Publications

the biphenyl- and 4-chlorobiphenyl-catabolic transposon tn4371, a member of a new family of genomic islands related to incp and ti plasmids.	the nucleotide sequence of the biphenyl catabolic transposon tn4371 has been completed and analyzed. it confirmed that the element has a mosaic structure made of several building blocks. in addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of achromobacter georgiopolitanum kks102, tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, pl ...	2003	12902278
the ti plasmid of agrobacterium tumefaciens harbors an attm-paralogous gene, aiib, also encoding n-acyl homoserine lactonase activity.	the agrobacterium tumefaciens c58 genome contains three putative n-acyl homoserine lactone (acyl-hsl) hydrolases, which are closely related to the lactonase aiia of bacillus. when expressed in escherichia coli, two of the putative acyl-hsl hydrolases, attm and aiib, conferred the ability to degrade acyl-hsls on the host. in erwinia strain 6276, the lactonases reduced the endogenous acyl-hsl level and the bacterial virulence in planta.	2003	12902298
comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.	zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. thus its transport is regulated by zinc repressors zur of proteobacteria and gram-positive bacteria from the bacillus group and adcr of bacteria from the streptococcus group. comparative computational analysis allowed us to identify binding signals of zur repressors gaaatgttatantataacatttc for gamma-proteobacteria, gtaatgtaataacattac for the agrobacterium group, gatatgttataacatatc for the rh ...	2003	12904577
application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.	a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes.	2003	12914674
control of sxt integration and excision.	the vibrio cholerae sxt element is a conjugative self-transmissible chromosomally integrating element that encodes resistance to multiple antibiotics. sxt integrates in a site-specific fashion at prfc and excises from the chromosome to form a circular but nonreplicative extrachromosomal form. both chromosomal integration and excision depend on an sxt-encoded recombinase, int. here we found that int is necessary and sufficient for sxt integration and that int expression in recipient cells require ...	2003	12923077
composition, acquisition, and distribution of the vi exopolysaccharide-encoding salmonella enterica pathogenicity island spi-7.	vi capsular polysaccharide production is encoded by the viab locus, which has a limited distribution in salmonella enterica serovars. in s. enterica serovar typhi, viab is encoded on a 134-kb pathogenicity island known as spi-7 that is located between partially duplicated trna(pheu) sites. functional and bioinformatic analysis suggests that spi-7 has a mosaic structure and may have evolved as a consequence of several independent insertion events. analysis of viab-associated dna in vi-positive s. ...	2003	12923078
regulation of the vitamin b12 metabolism and transport in bacteria by a conserved rna structural element.	cobalamin in the form of adenosylcobalamin (ado-cbl) is known to repress expression of genes for vitamin b(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of ado-cbl to 5'untranslated gene regions (5'utr). using comparative analysis of genes and regulatory regions, we identified a highly conserved rna structure, the b12-element, which is widely distributed in 5'utrs of vitamin b(12)-related genes in eubacteria. multiple alignment o ...	2003	12923257
a novel antimicrobial protein isolated from potato (solanum tuberosum) shares homology with an acid phosphatase.	the nucleotide and amino acids sequences for ap(1) will appear in the genbank(r) and ncbi databases under accession number ay297449. a novel antimicrobial protein (ap(1)) was purified from leaves of the potato ( solanum tuberosum, variety ms-42.3) with a procedure involving ammonium sulphate fractionation, molecular sieve chromatography with sephacryl s-200 and hydrophobic chromatography with butyl-sepharose using a fplc system. the inhibition spectrum investigation showed that ap(1) had good in ...	2003	12927022
intrinsic contributions of polar amino acid residues toward thermal stability of an abc-atpase of mesophilic origin.	the nucleotide-binding subunit of phosphate-specific transporter (pstb) from mesophilic bacterium, mycobacterium tuberculosis, is a unique atp-binding cassette (abc) atpase because of its unusual ability to hydrolyze atp at high temperature. in an attempt to define the basis of thermostability, we took a theoretical approach and compared amino acid composition of this protein to that of other pstbs from available bacterial genomes. interestingly, based on the content of polar amino acids, this p ...	2003	12931011
