Publications

functional expression of sinorhizobium meliloti bets, a high-affinity betaine transporter, in bradyrhizobium japonicum usda110.	among the rhizobiaceae, bradyrhizobium japonicum strain usda110 appears to be extremely salt sensitive, and the presence of glycine betaine cannot restore its growth in medium with an increased osmolarity (e. boncompagni, m. osteras, m. c. poggi, and d. le rudulier, appl. environ. microbiol. 65:2072-2077, 1999). in order to improve the salt tolerance of b. japonicum, cells were transformed with the bets gene of sinorhizobium meliloti. this gene encodes a major glycine betaine/proline betaine tra ...	2004	15466533
unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin).	efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ...	2004	15060050
identification of pimr as a positive regulator of pimaricin biosynthesis in streptomyces natalensis.	sequencing of the dna region on the left fringe of the pimaricin gene cluster revealed the presence of a 3.6-kb gene, pimr, whose deduced product (1,198 amino acid residues) was found to have amino acid sequence homology with bacterial regulatory proteins. database comparisons revealed that pimr represents the archetype of a new class of regulators, combining a streptomyces antibiotic regulatory protein (sarp)-like n-terminal section with a c-terminal half homologous to guanylate cyclases and la ...	2004	15090496
genome-wide comparison of the his-to-asp phosphorelay signaling components of three symbiotic genera of rhizobia.	histidine-to-aspartate (his-asp) phosphorelay (or two-component) systems are very common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli. the his-asp phosphorelay components include "sensor histidine kinase (hk)", "phosphotransfer intermediate (hpt)", and "response regulator (rr)". with special reference to three bacterial species (mesorhizobium loti, bradyrhizobium japonicum, sinorhizobium meliloti), each of which belongs to a ...	2004	15141946
expression islands clustered on the symbiosis island of the mesorhizobium loti genome.	rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. the establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. we developed a macroarray for mesorhizobium loti maff303099, a microsymbiont of the model legume lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. global transcriptional ...	2004	15060047
structural basis of ligand activation in a cyclic nucleotide regulated potassium channel.	here we describe the initial functional characterization of a cyclic nucleotide regulated ion channel from the bacterium mesorhizobium loti and present two structures of its cyclic nucleotide binding domain, with and without camp. the domains are organized as dimers with the interface formed by the linker regions that connect the nucleotide binding pocket to the pore domain. together, structural and functional data suggest the domains form two dimers on the cytoplasmic face of the channel. we pr ...	2004	15550244
structural and genetic characterization of the shigella boydii type 13 o antigen.	shigella is an important human pathogen. it is generally agreed that shigella and escherichia coli constitute a single species; the only exception is shigella boydii type 13, which is more distantly related to e. coli and other shigella forms and seems to represent another species. this gives s. boydii type 13 an important status in evolution. o antigen is the polysaccharide part of the lipopolysaccharide in the outer membrane of gram-negative bacteria and plays an important role in pathogenicit ...	2004	14702307
degradation pathway and generation of monohydroxamic acids from the trihydroxamate siderophore deferrioxamine b.	siderophores are avid ferric ion-chelating molecules that sequester the metal for microbes. microbes elicit siderophores in numerous and different environments, but the means by which these molecules reenter the carbon and nitrogen cycles is poorly understood. the metabolism of the trihydroxamic acid siderophore deferrioxamine b by a mesorhizobium loti isolated from soil was investigated. specifically, the pathway by which the compound is cleaved into its constituent monohydroxamates was examine ...	2004	14766561
biochemical and proteomic analysis of the magnetosome membrane in magnetospirillum gryphiswaldense.	we analyzed the biochemical composition of the magnetosome membrane (mm) in magnetospirillum gryphiswaldense. isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. the binding characteristics of mm-associated proteins were studied by selective solubilization and limited proteolysis. the mm-associated proteins ...	2004	14766587
comparison of the 1.85 a structure of cyp154a1 from streptomyces coelicolor a3(2) with the closely related cyp154c1 and cyps from antibiotic biosynthetic pathways.	the genus streptomyces produces two-thirds of microbially derived antibiotics. polyketides form the largest and most diverse group of these natural products. antibiotic diversity of polyketides is generated during their biosynthesis by several means, including postpolyketide modification performed by oxidoreductases, a broad group of enzymes including cytochrome p450 monooxygenases (cyps). cyps catalyze site-specific oxidation of macrolide antibiotic precursors significantly affecting antibiotic ...	2004	14691240
h protein of bacteriophage 16-3 and rkpm protein of sinorhizobium meliloti 41 are involved in phage adsorption.	the strain-specific capsular polysaccharide kr5 antigen of sinorhizobium meliloti 41 is required both for invasion of the symbiotic nodule and for the adsorption of bacteriophage 16-3. in order to know more about the genes involved in these events, bacterial mutants carrying an altered phage receptor were identified by using host range phage mutants. a representative mutation was localized in the rkpm gene by complementation and dna sequence analysis. a host range phage mutant isolated on these ...	2004	14996788
characteristic biological activities of lipopolysaccharides from sinorhizobium and mesorhizobium.	the biological actions of lipopolysaccharides (lpss) from sinorhizobium meliloti, mesorhizobium loti and escherichia coli were compared. in biological activities including lethality, production of tumor necrosis factor (tnf)-alpha and nitric oxide (no), adjuvant action and limulus activity, lps from s. meliloti exhibited stronger actions than lps from m. loti, but had a weaker action than lps from e. coli. on the other hand, m. loti lps showed a higher activity to activate human complement than ...	2004	15025821
