Publications

isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants.	the goal of this study was to initiate investigation of the genetics of bacterial poly-3-hydroxybutyrate (phb) metabolism at the community level. we constructed metagenome libraries from activated sludge and soil microbial communities in the broad-host-range incp cosmid prk7813. several unique clones were isolated from these libraries by functional heterologous complementation of a sinorhizobium meliloti bdha mutant, which is unable to grow on the phb cycle intermediate d-3-hydroxybutyrate due t ...	2006	16391068
fosfomycin resistance proteins: a nexus of glutathione transferases and epoxide hydrolases in a metalloenzyme superfamily.	three similar but mechanistically distinct fosfomycin resistance proteins that catalyze the opening of the oxirane ring of the antibiotic are known. fosa is a mn(ii) and k(+)-dependent glutathione transferase. fosb is a mg(2+)-dependent l-cysteine thiol transferase. fosx is a mn(ii)-dependent fosfomycin-specific epoxide hydrolase. the expression, purification, kinetic, and physical characteristics of six fosfomycin resistance proteins including the fosa proteins from transposon tn2921 and pseudo ...	2005	16399398
mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an indian tropical leguminous plant.	the bacterial strain sjt(t), along with 15 other mesophilic, neutrophilic and facultatively sulfur-oxidizing chemolithotrophic isolates, was isolated by enrichment on reduced sulfur compounds as the sole energy and electron source from soils immediately adjacent to the roots of clitoria ternatea, a slender leguminous herb of the lower gangetic plains of india. strain sjt(t) was able to oxidize thiosulfate and elemental sulfur for chemolithoautotrophic growth. 16s rrna and reca gene sequence-base ...	2006	16403872
a nucleoporin is required for induction of ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis.	nuclear-cytoplasmic partitioning and traffic between cytoplasmic and nuclear compartments are fundamental processes in eukaryotic cells. nuclear pore complexes mediate transport of proteins, rnas and ribonucleoprotein particles in and out of the nucleus. here we present positional cloning of a plant nucleoporin gene, nup133, essential for a symbiotic signal transduction pathway shared by rhizobium bacteria and mycorrhizal fungi. mutation of nup133 results in a temperature sensitive nodulation de ...	2006	16407163
identification of a ubiquinone-binding site that affects autophosphorylation of the sensor kinase regb.	rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. one of the key global redox regulators of the cell's metabolic physiology is the sensor kinase regb that controls the synthesis of numerous energy generation and utilization processes. in this study, we have succeeded in purifying full-length regb containing six transmembrane-spanning elements. exogenous addition of excess oxidized coenzyme q1 is capable of ...	2006	16407278
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.	recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...	2006	16407325
the epidermis-specific extracellular bodyguard controls cuticle development and morphogenesis in arabidopsis.	the outermost epidermal cell wall is specialized to withstand pathogens and natural stresses, and lipid-based cuticular polymers are the major barrier against incursions. the arabidopsis thaliana mutant bodyguard (bdg), which exhibits defects characteristic of the loss of cuticle structure not attributable to a lack of typical cutin monomers, unexpectedly accumulates significantly more cell wall-bound lipids and epicuticular waxes than wild-type plants. pleiotropic effects of the bdg mutation on ...	2006	16415209
identification and characterization of rbma, a novel protein required for the development of rugose colony morphology and biofilm structure in vibrio cholerae.	phase variation between smooth and rugose colony variants of vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. the rugose variant forms corrugated colonies, exhibits increased levels of resistance to osmotic, acid, and oxidative stresses, and has an enhanced capacity to form biofilms. many of these phenotypes are mediated in part by increased production of an exopolysaccharide termed vps. in this study, we compared total protein profiles ...	2006	16428409
regulation and properties of pstscab, a high-affinity, high-velocity phosphate transport system of sinorhizobium meliloti.	the properties and regulation of the pstscab-encoded pi uptake system from the alfalfa symbiont sinorhizobium meliloti are reported. we present evidence that the pstscab genes and the regulatory phoub genes are transcribed from a single promoter that contains two phob binding sites and that transcription requires phob. s. meliloti strain 1021 (rm1021) and its derivatives were found to carry a c deletion frameshift mutation in the pstc gene (designated pstc1021) that severely impairs activity of ...	2006	16428413
blast screening of chlamydial genomes to identify signature proteins that are unique for the chlamydiales, chlamydiaceae, chlamydophila and chlamydia groups of species.	chlamydiae species are of much importance from a clinical viewpoint. their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. the obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. thus, it is of importance to develop additional means for their identification and characterization.	2006	16436211
tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses.	most land plants can form a root symbiosis with arbuscular mycorrhizal (am) fungi for assimilation of inorganic phosphate from the soil. in contrast, the nitrogen-fixing root nodule symbiosis is almost completely restricted to the legumes. the finding that the two symbioses share common signaling components in legumes suggests that the evolutionarily younger nitrogen-fixing symbiosis has recruited functions from the more ancient am symbiosis. the recent advances in cloning of the genes required ...	2006	16452143
the genome of the novel phage rtp, with a rosette-like tail tip, is homologous to the genome of phage t1.	a new escherichia coli phage, named rtp, was isolated and shown to be closely related to phage t1. electron microscopy revealed that phage rtp has a morphologically unique tail tip consisting of four leaf-like structures arranged in a rosette, whereas phage t1 has thinner, flexible leaves that thicken toward the ends. in contrast to t1, rtp did not require fhua and tonb for infection. the 46.2-kb genome of phage rtp encodes 75 open reading frames, 47 of which are homologous to phage t1 genes. li ...	2006	16452425
