Publications

unique gtp-binding pocket and allostery of uridylate kinase from a gram-negative phytopathogenic bacterium.	using x-ray diffraction methodology, we have successfully determined the tertiary structures of the apo- and gtp-bound forms of uridylate kinase (umpk) from the gram-negative plant pathogen xanthomonas campestris with crystals grown under a strong magnetic field. the flexible atp- and ump-binding loops are clearly shown under this situation. x. campestris umpk contains a unique patch of noticeably positive nature from residue r100 to residue r127, allowing it to form a special gtp-binding pocket ...	2009	19059268
y4lo of rhizobium sp. strain ngr234 is a symbiotic determinant required for symbiosome differentiation.	type 3 (t3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial t3 secretion system, affect the nodulation of certain host legumes. the open reading frame y4lo of rhizobium sp. strain ngr234 encodes a protein with sequence similarities to t3 effectors from pathogenic bacteria (the yopj effector family). transcription studies showed that the promoter activity of y4lo depended on the transcriptional activator ttsi. recombinant y4lo protein expressed in escherichia coli did not ...	2009	19060155
y4lo of rhizobium sp. strain ngr234 is a symbiotic determinant required for symbiosome differentiation.	type 3 (t3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial t3 secretion system, affect the nodulation of certain host legumes. the open reading frame y4lo of rhizobium sp. strain ngr234 encodes a protein with sequence similarities to t3 effectors from pathogenic bacteria (the yopj effector family). transcription studies showed that the promoter activity of y4lo depended on the transcriptional activator ttsi. recombinant y4lo protein expressed in escherichia coli did not ...	2009	19060155
the role of ampr in regulation of l1 and l2 beta-lactamases in stenotrophomonas maltophilia.	stenotrophomonas maltophilia is known to produce at least two chromosomal-mediated inducible beta-lactamases, l1 and l2. gene l2, which encodes a class a beta-lactamase, and the adjacent ampr gene form an ampr-class a beta-lactamase module. l1 belongs to the class b beta-lactamase and has no neighbor ampr-like regulatory gene. in this study, the ampr-l2 module from s. maltophilia kh was compared with ampr-beta-lactamase modules from several microorganisms with respect to the ampr and beta-lactam ...	2009	19071216
regulation and activity of a zinc uptake regulator, zur, in corynebacterium diphtheriae.	regulation of metal ion homeostasis is essential to bacterial cell survival, and in most species it is controlled by metal-dependent transcriptional regulators. in this study, we describe a corynebacterium diphtheriae ferric uptake regulator-family protein, zur, that controls expression of genes involved in zinc uptake. by measuring promoter activities and mrna levels, we demonstrate that zur represses transcription of three genes (zrg, cmra, and troa) in zinc-replete conditions. all three of th ...	2009	19074382
regulation and activity of a zinc uptake regulator, zur, in corynebacterium diphtheriae.	regulation of metal ion homeostasis is essential to bacterial cell survival, and in most species it is controlled by metal-dependent transcriptional regulators. in this study, we describe a corynebacterium diphtheriae ferric uptake regulator-family protein, zur, that controls expression of genes involved in zinc uptake. by measuring promoter activities and mrna levels, we demonstrate that zur represses transcription of three genes (zrg, cmra, and troa) in zinc-replete conditions. all three of th ...	2009	19074382
a fatty acid messenger is responsible for inducing dispersion in microbial biofilms.	it is well established that in nature, bacteria are found primarily as residents of surface-associated communities called biofilms. these structures form in a sequential process initiated by attachment of cells to a surface, followed by the formation of matrix-enmeshed microcolonies, and culminating in dispersion of the bacteria from the mature biofilm. in the present study, we have demonstrated that, during growth, pseudomonas aeruginosa produces an organic compound we have identified as cis-2- ...	2009	19074399
a fatty acid messenger is responsible for inducing dispersion in microbial biofilms.	it is well established that in nature, bacteria are found primarily as residents of surface-associated communities called biofilms. these structures form in a sequential process initiated by attachment of cells to a surface, followed by the formation of matrix-enmeshed microcolonies, and culminating in dispersion of the bacteria from the mature biofilm. in the present study, we have demonstrated that, during growth, pseudomonas aeruginosa produces an organic compound we have identified as cis-2- ...	2009	19074399
application of recognition of individual genes-fluorescence in situ hybridization (ring-fish) to detect nitrite reductase genes (nirk) of denitrifiers in pure cultures and environmental samples.	denitrification is an alternative type of anaerobic respiration in which nitrate is reduced to gaseous products via nitrite. the key step in this process is the reduction of nitrite to nitric oxide, which is catalyzed by two structurally different but functionally equivalent forms of nitrite reductase encoded by the nirk and nirs genes. cultivation-independent studies based on these functional marker genes showed that in the environment there was a dominance of organisms with nirk and nirs genes ...	2008	19074610
application of recognition of individual genes-fluorescence in situ hybridization (ring-fish) to detect nitrite reductase genes (nirk) of denitrifiers in pure cultures and environmental samples.	denitrification is an alternative type of anaerobic respiration in which nitrate is reduced to gaseous products via nitrite. the key step in this process is the reduction of nitrite to nitric oxide, which is catalyzed by two structurally different but functionally equivalent forms of nitrite reductase encoded by the nirk and nirs genes. cultivation-independent studies based on these functional marker genes showed that in the environment there was a dominance of organisms with nirk and nirs genes ...	2008	19074610
an orphan luxr homolog of sinorhizobium meliloti affects stress adaptation and competition for nodulation.	the sin/expr quorum-sensing system of sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, medicago sativa. the luxr-type response regulators of the sin system include the synthase (sini)-associated sinr and the orphan regulator expr. interestingly, the s. meliloti rm1021 genome codes for four additional putative orphan luxr homologs whose regulatory roles remain to be identified. these response regulators contain the characteristic domains of the luxr ...	2009	19088317
