlp1, which serves as an energy taxis transducer. the tlp1 protein is predicted to have an n-terminal periplasmic region and a cytoplasmic c-terminal signaling module homologous to those of other chemorecep ...	2004	15375141