characterization of an agrobacterium tumefaciens d-psicose 3-epimerase that converts d-fructose to d-psicose.	the noncharacterized gene previously proposed as the d-tagatose 3-epimerase gene from agrobacterium tumefaciens was cloned and expressed in escherichia coli. the expressed enzyme was purified by three-step chromatography with a final specific activity of 8.89 u/mg. the molecular mass of the purified protein was estimated to be 132 kda of four identical subunits. mn2+ significantly increased the epimerization rate from d-fructose to d-psicose. the enzyme exhibited maximal activity at 50 degrees c ...	2006	16461638
catabolism of 1,5-anhydro-d-fructose in sinorhizobium morelense s-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-d-fructose reductase and its application in sugar analysis and rare sugar synthesis.	the bacterium sinorhizobium morelense s-30.7.5 was isolated by a microbial screening using the sugar 1,5-anhydro-d-fructose (af) as the sole carbon source. this strain metabolized af by a novel pathway involving its reduction to 1,5-anhydro-d-mannitol (am) and the further conversion of am to d-mannose by c-1 oxygenation. growth studies showed that the af metabolizing capability is not confined to s. morelense s-30.7.5 but is a more common feature among the rhizobiaceae. the af reducing enzyme wa ...	2006	16461673
tfam detects co-evolution of trna identity rules with lateral transfer of histidyl-trna synthetase.	we present tfam, an automated, statistical method to classify the identity of trnas. tfam, currently optimized for bacteria, classifies initiator trnas and predicts the charging identity of both typical and atypical trnas such as suppressors with high confidence. we show statistical evidence for extensive variation in trna identity determinants among bacterial genomes due to variation in overall tdna base content. with tfam we have detected the first case of eukaryotic-like trna identity rules i ...	2006	16473847
rhizobial exopolysaccharides: genetic control and symbiotic functions.	specific complex interactions between soil bacteria belonging to rhizobium, sinorhizobium, mesorhizobium, phylorhizobium, bradyrhizobium and azorhizobium commonly known as rhizobia, and their host leguminous plants result in development of root nodules. nodules are new organs that consist mainly of plant cells infected with bacteroids that provide the host plant with fixed nitrogen. proper nodule development requires the synthesis and perception of signal molecules such as lipochitooligosacchari ...	2006	16483356
a luxr/luxi-type quorum-sensing system in a plant bacterium, mesorhizobium tianshanense, controls symbiotic nodulation.	the ability of rhizobia to symbiotically fix nitrogen from the atmosphere when forming nodules on their plant hosts requires various signal transduction pathways. luxr-luxi-type quorum-sensing systems have been shown to be one of the players in a number of rhizobium species. in this study, we found that mesorhizobium tianshanense, a moderate-growth rhizobium that forms nodules on a number of licorice plants, produces multiple n-acyl homoserine lactone (ahl)-like molecules. a simple screen for ah ...	2006	16484206
the clc element of pseudomonas sp. strain b13, a genomic island with various catabolic properties.	pseudomonas sp. strain b13 is a bacterium known to degrade chloroaromatic compounds. the properties to use 3- and 4-chlorocatechol are determined by a self-transferable dna element, the clc element, which normally resides at two locations in the cell's chromosome. here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known cata ...	2006	16484212
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
aminoacyl-transferases and the n-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen.	the n-end rule relates the in vivo half-life of a protein to the identity of its n-terminal residue. primary destabilizing n-terminal residues (nd(p)) are recognized directly by the targeting machinery. the recognition of secondary destabilizing n-terminal residues (nd(s)) is preceded by conjugation of an nd(p) residue to nd(s) of a polypeptide substrate. in eukaryotes, ate1-encoded arginyl-transferases (r(d,e,c*)-transferases) conjugate arg (r), an nd(p) residue, to nd(s) residues asp (d), glu ...	2006	16492767
structure of mesorhizobium loti arylamine n-acetyltransferase 1.	the arylamine n-acetyltransferase (nat) enzymes have been found in a broad range of both eukaryotic and prokaryotic organisms. the nat enzymes catalyse the transfer of an acetyl group from acetyl co-enzyme a onto the terminal nitrogen of a range of arylamine, hydrazine and arylhydrazine compounds. recently, several nat structures have been reported from different prokaryotic sources including salmonella typhimurium, mycobacterium smegmatis and pseudomonas aeruginosa. bioinformatics analysis of t ...	2005	16508079
structure of mesorhizobium loti arylamine n-acetyltransferase 1.	the arylamine n-acetyltransferase (nat) enzymes have been found in a broad range of both eukaryotic and prokaryotic organisms. the nat enzymes catalyse the transfer of an acetyl group from acetyl co-enzyme a onto the terminal nitrogen of a range of arylamine, hydrazine and arylhydrazine compounds. recently, several nat structures have been reported from different prokaryotic sources including salmonella typhimurium, mycobacterium smegmatis and pseudomonas aeruginosa. bioinformatics analysis of t ...	2005	16508079
crystallization and preliminary x-ray crystallographic analysis of 2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase from pseudomonas sp. ma-1.	2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase (mhpco) catalyzes the conversion of an aromatic substrate, mhpc, to an aliphatic compound, alpha-(n-acetylaminomethylene)-succinic acid, and is involved in the degradation of vitamin b6 by the soil bacterium pseudomonas sp. ma-1. using only fad as a cofactor, mhpco is unique in catalyzing hydroxylation and subsequent aromatic ring cleavage without requiring a metal-ion cofactor. here, the crystallization of mhpco is reported together ...	2005	16511028
a putative polyketide-synthesis protein xc5357 from xanthomonas campestris: heterologous expression, crystallization and preliminary x-ray analysis.	xanthomonas campestris pv. campestris (xcc) is a gram-negative yellow-pigmented bacterium and is the causative agent of black rot, one of the major worldwide diseases of cruciferous crops. it also synthesizes a variety of polyketide metabolites that lead to important antibiotics. xc5357 is a putative 12.2 kda protein of unknown structure from xcc that is likely to be essential for polyketide synthesis. it was overexpressed in escherichia coli, purified and crystallized using the hanging-drop vap ...	2005	16511132
