Publications

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
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
concomitant induction of systemic resistance to pseudomonas syringae pv. lachrymans in cucumber by trichoderma asperellum (t-203) and accumulation of phytoalexins.	most studies on the reduction of disease incidence in soil treated with trichoderma asperellum have focused on microbial interactions rather than on plant responses. this study presents conclusive evidence for the induction of a systemic response against angular leaf spot of cucumber (pseudomonas syringae pv. lachrymans) following application of t. asperellum to the root system. to ascertain that t. asperellum was the only microorganism present in the root milieu, plants were grown in an aseptic ...	2003	14660384
efficient synthesis of a heptasaccharide, the repeating unit of the o-chain lipopolysaccharide produced by xanthomonas campestris strain 642.	alpha-l-rhap-(1-->3)-alpha-l-rhap-(1-->2)-alpha-l-rhap-(1-->3)-[beta-d-xylp-(1-->2)-][beta-d-xylp-(1-->4)-]alpha-l-rhap-(1-->3)-alpha-l-rhap, the repeating unit of the o-chain lipopolysaccharide produced by xanthomonas campestris strain 642 was synthesized as its methyl glycoside via 3-o-selective glycosylation of methyl alpha-l-rhamnopyranosyl-(1-->3)-2,4-di-o-benzoyl-alpha-l-rhamnopyranoside (9) with 2,3,4-tri-o-benzoyl-alpha-l-rhamnopyranosyl-(1-->3)-2,4-di-o-benzoyl-alpha-l-rhamnopyranosyl-( ...	2003	12706967
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
biofilm dispersal in xanthomonas campestris is controlled by cell-cell signaling and is required for full virulence to plants.	the rpf gene cluster of xanthomonas campestris pathovar campestris (xcc) is required for the pathogenesis of this bacterium to plants. several rpf genes are involved in the coordinate positive regulation of the production of virulence factors mediated by the small diffusible molecule dsf (for diffusible signal factor). rpff directs the synthesis of dsf, and a two-component sensory transduction system comprising rpfc and rpfg has been implicated in the perception of the dsf signal and signal tran ...	2003	12960398
evidence for dose-dependent effects on plant growth by stenotrophomonas strains from different origins.	to assess the influence of stenotrophomonas on plants, the interaction of 16 stenotrophomonas strains from clinical and environmental sources with strawberry plant seedlings was analysed.	2003	12969277
effect of azospirillum-mediated plant growth promotion on the development of bacterial diseases on fresh-market and cherry tomato.	plant growth-promoting (pgp) activity of two azospirillum strains and their effects on foliar and vascular bacterial diseases were evaluated on fresh market and cherry tomato.	2003	12969298
catalytic mechanism of thiol peroxidase from escherichia coli. sulfenic acid formation and overoxidation of essential cys61.	escherichia coli thiol peroxidase (tpx, p20, scavengase) is part of an oxidative stress defense system that uses reducing equivalents from thioredoxin (trx1) and thioredoxin reductase to reduce alkyl hydroperoxides. tpx contains three cys residues, cys(95), cys(82), and cys(61), and the latter residue aligns with the n-terminal active site cys of other peroxidases in the peroxiredoxin family. to identify the catalytically important cys, we have cloned and purified tpx and four mutants (c61s, c82 ...	2003	12514184
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
vgj phi, a novel filamentous phage of vibrio cholerae, integrates into the same chromosomal site as ctx phi.	we describe a novel filamentous phage, designated vgj phi, isolated from strain sg25-1 of vibrio cholerae o139, which infects all o1 (classical and el tor) and o139 strains tested. the sequence of the 7,542 nucleotides of the phage genome reveals that vgj phi has a distinctive region of 775 nucleotides and a conserved region with an overall genomic organization similar to that of previously characterized filamentous phages, such as ctx phi of v. cholerae and ff phages of escherichia coli. the co ...	2003	13129939
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
a nuclear protease required for flowering-time regulation in arabidopsis reduces the abundance of small ubiquitin-related modifier conjugates.	the arabidopsis mutant early in short days4 (esd4) shows extreme early flowering and alterations in shoot development. we have identified esd4 and demonstrate that it encodes a nuclear protein located predominantly at the periphery of the nucleus. esd4 contains a segment of >200 amino acids with strong similarity to yeast and animal proteases that are specific for the protein modifier small ubiquitin-related modifier (sumo). esd4 shows a similar function to these proteases in vitro and processes ...	2003	14507998
the unusual arabidopsis extensin gene atext1 is expressed throughout plant development and is induced by a variety of biotic and abiotic stresses.	we detail the expression of the arabidopsis thaliana (l.) heynh. atext1 extensin gene. atext1 is normally expressed in roots and inflorescences, and is induced by wounding, exogenously supplied salicylic acid, methyl jasmonate, auxins and brassinosteroids. northern assays and histochemical analysis of transgenics expressing an atext1:: gus fusion show that this gene is also induced by the brassica pathogen xanthomonas campestris pv. campestris and that this induction is restricted to tissues clo ...	2003	14520562
cleavage of the pseudomonas syringae type iii effector avrrpt2 requires a host factor(s) common among eukaryotes and is important for avrrpt2 localization in the host cell.	many phytopathogenic bacteria use a type iii secretion system to deliver type iii effector proteins into the host plant cell. the pseudomonas syringae type iii effector avrrpt2 is cleaved at a specific site when translocated into the host cell. in this study, we first demonstrate that the factor(s) required for avrrpt2 cleavage is present in extracts from animal and yeast cells, as well as plant cells. the cleavage factor in animal and plant cell extracts was heat labile but relatively insensiti ...	2003	14526114
[the extracellular proteases of the phytopathogenic bacterium xanthomonas campestris].	the culture liquids of three xanthomonas campestris pv. campestris strains were found to possess proteolytic activity. the culture liquid of strain b-611 with the highest proteolytic activity was fractionated by salting-out with ammonium sulfate, gel filtration, and ion-exchange chromatography. the electrophoretic analysis of active fractions showed the presence of two proteases in the culture liquid of strain b-611, the major of which being serine protease. the treatment of cabbage seedlings wi ...	2003	14526540
