| rapid screening for freshwater bacterial groups by using reverse line blot hybridization. | the identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. we present a set of 16s ribosomal rna gene-based oligonucleotide probes specific for 15 of these freshwater clusters. the probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of pcr products from many samples against an array of probes. the optimized assay was made stringent to discri ... | 2003 | 14532039 |
| genome sequences of two closely related vibrio parahaemolyticus phages, vp16t and vp16c. | two bacteriophages of an environmental isolate of vibrio parahaemolyticus were isolated and sequenced. the vp16t and vp16c phages were separated from a mixed lysate based on plaque morphology and exhibit 73 to 88% sequence identity over about 80% of their genomes. only about 25% of their predicted open reading frames are similar to genes with known functions in the genbank database. both phages have cos sites and open reading frames encoding proteins closely related to coliphage lambda's termina ... | 2003 | 14563879 |
| 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 |
| a gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. | plants have evolved sophisticated defense mechanisms against pathogen infections, during which resistance (r) genes play central roles in recognizing pathogens and initiating defense cascades. most of the cloned r genes share two common domains: the central domain, which encodes a nucleotide binding adaptor shared by apaf-1, certain r proteins, and ced-4 (nb-arc), plus a c-terminal region that encodes leu-rich repeats (lrr). in arabidopsis, a dominant mutant, suppressor of npr1-1, constitutive 1 ... | 2003 | 14576290 |
| enzyme-specific profiles for genome annotation: priam. | the advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. here we describe priam, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the enzyme database. priam relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each enzyme entry. automatically generated logical rules define which of these profile ... | 2003 | 14602924 |
| erecta, an lrr receptor-like kinase protein controlling development pleiotropically affects resistance to bacterial wilt. | bacterial wilt, one of the most devastating bacterial diseases of plants worldwide, is caused by ralstonia solanacearum and affects many important crop species. we show that several strains isolated from solanaceous crops in europe are pathogenic in different accessions of arabidopsis thaliana. one of these strains, 14.25, causes wilting symptoms in a. thaliana accession landsberg erecta (ler) and no apparent symptoms in accession columbia (col-0). disease development and bacterial multiplicatio ... | 2003 | 14617092 |
| role of the stationary growth phase sigma factor rpos of burkholderia pseudomallei in response to physiological stress conditions. | the burkholderia pseudomallei rpos gene was identified, and an rpos null mutant was constructed. the mutant was shown to have an increased sensitivity to carbon starvation and oxidative stress. by using rpos-lacz fusions, transcription of rpos was shown to be growth phase regulated, reaching a peak upon entry into stationary phase. | 2003 | 14617667 |
| 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 |
| xopc and xopj, two novel type iii effector proteins from xanthomonas campestris pv. vesicatoria. | pathogenicity of the gram-negative plant pathogen xanthomonas campestris pv. vesicatoria depends on a type iii secretion (tts) system which translocates bacterial effector proteins into the plant cell. previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the tts system. in this study, we characterized two of these genes, xopc and xopj. both genes encode xanthomonas outer proteins (xops) that were shown to be secreted by the tts sy ... | 2003 | 14645268 |
| gaca regulates symbiotic colonization traits of vibrio fischeri and facilitates a beneficial association with an animal host. | the gacs/gaca two-component system regulates the expression of bacterial traits during host association. although the importance of gacs/gaca as a regulator of virulence is well established, its role in benign associations is not clear, as mutations in either the gacs or gaca gene have little impact on the success of colonization in nonpathogenic associations studied thus far. using as a model the symbiotic association of the bioluminescent marine bacterium vibrio fischeri with its animal host, ... | 2003 | 14645281 |
| 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 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 |
| efficient degradation of 2,4,6-trichlorophenol requires a set of catabolic genes related to tcp genes from ralstonia eutropha jmp134(pjp4). | 2,4,6-trichlorophenol (2,4,6-tcp) is a hazardous pollutant. several aerobic bacteria are known to degrade this compound. one of these, ralstonia eutropha jmp134(pjp4), a well-known, versatile chloroaromatic compound degrader, is able to grow in 2,4,6-tcp by converting it to 2,6-dichlorohydroquinone, 6-chlorohydroxyquinol, 2-chloromaleylacetate, maleylacetate, and beta-ketoadipate. three enzyme activities encoded by tcp genes, 2,4,6-tcp monooxygenase (tcpa), 6-chlorohydroxyquinol 1,2-dioxygenase ... | 2003 | 14660355 |
| biochemical, genetic, and zoosporicidal properties of cyclic lipopeptide surfactants produced by pseudomonas fluorescens. | zoospores play an important role in the infection of plant and animal hosts by oomycetes and other zoosporic fungi. in this study, six fluorescent pseudomonas isolates with zoosporicidal activities were obtained from the wheat rhizosphere. zoospores of multiple oomycetes, including pythium species, albugo candida, and phytophthora infestans, were rendered immotile within 30 s of exposure to cell suspensions or cell culture supernatants of the six isolates, and subsequent lysis occurred within 60 ... | 2003 | 14660362 |
| specific and sensitive detection of ralstonia solanacearum in soil on the basis of pcr amplification of flic fragments. | ralstonia solanacearum is the causative agent of bacterial wilt in many important crops. a specific and sensitive pcr detection method that uses primers targeting the gene coding for the flagella subunit, flic, was established. based on the first flic gene sequence of r. solanacearum strain k60 available at genbank, the ral_flic pcr primer system was designed; this system yielded a single 724-bp product with the dnas of all of the r. solanacearum strains tested. however, r. pickettii and four en ... | 2003 | 14660373 |
