| enzymatic manganese(ii) oxidation by a marine alpha-proteobacterium. | a yellow-pigmented marine bacterium, designated strain sd-21, was isolated from surface sediments of san diego bay, san diego, calif., based on its ability to oxidize soluble mn(ii) to insoluble mn(iii, iv) oxides. 16s rrna analysis revealed that this organism was most closely related to members of the genus erythrobacter, aerobic anoxygenic phototrophic bacteria within the alpha-4 subgroup of the proteobacteria (alpha-4 proteobacteria). sd-21, however, has a number of distinguishing phenotypic ... | 2001 | 11526000 |
| mtnk, methylthioribose kinase, is a starvation-induced protein in bacillus subtilis. | methylthioadenosine, the main by-product of spermidine synthesis, is degraded in bacillus subtilis as adenine and methylthioribose. the latter is an excellent sulfur source and the precursor of quorum-sensing signalling molecules. nothing was known about methylthioribose recycling in this organism. | 2001 | 11545674 |
| ferrochelatase is present in brucella abortus and is critical for its intracellular survival and virulence. | brucella spp. are pathogenic bacteria that cause brucellosis, an animal disease which can also affect humans. although understanding the pathogenesis is important for the health of animals and humans, little is known about virulence factors associated with it. in order for chronic disease to be established, brucella spp. have developed the ability to survive inside phagocytes by evading cell defenses. it hides inside vacuoles, where it then replicates, indicating that it has an active metabolism ... | 2001 | 11553564 |
| the diversity of rhizobia nodulating beans in northwest argentina as a source of more efficient inoculant strains. | the common bean (phaseolus vulgaris l.) is cultivated widely in central and south america and particularly in the northwest of argentina. in order to describe the diversity of the common bean nodulating rhizobial population from the bean producing area in northwest argentina (nwa), a collection of about 400 isolates of common beans recovered from nodules and soil samples from nwa were characterized by using nifh-pcr, analysis of genes coding for 16s rrna and nodc, and rep-fingerprinting, respect ... | 2001 | 11566389 |
| genetic locus required for antigenic maturation of rhizobium etli ce3 lipopolysaccharide. | rhizobium etli modifies lipopolysaccharide (lps) structure in response to environmental signals, such as low ph and anthocyanins. these lps modifications result in the loss of reactivity with certain monoclonal antibodies. the same antibodies fail to recognize previously isolated r. etli mutant strain ce367, even in the absence of such environmental cues. chemical analysis of the lps in strain ce367 demonstrated that it lacked the terminal sugar of the wild-type o antigen, 2,3,4-tri-o-methylfuco ... | 2001 | 11567006 |
| identification of the partitioning site within the repabc-type replicon of the composite paracoccus versutus plasmid ptav1. | the replicator region of composite plasmid ptav1 of paracoccus versutus (included in mini-replicon ptav320) belongs to the family of repabc replicons commonly found in plasmids harbored by agrobacterium and rhizobium spp. the repabc replicons encode three genes clustered in an operon, which are involved in partitioning (repa and repb) and replication (repc). in order to localize the partitioning site of ptav320, the two identified incompatibility determinants of this mini-replicon (inc1, located ... | 2001 | 11591666 |
| the esat-6 gene cluster of mycobacterium tuberculosis and other high g+c gram-positive bacteria. | the genome of mycobacterium tuberculosis h37rv has five copies of a cluster of genes known as the esat-6 loci. these clusters contain members of the cfp-10 (lhp) and esat-6 (esat-6) gene families (encoding secreted t-cell antigens that lack detectable secretion signals) as well as genes encoding secreted, cell-wall-associated subtilisin-like serine proteases, putative abc transporters, atp-binding proteins and other membrane-associated proteins. these membrane-associated and energy-providing pro ... | 2001 | 11597336 |
| cloning of a genetically unstable cytochrome p-450 gene cluster involved in degradation of the pollutant ethyl tert-butyl ether by rhodococcus ruber. | rhodococcus ruber (formerly gordonia terrae) ifp 2001 is one of a few bacterial strains able to degrade ethyl tert-butyl ether (etbe), which is a major pollutant from gasoline. this strain was found to undergo a spontaneous 14.3-kbp chromosomal deletion, which results in the loss of the ability to degrade etbe. sequence analysis of the region corresponding to the deletion revealed the presence of a gene cluster, ethabcd, encoding a ferredoxin reductase, a cytochrome p-450, a ferredoxin, and a 10 ... | 2001 | 11673424 |
| dna sequence and mutational analysis of rhizobitoxine biosynthesis genes in bradyrhizobium elkanii. | we cloned and sequenced a cluster of genes involved in the biosynthesis of rhizobitoxine, a nodulation enhancer produced by bradyrhizobium elkanii. the nucleotide sequence of the cloned 28.4-kb dna region encompassing rtxa showed that several open reading frames (orfs) were located downstream of rtxa. a large-deletion mutant of b. elkanii, usda94 delta rtx::omega 1, which lacks rtxa, orf1 (rtxc), orf2, and orf3, did not produce rhizobitoxine, dihydrorhizobitoxine, or serinol. the broad-host-rang ... | 2001 | 11679318 |
| pathoadaptive mutations that enhance virulence: genetic organization of the cada regions of shigella spp. | pathoadaptive mutations improve the fitness of pathogenic species by modification of traits that interfere with factors (virulence and ancestral) required for survival in host tissues. a demonstrated pathoadaptive mutation is the loss of lysine decarboxylase (ldc) expression in shigella species that have evolved from ldc-expressing escherichia coli. previous studies demonstrated that the product of ldc activity, cadaverine, blocks the action of shigella enterotoxins and that the gene encoding ld ... | 2001 | 11705922 |
| genome trees constructed using five different approaches suggest new major bacterial clades. | the availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes. | 2001 | 11734060 |
| dynamics of genome architecture in rhizobium sp. strain ngr234. | bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. to address these issues, we have studied the dynamics of the genome architecture in rhizobium sp. strain ngr234 and analyzed its biological significa ... | 2002 | 11741857 |
| degradation of aromatics and chloroaromatics by pseudomonas sp. strain b13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate:succinyl-coenzyme a (coa) transferase and 3-oxoadipyl-coa thiolase. | 3-oxoadipate:succinyl-coenzyme a (coa) transferase and 3-oxoadipyl-coa thiolase carry out the ultimate steps in the conversion of benzoate and 3-chlorobenzoate to tricarboxylic acid cycle intermediates in bacteria utilizing the 3-oxoadipate pathway. this report describes the characterization of dna fragments with the overall length of 5.9 kb from pseudomonas sp. strain b13 that encode these enzymes. dna sequence analysis revealed five open reading frames (orfs) plus an incomplete one. orf1, of u ... | 2002 | 11741863 |
