Publications

evidence for a new sub-class of methionine sulfoxide reductases b with an alternative thioredoxin recognition signature.	methionine sulfoxide reductases catalyze the reduction of protein-bound methionine sulfoxide back to methionine via a thioredoxin-recycling process. two classes of methionine sulfoxide reductases, called msra and msrb, exist that display opposite stereoselectivities toward the sulfoxide function. although they are structurally unrelated, they share a similar chemical mechanism that includes three steps with 1) formation of a sulfenic acid intermediate with a concomitant release of 1 mol of methi ...	2004	15280355
cloning and partial characterization of zwittermicin a resistance gene cluster from bacillus thuringiensis subsp. kurstaki strain hd1.	the study seeks to shed light on the aminopolyol, broad-spectrum antibiotic zwittermicin a gene cluster of bacillus thuringiensis subsp. kurstaki hd1 and to identify any new uncharacterized genes with an eventual goal to establish a better understanding of the resistance gene cluster.	2004	15281929
integron integrase binds to bulged hairpin dna.	gene cassettes are short, monogenic dna elements that translocate between integrons through site-specific excision and integration. these events require that an integron-coded tyrosine recombinase forms a reactive complex with two sites, at least one of which belongs to the attc class. an attc site can be divided into two pairs of short repeats flanking a palindromic central region. the nucleotide sequence of attc among different cassettes varies extensively, implying that the site contains a st ...	2004	15289577
polyhydroxyalkanoate (pha) accumulation in sulfate-reducing bacteria and identification of a class iii pha synthase (phaec) in desulfococcus multivorans.	seven strains of sulfate-reducing bacteria (srb) were tested for the accumulation of polyhydroxyalkanoates (phas). during growth with benzoate desulfonema magnum accumulated large amounts of poly(3-hydroxybutyrate) [poly(3hb)]. desulfosarcina variabilis (during growth with benzoate), desulfobotulus sapovorans (during growth with caproate), and desulfobacterium autotrophicum (during growth with caproate) accumulated poly(3hb) that accounted for 20 to 43% of cell dry matter. desulfobotulus sapovor ...	2004	15294771
bactericidal activity of glycinecin a, a bacteriocin derived from xanthomonas campestris pv. glycines, on phytopathogenic xanthomonas campestris pv. vesicatoria cells.	the ability of glycinecin a, a bacteriocin derived from xanthomonas campestris pv. glycines 8ra, to kill closely related bacteria has been demonstrated previously by our group. in the present study, we aimed at determining the glycinecin a-induced cause of death. treatment with glycinecin a caused slow dissipation of membrane potential and rapid depletion of the ph gradient. glycinecin a treatment also induced leakage of potassium ions from x. campestris pv. vesicatoria yk93-4 cells and killed s ...	2004	15294776
xanthan gum production from cassava bagasse hydrolysate with xanthomonas campestris using alternative sources of nitrogen.	cassava bagasse was hydrolyzed using hcl and the hydrolysate was used for the production of xanthan gum using a bacterial culture of xanthomonas campestris. cassava bagasse hydrolysate with an initial concentration of approx 20 g of glucose/l proved to be the best substrate concentration for xanthan gum production. among the organic and inorganic nitrogen sources tested to supplement the medium-urea, yeast extract, peptone, potassium nitrate, and ammonium sulfate-potassium nitrate was most suita ...	2004	15304758
xanthan gum production by xanthomonas campestris w.t. fermentation from chestnut extract.	xanthomonas campestris w.t. was used for production of xanthan gum in fermentations with chestnut flour for the first time. fermentations were carried out with either chestnut flour or its soluble sugars (33.5%) and starch (53.6%), respectively, at 28 degrees c and 200 rpm at initial ph 7.0 in flasks. the effect of agitation rate (at 200, 400, and 600 rpm) on xanthan gum production was also studied in a 2-l batch reactor. it was found that xanthan production reaches a maximum value of 3.3 g/100 ...	1999	15304770
cloning and expression of afpa, a gene encoding an antifreeze protein from the arctic plant growth-promoting rhizobacterium pseudomonas putida gr12-2.	the arctic plant growth-promoting rhizobacterium pseudomonas putida gr12-2 secretes an antifreeze protein (afp) that promotes survival at subzero temperatures. the afp is unusual in that it also exhibits a low level of ice nucleation activity. a dna fragment with an open reading frame encoding 473 amino acids was cloned by pcr and inverse pcr using primers designed from partial amino acid sequences of the isolated afp. the predicted gene product, afpa, had a molecular mass of 47.3 kda, a pi of 3 ...	2004	15317770
different patterns of evolution for duplicated dna repair genes in bacteria of the xanthomonadales group.	dna repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. the importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.	2004	15333143
in search of rnase p rna from microbial genomes.	a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ...	2004	15337843
in vivo phosphorylation of partner switching regulators correlates with stress transmission in the environmental signaling pathway of bacillus subtilis.	exposure of bacteria to diverse growth-limiting stresses induces the synthesis of a common set of proteins which provide broad protection against future, potentially lethal stresses. among bacillus subtilis and its relatives, this general stress response is controlled by the sigmab transcription factor. signals of environmental and energy stress activate sigmab through a multicomponent network that functions via a partner switching mechanism, in which protein-protein interactions are governed by ...	2004	15342582
mutational analysis of xanthomonas harpin hpag identifies a key functional region that elicits the hypersensitive response in nonhost plants.	hpag is a type iii-secreted elicitor protein of xanthomonas axonopodis pv. glycines. we have determined the critical amino acid residues important for hypersensitive response (hr) elicitation by random and site-directed mutagenesis of hpag and its homolog xopa. a plasmid clone carrying hpag was mutagenized by site-directed mutagenesis, hydroxylamine mutagenesis, and error-prone pcr. a total of 52 mutants were obtained, including 51 single missense mutants and 1 double missense mutant. the hr eli ...	2004	15342594