structural elucidation of the o-chain of the lipopolysaccharide from xanthomonas campestris strain 8004.	a novel o-specific polysaccharide containing 3-acetamido-3-deoxy-alpha-d-fucose (fuc3nac) and d-rhamnose was isolated from the phenol-soluble lipopolysaccharide fraction of the plant associated bacterium xanthomonas campestris strain 8004. the structure, determined by means of chemical analysis and 1d and 2d nmr spectroscopy, showed a branched trisaccharide repeating unit, as shown below: [formula: see text].	2003	12543561
prospecting for novel biocatalysts in a soil metagenome.	the metagenomes of complex microbial communities are rich sources of novel biocatalysts. we exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. a 16s rrna sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera pseudomonas, agrobacterium, xanthomonas, microbulbifer, and janthinobacterium. total genomic dna from t ...	2003	14532085
8-hydroxy-(+)-delta-cadinene is a precursor to hemigossypol in gossypium hirsutum.	[(3)h](+)-delta-cadinene and its 8-hydroxy derivative, prepared from (1rs)-[1-(3)h]fpp by the action of one and two recombinant enzymes, respectively, were infiltrated into cotyledons of bacterial blight-resistant cotton plants as they biosynthesized sesquiterpene phytoalexins in response to infection by xanthomonas campestris pv. malvacearum. following both treatments, tritium appeared in the hplc fraction that contained hemigossypol. hemigossypol was isolated from the cotyledons that had been ...	2003	12946420
susceptible to intolerance--a range of hormonal actions in a susceptible arabidopsis pathogen response.	ethylene and salicylic acid (sa) are key intermediates in a host's response to pathogens. previously, we have shown using a tomato compatible interaction that ethylene and sa act sequentially and are essential for disease symptom production. here, we have examined the relationship between the two signals in the arabidopsis-xanthomonas campestris pv. campestris (xcc) compatible interaction. preventing sa accumulation by expression of the nahg gene reduced subsequent ethylene production and altere ...	2003	12535339
intracellular peptidoglycan hydrolases of the bacterium xanthomonas campestris xl-1.	a system of intracellular peptidoglycan hydrolases of xanthomonas campestris xl-1 comprises about 10 enzymes of different localization and substrate specificity. seven enzymes (a(1)-a(7)) are localized in cytosol, one enzyme (a(8)) in periplasm, and two enzymes (a(9), a(10)) were found in the fraction of cell walls and membranes. while the culture is entering the logarithmic growth stage from the stationary stage, a change occurs in the activity of the cytosolic enzymes: a(1) significantly incre ...	2003	12765529
identification of genes required for synthesis of the adhesive holdfast in caulobacter crescentus.	adhesion to both abiotic and biotic surfaces by the gram-negative prothescate bacterium caulobacter crescentus is mediated by a polar organelle called the "holdfast," which enables the bacterium to form stable monolayer biofilms. the holdfast, a complex polysaccharide composed in part of n-acetylglucosamine, localizes to the tip of the stalk (a thin cylindrical extension of the cell wall and membranes). we report here the isolation of adhesion mutants with transposon insertions in an uncharacter ...	2003	12562815
multiple hormones act sequentially to mediate a susceptible tomato pathogen defense response.	phytohormones regulate plant responses to a wide range of biotic and abiotic stresses. how a limited number of hormones differentially mediate individual stress responses is not understood. we have used one such response, the compatible interaction of tomato (lycopersicon esculentum) and xanthomonas campestris pv vesicatoria (xcv), to examine the interactions of jasmonic acid (ja), ethylene, and salicylic acid (sa). the role of ja was assessed using an antisense allene oxide cyclase transgenic l ...	2003	14551324
involvement of an inducible fructose phosphotransferase operon in streptococcus gordonii biofilm formation.	oral streptococci, such as streptococcus gordonii, are the predominant early colonizers that initiate biofilm formation on tooth surfaces. investigation of an s. gordonii::tn917-lac biofilm-defective mutant isolated by using an in vitro biofilm formation assay showed that the transposon insertion is near the 3' end of an open reading frame (orf) encoding a protein homologous to streptococcus mutans fruk. three genes, frur, fruk, and frui, were predicted to encode polypeptides that are part of th ...	2003	14563858
cadmium-induced adaptive resistance and cross-resistance to zinc in xanthomonas campestris.	cadmium (cd) and zinc (zn) are environmental pollutants affecting both soil and water. the toxicity resulting from the exposure of xanthomonas campestris, a soil bacterium and plant pathogen, to these metals was investigated. pretreatment of x. campestris with sub-lethal concentrations of cd induced adaptive protection against subsequent exposure to lethal doses of cd. moreover, cd-induced cells also showed cross-resistance to lethal concentrations of zn. these induced protections required newly ...	2003	14570280
high throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance.	virus-induced gene silencing was used to assess the function of random nicotiana benthamiana cdnas in disease resistance. out of 4992 cdnas tested from a normalized library, there were 79 that suppressed a hypersensitive response (hr) associated with pto-mediated resistance against pseudomonas syringae. however, only six of these clones blocked the pto-mediated suppression of p.syringae growth. the three clones giving the strongest loss of pto resistance had inserts corresponding to hsp90 and al ...	2003	14592968
hlm1, an essential signaling component in the hypersensitive response, is a member of the cyclic nucleotide-gated channel ion channel family.	the hypersensitive response (hr) in plants is a programmed cell death that is commonly associated with disease resistance. a novel mutation in arabidopsis, hlm1, which causes aberrant regulation of cell death, manifested by a lesion-mimic phenotype and an altered hr, segregated as a single recessive allele. broad-spectrum defense mechanisms remained functional or were constitutive in the mutant plants, which also exhibited increased resistance to a virulent strain of pseudomonas syringae pv toma ...	2003	12566578
flagellin glycosylation island in pseudomonas syringae pv. glycinea and its role in host specificity.	the deduced amino acid sequences of the flagellins of pseudomonas syringae pv. tabaci and p. syringae pv. glycinea are identical; however, their abilities to induce a hypersensitive reaction are clearly different. the reason for the difference seems to depend on the posttranslational modification of the flagellins. to investigate the role of this posttranslational modification in the interactions between plants and bacterial pathogens, we isolated genes that are potentially involved in the postt ...	2003	14594840