| a glutathione-dependent formaldehyde-activating enzyme (gfa) from paracoccus denitrificans detected and purified via two-dimensional proton exchange nmr spectroscopy. | the formation of s-hydroxymethylglutathione from formaldehyde and glutathione is a central reaction in the consumption of the cytotoxin formaldehyde in some methylotrophic bacteria as well as in many other organisms. we describe here the discovery of an enzyme from paracoccus denitrificans that accelerates this spontaneous condensation reaction. the rates of s-hydroxymethylglutathione formation and cleavage were determined under equilibrium conditions via two-dimensional proton exchange nmr spec ... | 2002 | 11741920 |
| the embl nucleotide sequence database. | the embl nucleotide sequence database (aka embl-bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. embl-bank is located and maintained at the european bioinformatics institute (ebi) near cambridge, uk. in an international collaboration with ddbj (japan) and genbank (usa), data are exchanged amongst the collaborating databases on a daily basis. major contributors to the embl database are individual scientists and genom ... | 2002 | 11752244 |
| dna data bank of japan (ddbj) for genome scale research in life science. | the dna data bank of japan (ddbj, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from japanese researchers. the increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases. the increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science ha ... | 2002 | 11752245 |
| the genome sequence of the facultative intracellular pathogen brucella melitensis. | brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and malta fever in humans. the genome of b. melitensis strain 16m was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 orfs. by using the bioinformatics suite ergo, 2,487 (78%) orfs were assigned functions. the origins of replication of the two chromosomes are similar to those of other alpha-proteobacter ... | 2002 | 11756688 |
| the genome sequence of the facultative intracellular pathogen brucella melitensis. | brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and malta fever in humans. the genome of b. melitensis strain 16m was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 orfs. by using the bioinformatics suite ergo, 2,487 (78%) orfs were assigned functions. the origins of replication of the two chromosomes are similar to those of other alpha-proteobacter ... | 2002 | 11756688 |
| cloning, sequence analysis, and expression in escherichia coli of the gene encoding an alpha-amino acid ester hydrolase from acetobacter turbidans. | the alpha-amino acid ester hydrolase from acetobacter turbidans atcc 9325 is capable of hydrolyzing and synthesizing beta-lactam antibiotics, such as cephalexin and ampicillin. n-terminal amino acid sequencing of the purified alpha-amino acid ester hydrolase allowed cloning and genetic characterization of the corresponding gene from an a. turbidans genomic library. the gene, designated aeha, encodes a polypeptide with a molecular weight of 72,000. comparison of the determined n-terminal sequence ... | 2002 | 11772629 |
| nolx of sinorhizobium fredii usda257, a type iii-secreted protein involved in host range determination, iis localized in the infection threads of cowpea (vigna unguiculata [l.] walp) and soybean (glycine max [l.] merr.) nodules. | sinorhizobium fredii usda257 forms nitrogen-fixing nodules on soybean (glycine max [l.] merr.) in a cultivar-specific manner. this strain forms nodules on primitive soybean cultivars but fails to nodulate agronomically improved north american cultivars. soybean cultivar specificity is regulated by the nolxwbtuv locus, which encodes part of a type iii secretion system (ttss). nolx, a soybean cultivar specificity protein, is secreted by ttss and shows homology to hrpf of the plant pathogen xanthom ... | 2002 | 11790754 |
| integrative genetic element that reverses the usual target gene orientation. | a genetic element integrating site specifically into a prokaryotic gene usually carries a copy of the 3' portion of that gene that restores the active gene even as the original is disrupted. a cryptic element in mesorhizobium loti instead carries a copy of the 5' end of the trna gene into which it integrated. this has implications for the evolution of new integrase-site combinations. | 2002 | 11790760 |
| hemk, a class of protein methyl transferase with similarity to dna methyl transferases, methylates polypeptide chain release factors, and hemk knockout induces defects in translational termination. | hemk, a universally conserved protein of unknown function, has high amino acid similarity with dna-(adenine-n6) methyl transferases (mtases). a certain mutation in hemk gene rescues the photosensitive phenotype of a ferrochelatase-deficient (hemh) mutant in escherichia coli. a hemk knockout strain of e. coli not only suffered severe growth defects, but also showed a global shift in gene expression to anaerobic respiration, as determined by microarray analysis, and this shift may lead to the abro ... | 2002 | 11805295 |
| significance of two distinct types of tryptophan synthase beta chain in bacteria, archaea and higher plants. | tryptophan synthase consists of two subunits, alpha and beta. two distinct subgroups of beta chain exist. the major group (trpeb_1) includes the well-studied beta chain of salmonella typhimurium. the minor group of beta chain (trpeb_2) is most frequently found in the archaea. most of the amino-acid residues important for catalysis are highly conserved between both trpe subfamilies. | 2002 | 11806827 |
| significance of two distinct types of tryptophan synthase beta chain in bacteria, archaea and higher plants. | tryptophan synthase consists of two subunits, alpha and beta. two distinct subgroups of beta chain exist. the major group (trpeb_1) includes the well-studied beta chain of salmonella typhimurium. the minor group of beta chain (trpeb_2) is most frequently found in the archaea. most of the amino-acid residues important for catalysis are highly conserved between both trpe subfamilies. | 2002 | 11806827 |
| a human mitochondrial transcription factor is related to rna adenine methyltransferases and binds s-adenosylmethionine. | a critical step toward understanding mitochondrial genetics and its impact on human disease is to identify and characterize the full complement of nucleus-encoded factors required for mitochondrial gene expression and mitochondrial dna (mtdna) replication. two factors required for transcription initiation from a human mitochondrial promoter are h-mtrna polymerase and the dna binding transcription factor, h-mttfa. however, based on studies in model systems, the existence of a second human mitocho ... | 2002 | 11809803 |
| rapid identification of probiotic lactobacillus biosurfactant proteins by proteinchip tandem mass spectrometry tryptic peptide sequencing. | a novel proteinchip-interfaced tandem mass spectrometer was employed to identify collagen binding proteins from biosurfactant produced by lactobacillus fermentum rc-14. on-chip tryptic digestion of the captured collagen binding proteins resulted in rapid sequence identification of five novel tryptic peptide sequences via collision-induced dissociation tandem mass spectrometry. | 2002 | 11823248 |