the pen1 syntaxin defines a novel cellular compartment upon fungal attack and is required for the timely assembly of papillae.	attack by the host powdery mildew erysiphe cichoracearum usually results in successful penetration and rapid proliferation of the fungus on arabidopsis. by contrast, the nonhost barley powdery mildew blumeria graminis f. sp. hordei (bgh) typically fails to penetrate arabidopsis epidermal cells. in both instances the plant secretes cell wall appositions or papillae beneath the penetration peg of the fungus. genetic screens for mutations that result in increased penetration of bgh on arabidopsis h ...	2004	15342780
comparison of atpase-encoding type iii secretion system hrcn genes in biocontrol fluorescent pseudomonads and in phytopathogenic proteobacteria.	type iii protein secretion systems play a key role in the virulence of many pathogenic proteobacteria, but they also occur in nonpathogenic, plant-associated bacteria. certain type iii protein secretion genes (e.g., hrcc) have been found in pseudomonas sp. strain sbw25 (and other biocontrol pseudomonads), but other type iii protein secretion genes, such as the atpase-encoding gene hrcn, have not been found. using both colony hybridization and a pcr approach, we show here that hrcn is nevertheles ...	2004	15345390
the pepper transcription factor capf1 confers pathogen and freezing tolerance in arabidopsis.	an erf/ap2-type transcription factor (capf1) was isolated by differential-display reverse transcription-pcr, following inoculation of the soybean pustule pathogen xanthomonas axonopodis pv glycines 8ra, which induces hypersensitive response in pepper (capsicum annuum) leaves. capf1 mrna was induced under conditions of biotic and abiotic stress. higher levels of capf1 transcripts were observed in disease-resistant tissue compared with susceptible tissue. capf1 expression was additionally induced ...	2004	15347795
complete genomic sequence of bacteriophage b3, a mu-like phage of pseudomonas aeruginosa.	bacteriophage b3 is a transposable phage of pseudomonas aeruginosa. in this report, we present the complete dna sequence and annotation of the b3 genome. dna sequence analysis revealed that the b3 genome is 38,439 bp long with a g+c content of 63.3%. the genome contains 59 proposed open reading frames (orfs) organized into at least three operons. of these orfs, the predicted proteins from 41 orfs (68%) display significant similarity to other phage or bacterial proteins. many of the predicted b3 ...	2004	15375138
an energy taxis transducer promotes root colonization by azospirillum brasilense.	motility responses triggered by changes in the electron transport system are collectively known as energy taxis. in azospirillum brasilense, energy taxis was shown to be the principal form of locomotor control. in the present study, we have identified a novel chemoreceptor-like protein, named tlp1, which serves as an energy taxis transducer. the tlp1 protein is predicted to have an n-terminal periplasmic region and a cytoplasmic c-terminal signaling module homologous to those of other chemorecep ...	2004	15375141
genomic plasticity of the causative agent of melioidosis, burkholderia pseudomallei.	burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. this gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern thailand where half of those affected die. here we report the complete genome of b. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of g ...	2004	15377794
the secretome of the plant pathogenic bacterium erwinia chrysanthemi.	erwinia chrysanthemi causes soft-rot diseases of many plants by secreting a battery of enzymes which degrade the plant cell walls. we initiated a proteomic analysis to create a reference map of the e. chrysanthemi secretome. extracellular proteins were isolated from e. chrysanthemi culture supernatants and resolved by two-dimensional electrophoresis. by analysis of mutants, western blotting, and matrix-assisted laser desorption/ionization-time of flight (maldi-tof) 55 spots representing 25 uniqu ...	2004	15378709
effect of dimer dissociation on activity and thermostability of the alpha-glucuronidase from geobacillus stearothermophilus: dissecting the different oligomeric forms of family 67 glycoside hydrolases.	the oligomeric organization of enzymes plays an important role in many biological processes, such as allosteric regulation, conformational stability and thermal stability. alpha-glucuronidases are family 67 glycosidases that cleave the alpha-1,2-glycosidic bond between 4-o-methyl-d-glucuronic acid and xylose units as part of an array of hemicellulose-hydrolyzing enzymes. currently, two crystal structures of alpha-glucuronidases are available, those from geobacillus stearothermophilus (agua) and ...	2004	15466046
characterization of plasmid por1 from ornithobacterium rhinotracheale and construction of a shuttle plasmid.	the bacterium ornithobacterium rhinotracheale has been recognized as an emerging pathogen in poultry since about 10 years ago. knowledge of this bacterium and its mechanisms of virulence is still very limited. here we report the development of a transformation system that enables genetic modification of o. rhinotracheale. the system is based on a cryptic plasmid, por1, that was derived from an o. rhinotracheale strain of serotype k. sequencing indicated that the plasmid consisted of 14,787 nucle ...	2004	15466524
transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium thermotoga maritima.	thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees c. a whole-genome cdna microarray was used to examine differential expression patterns between biofilm and planktonic populations. mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the ge ...	2004	15466556
variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice.	in animal pathogenic bacteria, horizontal gene transfer events (hgt) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (lps). as a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. since lps is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. although lps has been suggested as a ...	2004	15473911
a phylogenetic analysis of wadi el natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures.	samples of sediments and surrounding soda soils (ss) from the extremely saline and alkaline lakes of the wadi el natrun in the libyan desert, egypt, were obtained in october 2000. anaerobic enrichment cultures were grown from these samples, dna isolated, and the bacterial diversity assessed by 16s rrna gene clone analysis. clones derived from lake sediments (ls) most closely matched clostridium spp., natronoincola histidinovorans, halocella cellulolytica, bacillus spp., and the cytophaga-flexiba ...	2004	15480866