phenotypic and genotypic analysis of rhizobia isolated from pasture legumes native of sardinia and asinara island.	thirty-five rhizobial strains were isolated from nodules of lotus edulis, l. ornithopodioides, l. cytisoides, hedysarum coronarium, ornithopus compressus and scorpiurus muricatus growing in sardinia and asinara island. basic characteristics applied to identification of rhizobia such as symbiotic properties, antibiotic- and salt-resistance, temperate-sensitivities, utilization of different sources of carbon and nitrogen were studied. the results from the 74 metabolic tests were used for cluster a ...	2004	15031655
the prc-barrel domain of the ribosome maturation protein rimm mediates binding to ribosomal protein s19 in the 30s ribosomal subunits.	the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes. a deltarimm mutant is defective in 30s maturation and accumulates 17s rrna. to study the interaction of rimm with the 30s and its involvement in 30s maturation, rimm amino acid substitution mutants were constructed. a mutant rimm (rimm-yy-->aa), containing alanine substitutions for two adjacent tyrosines within the prc beta-barrel domain, showed a reduced binding to 30s and an accumula ...	2004	15496525
widespread presence of "bacterial-like" ppp phosphatases in eukaryotes.	in eukaryotes, ppp (protein phosphatase p) family is one of the two known protein phosphatase families specific for ser and thr. the role of ppp phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. unlike eukaryotic ppp phosphatases, bacterial members of the family have broad substrate specificity or may even be tyr-specific. moreover, one group of bacterial ppps are diadenosine tetraphosphatases, indicating that bacterial ppp phosphatases may not necessar ...	2004	15555063
complete nucleotide sequence of the conjugative tetracycline resistance plasmid pfbaot6, a member of a group of incu plasmids with global ubiquity.	this study presents the first complete sequence of an incu plasmid, pfbaot6. this plasmid was originally isolated from a strain of aeromonas caviae from hospital effluent (westmorland general hospital, kendal, united kingdom) in september 1997 (g. rhodes, g. huys, j. swings, p. mcgann, m. hiney, p. smith, and r. w. pickup, appl. environ. microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pfbaot6 is 84,748 bp long and has 94 predicted coding sequences, ...	2004	15574953
nucleotide sequences, genetic organization, and distribution of peu30 and pel60 from erwinia amylovora.	the nucleotide sequences, genetic organization, and distribution of plasmids peu30 (30,314 bp) and pel60 (60,145 bp) from the plant pathogen erwinia amylovora are described. the newly characterized peu30 and pel60 plasmids inhabited strains isolated in the western united states and lebanon, respectively. the gene content of peu30 resembled plasmids found in plant-associated bacteria, while that of pel60 was most similar to incl/m plasmids inhabiting enteric bacteria.	2004	15574957
a genetic locus necessary for rhamnose uptake and catabolism in rhizobium leguminosarum bv. trifolii.	rhizobium leguminosarum bv. trifolii mutants unable to catabolize the methyl-pentose rhamnose are unable to compete effectively for nodule occupancy. in this work we show that the locus responsible for the transport and catabolism of rhamnose spans 10,959 bp. mutations in this region were generated by transposon mutagenesis, and representative mutants were characterized. the locus contains genes coding for an abc-type transporter, a putative dehydrogenase, a probable isomerase, and a sugar kinas ...	2004	15576793
new insights into type ii nad(p)h:quinone oxidoreductases.	type ii nad(p)h:quinone oxidoreductases (ndh-2) catalyze the two-electron transfer from nad(p)h to quinones, without any energy-transducing site. ndh-2 accomplish the turnover of nad(p)h, regenerating the nad(p)(+) pool, and may contribute to the generation of a membrane potential through complexes iii and iv. these enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kda, containing a flavin moiety. there are a few compounds that can prevent their activity ...	2004	15590775
bacterial signal transduction network in a genomic perspective.	bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. the complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. comparative studies revealed certain general trends in the organization of diverse signalling systems. these include (i) modular structure of signalling proteins; (ii) comm ...	2004	15142243
the sinorhizobium meliloti fur gene regulates, with dependence on mn(ii), transcription of the sitabcd operon, encoding a metal-type transporter.	sinorhizobium meliloti is an alpha-proteobacterium able to induce nitrogen-fixing nodules on roots of specific legumes. in order to propagate in the soil and for successful symbiotic interaction the bacterium needs to sequester metals like iron and manganese from its environment. the metal uptake has to be in turn tightly regulated to avoid toxic effects. in this report we describe the characterization of a chromosomal region of s. meliloti encoding the sitabcd operon and the putative regulatory ...	2004	15150249
characterization of the icmh and icmf genes required for legionella pneumophila intracellular growth, genes that are present in many bacteria associated with eukaryotic cells.	legionella pneumophila, the causative agent of legionnaires' disease, replicates intracellularly within a specialized phagosome of mammalian and protozoan host cells, and the icm/dot type iv secretion system has been shown to be essential for this process. unlike all the other known icm/dot proteins, the icmf protein, which was described before, and the icmh protein, which is characterized here, have homologous proteins in many bacteria (such as yersinia pestis, salmonella enterica, rhizobium le ...	2004	15155646