elucidation of the o-chain structure from the lipopolysaccharide of agrobacterium tumefaciens strain c58.	a linear homopolysaccharide built of 3-alpha-l-6dtalp residues, randomly acetylated at position c-4, is described for the o-specific polysaccharide of agrobacterium tumefaciens strain c58. this structure, determined by spectroscopical and chemical methods, is strictly correlated to that of rhizobium loti strain nzp2213, which differs for the degree and the position of o-acetylation.	2003	12932373
a lotus japonicus beta-type carbonic anhydrase gene expression pattern suggests distinct physiological roles during nodule development.	a full-length cdna clone, designated ljca1, coding for a beta-type carbonic anhydrase (ca; ec: 4.2.1.1) was isolated from a lotus japonicus nodule cdna library. semi-quantitative rt-pcr analysis revealed that ljca1 codes for a nodule-specific ca, transcripts of which accumulate at maximum levels in young nodules at 14 days post-infection (d.p.i.). in situ hybridization and immunolocalization revealed that ljca1 transcripts and ljca1 polypeptides were present at high levels in all cell types of y ...	2003	12932831
purification and characterization of an immunogenic aminopeptidase of brucella melitensis.	an immunogenic aminopeptidase was purified from brucella melitensis strain vtrm1. the purification procedure consisted of ammonium sulfate fractionation and three chromatographic steps. this procedure resulted in a yield of 29% and a 144-fold increase in specific activity. the aminopeptidase appeared to be a monomeric enzyme with a molecular mass of 96 kda and an isoelectric point of 4.8. its activity was optimal at ph 7.0 at 40 degrees c. the enzyme was strongly inhibited by edta, 1,10-phenathr ...	2003	12933870
ehrlichia chaffeensis and anaplasma phagocytophilum lack genes for lipid a biosynthesis and incorporate cholesterol for their survival.	ehrlichia chaffeensis and anaplasma phagocytophilum are agents of human monocytic and granulocytic ehrlichioses, respectively. they are extremely sensitive to mechanical stress and are pleomorphic gram-negative bacteria. membrane incorporation of cholesterol from the eukaryotic host is known to be essential for other fragile and pleomorphic bacteria and mycoplasmas that lack a cell wall. thus, we tested whether cholesterol is required for e. chaffeensis and a. phagocytophilum. using a freeze fra ...	2003	12933880
evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.	shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire opero ...	2003	12952534
the cog database: an updated version includes eukaryotes.	the availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.	2003	12969510
does lowering glutamine synthetase activity in nodules modify nitrogen metabolism and growth of lotus japonicus?	a cdna encoding cytosolic glutamine synthetase (gs) from lotus japonicus was fused in the antisense orientation relative to the nodule-specific lbc3 promoter of soybean (glycine max) and introduced into l. japonicus via transformation with agrobacterium tumefaciens. among the 12 independent transformed lines into which the construct was introduced, some of them showed diminished levels of gs1 mrna and lower levels of gs activity. three of these lines were selected and their t(1) progeny was furt ...	2003	12970491
experimental determination and system level analysis of essential genes in escherichia coli mg1655.	defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. we used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of escherichia coli in rich media. we identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. functional context analysis of these data allows individual functional assignment ...	2003	13129938
characterization of a spontaneous nonmagnetic mutant of magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island.	frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium magnetospirillum gryphiswaldense msr-1. a nonmagnetic mutant, designated strain msr-1b, was isolated and characterized. the mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. the growth of strain msr-1b was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iro ...	2003	13129949
complete sequence of virulence plasmid pjm1 from the marine fish pathogen vibrio anguillarum strain 775.	the virulence plasmid pjm1 enables the fish pathogen vibrio anguillarum, a gram-negative polarly flagellated comma-shaped rod bacterium, to cause a highly fatal hemorrhagic septicemic disease in salmonids and other fishes, leading to epizootics throughout the world. the pjm1 plasmid 65,009-nucleotide sequence, with an overall g+c content of 42.6%, revealed genes and open reading frames (orfs) encoding iron transporters, nonribosomal peptide enzymes, and other proteins essential for the biosynthe ...	2003	13129954