hpab from xanthomonas campestris pv. vesicatoria acts as an exit control protein in type iii-dependent protein secretion.	the hrp (hypersensitive response and pathogenicity) gene cluster of the plant pathogenic bacterium xanthomonas campestris pv. vesicatoria encodes a type iii secretion (tts) system, which injects bacterial effector proteins into the plant cell. here, we characterized hpab (hpa, hrp-associated), which encodes a pathogenicity factor with typical features of a tts chaperone. we show that hpab is important for the efficient secretion of at least five effector proteins but is dispensable for the secre ...	2004	15491365
innate immunity in arabidopsis thaliana: lipopolysaccharides activate nitric oxide synthase (nos) and induce defense genes.	lipopolysaccharides (lps) are cell-surface components of gram-negative bacteria and are microbe-/pathogen-associated molecular patterns in animal pathosystems. as for plants, the molecular mechanisms of signal transduction in response to lps are not known. here, we show that arabidopsis thaliana reacts to lps with a rapid burst of no, a hallmark of innate immunity in animals. fifteen lps preparations (among them burkholderia cepacia, pseudomonas aeruginosa, and erwinia carotovora) as well as lip ...	2004	15498873
diversity and antagonistic potential of bacteria associated with bryophytes from nutrient-poor habitats of the baltic sea coast.	very little is known about the interaction of bryophytes with bacteria. therefore, we analyzed bacteria associated with three bryophyte species, tortula ruralis, aulacomnium palustre, and sphagnum rubellum, which represent typical moss species of three nutrient-poor plant communities at the southern baltic sea coast in germany. by use of two cultivation-independent techniques, denaturing gradient gel electrophoresis and single-strand conformation polymorphism analysis of the 16s ribosomal dna, a ...	2004	15528520
characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal dna terminal restriction fragment length polymorphism profiling.	progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (cf) patients. a greater understanding of these bacterial infections is needed to improve lung disease management. as culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (t-rf) length polymorphism profiling and 16s rrna clone data to characterize, without prior cultivation, the bacterial comm ...	2004	15528712
a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land.	the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ...	2004	15535883
the bag or the spindle: the cell factory at the time of systems' biology.	genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. as a first step, isolated genes (including those of the metagenome), or small gene clusters are improved and expressed in a variety of hosts. new techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a ...	2004	15537427
a genetic screen to isolate type iii effectors translocated into pepper cells during xanthomonas infection.	the bacterial pathogen xanthomonas campestris pv. vesicatoria (xcv) uses a type iii secretion system (ttss) to translocate effector proteins into host plant cells. the ttss is required for xcv colonization, yet the identity of many proteins translocated through this apparatus is not known. we used a genetic screen to functionally identify xcv ttss effectors. a transposon 5 (tn5)-based transposon construct including the coding sequence for the xcv avrbs2 effector devoid of its ttss signal was ran ...	2004	15545602
exploiting thiol modifications.		2004	15547642
identification and expression profiling of tomato genes differentially regulated during a resistance response to xanthomonas campestris pv. vesicatoria.	the gram-negative bacterium xanthomonas campestris pv. vesicatoria is the causal agent of spot disease in tomato and pepper. plants of the tomato line hawaii 7981 are resistant to race t3 of x. campestris pv. vesicatoria expressing the type iii effector protein avrxv3 and develop a typical hypersensitive response upon bacterial challenge. a combination of suppression subtractive hybridization and microarray analysis identified a large set of cdnas that are induced or repressed during the resista ...	2004	15553246
modulation of swarming and virulence by fatty acids through the rsba protein in proteus mirabilis.	after sensing external signals, proteus mirabilis undergoes a multicellular behavior called swarming which is coordinately regulated with the expression of virulence factors. here we report that exogenously added fatty acids could act as signals to regulate swarming in p. mirabilis. specifically, while oleic acid enhanced swarming, some saturated fatty acids, such as lauric acid, myristic acid, palmitic acid, and stearic acid, inhibited swarming. we also found that expression of hemolysin, which ...	2004	15557604
ornithine decarboxylase gene (caodc1) is specifically induced during tmv-mediated but salicylate-independent resistant response in hot pepper.	a gene encoding putative ornithine decarboxylase (odc) has been isolated by differential screening of a cdna library from the resistant hot pepper (capsicum annuum l.) inoculated with avirulent tobacco mosaic virus (tmv) pathotype p0. in hot pepper plants, transcripts of the caodc1 (c. annuum odc1) gene started to accumulate at 24 h post-inoculation of tmv-p0 and the signal was spread systemically. the transcript level of caodc1 was increased rapidly in a hot pepper resistant to xanthomonas camp ...	2004	15564537
characterisation of a secondary alcohol dehydrogenase from xanthomonas campestris dsm 3586.	the chromosomal locus np_636946 of xanthomonas campestris dsm 3586 (atcc 33913) which was earlier presumed to encode a quinoprotein glucose dehydrogenase has been cloned, expressed in escherichia coli and the recombinant enzyme has been characterised. it was found to have no glucose dehydrogenase activity but to be active on many different polyols and diols, aliphatic alcohols, certain aldonic acids and amino-sugars. the product of d: -gluconic acid oxidation was 5-keto-d: -gluconic acid. the en ...	2005	15565334
characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library.	it has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques. thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms. to isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the puc19 ...	2004	15574921
complete nucleotide sequence of the conjugative tetracycline resistance plasmid pfbaot6, a member of a group of incu plasmids with global ubiquity.	this study presents the first complete sequence of an incu plasmid, pfbaot6. this plasmid was originally isolated from a strain of aeromonas caviae from hospital effluent (westmorland general hospital, kendal, united kingdom) in september 1997 (g. rhodes, g. huys, j. swings, p. mcgann, m. hiney, p. smith, and r. w. pickup, appl. environ. microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pfbaot6 is 84,748 bp long and has 94 predicted coding sequences, ...	2004	15574953