genetic differences between two strains of xylella fastidiosa revealed by suppression subtractive hybridization.	suppression subtractive hybridization was used to rapidly identify 18 gene differences between a citrus variegated chlorosis (cvc) strain and a pierce's disease of grape (pd) strain of xylella fastidiosa. the results were validated as being highly representative of actual differences by comparison of the completely sequenced genome of a cvc strain with that of a pd strain.	2003	12571065
overexpression of the disease resistance gene pto in tomato induces gene expression changes similar to immune responses in human and fruitfly.	the pto gene encodes a serine/threonine protein kinase that confers resistance in tomato (lycopersicon esculentum) to pseudomonas syringae pv tomato strains that express the type iii effector protein avrpto. constitutive overexpression of pto in tomato, in the absence of avrpto, activates defense responses and confers resistance to several diverse bacterial and fungal plant pathogens. we have used a series of gene discovery and expression profiling methods to examine the effect of pto overexpres ...	2003	12913147
development of a phenomenological modeling approach for prediction of growth and xanthan gum production using xanthomonas campestris.	an unstructured kinetic model for xanthan production is described and fitted to experimental data obtained in a stirred batch reactor. the culture medium was composed of several nitrogen sources (soybean hydrolysates, ammonium and nitrate salts) consumed sequentially. the model proposed is able to describe this sequential consumption of nitrogen sources, the consumption of inorganic phosphate and carbon, the evolution of biomass, and production of xanthan. the parameter estimation has been perfo ...	2003	12790645
arabidopsis contains a large superfamily of acyl-activating enzymes. phylogenetic and biochemical analysis reveals a new class of acyl-coenzyme a synthetases.	acyl-activating enzymes are a diverse group of proteins that catalyze the activation of many different carboxylic acids, primarily through the formation of a thioester bond. this group of enzymes is found in all living organisms and includes the acyl-coenzyme a synthetases, 4-coumarate:coenzyme a ligases, luciferases, and non-ribosomal peptide synthetases. the members of this superfamily share little overall sequence identity, but do contain a 12-amino acid motif common to all enzymes that activ ...	2003	12805634
crystal structure of a putative methyltransferase from mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis.	bioinformatic analyses of whole genome sequences highlight the problem of identifying the biochemical and cellular functions of many gene products that are at present uncharacterized. the open reading frame rv3853 from mycobacterium tuberculosis has been annotated as meng and assumed to encode an s-adenosylmethionine (sam)-dependent methyltransferase that catalyzes the final step in menaquinone biosynthesis. the rv3853 gene product has been expressed, refolded, purified, and crystallized in the ...	2003	12837779
characterization of the xanthomonas axonopodis pv. glycines hrp pathogenicity island.	we sequenced an approximately 29-kb region from xanthomonas axonopodis pv. glycines that contained the hrp type iii secretion system, and we characterized the genes in this region by tn3-gus mutagenesis and gene expression analyses. from the region, hrp (hypersensitive response and pathogenicity) and hrc (hrp and conserved) genes, which encode type iii secretion systems, and hpa (hrp-associated) genes were identified. the characteristics of the region, such as the presence of many virulence gene ...	2003	12730176
honor thy symbionts.	our intestine is the site of an extraordinarily complex and dynamic environmentally transmitted consortial symbiosis. the molecular foundations of beneficial symbiotic host-bacterial relationships in the gut are being revealed in part from studies of simplified models of this ecosystem, where germ-free mice are colonized with specified members of the microbial community, and in part from comparisons of the genomes of members of the intestinal microbiota. the results emphasize the contributions o ...	2003	12923294
influence of nutritional factors on the nature, yield, and composition of exopolysaccharides produced by gluconacetobacter xylinus i-2281.	the influence of substrate composition on the yield, nature, and composition of exopolysaccharides (eps) produced by the food-grade strain gluconacetobacter xylinus i-2281 was investigated during controlled cultivations on mixed substrates containing acetate and either glucose, sucrose, or fructose. enzymatic activity analysis and acid hydrolysis revealed that two eps, gluconacetan and levan, were produced by g. xylinus. in contrast to other acetic acid strains, no exocellulose formation has bee ...	2003	14532066
characterization of two antagonistic strains of rahnella aquatilis isolated from soil in egypt.	in an attempt to obtain biological control agents for controlling bacterial spot of cucumber, over 250 bacterial strains were isolated from agricultural soil samples, collected from different localities in giza governorate (egypt) and screened for in vitro antibiosis towards xanthomonas campestris. only 2 strains showed antagonistic activity. they and their culture filtrates restricted the growth of a number of g- and g(+)-indicator bacteria. on chrome azurol s agar, both strains exhibited a mar ...	2003	15058195
characterization of dominantly negative mutant clya cytotoxin proteins in escherichia coli.	we report studies of the subcellular localization of the clya cytotoxic protein and of mutations causing defective translocation to the periplasm in escherichia coli. the ability of clya to translocate to the periplasm was abolished in deletion mutants lacking the last 23 or 11 amino acid residues of the c-terminal region. a naturally occurring clya variant lacking four residues (183 to 186) in a hydrophobic subdomain was retained mainly in the cytosolic fraction. these mutant proteins displayed ...	2003	12949101
glutathione and catalase provide overlapping defenses for protection against respiration-generated hydrogen peroxide in haemophilus influenzae.	glutathione is an abundant and ubiquitous low-molecular-weight thiol that may play a role in many cellular processes, including protection against the deleterious effects of reactive oxygen species. we address here the role of glutathione in protection against hydrogen peroxide (h2o2) in haemophilus influenzae and show that glutathione and catalase provide overlapping defense systems. h. influenzae is naturally glutathione deficient and imports glutathione from the growth medium. mutant h. influ ...	2003	12949108