a noncognate aminoacyl-trna synthetase that may resolve a missing link in protein evolution.	efforts to delineate the advent of many enzymes essential to protein translation are often limited by the fact that the modern genetic code evolved before divergence of the tree of life. glutaminyl-trna synthetase (glnrs) is one noteworthy exception to the universality of the translation apparatus. in eukaryotes and some bacteria, this enzyme is essential for the biosynthesis of gln-trnagln, an obligate intermediate in translation. glnrs is absent, however, in archaea, and most bacteria, organel ...	2003	13679580
isolation and molecular characterization of thiosulfate-oxidizing bacteria from an italian rice field soil.	in rice paddy soils an active cycling of sulfur compounds takes place. to elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. from the mpn enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. these strains were characterized by 16s rdna analyses. the isolates were affiliated to seven diffe ...	2003	14529188
lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of nepsilon-acetyl-beta-lysine and growth at high salinity.	the compatible solute n(epsilon)-acetyl-beta-lysine is unique to methanogenic archaea and is produced under salt stress only. however, the molecular basis for the salt-dependent regulation of n(epsilon)-acetyl-beta-lysine formation is unknown. genes potentially encoding lysine-2,3-aminomutase (abla) and beta-lysine acetyltransferase (ablb), which are assumed to catalyze n(epsilon)-acetyl-beta-lysine formation from alpha-lysine, were identified on the chromosomes of the methanogenic archaea metha ...	2003	14532061
low sequence similarity and gene content of symbiotic clusters of bradyrhizobium sp. wm9 (lupinus) indicate early divergence of "lupin" lineage in the genus bradyrhizobium.	two sequenced nodulation regions of lupin bradyrhizobium sp. wm9 carried the majority of genes involved in the nod factor production. the nod region i harbored: nola, nodd, noda, nodb, nodc, nods, nodi, nodj, nolo, nodz, fixr, nifa, fixa, nodm, nolk and noel. this gene arrangement resembled that found in the nodulation region of bradyrhizobium japonicum usda110, however strain wm9 harbored only one nodd gene copy, while the nodm, nolk and noel genes had no counterparts in the 410 kb symbiotic re ...	2003	14533715
plant recognition of symbiotic bacteria requires two lysm receptor-like kinases.	although most higher plants establish a symbiosis with arbuscular mycorrhizal fungi, symbiotic nitrogen fixation with rhizobia is a salient feature of legumes. despite this host range difference, mycorrhizal and rhizobial invasion shares a common plant-specified genetic programme controlling the early host interaction. one feature distinguishing legumes is their ability to perceive rhizobial-specific signal molecules. we describe here two lysm-type serine/threonine receptor kinase genes, nfr1 an ...	2003	14534578
d-xylose metabolism in hypocrea jecorina: loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded l-arabinitol-4-dehydrogenase.	with the goal of the genetic characterization of the d-xylose pathway in hypocrea jecorina (anamorph: trichoderma reesei), we cloned the xdh1 gene, encoding nad-xylitol dehydrogenase, which catalyzes the second step of fungal d-xylose catabolism. this gene encodes a 363-amino-acid protein which has a mass of 38 kda, belongs to the zinc-containing alcohol dehydrogenase family, exhibits high sequence identity to the published sequences of xylitol dehydrogenases from yeast origins, but contains a s ...	2003	14555469
the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons.	is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ...	2003	14563872
identification of quorum-sensing-regulated genes of burkholderia cepacia.	quorum sensing is a regulatory mechanism (operating in response to cell density) which in gram-negative bacteria usually involves the production of n-acyl homoserine lactones (hsl). quorum sensing in burkholderia cepacia has been associated with the regulation of expression of extracellular proteins and siderophores and also with the regulation of swarming and biofilm formation. in the present study, several quorum-sensing-controlled gene promoters of b. cepacia atcc 25416 were identified and ch ...	2003	14563881