associations of the major pseudopilin xpsg with xpsn (gspc) and secretin xpsd of xanthomonas campestris pv. campestris type ii secretion apparatus revealed by cross-linking analysis.	the major pseudopilin xpsg is an essential component of type ii secretion apparatus of xanthomonas campestris pv. campestris. along with other ancillary pseudopilins, it forms a pilus-like structure spanning between cytoplasmic and outer membranes. associations of pseudopilins with non-pseudopilin members of type ii secretion apparatus were not well documented, probably due to their dynamic or unstable nature. in this study, by treating intact cells with a cleavable cross-linker dithiobis(succin ...	2004	15590656
process of protein transport by the type iii secretion system.	the type iii secretion system (ttss) of gram-negative bacteria is responsible for delivering bacterial proteins, termed effectors, from the bacterial cytosol directly into the interior of host cells. the ttss is expressed predominantly by pathogenic bacteria and is usually used to introduce deleterious effectors into host cells. while biochemical activities of effectors vary widely, the ttss apparatus used to deliver these effectors is conserved and shows functional complementarity for secretion ...	2004	15590783
cas3p belongs to a seven-member family of capsule structure designer proteins.	the polysaccharide capsule is the main virulence factor of the basidiomycetous yeast cryptococcus neoformans. four genes (cap10, cap59, cap60, and cap64) essential for capsule formation have been previously identified, although their roles in the biosynthetic pathway remain unclear. a genetic and bioinformatics approach allowed the identification of six cap64-homologous genes, named cas3, cas31, cas32, cas33, cas34, and cas35, in the c. neoformans genome. this gene family is apparently specific ...	2004	15590825
mitochondrial cytochrome c1 is a collapsed di-heme cytochrome.	cytochrome c(1) from mitochondrial complex iii and the di-heme cytochromes c in the corresponding enzyme from epsilon-proteobacteria have so far been considered to represent unrelated cytochromes. a missing link protein discovered in the genome of the hyperthermophilic bacterium aquifex aeolicus, however, provides evidence for a close evolutionary relationship between these two cytochromes. the mono-heme cytochrome c(1) from a. aeolicus contains stretches of strong sequence homology toward the e ...	2004	15591339
the cytoskeleton as a regulator and target of biotic interactions in plants.		2004	15591444
the kata catalase gene is regulated by oxyr in both free-living and symbiotic sinorhizobium meliloti.	the characterization of an oxyr insertion mutant provides evidences that kata, which encodes the unique h2o2-inducible hpii catalase, is regulated by oxyr not only in free-living sinorhizobium meliloti but also in symbiotic s. meliloti. moreover, oxyr is expressed independently of exogenous h2o2 and downregulates its own expression in s. meliloti.	2005	15601722
cazfp1, cys2/his2-type zinc-finger transcription factor gene functions as a pathogen-induced early-defense gene in capsicum annuum.	a pepper zinc-finger protein gene, cazfp1 , encoding the cys2/his2-type zinc-finger transcription factor was isolated from pepper leaves inoculated with an avirulent strain bv5-4a of xanthomonas campestris pv. vesicatoria . the cazfp1 protein is a nuclear targeting protein, which functions as a transcriptional regulator. the full-length cazfp1 had no transcriptional activation activity, whereas the c-terminal region of cazfp1 had transactivation activity. the cazfp1 transcripts were constitutive ...	2004	15604723
comprehensive analysis of the extracellular proteins from xanthomonas campestris pv. campestris b100.	the extracellular proteome of xanthomonas campestris pv. campestris (xcc) cultivated in minimal medium was isolated from the cell-free culture supernatant and separated by two-dimensional gel electrophoresis. this technique resolved 97 clearly visible protein spots, which were excised, digested with trypsin and identified on the basis of their peptide mass fingerprints generated by matrix assisted laser desorption/ionisation-time of flight-mass spectrometry. using this approach 87 different prot ...	2005	15619296
the hrpk operon of pseudomonas syringae pv. tomato dc3000 encodes two proteins secreted by the type iii (hrp) protein secretion system: hopb1 and hrpk, a putative type iii translocator.	pseudomonas syringae is a gram-negative bacterial plant pathogen that is dependent on a type iii protein secretion system (ttss) and the effector proteins it translocates into plant cells for pathogenicity. the p. syringae ttss is encoded by hrp-hrc genes that reside in a central region of a pathogenicity island (pai). flanking one side of this pai is the exchangeable effector locus (eel). we characterized the transcriptional expression of the open reading frames (orfs) within the eel of p. syri ...	2005	15629936
a synonymous mutation in yersinia enterocolitica yope affects the function of the yope type iii secretion signal.	yersinia spp. inject virulence proteins called yops into the cytosol of target eukaryotic cells in an effort to evade phagocytic killing via a dedicated protein-sorting pathway termed type iii secretion. previous studies have proposed that, unlike other protein translocation mechanisms, yops are not recognized as substrates for secretion via a solely proteinaceous signal. rather, at least some of this information may be encoded within yop mrna. herein, we report that the first seven codons of yo ...	2005	15629941
evidence for two flagellar stators and their role in the motility of pseudomonas aeruginosa.	pseudomonas aeruginosa is a ubiquitous bacterium capable of twitching, swimming, and swarming motility. in this study, we present evidence that p. aeruginosa has two flagellar stators, conserved in all pseudomonads as well as some other gram-negative bacteria. either stator is sufficient for swimming, but both are necessary for swarming motility under most of the conditions tested, suggesting that these two stators may have different roles in these two types of motility.	2005	15629949
protection of xanthomonas against arsenic toxicity involves the peroxide-sensing transcription regulator oxyr.	arsenic has been shown to mediate its toxicity through induced generation of reactive oxygen species. here, we examined the role of oxidative stress-inducible genes (kata, ahpc and ohr) and their regulators (oxyr and ohrr) in the response to arsenic treatment in a plant pathogenic bacterium, xanthomonas campestris pv. phaseoli (xp). overproduction of peroxide-scavenging enzymes (kata, ahpcf and ohr) did not enhance arsenic tolerance in wild-type xp. furthermore, inactivation of kata, ahpc, ohr, ...	2005	15636745
diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbl) in differently managed agricultural soils.	a pcr-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) form i large-subunit genes (cbbl) as a functional marker of autotrophic bacteria that fix carbon dioxide via the calvin-benson-bassham cycle. we constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbl genes. the diversity of these cbbl genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. ...	2005	15640185
a clp gene homologue belonging to the crp gene family globally regulates lytic enzyme production, antimicrobial activity, and biological control activity expressed by lysobacter enzymogenes strain c3.	lysobacter enzymogenes strain c3, a biological control agent for plant diseases, produces multiple extracellular hydrolytic enzymes and displays antimicrobial activity against various fungal and oomycetous species. however, little is known about the regulation of these enzymes or their roles in antimicrobial activity and biocontrol. a study was undertaken to identify mutants of strain c3 affected in extracellular enzyme production and to evaluate their biocontrol efficacy. a single mini-tn5-lacz ...	2005	15640196
molecular characterization of resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in petroleum-contaminated soil.	pcr assays for analyzing resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in soil were developed. sequence analysis of amplicons showed that the pcr successfully retrieved transporter gene fragments from soil. most of the genes retrieved from petroleum-contaminated soils formed a cluster (cluster pcs) that was distantly related to known transporter genes. competitive pcr showed that the abundance of pcs genes is increased in petroleum-contaminated soil.	2005	15640241
sensitive and specific detection of xanthomonas campestris pv campestris by pcr using species-specific primers based on hrpf gene sequences.	a sensitive and specific assay was developed to detect bacterial black rot of crucifers caused by xanthomonas campestris pv. campestris (x. c. pv. campestris), in cabbage seed and plant. primers xcf and xcr from hrpf homologous to nolx, host recognition protein, were used to amplify a 525 bp dna fragment. pcr technique was applied to detect the pathogen in naturally infected seed and plant of cabbage. the pcr product was only produced from x. c. pv. campestris among 40 isolates of xanthomonas st ...	2004	15646387
in silico analysis of nonribosomal peptide synthetases of xanthomonas axonopodis pv. citri: identification of putative siderophore and lipopeptide biosynthetic genes.	the genomes of the plant pathogens xanthomonas axonopodis (xac) and xanthomonas campestris (xcc) were analysed with the aim of deducing their ability to produce nonribosomal peptides. nonribosomal peptide synthetase (nrps) genes were identified in two separate loci of xac. while the genes of locus 1 are common to both strains, locus 2 was only found in xac. dissection and phylogenetic analysis of the condensation and thioesterase domains of the nrpss of loci 1 and 2 of xac revealed homology, res ...	2004	15646388
induction of rapid detachment in shewanella oneidensis mr-1 biofilms.	active detachment of cells from microbial biofilms is a critical yet poorly understood step in biofilm development. we discovered that detachment of cells from biofilms of shewanella oneidensis mr-1 can be induced by arresting the medium flow in a hydrodynamic biofilm system. induction of detachment was rapid, and substantial biofilm dispersal started as soon as 5 min after the stop of flow. we developed a confocal laser scanning microscopy-based assay to quantify detachment. the extent of bioma ...	2005	15659679
expression profiling of virulence and pathogenicity genes of xanthomonas axonopodis pv. citri.	dna macroarrays of 279 genes of xanthomonas axonopodis pv. citri potentially associated with pathogenicity and virulence were used to compare the transcriptional alterations of this bacterium in response to two synthetic media. data analysis indicated that 31 genes were up-regulated by synthetic medium xvm2, while only 7 genes were repressed. the results suggest that xvm2 could be used as an in vitro system to identify candidate genes involved in pathogenesis of x. axonopodis pv. citri.	2005	15659697
antibacterial activity of seed proteins of robinia pseudoacacia.	a low molecular weight cationic peptide was isolated from robinia pseudoacacia seed and tested in vitro against seven bacteria (corynebacterium michiganense, staphylococcus aureus, bacillus subtilis, erwinia carotovora subsp. carotovora, pseudomonas syringae pv syringae, xanthomonas campestris pv campestris, and escherichia coli). the peptide inhibited the growth of the tested strains. the effective concentrations required for 50% inhibition of bacterial growth ranged between 20 and 120 microg m ...	2005	15664465
the genome sequence of xanthomonas oryzae pathovar oryzae kacc10331, the bacterial blight pathogen of rice.	the nucleotide sequence was determined for the genome of xanthomonas oryzae pathovar oryzae (xoo) kacc10331, a bacterium that causes bacterial blight in rice (oryza sativa l.). the genome is comprised of a single, 4 941 439 bp, circular chromosome that is g + c rich (63.7%). the genome includes 4637 open reading frames (orfs) of which 3340 (72.0%) could be assigned putative function. orthologs for 80% of the predicted xoo genes were found in the previously reported x.axonopodis pv. citri (xac) a ...	2005	15673718
molecular characterization of proteolytic cleavage sites of the pseudomonas syringae effector avrrpt2.	during infection of arabidopsis thaliana, the bacterium pseudomonas syringae pv tomato delivers the effector protein avrrpt2 into the plant cell cytosol. within the plant cell, avrrpt2 undergoes n-terminal processing and causes elimination of arabidopsis rin4. previous work established that avrrpt2 is a putative cysteine protease, and avrrpt2 processing and rin4 elimination require an intact predicted catalytic triad in that avrrpt2. in this work, proteolytic events that depend on avrrpt2 activi ...	2005	15684089
expression of heat-shock genes groesl in xanthomonas campestris is upregulated by clp in an indirect manner.	clp is a homologue of cyclic amp-receptor protein in xanthomonas campestris. in this study, proteomic analysis and western blotting showed that the clp mutant (tc820) of x. campestris synthesizes less groesl proteins than the parental p20h. the groesl upstream regions, nt -583 to -32 (552 bp) and nt -178 to -29 (150 bp) relative to the groesl initiation codon, were cloned for transcriptional fusion assays. the 150-bp region, bearing putative sigma24- and sigma32-binding sites and the circe eleme ...	2005	15686836