an orphan luxr homolog of sinorhizobium meliloti affects stress adaptation and competition for nodulation.	the sin/expr quorum-sensing system of sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, medicago sativa. the luxr-type response regulators of the sin system include the synthase (sini)-associated sinr and the orphan regulator expr. interestingly, the s. meliloti rm1021 genome codes for four additional putative orphan luxr homologs whose regulatory roles remain to be identified. these response regulators contain the characteristic domains of the luxr ...	2009	19088317
overexpression of lipid transfer protein (ltp) genes enhances resistance to plant pathogens and ltp functions in long-distance systemic signaling in tobacco.	the lipid signal is essential for the activation of plant defense responses, but downstream components of the signaling pathway are still poorly defined. to investigate the biological functions of pepper lipid transfer protein (ltp), we carried out virus-induced gene silencing (vigs) in pepper, constitutive expression of caltps and grafting experiments in the tobacco plant. suppression of endogenous caltpi and caltpii by vigs, respectively, resulted in enhanced susceptibility to xanthomonas camp ...	2009	19089429
xanthomonas campestris overcomes arabidopsis stomatal innate immunity through a dsf cell-to-cell signal-regulated virulence factor.	pathogen-induced stomatal closure is part of the plant innate immune response. phytopathogens using stomata as a way of entry into the leaf must avoid the stomatal response of the host. in this article, we describe a factor secreted by the bacterial phytopathogen xanthomonas campestris pv campestris (xcc) capable of interfering with stomatal closure induced by bacteria or abscisic acid (aba). we found that living xcc, as well as ethyl acetate extracts from xcc culture supernatants, are capable o ...	2009	19091877
heme-dependent metalloregulation by the iron response regulator (irr) protein in rhizobium and other alpha-proteobacteria.	perception and response to nutritional iron by bacteria is essential for viability, and for the ability to adapt to the environment. the iron response regulator (irr) is part of a novel regulatory scheme employed by rhizobium and other alpha-proteobacteria to control iron-dependent gene expression. bradyrhizobium japonicum senses iron through the status of heme biosynthesis to regulate gene expression, thus it responds to an iron-dependent process rather than to iron directly. irr mediates this ...	2009	19093075
heme-dependent metalloregulation by the iron response regulator (irr) protein in rhizobium and other alpha-proteobacteria.	perception and response to nutritional iron by bacteria is essential for viability, and for the ability to adapt to the environment. the iron response regulator (irr) is part of a novel regulatory scheme employed by rhizobium and other alpha-proteobacteria to control iron-dependent gene expression. bradyrhizobium japonicum senses iron through the status of heme biosynthesis to regulate gene expression, thus it responds to an iron-dependent process rather than to iron directly. irr mediates this ...	2009	19093075
mechanism of allosteric inhibition of n-acetyl-l-glutamate synthase by l-arginine.	n-acetylglutamate synthase (nags) catalyzes the first committed step in l-arginine biosynthesis in plants and micro-organisms and is subject to feedback inhibition by l-arginine. this study compares the crystal structures of nags from neisseria gonorrhoeae (ngnags) in the inactive t-state with l-arginine bound and in the active r-state complexed with coa and l-glutamate. under all of the conditions examined, the enzyme consists of two stacked trimers. each monomer has two domains: an amino acid ...	2009	19095660
elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in medicago truncatula.	exposure of medicago truncatula cell suspension cultures to pathogen or wound signals leads to accumulation of various classes of flavonoid and/or triterpene defense molecules, orchestrated via a complex signalling network in which transcription factors (tfs) are essential components.	2008	19102779
low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-iii secretion system in xanthomonas campestris pv. campestris.	xanthomonas campestris pathovar campestris (xcc) is a plant pathogenic bacterium and as such has to adapt to a variety of environments. during the course of disease, xcc colonizes the surface of its host, infects the xylem in the early stages, and develops a fully saprophytic life-style, aided by secreted degradative enzymes, in the late stages. to get some insight into this complex regulation, xcc was cultivated in the presence of low molecular weight host plant extract (<10 kda). from this exp ...	2009	19114064
functional characterization of the type iii secretion atpase hrcn from the plant pathogen xanthomonas campestris pv. vesicatoria.	many gram-negative plant and animal pathogenic bacteria employ a type iii secretion (t3s) system to inject effector proteins into the cytosol of eukaryotic host cells. the membrane-spanning t3s apparatus is associated with an atpase that presumably provides the energy for the secretion process. here, we describe the role of the predicted atpase hrcn from the plant pathogenic bacterium xanthomonas campestris pathovar vesicatoria. we show that hrcn hydrolyzes atp in vitro and is essential for t3s ...	2009	19114489
functional characterization of the type iii secretion atpase hrcn from the plant pathogen xanthomonas campestris pv. vesicatoria.	many gram-negative plant and animal pathogenic bacteria employ a type iii secretion (t3s) system to inject effector proteins into the cytosol of eukaryotic host cells. the membrane-spanning t3s apparatus is associated with an atpase that presumably provides the energy for the secretion process. here, we describe the role of the predicted atpase hrcn from the plant pathogenic bacterium xanthomonas campestris pathovar vesicatoria. we show that hrcn hydrolyzes atp in vitro and is essential for t3s ...	2009	19114489
origins of the xylella fastidiosa prophage-like regions and their impact in genome differentiation.	xylella fastidiosa is a gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced x. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. to better evaluate the recent evolution of the x. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and temecu ...	2008	19116666
simple adhesive-tape-based sampling of tomato surfaces combined with rapid fluorescence in situ hybridization for salmonella detection.	a simple adhesive-tape-based method for sampling of tomato surfaces was combined with fluorescence in situ hybridization for rapid culture-independent detection of salmonella strains. tapes could also be placed face-down on selective agar for on-tape enrichment of captured salmonella cells. overlay of cell-charged tapes with small volumes of liquid enrichment media enabled subsequent detection of tape-captured salmonella via flow cytometry.	2009	19124588