| 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 |
| identification of alka gene related to virulence of shigella flexneri 2a by mutational analysis. | in vivo induced genes are thought to play an important role during infection of host. alka was identified as an in vivo-induced gene by in vivo expression technology (ivet), but its virulence in shigella flexneri was not reported. the purpose of this study was to identify the role of alka gene in the pathogenesis of s. flexneri. | 2003 | 14669321 |
| characterization of the 101-kilobase-pair megaplasmid pkb1, isolated from the rubber-degrading bacterium gordonia westfalica kb1. | the complete sequence of the circular 101,016-bp megaplasmid pkb1 from the cis-1,4-polyisoprene-degrading bacterium gordonia westfalica kb1, which represents the first described extrachromosomal dna of a member of this genus, was determined. plasmid pkb1 harbors 105 open reading frames. the predicted products of 46 of these are significantly related to proteins of known function. plasmid pkb1 is organized into three functional regions that are flanked by insertion sequence (is) elements: (i) a r ... | 2004 | 14679241 |
| transcriptome analysis of the response of pseudomonas aeruginosa to hydrogen peroxide. | pseudomonas aeruginosa must often overcome a high concentration of oxidants to successfully infect the human host. we report here the results of a transcriptome profiling comparing cells treated with h(2)o(2) and untreated controls. the data indicate that the early response of p. aeruginosa to h(2)o(2) consists of an upregulation of protective mechanisms and a downregulation of primary metabolism. | 2004 | 14679246 |
| expression of l-ornithine ndelta-oxygenase (pvda) in fluorescent pseudomonas species: an immunochemical and in silico study. | omega-amino acid monooxygenases (ec 1.14.13.-), catalysing the formation of hydroxamate precursors of microbial siderophores (e.g., pyoverdine), have so far eluded structural and biochemical characterisation. here, the expression of recombinant l-ornithine-ndelta-oxygenase (pvda) from pseudomonas aeruginosa pao1 is reported. a library of eight monoclonal antibodies (mabs) directed against pvda has been generated. two mab families recognising the n- and c-terminal regions of pvda were identified. ... | 2004 | 14684153 |
| role of siderophore biosynthesis in virulence of staphylococcus aureus: identification and characterization of genes involved in production of a siderophore. | molecular determinants underlying the production of siderophores in the human and animal pathogen staphylococcus aureus and the contribution of siderophore production to the virulence of this bacterium have, until now, remained undefined. here, we show that s. aureus strains rn6390 and newman produce siderophore when the cells are starved for iron. we further identified and characterized a nine-gene, iron-regulated operon, designated sbn and situated between sirabc and gale on the s. aureus chro ... | 2004 | 14688077 |
| structure of hrcqb-c, a conserved component of the bacterial type iii secretion systems. | type iii secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. in addition, type iii secretion systems are also required for biogenesis of the bacterial flagellum. the hrcq(b) protein, a component of the secretion apparatus of pseudomonas ... | 2004 | 14694203 |
| structure of hrcqb-c, a conserved component of the bacterial type iii secretion systems. | type iii secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. in addition, type iii secretion systems are also required for biogenesis of the bacterial flagellum. the hrcq(b) protein, a component of the secretion apparatus of pseudomonas ... | 2004 | 14694203 |
| complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage d3112. | bacteriophage d3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen pseudomonas aeruginosa. to further our understanding of transposable phage in p. aeruginosa, we have sequenced the complete genome of d3112. the genome is 37,611 bp, with an overall g+c content of 65%. we have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes a and b) that have been previously characterized ... | 2004 | 14702309 |
| an evolutionary hot spot: the pngr234b replicon of rhizobium sp. strain ngr234. | rhizobium sp. strain ngr234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. since the overall organization of the ngr234 genome is strikingly similar to that of the narrow-host-range symbiont rhizobium meliloti strain 1021 (also known as sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? study of the early symbiotic genes of both bacteria (carried by the syma plasmids) did not provide obvious answers. yet, bo ... | 2004 | 14702322 |
| pseudomonas syringae type iii secretion system targeting signals and novel effectors studied with a cya translocation reporter. | pseudomonas syringae pv. tomato strain dc3000 is a pathogen of tomato and arabidopsis: the hrp-hrc-encoded type iii secretion system (ttss), which injects bacterial effector proteins (primarily called hop or avr proteins) into plant cells, is required for pathogenicity. in addition to being regulated by the hrpl alternative sigma factor, most avr or hop genes encode proteins with n termini that have several characteristic features, including (i) a high percentage of ser residues, (ii) an aliphat ... | 2004 | 14702323 |
| comparison of slime from tomato and banana strains of pseudomonas solanacearum. | | 1959 | 13818445 |
| propionyl-coenzyme a synthetases of ralstonia solanacearum and salmonella choleraesuis display atypical kinetics. | propionyl-coenzyme a synthetases (prpe) of salmonella choleraesuis and ralstonia solanacearum sharing 62% identity in amino acid sequence to each other were cloned, expressed in escherichia coli and purified. both enzymes catalyzed acetyl-, propionyl-, butyryl- and acrylyl-coenzyme a formation with the highest k(cat)/k(m) values for propionate. they displayed sigmoidal homotrophic autoactivation kinetics for propionate but not for the other acyl substrates tested. besides, substrate inhibition k ... | 2004 | 14706841 |
