Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| virulence of enteropathogenic escherichia coli, a global pathogen. | enteropathogenic escherichia coli (epec) remains an important cause of diarrheal disease worldwide. research into epec is intense and provides a good virulence model of other e. coli infections as well as other pathogenic bacteria. although the virulence mechanisms are now better understood, they are extremely complex and much remains to be learnt. the pathogenesis of epec depends on the formation of an ultrastructural lesion in which the bacteria make intimate contact with the host apical enter ... | 2003 | 12857773 |
| interplay of the czc system and two p-type atpases in conferring metal resistance to ralstonia metallidurans. | cadmium and zinc are removed from cells of ralstonia metallidurans by the czccba efflux pump and by two soft-metal-transporting p-type atpases, cada and znta. the czccba genes are located on plasmid pmol30, and the cada and znta genes are on the bacterial chromosome. expression of znta from r. metallidurans in escherichia coli predominantly mediated resistance to zinc, and expression of cada predominantly mediated resistance to cadmium. both transporters decreased the cellular content of zinc or ... | 2003 | 12867443 |
| a 65-kilobase pathogenicity island is unique to philadelphia-1 strains of legionella pneumophila. | nucleotide sequence analysis of an approximately 80-kb genomic region revealed an approximately 65-kb locus that bears hallmarks of a pathogenicity island. this locus includes homologues of a type iv secretion system, mobile genetic elements, and known virulence factors. comparative studies with other legionella pneumophila strains and serogroups indicated that this approximately 65-kb locus is unique to l. pneumophila serogroup 1 philadelphia-1 strains. | 2003 | 12867476 |
| phylogenetic analysis of bacterial and archaeal arsc gene sequences suggests an ancient, common origin for arsenate reductase. | the ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. the arsc gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. a survey of genbank shows that arsc appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects. | 2003 | 12877744 |
| host plant-dependent phenotypic reversion of ralstonia solanacearum from non-pathogenic to pathogenic forms via alterations in the phca gene. | ralstonia solanacearum is a plant pathogenic bacterium that undergoes a spontaneous phenotypic conversion (pc) from a wild-type pathogenic to a non-pathogenic form. pc is often associated with mutations in phca, which is a key virulence regulatory gene. until now, reversion to the wild-type pathogenic form has not been observed for pc variants and the biological significance of pc has been questioned. in this study, we characterized various alterations in phca (eight is element insertions, three ... | 2003 | 12890023 |
| benzoate-coenzyme a ligase from thauera aromatica: an enzyme acting in anaerobic and aerobic pathways. | in the denitrifying member of the beta-proteobacteria thauera aromatica, the anaerobic metabolism of aromatic acids such as benzoate or 2-aminobenzoate is initiated by the formation of the coenzyme a (coa) thioester, benzoyl-coa and 2-aminobenzoyl-coa, respectively. both aromatic substrates were transformed to the acyl-coa intermediate by a single coa ligase (amp forming) that preferentially acted on benzoate. this benzoate-coa ligase was purified and characterized as a 57-kda monomeric protein. ... | 2003 | 12897012 |
| spread of recombinant dna by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an acinetobacter sp. | transgenic potato plants with the nptii gene coding for neomycin phosphotransferase (kanamycin resistance) as a selection marker were examined for the spread of recombinant dna into the environment. we used the recombinant fusion of nptii with the tg4 terminator for a novel biomonitoring technique. this depended on natural transformation of acinetobacter sp. strain bd413 cells having in their genomes a terminally truncated nptii gene (nptii'; kanamycin sensitivity) followed by the tg4 terminator ... | 2003 | 12902229 |
| the biphenyl- and 4-chlorobiphenyl-catabolic transposon tn4371, a member of a new family of genomic islands related to incp and ti plasmids. | the nucleotide sequence of the biphenyl catabolic transposon tn4371 has been completed and analyzed. it confirmed that the element has a mosaic structure made of several building blocks. in addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of achromobacter georgiopolitanum kks102, tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, pl ... | 2003 | 12902278 |
| colonization of arabidopsis thaliana with salmonella enterica and enterohemorrhagic escherichia coli o157:h7 and competition by enterobacter asburiae. | enteric pathogens, such as salmonella enterica and escherichia coli o157:h7, have been shown to contaminate fresh produce. under appropriate conditions, these bacteria will grow on and invade the plant tissue. we have developed arabidopsis thaliana (thale cress) as a model system with the intention of studying plant responses to human pathogens. under sterile conditions and at 100% humidity, s. enterica serovar newport and e. coli o157:h7 grew to 10(9) cfu g(-1) on a. thaliana roots and to 2 x 1 ... | 2003 | 12902287 |