a developmental response to pathogen infection in arabidopsis.	we present evidence that susceptible arabidopsis plants accelerate their reproductive development and alter their shoot architecture in response to three different pathogen species. we infected 2-week-old arabidopsis seedlings with two bacterial pathogens, pseudomonas syringae and xanthomonas campestris, and an oomycete, peronospora parasitica. infection with each of the three pathogens reduced time to flowering and the number of aerial branches on the primary inflorescence. in the absence of co ...	2003	12970499
direct delivery of bacterial avirulence proteins into resistant arabidopsis protoplasts leads to hypersensitive cell death.	many bacterial avirulence (avr) proteins, including the pseudomonas syringae proteins, avrrpt2 and avrb, appear to be recognized inside the host plant cell by resistance mechanisms mediated by the cognate resistance (r) genes. it is thought that avr proteins are either delivered directly into the host cell via the bacterial type iii secretion system (ttss) or taken up by the plant cell following secretion into the apoplast through the ttss. recently, it was shown that the xanthomonas campestris ...	2003	12943547
molecular genetic analyses of potential beta-galactosidase genes in xanthomonas campestris.	xanthomonas campestris pv. campestris, which displays no significant beta-1,4-d-galactopyranosidase activity, has three annotated beta-galactosidase genes in the sequenced genome, designated gala, galb and galc herein. gala and galb are similar to glycosyl hydrolase (gh) family 2 enzymes, including escherichia coli lacz. gala and galb cannot express detectable activity even after being cloned in-frame and driven by the vector's promoter. galc is a gh35 enzyme homologous to the xanthomonas axonop ...	2003	15153767
identification and characterization of a unique adenosine kinase from mycobacterium tuberculosis.	adenosine kinase (ak) is a purine salvage enzyme that catalyzes the phosphorylation of adenosine to amp. in mycobacterium tuberculosis, ak can also catalyze the phosphorylation of the adenosine analog 2-methyladenosine (methyl-ado), the first step in the metabolism of this compound to an active form. purification of ak from m. tuberculosis yielded a 35-kda protein that existed as a dimer in its native form. adenosine (ado) was preferred as a substrate at least 30-fold (km = 0.8 +/- 0.08 microm) ...	2003	14594827
phya, a secreted protein of xanthomonas oryzae pv. oryzae, is required for optimum virulence and growth on phytic acid as a sole phosphate source.	xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. we have identified a novel virulence deficient mutant (bxo1691) of x. oryzae pv. oryzae that has a tn5 insertion in an open reading frame (phya; putative phytase a) encoding a 373-amino acid (aa) protein containing a 28-aa predicted signal peptide. extracellular protein profiles revealed that a 38-kda band is absent in phya mutants as compared with phya+ strains. a blast search with phya and its deduced polype ...	2003	14601665
activity of class iii peroxidases in the defense of cotton to bacterial blight.	cotton cotyledons displayed a hypersensitive reaction (hr) in the cultivar réba b50 after infiltration with the avirulent race 18 from xanthomonas campestris pv. malvacearum. two sets of peroxidases were associated with the hr time course. early but transient accumulation of peroxidase in material encapsulating the bacteria in intercellular areas was observed by immunocytochemistry at 3 h postinfection and coincided with the oxidative burst. total guaiacol-peroxidase activity was highly increase ...	2003	14601671
genomic approaches in xanthomonas campestris pv. vesicatoria allow fishing for virulence genes.	xanthomonas campestris pv. vesicatoria is an economically important pathogen of pepper and tomato and has been established as a model organism to study bacterial infection strategies. in the last two decades, intensive genetic and molecular analyses led to the isolation of many genes that play a role in the intimate molecular relationship with the host plant. essential for pathogenicity is a type iii protein secretion system, which delivers bacterial effector proteins into the host cell. current ...	2003	14651862
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
application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.	a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes.	2003	12914674
a pseudomonas syringae type iii effector suppresses cell wall-based extracellular defense in susceptible arabidopsis plants.	bacterial effector proteins secreted through the type iii secretion system (ttss) play a crucial role in causing plant and human diseases. although the ability of type iii effectors to trigger defense responses in resistant plants is well understood, the disease-promoting functions of type iii effectors in susceptible plants are largely enigmatic. previous microscopic studies suggest that in susceptible plants the ttss of plant-pathogenic bacteria transports suppressors of a cell wall-based plan ...	2003	12817082
expression of the apyrase-like apy1 genes in roots of medicago truncatula is induced rapidly and transiently by stress and not by sinorhizobium meliloti or nod factors.	the model legume medicago truncatula contains at least six apyrase-like genes, five of which (mtapy1;1, mtapy1;2, mtapy1;3, mtapy1;4, and mtapy1;5) are members of a legume-specific family, whereas a single gene (mtapy2) has closer homologs in arabidopsis. phylogenetic analysis has revealed that the proteins encoded by these two plant gene families are more similar to yeast (saccharomyces cerevisiae) gda1 and to two proteins encoded by newly described mammalian genes (enp5 and 6) than they are to ...	2003	12644663
detection and diversity assessment of xylella fastidiosa in field-collected plant and insect samples by using 16s rrna and gyrb sequences.	the causal agent of diseases in many economically important plants is attributed to the xylem-limited bacterium xylella fastidiosa. the detection of this plant pathogen has been hampered due to its difficult isolation and slow growth on plates. nearly complete nucleotide sequences of the 16s rrna gene and partial sequences of the gyrb gene were determined for 18 strains of x. fastidiosa isolated from different plant hosts. a phylogenetic analysis, based on gyrb, grouped strains in three clusters ...	2003	12839807