| the hemk gene in escherichia coli encodes the n(5)-glutamine methyltransferase that modifies peptide release factors. | class 1 peptide release factors (rfs) in escherichia coli are n(5)-methylated on the glutamine residue of the universally conserved ggq motif. one other protein alone has been shown to contain n(5)-methylglutamine: e.coli ribosomal protein l3. we identify the l3 methyltransferase as yfcb and show that it methylates ribosomes from a yfcb strain in vitro, but not rf1 or rf2. hemk, a close orthologue of yfcb, is shown to methylate rf1 and rf2 in vitro. hemk is immediately downstream of and co-expre ... | 2002 | 11847124 |
| raiir genes are part of a quorum-sensing network controlled by cini and cinr in rhizobium leguminosarum. | analysis of n-acyl-l-homoserine lactones (ahls) produced by rhizobium leguminosarum bv. viciae indicated that there may be a network of quorum-sensing regulatory systems producing multiple ahls in this species. using a strain lacking a symbiosis plasmid, which carries some of the quorum-sensing genes, we isolated mutations in two genes (raii and rair) that are required for production of ahls. the raiir genes are located adjacent to dad genes (involved in d-alanine catabolism) on a large indigeno ... | 2002 | 11872711 |
| heat shock proteome of agrobacterium tumefaciens: evidence for new control systems. | the regulation of agrobacterium tumefaciens heat shock genes involves a transcriptional activator (rpoh) and repressor elements (hrca-circe). using proteome analysis and mutants in these control elements, we show that the heat shock induction of 32 (out of 56) heat shock proteins is independent of rpoh and hrca. these results indicate the existence of additional regulatory factors in the a. tumefaciens heat shock response. | 2002 | 11872730 |
| differences between subcultures of the mesorhizobium loti type strain from different culture collections. | because of differences in the reported 16s rrna gene sequence of the mesorhizobium loti type strain available from different culture collections, we collected different subcultures of this strain and compared them by 16s rdna sequencing, sds-page of whole-cell protein extracts and rapd-pcr. our results indicate that the 16s rdna sequence differences can be explained by the presence of two different organisms in one of the subcultures. in addition, even for subcultures of the type strain that had ... | 2001 | 11876362 |
| complete genomic sequence of sfv, a serotype-converting temperate bacteriophage of shigella flexneri. | bacteriophage sfv is a temperate serotype-converting phage of shigella flexneri. sfv encodes the factors involved in type v o-antigen modification, and the serotype conversion and integration-excision modules of the phage have been isolated and characterized. we now report on the complete sequence of the sfv genome (37,074 bp). a total of 53 open reading frames were predicted from the nucleotide sequence, and analysis of the corresponding proteins was used to construct a functional map. the gene ... | 2002 | 11889106 |
| genome sequence and analysis of the oral bacterium fusobacterium nucleatum strain atcc 25586. | we present a complete dna sequence and metabolic analysis of the dominant oral bacterium fusobacterium nucleatum. although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens porphyromonas gingivalis and bacteroides forsythus. the f. nucleatum strain atcc 25586 genome was assembled from shotgun sequences and analyzed using the ergo bioinformatics suite (http://www.integratedgenomics ... | 2002 | 11889109 |
| the nucleotide sequence of shiga toxin (stx) 2e-encoding phage phip27 is not related to other stx phage genomes, but the modular genetic structure is conserved. | in this study we determined the complete nucleotide sequence of shiga toxin 2e-encoding bacteriophage phi p27, isolated from the shiga toxin-producing escherichia coli patient isolate 2771/97. phi p27 is integrated as a prophage in the chromosomal yece gene. this integration generates identity segments of attl and attr sites with lengths of 11 nucleotides. the integrated prophage genome has a size of 42,575 bp. we identified 58 open reading frames (orfs), each with a length of >150 nucleotides. ... | 2002 | 11895953 |
| use of the caulobacter crescentus genome sequence to develop a method for systematic genetic mapping. | the functional analysis of sequenced genomes will be facilitated by the development of tools for the rapid mapping of mutations. we have developed a systematic approach to genetic mapping in caulobacter crescentus that is based on bacteriophage-mediated transduction of strategically placed antibiotic resistance markers. the genomic dna sequence was used to identify sites distributed evenly around the chromosome at which plasmids could be nondisruptively integrated. dna fragments from these sites ... | 2002 | 11914347 |
| ania regulates reserve polymer accumulation and global protein expression in rhizobium etli. | previously, it was reported that the oxidative capacity and ability to grow on carbon sources such as pyruvate and glucose were severely diminished in the rhizobium etli phac::omegasm(r)/sp(r) mutant car1, which is unable to synthesize poly-beta-hydroxybutyric acid (phb) (m. a. cevallos, s. encarnación, a. leija, y. mora, and j. mora, j. bacteriol. 178:1646-1654, 1996). by random tn5 mutagenesis of the phac strain, we isolated the mutants vem57 and vem58, both of which contained single tn5 inser ... | 2002 | 11914361 |
| selenoprotein r is a zinc-containing stereo-specific methionine sulfoxide reductase. | selenoprotein r (selr) is a mammalian selenocysteine-containing protein with no known function. here we report that cysteine homologs of selr are present in all organisms except certain parasites and hyperthermophiles, and this pattern of occurrence closely matches that of only one protein, peptide methionine sulfoxide reductase (msra). moreover, in several genomes, selr and msra genes are fused or clustered, and their expression patterns suggest a role of both proteins in protection against oxi ... | 2002 | 11929995 |
| rhizobial acyl carrier proteins and their roles in the formation of bacterial cell-surface components that are required for the development of nitrogen-fixing root nodules on legume hosts. | acyl carrier protein (acp) of escherichia coli is a small acidic protein which functions as carrier of growing acyl chains during their biosynthesis and as donor of acyl chains during transfer to target molecules. this unique acp of e. coli is expressed constitutively. in more complex bacteria, multiple acps are present, indicating a channeling of pools of multi-carbon units into different biosynthetic routes. in rhizobia, for example, besides the constitutive acp (acpp) involved in the biosynth ... | 2002 | 11959430 |