| pathogenicity islands in bacterial pathogenesis. | in this review, we focus on a group of mobile genetic elements designated pathogenicity islands (pai). these elements play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants. characteristic molecular features of pai of important human pathogens and their role in pathogenesis are described. the availability of a large number of genome sequences of pathogenic bacteria and their benign relatives currently offers a ... | 2004 | 14726454 |
| illuminating the molecular basis of gene-for-gene resistance; arabidopsis thaliana rrs1-r and its interaction with ralstonia solanacearum popp2. | elucidation of the molecular basis of gene-for-gene interactions between disease-resistance (r) genes and pathogen avirulence (avr) genes has been a holy grail of plant pathology for the past decade. recent studies of the r-avr interaction between rrs1-r and popp2 by laurent deslandes et al. provide new insights and suggest a direct physical association of the encoded proteins in support of a simplistic receptor-ligand model. however, careful consideration of the experimental findings reveals th ... | 2004 | 14729210 |
| direct glutaminyl-trna biosynthesis and indirect asparaginyl-trna biosynthesis in pseudomonas aeruginosa pao1. | the genomic sequence of pseudomonas aeruginosa pao1 was searched for the presence of open reading frames (orfs) encoding enzymes potentially involved in the formation of gln-trna and of asn-trna. we found orfs similar to known glutamyl-trna synthetases (glurs), glutaminyl-trna synthetases (glnrs), aspartyl-trna synthetases (asprs), and trimeric trna-dependent amidotransferases (adt) but none similar to known asparaginyl-trna synthetases (asnrs). the absence of asnrs was confirmed by biochemical ... | 2004 | 14729703 |
| differential expression of two paralogous genes of bacillus subtilis encoding single-stranded dna binding protein. | the bacillus subtilis genome comprises two paralogous single-stranded dna binding protein (ssb) genes, ssb and ywph, which show distinct expression patterns. the main ssb gene is strongly expressed during exponential growth and is coregulated with genes encoding the ribosomal proteins s6 and s18. the gene organization rpsf-ssb-rpsr as observed in b. subtilis is found in many gram-positive as well as some gram-negative bacteria, but not in escherichia coli. the ssb gene is essential for cell viab ... | 2004 | 14762004 |
| antifungal activity of beta-asarone from rhizomes of acorus gramineus. | an antifungal substance was isolated from the extract of acorus gramineus using various chromatographic procedures. the antibiotic was identified as beta-asarone, cis-2,4,5-trimethoxy-1-propenylbenzene, on the basis of the high-resolution ei-mass, nmr, and uv spectral data. beta-asarone completely inhibited mycelial growth of some plant pathogenic fungi, cladosporium cucumerinum,colletotrichum orbiculare, magnaporthe grisea, and pythium ultimum, in a range of 0.5-30 microg/ml. the growth of baci ... | 2004 | 14969530 |
| transcriptional profiling of caulobacter crescentus during growth on complex and minimal media. | microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (pye) and minimal salts medium with glucose or xylose as the carbon source. nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. the differentially expressed genes included many encoding transport systems, most notably di ... | 2004 | 14973021 |
| teir, a luxr-type transcription factor required for testosterone degradation in comamonas testosteroni. | we have identified a new steroid-inducible gene (designated teir [testosterone-inducible regulator]) in comamonas testosteroni that is required for testosterone degradation. nucleotide sequence analysis of teir predicts a 391-amino-acid protein which shows homology between residues 327 and 380 (c-terminal domain) to the luxr helix-turn-helix dna binding domain and between residues 192 and 227 to the pas sensor domain. this domain distribution resembles that described for trar, a specific transcr ... | 2004 | 14973025 |
| vpst is a transcriptional regulator required for expression of vps biosynthesis genes and the development of rugose colonial morphology in vibrio cholerae o1 el tor. | vibrio cholerae switches between smooth and rugose colonial variants. the rugose variant produces more vibrio polysaccharides (vps(el tor)) and forms well-developed biofilms. both phenotypes depend on expression of vps biosynthesis genes. we identified a positive transcriptional regulator of vps gene expression, vpst, which is homologous to response regulators of two-component regulatory systems. disruption of vpst in the rugose variant yields smooth colonies, prevents formation of mature biofil ... | 2004 | 14973043 |
| evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of paederus fuscipes beetles. | pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. it is used by apparently all members of the rove beetle genera paederus and paederidus as a chemical defense against predators. however, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. we have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-uncultu ... | 2004 | 14973122 |
| the melampsora lini avrl567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells. | the linum usitatissimum (flax) l gene alleles, which encode nucleotide binding site-leu rich repeat class intracellular receptor proteins, confer resistance against the melampsora lini (flax rust) fungus. at least 11 different l resistance specificities are known, and the corresponding avirulence genes in m. lini map to eight independent loci, some of which are complex and encode multiple specificities. we identified an m. lini cdna marker that cosegregates in an f2 rust family with a complex lo ... | 2004 | 14973158 |
| evidence for a hybrid genomic island in verocytotoxin-producing escherichia coli cl3 (serotype o113:h21) containing segments of edl933 (serotype o157:h7) o islands 122 and 48. | genomic o island 122 (oi-122) of the verocytotoxin-producing escherichia coli (vtec) strain edl933 contains four putative virulence genes, z4321, z4326, z4332, and z4333. however, strain cl3 (serotype o113:h21) contains only z4321, not the other three genes. to determine whether z4321 is part of a different genomic island in cl3, a region of 27,293 bp up- and downstream of z4321 was sequenced and found to contain elements of two different edl933 genomic islands (oi-48 and oi-122) and a yersinia ... | 2004 | 14977955 |
