Publications

secrets of soil survival revealed by the genome sequence of arthrobacter aurescens tc1.	arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. the genome of arthrobacter aurescens strain tc1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, ptc1 and p ...	2006	17194220
identification of amino acid residues involved in substrate specificity of plant acyl-acp thioesterases using a bioinformatics-guided approach.	the large amount of available sequence information for the plant acyl-acp thioesterases (tes) made it possible to use a bioinformatics-guided approach to identify amino acid residues involved in substrate specificity. the conserved property difference locator (cpdl) program allowed the identification of putative specificity-determining residues that differ between the fata and fatb te classes. six of the fata residue differences identified by cpdl were incorporated into the fatb-like parent via ...	2007	17201914
redox-induced changes in flavin structure and roles of flavin n(5) and the ribityl 2'-oh group in regulating puta--membrane binding.	puta is a novel flavoprotein in escherichia coli that switches from a transcriptional repressor to a membrane-bound proline catabolic enzyme. previous crystallographic studies of the puta proline dehydrogenase (prodh) domain under oxidizing conditions revealed that fad n(5) and the ribityl 2'-oh group form hydrogen bonds with arg431 and arg556, respectively. here we identify molecular interactions in the puta prodh active site that underlie redox-dependent functional switching of puta. we report ...	2007	17209558
ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.	the amount of lateral gene transfer (lgt) that has occurred in microbial evolution is heavily debated. efforts to quantify lgt through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by lgt, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. here we present a simple method that is independent of gene-tree comparisons to estimate the lgt rate among s ...	2007	17213324
gentisate 1,2-dioxygenase from xanthobacter polyaromaticivorans 127w.	a putative gentisate 1,2-dioxygenase was encoded in the dibenzothiophene degradation gene cluster (dbd) from xanthobacter polyaromaticivorans 127w. the deduced amino acid sequence showed high sequence similarity with gentisate dioxygenases from pseudomonas alcaligenes (aad49427, 65% identical), bradyrhizobium japonicum (np_766750, 64%), and p. aeruginosa (zp_00135722, 54%), and moderate similarity with 1-hydroxy-2-naphthoate dioxygenase from nocardioides sp. kp7 (baa31235, 33%) and salicylate di ...	2007	17213679
the lipopolysaccharide of sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant medicago truncatula.	in the establishment of symbiosis between medicago truncatula and the nitrogen-fixing bacterium sinorhizobium meliloti, the lipopolysaccharide (lps) of the microsymbiont plays an important role as a signal molecule. it has been shown in cell cultures that the lps is able to suppress an elicitor-induced oxidative burst. to investigate the effect of s. meliloti lps on defense-associated gene expression, a microarray experiment was performed. for evaluation of the m. truncatula microarray datasets, ...	2007	17220366
structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.	the aryl hydrocarbon receptor (ahr) is a ligand-dependent transcription factor that is activated by a structurally diverse array of synthetic and natural chemicals, including toxic halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (tcdd). analysis of the molecular events occurring in the ahr ligand binding and activation processes requires structural information on the ahr per-arnt-sim (pas) b-containing ligand binding domain, for which no experimentally determined st ...	2007	17223691
rhizobitoxine production in agrobacterium tumefaciens c58 by bradyrhizobium elkanii rtxacdefg genes.	we examined the genetic basis and transfer for production of rhizobitoxine, an inhibitor of ethylene biosynthesis in plants, directed by the rtx genes of bradyrhizobium elkanii. comparison with genome sequences of bradyrhizobium japonicum and xanthomonas oryzae suggests that the rtx genes extend from the previously identified rtxac genes through four additional genes rtxdefg. reverse transcription-pcr analysis showed that the rtxacdefg genes are expressed as an operon. mutational analysis indica ...	2007	17227467
molecular dissection of diheme cytochrome c gene from soil isolate of a gram negative, facultative chemolithotrophic sulfur oxidizer.	a gram negative chemolithotrophic bacterium (rpi) with facultative mode of nutrition was isolated from the soil. enzymological studies confirmed presence of thiosulphate oxidase, sulphite oxidase and rhodanese, all of which play role in sulfur metabolism pathway. a set of degenerate oligonucleotide primer pairs was used for thermal amplification of a major part of the coding region of the cytochrome c gene locus of this bacterium. nucleotide and translated amino acid sequence revealed the gene t ...	2004	17240791
characterization and expression patterns of sinorhizobium meliloti tmrna (ssra).	tmrna (ssra) in sinorhizobium meliloti is a small rna annotated by homology with the bradyrhizobium japonicum sra molecule. here, this molecule is described in sinorhizobium meliloti as a model for such molecules in alphaproteobacteria subgroup-2. northern blot analysis and mapping of both 5' and 3' ends of this tmrna allow the identification of two pieces: a 214 nt mrna-like domain and an 82 nt trna-like domain, both highly stable, whereas the premature form is unstable. transcriptional studies ...	2007	17241239
a novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with comamonas sp. strain cnb-1.	comamonas sp. strain cnb-1 degrades nitrobenzene and chloronitrobenzene via the intermediates 2-aminomuconate and 2-amino-5-chloromuconate, respectively. deamination of these two compounds results in the release of ammonia, which is used as a source of nitrogen for bacterial growth. in this study, a novel deaminase was purified from comamonas strain cnb-1, and the gene (cnbz) encoding this enzyme was cloned. the n-terminal sequence and peptide fingerprints of this deaminase were determined, and ...	2007	17259310
monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16s rrna gene-based analyses.	the diversity and dynamics of bacterial populations in saint-nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (sscp) fingerprinting and sequencing of 16s rrna genes. the dominant clones, among 125 16s rrna genes isolated from milk, belonged to members of the firmicutes (58% of the total clones) affiliated mainly with the orders clostridiales and the lactobacillales, followed by ...	2007	17259356