sm-like proteins in eubacteria: the crystal structure of the hfq protein from escherichia coli.	the hfq protein was discovered in escherichia coli in the early seventies as a host factor for the qbeta phage rna replication. during the last decade, it was shown to be involved in many rna processing events and remote sequence homology indicated a link to spliceosomal sm proteins. we report the crystal structure of the e.coli hfq protein showing that its monomer displays a characteristic sm-fold and forms a homo-hexamer, in agreement with former biochemical data. overall, the structure of the ...	2003	12853626
simultaneous analysis of phytohormones, phytotoxins, and volatile organic compounds in plants.	phytohormones regulate the protective responses of plants against both biotic and abiotic stresses by means of synergistic or antagonistic actions referred to as signaling crosstalk. a bottleneck in crosstalk research is the quantification of numerous interacting phytohormones and regulators. the chemical analysis of salicylic acid, jasmonic acid, indole-3-acetic acid, and abscisic acid is typically achieved by using separate and complex methodologies. moreover, pathogen-produced phytohormone mi ...	2003	12874387
productivity improvement in xanthan gum fermentation using multiple substrate optimization.	a novel and more comprehensive formulation of the optimal control problem that reflects the operational requirements of a typical industrial fermentation has been proposed in this work. this formulation has been applied to a fed-batch bioreactor with three control variables, i.e., feed rates of carbon source, nitrogen source, and an oxygen source, to result in a 148.7% increase in product formation. xanthan gum production using xanthomonas campestris has been used as the model system for this op ...	2003	12892481
flagellin gene flic of xanthomonas campestris is upregulated by transcription factor clp.	clp, a homologue of cyclic amp receptor protein (crp), of xanthomonas campestris regulates the expression of many genes. in this study, proteomic analysis showed the amounts of several extracellular proteins in a clp mutant to be reduced, including the flagellin encoded by flic. transcriptional fusion assay showed that activity of flic promoter is reduced by 2.3-fold in clp mutant compared to the wild-type, coincident with the protein levels. the clp mutant is slightly reduced in motility; howev ...	2003	12893272
[the bactericidal activity of lectins from nitrogen-fixing bacilli].	lectins i and ii isolated from the nitrogen-fixing soil bacterium paenibacillus polymyxa 1460 were found to be able to suppress the growth of rhizobium leguminosarum 252 and bacillus subtilis 36 at nearly all the concentrations tested (from 1 to 10 micrograms/ml). lectin i was also inhibitory to azospirillum brasilense 245 and erwinia carotovora subsp. citrulis 603, while lectin ii exerted bactericidal activity against xanthomonas campestris b-610 and b-611 and a. brasilense 245. the bacillar le ...	2003	12901008
asexual development is increased in neurospora crassa cat-3-null mutant strains.	we use asexual development of neurospora crassa as a model system with which to determine the causes of cell differentiation. air exposure of a mycelial mat induces hyphal adhesion, and adherent hyphae grow aerial hyphae that, in turn, form conidia. previous work indicated the development of a hyperoxidant state at the start of these morphogenetic transitions and a large increase in catalase activity during conidiation. catalase 3 (cat-3) increases at the end of exponential growth and is induced ...	2003	12912899
prophage genomics.	the majority of the bacterial genome sequences deposited in the national center for biotechnology information database contain prophage sequences. analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile dna elements, and massive dna deletion. we review the technical difficulties in defining such altered prophage sequ ...	2003	12794192
the mosaic structure of the symbiotic plasmid of rhizobium etli cfn42 and its relation to other symbiotic genome compartments.	symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. in rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. to understand the structure and evolution of the symbiotic genome compartments (sgcs), it is necessary to analyze their common genetic content and organization as well as to study their differences. to date, five sgcs belonging to distinct spec ...	2003	12801410
survivability and long-term preservation of bacteria in water and in phosphate-buffered saline.	to evaluate the suitability of using sterile water and phosphate-buffered saline (pbs) for preservation of bacteria pathogenic to plants or humans.	2003	12803555
three pathogen-inducible genes encoding lipid transfer protein from pepper are differentially activated by pathogens, abiotic, and environmental stresses.	the three cdna clones, caltpi, caltpii, and caltpiii, corresponding to pepper lipid transfer protein (ltp) genes were isolated from a pepper (capsicum annuum) cdna library from hypersensitive response (hr) lesions of leaves infected with xanthomonas campestris pv. vesicatoria. the caltp genes are well conserved in their coding region with 57-72% identity at the amino acid level, but display 72-83% identity at the nucleotide sequence level. the transcripts of the three caltp genes differentially ...	2003	12803619
small ubiquitin-like modifier modulates abscisic acid signaling in arabidopsis.	post-translational modification of proteins by small polypeptides, such as ubiquitin, has emerged as a common and important mechanism for regulating protein function. small ubiquitin-like modifier (sumo) is a small protein that is structurally related to but functionally different from ubiquitin. we report the identification and functional analysis of atsumo1, atsumo2, and atsce1a as components of the sumo conjugation (sumoylation) pathway in arabidopsis. in yeast-two hybrid assays, atsumo1/2 in ...	2003	12782728
consensus-degenerate hybrid oligonucleotide primers for amplification of priming glycosyltransferase genes of the exopolysaccharide locus in strains of the lactobacillus casei group.	a primer design strategy named codehop (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (gt) gene in strains of the lactobacillus casei group. each hybrid primer consisted of a short 3' degenerate core based on four highly conserved amino acids and a longer 5' consensus clamp region based on six sequences of the priming gt gene products from exopolysaccharide (eps)-producing bacteria. the hybr ...	2003	12788729