insight into the structure of mesorhizobium loti arylamine n-acetyltransferase 2 (mlnat2): a biochemical and computational study.	the arylamine n-acetyltransferases (nat; ec 2.3.1.5) are xenobiotic-metabolizing enzymes (xme) that catalyze the transfer of an acetyl group from acetylcoa (ac-coa) to arylamine, hydrazines and their n-hydroxylated metabolites. eukaryotes may have up to three nat isoforms, but mesorhizobium loti is the only prokaryote with two functional nat isoforms (mlnat1 and mlnat2). the three-dimensional structure of mlnat1 has been determined (holton, s.j., dairou, j., sandy, j., rodrigues-lima, f., dupret ...	2006	16513121
the pea nodule environment restores the ability of a rhizobium leguminosarum lipopolysaccharide acpxl mutant to add 27-hydroxyoctacosanoic acid to its lipid a.	members of the rhizobiaceae contain 27-hydroxyoctacosanoic acid (27ohc(28:0)) in their lipid a. a rhizobium leguminosarum 3841 acpxl mutant (named here rlv22) lacking a functional specialized acyl carrier lacked 27ohc(28:0) in its lipid a, had altered growth and physiological properties (e.g., it was unable to grow in the presence of an elevated salt concentration [0.5% nacl]), and formed irregularly shaped bacteroids, and the synchronous division of this mutant and the host plant-derived symbio ...	2006	16513742
motd of sinorhizobium meliloti and related alpha-proteobacteria is the flagellar-hook-length regulator and therefore reassigned as flik.	the flagella of the soil bacterium sinorhizobium meliloti differ from the enterobacterial paradigm in the complex filament structure and modulation of the flagellar rotary speed. the mode of motility control in s. meliloti has a molecular corollary in two novel periplasmic motility proteins, motc and mote, that are present in addition to the ubiquitous mota/motb energizing proton channel. a fifth motility gene is located in the mot operon downstream of the motb and motc genes. its gene product w ...	2006	16513744
genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium nitrobacter winogradskyi nb-255.	the alphaproteobacterium nitrobacter winogradskyi (atcc 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. there were extensive similarities to genes in two alphaproteobacteria, bradyrhizobium japonicum usda110 (1,300 genes) and rhodopseudomonas palustris cga009 cg (815 genes). genes encoding p ...	2006	16517654
transformation of rhizobia with broad-host-range plasmids by using a freeze-thaw method.	several species of rhizobia were successfully transformed with broad-host-range plasmids of different replicons by using a modified freeze-thaw method. a generic binary vector (ppzp211) was maintained in mesorhizobium loti without selection and stably inherited during nodulation. the method could extend the potential of rhizobia as a vehicle for plant transformation.	2006	16517691
making ends meet: repairing breaks in bacterial dna by non-homologous end-joining.	dna double-strand breaks (dsbs) are one of the most dangerous forms of dna lesion that can result in genomic instability and cell death. therefore cells have developed elaborate dsb-repair pathways to maintain the integrity of genomic dna. there are two major pathways for the repair of dsbs in eukaryotes: homologous recombination and non-homologous end-joining (nhej). until very recently, the nhej pathway had been thought to be restricted to the eukarya. however, an evolutionarily related nhej a ...	2006	16518468
the rhizobium etli sigma70 (siga) factor recognizes a lax consensus promoter.	a collection of rhizobium etli promoters was isolated from a genomic dna library constructed in the promoter-trap vector pbbmcs53, by their ability to drive the expression of a gusa reporter gene. thirty-seven clones were selected, and their transcriptional start-sites were determined. the upstream sequence of these 37 start-sites, and the sequences of seven previously identified promoters were compared. on the basis of sequence conservation and mutational analysis, a consensus sequence cttgacn1 ...	2006	16528104
paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms.	while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ...	2006	16529662
characterization of a periplasmic s1-like nuclease coded by the mesorhizobium loti symbiosis island.	dna sequences encoding hypothetical proteins homologous to s1 nuclease from aspergillus oryzae are found in many organisms including fungi, plants, pathogenic bacteria, and eukaryotic parasites. one of these is the m1 nuclease of mesorhizobium loti which we demonstrate herein to be an enzymatically active, soluble, and stable s1 homolog that lacks the extensive mannosyl-glycosylation found in eukaryotic s1 nuclease homologs. we have expressed the cloned m1 protein in m. loti and purified recombi ...	2006	16529713
absence of substrate channeling between active sites in the agrobacterium tumefaciens ispdf and ispe enzymes of the methyl erythritol phosphate pathway.	the conversion of 2-c-methyl-d-erythritol 4-phosphate (mep) to 2-c-methyl-d-erythritol 2,4-cyclodiphosphate (cmedp) in the mep entry into the isoprenoid biosynthetic pathway occurs in three consecutive steps catalyzed by the ispd, ispe, and ispf enzymes, respectively. in agrobacterium tumefaciens the ispd and ispf genes are fused to encode a bifunctional enzyme that catalyzes the first (synthesis of 4-diphosphocytidyl-2-c-methyl d-erythritol) and third (synthesis of 2-c-methyl-d-erythritol 2,4-c ...	2006	16533036
score-based prediction of genomic islands in prokaryotic genomes using hidden markov models.	horizontal gene transfer (hgt) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. it is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes hgt from gene genesis, duplications or mutations. for a precise characterization, algorithms are needed that identify transfer events with high reliability. frequently, the transferred pieces of dna have a considerable length, comprise several gene ...	2006	16542435
molecular cloning, expression and characterization of pyridoxamine-pyruvate aminotransferase.	pyridoxamine-pyruvate aminotransferase is a plp (pyridoxal 5'-phosphate) (a coenzyme form of vitamin b6)-independent aminotransferase which catalyses a reversible transamination reaction between pyridoxamine and pyruvate to form pyridoxal and l-alanine. the gene encoding the enzyme has been identified, cloned and overexpressed for the first time. the mlr6806 gene on the chromosome of a symbiotic nitrogen-fixing bacterium, mesorhizobium loti, encoded the enzyme, which consists of 393 amino acid r ...	2006	16545075
role of murf in cell wall biosynthesis: isolation and characterization of a murf conditional mutant of staphylococcus aureus.	the staphylococcus aureus murf gene was placed under the control of a promoter inducible by iptg (isopropyl-beta-d-thiogalactopyranoside). it was demonstrated that murf is an essential gene; it is cotranscribed with ddla and growth rate, level of beta-lactam antibiotic resistance, and rates of transcription of the meca and pbpb genes paralleled the rates of transcription of murf. at suboptimal concentrations of the inducer, a udp-linked muramyl tripeptide accumulated in the cytoplasm in parallel ...	2006	16547042