pleiotropic effects of mutations that alter the sinorhizobium meliloti cytochrome c respiratory system.	using transposon mutagenesis, mutations have been isolated in several genes (ccda, cycm, ccmc, ccmb and senc) that play a role in sinorhizobium meliloti cytochrome metabolism. as in other bacteria, mutations in the s. meliloti ccda, ccmb and ccmc genes resulted in the absence of all c-type cytochromes. however, the s. meliloti ccda mutant also lacked cytochrome oxidase aa(3), a defect that does not appear to have been reported for other bacteria. the aa(3)-type cytochromes were also missing from ...	2007	17259611
the contribution of bacteroidal nitrate and nitrite reduction to the formation of nitrosylleghaemoglobin complexes in soybean root nodules.	it is becoming recognized that leghaemoglobin constitutes an important buffer for the cytotoxic nitric oxide radical (no()) in root nodules, although the sources of this no() within nodules are unclear. in bradyrhizobium japonicum bacteroids, no() can be produced through the denitrification process, during which nitrate is reduced to nitrite by the periplasmic nitrate reductase nap, and nitrite is reduced to no() by the respiratory nitrite reductase nirk. to assess the contribution of bacter ...	2007	17259612
the small fnr regulon of neisseria gonorrhoeae: comparison with the larger escherichia coli fnr regulon and interaction with the narq-narp regulon.	neisseria gonorrhoeae can survive during oxygen starvation by reducing nitrite to nitrous oxide catalysed by the nitrite and nitric oxide reductases, ania and norb. the oxygen-sensing transcription factor, fnr, is essential for transcription activation at the ania promoter, and full activation also requires the two-component regulatory system, narq-narp, and the presence of nitrite. the only other gene known to be activated by the gonococcal fnr is ccp encoding a cytochrome c peroxidase, and no ...	2007	17261178
variability in bradyrhizobium japonicum and b. elkanii seven years after introduction of both the exotic microsymbiont and the soybean host in a cerrados soil.	the plasticity of rhizobial genomes is far greater than previously thought, with complex genomic recombination events that may be accelerated by the often stressful environmental conditions of the tropics. this study aimed at evaluating changes in soybean rhizobia due to adaptation to inhospitable environmental conditions (high temperatures, drought, and acid soils) in the brazilian cerrados. both the host plant and combinations of four strains of soybean bradyrhizobium were introduced in an unc ...	2007	17265000
a complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in rhodobacter sphaeroides.	bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. approximately 40 proteins are required for the assembly and functionality of this structure. rhodobacter sphaeroides has two flagellar systems. one of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. in this work we found th ...	2007	17293429
characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis.	members of the gammaproteobacterial clade nor5/om60 regularly form an abundant part, up to 11%, of the bacterioplankton community in coastal systems during the summer months. here, we report the nearly complete genome sequence of one cultured representative, congregibacter litoralis strain kt71, isolated from north sea surface water. unexpectedly, a complete photosynthesis superoperon, including genes for accessory pigments, was discovered. it has a high sequence similarity to bac clones from mo ...	2007	17299055
evidence of horizontal transfer of symbiotic genes from a bradyrhizobium japonicum inoculant strain to indigenous diazotrophs sinorhizobium (ensifer) fredii and bradyrhizobium elkanii in a brazilian savannah soil.	the importance of horizontal gene transfer (hgt) in the evolution and speciation of bacteria has been emphasized; however, most studies have focused on genes clustered in pathogenesis and very few on symbiosis islands. both soybean (glycine max [l.] merrill) and compatible bradyrhizobium japonicum and bradyrhizobium elkanii strains are exotic to brazil and have been massively introduced in the country since the early 1960s, occupying today about 45% of the cropped land. for the past 10 years, ou ...	2007	17308185
genetic diversity of rhizobia associated with desmodium species grown in china.	desmodia are leguminous plants used as important forage and herbal medicine in china. little information is available about the nodule bacteria of desmodium species. to understand the genetic diversity of rhizobia associated with desmodium species grown in china, isolates from temperate and subtropical regions were obtained and analysed.	2007	17309506
living without fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium rhizobium and other alpha-proteobacteria.	the alpha-proteobacteria include several important genera, including the symbiotic n(2)-fixing "rhizobia", the plant pathogen agrobacterium, the mammalian pathogens brucella, bartonella as well as many others that are of environmental or other interest--including rhodobacter, caulobacter and the hugely abundant marine genus pelagibacter. only a few species--mainly different members of the rhizobia--have been analyzed directly for their ability to use and to respond to iron. these studies, howeve ...	2007	17310401
comparative analysis of hmuo function and expression in corynebacterium species.	we have constructed defined deletions in the hmuo gene from corynebacterium diphtheriae and corynebacterium ulcerans and show that the c. ulcerans hmuo mutation results in a significant reduction in hemoglobin-iron utilization, whereas in c. diphtheriae strains, deletion of hmuo caused no or only partial reduction in the utilization of heme as an iron source. we also show that expression from the c. ulcerans hmuo promoter exhibits minimal regulation by iron and heme whereas transcription from th ...	2007	17322319
two host-induced ralstonia solanacearum genes, acra and dinf, encode multidrug efflux pumps and contribute to bacterial wilt virulence.	multidrug efflux pumps (mdrs) are hypothesized to protect pathogenic bacteria from toxic host defense compounds. we created mutations in the ralstonia solanacearum acra and dinf genes, which encode putative mdrs in the broad-host-range plant pathogen. both mutations reduced the ability of r. solanacearum to grow in the presence of various toxic compounds, including antibiotics, phytoalexins, and detergents. both acrab and dinf mutants were significantly less virulent on the tomato plant than the ...	2007	17337552