inactivation of the flagellin gene flaa in magnetospirillum gryphiswaldense results in nonmagnetotactic mutants lacking flagellar filaments.	magnetotactic bacteria synthesize magnetosomes, which cause them to orient and migrate along magnetic field lines. the analysis of magnetotaxis and magnetosome biomineralization at the molecular level has been hindered by the unavailability of genetic methods, namely the lack of a means to introduce directed gene-specific mutations. here we report a method for knockout mutagenesis by homologous recombination in magnetospirillum gryphiswaldense. multiple flagellin genes, which are unlinked in the ...	2004	15184166
regb/rega, a highly conserved redox-responding global two-component regulatory system.	the reg regulon from rhodobacter capsulatus and rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. the redox signal that is detected by the membrane-bound sensor kinase, regb, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c o ...	2004	15187184
infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes.	bacteria belonging to the genera rhizobium, mesorhizobium, sinorhizobium, bradyrhizobium, and azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. the interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that aris ...	2004	15187185
sinorhizobium meliloti sulfotransferase that modifies lipopolysaccharide.	sinorhizobium meliloti is a gram-negative soil bacterium found either in free-living form or as a nitrogen-fixing endosymbiont of a plant structure called the nodule. symbiosis between s. meliloti and its plant host alfalfa is dependent on bacterial transcription of nod genes, which encode the enzymes responsible for synthesis of nod factor. s. meliloti nod factor is a lipochitooligosaccharide that undergoes a sulfate modification essential for its biological activity. sulfate also modifies the ...	2004	15205418
mutational analysis and biochemical characterization of the burkholderia thailandensis dw503 quorum-sensing network.	numerous gram-negative bacteria communicate and regulate gene expression through a cell density-responsive mechanism termed quorum sensing (qs), which involves the synthesis and perception of diffusible n-acyl-homoserine lactones (ahl). in this study we genetically and physiologically characterized the burkholderia thailandensis dw503 qs network. in silico analysis of the b. thailandensis genome revealed the presence of at least three ahl synthases (ahs) and five transcriptional regulators belon ...	2004	15205437
the louse-borne human pathogen bartonella quintana is a genomic derivative of the zoonotic agent bartonella henselae.	we present the complete genomes of two human pathogens, bartonella quintana (1,581,384 bp) and bartonella henselae (1,931,047 bp). the two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. a primary difference between the two pathogens is their reservoir ecology. whereas b. quintana is a specialist, using ...	2004	15210978
two c-p lyase operons in pseudomonas stutzeri and their roles in the oxidation of phosphonates, phosphite, and hypophosphite.	dna sequencing and analysis of two distinct c-p lyase operons in pseudomonas stutzeri wm88 were completed. the htxabcdefghijklmn operon encodes a hypophosphite-2-oxoglutarate dioxygenase (htxa), whereas the predicted amino acid sequences of htxb to htxn are each homologous to the components of the escherichia coli phn operon, which encodes c-p lyase, although homologs of e. coli phnf and phno are absent. the genes in the htx operon are cotranscribed based on gene organization, and the presence o ...	2004	15231805
characterization of nopp, a type iii secreted effector of rhizobium sp. strain ngr234.	the type three secretion system (ttss) encoded by pngr234a, the symbiotic plasmid of rhizobium sp. strain ngr234, is responsible for the flavonoid- and nodd1-dependent secretion of nodulation outer proteins (nops). abolition of secretion of all or specific nops significantly alters the nodulation ability of ngr234 on many of its hosts. in the closely related strain rhizobium fredii usda257, inactivation of the ttss modifies the host range of the mutant so that it includes the improved glycine ma ...	2004	15231809
properties of a novel thermostable glucoamylase from the hyperthermophilic archaeon sulfolobus solfataricus in relation to starch processing.	a gene (ssg) encoding a putative glucoamylase in a hyperthermophilic archaeon, sulfolobus solfataricus, was cloned and expressed in escherichia coli, and the properties of the recombinant protein were examined in relation to the glucose production process. the recombinant glucoamylase was extremely thermostable, with an optimal temperature at 90 degrees c. the enzyme was most active in the ph range from 5.5 to 6.0. the enzyme liberated beta-d-glucose from the substrate maltotriose, and the subst ...	2004	15240266
molecular analysis of carbon monoxide-oxidizing bacteria associated with recent hawaiian volcanic deposits.	genomic dna extracts from four sites at kilauea volcano were used as templates for pcr amplification of the large subunit (coxl) of aerobic carbon monoxide dehydrogenase. the sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. pcr primers amplified coxl sequences from the omp clade of co oxidizers, which includes isolates such as oligotropha carboxidovorans, mycobacterium tuber ...	2004	15240307
fur is involved in manganese-dependent regulation of mnta (sita) expression in sinorhizobium meliloti.	fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. in this work we analyzed the phenotype of a fur mutant in sinorhizobium meliloti, an alpha-proteobacterium that fixes n(2) in association with host plants. we demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a fur-independent manner. however, manganese-dependent expressi ...	2004	15240318
lotus japonicus ljkup is induced late during nodule development and encodes a potassium transporter of the plasma membrane.	the kup family of potassium transporters in plants is large but poorly characterized. we isolated and characterized the first kup transporter from a legume, ljkup of lotus japonicus. although expressed throughout plants, ljkup transcript levels were highest in nodules. induction of ljkup expression occurred late during nodule development, at a time of rapid organ expansion. a high level of ljkup expression was maintained in mature, full-sized nodules. however, induction of ljkup expression was i ...	2004	15242173
fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy.	a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ...	2004	15060178
root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...	2004	15066803