| biosynthetic gene cluster of simocyclinone, a natural multihybrid antibiotic. | the entire simocyclinone biosynthetic cluster (sim gene cluster) from the producer streptomyces antibioticus tü6040 was identified on six overlapping cosmids (1n1, 5j10, 2l16, 2p6, 4g22, and 1k3). in total, 80.7 kb of dna from these cosmids was sequenced, and the analysis revealed 49 complete open reading frames (orfs). these orfs include genes responsible for the formation and attachment of four different moieties originating from at least three different pools of primary metabolites. also in t ... | 2002 | 11959542 |
| structural, functional, and evolutionary analysis of moez, a gene encoding an enzyme required for the synthesis of the pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid). | pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. six genbank sequences code for proteins similar in structure to moez, a p. stutzeri protein necessary for the synthesis of pdtc. | 2002 | 11972321 |
| over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? | the survival of individual organisms facing stress is enhanced by the induction of a set of changes. as the intensity, duration and nature of stress is highly variable, the optimal response to stress may be unpredictable. to face such an uncertain future, it may be advantageous for a clonal population to increase its phenotypic heterogeneity (bet-hedging), ensuring that at least a subset of cells would survive the current stress. with current techniques, assessing the extent of this variability ... | 2002 | 11972324 |
| genes from pseudomonas sp. strain bs involved in the conversion of l-2-amino-delta(2)-thiazolin-4-carbonic acid to l-cysteine. | dl-2-amino-delta(2)-thiazolin-4-carbonic acid (dl-atc) is a substrate for cysteine synthesis in some bacteria, and this bioconversion has been utilized for cysteine production in industry. we cloned a dna fragment containing the genes involved in the conversion of l-atc to l-cysteine from pseudomonas sp. strain bs. the introduction of this dna fragment into escherichia coli cells enabled them to convert l-atc to cysteine via n-carbamyl-l-cysteine (l-ncc) as an intermediate. the smallest recombin ... | 2002 | 11976087 |
| characterization of a class ii defective transposon carrying two haloacetate dehalogenase genes from delftia acidovorans plasmid puo1. | the two haloacetate dehalogenase genes, dehh1 and dehh2, on the 65-kb plasmid puo1 from delftia acidovorans strain b were found to be located on transposable elements. the dehh2 gene was carried on an 8.9-kb class i composite transposon (tnhad1) that was flanked by two directly repeated copies of is1071, is1071l and is1071r. the dehh1 gene was also flanked by is1071l and a truncated version of is1071 (is1071n). tnhad1, dehh1, and is1071n were located on a 15.6-kb class ii transposon (tnhad2) who ... | 2002 | 11976102 |
| engineering the rhizobium leguminosarum bv. viciae hydrogenase system for expression in free-living microaerobic cells and increased symbiotic hydrogenase activity. | rhizobium leguminosarum bv. viciae upm791 induces hydrogenase activity in pea (pisum sativum l.) bacteroids but not in free-living cells. the symbiotic induction of hydrogenase structural genes (hupsl) is mediated by nifa, the general regulator of the nitrogen fixation process. so far, no culture conditions have been found to induce nifa-dependent promoters in vegetative cells of this bacterium. this hampers the study of the r. leguminosarum hydrogenase system. we have replaced the native nifa-d ... | 2002 | 11976122 |
| high-density microarray of small-subunit ribosomal dna probes. | ribosomal dna sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. as a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rrna genes. the genechip (affymetrix co ... | 2002 | 11976131 |
| a complete sequence of the t. tengcongensis genome. | thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in tengchong, china. using a whole-genome-shotgun method, we sequenced its 2,689,445-bp genome from an isolate, mb4(t) (genbank accession no. ae008691). the genome encodes 2588 predicted coding sequences (cds). among them, 1764 (68.2%) are classified according to homology to other documented proteins, and the rest, 824 cds (31.8%), are functionally unknown. one of ... | 2002 | 11997336 |
| a novel type of uracil-dna glycosylase mediating repair of hydrolytic dna damage in the extremely thermophilic eubacterium thermus thermophilus. | spontaneous hydrolytic deamination of dna cytosine and 5-methyl-cytosine residues is an abundant source of c/g (5-mec/g) to t/a transition mutations. as a result of this pressure, at least six different families of enzymes have evolved that initiate repair at u/g (t/g) mispairs, the relevant pre-mutagenic intermediates. the necessarily higher rate of the process at elevated temperatures must pose a correspondingly accentuated problem to contemporary thermophilic organisms and may have been a ser ... | 2002 | 12000829 |
| evolving insights: symbiosis islands and horizontal gene transfer. | | 2002 | 12003923 |
| redundancy in periplasmic binding protein-dependent transport systems for trehalose, sucrose, and maltose in sinorhizobium meliloti. | we have identified a cluster of six genes involved in trehalose transport and utilization (thu) in sinorhizobium meliloti. four of these genes, thue, -f, -g, and -k, were found to encode components of a binding protein-dependent trehalose/maltose/sucrose abc transporter. their deduced gene products comprise a trehalose/maltose-binding protein (thue), two integral membrane proteins (thuf and thug), and an atp-binding protein (thuk). in addition, a putative regulatory protein (thur) was found dive ... | 2002 | 12003938 |
| comparative sequence analysis of the symbiosis island of mesorhizobium loti strain r7a. | the mesorhizobium loti strain r7a symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to lotus symbionts. it integrates into a phenylalanine trna gene in a process mediated by a p4-type integrase encoded at the left end of the element. we have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of m. loti s ... | 2002 | 12003951 |
| cau-1, a subclass b3 metallo-beta-lactamase of low substrate affinity encoded by an ortholog present in the caulobacter crescentus chromosome. | the sequenced chromosome of caulobacter crescentus cb15 encodes a hypothetical protein that exhibits significant similarity (30 to 35% identical residues) to metallo-beta-lactamases of subclass b3. an allelic variant of this gene (divergent by 3% of its nucleotides) was cloned in escherichia coli from c. crescentus type strain dsm4727. expression studies confirmed the metallo-beta-lactamase activity of its product, cau-1. the enzyme produced in e. coli was purified by two ion-exchange chromatogr ... | 2002 | 12019096 |
| expression cloning and characterization of the c28 acyltransferase of lipid a biosynthesis in rhizobium leguminosarum. | an unusual feature of lipid a from plant endosymbionts of the rhizobiaceae family is the presence of a 27-hydroxyoctacosanoic acid (c28) moiety. an enzyme that incorporates this acyl chain is present in extracts of rhizobium leguminosarum, rhizobium etli, and sinorhizobium meliloti but not escherichia coli. the enzyme transfers 27-hydroxyoctacosanate from a specialized acyl carrier protein (acpxl) to the precursor kdo2 ((3-deoxy-d-manno-octulosonic acid)2)-lipid iv(a). we now report the identifi ... | 2002 | 12019272 |