nutritional similarity between leaf-associated nonpathogenic bacteria and the pathogen is not predictive of efficacy in biological control of bacterial spot of tomato.	it has been demonstrated that for a nonpathogenic, leaf-associated bacterium, effectiveness in the control of bacterial speck of tomato is correlated with the similarity in the nutritional needs of the nonpathogenic bacterium and the pathogen pseudomonas syringae pv. tomato. this relationship was investigated further in this study by using the pathogen xanthomonas campestris pv. vesicatoria, the causal agent of bacterial spot of tomato, and a collection of nonpathogenic bacteria isolated from to ...	2003	12788754
physical interaction between rrs1-r, a protein conferring resistance to bacterial wilt, and popp2, a type iii effector targeted to the plant nucleus.	rrs1-r confers broad-spectrum resistance to several strains of the causal agent of bacterial wilt, ralstonia solanacearum. although genetically defined as recessive, this r gene encodes a protein whose structure combines the tir-nbs-lrr domains found in several r proteins and a wrky motif characteristic of some plant transcriptional factors and behaves as a dominant gene in transgenic susceptible plants. here we show that popp2, a r. solanacearum type iii effector, which belongs to the yopj/avrr ...	2003	12788974
quorum sensing in plant-pathogenic bacteria.	quorum sensing (qs) allows bacteria to assess their local population density and/or physical confinement via the secretion and detection of small, diffusible signal molecules. this review describes how phytopathogenic bacteria have incorporated qs mechanisms into complex regulatory cascades that control genes for pathogenicity and colonization of host surfaces. traits regulated by qs include the production of extracellular polysaccharides, degradative enzymes, antibiotics, siderophores, and pigm ...	2003	12730390
ethylene insensitivity modulates ozone-induced cell death in birch.	we have used genotypic variation in birch (betula pendula roth) to investigate the roles of ozone (o(3))-induced ethylene (et), jasmonic acid, and salicylic acid in the regulation of tissue tolerance to o(3). of these hormones, et evolution correlated best with o(3)-induced cell death. disruption of et perception by transformation of birch with the dominant negative mutant allele etr1-1 of the arabidopsis et receptor gene etr1 or blocking of et perception with 1-methylcyclopropene reduced but di ...	2003	12746524
differential effects of elevated ozone on two hybrid aspen genotypes predisposed to chronic ozone fumigation. role of ethylene and salicylic acid.	the role of ethylene (et) signaling in the responses of two hybrid aspen (populus tremula l. x p. tremuloides michx.) clones to chronic ozone (o(3); 75 nl l(-1)) was investigated. the hormonal responses differed between the clones; the o(3)-sensitive clone 51 had higher et evolution than the tolerant clone 200 during the exposure, whereas the free salicylic acid concentration in clone 200 was higher than in clone 51. the cellular redox status, measured as glutathione redox balance, did not diffe ...	2003	12746525
expression of putative pathogenicity-related genes in xylella fastidiosa grown at low and high cell density conditions in vitro.	xylella fastidiosa is the causal agent of economically important plant diseases, including citrus variegated chlorosis and pierce's disease. hitherto, there has been no information on the molecular mechanisms controlling x. fastidiosa-plant interactions. to determine whether predicted open reading frames (orfs) encoding putative pathogenicity-related factors were expressed by x. fastidiosa 9a5c cells grown at low (lcd) and high cell density (hcd) conditions in liquid modified pw medium, reverse ...	2003	12757950
pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in p. syringae pv. syringae b728a.	pseudomonas syringae is a plant pathogen whose pathogenicity and host specificity are thought to be determined by hop/avr effector proteins injected into plant cells by a type iii secretion system. p. syringae pv. syringae b728a, which causes brown spot of bean, is a particularly well-studied strain. the type iii secretion system in p. syringae is encoded by hrp (hypersensitive response and pathogenicity) and hrc (hrp conserved) genes, which are clustered in a pathogenicity island with a tripart ...	2003	12670984
isolation and antifungal and antioomycete activities of aerugine produced by pseudomonas fluorescens strain mm-b16.	the bacterial strain mm-b16, which showed strong antifungal and antioomycete activity against some plant pathogens, was isolated from a mountain forest soil in korea. based on the physiological and biochemical characteristics and 16s ribosomal dna sequence analysis, the bacterial strain mm-b16 was identical to pseudomonas fluorescens. an antibiotic active against colletotrichum orbiculare and phytophthora capsici in vitro and in vivo was isolated from the culture filtrates of p. fluorescens stra ...	2003	12676678
type ii protein secretion in pseudomonas aeruginosa: the pseudopilus is a multifibrillar and adhesive structure.	the type ii secretion pathway of pseudomonas aeruginosa is involved in the extracellular release of various toxins and hydrolytic enzymes such as exotoxin a and elastase. this pathway requires the function of a macromolecular complex called the xcp secreton. the xcp secreton shares many features with the machinery involved in type iv pilus assembly. more specifically, it involves the function of five pilin-like proteins, the xcpt-x pseudopilins. we show that, upon overexpression, the xcpt pseudo ...	2003	12700254
the pair of bacteriophytochromes from agrobacterium tumefaciens are histidine kinases with opposing photobiological properties.	bacteriophytochrome photoreceptors (bphps) are a family of phytochrome-like sensor kinases that help a wide variety of bacteria respond to their light environment. in agrobacterium tumefaciens, a unique pair of bphps with potentially opposing roles in light sensing are present. both atbphps contain an n-terminal chromophore-binding domain that covalently attaches a biliverdin chromophore. whereas atbphp1 assumes a pr ground state, atbphp2 is unusual in that it assumes a pfr ground state that is ...	2003	12604773
origin and evolution of circadian clock genes in prokaryotes.	regulation of physiological functions with approximate daily periodicity, or circadian rhythms, is a characteristic feature of eukaryotes. until recently, cyanobacteria were the only prokaryotes reported to possess circadian rhythmicity. it is controlled by a cluster of three genes: kaia, kaib, and kaic. using sequence data of approximately 70 complete prokaryotic genomes from the various public depositories, we show here that the kai genes and their homologs have quite a different evolutionary ...	2003	12604787