urease-encoding genes in ammonia-oxidizing bacteria.	many but not all ammonia-oxidizing bacteria (aob) produce urease (urea amidohydrolase, ec 3.5.1.5) and are capable of using urea for chemolithotrophic growth. we sequenced the urease operons from two aob, the beta-proteobacterium nitrosospira sp. strain npav and the gamma-proteobacterium nitrosococcus oceani. in both organisms, all seven urease genes were contiguous: the three structural urease genes ureabc were preceded and succeeded by the accessory genes ured and ureefg, respectively. green f ...	2004	15066830
omega-amino acid:pyruvate transaminase from alcaligenes denitrificans y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.	alcaligenes denitrificans y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (apta) was cloned. the gene was functionally expressed in escherichia coli bl21 by using an isopropyl-beta-d-thiogalactopyranoside (iptg)-inducible pet expression system (9.6 u/mg), and the recombinant apta was purified to show a specific a ...	2004	15066855
characterization of three functional high-affinity ammonium transporters in lotus japonicus with differential transcriptional regulation and spatial expression.	ammonium is a primary source of nitrogen for plants. in legume plants ammonium can also be obtained by symbiotic nitrogen fixation, and nh(4)(+) is also a regulator of early and late symbiotic interaction steps. ammonium transporters are likely to play important roles in the control of nodule formation as well as in nitrogen assimilation. two new genes, ljamt1;2 and ljamt1;3, were cloned from lotus japonicus. both were able to complement the growth defect of a yeast (saccharomyces cerevisiae) am ...	2004	15075393
microorganisms resistant to free-living amoebae.	free-living amoebae feed on bacteria, fungi, and algae. however, some microorganisms have evolved to become resistant to these protists. these amoeba-resistant microorganisms include established pathogens, such as cryptococcus neoformans, legionella spp., chlamydophila pneumoniae, mycobacterium avium, listeria monocytogenes, pseudomonas aeruginosa, and francisella tularensis, and emerging pathogens, such as bosea spp., simkania negevensis, parachlamydia acanthamoebae, and legionella-like amoebal ...	2004	15084508
the pgaabcd locus of escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation.	production of a polysaccharide matrix is a hallmark of bacterial biofilms, but the composition of matrix polysaccharides and their functions are not widely understood. previous studies of the regulation of escherichia coli biofilm formation suggested the involvement of an unknown adhesin. we now establish that the pgaabcd (formerly ycdsrqp) locus affects biofilm development by promoting abiotic surface binding and intercellular adhesion. all of the pga genes are required for optimal biofilm form ...	2004	15090514
new rna motifs suggest an expanded scope for riboswitches in bacterial genetic control.	the expression of certain genes involved in fundamental metabolism is regulated by metabolite-binding "riboswitch" elements embedded within their corresponding mrnas. we have identified at least six additional elements within the bacillus subtilis genome that exhibit characteristics of riboswitch function (glms, gcvt, ydao/yuaa, ykkc/yxkd, ykok, and yybp/ykoy). these motifs exhibit extensive sequence and secondary-structure conservation among many bacterial species and occur upstream of related ...	2004	15096624
cloning and characterization of the gene encoding the major cell-associated phospholipase a of legionella pneumophila, plab, exhibiting hemolytic activity.	legionella pneumophila, the causative agent of legionnaires' disease, is an intracellular pathogen of amoebae, macrophages, and epithelial cells. the pathology of legionella infections involves alveolar cell destruction, and several proteins of l. pneumophila are known to contribute to this ability. by screening a genomic library of l. pneumophila, we found an additional l. pneumophila gene, plab, which coded for a hemolytic activity and contained a lipase consensus motif in its deduced protein ...	2004	15102773
transgenic lotus japonicus with an ethylene receptor gene cm-ers1/h70a enhances formation of infection threads and nodule primordia.	ethylene inhibits the establishment of symbiosis between rhizobia and legumes. to examine how and when endogenous ethylene inhibits rhizobial infection and nodulation, we produced transgenic lotus japonicus carrying the mutated melon ethylene receptor gene cm-ers1/h70a that confers ethylene insensitivity and fixes the transgene in the t(3) generation. the resultant transgenic plants showed reduced ethylene sensitivity because of 1-aminocyclopropane-1-carboxylate resistance and increased flowerin ...	2004	15111717
patterns of bacterial gene movement.	lateral gene transfer has emerged as an important force in bacterial evolution. a substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. in this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. we have analyzed 50 bacterial complete genomes from nine groups. for each group we use a 16s rrna phylogeny and a comparison of protein similarity to map gene insertions/deletions ont ...	2004	15115802
comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from methylocystis strain sc2.	in addition to the conventional pmoa gene (pmoa1) encoding the active site polypeptide of particulate methane monooxygenase, a novel pmoa gene copy (pmoa2) is widely distributed among type ii methanotrophs (methane-oxidizing bacteria [mob]) (m. tchawa yimga, p. f. dunfield, p. ricke, j. heyer, and w. liesack, appl. environ. microbiol. 69:5593-5602, 2003). here we report that the pmoa1 and pmoa2 gene copies in the type ii mob methylocystis strain sc2 are each part of a complete pmocab gene cluste ...	2004	15128567
the nitrogen-fixing symbiotic bacterium mesorhizobium loti has and expresses the gene encoding pyridoxine 4-oxidase involved in the degradation of vitamin b6.	the gene product of mll6785 of a nitrogen-fixing symbiotic bacterium mesorhizobium loti maff303099 was identified as pyridoxine 4-oxidase, the first enzyme in the vitamin b6-degradation pathway. the gene was cloned and ligated into pet-21a+. escherichia coli bl21(de3) was co-transformed with the constructed plasmid plus pky206 containing groesl genes encoding chaperonins. the overexpressed protein was purified to homogeneity by the ammonium sulfate fractionation and three chromatography steps. t ...	2004	15135526