hpdr is a transcriptional activator of sinorhizobium meliloti hpda, which encodes a herbicide-targeted 4-hydroxyphenylpyruvate dioxygenase.	sinorhizobium meliloti hpda, which encodes the herbicide target 4-hydroxyphenylpyruvate dioxygenase, is positively regulated by hpdr. gel mobility shift and dnase i footprinting analyses revealed that hpdr binds to a region that spans two conserved direct-repeat sequences within the hpdr-hpda intergenic space. hpdr-dependent hpda transcription occurs in the presence of 4-hydroxyphenylpyruvate, tyrosine, and phenylalanine, as well as during starvation.	2007	17337579
structure and characterization of a novel chicken biotin-binding protein a (bbp-a).	the chicken genome contains a bbp-a gene showing similar characteristics to avidin family genes. in a previous study we reported that the bbp-a gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ligand-binding site of avidin.	2007	17343730
structure and kinetics of monofunctional proline dehydrogenase from thermus thermophilus.	proline dehydrogenase (prodh) and delta(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) catalyze the two-step oxidation of proline to glutamate. they are distinct monofunctional enzymes in all eukaryotes and some bacteria but are fused into bifunctional enzymes known as proline utilization a (puta) in other bacteria. here we report the first structure and biochemical data for a monofunctional prodh. the 2.0-a resolution structure of thermus thermophilus prodh reveals a distorted (betaalpha)(8) ...	2007	17344208
discovery of a mandelonitrile hydrolase from bradyrhizobium japonicum usda110 by rational genome mining.	a mandelonitrile hydrolase bll6402 from bradyrhizobium japonicum usda110 was predicted by rational genome mining, i.e. combining traditional genome mining with functional analysis of the genetic organization of the putative nitrilase gene within the chromosome of microorganisms. this putative gene was cloned and over-expressed in escherichia coli, and the encoded protein was purified to give a nitrilase with a molecular mass of about 37kda. the molecular weight of the holoenzyme was about 455kda ...	2007	17350705
amp-forming acetyl-coa synthetases in archaea show unexpected diversity in substrate utilization.	adenosine monophosphate (amp)-forming acetyl-coa synthetase (acs; acetate:coa ligase (amp-forming), ec 6.2.1.1) is a key enzyme for conversion of acetate to acetyl-coa, an essential intermediate at the junction of anabolic and catabolic pathways. phylogenetic analysis of putative short and medium chain acyl-coa synthetase sequences indicates that the acss form a distinct clade from other acyl-coa synthetases. within this clade, the archaeal acss are not monophyletic and fall into three groups co ...	2007	17350930
amp-forming acetyl-coa synthetases in archaea show unexpected diversity in substrate utilization.	adenosine monophosphate (amp)-forming acetyl-coa synthetase (acs; acetate:coa ligase (amp-forming), ec 6.2.1.1) is a key enzyme for conversion of acetate to acetyl-coa, an essential intermediate at the junction of anabolic and catabolic pathways. phylogenetic analysis of putative short and medium chain acyl-coa synthetase sequences indicates that the acss form a distinct clade from other acyl-coa synthetases. within this clade, the archaeal acss are not monophyletic and fall into three groups co ...	2007	17350930
flagellin diversity in clostridium botulinum groups i and ii: a new strategy for strain identification.	strains of clostridium botulinum are traditionally identified by botulinum neurotoxin type; however, identification of an additional target for typing would improve differentiation. isolation of flagellar filaments and analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) showed that c. botulinum produced multiple flagellin proteins. nano-liquid chromatography-tandem mass spectrometry (nlc-ms/ms) analysis of in-gel tryptic digests identified peptides in all flagellin b ...	2007	17351097
the sorcerer ii global ocean sampling expedition: expanding the universe of protein families.	metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. we used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million global ocean sampling (gos) sequences. the gos dataset covers nearly all known prokaryotic protein families. a total of 3,995 medium- and large-sized clusters consi ...	2007	17355171
molecular diversity of legume root-nodule bacteria in kakadu national park, northern territory, australia.	symbiotic relationships between leguminous plants (family fabaceae) and nodule-forming bacteria in australia native ecosystems remain poorly characterized despite their importance. most studies have focused on temperate parts of the country, where the use of molecular approaches have already revealed the presence of bradyrhizobium, ensifer (formerly sinorhizobium), mesorhizobium and rhizobium genera of legume root-nodule bacteria. we here provide the first molecular characterization of nodulatin ...	2007	17356689
quorum-sensing regulation in rhizobia and its role in symbiotic interactions with legumes.	legume-nodulating bacteria (rhizobia) usually produce n-acyl homoserine lactones, which regulate the induction of gene expression in a quorum-sensing (or population-density)-dependent manner. there is significant diversity in the types of quorum-sensing regulatory systems that are present in different rhizobia and no two independent isolates worked on in detail have the same complement of quorum-sensing genes. the genes regulated by quorum sensing appear to be rather diverse and many are associa ...	2007	17360278
heterologous expression and identification of the genes involved in anaerobic degradation of 1,3-dihydroxybenzene (resorcinol) in azoarcus anaerobius.	azoarcus anaerobius, a strictly anaerobic, gram-negative bacterium, utilizes resorcinol as a sole carbon and energy source with nitrate as an electron acceptor. previously, we showed that resorcinol degradation by this bacterium is initiated by two oxidative steps, both catalyzed by membrane-associated enzymes that lead to the formation of hydroxyhydroquinone (hhq; 1,2,4-benzenetriol) and 2-hydroxy-1,4-benzoquinone (hbq). this study presents evidence for the further degradation of hbq in cell ex ...	2007	17369298
devs, a heme-containing two-component oxygen sensor of mycobacterium tuberculosis.	mycobacterium tuberculosis can exist in the actively growing state of the overt disease or in a latent quiescent state that can be induced, among other things, by anaerobiosis. eradication of the latent state is particularly difficult with the available drugs and requires prolonged treatment. devs is a member of the devs-devr two-component regulatory system that is thought to mediate the cellular response to anaerobiosis. here we report the cloning, expression, and initial characterization of a ...	2007	17371046