| metagenomic profiling: microarray analysis of an environmental genomic library. | genomic libraries derived from environmental dna (metagenomic libraries) are useful for characterizing uncultured microorganisms. however, conventional library-screening techniques permit characterization of relatively few environmental clones. here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with dna from a set of groundwater isolates, reference strains, and communities. a cosmid library derived from a microcosm of groundwater microorgan ... | 2003 | 12902288 |
| regulation of the vitamin b12 metabolism and transport in bacteria by a conserved rna structural element. | cobalamin in the form of adenosylcobalamin (ado-cbl) is known to repress expression of genes for vitamin b(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of ado-cbl to 5'untranslated gene regions (5'utr). using comparative analysis of genes and regulatory regions, we identified a highly conserved rna structure, the b12-element, which is widely distributed in 5'utrs of vitamin b(12)-related genes in eubacteria. multiple alignment o ... | 2003 | 12923257 |
| spatial stochastic simulation offers potential as a quantitative method for pest risk analysis. | pest risk analysis represents an emerging field of risk analysis that evaluates the potential risks of the introduction and establishment of plant pests into a new geographic location and then assesses the management options to reduce those potential risks. development of new and adapted methodology is required to answer questions concerning pest risk analysis of exotic plant pests. this research describes a new method for predicting the potential establishment and spread of a plant pest into ne ... | 2003 | 12926559 |
| a novel antimicrobial protein isolated from potato (solanum tuberosum) shares homology with an acid phosphatase. | the nucleotide and amino acids sequences for ap(1) will appear in the genbank(r) and ncbi databases under accession number ay297449. a novel antimicrobial protein (ap(1)) was purified from leaves of the potato ( solanum tuberosum, variety ms-42.3) with a procedure involving ammonium sulphate fractionation, molecular sieve chromatography with sephacryl s-200 and hydrophobic chromatography with butyl-sepharose using a fplc system. the inhibition spectrum investigation showed that ap(1) had good in ... | 2003 | 12927022 |
| the complete genome sequence of the arabidopsis and tomato pathogen pseudomonas syringae pv. tomato dc3000. | we report the complete genome sequence of the model bacterial pathogen pseudomonas syringae pathovar tomato dc3000 (dc3000), which is pathogenic on tomato and arabidopsis thaliana. the dc3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 orfs. we identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type iii secretion system effector proteins. many of the virule ... | 2003 | 12928499 |
| evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. | shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire opero ... | 2003 | 12952534 |
| an improved probability mapping approach to assess genome mosaicism. | maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. however, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. here we extend the probability mapping approach by improving taxon sampling o ... | 2003 | 12974984 |
| reactive oxygen species and ethylene play a positive role in lateral root base nodulation of a semiaquatic legume. | lateral root base nodulation on the tropical, semiaquatic legume sesbania rostrata results from two coordinated, nod factor-dependent processes: formation of intercellular infection pockets and induction of cell division. infection pocket formation is associated with cell death and production of hydrogen peroxide. pharmacological experiments showed that ethylene and reactive oxygen species mediate nod factor responses and are required for nodule initiation, whereby induction of division and infe ... | 2003 | 12975522 |
| experimental determination and system level analysis of essential genes in escherichia coli mg1655. | defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. we used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of escherichia coli in rich media. we identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. functional context analysis of these data allows individual functional assignment ... | 2003 | 13129938 |
| comparison of slime from tomato and banana strains of pseudomonas solanacearum. | 1959 | 13818445 | |
| taxonomic analysis with the electronic computer of some xanthomonas and pseudomonas species. | colwell, r. r. (university of washington, seattle) and j. liston. taxonomic analysis with the electronic computer of some xanthomonas and pseudomonas species. j. bacteriol. 82:913-919. 1961.-forty organisms, including 16 xanthomonas spp., 5 strains of pseudomonas solanacearum, 4 strains of p. aeruginosa, 6 strains of p. fluorescens, 5 freshly isolated strains of pseudomonads, as well as the american type culture collection strains of flavobacterium aquatile, vibrio cuneatus, vibrio metschnikovii ... | 1961 | 13880721 |
| ethylene production by pseudomonas solanacearum. | 1964 | 14167811 | |