excision and integration of cassettes by an integron integrase of nitrosomonas europaea.	we found in the environmental strain nitrosomonas europaea a chromosomal integron-like structure with an integrase gene, inti(neu). we have tested the capacity of the intineu integrase to excise and integrate several resistance gene cassettes. the results allow us to consider intineu a new functional integron integrase.	2003	12618471
the rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.	the rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. they are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. on the basis of experimental studies with the developmental regulator rhomboid from drosophila and the aara protein from the bacterium providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose ...	2003	12620104
lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in xylella species and in heterocystous cyanobacteria.	tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. a seven-gene cluster in xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-coa synthetase, and trpr. a second gene block, present in the anabaena/nostoc lineage, but not in other cyanobacteria, contains a near ...	2003	12620124
xanosporic acid, an intermediate in bacterial degradation of the fungal phototoxin cercosporin.	the red fungal perylenequinone phototoxin cercosporin is oxidized by xanthomonas campestris pv zinniae to a non-toxic, unstable green metabolite xanosporic acid, identified via its lactone as 1,12-bis(2'r-hydroxypropyl)-4,9-dihydroxy-6,7-methylenedioxy-11-methoxy-3-oxaperylen-10h-10-one-2-carboxylic acid. xanosporolactone was isolated in approximately 2:1 ratio of m:p atropisomers.	2003	12620324
construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on escherichia coli.	enrichment of microorganisms with special traits and the construction of metagenomic libraries by direct cloning of environmental dna have great potential for identifying genes and gene products for biotechnological purposes. we have combined these techniques to isolate novel genes conferring oxidation of short-chain (c(2) to c(4)) polyols or reduction of the corresponding carbonyls. in order to favor the growth of microorganisms containing the targeted genes, samples collected from four differe ...	2003	12620823
prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of pseudomonas fluorescens strain ku-7.	the 2-nitrobenzoic acid degradation pathway of pseudomonas fluorescens strain ku-7 proceeds via a novel 3-hydroxyanthranilate intermediate. in this study, we cloned and sequenced a 19-kb dna locus of strain ku-7 that encompasses the 3-hydroxyanthranilate meta-cleavage pathway genes. the gene cluster, designated nbaexhjigfcdr, is organized tightly and in the same direction. the nbac and nbad gene products were found to be novel homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and ...	2003	12620844
a suppressor of the menadione-hypersensitive phenotype of a xanthomonas campestris pv. phaseoli oxyr mutant reveals a novel mechanism of toxicity and the protective role of alkyl hydroperoxide reductase.	we isolated menadione-resistant mutants of xanthomonas campestris pv. phaseoli oxyr (oxyr(xp)). the oxyrr2(xp) mutant was hyperresistant to the superoxide generators menadione and plumbagin and was moderately resistant to h(2)o(2) and tert-butyl hydroperoxide. analysis of enzymes involved in oxidative-stress protection in the oxyrr2(xp) mutant revealed a >10-fold increase in ahpc and ahpf levels, while the levels of superoxide dismutase (sod), catalase, and the organic hydroperoxide resistance p ...	2003	12591894
differences between pseudomonas syringae pv. syringae b728a and pantoea agglomerans brt98 in epiphytic and endophytic colonization of leaves.	the leaf colonization strategies of two bacterial strains were investigated. the foliar pathogen pseudomonas syringae pv. syringae strain b728a and the nonpathogen pantoea agglomerans strain brt98 were marked with a green fluorescent protein, and surface (epiphytic) and subsurface (endophytic) sites of bean and maize leaves in the laboratory and the field were monitored to see if populations of these strains developed. the populations were monitored using both fluorescence microscopy and counts ...	2003	12571050
enhancement of population size of a biological control agent and efficacy in control of bacterial speck of tomato through salicylate and ammonium sulfate amendments.	sodium salicylate and ammonium sulfate were applied to leaf surfaces along with suspensions of the biological control agents pseudomonas syringae cit7(pnah7), which catabolizes salicylate, and cit7, which does not catabolize salicylate, to determine whether enhanced biological control of bacterial speck of tomato could be achieved. foliar amendment with salicylate alone significantly enhanced the population size and the efficacy of cit7(pnah7), but not of cit7, on tomato leaves. application of a ...	2003	12571060
prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey.	the twin-arginine translocation (tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. however, the extent to which this pathway is used among the prokaryotes is not known. by using a genomic approach, a comprehensive list of putative tat substrates for 84 diverse prokaryotes was established. strikingly, the results indicate that the tat pathway is utilized to highly varying extents. furthermore, while many prokaryotes use thi ...	2003	12562823
identification of the pepper sar8.2 gene as a molecular marker for pathogen infection, abiotic elicitors and environmental stresses in capsicum annuum.	pepper ( capsicum annuum l.) sar8.2 genes, designated casar82a, b and c, which are induced by all the biotic and abiotic stresses, were isolated from a pepper cdna library constructed with the mrnas from pepper plants infected with xanthomonas campestris pv. vesicatoria. the pepper casar82a, b and c gene products, which are very similar to each other in amino acid sequences, have 43-50% homology with those of tobacco sar8.2 genes. the casar8.2 genes were not constitutively expressed in any of th ...	2003	12520329
cloning and characterization of kata, encoding the major monofunctional catalase from xanthomonas campestris pv. phaseoli and characterization of the encoded catalase kata.	the first cloning and characterization of the gene kata, encoding the major catalase (kata), from xanthomonas is reported. a reverse genetic approach using a synthesized kata-specific dna probe to screen a x. campestris pv. phaseoli genomic library was employed. a positively hybridizing clone designated pkat29 that contained a full-length kata was isolated. analysis of the nucleotide sequence revealed an open reading frame of 1,521 bp encoding a 507-amino acid protein with a theoretical molecula ...	2003	12520360