xc1028 from xanthomonas campestris adopts a pilz domain-like structure without a c-di-gmp switch.	the crystal structure of xc1028 from xanthomonas campestris has been determined to a resolution of 2.15 a using the multiple anomalous dispersion approach. it bears significant sequence identity and similarity values of 64.10% and 70.09%, respectively, with pa2960, a protein indispensable for type iv pilus-mediated twitching motility, after which the pilz motif was first named. however, both xc1028 and pa2960 lack detectable c-di-gmp binding capability. although xc1028 adopts a structure compris ...	2009	19127589
oxidation of a single active site suffices for the functional inactivation of the dimeric bacillus subtilis ohrr repressor in vitro.	bacillus subtilis ohrr is a dimeric repressor that senses organic peroxides and regulates the expression of the ohra peroxiredoxin. derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overoxidation to the sulfinic or sulfonic acids. we expressed a single-chain ohrr (scohrr) in which the two monomers were connected by a short amino-acid linker. scohrr variants containi ...	2009	19129220
enhanced fructooligosaccharides and inulinase production by a xanthomonas campestris pv. phaseoli km 24 mutant.	xanthomonas campestris pv phaseoli produced an extracellular endoinulinase (9.24 +/- 0.03 u ml(-1)) in an optimized medium comprising of 3% sucrose and 2.5% tryptone. x. campestris pv. phaseoli was further subjected to ethylmethanesulfonate mutagenesis and the resulting mutant, x. campestris pv. phaseoli km 24 demonstrated inulinase production of 22.09 +/- 0.03 u ml(-1) after 18 h, which was 2.4-fold higher than that of the wild type. inulinase production by this mutant was scaled up using sucro ...	2009	19130092
a comparison between shaker and bioreactor performance based on the kinetic parameters of xanthan gum production.	xanthan gum production was studied using sugarcane broth as the raw material and batch fermentation by xanthomonas campestris pv. campestris nrrl b-1459. the purpose of this study was to optimize the variables of sucrose, yeast extract, and ammonium nitrate concentrations and to determine the kinetic parameters of this bioreaction under optimized conditions. the effects of yeast extract and ammonium nitrate concentrations for a given sucrose concentration (12.1-37.8 g l(-1)) were evaluated by ce ...	2009	19130306
flagellar biogenesis of xanthomonas campestris requires the alternative sigma factors rpon2 and flia and is temporally regulated by flha, flhb, and flgm.	in prokaryotes, flagellar biogenesis is a complicated process involving over 40 genes. the phytopathogen xanthomonas campestris pv. campestris possesses a single polar flagellum, which is essential for the swimming motility. a sigma54 activator, fleq, has been shown to be required for the transcriptional activation of the flagellar type iii secretion system (f-t3ss), rod, and hook proteins. one of the two rpon genes, rpon2, encoding sigma54, is essential for flagellation. rpon2 and fleq direct t ...	2009	19136588
imbalanced lignin biosynthesis promotes the sexual reproduction of homothallic oomycete pathogens.	lignin is incorporated into plant cell walls to maintain plant architecture and to ensure long-distance water transport. lignin composition affects the industrial value of plant material for forage, wood and paper production, and biofuel technologies. industrial demands have resulted in an increase in the use of genetic engineering to modify lignified plant cell wall composition. however, the interaction of the resulting plants with the environment must be analyzed carefully to ensure that there ...	2009	19148278
fabrication of modified release tablet formulation of metoprolol succinate using hydroxypropyl methylcellulose and xanthan gum.	the present investigation was undertaken to fabricate modified release tablet of metoprolol succinate using hydroxypropyl methylcellulose (hpmc) and xanthan gum as a matrixing agent. a 3(2) full factorial design was employed for the optimization of formulation. the percentage drug released at a given time (y (60), y (240) and y (720)) and the time required for a given percentage of drug to be released (t (50%)) were selected as dependent variables. the in vitro drug dissolution study was carried ...	2009	19148762
the safety of polyglycoplex (pgx) as shown in a 90-day rodent feeding study.	this study was designed to evaluate the safety of polyglycoplex (pgx), a novel viscous dietary polysaccharide (fiber), when administered to sprague dawley(r) rats in the diet for 90 days.	2009	19149876
biotic and abiotic stimulation of root epidermal cells reveals common and specific responses to arbuscular mycorrhizal fungi.	during arbuscular mycorrhizal (am) colonization, a focal accumulation of organelles occurs in root epidermal cells, prior to fungal penetration, beneath adhering hyphopodia. this is followed by the appearance of the prepenetration apparatus (ppa), a transcellular column of cytoplasm connected to the nucleus and rich in cytoskeleton and secretory endomembranes. this apparatus appears to be responsible for the construction of an apoplastic compartment that confines the fungus within the cell lumen ...	2009	19151131
chromosome-based genetic complementation system for xylella fastidiosa.	xylella fastidiosa is a xylem-limited, gram-negative bacterium that causes pierce's disease of grapevine. here, we describe the construction of four vectors that facilitate the insertion of genes into a neutral site (ns1) in the x. fastidiosa chromosome. these vectors carry a cole1-like (pmb1) replicon and dna sequences from ns1 flanking a multiple-cloning site and a resistance marker for one of the following antibiotics: chloramphenicol, erythromycin, gentamicin, or kanamycin. in x. fastidiosa, ...	2009	19151176
environmental control in tea fields to reduce infection by pseudomonas syringae pv. theae.	bacterial shoot blight (bsb) disease, caused by pseudomonas syringae pv. theae, is a major bacterial disease of tea plants in japan. bsb mainly occurs in the low-temperature season, and lesion formation by p. syringae pv. theae is enhanced by both low temperature and the presence of ice nucleation-active xanthomonas campestris (inax), which catalyzes ice formation at -2 to -4 degrees c and is frequently co-isolated with p. syringae pv. theae from tea plants. low temperature is thus the most impo ...	2009	19159313
rodz, a component of the bacterial core morphogenic apparatus.	the molecular basis of bacterial cell morphogenesis remains largely an open question. here we discover a morphogenic protein, rodz, which is widely conserved across the bacterial kingdom. in caulobacter crescentus, rodz is essential for viability and is involved in all aspects of this organism's complex morphology. depletion or over-production of rodz results in grossly misshapen cells with stalk defects. rodz exhibits a localization pattern during the cell cycle corresponding to sites of active ...	2009	19164570