| analysis of mesorhizobium loti glycogen operon: effect of phosphoglucomutase (pgm) and glycogen synthase (g/ga) null mutants on nodulation of lotus tenuis. | the phosphoglucomutase (pgm) gene codes for a key enzyme required for the formation of udp-glucose and adp-glucose, the sugar donors for the biosynthesis of glucose containing polysaccharides. a mesorhizobium loti pgm null mutant obtained in this study contains an altered form of lipopolysaccharide (lps), lacks exopolysaccharide (eps), beta cyclic glucan, and glycogen and is unable to nodulate lotus tenuis. the nonnodulating phenotype of the pgm mutant was not due to the absence of glycogen, sin ... | 2002 | 12026175 |
| expressed sequence tags from roots and nodule primordia of lotus japonicus infected with mesorhizobium loti. | messenger rna from young lotus japonicus roots carrying root nodule primordia appearing after inoculation with mesorhizobium loti bacteria were used to construct a cdna expression library. single-pass sequencing employing colony-polymerase chain reaction (pcr) and analysis of pcr products established a total of 2,397 new expressed sequence tags (ests). we have putatively identified 1,236 known and 484 hypothetical proteins coded by the corresponding mrnas. the remaining cdnas are unknown (316) o ... | 2002 | 12026176 |
| a novel type of conserved dna-binding domain in the transcriptional regulators of the algr/agra/lytr family. | sequence analysis of bacterial genomes revealed a novel dna-binding domain. this domain is found in several response regulators of the two-component signal transduction system, such as pseudomonas aeruginosa algr, involved in the regulation of alginate biosynthesis and in the pathogenesis of cystic fibrosis; clostridium perfringens virr, a regulator of virulence factors, and in several regulators of bacteriocin biosynthesis, previously unified in the agra/come family. most of the transcriptional ... | 2002 | 12034833 |
| prevalent bacterial species and novel phylotypes in advanced noma lesions. | the purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16s ribosomal dna bacterial genes from dna isolated from advanced noma lesions of four nigerian children were pcr amplified with universally conserved primers and spirochetal selective primers and cloned into escherichia coli. partial 16s rrna sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or close ... | 2002 | 12037085 |
| functional analysis of sinorhizobium meliloti genes involved in biotin synthesis and transport. | external biotin greatly stimulates bacterial growth and alfalfa root colonization by sinorhizobium meliloti strain 1021. several genes involved in responses to plant-derived biotin have been identified in this bacterium, but no genes required for biotin transport are known, and not all loci required for biotin synthesis have been assigned. searches of the s. meliloti genome database in combination with complementation tests of escherichia coli biotin auxotrophs indicate that biotin synthesis pro ... | 2002 | 12039741 |
| identification and isolation of genes involved in poly(beta-hydroxybutyrate) biosynthesis in azospirillum brasilense and characterization of a phbc mutant. | like many other prokaryotes, rhizobacteria of the genus azospirillum produce high levels of poly(beta-hydroxybutyrate) (phb) under suboptimal growth conditions. utilization of phb by bacteria under stress has been proposed as a mechanism that favors their compatible establishment in competitive environments, thus showing great potential for the improvement of bacterial inoculants for plants and soils. the three genes that are considered to be essential in the phb biosynthetic pathway, phba (beta ... | 2002 | 12039753 |
| key role of bacterial nh(4)(+) metabolism in rhizobium-plant symbiosis. | symbiotic nitrogen fixation is carried out in specialized organs, the nodules, whose formation is induced on leguminous host plants by bacteria belonging to the family rhizobiaceae: nodule development is a complex multistep process, which requires continued interaction between the two partners and thus the exchange of different signals and metabolites. nh(4)(+) is not only the primary product but also the main regulator of the symbiosis: either as ammonium and after conversion into organic compo ... | 2002 | 12040124 |
| lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. | glutathione is found primarily in eukaryotes and in gram-negative bacteria. it has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. to evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase. | 2002 | 12049666 |
| in silico sequence analysis of arylamine n-acetyltransferases: evidence for an absence of lateral gene transfer from bacteria to vertebrates and first description of paralogs in bacteria. | the arylamine n-acetyltransferases (nats) are xenobiotic-metabolizing enzymes responsible for the biotransformation of various arylamine and heterocyclic amines, including drugs and carcinogenic compounds. nat and nat-like genes have been identified in several vertebrate and eubacterial species. little is known about their evolutionary history, but the horizontal transfer of nat genes from bacteria to vertebrates was recently suggested [s. salzberg, o. white, j. peterson, j. eisen, science 292 ( ... | 2002 | 12054539 |
| the rhizobium etli cyac product: characterization of a novel adenylate cyclase class. | adenylate cyclases (acs) catalyze the formation of 3',5'-cyclic amp (camp) from atp. a novel ac-encoding gene, cyac, was isolated from rhizobium etli by phenotypic complementation of an escherichia coli cya mutant. the functionality of the cyac gene was corroborated by its ability to restore camp accumulation in an e. coli cya mutant. further, overexpression of a male::cyac fusion protein allowed the detection of significant ac activity levels in cell extracts of an e. coli cya mutant. cyac is u ... | 2002 | 12057950 |
| contribution of membrane-binding and enzymatic domains of penicillin binding protein 5 to maintenance of uniform cellular morphology of escherichia coli. | four low-molecular-weight penicillin binding proteins (lmw pbps) of escherichia coli are closely related and have similar dd-carboxypeptidase activities (pbps 4, 5, and 6 and dacd). however, only one, pbp 5, has a demonstrated physiological function. in its absence, certain mutants of e. coli have altered diameters and lose their uniform outer contour, resulting in morphologically aberrant cells. to determine what differentiates the activities of these lmw pbps, we constructed fusion proteins co ... | 2002 | 12057958 |
| identification of the lipooligosaccharide biosynthesis gene lic2b as a putative virulence factor in strains of nontypeable haemophilus influenzae that cause otitis media. | nontypeable (nt) strains of haemophilus influenzae are an important cause of acute otitis media (om). the pathogenic process by which nt h. influenzae strains cause om is poorly understood. in order to identify specific virulence factors important for om pathogenesis, genomic subtraction of the nt h. influenzae middle ear isolate g622 against h. influenzae strain rd was conducted and the resulting subtraction products were used to screen a panel of h. influenzae isolates. subtraction identified ... | 2002 | 12065495 |
| genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino acid substitution in bovine staphylococcus aureus. | staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. we here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, rf122, and the recently sequenced human-associated clones, mu50 and n315, of staphylococcus aureus. a shotgun sequence survey of approximately 10% of the rf122 genome identified numerous unique sequences and those with elevated rates of nonsynonymous substitution. taken together, these analyses show that ... | 2002 | 12065548 |
| the rna polymerase alpha subunit from sinorhizobium meliloti can assemble with rna polymerase subunits from escherichia coli and function in basal and activated transcription both in vivo and in vitro. | sinorhizobium meliloti, a gram-negative soil bacterium, forms a nitrogen-fixing symbiotic relationship with members of the legume family. to facilitate our studies of transcription in s. meliloti, we cloned and characterized the gene for the alpha subunit of rna polymerase (rnap). s. meliloti rpoa encodes a 336-amino-acid, 37-kda protein. sequence analysis of the region surrounding rpoa identified six open reading frames that are found in the conserved gene order secy (secy)-adk (adk)-rpsm (s13) ... | 2002 | 12081950 |
| export of l-isoleucine from corynebacterium glutamicum: a two-gene-encoded member of a new translocator family. | bacteria possess amino acid export systems, and corynebacterium glutamicum excretes l-isoleucine in a process dependent on the proton motive force. in order to identify the system responsible for l-isoleucine export, we have used transposon mutagenesis to isolate mutants of c. glutamicum sensitive to the peptide isoleucyl-isoleucine. in one such mutant, strong peptide sensitivity resulted from insertion into a gene designated brnf encoding a hydrophobic protein predicted to possess seven transme ... | 2002 | 12081967 |
| purification, molecular cloning, and characterization of pyridoxine 4-oxidase from microbacterium luteolum. | pyridoxine 4-oxidase (ec 1.1.3.12, pn 4-oxidase), which catalyzes the oxidation of pn by oxygen or other hydrogen acceptors to form pyridoxal and hydrogen peroxide or reduced forms of the acceptors, respectively, was purified for the first time to homogeneity from microbacterium luteolum yk-1 (=aureobacterium luteolum yk-1). the purified enzyme required fad for its catalytic activity and stability. the enzyme was a monomeric protein with the subunit molecular mass of 53,000 +/- 1,000 da. pn was ... | 2002 | 12092811 |
| rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (bra/liv) of the abc family. | amino acid uptake by rhizobium leguminosarum is dominated by two abc transporters, the general amino acid permease (aap) and the branched-chain amino acid permease (bra(rl)). characterization of the solute specificity of bra(rl) shows it to be the second general amino acid permease of r. leguminosarum. although bra(rl) has high sequence identity to members of the family of hydrophobic amino acid transporters (haat), it transports a broad range of solutes, including acidic and basic polar amino a ... | 2002 | 12107123 |
| cloning and characterization of the phosphatidylserine synthase gene of agrobacterium sp. strain atcc 31749 and effect of its inactivation on production of high-molecular-mass (1-->3)-beta-d-glucan (curdlan). | genes involved in the production of the extracellular (1-->3)-beta-glucan, curdlan, by agrobacterium sp. strain atcc 31749 were described previously (stasinopoulos et al., glycobiology 9:31-41, 1999). to identify additional curdlan-related genes whose protein products occur in the cell envelope, the transposon tnphoa was used as a specific genetic probe. one mutant was unable to produce high-molecular-mass curdlan when a previously uncharacterized gene, pss(ag), encoding a 30-kda, membrane-assoc ... | 2002 | 12107128 |
| genomic and functional analyses of sxt, an integrating antibiotic resistance gene transfer element derived from vibrio cholerae. | sxt is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. in recent years, sxt-related conjugative, self-transmissible integrating elements have become widespread in asian vibrio cholerae. we have determined the 100-kb dna sequence of sxt. this element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many gene ... | 2002 | 12107144 |
| identification of klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. | klebsiella pneumoniae is an opportunistic pathogen responsible for nosocomial infections that initially colonize the intestinal tract of patients. signature-tagged mutagenesis was used to identify genes required for this function. a library of 2,200 mutants was analyzed for the inability of the mutants to survive in a murine model of intestinal colonization and to adhere to human intestinal cells (int-407) in vitro. twenty-nine attenuated mutants were selected for further analyses after competit ... | 2002 | 12117993 |
| regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. | the riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. a model for regulation based on formation of alternative rna structures involving the rfn elements is suggested. in gram-positive bacteria including actinomycetes, thermotoga, thermus and deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most gram-negative bacteria, the riboflavin biosynthesis ... | 2002 | 12136096 |
| suppressive subtractive hybridization detects extensive genomic diversity in thermotoga maritima. | comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. such studies have focused mainly on pathogens; here, we examined thermotoga maritima, a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. the genome sequence of t. maritima msb8 is available, and dna from this strain served as a reference to obtain strain-specific sequences from thermotoga sp. strain rq2, a very clos ... | 2002 | 12142418 |
| n-acyl-homoserine lactone inhibition of rhizobial growth is mediated by two quorum-sensing genes that regulate plasmid transfer. | the growth of some strains of rhizobium leguminosarum bv. viciae is inhibited by n-(3-hydroxy-7-cis tetradecenoyl)-l-homoserine lactone (3oh-c(14:1)-hsl), which was previously known as the small bacteriocin before its characterization as an n-acyl homoserine lactone (ahl). tn5-induced mutants of r. leguminosarum bv. viciae resistant to 3oh-c(14:1)-hsl were isolated, and mutations in two genes were identified. these genes, bisr and trir, which both encode luxr-type regulators required for plasmid ... | 2002 | 12142421 |
| functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer. | functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ... | 2002 | 12142429 |