in search of rnase p rna from microbial genomes.	a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ...	2004	15337843
occurrence and potential diagnostic applications of serological cross-reactivities between brucella and other alpha-proteobacteria.	agrobacterium, sinorhizobium, and ochrobactrum are genera closely related to brucella but, in contrast to the latter, are not pathogenic for humans and animals. we studied by an indirect enzyme-linked immunosorbent assay (elisa) the reactivities of brucellosis sera against cytosolic (cyt) and membrane (ma) antigens from these nonpathogenic bacteria, and we evaluated the potential usefulness of these cross-reactions for the diagnosis of brucellosis in humans, sheep, cows, and dogs. canine infecti ...	2004	15358645
genome-wide molecular clock and horizontal gene transfer in bacterial evolution.	we describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. the approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straig ...	2004	15375139
production of amino acids by rhizobium, mesorhizobium and sinorhizobium strains in chemically defined media.	five strains of rhizobium spp, one strain of mesorhizobium loti and two strains of sinorhizobium meliloti were tested for their ability to grow in chemically-defined medium lacking growth factor. qualitative and quantitative production of aspartic acid, serine, glutamic acid, glycine, histidine, threonine, arginine, alanine, proline, cysteine, tyrosine, valine, methionine, lysine, isoleucine, leucine, and phenylalanine was determined by the use of mannitol as sole carbon source. strains of rhizo ...	2004	15378411
release of periplasmic proteins of brucella suis upon acidic shock involves the outer membrane protein omp25.	the survival and replication of brucella in macrophages is initially triggered by a low intraphagosomal ph. in order to identify proteins released by brucella during this early acidification step, we analyzed brucella suis conditioned medium at various ph levels. no significant proteins were released at ph 4.0 in minimal medium or citrate buffer, whereas in acetate buffer, b. suis released a substantial amount of soluble proteins. comparison of 13 n-terminal amino acid sequences determined by ed ...	2004	15385468
the ton system, an abc transporter, and a universally conserved gtpase are involved in iron utilization by brucella melitensis 16m.	brucella spp. are gram-negative intracellular facultative pathogens that are known to produce 2,3-dihydroxybenzoic acid (dhba), a catechol siderophore that is essential for full virulence in the natural host. the mechanism of dhba entry into brucella and other gram-negative bacteria is poorly understood. using mini-tn5kmcat mutagenesis, we created a transposon library of brucella melitensis 16m and isolated 32 mutants with a defect in iron acquisition or assimilation. three of these transposon m ...	2004	15385478
the structure and ligand binding properties of the b. subtilis ykof gene product, a member of a novel family of thiamin/hmp-binding proteins.	the crystal structure of the bacillus subtilis ykof gene product, a protein involved in the hydroxymethyl pyrimidine (hmp) salvage pathway, was solved by the multiwavelength anomalous dispersion (mad) method and refined with data extending to 1.65 a resolution. the atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the act and ram-domains. each repeat shows a re ...	2004	15451668
complete genome sequence of the industrial bacterium bacillus licheniformis and comparisons with closely related bacillus species.	bacillus licheniformis is a gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. this species is closely related to the well studied model organism bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature.	2004	15461803
expression profiling in medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program.	in this study, we describe a large-scale expression-profiling approach to identify genes differentially regulated during the symbiotic interaction between the model legume medicago truncatula and the nitrogen-fixing bacterium sinorhizobium meliloti. macro- and microarrays containing about 6,000 probes were generated on the basis of three cdna libraries dedicated to the study of root symbiotic interactions. the experiments performed on wild-type and symbiotic mutant material led us to identify a ...	2004	15466239
expression of an exogenous 1-aminocyclopropane-1-carboxylate deaminase gene in sinorhizobium meliloti increases its ability to nodulate alfalfa.	1-aminocyclopropane-1-carboxylate (acc) deaminase has been found in various plant growth-promoting rhizobacteria, including rhizobia. this enzyme degrades acc, the immediate precursor of ethylene, and thus decreases the biosynthesis of ethylene in higher plants. the acc deaminase of rhizobium leguminosarum bv. viciae 128c53k was previously reported to be able to enhance nodulation of peas. the acc deaminase structural gene (acds) and its upstream regulatory gene, a leucine-responsive regulatory ...	2004	15466529
where does bacterial replication start? rules for predicting the oric region.	three methods, based on dna asymmetry, the distribution of dnaa boxes and dnaa gene location, were applied to identify the putative replication origins in 120 chromosomes. the chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. dna asymmetry is the most universal method of putative oric identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. the three meth ...	2004	15258248
a novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101.	p-nitrophenol (4-np) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. to date, several 4-np-degrading bacteria have been isolated; however, the genetic information remains very limited. in this study, a novel 4-np degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101, was identified and characterized. the deduced amino acid sequences of npcb, npca, and npcc showed identity with phenol 2-hydroxylase compon ...	2004	15262926