regulation of resistance to copper in xanthomonas axonopodis pv. vesicatoria.	copper-resistant strains of xanthomonas axonopodis pv. vesicatoria were previously shown to carry plasmid-borne copper resistance genes related to the cop and pco operons of pseudomonas syringae and escherichia coli, respectively. however, instead of the two-component (coprs and pcors) systems determining copper-inducible expression of the operons in p. syringae and e. coli, a novel open reading frame, copl, was found to be required for copper-inducible expression of the downstream multicopper o ...	2005	15691931
effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria.	soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. we investigated the effects of three factors on viable counts, assessed as numbers of cfu on solid media, and on the phy ...	2005	15691937
genetic and physiological analysis of the major oxyr-regulated kata from xanthomonas campestris pv. phaseoli.	kata encodes the major catalase that accounts for 90 % of the total catalase activity present in xanthomonas campestris pv. phaseoli. kata is located upstream of an orf designated anka encoding a cytoplasmic membrane protein homologous to eukaryotic ankyrin. transcriptional analysis of kata and anka identified two kata transcripts: a major monocistronic kata transcript and a minor bicistronic kata-anka transcript. kata expression was induced in the presence of various oxidants including h2o2, or ...	2005	15699208
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
pseudomonas aeruginosa fiml regulates multiple virulence functions by intersecting with vfr-modulated pathways.	virulence of pseudomonas aeruginosa involves the co-ordinate expression of a range of factors including type iv pili (tfp), the type iii secretion system (ttss) and quorum sensing. tfp are required for twitching motility, efficient biofilm formation, and for adhesion and type iii secretion (tts)-mediated damage to mammalian cells. we describe a novel gene (fiml) that is required for tfp biogenesis and function, for tts and for normal biofilm development in p. aeruginosa. the predicted product of ...	2005	15720546
endocytosis of xanthomonas campestris pathovar campestris lipopolysaccharides in non-host plant cells of nicotiana tabacum.	the specific recognition of phytopathogenic bacteria by plant cells is generally mediated by a number of signal molecules. the elicitor-active lipopolysaccharides (lps) of the phytopathogenic bacterium xanthomonas campestris pv. campestris (x.c.c) are recognized by its non-host plant nicotiana tabacum (n.t.). this lps was purified and labelled with fluorescein isothiocyanate (fitc) for monitoring the fate of these signal molecules in intact plant cells of tobacco. in this study we were able to s ...	2005	15720635
structural analyses of novel glycerophosphorylated alpha-cyclosophorohexadecaoses isolated from x. campestris pv. campestris.	novel periplasmic anionic cyclic glucans produced by xanthomonas campestris pv. campestris were isolated by trichloroacetic acid treatment and various chromatographic techniques. no report has been made on the presence of substituted cyclic glucans of the xanthomonas species. we show, for the first time, that x. campestris pv. campestris produces the anionic cyclic glucans with phosphoglycerol residues, the presence of which can be predicted by analyzing the sequence database with the aid of the ...	2005	15721339
molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria.	we report the cloning and functional characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. this is the first gene of this type from any nematode species. we show that a similar cdna is also present in another closely related species b. mucronatus, but that similar sequences are not present in any other nematode studied to date. the b. xylophilus gene is expressed solely in the oesophageal gland cel ...	2005	15727561
variation in the strength of selected codon usage bias among bacteria.	among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. however, in other species selection appears to have been ineffective. here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. the approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. the ...	2005	15728743
induction of some defense-related genes and oxidative burst is required for the establishment of systemic acquired resistance in capsicum annuum.	the inoculation of primary pepper leaves with an avirulent strain of xanthomonas campestris pv. vesicatoria induced systemic acquired resistance (sar) in the non-inoculated, secondary leaves. this sar response was accompanied by the systemic expression of the defense-related genes, a systemic microoxidative burst generating h2o2, and the systemic induction of both ion-leakage and callose deposition in the non-inoculated, secondary leaves. some defense-related genes including those encoding pr-1, ...	2005	15729568
crystal structure of n-acetylornithine transcarbamylase from xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.	we have identified in xanthomonas campestris a novel n-acetylornithine transcarbamylase that replaces ornithine transcarbamylase in the canonic arginine biosynthetic pathway of several eubacteria. the crystal structures of the protein in the presence and absence of the reaction product, n-acetylcitrulline, were determined. this new family of transcarbamylases lacks the dxxsmg motif that is characteristic of all ornithine transcarbamylases (otcases) and contains a novel proline-rich loop that for ...	2005	15731101
powerful screens for bacterial virulence proteins.		2005	15738387
prokaryotic phylogenies inferred from protein structural domains.	the determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. in this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. the evolution of the structura ...	2005	15741510
the conserved xanthomonas campestris pv. vesicatoria effector protein xopx is a virulence factor and suppresses host defense in nicotiana benthamiana.	nicotiana benthamiana leaves display a visible plant cell death response when infiltrated with a high titer inoculum of the non-host pathogen, xanthomonas campestris pv. vesicatoria (xcv). this visual phenotype was used to identify overlapping cosmid clones from a genomic cosmid library constructed from the xcv strain, gm98-38. individual cosmid clones from the xcv library were conjugated into x. campestris pv. campestris (xcc) and exconjugants were scored for an altered visual high titer inocul ...	2005	15743446
comparative genomic analysis of the ppt23a plasmid family of pseudomonas syringae.	members of the ppt23a plasmid family of pseudomonas syringae play an important role in the interaction of this bacterial pathogen with host plants. complete sequence analysis of several ppt23a family plasmids (pfps) has provided a glimpse of the gene content and virulence function of these plasmids. we constructed a macroarray containing 161 genes to estimate and compare the gene contents of 23 newly analyzed and eight known pfps from 12 pathovars of p. syringae, which belong to four genomospeci ...	2005	15743960