| [experiment on extraction, sulfonate of paeonol and its antibiotic effect on plant pathogen]. | paeonol contents in root barks, cores, stems and leaves of paeonia suffruticosa andr. from nanling county, anhui province were determined and paeonol was extracted with alcohol, acid alcohol and alkali alcohol. sodium paeonol sulfonate was synthesized by treating paeonol with concentrated sulfuric acid and oleums, and its physicochemical properties were surveyed by hplc, tlc, ftir and uv. antibiotic experiment on plant pathogenic fungi and bacteria showed that paeonol and sodium paeonol sulfonat ... | 2003 | 14989057 |
| comparative analysis of protein domain organization. | we have developed a set of graph theory-based tools, which we call comparative analysis of protein domain organization (cado), to survey and compare protein domain organizations of different organisms. in the language of cado, the organization of protein domains in a given organism is shown as a domain graph in which protein domains are represented as vertices, and domain combinations, defined as instances of two domains found in one protein, are represented as edges. cado provides a new way to ... | 2004 | 14993202 |
| phosphatidylethanolamine is not essential for growth of sinorhizobium meliloti on complex culture media. | in addition to phosphatidylglycerol (pg), cardiolipin (cl), and phosphatidylethanolamine (pe), sinorhizobium meliloti also possesses phosphatidylcholine (pc) as a major membrane lipid. the biosynthesis of pc in s. meliloti can occur via two different routes, either via the phospholipid n-methylation pathway, in which pe is methylated three times in order to obtain pc, or via the phosphatidylcholine synthase (pcs) pathway, in which choline is condensed with cdp-diacylglycerol to obtain pc directl ... | 2004 | 14996797 |
| visualization of the phylogenetic content of five genomes using dekapentagonal maps. | the methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. if the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. analyses of genomes representing five photosynthetic ... | 2004 | 15003123 |
| novel pathway of salicylate degradation by streptomyces sp. strain wa46. | a novel salicylate-degrading streptomyces sp., strain wa46, was identified by uv fluorescence on solid minimal medium containing salicylate; trace amounts of gentisate were detected by high-pressure liquid chromatography when strain wa46 was grown with salicylate. pcr amplification of wa46 dna with degenerate primers for gentisate 1,2-dioxygenase (gdo) genes produced an amplicon of the expected size. sequential pcr with nested gdo primers was then used to identify a salicylate degradation gene c ... | 2004 | 15006746 |
| diverse organization of genes of the beta-ketoadipate pathway in members of the marine roseobacter lineage. | members of the roseobacter lineage, an ecologically important marine clade within the class alpha-proteobacteria, harbor genes for the protocatechuate branch of the beta-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. the genes of this pathway are typically clustered, although gene order varies among organisms. here we characterize genes linked to pcah and -g, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the roseobacter lin ... | 2004 | 15006791 |
| molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface. | lateral gene transfer (lgt) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. to date, lgt has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. here we used a combination of molecular analyses to investigate the role of lgt in the evolution of metal homeostasis in lead-resistant subsurface bacteria. a nested pcr a ... | 2004 | 15006795 |
| wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including ralstonia eutropha and related species, and proposal of ralstonia [pseudomonas] syzygii (roberts et al. 1990) comb. nov. | comparative 16s rdna sequence analysis indicates that two distinct sublineages, with a sequence dissimilarity of >4 % (bootstrap value, 100 %), exist within the genus ralstonia: the ralstonia eutropha lineage, which comprises ralstonia basilensis, ralstonia campinensis, r. eutropha, ralstonia gilardii, ralstonia metallidurans, ralstonia oxalatica, ralstonia paucula, ralstonia respiraculi and ralstonia taiwanensis; and the ralstonia pickettii lineage, which comprises ralstonia insidiosa, ralstoni ... | 2004 | 15023939 |
| a dna adenine methyltransferase of escherichia coli that is cell cycle regulated and essential for viability. | dna sequence analysis revealed that the putative yhdj dna methyltransferase gene of escherichia coli is 55% identical to the nostoc sp. strain pcc7120 gene encoding dna methyltransferase avaiii, which methylates adenine in the recognition sequence, atgcat. the yhdj gene was cloned, and the enzyme was overexpressed and purified. methylation and restriction analysis showed that the dna methyltransferase methylates the first adenine in the sequence atgcat. this dna methylation was found to be regul ... | 2004 | 15028690 |
| structural basis for host recognition by the haemophilus influenzae hia autotransporter. | haemophilus influenzae is an important human pathogen that initiates infection by colonizing the upper respiratory tract. the h. influenzae hia autotransporter is an adhesive protein that promotes adherence to respiratory epithelial cells. hia adhesive activity resides in two homologous binding domains, called hiabd1 and hiabd2. these domains interact with the same host cell receptor, but bind with different affinities. in this report, we describe the crystal structure of the high-affinity hiabd ... | 2004 | 15029242 |
| the lspb protein is involved in the secretion of the lspa1 and lspa2 proteins by haemophilus ducreyi. | the lspa1 and lspa2 proteins of haemophilus ducreyi 35000 are two very large macromolecules that can be detected in concentrated culture supernatant fluid. both of these proteins exhibit homology with the n-terminal region of the bordetella pertussis filamentous hemagglutinin (fha), which is involved in secretion of the latter macromolecule. the lspa2 open reading frame is flanked upstream by a gene, lspb, that encodes a predicted protein with homology to the b. pertussis fhac outer membrane pro ... | 2004 | 15039306 |