comparative whole-genome hybridization reveals genomic islands in brucella species.	brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and malta fever in humans. based on host preference, the genus is divided into six species. brucella abortus, b. melitensis, and b. suis are pathogenic to humans, whereas b. ovis and b. neotomae are nonpathogenic to humans and b. canis human infections are rare. limited genome diversity exists among brucella species. comparison of brucella species whole genomes is, therefore, likel ...	2004	15262941
the homogentisate pathway: a central catabolic pathway involved in the degradation of l-phenylalanine, l-tyrosine, and 3-hydroxyphenylacetate in pseudomonas putida.	pseudomonas putida metabolizes phe and tyr through a peripheral pathway involving hydroxylation of phe to tyr (phhab), conversion of tyr into 4-hydroxyphenylpyruvate (tyrb), and formation of homogentisate (hpd) as the central intermediate. homogentisate is then catabolized by a central catabolic pathway that involves three enzymes, homogentisate dioxygenase (hmga), fumarylacetoacetate hydrolase (hmgb), and maleylacetoacetate isomerase (hmgc), finally yielding fumarate and acetoacetate. whereas t ...	2004	15262943
yapi, a new yersinia pseudotuberculosis pathogenicity island.	pathogenicity islands (pais) are chromosomal clusters of pathogen-specific virulence genes often found at trna loci. in the yersinia pseudotuberculosis 32777 chromosome, we characterized a 98-kb segment that has all of the characteristic features of a pai, including insertion in a (phenylalanine) trna gene, the presence of a bacteriophage-like integrase-encoding gene, and direct repeats at the integration sites. the g+c content of the segment ranges from 31 to 60%, reflecting a genetic mosaic: t ...	2004	15271940
sequencing and analysis of the large virulence plasmid plvpk of klebsiella pneumoniae cg43.	we have determined the entire dna sequence of plvpk, which is a 219-kb virulence plasmid harbored in a bacteremic isolate of klebsiella pneumoniae. a total of 251 open reading frames (orfs) were annotated, of which 37% have homologous genes of known function, 31% match the hypothetical genes in the genbank database, and the remaining 32% are novel sequences. the obvious virulence-associated genes carried by the plasmid are the capsular polysaccharide synthesis regulator rmpa and its homolog rmpa ...	2004	15276215
excision of the shigella resistance locus pathogenicity island in shigella flexneri is stimulated by a member of a new subgroup of recombination directionality factors.	pathogenicity islands are capable of excision and insertion within bacterial chromosomes. we describe a protein, rox, that stimulates excision of the shigella resistance locus pathogenicity island in shigella flexneri. sequence analysis suggests that rox belongs to a new subfamily of recombination directionality factors, which includes proteins from p4, enterohemorrhagic escherichia coli, and yersinia pestis.	2004	15292162
real-time taqman pcr for quantifying oral bacteria during biofilm formation.	a taqman pcr was developed for quantifying early colonizer microorganisms in dental biofilms. to design species-specific primers and taqman probes, genomic subtractive hybridization was used. this quantitative assay in combination with subtractive hybridization may be of value in the study of microbial ecosystems consisting of related species that are involved in the formation and etiology of biofilms.	2004	15297540
identification and transcriptional control of caulobacter crescentus genes encoding proteins containing a cold shock domain.	the cold shock proteins are small peptides that share a conserved domain, called the cold shock domain (csd), that is important for nucleic acid binding. the caulobacter crescentus genome has four csp genes that encode proteins containing csds. three of these (cspa, cspb, and cspc) encode peptides of about 7 kda and are very similar to the cold shock proteins of other bacteria. analysis by reverse transcription-pcr of the fourth gene (cspd), which was previously annotated as encoding a 7-kda pro ...	2004	15317764
conservation of functional domain structure in bicarbonate-regulated "soluble" adenylyl cyclases in bacteria and eukaryotes.	soluble adenylyl cyclase (sac) is an evolutionarily conserved bicarbonate sensor. in mammals, it is responsible for bicarbonate-induced, camp-dependent processes in sperm required for fertilization and postulated to be involved in other bicarbonate- and carbon dioxide-dependent functions throughout the body. among eukaryotes, sac-like cyclases have been detected in mammals and in the fungi dictyostelium; these enzymes display extensive similarity extending through two cyclase catalytic domains a ...	2004	15322879
terbinafine resistance mediated by salicylate 1-monooxygenase in aspergillus nidulans.	resistance to antifungal agents is a recurring and growing problem among patients with systemic fungal infections. uv-induced aspergillus nidulans mutants resistant to terbinafine have been identified, and we report here the characterization of one such gene. a sib-selected, 6.6-kb genomic dna fragment encodes a salicylate 1-monooxygenase (sala), and a fatty acid synthase subunit (fasc) confers terbinafine resistance upon transformation of a sensitive strain. subfragments carrying sala but not f ...	2004	15328121
different patterns of evolution for duplicated dna repair genes in bacteria of the xanthomonadales group.	dna repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. the importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.	2004	15333143
ion channel structure and the promise of bacteria: cyclic nucleotide-gated channels in the queue.		2004	15337818
large-scale analysis of gene expression profiles during early stages of root nodule formation in a model legume, lotus japonicus.	gene expression profiles during early stages of formation of symbiotic nitrogen-fixing nodules in a model legume lotus japonicus were analyzed by means of a cdna array of 18,144 non-redundant expressed sequence tags (ests) isolated from l. japonicus. expression of a total of 1,076 genes was significantly accelerated during the successive stages that represent infection of mesorhizobium loti, nodule primordium initiation, nodule organogenesis, and the onset of nitrogen fixation. these include 32 ...	2004	15500251