biosynthesis of auxin by the gram-positive phytopathogen rhodococcus fascians is controlled by compounds specific to infected plant tissues.	the role and metabolism of indole-3-acetic acid in gram-negative bacteria is well documented, but little is known about indole-3-acetic acid biosynthesis and regulation in gram-positive bacteria. the phytopathogen rhodococcus fascians, a gram-positive organism, incites diverse developmental alterations, such as leafy galls, on a wide range of plants. phenotypic analysis of a leafy gall suggests that auxin may play an important role in the development of the symptoms. we show here for the first t ...	2005	15746315
poly(a) polymerase modification and reverse transcriptase pcr amplification of environmental rna.	we describe a combination of two established techniques for a novel application for constructing full-length cdna clone libraries from environmental rna. the cdna was cloned without the use of prescribed primers that target specific genes, and the procedure did not involve random priming. purified rna was first modified by addition of a poly(a) tail and then was amplified by using a commercially available reverse transcriptase pcr (rt-pcr) cdna synthesis kit. to demonstrate the feasibility of th ...	2005	15746328
isolation and characterization of novel giant stenotrophomonas maltophilia phage phisma5.	stenotrophomonas maltophilia is one of the most prevalent opportunistic bacteria causing nosocomial infections. it has become problematic because most of the isolates are resistant to multiple antibiotics, and therefore, development of phage therapy has attracted strong attention. in this study, eight s. maltophilia phages were isolated from clinical samples including patient specimens, catheter-related devices, and wastewater. these phages can be divided into four distinct groups based on host ...	2005	15746341
genomic analysis of bacteriophage phijl001: insights into its interaction with a sponge-associated alpha-proteobacterium.	bacteriophage phijl001 infects a novel marine bacterium in the alpha subclass of the proteobacteria isolated from the marine sponge ircinia strobilina. phijl001 is a siphovirus and forms turbid plaques on its host. the genome sequence of phijl001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. the complete genome sequence of phijl001 comprised 63,469 bp with an overall g+c content of 62%. the genome has 91 predicted ...	2005	15746365
molecular genetic evidence for the role of sgt1 in the intramolecular complementation of bs2 protein activity in nicotiana benthamiana.	pepper plants (capsicum annuum) containing the bs2 resistance gene are resistant to strains of xanthomonas campestris pv vesicatoria (xcv) expressing the bacterial effector protein avrbs2. avrbs2 is delivered directly to the plant cell via the type iii protein secretion system (ttss) of xcv. upon recognition of avrbs2 by plants expressing the bs2 gene, a signal transduction cascade is activated leading to a bacterial disease resistance response. here, we describe a novel pathosystem that consist ...	2005	15749757
integrons in xanthomonas: a source of species genome diversity.	integrons are best known for assembling antibiotic resistance genes in clinical bacteria. they capture genes by using integrase-mediated site-specific recombination of mobile gene cassettes. integrons also occur in the chromosomes of many bacteria, notably beta- and gamma-proteobacteria. in a survey of xanthomonas, integrons were found in all 32 strains representing 12 pathovars of two species. their chromosomal location was downstream from the acid dehydratase gene, ilvd, suggesting that an int ...	2005	15755815
detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.	diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. this concept was first demonstrated for the members of the family rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and anima ...	2005	15755957
the capsular polysaccharide biosynthesis of streptococcus pneumoniae serotype 8: functional identification of the glycosyltransferase wcis (cap8h).	cps (capsular polysaccharide) is a major virulence factor in streptococcus pneumoniae. biosynthesis of cps ru (repeat unit) proceeds by sequential transfer of sugar residues from the appropriate sugar donor to an activated lipid carrier by committed gts (glycosyltransferases). while the nucleotide sequence of many cps loci is already known, the real substrate specificity of the hypothetical gts, as well as the sequence of sugar addition is unclear. in the present paper, we report the biochemical ...	2005	15766331
nmr structure note--solution structure of a bacterial bola-like protein xc975 from a plant pathogen xanthomonas campestris pv. campestris.		2005	15772757
pseudoxanthomonas koreensis sp. nov. and pseudoxanthomonas daejeonensis sp. nov.	gram-negative, non-spore-forming, rod-shaped bacteria, t7-09(t) and tr6-08(t), were isolated from soil from a ginseng field in south korea and characterized to determine their taxonomic position. 16s rrna gene sequence analysis showed that the two isolates shared 99.5 % sequence similarity. strains t7-09(t) and tr6-08(t) were shown to belong to the proteobacteria and showed the highest levels of sequence similarity to pseudoxanthomonas broegbernensis dsm 12573(t) (98.1 %), pseudoxanthomonas mexi ...	2005	15774663
identification of a tcpc-tcpq outer membrane complex involved in the biogenesis of the toxin-coregulated pilus of vibrio cholerae.	the toxin-coregulated pilus (tcp) of vibrio cholerae and the soluble tcpf protein that is secreted via the tcp biogenesis apparatus are essential for intestinal colonization. the tcp biogenesis apparatus is composed of at least nine proteins but is largely uncharacterized. tcpc is an outer membrane lipoprotein required for tcp biogenesis that is a member of the secretin protein superfamily. in the present study, analysis of tcpc in a series of strains deficient in each of the tcp biogenesis prot ...	2005	15774863
effects on promoter activity of base substitutions in the cis-acting regulatory element of hrpxo regulons in xanthomonas oryzae pv. oryzae.	in xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight of rice, hrpxo is known to be a transcriptional regulator for the hypersensitive response and pathogenicity (hrp) genes. several hrpxo regulons are preceded by a consensus sequence (ttcgc-n(15)-ttcgc), called the plant-inducible promoter (pip) box, which is required for expression of the gene that follows. thus, the pip box can be an effective marker for screening hrpxo regulons from the genome database. it is not known, ...	2005	15774873