| comparative genomics of gene-family size in closely related bacteria. | the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. | 2004 | 15059260 |
| organization of lin genes and is6100 among different strains of hexachlorocyclohexane-degrading sphingomonas paucimobilis: evidence for horizontal gene transfer. | the organization of lin genes and is6100 was studied in three strains of sphingomonas paucimobilis (b90a, sp+, and ut26) which degraded hexachlorocyclohexane (hch) isomers but which had been isolated at different geographical locations. dna-dna hybridization data revealed that most of the lin genes in these strains were associated with is6100, an insertion sequence classified in the is6 family and initially found in mycobacterium fortuitum. eleven, six, and five copies of is6100 were detected in ... | 2004 | 15060023 |
| the pmli-pmlr quorum-sensing system in burkholderia pseudomallei plays a key role in virulence and modulates production of the mpra protease. | burkholderia pseudomallei is the causative agent of melioidosis, an often fatal infection of humans and animals. the virulence of this pathogen is thought to depend on a number of secreted proteins, including the mpra metalloprotease. we observed that mpra is produced upon entry into the stationary phase, when the cell density is high, and this prompted us to study cell density-dependent regulation in b. pseudomallei. a search of the b. pseudomallei genome led to identification of a quorum-sensi ... | 2004 | 15060030 |
| characterization of the cis-acting regulatory element controlling hrpb-mediated activation of the type iii secretion system and effector genes in ralstonia solanacearum. | the ability of ralstonia solanacearum to cause disease on plants depends on its type iii secretion system (ttss) encoded by hrp genes. the expression of hrp genes and known ttss substrates is coordinately regulated by hrpb, a member of the arac family of transcriptional regulators. two hrpb-regulated promoters (hrpy and popabc) were characterized by deletion analysis, and the hrpb-dependent activation of these promoters was found to be conferred by a 25-nucleotide dna element, the hrp(ii) box (t ... | 2004 | 15060033 |
| fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy. | a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ... | 2004 | 15060178 |
| genome features of leptospira interrogans serovar copenhageni. | we report novel features of the genome sequence of leptospira interrogans serovar copenhageni, a highly invasive spirochete. leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in mammals. genomic sequence analysis reveals the presence of a competent transport system with 13 families of genes encoding for major transporters including a three-member component efflux system compatible with the long-term survival of this organ ... | 2004 | 15064809 |
| genetic evidence that the vibrio cholerae monolayer is a distinct stage in biofilm development. | biofilm development is conceived as a developmental process in which free swimming cells attach to a surface, first transiently and then permanently, as a single layer. this monolayer of immobilized cells gives rise to larger cell clusters that eventually develop into the biofilm, a three-dimensional structure consisting of large pillars of bacteria interspersed with water channels. previous studies have shown that efficient development of the vibrio cholerae biofilm requires a combination of pi ... | 2004 | 15066042 |
| urease-encoding genes in ammonia-oxidizing bacteria. | many but not all ammonia-oxidizing bacteria (aob) produce urease (urea amidohydrolase, ec 3.5.1.5) and are capable of using urea for chemolithotrophic growth. we sequenced the urease operons from two aob, the beta-proteobacterium nitrosospira sp. strain npav and the gamma-proteobacterium nitrosococcus oceani. in both organisms, all seven urease genes were contiguous: the three structural urease genes ureabc were preceded and succeeded by the accessory genes ured and ureefg, respectively. green f ... | 2004 | 15066830 |
| omega-amino acid:pyruvate transaminase from alcaligenes denitrificans y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines. | alcaligenes denitrificans y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (apta) was cloned. the gene was functionally expressed in escherichia coli bl21 by using an isopropyl-beta-d-thiogalactopyranoside (iptg)-inducible pet expression system (9.6 u/mg), and the recombinant apta was purified to show a specific a ... | 2004 | 15066855 |
| gene prediction using the self-organizing map: automatic generation of multiple gene models. | many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. it is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. | 2004 | 15070404 |
| structure of the polyketide cyclase snoal reveals a novel mechanism for enzymatic aldol condensation. | snoal belongs to a family of small polyketide cyclases, which catalyse ring closure steps in the biosynthesis of polyketide antibiotics produced in streptomyces. several of these antibiotics are among the most used anti-cancer drugs currently in use. the crystal structure of snoal, involved in nogalamycin biosynthesis, with a bound product, has been determined to 1.35 a resolution. the fold of the subunit can be described as a distorted alpha+beta barrel, and the ligand is bound in the hydrophob ... | 2004 | 15071504 |
| divergence and redundancy of 16s rrna sequences in genomes with multiple rrn operons. | the level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16s rrna-based methods. furthermore, the occurrence of widespread horizontal gene transfer (hgt) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. for this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16s rrna sequences were evaluated. bacterial genomes display up to 15 operons ... | 2004 | 15090503 |