bacteriophage st64b, a genetic mosaic of genes from diverse sources isolated from salmonella enterica serovar typhimurium dt 64.	the complete sequence of the double-stranded dna (dsdna) genome of the salmonella enterica serovar typhimurium st64b bacteriophage was determined. the 40,149-bp genomic sequence of st64b has an overall g+c content of 51.3% and is distinct from that of p22. the genome architecture is similar to that of the lambdoid phages, particularly that of coliphage lambda. most of the putative tail genes showed sequence similarity to tail genes of mu, a nonlambdoid phage. in addition, it is likely that these ...	2003	14563886
convergent neofunctionalization by positive darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene.	gene duplication is a primary source of molecular substrate for the emergence of evolutionary novelties. the chances for redundant gene sequences to evolve new functions are small compared with the probability that the copies become disabled by deleterious mutations. functional divergence after gene duplication can result in two alternative evolutionary fates: one copy acquires a novel function (neofunctionalization), or each copy adopts part of the tasks of their parental gene (subfunctionaliza ...	2003	14576276
one step assembly of multiple dna fragments with a designed order and orientation in bacillus subtilis plasmid.	a universal method to reconstitute sets of genes was developed. owing to the intrinsic nature of the plasmid establishment mechanism in bacillus subtilis, the assembly of five antibiotic resistance genes with a defined order and orientation was achieved. these five fragments and the plasmid have three-base protruding sequences at both ends. the protruding sequences are designed so that each fragment is ligated once in a row according to the pairing. ligation by t4 dna ligase in the presence of 1 ...	2003	14576333
gamma-proteobacteria aquicella lusitana gen. nov., sp. nov., and aquicella siphonis sp. nov. infect protozoa and require activated charcoal for growth in laboratory media.	several isolates, belonging to two new species of the same novel genus of gamma-proteobacteria, were recovered from drilled well (borehole) and spa water at são gemil in central portugal. these organisms are phylogenetically most closely related to the strictly intracellular uncultured species of the genus rickettsiella, which cause disease in arthropods, and to the facultatively intracellular species of the genus legionella, some of which cause legionnaires' disease and pontiac fever. the são g ...	2003	14602611
usefulness of rpob gene sequencing for identification of afipia and bosea species, including a strategy for choosing discriminative partial sequences.	bacteria belonging to the genera afipia and bosea are amoeba-resisting bacteria that have been recently reported to colonize hospital water supplies and are suspected of being responsible for intensive care unit-acquired pneumonia. identification of these bacteria is now based on determination of the 16s ribosomal dna sequence. however, the 16s rrna gene is not polymorphic enough to ensure discrimination of species defined by dna-dna relatedness. the complete rpob sequences of 20 strains were fi ...	2003	14602635
coevolution of an aminoacyl-trna synthetase with its trna substrates.	glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ...	2003	14615592
identification and characterization of genes required for biosynthesis and transport of the siderophore vibrioferrin in vibrio parahaemolyticus.	in response to low iron availability, vibrio parahaemolyticus synthesizes and secretes a polyhydroxycarboxylate-type siderophore vibrioferrin which is composed of 1 mol each of 2-ketoglutaric acid, l-alanine, ethanolamine, and citric acid. we have previously reported the cloning and characterization of the pvua gene, which encodes the 78-kda outer membrane receptor protein for ferric vibrioferrin. in this study, nine genes involved in the biosynthesis and transport of vibrioferrin have been iden ...	2003	14617658
a dna element recognised by the molybdenum-responsive transcription factor mode is conserved in proteobacteria, green sulphur bacteria and archaea.	the transition metal molybdenum is essential for life. escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an abc transport system. in e. coli and other proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor mode.	2003	14641908
purification of the formate-tetrahydrofolate ligase from methylobacterium extorquens am1 and demonstration of its requirement for methylotrophic growth.	the serine cycle methylotroph methylobacterium extorquens am1 contains two pterin-dependent pathways for c(1) transfers, the tetrahydrofolate (h(4)f) pathway and the tetrahydromethanopterin (h(4)mpt) pathway, and both are required for growth on c(1) compounds. with the exception of formate-tetrahydrofolate ligase (ftfl, alternatively termed formyl-h(4)f synthetase), all of the genes encoding the enzymes comprising these two pathways have been identified, and the corresponding gene products have ...	2003	14645277