oxa-60, a chromosomal, inducible, and imipenem-hydrolyzing class d beta-lactamase from ralstonia pickettii.	a chromosomally encoded oxacillinase, oxa-22, had been characterized from ralstonia pickettii pic-1 that did not explain by itself the resistance profile of this strain to beta-lactams. thus, further analysis of the genetic background of this species led to the identification of another oxacillinase, oxa-60, that was expressed only after beta-lactam induction. this chromosomally encoded oxacillinase shared 19% amino acid identity with oxa-22. it has a narrow-spectrum hydrolysis profile that incl ...	2004	15504844
transfer of the symbiotic plasmid of rhizobium etli cfn42 requires cointegration with p42a, which may be mediated by site-specific recombination.	plasmid p42a from rhizobium etli cfn42 is self-transmissible and indispensable for conjugative transfer of the symbiotic plasmid (psym). most psym transconjugants also inherit p42a. psym transconjugants that lack p42a always contain recombinant psyms, which we designated rpsyms. rpsyms do not contain some psym segments and instead have p42a sequences, including the replication and transfer regions. these novel recombinant plasmids are compatible with wild-type psym, incompatible with p42a, and ...	2004	15516565
a novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin.	a novel alanine dehydrogenase (aladh) showing no significant amino acid sequence homology with previously known bacterial aladhs was purified to homogeneity from the soluble fraction of the hyperthermophilic archaeon archaeoglobus fulgidus. aladh catalyzed the reversible, nad+-dependent deamination of l-alanine to pyruvate and nh4+. nadp(h) did not serve as a coenzyme. the enzyme is a homodimer of 35 kda per subunit. the km values for l-alanine, nad+, pyruvate, nadh, and nh4+ were estimated at 0 ...	2004	15516582
characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal dna terminal restriction fragment length polymorphism profiling.	progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (cf) patients. a greater understanding of these bacterial infections is needed to improve lung disease management. as culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (t-rf) length polymorphism profiling and 16s rrna clone data to characterize, without prior cultivation, the bacterial comm ...	2004	15528712
bartonella adhesin a mediates a proangiogenic host cell response.	bartonella henselae causes vasculoproliferative disorders in humans. we identified a nonfimbrial adhesin of b. henselae designated as bartonella adhesin a (bada). bada is a 340-kd outer membrane protein encoded by the 9.3-kb bada gene. it has a modular structure and contains domains homologous to the yersinia enterocolitica nonfimbrial adhesin (yersinia adhesin a). expression of bada was restored in a bada-deficient transposon mutant by complementation in trans. bada mediates the binding of b. h ...	2004	15534369
a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land.	the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ...	2004	15535883
unexpectedly diverse mesorhizobium strains and rhizobium leguminosarum nodulate native legume genera of new zealand, while introduced legume weeds are nodulated by bradyrhizobium species.	the new zealand native legume flora are represented by four genera, sophora, carmichaelia, clianthus, and montigena. the adventive flora of new zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in new zealand. the success of the introduced species may be due, at least in part, to the nature of their rhizobial sym ...	2004	15466541
comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.	recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ...	2004	15466593
the complete genomic sequence of nocardia farcinica ifm 10152.	we determined the genomic sequence of nocardia farcinica ifm 10152, a clinical isolate, and revealed the molecular basis of its versatility. the genome consists of a single circular chromosome of 6,021,225 bp with an average g+c content of 70.8% and two plasmids of 184,027 (pnf1) and 87,093 (pnf2) bp with average g+c contents of 67.2% and 68.4%, respectively. the chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as w ...	2004	15466710
symbiotic phenotypes and translocated effector proteins of the mesorhizobium loti strain r7a virb/d4 type iv secretion system.	the symbiosis island of mesorhizobium loti strain r7a contains genes with strong similarity to the structural vir genes (virb1-11; vird4) of agrobacterium tumefaciens that encode the type iv secretion system (t4ss) required for t-dna transfer to plants. in contrast, m. loti strain maff303099 lacks these genes but contains genes not present in strain r7a that encode a type iii secretion system (t3ss). here we show by hybridization analysis that most m. loti strains contain the virb/d4 t4ss and no ...	2004	15469524
variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice.	in animal pathogenic bacteria, horizontal gene transfer events (hgt) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (lps). as a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. since lps is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. although lps has been suggested as a ...	2004	15473911
generation of the brucella melitensis orfeome version 1.1.	the bacteria of the brucella genus are responsible for a worldwide zoonosis called brucellosis. they belong to the alpha-proteobacteria group, as many other bacteria that live in close association with a eukaryotic host. importantly, the brucellae are mainly intracellular pathogens, and the molecular mechanisms of their virulence are still poorly understood. using the complete genome sequence of brucella melitensis, we generated a database of protein-coding open reading frames (orfs) and constru ...	2004	15489343
regulatory role of rhizobium etli cnpaf512 fnrn during symbiosis.	the rhizobium etli cnpaf512 fnrn gene was identified in the fixabcx rpon(2) region. the corresponding protein contains the hallmark residues characteristic of proteins belonging to the class ib group of fnr-related proteins. the expression of r. etli fnrn is highly induced under free-living microaerobic conditions and during symbiosis. this microaerobic and symbiotic induction of fnrn is not controlled by the sigma factor rpon and the symbiotic regulator nifa or fixlj, but it is due to positive ...	2004	15006745