| the pgaabcd locus of escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. | production of a polysaccharide matrix is a hallmark of bacterial biofilms, but the composition of matrix polysaccharides and their functions are not widely understood. previous studies of the regulation of escherichia coli biofilm formation suggested the involvement of an unknown adhesin. we now establish that the pgaabcd (formerly ycdsrqp) locus affects biofilm development by promoting abiotic surface binding and intercellular adhesion. all of the pga genes are required for optimal biofilm form ... | 2004 | 15090514 |
| physiologic and proteomic evidence for a role of nitric oxide in biofilm formation by nitrosomonas europaea and other ammonia oxidizers. | no, a free radical gas, is the signal for nitrosomonas europaea cells to switch between different growth modes. at an no concentration of more than 30 ppm, biofilm formation by n. europaea was induced. no concentrations below 5 ppm led to a reversal of the biofilm formation, and the numbers of motile and planktonic (motile-planktonic) cells increased. in a proteomics approach, the proteins expressed by n. europaea were identified. comparison studies of the protein patterns of motile-planktonic a ... | 2004 | 15090520 |
| genome of staphylococcal phage k: a new lineage of myoviridae infecting gram-positive bacteria with a low g+c content. | phage k is a polyvalent phage of the myoviridae family which is active against a wide range of staphylococci. phage genome sequencing revealed a linear dna genome of 127,395 bp, which carries 118 putative open reading frames. the genome is organized in a modular form, encoding modules for lysis, structural proteins, dna replication, and transcription. interestingly, the structural module shows high homology to the structural module from listeria phage a511, suggesting intergenus horizontal trans ... | 2004 | 15090528 |
| segmentally variable genes: a new perspective on adaptation. | genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. we have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping function ... | 2004 | 15094797 |
| dna repair in chromobacterium violaceum. | chromobacterium violaceum is a gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the negro river in the brazilian amazon. this bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. c. violaceum promotes the solubilization of gold in a mercur ... | 2004 | 15100997 |
| a new ralstonia solanacearum high-affinity mannose-binding lectin rs-iil structurally resembling the pseudomonas aeruginosa fucose-specific lectin pa-iil. | the plant pathogen ralstonia solanacearum produces two lectins, each with different affinity to fucose. we described previously the properties and sequence of the first lectin, rsl (subunit m(r) 9.9 kda), which is related to fungal lectins (sudakevitz, d., imberty, a., and gilboa-garber, n., 2002, j biochem 132: 353-358). the present communication reports the discovery of the second one, rs-iil (subunit m(r) 11.6 kda), a tetrameric lectin, with high sequence similarity to the fucose-binding lect ... | 2004 | 15101976 |
| negative cross-communication among wheat rhizosphere bacteria: effect on antibiotic production by the biological control bacterium pseudomonas aureofaciens 30-84. | phenazine antibiotic production in the biological control bacterium pseudomonas aureofaciens 30-84 is regulated in part via the phzr/phzi n-acyl homoserine lactone (ahl) system. previous work showed that a subpopulation of the wheat rhizosphere community positively affected phenazine gene expression in strain 30-84 via ahl signals (e. a. pierson, d. w. wood, j. a. cannon, f. m. blachere, and l. s. pierson iii, mol. plant-microbe interact. 11:1078-1084, 1998). in the present work, a second subpop ... | 2004 | 15128573 |
| identification and characterization of the dna-binding domain of the multifunctional puta flavoenzyme. | the puta flavoprotein from escherichia coli is a transcriptional repressor and a bifunctional enzyme that regulates and catalyzes proline oxidation. puta represses transcription of genes puta and putp by binding to the control dna region of the put regulon. the objective of this study is to define and characterize the dna binding domain of puta. the dna binding activity of puta, a 1320 amino acid polypeptide, has been localized to n-terminal residues 1-261. after exploring a potential dna-bindin ... | 2004 | 15155740 |
| a core catalytic domain of the tyra protein family: arogenate dehydrogenase from synechocystis. | the tyra protein family includes prephenate dehydrogenases, cyclohexadienyl dehydrogenases and tyra(a)s (arogenate dehydrogenases). tyra(a) from synechocystis sp. pcc 6803, encoding a 30 kda tyra(a) protein, was cloned into an overexpression vector in escherichia coli. tyra(a) was then purified to apparent homogeneity and characterized. this protein is a model structure for a catalytic core domain in the tyra superfamily, uncomplicated by allosteric or fused domains. competitive inhibitors actin ... | 2004 | 15171683 |
| identification of mdod, an mdog paralog which encodes a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures. | osmoregulated periplasmic glucans (opgs) of escherichia coli are anionic and highly branched oligosaccharides that accumulate in the periplasmic space in response to low osmolarity of the medium. the glucan length, ranging from 5 to 12 glucose residues, is under strict control. two genes that form an operon, mdogh, govern glucose backbone synthesis. the new gene mdod, which appears to be a paralog of mdog, was characterized in this study. cassette inactivation of mdod resulted in production of o ... | 2004 | 15175282 |
| genomic diversity of burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a burkholderia mallei-specific prophage in b. pseudomallei 1026b. | burkholderia pseudomallei is the etiologic agent of the disease melioidosis and is a category b biological threat agent. the genomic sequence of b. pseudomallei k96243 was recently determined, but little is known about the overall genetic diversity of this species. suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of b. pseudomallei, 1026b and k96243. numerous mobile genetic elements, including a temperate bacteriophage de ... | 2004 | 15175308 |
| diversity in chemotaxis mechanisms among the bacteria and archaea. | the study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. in bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. most insights into the processes involved have come from studies of escherichia coli over the last three decades. however, in the last 10 years, with the sequ ... | 2004 | 15187186 |