time-resolved crystallographic studies of the heme domain of the oxygen sensor fixl: structural dynamics of ligand rebinding and their relation to signal transduction.	the fixl protein of bradyrhizobium japonicum is a dimeric oxygen sensor responsible for initiating regulation of transcription of genes encoding proteins involved in nitrogen fixation and oxidative stress. it consists of an n-terminal heme-bound pas domain, denoted bjfixlh, and a c-terminal histidine kinase domain whose enzymatic activity depends on the ligation state of the heme. to investigate the molecular basis for this dependence and the dynamics associated with conversion between ligated a ...	2007	17385895
functional anthology of intrinsic disorder. 2. cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.	biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. however, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actu ...	2007	17391015
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
an extracytoplasmic function sigma factor acts as a general stress response regulator in sinorhizobium meliloti.	sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. sixty stress response genes were thus found to be up-regulated under both conditions. one of them, rpoe2 (smc01506), encodes a putative extracytoplasmic function (ecf) sigma factor. we showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry i ...	2007	17400745
responses of rhizobia to desiccation in relation to osmotic stress, oxygen, and temperature.		2007	17400779
diversification of lupine bradyrhizobium strains: evidence from nodulation gene trees.	bradyrhizobium strains isolated in europe from genisteae and serradella legumes form a distinct lineage, designated clade ii, on nodulation gene trees. clade ii bradyrhizobia appear to prevail also in the soils of western australia and south africa following probably accidental introduction with seeds of their lupine and serradella hosts. given this potential for dispersal, we investigated bradyrhizobium isolates originating from a range of native new world lupines, based on phylogenetic analyse ...	2007	17400786
crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, dbja, from bradyrhizobium japonicum usda110.	haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. the haloalkane dehalogenase dbja constitutes a novel substrate-specificity class with high catalytic activity for beta-methylated haloalkanes. in order to reveal the mechanism of its substrate specificity, dbja has been crystallized using the hanging-drop vapour-diffusion method. the best crystals were obtained using the microseeding technique with a reservoir solution consisting of 17-19.5%(w/v) pe ...	2007	17401198
a tale of two oxidation states: bacterial colonization of arsenic-rich environments.	microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ...	2007	17432936
flavone synthases from medicago truncatula are flavanone-2-hydroxylases and are important for nodulation.	flavones are important copigments found in the flowers of many higher plants and play a variety of roles in plant adaptation to stress. in medicago species, flavones also act as signal molecules during symbiotic interaction with the diazotropic bacterium sinorhizobium meliloti. they are the most potent nod gene inducers found in root exudates. however, flavone synthase ii (fns ii), the key enzyme responsible for flavone biosynthesis, has not been characterized in medicago species. we cloned two ...	2007	17434990
subpicosecond oxygen trapping in the heme pocket of the oxygen sensor fixl observed by time-resolved resonance raman spectroscopy.	dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein fixl constitutes the first step in hypoxia-induced signaling. in the present study, the photodissociation of the heme-o2 bond was used to synchronize this event, and time-resolved resonance raman (tr(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. tr(3) measurements on heme-oxycomplexes are highly challenging and have not yet b ...	2007	17446273
rhizavidin from rhizobium etli: the first natural dimer in the avidin protein family.	rhizobium etli cfn42 is a symbiotic nitrogen-fixing bacterium of the common bean phaseolus vulgaris. the symbiotic plasmid p42d of r. etli comprises a gene encoding a putative (strept)avidin-like protein, named rhizavidin. the amino acid sequence identity of rhizavidin in relation to other known avidin-like proteins is 20-30%. the amino acid residues involved in the (strept)avidin-biotin interaction are well conserved in rhizavidin. the structural and functional properties of rhizavidin were car ...	2007	17447892
trehalose biosynthesis in rhizobium leguminosarum bv. trifolii and its role in desiccation tolerance.	rhizobium leguminosarum bv. trifolii forms nitrogen-fixing root nodules on the pasture legume trifolium repens, and t. repens seed is often coated with a compatible r. leguminosarum bv. trifolii strain prior to sowing. however, significant losses in bacterial viability occur during the seed-coating process and during storage of the coated seeds, most likely due to desiccation stress. the disaccharide trehalose is known to function as an osmoprotectant, and trehalose accumulation due to de novo b ...	2007	17449695
diversity and relationships of bradyrhizobia from legumes native to eastern north america.	dna sequencing and polymerase chain reaction (pcr) assays with lineage-specific primers were used to analyze the diversity of 276 isolates of bradyrhizobium sp. nodule bacteria associated with 13 native legumes species in the northeastern united states, representing eight genera in six legume tribes. a pcr screen with two primer pairs in the rrna region indicated that seven of the legume species were exclusively associated with strains having markers resembling bradyrhizobium elkanii, while the ...	2006	17473884
mycorrhizal and rhizobial colonization of genetically modified and conventional soybeans.	we grew plants of nine soybean varieties, six of which were genetically modified to express transgenic cp4-epsps, in the presence of bradyrhizobium japonicum and arbuscular mycorrhizal fungi. mycorrhizal colonization and nodule abundance and mass differed among soybean varieties; however, in no case was variation significantly associated with the genetic modification.	2007	17483262
a memory of oxygen binding explains the dose response of the heme-based sensor fixl.	bradyrhizobium japonicum fixl is a modular oxygen sensor that directs adaptations to hypoxia by coupling the status of a heme-binding domain to a histidine-protein kinase activity. the oxygen-bound form is the "off-state". the unliganded form is the "on-state" active kinase that phosphorylates a transcription factor, fixj. we have developed methods to optimize the kinase reactions of fixl and measure the turnover rates (kcat) for reactions catalyzed by highly inhibited states of this sensor at c ...	2007	17487983