eukaryotic control on bacterial cell cycle and differentiation in the rhizobium-legume symbiosis.	symbiosis between legumes and rhizobium bacteria leads to the formation of root nodules where bacteria in the infected plant cells are converted into nitrogen-fixing bacteroids. nodules with a persistent meristem are indeterminate, whereas nodules without meristem are determinate. the symbiotic plant cells in both nodule types are polyploid because of several cycles of endoreduplication (genome replication without mitosis and cytokinesis) and grow consequently to extreme sizes. here we demonstra ...	2006	16547129
brucella spp noncanonical lps: structure, biosynthesis, and interaction with host immune system.	brucella spp. are facultative intracellular pathogens that have the ability to survive and multiply in professional and non-professional phagocytes, and cause abortion in domestic animals and undulant fever in humans. several species are recognized within the genus brucella and this classification is mainly based on the difference in pathogenicity and in host preference. brucella strains may occur as either smooth or rough, expressing smooth lps (s-lps) or rough lps (r-lps) as major surface anti ...	2006	16556309
novel carbapenem-hydrolyzing oxacillinase oxa-62 from pandoraea pnomenusa.	pandoraea spp. are gram-negative, glucose nonfermenting rods detectable in blood cultures and sputa of cystic fibrosis patients. they are resistant to various antibiotic groups, with imipenem being the only active beta-lactam. we isolated an imipenem-resistant (mic, 64 microg/ml) pandoraea pnomenusa strain from a cystic fibrosis patient. cloning and sequencing identified two beta-lactamases of bush group 2d, namely, the known oxa-33, located on an integron, and the novel carbapenem-hydrolyzing o ...	2006	16569848
cloning, functional expression and characterization of mesorhizobium loti arylamine n-acetyltransferases: rhizobial symbiosis supplies leguminous plants with the xenobiotic n-acetylation pathway.	arylamine n-acetyltransferases (nats) are xenobiotic-metabolizing enzymes involved in the detoxification of numerous aromatic chemicals. the nat-dependent n-acetylation pathway has not previously been detected in plants. we demonstrate here the occurrence of the nat-dependent pathway in leguminous plants, due to symbiosis with mesorhizobium loti. we cloned two nat enzymes from m. loti and showed that these two recombinant enzymes catalysed the n-acetylation of several known nat substrates, inclu ...	2006	16573698
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
expression of a complete soybean leghemoglobin gene in root nodules of transgenic lotus corniculatus.	the complete soybean leghemoglobin lbc(3) gene was transferred into the legume lotus corniculatus using an agrobacterium rhizogenes vector system. organ-specific expression of the soybean gene was observed in root nodules formed on regenerated transgenic plants after infection with rhizobium loti. the primary transcript was processed in the same way as in soybean nodules and the resulting mrna was translated into lbc(3) protein. quantitative determination of the lbc(3) protein in nodules of tran ...	1987	16593870
update of the nad(p)h:quinone oxidoreductase (nqo) gene family.	the nad(p)h:quinone acceptor oxidoreductase (nqo) gene family belongs to the flavoprotein clan and, in the human genome, consists of two genes (nqo1 and nqo2). these two genes encode cytosolic flavoenzymes that catalyse the beneficial two-electron reduction of quinones to hydroquinones. this reaction prevents the unwanted one-electron reduction of quinones by other quinone reductases; one-electron reduction results in the formation of reactive oxygen species, generated by redox cycling of semiqu ...	2006	16595077
identification of sinorhizobium meliloti early symbiotic genes by use of a positive functional screen.	the soil bacterium sinorhizobium meliloti establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. the complexity of the changes of alfalfa root structures during symbiosis and the amount of s. meliloti genes with unknown functions raised the possibility that more s. meliloti genes may be required for early stages of the symbiosis. a positive functional screen of the entire s. meliloti genome for symbiotic genes was carried ...	2006	16597978
spontaneous root-nodule formation in the model legume lotus japonicus: a novel class of mutants nodulates in the absence of rhizobia.	root-nodule development in legumes is an inducible developmental process initially triggered by perception of lipochitin-oligosaccharide signals secreted by the bacterial microsymbiont. in nature, rhizobial colonization and invasion of the legume root is therefore a prerequisite for formation of nitrogen-fixing root nodules. here, we report isolation and characterization of chemically induced spontaneously nodulating mutants in a model legume amenable to molecular genetics. six mutant lines of l ...	2006	16610740
functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine a.	a 45 kb dna sequencing analysis from streptomyces hygroscopicus 5008 involved in validamycin a (val-a) biosynthesis revealed 16 structural genes, 2 regulatory genes, 5 genes related transport, transposition/integration or tellurium resistance; another 4 genes had no obvious identity. the val-a biosynthetic pathway was proposed, with assignment of the required genetic functions confined to the sequenced region. a cluster of eight reassembled genes was found to support val-a synthesis in a heterol ...	2006	16632251
the genome of rhizobium leguminosarum has recognizable core and accessory components.	rhizobium leguminosarum is an alpha-proteobacterial n2-fixing symbiont of legumes that has been the subject of more than a thousand publications. genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. we have sequenced the genome of r. leguminosarum biovar viciae strain 3841.	2006	16640791
genome of crocodilepox virus.	here, we present the genome sequence, with analysis, of a poxvirus infecting nile crocodiles (crocodylus niloticus) (crocodilepox virus; crv). the genome is 190,054 bp (62% g+c) and predicted to contain 173 genes encoding proteins of 53 to 1,941 amino acids. the central genomic region contains genes conserved and generally colinear with those of other chordopoxviruses (chpvs). crv is distinct, as the terminal 33-kbp (left) and 13-kbp (right) genomic regions are largely crv specific, containing 4 ...	2006	16641289