| swimming motility, a virulence trait of ralstonia solanacearum, is regulated by flhdc and the plant host environment. | swimming motility allows the bacterial wilt pathogen ralstonia solanacearum to efficiently invade and colonize host plants. however, the bacteria are essentially nonmotile once inside plant xylem vessels. to determine how and when motility genes are expressed, we cloned and mutated flhdc, which encodes a major regulator of flagellar biosynthesis and bacterial motility. an flhdc mutant was nonmotile and less virulent than its wild-type parent on both tomato and arabidopsis; on arabidopsis, the fl ... | 2004 | 15195951 |
| flagellin is not a major defense elicitor in ralstonia solanacearum cells or extracts applied to arabidopsis thaliana. | the phytopathogenic bacterium ralstonia solanacearum requires motility for full virulence, and its flagellin is a candidate pathogen-associated molecular pattern that may elicit plant defenses. boiled extracts from r. solanacearum contained a strong elicitor of defense-associated responses. however, r. solanacearum flagellin is not this elicitor, because extracts from wild-type bacteria and flic or flhdc mutants defective in flagellin production all elicited similar plant responses. equally impo ... | 2004 | 15195952 |
| mutational analysis and biochemical characterization of the burkholderia thailandensis dw503 quorum-sensing network. | numerous gram-negative bacteria communicate and regulate gene expression through a cell density-responsive mechanism termed quorum sensing (qs), which involves the synthesis and perception of diffusible n-acyl-homoserine lactones (ahl). in this study we genetically and physiologically characterized the burkholderia thailandensis dw503 qs network. in silico analysis of the b. thailandensis genome revealed the presence of at least three ahl synthases (ahs) and five transcriptional regulators belon ... | 2004 | 15205437 |
| variation in the effectors of the type iii secretion system among photorhabdus species as revealed by genomic analysis. | entomopathogenic bacteria of the genus photorhabdus harbor a type iii secretion system. this system was probably acquired prior to the separation of the species within this genus. furthermore, the core components of the secretion machinery are highly conserved but the predicted effectors differ between photorhabdus luminescens and p. asymbiotica, two highly related species with different hosts. | 2004 | 15205440 |
| identification of burkholderia cenocepacia genes required for bacterial survival in vivo. | burkholderia cenocepacia (formerly burkholderia cepacia complex genomovar iii) causes chronic lung infections in patients with cystic fibrosis. in this work, we used a modified signature-tagged mutagenesis (stm) strategy for the isolation of b. cenocepacia mutants that cannot survive in vivo. thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 b. cenocepacia transposon mutants, arranged in pools of ... | 2004 | 15213146 |
| inventory and functional analysis of the large hrp regulon in ralstonia solanacearum: identification of novel effector proteins translocated to plant host cells through the type iii secretion system. | the ability of ralstonia solanacearum strain gmi1000 to cause disease on a wide range of host plants (including most solanaceae and arabidopsis thaliana) depends on genes activated by the regulatory gene hrpb. hrpb controls the expression of the type iii secretion system (ttss) and pathogenicity effectors transiting through this pathway. in order to establish the complete repertoire of ttss-dependent effectors belonging to the hrp regulon and to start their functional analysis, we developed a ra ... | 2004 | 15225308 |
| first characterization of an archaeal gtp-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon thermococcus kodakaraensis kod1. | phosphoenolpyruvate carboxykinase (pck), which catalyzes the nucleotide-dependent, reversible decarboxylation of oxaloacetate to yield phosphoenolpyruvate and co2, is one of the important enzymes in the interconversion between c3 and c4 metabolites. this study focused on the first characterization of the enzymatic properties and expression profile of an archaeal pck from the hyperthermophilic archaeon thermococcus kodakaraensis (pcktk). pcktk showed 30 to 35% identities to gtp-dependent pcks fro ... | 2004 | 15231795 |
| global gene expression in staphylococcus aureus biofilms. | we previously demonstrated that mutation of the staphylococcal accessory regulator (sara) in a clinical isolate of staphylococcus aureus (uams-1) results in an impaired capacity to form a biofilm in vitro (k. e. beenken, j. s. blevins, and m. s. smeltzer, infect. immun. 71:4206-4211, 2003). in this report, we used a murine model of catheter-based biofilm formation to demonstrate that a uams-1 sara mutant also has a reduced capacity to form a biofilm in vivo. surprisingly, mutation of the uams-1 ... | 2004 | 15231800 |
| arabidopsis cyp86a2 represses pseudomonas syringae type iii genes and is required for cuticle development. | pseudomonas syringae relies on type iii secretion system to deliver effector proteins into the host cell for parasitism. type iii genes are induced in planta, but host factors affecting the induction are poorly understood. here we report on the identification of an arabidopsis mutant, att1 (for aberrant induction of type three genes), that greatly enhances the expression of bacterial type iii genes avrpto and hrpl. att1 plants display enhanced disease severity to a virulent strain of p. syringae ... | 2004 | 15241470 |
| identification of a bifunctional enzyme mnmc involved in the biosynthesis of a hypermodified uridine in the wobble position of trna. | the gene encoding the bifunctional enzyme mnmc that catalyzes the two last steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2u) in trna has been previously mapped at about 50 min on the escherichia coli k12 chromosome, but to date the identity of the corresponding enzyme has not been correlated with any of the known open reading frames (orfs). using the protein fold-recognition approach, we predicted that the 74-kda product of the yfck orf located at 52.6 min and annotated as ... | 2004 | 15247431 |