auxin and nitric oxide control indeterminate nodule formation.	rhizobia symbionts elicit root nodule formation in leguminous plants. nodule development requires local accumulation of auxin. both plants and rhizobia synthesise auxin. we have addressed the effects of bacterial auxin (iaa) on nodulation by using sinorhizobium meliloti and rhizobium leguminosarum bacteria genetically engineered for increased auxin synthesis.	2007	17488509
identification of bacteria on the surface of clinically infected and non-infected prosthetic hip joints removed during revision arthroplasties by 16s rrna gene sequencing and by microbiological culture.	it has been postulated that bacteria attached to the surface of prosthetic hip joints can cause localised inflammation, resulting in failure of the replacement joint. however, diagnosis of infection is difficult with traditional microbiological culture methods, and evidence exists that highly fastidious or non-cultivable organisms have a role in implant infections. the purpose of this study was to use culture and culture-independent methods to detect the bacteria present on the surface of prosth ...	2007	17501992
functional characterization of the sinorhizobium meliloti acetate metabolism genes acea, smc00767, and glcb.	the genes encoding malate synthase (glcb) and isocitrate lyase (acea) and a 240-bp open reading frame (smc00767) located downstream of acea were isolated and functionally characterized in sinorhizobium meliloti. independent and double interposon mutants of each gene were constructed, and the corresponding phenotypes were analyzed. acea mutants failed to grow on acetate, and mutants deficient in smc00767 were also affected in acetate utilization. in contrast, mutants deficient in glcb grew on ace ...	2007	17526694
diversity and geographical distribution of rhizobia associated with lespedeza spp. in temperate and subtropical regions of china.	eighty-eight root-nodule isolates from lespedeza spp. grown in temperate and subtropical regions of china were characterized by a polyphasic approach. nine clusters were defined in numerical taxonomy and sds-page analysis of whole cell proteins. based upon further characterizations of amplified 16s rdna restriction analysis (ardra), pcr-based restriction fragment length polymorphism of ribosomal igs, 16s rdna sequence analysis and dna-dna hybridization, these isolates were identified as bradyrhi ...	2007	17530227
genetic diversity of rhizobia associated with acacia longifolia in two stages of invasion of coastal sand dunes.	we examined the genetic diversity of root nodule bacteria associated with the australian legume acacia longifolia in two stages of invasion of a coastal sand dune system. all isolates belonged to the genus bradyrhizobium. a higher diversity was found in the long-established trees. the results suggest the introduction of exotic bradyrhizobia with the plant.	2007	17545318
agrobacterium tumefaciens fur has important physiological roles in iron and manganese homeostasis, the oxidative stress response, and full virulence.	in agrobacterium tumefaciens, the balance between acquiring enough iron and avoiding iron-induced toxicity is regulated in part by fur (ferric uptake regulator). a fur mutant was constructed to address the physiological role of the regulator. atypically, the mutant did not show alterations in the levels of siderophore biosynthesis and the expression of iron transport genes. however, the fur mutant was more sensitive than the wild type to an iron chelator, 2,2'-dipyridyl, and was also more resist ...	2007	17545320
medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress.	drought is one of the environmental factors most affecting crop production. under drought, symbiotic nitrogen fixation is one of the physiological processes to first show stress responses in nodulated legumes. this inhibition process involves a number of factors whose interactions are not yet understood. this work aims to further understand changes occurring in nodules under drought stress from a proteomic perspective. drought was imposed on medicago truncatula 'jemalong a17' plants grown in sym ...	2007	17545507
structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins.	the binding of a cofactor to a protein matrix often involves a reorganization of the polypeptide structure. b hemoproteins provide multiple examples of this behavior. in this minireview, selected monomeric and single b heme proteins endowed with distinct topological properties are inspected for the extent of induced refolding upon heme binding. to complement the data reported in the literature, original results are presented on a two-on-two globin of cyanobacterial origin (synechococcus sp. pcc ...	2007	17550789
auxin influx activity is associated with frankia infection during actinorhizal nodule formation in casuarina glauca.	plants from the casuarinaceae family enter symbiosis with the actinomycete frankia leading to the formation of nitrogen-fixing root nodules. we observed that application of the auxin influx inhibitor 1-naphtoxyacetic acid perturbs actinorhizal nodule formation. this suggests a potential role for auxin influx carriers in the infection process. we therefore isolated and characterized homologs of the auxin influx carrier (aux1-lax) genes in casuarina glauca. two members of this family were found to ...	2007	17556507
involvement of a soybean atp-binding cassette-type transporter in the secretion of genistein, a signal flavonoid in legume-rhizobium symbiosis.	legume plants have an ability to fix atmospheric nitrogen into nutrients via symbiosis with soil microbes. as the initial event of the symbiosis, legume plants secrete flavonoids into the rhizosphere to attract rhizobia. secretion of flavonoids is indispensable for the establishment of symbiotic nitrogen fixation, but almost nothing is known about the membrane transport mechanism of flavonoid secretion from legume root cells. in this study, we performed biochemical analyses to characterize the t ...	2007	17556512
nutrient sharing between symbionts.		2007	17556524
genomes of the symbiotic nitrogen-fixing bacteria of legumes.		2007	17556525
dominant role of the cbb3 oxidase in regulation of photosynthesis gene expression through the prrba system in rhodobacter sphaeroides 2.4.1.	in this study, the h303a mutant form of the cbb(3) oxidase (h303a oxidase), which has the h303a mutation in its catalytic subunit (ccon), was purified from rhodobacter sphaeroides. the h303a oxidase showed the same catalytic activity as did the wild-type form of the oxidase (wt oxidase). the heme contents of the mutant and wt forms of the cbb(3) oxidase were also comparable. however, the puf and puc operons, which are under the control of the prrba two-component system, were shown to be derepres ...	2007	17557830