localized changes in flavonoid biosynthesis in roots of lotus pedunculatus after infection by rhizobium loti.	two-dimensional paper chromatography in four solvent systems, high-sensitivity spray reagents, and uv absorption spectroscopy were used to separate and characterize flavonoids and isoflavonoids in roots and root nodules of 20-d-old lotus pedunculatus cav. seedlings were grown either under sterile conditions or after inoculation with fix(+) or fix(-) strains of rhizobium loti. flavonoids rather than isoflavonoids predominated in all tissues. flavonoid profiles in sterile and denodulated root tiss ...	1992	16652981
plasmid pcar3 contains multiple gene sets involved in the conversion of carbazole to anthranilate.	the carbazole degradative car-i gene cluster (caraaibaibbiciaci) of sphingomonas sp. strain ka1 is located on the 254-kb circular plasmid pcar3. carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (cardo; caraaiaci), meta-cleavage enzyme (carbaibbi), and hydrolase (carci). cardo is a three-component dioxygenase, and caraai and caraci are its terminal oxygenase and ferredoxin components. the car-i gene cluster lacks the gene encoding the ferredoxin reductase component ...	2006	16672458
environmental whole-genome amplification to access microbial populations in contaminated sediments.	low-biomass samples from nitrate and heavy metal contaminated soils yield dna amounts that have limited use for direct, native analysis and screening. multiple displacement amplification (mda) using phi29 dna polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. by first amplifying the genomic dna (gdna), biodiversity analysis and gdna library construction of microbes found in contaminated soils were made possible. the mda method was validated by an ...	2006	16672469
isolation and biochemical characterization of two novel metagenome-derived esterases.	the metagenomes of uncultured microbial communities are rich sources for novel biocatalysts. in this study, esterase esta3 was derived from a drinking water metagenome, and esterase estce1 was derived from a soil metagenome. both esterases are approximately 380 amino acids in size and show similarity to beta-lactamases, indicating that they belong to family viii of the lipases/esterases. esta3 had a temperature optimum at 50 degrees c and a ph optimum at ph 9.0. it was remarkably active and very ...	2006	16672512
sequence analysis of the 144-kilobase accessory plasmid psmesm11a, isolated from a dominant sinorhizobium meliloti strain identified during a long-term field release experiment.	the genome of sinorhizobium meliloti type strain rm1021 consists of three replicons: the chromosome and two megaplasmids, psyma and psymb. additionally, many indigenous s. meliloti strains possess one or more smaller plasmids, which represent the accessory genome of this species. here we describe the complete nucleotide sequence of an accessory plasmid, designated psmesm11a, that was isolated from a dominant indigenous s. meliloti subpopulation in the context of a long-term field release experim ...	2006	16672515
multiple groesl operons are not key targets of rpoh1 and rpoh2 in sinorhizobium meliloti.	among the rhizobia that establish nitrogen-fixing nodules on the roots of host plants, many contain multiple copies of genes encoding the sigma factor rpoh and the chaperone groel/groes. in sinorhizobium meliloti there are two rpoh genes, four groesl operons, and one groel gene. rpoh1 mutants are defective for growth at high temperature and form ineffective nodules, rpoh1 rpoh2 double mutants are unable to form nodules, and groesl1 mutants form ineffective nodules. to explore the roles of rpoh1 ...	2006	16672605
flavonoid-inducible modifications to rhamnan o antigens are necessary for rhizobium sp. strain ngr234-legume symbioses.	rhizobium sp. strain ngr234 produces a flavonoid-inducible rhamnose-rich lipopolysaccharide (lps) that is important for the nodulation of legumes. many of the genes encoding the rhamnan part of the molecule lie between 87 degrees and 110 degrees of pngr234a, the symbiotic plasmid of ngr234. computational methods suggest that 5 of the 12 open reading frames (orfs) within this arc are involved in synthesis (and subsequent polymerization) of l-rhamnose. two others probably play roles in the transpo ...	2006	16672619
genome sequence of rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.	the recently sequenced rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with dna transfer, suggesting that ancestral rickettsiae might have been endowed with a conjugation apparatus. here we present the genome sequence of rickettsia bellii, the earliest diverging species of known rickettsiae. the 1,552,076 base pair-long chromosome does not exhibit the colinearity observed between other rickettsia genomes, and encodes a complete set of putative con ...	2006	16703114
genome prediction of phob regulated promoters in sinorhizobium meliloti and twelve proteobacteria.	in proteobacteria, genes whose expression is modulated in response to the external concentration of inorganic phosphate are often regulated by the phob protein which binds to a conserved motif (pho box) within their promoter regions. using a position weight matrix algorithm derived from known pho box sequences, we identified 96 putative pho regulon members whose promoter regions contained one or more pho boxs in the sinorhizobium meliloti genome. expression of these genes was examined through as ...	2006	16717279
postgenomic scan of metallo-beta-lactamase homologues in rhizobacteria: identification and characterization of bjp-1, a subclass b3 ortholog from bradyrhizobium japonicum.	the diffusion of metallo-beta-lactamases (mbls) among clinically important human pathogens represents a therapeutic issue of increasing importance. however, the origin of these resistance determinants is largely unknown, although an important number of proteins belonging to the mbl superfamily have been identified in microbial genomes. in this work, we analyzed the distribution and function of genes encoding mbl-like proteins in the class rhizobiales. among 12 released complete genomes of member ...	2006	16723554
structural classification of bacterial response regulators: diversity of output domains and domain combinations.	chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ...	2006	16740923
cbra is a stationary-phase regulator of cell surface physiology and legume symbiosis in sinorhizobium meliloti.	sinorhizobium meliloti produces an exopolysaccharide called succinoglycan that plays a critical role in promoting symbiosis with its host legume, alfalfa (medicago sativa). we performed a transposon mutagenesis and screened for mutants with altered succinoglycan production and a defect in symbiosis. in this way, we identified a putative two-component histidine kinase associated with a pas sensory domain, now designated cbra (calcofluor-bright regulator a). the cbra::tn5 mutation causes overprodu ...	2006	16740957
analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants.	polyethylene glycol dehydrogenase (pegdh) from sphingopyxis terrae (formerly sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a homodimeric structure. its amino acid sequence shows 28.5 to 30.5% identity with glucose oxidases from aspergillus niger and penicillium amagasakiense. the adp-binding site and the signature 1 and 2 consensus sequences of glucose-methanol-choline oxidoreductases are present in pegdh. based on three-di ...	2006	16751555
construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.	to infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. in contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional r ...	2006	16753070
biosynthesis of ascorbic acid in legume root nodules.	ascorbic acid (vitamin c) is a major antioxidant and redox buffer, but is also involved in other critical processes of plants. recently, the hypothesis has been proposed that legume nodules are unable to synthesize ascorbate and have to import it from the shoot or root, thus providing a means by which the plant regulates nodule senescence. the last step of ascorbate biosynthesis in plants is catalyzed by l-galactono-1,4-lactone dehydrogenase (galldh). the mrnas encoding galldh and three other en ...	2006	16766673
quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.	lateral gene transfer (lgt) is now accepted as an important factor in the evolution of prokaryotes. establishment of the occurrence of lgt is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual gc composition or codon usage within a genome, and identification of similarities between distant species as determined by best blast hits. we explore quantitative assessments of these strategies to study the prokaryotic trai ...	2006	16769896
knockdown of an arbuscular mycorrhiza-inducible phosphate transporter gene of lotus japonicus suppresses mutualistic symbiosis.	cdna for a major arbuscular mycorrhiza (am)-inducible phosphate (pi) transporter of lotus japonicus, ljpt3, was isolated from glomus mosseae-colonized roots. the ljpt3 transcript was expressed in arbuscule-containing cells of the inner cortex. the transport activity of the gene product was confirmed by the complementation of a yeast mutant that lacks high-affinity pi transporters. in contrast to most am-inducible pi transporters thus far reported, ljpt3 has an amino acid sequence that has much i ...	2006	16774930
denitrification ability of rhizobial strains isolated from lotus sp.	ten rhizobial strains isolated from lotus sp. have been characterized by their ability to denitrify. out of the 10 strains, the five slow-growing isolates grew well under oxygen-limiting conditions with nitrate as a sole nitrogen source, and accumulated nitrous oxide in the growth medium when acetylene was used to inhibit nitrous oxide reductase activity. all five strains contained dna homologous to the bradyrhizobium japonicum nirk, norbdq and nosz genes. in contrast, fast-growing lotus rhizobi ...	2006	16779640
a matrix-assisted laser desorption/ionization mass spectrometry approach to the lipid a from mesorhizobium loti.	the isolation, purification and analysis of the lipid a obtained from mesorhizobium loti ayac 1 bii strain is presented. analysis of the carbohydrate moiety after acid hydrolysis by high-ph anion-exchange chromatography with pulse amperometric detection (hpaec-pad) showed the presence of glucosamine and galacturonic acid as the only sugar components. gas chromatographic (gc) and gc/mass spectrometric (ms) analysis of the fatty acids revealed the presence of 3-oh-c12:0; 3-oh-c13:0; 3-oh-c20:0 and ...	2006	16779872
comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms.	hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ...	2006	16780600
activation of the global gene regulator prra (rega) from rhodobacter sphaeroides.	prra is a global transcription regulator activated upon phosphorylation by its cognate kinase prrb in response to low oxygen levels in rhodobacter sphaeroides. here we show by gel filtration, analytical ultracentrifugation, and nmr diffusion measurements that treatment of prra with a phosphate analogue, bef(3)(-), results in dimerization of the protein, producing a protein that binds dna. no dimeric species was observed in the absence of bef(3)(-). upon addition of bef(3)(-), the inhibitory acti ...	2006	16784239
flavin adenine dinucleotide-dependent 4-phospho-d-erythronate dehydrogenase is responsible for the 4-phosphohydroxy-l-threonine pathway in vitamin b6 biosynthesis in sinorhizobium meliloti.	the vitamin b6 biosynthetic pathway in sinorhizobium meliloti is similar to that in escherichia coli k-12; in both organisms this pathway includes condensation of two intermediates, 1-deoxy-d-xylulose 5-phosphate and 4-phosphohydroxy-l-threonine (4pht). here, we report cloning of a gene designated pdxr that functionally corresponds to the pdxb gene of e. coli and encodes a dye-linked flavin adenine dinucleotide-dependent 4-phospho-d-erythronate (4pe) dehydrogenase. this enzyme catalyzes the oxid ...	2006	16788172
fixj: a major regulator of the oxygen limitation response and late symbiotic functions of sinorhizobium meliloti.	sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, nifa and fixk, respectively, which are controlled by a two-component regulatory system fixlj in response to low-oxygen conditions. in order to identify the fixlj regulon, gene expression profiles were d ...	2006	16788198
popf1 and popf2, two proteins secreted by the type iii protein secretion system of ralstonia solanacearum, are translocators belonging to the hrpf/nopx family.	ralstonia solanacearum gmi1000 is a gram-negative plant pathogen which contains an hrp gene cluster which codes for a type iii protein secretion system (ttss). we identified two novel hrp-secreted proteins, called popf1 and popf2, which display similarity to one another and to putative ttss translocators, hrpf and nopx, from xanthomonas spp. and rhizobia, respectively. they also show similarities with ttss translocators of the yopb family from animal-pathogenic bacteria. both popf1 and popf2 bel ...	2006	16788199
effects of endogenous salicylic acid on nodulation in the model legumes lotus japonicus and medicago truncatula.	the exogenous addition of salicylic acid (sa) was previously shown to inhibit indeterminate but not determinate-type nodulation. we sought to extend these results by modulating endogenous levels of sa through the transgenic expression of salicylate hydroxylase (nahg) in both stably transformed lotus japonicus and composite medicago truncatula plants. nahg expression in l. japonicus resulted in a marked reduction of sa levels. this reduction correlated with an increase in the number of infections ...	2006	16798946