convergent evolution of amadori opine catabolic systems in plasmids of agrobacterium tumefaciens.	deoxyfructosyl glutamine (dfg, referred to elsewhere as dfg) is a naturally occurring amadori compound found in rotting fruits and vegetables. dfg also is an opine and is found in tumors induced by chrysopine-type strains of agrobacterium tumefaciens. such strains catabolize this opine via a pathway coded for by their plasmids. nt1, a derivative of the nopaline-type a. tumefaciens strain c58 lacking ptic58, can utilize dfg as the sole carbon source. genes for utilization of dfg were mapped to th ...	2003	12511498
novel methylotrophy genes of methylobacterium extorquens am1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase.	ten novel methylotrophy genes of the facultative methylotroph methylobacterium extorquens am1 were identified from a transposon mutagenesis screen. one of these genes encodes a product having identity with dihydrofolate reductase (dhfr). this mutant has a c(1)-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (h(4)mpt)-dependent formaldehyde oxidation. these results suggest that this gene, dmra, may encode dihydrome ...	2003	12511515
gene cloning, purification, and characterization of a phosphodiesterase from delftia acidovorans.	a novel phosphodiesterase (pdea) was purified from delftia acidovorans, the gene encoding the enzyme was cloned and expressed in escherichia coli, and the recombinant enzyme was purified to apparent homogeneity and characterized. pdea is an 85-kda trimer that exhibits maximal activity at 65 degrees c and ph 10 even though it was isolated from a mesophilic bacterium. although pdea exhibited both mono- and diesterase activity, it was most active on the phosphodiester bis(p-nitrophenyl)phosphate wi ...	2003	12514034
formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups.	sixty-two partial formyltetrahydrofolate synthetase (fthfs) structural gene sequences were recovered from roots of salt marsh plants, including spartina alterniflora, salicornia virginica, and juncus roemerianus. only s. alterniflora roots yielded sequences grouping with fthfs sequences from known acetogens. most other fthfs or fthfs-like sequences grouped with those from sulfate-reducing bacteria. several sequences that grouped with sphingomonas paucimobilis ligh were also recovered.	2003	12514064
the structure of actva-orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis.	actva-orf6 monooxygenase from streptomyces coelicolor that catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway is a member of a class of small monooxygenases that carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. the overall structure is a ferredoxin-like fold with a novel dimeric assembly, indicating that the widely represented ferredoxin fold may ...	2003	12514126
new connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated rna decay system.	several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. recent findings suggest that chromosomally encoded copies of toxins and antitoxins of post-segregational cell killing systems - such as the rele system - might function as regulatory switches under stress conditions. the rele toxin cleaves ribosome-associated transcripts, whereas another post-segregational cell killing toxin, pare, functions as a gyrase inhibitor.	2003	14659018
identification and characterization of the ddlb, ftsq and ftsa genes upstream of ftsz in bartonella bacilliformis and bartonella henselae.	homologues of the cell division protein ftsz were previously identified in bartonella bacilliformis and bartonella henselae. we report herein that ftsz is located at the distal end of an operon that includes ddlb, ftsq, and ftsa. these genes code for homologues of d-alanine d-alanine ligase, an enzyme involved in cell wall biosynthesis, and ftsq, and ftsa, which are involved in cell division. the ddlb, ftsq, and ftsa proteins from bartonella species are most homologous to proteins in closely rel ...	2003	14659047
identification and distribution of insertion sequences of paracoccus solventivorans.	three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ...	2003	14660342
molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity.	isolates belonging to six genera not previously known to oxidize co were obtained from enrichments with aquatic and terrestrial plants. dna from these and other isolates was used in pcr assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxl). coxl and putative coxl fragments were amplified from known co oxidizers (e.g., oligotropha carboxidovorans and bradyrhizobium japonicum), from novel co-oxidizing isolates (e.g., aminobacter sp. strain cox, burkholderia sp. strain lu ...	2003	14660374