an approach to characterizing single-subunit mutations in multimeric prepores and pores of anthrax protective antigen.	heptameric pores formed by the protective antigen (pa) moiety of anthrax toxin translocate the intracellular effector moieties of the toxin across the endosomal membrane to the cytosol of mammalian cells. we devised a protocol to characterize the effects of individual mutations in a single subunit of heptameric pa prepores (pore precursors) or pores. we prepared monomeric pa containing a test mutation plus an innocuous cys-replacement mutation at a second residue (lys563, located on the external ...	2009	19165720
the tep1 gene of sinorhizobium meliloti coding for a putative transmembrane efflux protein and n-acetyl glucosamine affect nod gene expression and nodulation of alfalfa plants.	soil bacteria collectively known as rhizobium, characterized by their ability to establish beneficial symbiosis with legumes, share several common characteristics with pathogenic bacteria when infecting the host plant. recently, it was demonstrated that a fadd mutant of sinorhizobium meliloti is altered in the control of swarming, a type of co-ordinated movement previously associated with pathogenicity, and is also impaired in nodulation efficiency on alfalfa roots. in the phytopathogen xanthomo ...	2009	19173735
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
genome sequence of desulfobacterium autotrophicum hrm2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.	sulfate-reducing bacteria (srb) belonging to the metabolically versatile desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. desulfobacterium autotrophicum hrm2 is the first member of this ecophysiologically important group with a now available genome sequence. with 5.6 megabasepairs (mbp) the genome of db. autotrophicum hrm2 is about 2 mbp larger than the sequenced genomes of other sulfate reducers (srb). a h ...	2009	19187283
a filamentous hemagglutinin-like protein of xanthomonas axonopodis pv. citri, the phytopathogen responsible for citrus canker, is involved in bacterial virulence.	xanthomonas axonopodis pv. citri, the phytopathogen responsible for citrus canker has a number of protein secretion systems and among them, at least one type v protein secretion system belonging to the two-partner secretion pathway. this system is mainly associated to the translocation of large proteins such as adhesins to the outer membrane of several pathogens. xanthomonas axonopodis pv. citri possess a filamentous hemagglutinin-like protein in close vicinity to its putative transporter protei ...	2009	19194503
phylogenetic structure of xanthomonas determined by comparison of gyrb sequences.	previously, we have produced a phylogeny of species type strains from the plant-pathogenic genus xanthomonas based on gyrb sequences. to evaluate this locus further for species and infraspecies identification, we sequenced an additional 203 strains comprising all the pathovar reference strains (which have defined plant hosts), 67 poorly characterized pathovars, currently classified as xanthomonas campestris, and 59 unidentified xanthomonads. the well-characterized pathovars grouped either in cla ...	2009	19196764
emma 2--a mage-compliant system for the collaborative analysis and integration of microarray data.	understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. attempts to standardize the annotation of microarray data include the minimum information about a microarray experiment (miame) recommendations, the mage-ml format for data interchange, and the use of controlled vocabularies or ontologies. the existing software systems for microarray data analysis implement the mentioned standards only partially and are often ...	2009	19200358
minimum contradiction matrices in whole genome phylogenies.	minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ...	2008	19204821
lactic acid bacteria from fresh fruit and vegetables as biocontrol agents of phytopathogenic bacteria and fungi.	this study evaluated the efficacy of lactic acid bacteria (lab) isolated from fresh fruits and vegetables as biocontrol agents against the phytopathogenic and spoilage bacteria and fungi, xanthomonas campestris, erwinia carotovora, penicillium expansum, monilinia laxa, and botrytis cinerea. the antagonistic activity of 496 lab strains was tested in vitro and all tested microorganisms except p. expansum were inhibited by at least one isolate. the 496 isolates were also analyzed for the inhibition ...	2008	19204894
substrate-protein interaction in human tryptophan dioxygenase: the critical role of h76.	the initial and rate-limiting step of the kynurenine pathway in humans involves the oxidation of tryptophan to n-formyl kynurenine catalyzed by two hemeproteins, tryptophan 2,3-dioxygenase (htdo) and indoleamine 2,3-dioxygenase (hido). in htdo, the conserved h76 residue is believed to act as an active site base to deprotonate the indole nh group of trp, the initial step of the trp oxidation reaction. in hido, this histidine is replaced by a serine. to investigate the role of the h76, we have stu ...	2009	19209904
functional expression of a bacterial xylose isomerase in saccharomyces cerevisiae.	in industrial fermentation processes, the yeast saccharomyces cerevisiae is commonly used for ethanol production. however, it lacks the ability to ferment pentose sugars like d-xylose and l-arabinose. heterologous expression of a xylose isomerase (xi) would enable yeast cells to metabolize xylose. however, many attempts to express a prokaryotic xi with high activity in s. cerevisiae have failed so far. we have screened nucleic acid databases for sequences encoding putative xis and finally were a ...	2009	19218403
characterization of regulatory pathways in xylella fastidiosa: genes and phenotypes controlled by gaca.	the xylem-limited, insect-transmitted bacterium xylella fastidiosa causes pierce's disease in grapes through cell aggregation and vascular clogging. gaca controls various physiological processes and pathogenicity factors in many gram-negative bacteria, including biofilm formation in pseudomonas syringae pv. tomato dc3000. cloned gaca of x. fastidiosa was found to restore the hypersensitive response and pathogenicity in gaca mutants of p. syringae pv. tomato dc3000 and erwinia amylovora. a gaca m ...	2009	19218414
target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.	to study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common tim barrel fold and catalyze a wide range of chemical reactions. here, we describe a collaboration between the enzyme specificity consortium (enspec) and the new york sgx research center for structural genomics (nysgxrc) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. using sequence- and s ...	2009	19219566
co-regulation of xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system ravs/ravr.	xanthomonas campestris pv. campestris (xcc) is known to regulate virulence through a quorum-sensing mechanism. detection of the quorum-sensing signal dsf by sensor rpfc leads to activation of the response regulator rpfg, which influences virulence by degrading cyclic-di-gmp and by subsequent increasing expression of the global regulator clp. in this study, we show that mutation of a response regulator ravr containing the ggdef-eal domains decreases xcc virulence factor production. the functional ...	2009	19220743