plant lectin-like bacteriocin from a rhizosphere-colonizing pseudomonas isolate.	rhizosphere isolate pseudomonas sp. strain bw11m1, which belongs to the pseudomonas putida cluster, secretes a heat- and protease-sensitive bacteriocin which kills p. putida gr12-2r3. the production of this bacteriocin is enhanced by dna-damaging treatment of producer cells. we isolated a tnmod mutant of strain bw11m1 that had lost the capacity to inhibit the growth of strain gr12-2r3. a wild-type genomic fragment encompassing the transposon insertion site was shown to confer the bacteriocin phe ...	2003	12533465
recombination activity of a distinctive integron-gene cassette system associated with pseudomonas stutzeri populations in soil.	class 1 integrons have strongly influenced the evolution of multiple antibiotic resistance. diverse integrons have recently been detected directly in a range of natural environments. in order to characterize the properties of these environmental integrons, we sought to isolate organisms containing integrons from soils, which resulted in the isolation of pseudomonas stutzeri strain q. further isolation efforts targeted at this species resulted in recovery of two other strains (p and bam). 16s rrn ...	2003	12533467
comparative analyses of the complete genome sequences of pierce's disease and citrus variegated chlorosis strains of xylella fastidiosa.	xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. x. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the american continent, and induces diverse disease phenotypes. previous molecular analyses indicated three distinct groups of x. fastidiosa isolates that were expected to be genetically divergent. here we r ...	2003	12533478
traffic at the tmrna gene.	a partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmrna gene (ssra) than for any type of trna gene. horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. diverse elements use ssra; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssra, and almost every s ...	2003	12533482
characterization of a novel intracellular endopeptidase of the alpha/beta hydrolase family from streptomyces coelicolor a3(2).	in a proteasome-lacking mutant of streptomyces coelicolor a3(2), an intracellular enzyme with chymotrypsin-like activity, absent from the wild type, was detected. complementation that restored proteasome function did not suppress expression of the endopeptidase. since the enzyme was not found in two other s. coelicolor proteasome mutants, its expression probably resulted from a secondary mutation arisen in the proteasome mutant. purification of the endopeptidase revealed its identity to sco7095, ...	2003	12511496
genomic comparison of salmonella enterica serovars and salmonella bongori by use of an s. enterica serovar typhimurium dna microarray.	the genus salmonella consists of over 2,200 serovars that differ in their host range and ability to cause disease despite their close genetic relatedness. the genetic factors that influence each serovar's level of host adaptation, how they evolved or were acquired, their influence on the evolution of each serovar, and the phylogenic relationships between the serovars are of great interest as they provide insight into the mechanisms behind these differences in host range and disease progression. ...	2003	12511502
a colonization factor (production of lateral flagella) of mesophilic aeromonas spp. is inactive in aeromonas salmonicida strains.	the nine laf (lateral flagellum) genes of mesophilic aeromonads are in the aeromonas salmonicida genome. the laf genes are functional, except for lafa (flagellin gene), which was inactivated by transposase 8 (is3 family). a pathogenic characteristic of mesophilic aeromonads (lateral flagella) is abolished in this specialized pathogen with a narrow host range.	2003	12514057
glutathione s-transferase isoenzymes from streptomyces griseus.	an inducible, cytosolic glutathione s-transferase (gst) was purified from streptomyces griseus. gst isoenzymes with pi values of 6.8 and 7.9 used standard gst substrates including 1-chloro-2,4-dinitrobenzene. gst had subunit and native m(r)s of 24 and 48, respectively, and the n-terminal sequence smilxywdiirglpah.	2003	12514067
oxyr acts as a repressor of catalase expression in neisseria gonorrhoeae.	it has been reported that neisseria gonorrhoeae possesses a very high level of catalase activity, but the regulation of catalase expression has not been investigated extensively. in escherichia coli and salmonella enterica serovar typhimurium, it has been demonstrated that oxyr is a positive regulator of hydrogen peroxide-inducible genes, including the gene encoding catalase. the oxyr gene from n. gonorrhoeae was cloned and used to complement an e. coli oxyr mutant, confirming its identity and f ...	2003	12496210
the secb chaperone is bifunctional in serratia marcescens: secb is involved in the sec pathway and required for hasa secretion by the abc transporter.	hasa is the secreted hemophore of the heme acquisition system (has) of serratia marcescens. it is secreted by a specific abc transporter apparatus composed of three proteins: hasd, an inner membrane abc protein; hase, another inner membrane protein; and hasf, a tolc homolog. except for hasf, the structural genes of the has system are encoded by an iron-regulated operon. in previous studies, this secretion system has been reconstituted in escherichia coli, where it requires the presence of the se ...	2003	12486043
versatility of aminoglycosides and prospects for their future.	aminoglycoside antibiotics have had a major impact on our ability to treat bacterial infections for the past half century. whereas the interest in these versatile antibiotics continues to be high, their clinical utility has been compromised by widespread instances of resistance. the multitude of mechanisms of resistance is disconcerting but also illuminates how nature can manifest resistance when bacteria are confronted by antibiotics. this article reviews the most recent knowledge about the mec ...	2003	12857776
tmrdb (tmrna database).	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ...	2003	12520048
recent advances in petroleum microbiology.	recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. the physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. new molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystem ...	2003	14665675
from gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria.	the rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. however, extensive lateral gene transfer (lgt) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. the group for which cases of lgt are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-proteobacteria, an ...	2003	12975657