metagenome survey of biofilms in drinking-water networks.	most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. first, a sequence analysis of 650 16s rrna clones indicated a high diversity within the biofilm communities, with the ma ...	2003	14660379
pathways for phosphatidylcholine biosynthesis in bacteria.	phosphatidylcholine (pc) is the major membrane-forming phospholipid in eukaryotes with important structural and signalling functions. although many prokaryotes lack pc, it can be found in significant amounts in membranes of rather diverse bacteria. two pathways for pc biosynthesis are known in bacteria, the methylation pathway and the phosphatidylcholine synthase (pcs) pathway. in the methylation pathway, phosphatidylethanolamine is methylated three times to yield pc, in reactions catalysed by o ...	2003	14663079
trans-editing of mischarged trnas.	aminoacyl-trna synthetases (aarss) are multidomain proteins that specifically attach amino acids to their cognate trnas. their most conserved, and presumably evolutionarily oldest, domains are the catalytic cores, which activate amino acids and transfer them to the 3' ends of trnas. additional domains appended to or inserted in the body of aarss increase efficiency and specificity of the aminoacylation process, either by providing additional trna contacts, or by hydrolyzing noncognate amino acid ...	2003	14663147
quorum sensing in nitrogen-fixing rhizobia.	members of the rhizobia are distinguished for their ability to establish a nitrogen-fixing symbiosis with leguminous plants. while many details of this relationship remain a mystery, much effort has gone into elucidating the mechanisms governing bacterium-host recognition and the events leading to symbiosis. several signal molecules, including plant-produced flavonoids and bacterially produced nodulation factors and exopolysaccharides, are known to function in the molecular conversation between ...	2003	14665677
mechanistic diversity of fosfomycin resistance in pathogenic microorganisms.	microbial resistance to the antibiotic fosfomycin [(1r,2s)-epoxypropylphosphonic acid, 1] is known to be mediated by thiol transferase enzymes fosa and fosb, which catalyze the addition of glutathione and l-cysteine to c1 of the oxirane, respectively. a probe of the microbial genome database reveals a related group of enzymes (fosx). the genes mlr3345 from mesorhizobium loti and lmo1702 from listeria monocytogenes were cloned and the proteins expressed. this heretofore unrecognized group of enzy ...	2003	14677948
protein profile of symbiotic bacteria mesorhizobium loti maff303099 in mid-growth phase.	expressed proteins in cultured symbiotic bacteria (mesorhizobium loti maff303099) in the mid-growth phase were proteomically analyzed by two-dimensional polyacrylamide gel electrophoresis (2d-page) and capillary high-performance liquid chromatography coupled with an ion-trap mass spectrometry (ms). the genome sequence data of m. loti were used to identify the analyzed proteins. we identified 114 of the 127 proteins analyzed on 2d-page gel with some microheterogenities which were caused by post-t ...	2003	14730152
domain organization of the mscs mechanosensitive channel of escherichia coli.	the major structural features of the escherichia coli mscs mechanosensitive channel protein have been explored using alkaline phosphatase (phoa) fusions, precise deletions and site-directed mutations. phoa protein fusion data, combined with the positive-inside rule, strongly support a model in which mscs crosses the membrane three times, adopting an n(out)-c(in) configuration. deletion data suggest that the c-terminal domain of the protein is essential for the stability of the mscs channel, wher ...	2003	12505982
a glutamate mutase is involved in the biosynthesis of the lipopeptide antibiotic friulimicin in actinoplanes friuliensis.	actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin. this antibiotic is active against gram-positive bacteria such as multiresistant enterococcus and staphylococcus strains. it consists of 10 amino acids that form a ring structure and 1 exocyclic amino acid to which an acyl residue is attached. by a reverse genetic approach, biosynthetic genes were identified that are required for the nonribosomal synthesis of the antibiotic. in close proximity two genes (glma and glmb) were ...	2003	12543643
biosynthesis of phosphatidylcholine in bacteria.	phosphatidylcholine (pc) is the major membrane-forming phospholipid in eukaryotes and can be synthesized by either of two pathways, the methylation pathway or the cdp-choline pathway. many prokaryotes lack pc, but it can be found in significant amounts in membranes of rather diverse bacteria and based on genomic data, we estimate that more than 10% of all bacteria possess pc. enzymatic methylation of phosphatidylethanolamine via the methylation pathway was thought to be the only biosynthetic pat ...	2003	12547654