a solanum lycopersicum x solanum pimpinellifolium linkage map of tomato displaying genomic locations of r-genes, rgas, and candidate resistance/defense-response ests.	we have identified an accession (la2093) within the tomato wild species solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. to utilize the full genetic potential of la2093 in tomato breeding, we have developed a linkage map based on an f(2) population of a cross between la2093 and a tomato breeding line, using 115 rflp, 94 est, and 41 rga markers. the map spanned 1002.4 cm of the 12 tomato chromosomes with an average ...	2008	19223983
a solanum lycopersicum x solanum pimpinellifolium linkage map of tomato displaying genomic locations of r-genes, rgas, and candidate resistance/defense-response ests.	we have identified an accession (la2093) within the tomato wild species solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. to utilize the full genetic potential of la2093 in tomato breeding, we have developed a linkage map based on an f(2) population of a cross between la2093 and a tomato breeding line, using 115 rflp, 94 est, and 41 rga markers. the map spanned 1002.4 cm of the 12 tomato chromosomes with an average ...	2008	19223983
export of functional streptomyces coelicolor alditol oxidase to the periplasm or cell surface of escherichia coli and its application in whole-cell biocatalysis.	streptomyces coelicolor a3(2) alditol oxidase (aldo) is a soluble monomeric flavoprotein in which the flavin cofactor is covalently linked to the polypeptide chain. aldo displays high reactivity towards different polyols such as xylitol and sorbitol. these characteristics make aldo industrially relevant, but full biotechnological exploitation of this enzyme is at present restricted by laborious and costly purification steps. to eliminate the need for enzyme purification, this study describes a w ...	2009	19224207
visualization of novel virulence activities of the xanthomonas type iii effectors avrbs1, avrbs3 and avrbs4.	xanthomonas campestris pv. vesicatoria secretes at least 20 effector proteins through the type iii secretion system directly into plant cells. in this study, we uncovered virulence activities of the effector proteins avrbs1, avrbs3 and avrbs4 using agrobacterium-mediated transient expression of the corresponding genes in nicotiana benthamiana, followed by microscopic analyses. we showed that, in addition to the nuclear-localized avrbs3, the effector avrbs1, which localizes to the plant cell cyto ...	2009	19236567
structure and function of pseudomonas aeruginosa protein pa1324 (21-170).	pseudomonas aeruginosa is the prototypical biofilm-forming gram-negative opportunistic human pathogen. p. aeruginosa is causatively associated with nosocomial infections and with cystic fibrosis. antibiotic resistance in some strains adds to the inherent difficulties that result from biofilm formation when treating p. aeruginosa infections. transcriptional profiling studies suggest widespread changes in the proteome during quorum sensing and biofilm development. many of the proteins found to be ...	2009	19241370
survival and dissemination of escherichia coli o157:h7 on physically and biologically damaged lettuce plants.	the ecology of the vegetable leaf surface is important to the survival of enteric pathogens. understanding changes in ecological parameters during the preharvest stages of production can lead to development of approaches to minimize the hazard of contamination of fresh fruits and vegetables with foodborne pathogens. in this study, survival levels of escherichia coli o157 over a 10-day period were compared among traumatically injured, phytopathogen-damaged, and healthy lettuce plants. leaves from ...	2008	19244888
the zur of xanthomonas campestris is involved in hypersensitive response and positively regulates the expression of the hrp cluster via hrpx but not hrpg.	in bacteria, zur is a key regulator for zinc homeostasis. our previous work has shown that, in the phytopathogen xanthomonas campestris pv. campestris, in addition to regulating zinc homeostasis, zur is essential for full virulence. here, we demonstrate that the x. campestris pv. campestris zur is involved in hypersensitive response (hr) and positively regulates the transcription of hrpa to hrpf operons and hrpx but not hrpg. constitutively expressing hrpx but not hrpg in the zur mutant could by ...	2009	19245326
new developments in microbial interspecies signaling.	there is a growing appreciation that in addition to well-documented intraspecies quorum sensing systems, small molecules act as signals between microbes of different species. this review will focus on how bacterial small molecules modulate these interspecies interactions. we will particularly emphasize complex relationships such as those between microbes and insects, interactions resulting in non-antagonistic outcomes (i.e. developmental and morphological processes), how co-culture can lead to t ...	2009	19251475
a stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure.	stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. strains have been assigned to genogroups using amplified fragment length polymorphism. hence, isolates of environmental and clinical origin predominate in different groups. a multilocus sequence typing (mlst) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. se ...	2009	19251858
the structure of nmb1585, a marr-family regulator from neisseria meningitidis.	the structure of the marr-family transcription factor nmb1585 from neisseria meningitidis has been solved using data extending to a resolution of 2.1 a. overall, the dimeric structure resembles those of other marr proteins, with each subunit comprising a winged helix-turn-helix (whth) domain connected to an alpha-helical dimerization domain. the spacing of the recognition helices of the whth domain indicates that nmb1585 is pre-configured for dna binding, with a putative inducer pocket that is l ...	2009	19255465
characterization of citrus sinensis type 1 mitochondrial alternative oxidase and expression analysis in biotic stress.	the higher plant mitochondrial electron transport chain contains an alternative pathway that ends with the aox (alternative oxidase). the aox proteins are encoded by a small gene family composed of two discrete gene subfamilies. aox1 is present in both monocot and eudicot plants, whereas aox2 is only present in eudicot plants. we isolated a genomic clone from citrus sinensis containing the aox1a gene. the orange aox1a consists of four exons interrupted by three introns and its promoter harbours ...	2009	19257856
pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria.	many bacteria export extracellular polysaccharides (eps) and capsular polysaccharides (cps). these polymers exhibit remarkably diverse structures and play important roles in the biology of free-living, commensal, and pathogenic bacteria. eps and cps production represents a major challenge because these high-molecular-weight hydrophilic polymers must be assembled and exported in a process spanning the envelope, without compromising the essential barrier properties of the envelope. emerging eviden ...	2009	19258536