| mutational analysis of the tola c-terminal domain of escherichia coli and genetic evidence for an interaction between tola and tolb. | the tol proteins are involved in the outer membrane stability of gram-negative bacteria. the c-terminal domain of tola was mutagenized to identify residues important for its functions. the isolation of suppressor mutants of tola mutations in the tolb gene confirmed an interaction between tolaiii and the n-terminal domain of tolb. | 2002 | 12142433 |
| plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by terrabacter sp. strain yk3. | the genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of pcr primers designed by using conserved sequences of the dioxygenase alpha subunit genes. one sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: terrabacter sp. strains yk1 and yk3, rhodococcus sp. strain yk2, and microbacterium sp. strain yk18. a 5.2-kb psti fragment encoding the alpha and beta subunits of the terminal diox ... | 2002 | 12147464 |
| cloning and expression of the haloalkane dehalogenase gene dhma from mycobacterium avium n85 and preliminary characterization of dhma. | haloalkane dehalogenases are microbial enzymes that catalyze cleavage of the carbon-halogen bond by a hydrolytic mechanism. until recently, these enzymes have been isolated only from bacteria living in contaminated environments. in this report we describe cloning of the dehalogenase gene dhma from mycobacterium avium subsp. avium n85 isolated from swine mesenteric lymph nodes. the dhma gene has a g+c content of 68.21% and codes for a polypeptide that is 301 amino acids long and has a calculated ... | 2002 | 12147465 |
| comparative genomic analysis of plant-associated bacteria. | this review deals with a comparative analysis of seven genome sequences from plant-associated bacteria. these are the genomes of agrobacterium tumefaciens, mesorhizobium loti, sinorhizobium meliloti, xanthomonas campestris pv campestris, xanthomonas axonopodis pv citri, xylella fastidiosa, and ralstonia solanacearum. genome structure and the metabolism pathways available highlight the compromise between the genome size and lifestyle. despite the recognized importance of the type iii secretion sy ... | 2002 | 12147758 |
| identification and characterization of a brucella abortus atp-binding cassette transporter homolog to rhizobium meliloti exsa and its role in virulence and protection in mice. | brucella abortus is a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. the mechanism of virulence of brucella spp. is not fully understood yet. furthermore, genes that allow brucella to reach the intracellular niche and to interact with host cells need to be identified. using the genomic survey sequence (gss) approach, we identified the gene encoding an atp-binding cassette (abc) transporter of b. abortus strain s2308. the deduce ... | 2002 | 12183550 |
| r391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. | the conjugative, chromosomally integrating element r391 is the archetype of the incj class of mobile genetic elements. originally found in a south african providencia rettgeri strain, r391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic dna repair. while initially described as a plasmid, r391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the sxt element f ... | 2002 | 12193633 |
| role of tfxe, but not tfxg, in trifolitoxin resistance. | eight genes, tfxabcdefg and tfua, confer production of trifolitoxin (tfx), a ribosomally synthesized, posttranslationally modified peptide antibiotic, in tfx-sensitive alpha-proteobacteria. an in-frame deletion in tfxe significantly reduced a strain's resistance to tfx in comparison to that of an otherwise identical construct containing wild-type tfxe. the deletion of tfxg had no effect on tfx resistance. nevertheless, rnase protection assays showed that tfxe and tfxg are transcribed, showing th ... | 2002 | 12200284 |
| predicted structure and phyletic distribution of the rna-binding protein hfq. | hfq, a bacterial rna-binding protein, was recently shown to contain the sm1 motif, a characteristic of sm and lsm proteins that function in rna processing events in archaea and eukaryotes. in this report, comparative structural modeling was used to predict a three-dimensional structure of the hfq core sequence. the predicted structure aligns with most major features of the methanobacterium thermoautotrophicum lsm protein structure. conserved residues in hfq are positioned at the same structural ... | 2002 | 12202750 |
| temperature-regulated transcription in the pathogenic fungus cryptococcus neoformans. | the basidiomycete fungus cryptococcus neoformans is an opportunistic pathogen of worldwide importance that causes meningitis, leading to death in immunocompromised individuals. unlike many basidiomycete fungi, c. neoformans is thermotolerant, and its ability to grow at 37 degrees c is considered to be a virulence factor. we used serial analysis of gene expression (sage) to characterize the transcriptomes of c. neoformans strains that represent two varieties with different polysaccharide capsule ... | 2002 | 12213776 |
| purification, substrate range, and metal center of atzc: the n-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. | n-isopropylammelide isopropylaminohydrolase, atzc, the third enzyme in the atrazine degradation pathway in pseudomonas sp. strain adp, catalyzes the stoichiometric hydrolysis of n-isopropylammelide to cyanuric acid and isopropylamine. the atzc gene was cloned downstream of the tac promoter and expressed in escherichia coli, where the expressed enzyme comprised 36% of the soluble protein. atzc was purified to homogeneity by ammonium sulfate precipitation and phenyl column chromatography. it has a ... | 2002 | 12218024 |
| a monocarboxylate permease of rhizobium leguminosarum is the first member of a new subfamily of transporters. | amino acid transport by rhizobium leguminosarum is dominated by two abc transporters, the general amino acid permease (aap) and the branched-chain amino acid permease (bra). however, mutation of these transporters does not prevent this organism from utilizing alanine for growth. an r. leguminosarum permease (mctp) has been identified which is required for optimal growth on alanine as a sole carbon and nitrogen source. characterization of mctp confirmed that it transports alanine (k(m) = 0.56 mm) ... | 2002 | 12218032 |
| the escherichia coli metd locus encodes an abc transporter which includes abc (metn), yaee (meti), and yaec (metq). | we report that the genes abc, yaec, and yaee comprise metd, an escherichia coli locus encoding a dl-methionine uptake system. metd is an abc transporter with abc the atpase, yaee the permease, and yaec the likely substrate binding protein. expression of these genes is regulated by l-methionine and metj, a common repressor of the methionine regulon. we propose to rename abc, yaee, and yaec as metn, meti, and metq, respectively. | 2002 | 12218041 |
| the two-component system bvrr/bvrs essential for brucella abortus virulence regulates the expression of outer membrane proteins with counterparts in members of the rhizobiaceae. | the brucella bvrr/bvrs two-component regulatory system is homologous to the chvi/chvg systems of sinorhizobium meliloti and agrobacterium tumefaciens necessary for endosymbiosis and pathogenicity in plants. bvrr/bvrs controls cell invasion and intracellular survival. probing the surface of bvrr and bvrs transposon mutants with monoclonal antibodies showed all described major outer membrane proteins (omps) but omp25, a protein known to be involved in brucella virulence. absence of omp25 expressio ... | 2002 | 12218183 |