putative porin of bradyrhizobium sp. (lupinus) bacteroids induced by glyphosate.	application of glyphosate (n-[phosphonomethyl] glycine) to bradyrhizobium sp. (lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. the most significant change was the presence of a 44-kda polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mm). the polypeptide has been characterized by the amino acid sequencing of its n terminus and the isolation and nucleic acid sequencing of its encoding gene. it is putativ ...	2007	17557843
sinorhizobium meliloti fur-like (mur) protein binds a fur box-like sequence present in the mnta promoter in a manganese-responsive manner.	in sinorhizobium meliloti, the mur(sm) protein, a homologue of the ferric uptake regulator (fur), mediates manganese-dependent regulation of the mntabcd manganese uptake system. in this study, we analyzed mur(sm) binding to the promoter region of the s. meliloti mnta gene. we demonstrated that mur(sm) protein binds with high affinity to the promoter region of mnta gene in a manganese-responsive manner. moreover, the results presented here indicate that two monomers, or one dimer, of mur(sm) bind ...	2007	17557847
a semi-quantitative gelc-ms analysis of temporal proteome expression in the emerging nosocomial pathogen ochrobactrum anthropi.	the alpha-proteobacteria are capable of interaction with eukaryotic cells, with some members, such as ochrobactrum anthropi, capable of acting as human pathogens. o. anthropi has been the cause of a growing number of hospital-acquired infections; however, little is known about its growth, physiology and metabolism. we used proteomics to investigate how protein expression of this organism changes with time during growth.	2007	17567905
dissection of the bradyrhizobium japonicum nifa+sigma54 regulon, and identification of a ferredoxin gene (fdxn) for symbiotic nitrogen fixation.	hierarchically organized regulatory proteins form a complex network for expression control of symbiotic and accessory genes in the nitrogen-fixing soybean symbiont bradyrhizobium japonicum. a genome-wide survey of regulatory interactions was made possible with the design of a custom-made gene chip. here, we report the first use of the microarray in a comprehensive and complete characterization of the b. japonicum nifa+sigma(54) regulon which forms an important node in the entire network. compara ...	2007	17569992
transcriptional regulation of the heme binding protein gene family of bartonella quintana is accomplished by a novel promoter element and iron response regulator.	we previously identified a five-member family of hemin-binding proteins (hbp's) of bartonella quintana that bind hemin on the outer surface but share no homology with known bacterial heme receptors. subsequently, we demonstrated that expression of the hbp family is significantly influenced by oxygen, heme, and temperature conditions encountered by the pathogen in the human host and the body louse vector; e.g., we observed a dramatic (>100-fold) increase in hbpc transcript levels in response to t ...	2007	17576755
responses of pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration.	pseudomonas aeruginosa in the lungs of cystic fibrosis patients grows to high densities in mucopurulent material that is depleted in oxygen. some have concluded that growth in these circumstances is dependent on anaerobic nitrate respiration. here we present data in favour of the alternative hypothesis that microaerobic respiration is the predominant mode of p. aeruginosa growth in the cystic fibrosis lung. we found that p. aeruginosa strain pao1 and a mucoid derivative of strain pao1 each grew ...	2007	17581126
mptpb, a virulence factor from mycobacterium tuberculosis, exhibits triple-specificity phosphatase activity.	bacterial pathogens have developed sophisticated mechanisms of evading the immune system to survive in infected host cells. central to the pathogenesis of mycobacterium tuberculosis is the arrest of phagosome maturation, partly through interference with ptdins signalling. the protein phosphatase mptpb is an essential secreted virulence factor in m. tuberculosis. a combination of bioinformatics analysis, enzyme kinetics and substrate-specificity characterization revealed that mptpb exhibits both ...	2007	17584180
a large gene cluster in burkholderia xenovorans encoding abietane diterpenoid catabolism.	abietane diterpenoids are defense compounds synthesized by trees that are abundant in natural environments and occur as significant pollutants from pulp and paper production. burkholderia xenovorans lb400 has diverse catabolic capabilities and represents an important group of heterotrophic bacteria in soil environments. the genome sequence of lb400 revealed homologs of the dit genes of pseudomonas abietaniphila bkme-9, which encode abietane diterpenoid degradation. lb400 grew on abietic acid (ab ...	2007	17586638
dost and devs are oxygen-switched kinases in mycobacterium tuberculosis.	exposure of mycobacterium tuberculosis to hypoxia is known to alter the expression of many genes, including ones thought to be involved in latency, via the transcription factor devr (also called dosr). two sensory kinases, dost and devs (also called doss), control the activity of devr. we show that, like devs, dost contains a heme cofactor within an n-terminal gaf domain. for full-length dost and devs, we determined the ligand-binding parameters and the rates of atp reaction with the liganded an ...	2007	17600145
promoters of orthologous glycine max and lotus japonicus nodulation autoregulation genes interchangeably drive phloem-specific expression in transgenic plants.	the nodule autoregulation receptor kinase (gmnark) of soybean (glycine max) is essential for the systemic autoregulation of nodulation. based on quantitative reverse-transcriptase polymerase chain reaction, gmnark is ex-pressed to varying levels throughout the plant; the transcript was detected at high levels in mature leaves and roots but to a lesser extent in young leaves, shoot tips, and nodules. the transcript level was not significantly affected by bradyrhizobium japonicum during the first ...	2007	17601165
bacterial cyclic beta-(1,2)-glucan acts in systemic suppression of plant immune responses.	although cyclic glucans have been shown to be important for a number of symbiotic and pathogenic bacterium-plant interactions, their precise roles are unclear. here, we examined the role of cyclic beta-(1,2)-glucan in the virulence of the black rot pathogen xanthomonas campestris pv campestris (xcc). disruption of the xcc nodule development b (ndvb) gene, which encodes a glycosyltransferase required for cyclic glucan synthesis, generated a mutant that failed to synthesize extracellular cyclic be ...	2007	17601826