conventional and pcr detection of aphelenchoides fragariae in diverse ornamental host plant species.	a pcr-based diagnostic assay was developed for early detection and identification of aphelenchoides fragariae directly in host plant tissues using the species-specific primers afragfl and afragrl that amplify a 169-bp fragment in the internal transcribed spacer (its1) region of ribosomal dna. these species-specific primers did not amplify dna from aphelenchoides besseyi or aphelenchoides ritzemabosi. the pcr assay was sensitive, detecting a single nematode in a background of plant tissue extract ...	2007	19259510
pseudomonas syringae hrpp is a type iii secretion substrate specificity switch domain protein that is translocated into plant cells but functions atypically for a substrate-switching protein.	pseudomonas syringae delivers virulence effector proteins into plant cells via an hrp1 type iii secretion system (t3ss). p. syringae pv. tomato dc3000 hrpp has a c-terminal, putative t3ss substrate specificity switch domain, like yersinia yscp. a deltahrpp dc3000 mutant could not cause disease in tomato or elicit a hypersensitive response (hr) in tobacco, but the hr could be restored by expression of hrpp in trans. though hrpp is a relatively divergent protein in the t3ss of different p. syringa ...	2009	19270091
enzyme-linked immunosorbent assay on nitrocellulose membranes (dot-elisa) in the serodiagnosis of plant pathogenic bacteria.	the usefulness of enzyme-linked immunosorbent assay on nitrocellulose membranes (dot-elisa) for diagnosis and identification of plant pathogenic bacteria was tested. five pathovars of xanthomonas campestris and two antisera, one produced against pv. vesicatoria and the other against pv. translucens, were used in a model system. a 10-min incubation of the bacterial cells, dot blotted on membranes, in diluted sera, followed by either alkaline phosphatase conjugated protein a or goat antirabbit glo ...	1987	19271341
protein secretion systems in bacterial-host associations, and their description in the gene ontology.	protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ...	2009	19278550
common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the gene ontology.	a wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. these molecules, termed effectors, commonly target the host defense signaling pathways in order to suppress the defense response. others target the gene expression machinery or trigger specific modifications to host morphology or physiology that promote the nutrition and proliferation ...	2009	19278551
initial in vitro evaluations of the antibacterial activities of glucosinolate enzymatic hydrolysis products against plant pathogenic bacteria.	the aim of the study was to evaluate the in vitro antibacterial effects of glucosinolate hydrolysis products (ghp) against plant pathogenic micro-organisms namely agrobacterium tumefaciens, erwinia chrysanthemi, pseudomonas cichorii, pseudomonas tomato, xanthomonas campestris and xanthomonas juglandis.	2009	19291239
the three-dimensional structure of the cytoplasmic domains of epsf from the type 2 secretion system of vibrio cholerae.	the type 2 secretion system (t2ss), a multi-protein machinery that spans both the inner and the outer membranes of gram-negative bacteria, is used for the secretion of several critically important proteins across the outer membrane. here we report the crystal structure of the n-terminal cytoplasmic domain of epsf, an inner membrane spanning t2ss protein from vibrio cholerae. this domain consists of a bundle of six anti-parallel helices and adopts a fold that has not been described before. the lo ...	2009	19324092
an adenosine kinase exists in xanthomonas campestris pathovar campestris and is involved in extracellular polysaccharide production, cell motility, and virulence.	adenosine kinase (adk) is a purine salvage enzyme and a typical housekeeping enzyme in eukaryotes which catalyzes the phosphorylation of adenosine to form amp. since prokaryotes synthesize purines de novo and no endogenous adk activity is detectable in escherichia coli, adk has long been considered to be rare in bacteria. to date, only two prokaryotes, both of which are gram-positive bacteria, have been reported to contain adk. here we report that the gram-negative bacterium xanthomonas campestr ...	2009	19329636
a family of bacterial cysteine protease type iii effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes.	bacterial phytopathogens employ a type iii secretion system to deliver effector proteins into the plant cell to suppress defense pathways; however, the molecular mechanisms and subcellular localization strategies that drive effector function largely remain a mystery. here, we demonstrate that the plant plasma membrane is the primary site for subcellular localization of the pseudomonas syringae effector avrpphb and five additional cysteine protease family members. avrpphb and two avrpphb-like eff ...	2009	19346252
identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway.	caprazamycins are potent anti-mycobacterial liponucleoside antibiotics isolated from streptomyces sp. mk730-62f2 and belong to the translocase i inhibitor family. their complex structure is derived from 5'-(beta-o-aminoribosyl)-glycyluridine and comprises a unique n-methyldiazepanone ring. the biosynthetic gene cluster has been identified, cloned, and sequenced, representing the first gene cluster of a translocase i inhibitor. sequence analysis revealed the presence of 23 open reading frames put ...	2009	19351877
purification and characterization of a novel antifungal protein from bacillus subtilis strain b29.	an antifungal protein was isolated from a culture of bacillus subtilis strain b29. the isolation procedure comprised ion exchange chromatography on diethylaminoethyl (deae)-52 cellulose and gel filtration chromatography on bio-gel p-100. the protein was absorbed on deae-cellulose and bio-gel p-100. the purified antifungal fraction was designated as b29i, with a molecular mass of 42.3 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page), pi value 5.69 by isoelectric focusin ...	2009	19353744
over-expression of a tomato n-acetyl-l-glutamate synthase gene (slnags1) in arabidopsis thaliana results in high ornithine levels and increased tolerance in salt and drought stresses.	a single copy of the n-acetyl-l-glutamate synthase gene (slnags1) has been isolated from tomato. the deduced amino acid sequence consists of 604 amino acids and shows a high level of similarity to the predicted arabidopsis nags1 and nags2 proteins. furthermore, the n-terminus argb domain and the c-terminus arga domain found in slnags1 are similar to the structural arrangements that have been reported for other predicted nags proteins. slnags1 was expressed at high levels in all aerial organs, an ...	2009	19357433