| a new and sensitive co-operational polymerase chain reaction for rapid detection of ralstonia solanacearum in water. | three primers from 16s rrna were successfully assayed simultaneously in one reaction for sensitive detection of ralstonia solanacearum in watercourses. the protocol is a modification of the co-operational polymerase chain reaction (co-pcr), which allows the simultaneous and co-operational action of the primers. it specifically amplified r. solanacearum strains belonging to biovars 1, 2 and 4. no products were obtained from any of the 162 unidentified isolates from river water. the sensitivity of ... | 2003 | 14500017 |
| the complete genome sequence of chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. | chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) approximately 500 orfs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) widespread utilization of quorum sensing for control of inducible systems, all of ... | 2003 | 14500782 |
| osmotic adaptation of thermus thermophilus rq-1: lesson from a mutant deficient in synthesis of trehalose. | strains of thermus thermophilus accumulate primarily trehalose and smaller amounts of mannosylglycerate in response to salt stress in yeast extract-containing media (o. c. nunes, c. m. manaia, m. s. da costa, and h. santos, appl. environ. microbiol. 61:2351-2357, 1995). a 2.4-kbp dna fragment from t. thermophilus strain rq-1 carrying otsa (encoding trehalose-phosphate synthase [tps]), otsb (encoding trehalose-phosphate phosphatase [tpp]), and a short sequence of the 5' end of tres (trehalose syn ... | 2003 | 14526004 |
| 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 |
| community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. | we investigated communities of denitrifying bacteria from adjacent meadow and forest soils. our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosz, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. denit ... | 2003 | 14532052 |
| 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 |
| laf3, a novel factor required for normal phytochrome a signaling. | phytochrome a (phya) is the photolabile plant light receptor that mediates broad spectrum very low-fluence responses and high irradiance responses to continuous far-red light (frc). an arabidopsis mutant laf3-1 (long after far-red 3) was recovered from a screen for transposon-tagged mutants that exhibit reduced inhibition of hypocotyl elongation in frc. the laf phenotype correlated well with a strongly attenuated disappearance of xtr7 transcript in frc. the effects of laf3-1 on phya-controlled c ... | 2003 | 14645728 |
| 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 |
| ccpa-dependent carbon catabolite repression in bacteria. | carbon catabolite repression (ccr) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. in gram-positive bacteria, ccpa-dependent ccr is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate hpr at a serine residue at the expense of atp. the reaction is catalyzed by hpr kinase, which is activated by glycolytic intermediates. in this review, the distribution of ccpa-dependent ccr among bacteria is inv ... | 2003 | 14665673 |
| 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 |
| 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 |
| nitrous oxide reductase (nosz) gene fragments differ between native and cultivated michigan soils. | the effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosz) fragments from denitrifying prokaryotes in native and cultivated soil was explored. thirty-six soil cores were composited from each of the two soil management conditions. nosz gene fragments were amplified from triplicate samples, and pcr products were cloned and screened by restriction fragment length polymorphism (rflp). the total nosz rflp profiles increased in similarity with soil sa ... | 2004 | 14711656 |
| 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 |
| prediction of rna-binding proteins from primary sequence by a support vector machine approach. | elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ... | 2004 | 14970381 |
| 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 |
| microarray-based identification of bacteria in clinical samples by solid-phase pcr amplification of 23s ribosomal dna sequences. | the rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. we describe a dna microarray-based pcr approach for the quick detection and identification of bacteria from cervical swab specimens from mares. this on-chip pcr method combines the amplification of a variable region of bacterial 23s ribosomal dna and the simultaneous sequence-specific detection on a solid phase. the solid phase contains bacterial species-specific primers co ... | 2004 | 15004052 |
| 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 |
| evaluation of monocot and eudicot divergence using the sugarcane transcriptome. | over 40,000 sugarcane (saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and dna sequences from other angiosperms, including the genomes of arabidopsis and rice (oryza sativa). approximately two-thirds of the sugarcane transcriptome have similar sequences in arabidopsis. these sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angi ... | 2004 | 15020759 |
| 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 |
| sigi: score-based identification of genomic islands. | genomic islands can be observed in many microbial genomes. these stretches of dna have a conspicuous composition with regard to sequence or encoded functions. genomic islands are assumed to be frequently acquired via horizontal gene transfer. for the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands. | 2004 | 15113412 |