control of degp-dependent degradation of c-type cytochromes by heme and the cytochrome c maturation system in escherichia coli.	c-type cytochromes are located partially or completely in the periplasm of gram-negative bacteria, and the heme prosthetic group is covalently bound to the protein. the cytochrome c maturation (ccm) multiprotein system is required for transport of heme to the periplasm and its covalent linkage to the peptide. other cytochromes and hemoglobins contain a noncovalently bound heme and do not require accessory proteins for assembly. here we show that bradyrhizobium japonicum cytochrome c550 polypepti ...	2007	17616605
novel alphaproteobacterial root nodule symbiont associated with lupinus texensis.	phylogenetic analysis of rrna gene, reca, noda, nifd, and nifh sequences suggested that nitrogen-fixing symbionts from two populations of lupinus texensis acquired the capacity for nodule symbiosis separately from other rhizobia in the alphaproteobacteria. their closest 16s rrna relatives were the nonsymbiotic taxa chelatococcus, bosea, and balneomonas.	2007	17616612
[efficacy of biological preparations of soybean root nodule bacteria modified with a homologous lectin].	the effect of various biopreparations of the root nodule bacterium bradyrhizobium japonicum, modified with a homologous lectin, on the virulence of rhizobia, the nitrogen-fixing activity of root nodules, and the productivity of the soybean (glycine max (l.) merr.) was studied. it was shown that a homologous lectin, added to a bacterial suspension when manufacturing biopreparations on a liquid and solid support, increases the efficiency of the soybean symbiotic system and the productivity of the ...	2007	17619577
human endonuclease viii-like (neil) proteins in the giant dna mimivirus.	endonuclease viii (nei), which recognizes and repairs oxidized pyrimidines in the base excision repair (ber) pathway, is sparsely distributed among both the prokaryotes and eukaryotes. recently, we and others identified three homologs of escherichia coli endonuclease viii-like (neil) proteins in humans. here, we report identification of human neil homologs in mimivirus, a giant dna virus that infects acanthamoeba. characterization of the two mimiviral homologs, mvnei1 and mvnei2, showed that the ...	2007	17627905
how rhizobial symbionts invade plants: the sinorhizobium-medicago model.	nitrogen-fixing rhizobial bacteria and leguminous plants have evolved complex signal exchange mechanisms that allow a specific bacterial species to induce its host plant to form invasion structures through which the bacteria can enter the plant root. once the bacteria have been endocytosed within a host-membrane-bound compartment by root cells, the bacteria differentiate into a new form that can convert atmospheric nitrogen into ammonia. bacterial differentiation and nitrogen fixation are depend ...	2007	17632573
comparative genomic reconstruction of transcriptional regulatory networks in bacteria.		2007	17636889
origins of flagellar gene operons and secondary flagellar systems.	forty-one flagellated species representing 11 bacterial phyla were used to investigate the origin of secondary flagellar systems and the structure and formation of flagellar gene operons over the course of bacterial evolution. secondary (i.e., lateral) flagellar systems, which are harbored by five of the proteobacterial species considered, originated twice, once in the alphaproteobacterial lineage and again in the common ancestor of the beta- and gammaproteobacteria. the order and organization o ...	2007	17644605
transcriptional and physiological responses of bradyrhizobium japonicum to desiccation-induced stress.	the growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. in this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of bradyrhizobium japonicum to drought. desiccation of cells resulted in the differential expression of 15 to 20% of the 8,453 [corrected] b. japonicum open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed ...	2007	17660288
region 2.1 of the escherichia coli heat-shock sigma factor rpoh (sigma32) is necessary but not sufficient for degradation by the ftsh protease.	the cellular level of the escherichia coli heat-shock sigma factor rpoh (sigma32) is negatively controlled by chaperone-mediated proteolysis through the essential metalloprotease ftsh. point mutations in the highly conserved region 2.1 stabilize rpoh in vivo. to assess the importance of this turnover element, hybrid proteins were constructed between e. coli rpoh and bradyrhizobium japonicum rpoh1, a stable rpoh protein that differs from region 2.1 of e. coli rpoh at several positions. nine amino ...	2007	17660420
identification of genes encoding trna modification enzymes by comparative genomics.	as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ...	2007	17673083
rasta-bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes.	toxin/antitoxin (ta) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. we present rasta-bacteria, an automated method allowing quick and reliable identification of ta loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. the tool successfully confirmed all reported ta systems, and spotted new putative loci upon screening of sequenced genomes. rasta-bacteria i ...	2007	17678530
homologous cpn60 genes in rhizobium leguminosarum are not functionally equivalent.	many bacteria possess 2 or more genes for the chaperonin groel and the cochaperonin groes. in particular, rhizobial species often have multiple groel and groes genes, with a high degree of amino-acid similarity, in their genomes. the rhizobium leguminosarum strain a34 has 3 complete groe operons, which we have named cpn.1, cpn.2 and cpn.3. previously we have shown the cpn. 1 operon to be essential for growth, but the two other cpn operons to be dispensable. here, we have investigated the extent ...	2007	17688191
lysm domains mediate lipochitin-oligosaccharide recognition and nfr genes extend the symbiotic host range.	legume-rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. we show here that expression of lotus japonicus nfr1 and nfr5 nod-factor receptor genes in medicago truncatula and l. filicaulis, extends their host range to include bacterial strains, mesorhizobium loti or dzl, normally infecting l. japonicus. as a result, th ...	2007	17690687
the glycine max xylem sap and apoplast proteome.	molecular signaling interactions in the plant apoplast are important for defense and developmental responses. we examined the soybean proteome of the apoplastic conduit of root-to-shoot communication, the xylem stream, using gel electrophoresis combined with two types of tandem mass spectrometry. we examined soybeans for the presence of a bradyrhizobium japonicum-induced, long distance developmental signal that controls autoregulation of nodulation (aon) to determine if xylem proteins (xps) were ...	2007	17696379