osmotic upshift transiently inhibits uptake via abc transporters in gram-negative bacteria.	atp-binding cassette transporters from several rhizobia and salmonella enterica serovar typhimurium, but not secondarily coupled systems, were inhibited by high concentrations (100 to 500 mm) of various osmolytes, an effect reversed by the removal of the osmolyte. abc systems were also inactivated in isolated pea bacteroids, probably due to the obligatory use of high-osmolarity isolation media. measurement of nutrient cycling in isolated pea bacteroids is impeded by this effect.	2006	16816205
rnai knock-down of enod40s leads to significant suppression of nodule formation in lotus japonicus.	enod40 is one of the most intriguing early nodulin genes that is known to be induced very early in response to interaction of legume plants with symbiotic rhizobium bacteria, but its function in the nodulation process is still not known. lotus japonicus has two enod40 genes: ljenod40-1 is abundantly induced in very early stages of bacterial infection or nod factor application, whereas ljenod40-2 is abundantly expressed only in mature nodules. we generated transgenic lines of l. japonicus with an ...	2006	16816411
expression of the 1-aminocyclopropane-1-carboxylic acid deaminase gene requires symbiotic nitrogen-fixing regulator gene nifa2 in mesorhizobium loti maff303099.	many soil bacteria contain 1-aminocyclopropane-1-carboxylic acid (acc) deaminase, which degrades acc, a precursor of the phytohormone ethylene. in order to examine the regulation of the acds gene encoding acc deaminase in mesorhizobium loti maff303099 during symbiosis with the host legume lotus japonicus, we introduced the beta-glucuronidase (gus) gene into acds so that gus was expressed under control of the acds promoter, and we also generated disruption mutants with mutations in a nitrogen fix ...	2006	16820494
identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, mesorhizobium loti.	we have found for the first time that a chromosomal gene, mlr6807, in mesorhizobium loti encodes a new tetrameric pyridoxal 4-dehydrogenase (pldh). the recombinant enzyme expressed in escherichia coli cells was homogenously purified and characterized. the enzyme consisted of four subunits each with a molecular weight of 26,000+/-1000, and exhibited km and kcat values of 91+/-2 microm and 149+/-1s(-1), respectively. pldh used nad+ as a cosubstrate, showed no activity toward sugars, and belonged t ...	2006	16824480
detecting non-orthology in the cogs database and other approaches grouping orthologs using genome-specific best hits.	correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. we present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the cogs database. the algorithm works with pairwise distance estimates, rather than computationally expensive and error-pr ...	2006	16835308
a novel fix- symbiotic mutant of lotus japonicus, ljsym105, shows impaired development and premature deterioration of nodule infected cells and symbiosomes.	nitrogen-fixing symbiosis between legume plants and rhizobia is established through complex interactions between two symbiotic partners. to identify the host legume genes that play crucial roles in such interactions, we isolated a novel fix- mutant, ljsym105, from a model legume lotus japonicus mg-20. the ljsym105 plants displayed nitrogen-deficiency symptoms after inoculation with mesorhizobium loti under nitrogen-free conditions, but their growth recovered when supplied with nitrogen-rich nutr ...	2006	16838790
new nodulation mutants responsible for infection thread development in lotus japonicus.	legume plants develop specialized root organs, the nodules, through a symbiotic interaction with rhizobia. the developmental process of nodulation is triggered by the bacterial microsymbiont but regulated systemically by the host legume plants. using ethylmethane sulfonate mutagenesis as a tool to identify plant genes involved in symbiotic nodule development, we have isolated and analyzed five nodulation mutants, ljsym74-3, ljsym79-2, ljsym79-3, ljsym80, and ljsym82, from the model legume lotus ...	2006	16838792
bacterial regulatory networks are extremely flexible in evolution.	over millions of years the structure and complexity of the transcriptional regulatory network (trn) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. in order to understand the plasticity of trns in bacteria, we studied the conservation of currently known trns of the two model organisms escherichia coli k12 and bacillus subtilis across complete genomes including bacteria, archaea and eukarya at three different levels: individual componen ...	2006	16840530
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
characterization of the beta-ketoadipate pathway in sinorhizobium meliloti.	aromatic compounds represent an important source of energy for soil-dwelling organisms. the beta-ketoadipate pathway is a key metabolic pathway involved in the catabolism of the aromatic compounds protocatechuate and catechol, and here we show through enzymatic analysis and mutant analysis that genes required for growth and catabolism of protocatechuate in the soil-dwelling bacterium sinorhizobium meliloti are organized on the psymb megaplasmid in two transcriptional units designated pcadchgb an ...	2006	16885292
protein-translocating trimeric autotransporters of gram-negative bacteria.		2006	16885434
activity of rhodobacter sphaeroides rpohii, a second member of the heat shock sigma factor family.	we have identified a second rpoh homolog, rpoh(ii), in the alpha-proteobacterium rhodobacter sphaeroides. primary amino acid sequence comparisons demonstrate that r. sphaeroides rpoh(ii) belongs to a phylogenetically distinct group with rpoh orthologs from alpha-proteobacteria that contain two rpoh genes. like its previously identified paralog, rpoh(i), rpoh(ii) is able to complement the temperature-sensitive phenotype of an escherichia coli sigma(32) (rpoh) mutant. in addition, we show that rec ...	2006	16885439
a novel esterase from ralstonia sp. m1: gene cloning, sequencing, high-level expression and characterization.	a newly isolated gene from ralstonia sp. m1, encoding an esterase, was cloned in escherichia coli and its nucleotide sequence determined. the 1.6kb insert revealed one complete open reading frame, predicted to encode an esterase (320 aa, 34.1kda) with a pi of 9.86. estr contained a putative oxyanion hole h36g37, a conserved pentapeptide g103hslg107 and a conserved catalytic his265 and asp237. the estr sequence shared 64-70 and 44-48% identity with the hydrolases/acyltransferases from burkholderi ...	2007	16893659