whole-genome sequence variation among multiple isolates of pseudomonas aeruginosa.	whole-genome shotgun sequencing was used to study the sequence variation of three pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain pao1. the majority of the pao1 genome is represented in these strains; however, at least three prominent islands of pao1-specific sequence are apparent. conversely, approximately 10% of the sequencing reads derived from each isolate fail to ...	2003	12562802
prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey.	the twin-arginine translocation (tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. however, the extent to which this pathway is used among the prokaryotes is not known. by using a genomic approach, a comprehensive list of putative tat substrates for 84 diverse prokaryotes was established. strikingly, the results indicate that the tat pathway is utilized to highly varying extents. furthermore, while many prokaryotes use thi ...	2003	12562823
characterization of a thermostable d-stereospecific alanine amidase from brevibacillus borstelensis bcs-1.	a gene encoding a new thermostable d-stereospecific alanine amidase from the thermophile brevibacillus borstelensis bcs-1 was cloned and sequenced. the molecular mass of the purified enzyme was estimated to be 199 kda after gel filtration chromatography and about 30 kda on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the enzyme could be composed of a hexamer with identical subunits. the purified enzyme exhibited strong amidase activity towards d-amino acid-containin ...	2003	12571020
salicylic acid inhibits indeterminate-type nodulation but not determinate-type nodulation.	lcos (lipochitin oligosaccharides, nod factors) produced by the rhizobial symbiote of vicia sativa subsp. nigra (vetch, an indeterminate-type nodulating plant) are mitogenic when carrying an 18:4 acyl chain but not when carrying an 18:1 acyl chain. this suggests that the 18:4 acyl chain specifically contributes to signaling in indeterminate-type nodulation. in a working hypothesis, we speculated that the 18:4 acyl chain is involved in oxylipin signaling comparable to, for example, signaling by d ...	2003	12580285
a mannosyl transferase required for lipopolysaccharide inner core assembly in rhizobium leguminosarum. purification, substrate specificity, and expression in salmonella waac mutants.	the lipopolysaccharide (lps) core domain of gram-negative bacteria plays an important role in outer membrane stability and host interactions. little is known about the biochemical properties of the glycosyltransferases that assemble the lps core. we now report the purification and characterization of the rhizobium leguminosarum mannosyl transferase lpcc, which adds a mannose unit to the inner 3-deoxy-d-manno-octulosonic acid (kdo) moiety of the lps precursor, kdo(2)-lipid iv(a). lpcc containing ...	2003	12591937
algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.	comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (hgt), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. this complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task.	2003	12515582
reductive genome evolution in buchnera aphidicola.	we have sequenced the genome of the intracellular symbiont buchnera aphidicola from the aphid baizongia pistacea. this strain diverged 80-150 million years ago from the common ancestor of two previously sequenced buchnera strains. here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. as a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. comparison of the 618-kb (kbp) g ...	2003	12522265
noti passporting to identify species composition of complex microbial systems.	we describe here a new method for large-scale scanning of microbial genomes on a quantitative and qualitative basis. to achieve this aim we propose to create noti passports: databases containing noti tags. we demonstrated that these tags comprising 19 bp of sequence information could be successfully generated using dna isolated from intestinal or fecal samples. such noti passports allow the discrimination between closely related bacterial species and even strains. this procedure for generating r ...	2003	12527794