| a global ph sensor: agrobacterium sensor protein chvg regulates acid-inducible genes on its two chromosomes and ti plasmid. | a sensor protein chvg is part of a chromosomally encoded two-component regulatory system chvg/chvi that is important for the virulence of agrobacterium tumefaciens. however, it is not clear what genes chvg regulates or what signal(s) it senses. in this communication, we demonstrate that chvg is involved in the regulation of acid-inducible genes, including aopb and kata, residing on the circular and linear chromosomes, respectively, and the tumor-inducing (ti)-plasmid-harbored vir genes, virb and ... | 2002 | 12218184 |
| a conserved mechanism for extracellular signaling in eukaryotes and prokaryotes. | epidermal growth factor receptor (egfr) is a key mediator of cell communication during animal development and homeostasis. in drosophila, the signaling event is commonly regulated by the polytopic membrane protein rhomboid (rho), which mediates the proteolytic activation of egfr ligands, allowing the secretion of the active signal. until very recently, the biochemical function of rho had remained elusive. it is now believed that drosophila rho is the founder member of a previously undescribed fa ... | 2002 | 12221285 |
| effect of omp10 or omp19 deletion on brucella abortus outer membrane properties and virulence in mice. | the distinctive properties of brucella outer membrane have been considered to be critical for brucella sp. virulence. among the outer membrane molecules possibly related to these properties, omp10 and omp19 are immunoreactive outer membrane lipoproteins. moreover, these proteins of brucella could constitute a new family of outer membrane proteins specifically encountered in the family rhizobiaceae: we evaluated the impact of omp10 or omp19 deletion on brucella abortus outer membrane properties a ... | 2002 | 12228280 |
| rapid colorimetric quantification of lipo-chitooligosaccharides from mesorhizobium loti and sinorhizobium meliloti. | nod factors are lipids with a chitinlike headgroup produced by gram-negative rhizobium bacteria. these lipo-chitooligosaccharides (lcos) are essential signaling molecules for accomplishing symbiosis between the bacteria and roots of legume plants. despite their important role in the rhizobium-legume interaction, no fast and sensitive nod factor quantification methods exist. here, we report two different quantification methods. the first is based on the enzymatic hydrolysis of nod factors to rele ... | 2002 | 12236592 |
| the brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. | the 3.31-mb genome sequence of the intracellular pathogen and potential bioterrorism agent, brucella suis, was determined. comparison of b. suis with brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. analysis of the b. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bac ... | 2002 | 12271122 |
| comparative genome analysis of the alpha -proteobacteria: relationships between plant and animal pathogens and host specificity. | | 2002 | 12271145 |
| the exopolyphosphatase gene from sulfolobus solfataricus: characterization of the first gene found to be involved in polyphosphate metabolism in archaea. | inorganic polyphosphate (polyp) polymers are widely distributed in all kinds of organisms. although the presence of polyp in members of the domain archaea has been described, at present nothing is known about the enzymology of polyp metabolism or the genes involved in this domain. we have cloned, sequenced, and overexpressed an exopolyphosphatase (ppx) gene (ppx) from thermophilic sulfolobus solfataricus. the gene codes for a functional ppx and possesses an open reading frame for 417 amino acids ... | 2002 | 12324325 |
| complete sequence and organization of pbtoxis, the toxin-coding plasmid of bacillus thuringiensis subsp. israelensis. | the entire 127,923-bp sequence of the toxin-encoding plasmid pbtoxis from bacillus thuringiensis subsp. israelensis is presented and analyzed. in addition to the four known cry and two known cyt toxins, a third cyt-type sequence was found with an additional c-terminal domain previously unseen in such proteins. many plasmid-encoded genes could be involved in several functions other than toxin production. the most striking of these are several genes potentially affecting host sporulation and germi ... | 2002 | 12324359 |
| conservation of the biotin regulon and the bira regulatory signal in eubacteria and archaea. | biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. the strict control of biotin biosynthesis in escherichia coli is mediated by the bifunctional bira protein, which acts both as a biotin-protein ligase and as a transcriptional repressor of the biotin operon. little is known about regulation of biotin biosynthesis in other bacteria. using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the bira r ... | 2002 | 12368242 |
| distribution and evolution of von willebrand/integrin a domains: widely dispersed domains with roles in cell adhesion and elsewhere. | the von willebrand a (vwa) domain is a well-studied domain involved in cell adhesion, in extracellular matrix proteins, and in integrin receptors. a number of human diseases arise from mutations in vwa domains. we have analyzed the phylogenetic distribution of this domain and the relationships among approximately 500 proteins containing this domain. although the majority of vwa-containing proteins are extracellular, the most ancient ones, present in all eukaryotes, are all intracellular proteins ... | 2002 | 12388743 |
| poly-beta-hydroxybutyrate biosynthesis in the facultative methylotroph methylobacterium extorquens am1: identification and mutation of gap11, gap20, and phar. | methylobacterium extorquens am1, a serine cycle facultative methylotroph, accumulates poly-beta-hydroxybutyrate (phb) as a carbon and energy reserve material during growth on both multicarbon- and single-carbon substrates. recently, the identification and mutation of the genes involved in the biosynthesis and degradation of phb have been described for this bacterium, demonstrating that two of the genes of the phb cycle (phaa and phab) are also involved in c(1) and c(2) metabolism, as part of a n ... | 2002 | 12399487 |
| a new species of devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume neptunia natans (l.f.) druce. | rhizobia are the common bacterial symbionts that form nitrogen-fixing root nodules in legumes. however, recently other bacteria have been shown to nodulate and fix nitrogen symbiotically with these plants. neptunia natans is an aquatic legume indigenous to tropical and subtropical regions and in african soils is nodulated by allorhizobium undicola. this legume develops an unusual root-nodule symbiosis on floating stems in aquatic environments through a unique infection process. here, we analyzed ... | 2002 | 12406707 |