molecular and functional analysis of nicotinate catabolism in eubacterium barkeri.	the anaerobic soil bacterium eubacterium barkeri catabolizes nicotinate to pyruvate and propionate via a unique fermentation. a full molecular characterization of nicotinate fermentation in this organism was accomplished by the following results: (i) a 23.2-kb dna segment with a gene cluster encoding all nine enzymes was cloned and sequenced, (ii) two chiral intermediates were discovered, and (iii) three enzymes were found, completing the hitherto unknown part of the pathway. nicotinate dehydrog ...	2006	16894175
the relaxase of the rhizobium etli symbiotic plasmid shows nic site cis-acting preference.	genetic and biochemical characterization of traa, the relaxase of symbiotic plasmid pretcfn42d from rhizobium etli, is described. after purifying the relaxase domain (n265traa), we demonstrated nic binding and cleavage activity in vitro and thus characterized for the first time the nick site (nic) of a plasmid in the family rhizobiaceae. we studied the range of n265traa relaxase specificity in vitro by testing different oligonucleotides in binding and nicking assays. in addition, the ability of ...	2006	16916896
a cytosolic arabidopsis d-xylulose kinase catalyzes the phosphorylation of 1-deoxy-d-xylulose into a precursor of the plastidial isoprenoid pathway.	plants are able to integrate exogenous 1-deoxy-d-xylulose (dx) into the 2c-methyl-d-erythritol 4-phosphate pathway, implicated in the biosynthesis of plastidial isoprenoids. thus, the carbohydrate needs to be phosphorylated into 1-deoxy-d-xylulose 5-phosphate and translocated into plastids, or vice versa. an enzyme capable of phosphorylating dx was partially purified from a cell-free arabidopsis (arabidopsis thaliana) protein extract. it was identified by mass spectrometry as a cytosolic protein ...	2006	16920870
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
molecular details of camp generation in mammalian cells: a tale of two systems.	the second messenger camp has been extensively studied for half a century, but the plethora of regulatory mechanisms controlling camp synthesis in mammalian cells is just beginning to be revealed. in mammalian cells, camp is produced by two evolutionary related families of adenylyl cyclases, soluble adenylyl cyclases (sac) and transmembrane adenylyl cyclases (tmac). these two enzyme families serve distinct physiological functions. they share a conserved overall architecture in their catalytic do ...	2006	16934836
isocitrate dehydrogenase of bradyrhizobium japonicum is not required for symbiotic nitrogen fixation with soybean.	a mutant strain of bradyrhizobium japonicum usda110 lacking isocitrate dehydrogenase activity was created to determine whether this enzyme was required for symbiotic nitrogen fixation with soybean (glycine max cv. williams 82). the isocitrate dehydrogenase mutant, strain 5051, was constructed by insertion of a streptomycin resistance gene cassette. the mutant was devoid of isocitrate dehydrogenase activity and of immunologically detectable protein, indicating there is only one copy in the genome ...	2006	16936027
rapid in situ evolution of nodulating strains for biserrula pelecinus l. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant.	diverse rhizobia able to nodulate biserrula pelecinus evolved following in situ transfer of noda and nifh from an inoculant to soil bacteria. transfer of these chromosomal genes and the presence of an identical integrase gene adjacent to a phe trna gene in both the inoculant and recipients indicate that there was lateral transfer of a symbiosis island.	2006	16936054
the hmuq and hmud genes from bradyrhizobium japonicum encode heme-degrading enzymes.	utilization of heme by bacteria as a nutritional iron source involves the transport of exogenous heme, followed by cleavage of the heme macrocycle to release iron. bradyrhizobium japonicum can use heme as an iron source, but no heme-degrading oxygenase has been described. here, bioinformatics analyses of the b. japonicum genome identified two paralogous genes renamed hmuq (bll7075) and hmud (bll7423) that encode proteins with weak similarity to the heme-degrading monooxygenase isdg from staphylo ...	2006	16952937
thiamine is synthesized by a salvage pathway in rhizobium leguminosarum bv. viciae strain 3841.	in the absence of added thiamine, rhizobium leguminosarum bv. viciae strain 3841 does not grow in liquid medium and forms only "pin" colonies on agar plates, which contrasts with the good growth of sinorhizobium meliloti 1021, mesorhizobium loti 303099, and rhizobium etli cfn42. these last three organisms have thicoge genes, which are essential for de novo thiamine synthesis. while r. leguminosarum bv. viciae 3841 lacks thicoge, it does have thimed. mutation of thim prevented formation of pin co ...	2006	16952958
refuting phylogenetic relationships.	phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. this constitutes an important methodologic dimension not often taken into account. here we address this dimension in the context of concatenation approaches to phylogeny.	2006	16956399
exopolysaccharide production by some rhizobium strain in culture.	eight rhizobium strains were screened for exopolysaccharide production during growth in yeast extract mannitol medium. a strain of rhizobium loti produced more than 250 mg of exopolysaccharide/100 ml of culture during the stationary phase of growth. exopolysaccharide production was favoured by maltose and mannitol but n2 supplementation could not affect the production siginificantly. preliminary studies indicate that the polymer contains 16% protein and 73.5% carbohydrate being composed of gluco ...	1998	16961205
extracellular atp in plants. visualization, localization, and analysis of physiological significance in growth and signaling.	extracellular atp (eatp) in animals is well documented and known to play an important role in cellular signaling (e.g. at the nerve synapse). the existence of eatp has been postulated in plants; however, there is no definitive experimental evidence for its presence or an explanation as to how such a polar molecule could exit the plant cell and what physiological role it may play in plant growth and development. the presence of eatp in plants (medicago truncatula) was detected by constructing a n ...	2006	16963521
complete nucleotide sequence of an exogenously isolated plasmid, plb1, involved in gamma-hexachlorocyclohexane degradation.	the alpha-proteobacterial strain sphingobium japonicum ut26 utilizes a highly chlorinated pesticide, gamma-hexachlorocyclohexane (gamma-hch), as a sole source of carbon and energy, and haloalkane dehalogenase linb catalyzes the second step of gamma-hch degradation in ut26. functional complementation of a linb mutant of ut26, ut26db, was performed by the exogenous plasmid isolation technique using hch-contaminated soil, leading to our successful identification of a plasmid, plb1, carrying the lin ...	2006	16963556