origin of the 2-amino-2-deoxy-gluconate unit in rhizobium leguminosarum lipid a. expression cloning of the outer membrane oxidase lpxq.	an unusual feature of the lipid a from the plant endosymbionts rhizobium etli and rhizobium leguminosarum is the presence of a proximal sugar unit consisting of a 2-amino-2-deoxy-gluconate moiety in place of glucosamine. an outer membrane oxidase that generates the 2-amino-2-deoxy-gluconate unit from a glucosamine-containing precursor is present in membranes of r. leguminosarum and r. etli but not in s. meliloti or escherichia coli. we now report the identification of a hybrid cosmid that direct ...	2003	12531908
comparative analyses of the complete genome sequences of pierce's disease and citrus variegated chlorosis strains of xylella fastidiosa.	xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. x. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the american continent, and induces diverse disease phenotypes. previous molecular analyses indicated three distinct groups of x. fastidiosa isolates that were expected to be genetically divergent. here we r ...	2003	12533478
traffic at the tmrna gene.	a partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmrna gene (ssra) than for any type of trna gene. horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. diverse elements use ssra; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssra, and almost every s ...	2003	12533482
regulation of expression of symbiotic genes in rhizobium sp. ngr234.	research in the field of rhizobium-legume symbiosis faces a new challenge: integrate the wealth of information generated by genomic projects. the goal: apprehend the complexity of the molecular mechanisms involved in symbiotic associations. at the time of writing, the genomes of three micro-symbionts (bradyrhizobium japonicum, mesorhizobium loti and sinorhizobium meliloti) have been sequenced, and two more (those of rhizobium leguminosarum and rhizobium etli) will be completed in the near future ...	2003	15242276
roses by other names: taxonomy of the rhizobiaceae.		2003	12730155
use of cdna microarrays to monitor transcriptional responses of the chestnut blight fungus cryphonectria parasitica to infection by virulence-attenuating hypoviruses.	hypoviruses are a family of cytoplasmically replicating rna viruses of the chestnut blight fungus cryphonectria parasitica. members of this mycovirus family persistently alter virulence (hypovirulence) and related fungal developmental processes, including asexual and sexual sporulation. in order to gain a better understanding of the molecular basis for these changes, we have developed a c. parasitica cdna microarray to monitor global transcriptional responses to hypovirus infection. in this repo ...	2003	14665460
biochemical and molecular characterization of transgenic lotus japonicus plants constitutively over-expressing a cytosolic glutamine synthetase gene.	higher plants assimilate nitrogen in the form of ammonia through the concerted activity of glutamine synthetase (gs) and glutamate synthase (gogat). the gs enzyme is either located in the cytoplasm (gs1) or in the chloroplast (gs2). to understand how modulation of gs activity affects plant performance, lotus japonicus l. plants were transformed with an alfalfa gs1 gene driven by the camv 35s promoter. the transformants showed increased gs activity and an increase in gs1 polypeptide level in all ...	2004	15197594
oxygen-controlled bacterial growth in the sponge suberites domuncula: toward a molecular understanding of the symbiotic relationships between sponge and bacteria.	sponges (phylum porifera), known to be the richest producers among the metazoans of bioactive secondary metabolites, are assumed to live in a symbiotic relationship with microorganisms, especially bacteria. until now, the molecular basis of the mutual symbiosis, the exchange of metabolites for the benefit of the other partner, has not been understood. we show with the demosponge suberites domuncula as a model that the sponge expresses under optimal aeration conditions the enzyme tyrosinase, whic ...	2004	15066829
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
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
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
a cyclic nucleotide modulated prokaryotic k+ channel.	a search of prokaryotic genomes uncovered a gene from mesorhizobium loti homologous to eukaryotic k(+) channels of the s4 superfamily that also carry a cyclic nucleotide binding domain at the cooh terminus. the gene was cloned from genomic dna, and the protein, denoted mlok1, was overexpressed in escherichia coli and purified. gel filtration analysis revealed a heterogeneous distribution of protein sizes which, upon inclusion of cyclic nucleotide, coalesces into a homogeneous population, eluting ...	2004	15337819
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
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
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