first gene cassettes of integrons as targets in finding adaptive genes in metagenomes.	the first gene cassettes of integrons are involved in the last adaptation response to changing conditions and are also the most expressed. we propose a rapid method for the selection of clones carrying an integron first gene cassette that is useful for finding adaptive genes in environmental metagenomic libraries.	2009	19363073
a high-resolution map of the grp1 locus on chromosome v of potato harbouring broad-spectrum resistance to the cyst nematode species globodera pallida and globodera rostochiensis.	the grp1 locus confers broad-spectrum resistance to the potato cyst nematode species globodera pallida and globodera rostochiensis and is located in the gp21-gp179 interval on the short arm of chromosome v of potato. a high-resolution map has been developed using the diploid mapping population rham026, comprising 1,536 genotypes. the flanking markers gp21 and gp179 have been used to screen the 1,536 genotypes for recombination events. interval mapping of the resistances to g. pallida pa2 and g. ...	2009	19363662
xanthomonas t3s effector xopn suppresses pamp-triggered immunity and interacts with a tomato atypical receptor-like kinase and tft1.	xopn is a virulence factor from xanthomonas campestris pathovar vesicatoria (xcv) that is translocated into tomato (solanum lycopersicum) leaf cells by the pathogen's type iii secretion system. xcv deltaxopn mutants are impaired in growth and have reduced ability to elicit disease symptoms in susceptible tomato leaves. we show that xopn action in planta reduced pathogen-associated molecular pattern (pamp)-induced gene expression and callose deposition in host tissue, indicating that xopn suppres ...	2009	19366901
the transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.	metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes. if genes encoding metabolic enzymes are horizontally transferred and are advantageous, they are likely to become fixed. horizontal gene transfer (hgt) has played a key role in prokaryotic evolution and its importance in eukaryotes is increasingly evident. high levels of endosymbiotic gene transfer (egt) accompanied the establishment of plast ...	2009	19368726
glyceraldehyde-3-phosphate dehydrogenase of xanthomonas campestris pv. campestris is required for extracellular polysaccharide production and full virulence.	glyceraldehyde-3-phosphate dehydrogenase (gapdh) plays an important role in glucose catabolism, converting glyceraldehyde 3-phosphates to 1,3-bisphosphoglycerates. open reading frame (orf) xc_0972 in the genome of xanthomonas campestris pv. campestris (xcc) strain 8004 is the only orf in this strain annotated to encode a gapdh. in this work, we have demonstrated genetically that this orf encodes a unique gapdh in xcc strain 8004, which seems to be constitutively expressed. a gapdh-deficient muta ...	2009	19372163
misexpression of fatty acid elongation1 in the arabidopsis epidermis induces cell death and suggests a critical role for phospholipase a2 in this process.	very-long-chain fatty acids (vlcfas) are important functional components of various lipid classes, including cuticular lipids in the higher plant epidermis and lipid-derived second messengers. here, we report the characterization of transgenic arabidopsis thaliana plants that epidermally express fatty acid elongation1 (fae1), the seed-specific beta-ketoacyl-coa synthase (kcs) catalyzing the first rate-limiting step in vlcfa biosynthesis. misexpression of fae1 changes the vlcfas in different clas ...	2009	19376931
deletions in the repertoire of pseudomonas syringae pv. tomato dc3000 type iii secretion effector genes reveal functional overlap among effectors.	the gamma-proteobacterial plant pathogen pseudomonas syringae pv. tomato dc3000 uses the type iii secretion system to inject ca. 28 avr/hop effector proteins into plants, which enables the bacterium to grow from low inoculum levels to produce bacterial speck symptoms in tomato, arabidopsis thaliana, and (when lacking hopq1-1) nicotiana benthamiana. the effectors are collectively essential but individually dispensable for the ability of the bacteria to defeat defenses, grow, and produce symptoms ...	2009	19381254
the quorum sensing-dependent gene katg of burkholderia glumae is important for protection from visible light.	quorum sensing (qs) plays important roles in the pathogenicity of burkholderia glumae, the causative agent of bacterial rice grain rot. we determined how qs is involved in catalase expression in b. glumae. the qs-defective mutant of b. glumae exhibited less catalase activity than wild-type b. glumae. a beta-glucuronidase assay of a katg::tn3-gusa78 reporter fusion protein revealed that katg expression is under the control of qs. furthermore, katg expression was upregulated by qsmr, a transcripti ...	2009	19395481
an icmf family protein, implm, is an integral inner membrane protein interacting with impkl, and its walker a motif is required for type vi secretion system-mediated hcp secretion in agrobacterium tumefaciens.	an intracellular multiplication f (icmf) family protein is a conserved component of a newly identified type vi secretion system (t6ss) encoded in many animal and plant-associated proteobacteria. we have previously identified impl(m), an icmf family protein that is required for the secretion of the t6ss substrate hemolysin-coregulated protein (hcp) from the plant-pathogenic bacterium agrobacterium tumefaciens. in this study, we characterized the topology of impl(m) and the importance of its nucle ...	2009	19395482
mapping of loci from solanum lycopersicoides conferring resistance or susceptibility to botrytis cinerea in tomato.	cultivated tomato (solanum lycopersicum, syn. lycopersicon esculentum) is susceptible to the necrotrophic ascomycete and causal agent of gray mold, botrytis cinerea. resistance to this fungal pathogen is elevated in wild relatives of tomato, including solanum lycopersicoides. an introgression line population (il) containing chromosomal segments of s. lycopersicoides within the background of tomato cv. vf36 was used to screen the genome for foliar resistance and susceptibility to b. cinerea. base ...	2009	19399472
a qrt-pcr-based method for the measurement of rrn operon copy number.	to develop a convenient and accurate method for estimating the rrn operon copy number (y(rrn)) in cells of pure prokaryotic cultures based on quantitative real-time polymerase chain reaction (qrt-pcr).	2009	19413774
ampdi is involved in expression of the chromosomal l1 and l2 beta-lactamases of stenotrophomonas maltophilia.	two ampd homologues, ampd(i) and ampd(ii), of stenotrophomonas maltophilia have been cloned and analyzed. comparative genomic analysis revealed that the genomic context of the ampd(ii) genes is quite different, whereas that of the ampd(i) genes is more conserved in s. maltophilia strains. the ampd system of s. maltophilia is distinct from that of the enterobacteriaceae and pseudomonas aeruginosa in three respects. (i) ampd(i) of s. maltophilia is not encoded in an ampde operon, in contrast to wh ...	2009	19414581