human wild-type alanine:glyoxylate aminotransferase and its naturally occurring g82e variant: functional properties and physiological implications.	human hepatic peroxisomal agt (alanine:glyoxylate aminotransferase) is a plp (pyridoxal 5'-phosphate)-dependent enzyme whose deficiency causes primary hyperoxaluria type i, a rare autosomal recessive disorder. to acquire experimental evidence for the physiological function of agt, the k(eq),(overall) of the reaction, the steady-state kinetic parameters of the forward and reverse reactions, and the pre-steady-state kinetics of the half-reactions of the plp form of agt with l-alanine or glycine an ...	2007	17696873
brucella abortus requires the heme transporter bhua for maintenance of chronic infection in balb/c mice.	the gene annotated bab2_1150 in the brucella abortus 2308 genome sequence is predicted to encode a homolog of the well-characterized heme transporter shua of shigella dysenteriae and accordingly has been given the designation bhua (brucella heme utilization). phenotypic analysis of an isogenic bhua mutant derived from b. abortus 2308 verified that there is a link between bhua and the ability of the parent strain to use heme as an iron source in in vitro assays. maximum expression of bhua in b. a ...	2007	17709407
selection against spurious promoter motifs correlates with translational efficiency across bacteria.	because binding of rnap to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of dna motifs capable of rnap-binding across the genome. here we analyze the distribution of the -10 promoter motifs that bind the sigma(70) subunit of rnap in 42 bacterial genomes. we show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequ ...	2007	17710145
reduced carbon availability to bacteroids and elevated ureides in nodules, but not in shoots, are involved in the nitrogen fixation response to early drought in soybean.	nitrogen fixation (nf) in soybean (glycine max l. merr.) is highly sensitive to soil drying. this sensitivity has been related to an accumulation of nitrogen compounds, either in shoots or in nodules, and a nodular carbon flux shortage under drought. to assess the relative importance of carbon and nitrogen status on nf regulation, the responses to the early stages of drought were monitored with two soybean cultivars with known contrasting tolerance to drought. in the sensitive cultivar ('biloxi' ...	2007	17720761
genome analysis of minibacterium massiliensis highlights the convergent evolution of water-living bacteria.	filtration usually eliminates water-living bacteria. here, we report on the complete genome sequence of minibacterium massiliensis, a beta-proteobacteria that was recovered from 0.22-mum filtered water used for patients in the hospital. the unexpectedly large 4,110,251-nucleotide genome sequence of m. massiliensis was determined using the traditional shotgun sequencing approach. bioinformatic analyses shows that the m. massiliensis genome sequence illustrates characteristic features of water-liv ...	2007	17722982
mutant strains of rhizobium japonicum with increased ability to fix nitrogen for soybean.	a strain of rhizobium japonicum used in commercial inoculants was mutagenized and screened by a rapid effectiveness assay with soybean plants. two mutant strains nodulated the roots earlier than the wild type and also expressed greater symbiotic nitrogen-fixing activity than the wild type in the presence and absence of fixed nitrogen. in addition, one of the mutants formed more root nodules than the wild type. plants inoculated with these strains had increased dry weights ( approximately 60 perc ...	1978	17729899
soybean lines lacking the 120,000-dalton seed lectin.	seeds of 102 lines of glycine max (l.) merr., the soybean, were screened quantitatively for the presence of the 120,000-dalton soybean lectin. wide variation in the content of this lectin was noted, and five lines of soybean whose seed totally lacked the lectin were identified. roots of all five lines were effectively nodulated by several strains of rhizobium japonicum, thus indicating that the 120,000-dalton soybean seed lectin is probably not required for the initiation of soybean-rhizobium sy ...	1978	17738723
a nodule-specific plant protein (nodulin-35) from soybean.	nodulin-35, a 35,000-molecular-weight protein, is present in soybean root nodules developed by different strains of rhizobium japonicum, irrespective of their effectiveness in fixing atmospheric nitrogen. this protein is not detected in uninfected plants and bacteroids or in free-living rhizobium and appears to be synthesized by the plant during the formation of root nodules.	1979	17750321
mutants of rhizobium japonicum with increased hydrogenase activity.	some strains of rhizobium japonicum can use hydrogen as an energy source for growth under microaerophilic conditions. mutant strains have been selected that use hydrogen in the presence of high partial pressures of oxygen. the mutants contain more hydrogenase than the parent strain, both as free-living cells and as bacteroids in nitrogen-fixing soybean root nodules.	1983	17754553
structural basis for light-dependent signaling in the dimeric lov domain of the photosensor ytva.	the photosensor ytva binds flavin mononucleotide and regulates the general stress reaction in bacillus subtilis in response to blue light illumination. it belongs to the family of light-oxygen-voltage (lov) proteins that were first described in plant phototropins and form a subgroup of the per-arnt-sim (pas) superfamily. here, we report the three-dimensional structure of the lov domain of ytva in its dark and light states. the protein assumes the global fold common to all pas domains and dimeriz ...	2007	17764689
impact of plant functional group, plant species, and sampling time on the composition of nirk-type denitrifier communities in soil.	we studied the influence of eight nonleguminous grassland plant species belonging to two functional groups (grasses and forbs) on the composition of soil denitrifier communities in experimental microcosms over two consecutive years. denitrifier community composition was analyzed by terminal restriction fragment length polymorphism (t-rflp) of pcr-amplified nirk gene fragments coding for the copper-containing nitrite reductase. the impact of experimental factors (plant functional group, plant spe ...	2007	17766442
evidence for an inter-organismic heme biosynthetic pathway in symbiotic soybean root nodules.	the successful symbiosis of soybean with bradyrhizobium japonicum depends on their complex interactions, culminating in the development and maintenance of root nodules. a b. japonicum mutant defective in heme synthesis in culture was able to produce heme as a result of its symbiotic association with the soybean host. the bacterial mutant was incapable of synthesizing the committed heme precursor delta-aminolevulinic acid (ala), but nodule plant cells formed ala from glutamate. in addition, exoge ...	1991	17799282