identification of new protein-protein interactions involving the products of the chromosome- and plasmid-encoded type iv secretion loci of the phytopathogen xanthomonas axonopodis pv. citri.	the recently sequenced genome of the bacterial plant pathogen xanthomonas axonopodis pv. citri contains two virb gene clusters, one on the chromosome and one on a 64-kb plasmid, each of which codes for a previously uncharacterized type iv secretion system (t4ss). here we used a yeast two-hybrid assay to identify protein-protein interactions in these two systems. our results revealed interactions between known t4ss components as well as previously uncharacterized interactions involving hypothetic ...	2005	15774874
the type iii-dependent hrp pilus is required for productive interaction of xanthomonas campestris pv. vesicatoria with pepper host plants.	the plant pathogenic bacterium xanthomonas campestris pv. vesicatoria expresses a type iii secretion system that is necessary for both pathogenicity in susceptible hosts and the induction of the hypersensitive response in resistant plants. this specialized protein transport system is encoded by a 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. here we show that x. campestris pv. vesicatoria produces filamentous structures, the hrp pili, at the cell surface under hrp-inducing ...	2005	15774889
caalaat1 catalyzes the alanine: 2-oxoglutarate aminotransferase reaction during the resistance response against tobacco mosaic virus in hot pepper.	hot pepper (capsicum annuum l. cv. bugang) plants exhibit a hypersensitive response (hr) upon infection by tobacco mosaic virus (tmv) pathotype p0. to elucidate molecular mechanism that underlies this resistance, hot pepper cv. bugang leaves were inoculated with tmv-p0 and genes specifically up-regulated during the hr were isolated by differential screening. one of the clones, caalaat1 encoding a putative alanine aminotransferase (ec 2.6.1.2) exhibited organ-specific expression pattern and the t ...	2005	15782348
evolutionary origins of genomic repertoires in bacteria.	explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. in eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (lgt) can also contribute substantially to genome contents. to determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the gamma-proteobacteria. we show that, although the ...	2005	15799709
functional insights from the distribution and role of homopeptide repeat-containing proteins.	expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ...	2005	15805494
comprehensive characterization of the contribution of individual sigb-dependent general stress genes to stress resistance of bacillus subtilis.	the sigma(b)-dependent general stress regulon of bacillus subtilis comprises more than 150 members. induction of this regulon by imposition of environmental or metabolic stress confers multiple, nonspecific, and preemptive stress resistance to nongrowing, nonsporulated cells of b. subtilis. in this study we performed a regulon-wide phenotypic screening analysis to determine the stress sensitivity profiles of 94 mutants defective in candidate members of the general stress regulon that were previo ...	2005	15805528
comparative analyses of xanthomonas and xylella complete genomes.	computational analyses of four bacterial genomes of the xanthomonadaceae family reveal new unique genes that may be involved in adaptation, pathogenicity, and host specificity. the xanthomonas genus presents 3636 unique genes distributed in 1470 families, while xylella genus presents 1026 unique genes distributed in 375 families. among xanthomonas-specific genes, we highlight a large number of cell wall degrading enzymes, proteases, and iron receptors, a set of energy metabolism genes, second co ...	2005	15805778
dimerization of the bacterial effector protein avrbs3 in the plant cell cytoplasm prior to nuclear import.	the effector protein avrbs3 from the bacterial phytopathogen xanthomonas campestris pv. vesicatoria is translocated into the plant cell where it specifically induces hypertrophy symptoms or the hypersensitive reaction. activity of avrbs3 depends on nuclear localization signals (nlss) and an acidic activation domain, suggesting a role in regulation of plant transcription. here, we show that avrbs3 dimerizes in the plant cell prior to its nuclear import. avrbs3 deletion derivatives were tested in ...	2005	15807781
co-evolution of trna 3' trailer sequences with 3' processing enzymes in bacteria.	maturation of the trna 3' terminus is a complicated process in bacteria. usually, it is initiated by an endonucleolytic cleavage carried out by rnase e and z in different bacteria. in escherichia coli, rnase e cleaves au-rich sequences downstream of trna, producing processing intermediates with a few extra residues at the 3' end; these are then removed by exoribonuclease trimming to generate the mature 3' end. here we show that essentially all e. coli trna precursors contain a potential rnase e ...	2005	15811923
exposure to cadmium elevates expression of genes in the oxyr and ohrr regulons and induces cross-resistance to peroxide killing treatment in xanthomonas campestris.	cadmium is an important heavy metal pollutant. for this study, we investigated the effects of cadmium exposure on the oxidative stress responses of xanthomonas campestris, a soil and plant pathogenic bacterium. the exposure of x. campestris to low concentrations of cadmium induces cross-protection against subsequent killing treatments with either h2o2 or the organic hydroperoxide tert-butyl hydroperoxide (tbooh), but not against the superoxide generator menadione. the cadmium-induced resistance ...	2005	15812010
xanthomonas axonopodis pv. phaseoli var. fuscans is aggregated in stable biofilm population sizes in the phyllosphere of field-grown beans.	the occurrence of "xanthomonas axonopodis pv. phaseoli var. fuscans" (proposed name) populations as biofilms on bean leaves was investigated during three field experiments on plots established with naturally contaminated bean seeds. behavior of aggregated versus solitary populations was determined by quantification of culturable cells in different fractions of the epiphytic population separated by particle size. x. axonopodis pv. phaseoli var. fuscans population dynamic studies confirmed an asym ...	2005	15812033
characterization of a mobile clpl gene from lactobacillus rhamnosus.	two genes encoding clpl atpase proteins were identified in a probiotic lactobacillus rhamnosus strain, e-97800. sequence analyses revealed that the genes, designated clpl1 and clpl2, share 80% identity. the clpl2 gene showed the highest degree of identity (98.5%) to a clpl gene from lactobacillus plantarum wcfsi, while it was not detected in three other l. rhamnosus strains studied. according to northern analyses, the expression of clpl1 and the clpl2 were induced during heat shock by > 20- and ...	2005	15812039