fabrication of triple-layer matrix tablets of venlafaxine hydrochloride using xanthan gum.	the objective of present investigation was to develop venlafaxine hydrochloride-layered tablets for obtaining sustained drug release. the tablets containing venlafaxine hydrochloride 150 mg were prepared by wet granulation technique using xanthan gum in the middle layer and barrier layers. the granules and tablets were characterized. the in vitro drug dissolution study was conducted in distilled water. the tablets containing two lower strengths were also developed using the same percentage compo ...	2009	19444618
glycine-aspartic_ acid-serine-leucine esterase xcc_ est from xanthomonas campestris pv. campestris 8004 and its esterase domain: gene expression in escherichia coli, refolding and characterization.	to characterize the gdsl (glycine, aspartic acid, serine and leucine motif in protein sequence) esterase xcc_ est from xanthomonas campestris pv. campestris (xcc) 8004.	2009	19445174
the xanthomonas campestris pv. vesicatoria type iii effector protein xopj inhibits protein secretion: evidence for interference with cell wall-associated defense responses.	the phytopathogenic bacterium xanthomonas campestris pv. vesicatoria uses the type iii secretion system (t3ss) to inject effector proteins into cells of its solanaceous host plants. it is generally assumed that these effectors manipulate host pathways to favor bacterial replication and survival. however, the molecular mechanisms by which type iii effectors suppress host defense responses are far from being understood. based on sequence similarity, xanthomonas outer protein j (xopj) is a member o ...	2009	19445590
substrate specificity of a mannose-6-phosphate isomerase from bacillus subtilis and its application in the production of l-ribose.	the uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from bacillus subtilis was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme was observed at ph 7.5 and 40 degrees c in the presence of 0.5 mm co(2+). the isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the c-2 and c-3 positions, such as the d and l forms of ribose, lyxose, talose, mannose, and allose. the en ...	2009	19447949
recognition of avrbs3-like proteins is mediated by specific binding to promoters of matching pepper bs3 alleles.	the pepper (capsicum annuum) bacterial spot (bs) resistance gene bs3 and its allelic variant bs3-e mediate recognition of the xanthomonas campestris pv vesicatoria type iii effector protein avrbs3 and its deletion derivative avrbs3deltarep16. recognition specificity resides in the bs3 and bs3-e promoters and is determined by a defined promoter region, the upa (for up-regulated by avrbs3) box. using site-directed mutagenesis, we defined the exact boundaries of the upa(avrbs3) box of the bs3 promo ...	2009	19448036
edgar: a software framework for the comparative analysis of prokaryotic genomes.	the introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. as one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. a main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.	2009	19457249
type iii protein secretion in plant pathogenic bacteria.		2009	19458111
mutation in the rgd motif decreases the esterase activity of xcc_est.	five truncated constructs of xcc_est gdsl esterase from xanthomonas campestris were heterologously expressed and purified. the truncated constructs with a rgd motif had higher specific activities than those without the motif. the specific activity of wild-type xcc_est was 32.5 +/- 2.7 u/mg, while the rgd mutant was 12.5 +/- 4.9 u/mg. moreover, we expressed mature forms of the xcc_est protein and the rgd mutant as inclusion bodies and, after refolding, there was no significant difference between ...	2009	19458922
fermentation performance and structure characteristics of xanthan produced by xanthomonas campestris with a glucose/xylose mixture.	the ability of xanthomonas campestris to convert glucose and xylose to xanthan and the structure of xanthan derived from the glucose/xylose mixture media are important when the lignocelluloses hydrolysate was used in xanthan production. in this paper, the features related to xanthan fermentation in the glucose/xylose mixture media and the structures of xanthan derived from the mixture media were studied. glucose was the preferred carbon source to produce xanthan while xylose was also utilized wi ...	2010	19459070
a plasmid rk2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species.	the majority of microorganisms in natural environments are difficult to cultivate, but their genes can be studied via metagenome libraries. to enhance the chances that these genes become expressed we here report the construction of a broad-host-range plasmid vector (prs44) for fosmid and bacterial artificial chromosome (bac) cloning. prs44 can be efficiently transferred to numerous hosts by conjugation. it replicates in such hosts via the plasmid rk2 origin of replication, while in escherichia c ...	2009	19459950
systems level analysis of two-component signal transduction systems in erwinia amylovora: role in virulence, regulation of amylovoran biosynthesis and swarming motility.	two-component signal transduction systems (tcsts), consisting of a histidine kinase (hk) and a response regulator (rr), represent a major paradigm for signal transduction in prokaryotes. tcsts play critical roles in sensing and responding to environmental conditions, and in bacterial pathogenesis. most tcsts in erwinia amylovora have either not been identified or have not yet been studied.	2009	19470164
detailed analysis of the dna recognition motifs of the xanthomonas type iii effectors avrbs3 and avrbs3deltarep16.	the gram-negative phytopathogenic bacterium xanthomonas campestris pv. vesicatoria (xcv) employs a type iii secretion system to translocate effector proteins into plant cells where they modulate host signaling pathways to the pathogen's benefit. the effector protein avrbs3 acts as a eukaryotic transcription factor and induces the expression of plant genes termed upa (up-regulated by avrbs3). here, we describe 11 new upa genes from bell pepper that are induced by avrbs3 early after infection with ...	2009	19473322
analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.	the hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. the fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme a-binding enzymes with a variety of substrates located at their active sites.	2009	19473548
the fractionated orthology of bs2 and rx/gpa2 supports shared synteny of disease resistance in the solanaceae.	comparative genomics provides a powerful tool for the identification of genes that encode traits shared between crop plants and model organisms. pathogen resistance conferred by plant r genes of the nucleotide-binding-leucine-rich-repeat (nb-lrr) class is one such trait with great agricultural importance that occupies a critical position in understanding fundamental processes of pathogen detection and coevolution. the proposed rapid rearrangement of r genes in genome evolution would make compara ...	2009	19474202