| the complex structure of polyhydroxybutyrate (phb) granules: four orthologous and paralogous phasins occur in ralstonia eutropha. | analysis of the genome sequence of the polyhydroxyalkanoate- (pha) accumulating bacterium ralstonia eutropha strain h16 revealed three homologues (phap2, phap3 and phap4) of the phasin protein phap1. phap1 is known to constitute the major component of the layer at the surface of poly(3-hydroxybutyrate), poly(3hb), granules. phap2, phap3 and phap4 exhibited 42, 49 and 45 % identity or 61, 62 and 63 % similarity to phap1, respectively. the calculated molecular masses of phap1, phap2, phap3 and pha ... | 2004 | 15256572 |
| 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 |
| pspg, a new member of the yersinia enterocolitica phage shock protein regulon. | the yersinia enterocolitica phage shock protein (psp) system is induced when the ysc type iii secretion system is produced or when only the yscc secretin component is synthesized. some psp null mutants have a growth defect when yscc is produced and a severe virulence defect in animals. the y. enterocolitica psp locus is made up of two divergently transcribed cistrons, pspf and pspabcdycjxf. pspa operon expression is dependent on rpon (sigma(54)) and the enhancer-binding protein pspf. previous da ... | 2004 | 15262928 |
| the global regulator genes from biocontrol strain serratia plymuthica ic1270: cloning, sequencing, and functional studies. | the biocontrol activity of various fluorescent pseudomonads towards plant-pathogenic fungi is dependent upon the gaca/gacs-type two-component system of global regulators and the rpos transcription sigma factor. in particular, these components are required for the production of antifungal antibiotics and exoenzymes. to investigate the effects of these global regulators on the expression of biocontrol factors by plant-associated bacteria other than pseudomonas spp., gaca/gacs and rpos homologues w ... | 2004 | 15262936 |
| 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 |
| genome sequence of the enterobacterial phytopathogen erwinia carotovora subsp. atroseptica and characterization of virulence factors. | the bacterial family enterobacteriaceae is notable for its well studied human pathogens, including salmonella, yersinia, shigella, and escherichia spp. however, it also contains several plant pathogens. we report the genome sequence of a plant pathogenic enterobacterium, erwinia carotovora subsp. atroseptica (eca) strain scri1043, the causative agent of soft rot and blackleg potato diseases. approximately 33% of eca genes are not shared with sequenced enterobacterial human pathogens, including s ... | 2004 | 15263089 |
| 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 |
| lessons learned from the genome analysis of ralstonia solanacearum. | ralstonia solanacearum is a devastating plant pathogen with a global distribution and an unusually wide host range. this bacterium can also be free-living as a saprophyte in water or in the soil in the absence of host plants. the availability of the complete genome sequence from strain gmi1000 provided the basis for an integrative analysis of the molecular traits determining the adaptation of the bacterium to various environmental niches and pathogenicity toward plants. this review summarizes cu ... | 2004 | 15283662 |
| in different organisms, the mode of interaction between two signaling proteins is not necessarily conserved. | although interfaces mediating protein-protein interactions are thought to be under strong evolutionary constraints, binding of the chemotaxis histidine kinase chea to its phosphorylation target chey suggests otherwise. the structure of thermotoga maritima chea domain p2 in complex with chey reveals a different association than that observed for the same escherichia coli proteins. similar regions of chey bind chea p2 in the two systems, but the chea p2 domains differ by an approximately 90 degree ... | 2004 | 15289606 |
| x-ray analysis of crystals of polygalacturonase a from pseudomonas solanacearum. | crystals of the pectolytic protein, polygalacturonase a, have been obtained from polyethylene glycol 8000 using vapor diffusion methods. the 52.4 kda protein is secreted by the plant pathogenic bacteria pseudomonas solanacearum, and is important in the virulence of this plant pathogen. the protein crystallizes in space group p2(1) and has unit-cell parameters of a = 101.9, b = 124.6, c = 48.1 a, and beta= 105 degrees 50'. the crystal has two molecules in the asymmetric unit, and diffracts maxima ... | 1995 | 15299786 |
| distribution and sequence analysis of a family of type ill-dependent effectors correlate with the phylogeny of ralstonia solanacearum strains. | in ralstonia solanacearum, we previously have reported on the characterization of popp1 and popp2 genes. these genes encode type iii-dependent pathogenicity effectors related to the large family of avrrxv/yopj cysteine proteases that are shared among pathogens of plants and animals. in this study, we identify a third gene, named popp3, that is inactivated in the genome sequence of strain gmi1000 by insertion of a copy of the insertion sequence isrso13. the three popp genes are localized on two l ... | 2004 | 15305614 |
| the hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. | the hotdog fold was initially identified in the structure of escherichia coli faba and subsequently in 4-hydroxybenzoyl-coa thioesterase from pseudomonas sp. strain cbs. since that time structural determinations have shown a number of other apparently unrelated proteins also share the hotdog fold. | 2004 | 15307895 |
| a putative polyketide synthase/peptide synthetase from magnaporthe grisea signals pathogen attack to resistant rice. | isolates of the rice blast fungus magnaporthe grisea that carry the gene encoding avirulence conferring enzyme1 (ace1) are specifically recognized by rice (oryza sativa) cultivars carrying the resistance gene pi33. this recognition enables resistant plants to activate a defense response. ace1 was isolated by map-based cloning and encodes a putative hybrid between a polyketide synthase and a nonribosomal peptide synthetase, enzymes involved in microbial secondary metabolism. ace1 is expressed exc ... | 2004 | 15319478 |
| 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 |