characteristics of a new enantioselective thermostable dipeptidase from brevibacillus borstelensis bcs-1 and its application to synthesis of a d-amino-acid-containing dipeptide.	a new thermostable dipeptidase gene was cloned from the thermophile brevibacillus borstelensis bcs-1 by genetic complementation of the d-glu auxotroph escherichia coli wm335 on a plate containing d-ala-d-glu. nucleotide sequence analysis revealed that the gene included an open reading frame coding for a 307-amino-acid sequence with an m(r) of 35,000. the deduced amino acid sequence of the dipeptidase exhibited 52% similarity with the dipeptidase from listeria monocytogenes. the enzyme was purifi ...	2004	15006780
diverse organization of genes of the beta-ketoadipate pathway in members of the marine roseobacter lineage.	members of the roseobacter lineage, an ecologically important marine clade within the class alpha-proteobacteria, harbor genes for the protocatechuate branch of the beta-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. the genes of this pathway are typically clustered, although gene order varies among organisms. here we characterize genes linked to pcah and -g, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the roseobacter lin ...	2004	15006791
phylogenomics of the reproductive parasite wolbachia pipientis wmel: a streamlined genome overrun by mobile genetic elements.	the complete sequence of the 1,267,782 bp genome of wolbachia pipientis wmel, an obligate intracellular bacteria of drosophila melanogaster, has been determined. wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. analysis of the wmel genome, in particular phylogenomic comparisons with other intracellular bacteria, has reveale ...	2004	15024419
evolutionarily conserved regions and hydrophobic contacts at the superfamily level: the case of the fold-type i, pyridoxal-5'-phosphate-dependent enzymes.	the wealth of biological information provided by structural and genomic projects opens new prospects of understanding life and evolution at the molecular level. in this work, it is shown how computational approaches can be exploited to pinpoint protein structural features that remain invariant upon long evolutionary periods in the fold-type i, plp-dependent enzymes. a nonredundant set of 23 superposed crystallographic structures belonging to this superfamily was built. members of this family typ ...	2004	15498941
islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their dna site specificities.	prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. integration usually occurs within a trna or tmrna gene, splitting the gene, yet sequences within the island restore the disrupted gene. the regenerated rna gene and the displaced fragment of that gene thus mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequences. our algorithm generates a list of trna and tmrna ...	2004	14681358
trends between gene content and genome size in prokaryotic species with larger genomes.	although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. we have compared 115 completed prokaryotic genomes by using the clusters of orthologous groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategie ...	2004	14973198
codon usage bias from trna's point of view: redundancy, specialization, and efficient decoding for translation optimization.	the selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and trna content in the framework of translation optimization. because most studies have focused only on codon usage, we analyzed the trna gene pool of 102 bacterial species. we show that as minimal generation times get shorter, the genomes contain more trna genes, but fewer anticodon species. surprisingly, despite the wide g+c variation of ...	2004	15479947
cpndb: a chaperonin sequence database.	type i chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. sequences of cpn60 genes, encoding 60-kda chaperonin protein subunits (cpn60, also known as groel or hsp60), are useful for phylogenetic studies and as targets for detection and identification of organisms. conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal pcr primers. here, we introduce cpndb, a curated collectio ...	2004	15289485
root-knot nematodes and bacterial nod factors elicit common signal transduction events in lotus japonicus.	the symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [nod factors (nf)]. using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living lotus japonicus root hairs, which precede root-hair deformation and reflect one of the earliest host responses to nf. remarkably, plant-parasitic root-knot nematodes (rkn) invoke a cytoskeletal response identical to that seen in r ...	2005	15710894
gene cassettes potentially encoding fosfomycin resistance determinants.		2005	15673790
the two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure.	the origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. until recently, too little phylogenetic information was available to address this issue by using multiple characters for many lineages.	2005	16207356
activation of olfactory-type cyclic nucleotide-gated channels is highly cooperative.	cyclic nucleotide-gated (cng) ion channels play a key role in the sensory transduction of vision and olfaction. the channels are opened by the binding of cyclic nucleotides. native olfactory cng channels are heterotetramers of cnga2, cnga4, and cngb1b subunits. upon heterologous expression, only cnga2 subunits can form functional homotetrameric channels. it is presently not known how the binding of the ligands to the four subunits is translated to channel opening. we studied activation of olfact ...	2005	16081488
correctly identifying the streptothricin resistance gene cassette.		2005	16082007
seven lotus japonicus genes required for transcriptional reprogramming of the root during fungal and bacterial symbiosis.	a combined genetic and transcriptome analysis was performed to study the molecular basis of the arbuscular mycorrhiza (am) symbiosis. by testing the am phenotype of nodulation-impaired mutants and complementation analysis, we defined seven lotus japonicus common symbiosis genes (symrk, castor, pollux, sym3, sym6, sym15, and sym24) that are required for both fungal and bacterial entry into root epidermal or cortical cells. to describe the phenotype of these mutants at the molecular level, we scre ...	2005	15980262
microbial k+ channels.		2005	15897296
peace talks and trade deals. keys to long-term harmony in legume-microbe symbioses.		2005	15824283