Publications

lempk3 is a mitogen-activated protein kinase with dual specificity induced during tomato defense and wounding responses.	mitogen-activated protein (map) kinase cascades are readily activated during the response of plants to avirulent pathogens or to pathogen-derived elicitors. here we show that the tomato map kinase lempk3 is specifically induced at the mrna level during elicitation of the hypersensitive response in resistant plants infected by avirulent strains of the phytopathogenic bacteria xanthomonas campestris pv. vesicatoria and pseudomonas syringae pv. tomato, as well as upon treatment with the fungal elic ...	2004	14742423
cell-cell signaling controls xylella fastidiosa interactions with both insects and plants.	xylella fastidiosa, which causes pierce's disease of grapevine and other important plant diseases, is a xylem-limited bacterium that depends on insect vectors for transmission. although many studies have addressed disease symptom development and transmission of the pathogen by vectors, little is known about the bacterial mechanisms driving these processes. recently available x. fastidiosa genomic sequences and molecular tools have provided new routes for investigation. here, we show that a diffu ...	2004	14755059
distribution and phylogenetic analysis of family 19 chitinases in actinobacteria.	in organisms other than higher plants, family 19 chitinase was first discovered in streptomyces griseus hut6037, and later, the general occurrence of this enzyme in streptomyces species was demonstrated. in the present study, the distribution of family 19 chitinases in the class actinobacteria and the phylogenetic relationship of actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. forty-nine strains were chosen to cover almost all the suborders of ...	2004	14766598
importance of opghxcv of xanthomonas campestris pv. vesicatoria in host-parasite interactions.	tn5 insertion mutants of xanthomonas campestris pv. vesicatoria were inoculated into tomato and screened for reduced virulence. one mutant exhibited reduced aggressiveness and attenuated growth in planta. southern blot analyses indicated that the mutant carried a single tn5 insertion not associated with previously cloned pathogenicity-related genes of x. campestris pv. vesicatoria. the wild-type phenotype of this mutant was restored by one recombinant plasmid (popg361) selected from a genomic li ...	2004	14964529
nopl, an effector protein of rhizobium sp. ngr234, thwarts activation of plant defense reactions.	bacterial effector proteins delivered into eukaryotic cells via bacterial type iii secretion systems are important virulence factors in plant-pathogen interactions. type iii secretion systems have been found in rhizobium species that form symbiotic, nitrogen-fixing associations with legumes. one such bacterium, rhizobium sp. ngr234, secretes a number of type iii effectors, including nodulation outer protein l (nopl, formerly y4xl). here, we show that expression of nopl in tobacco (nicotiana taba ...	2004	14966249
antifungal activity of beta-asarone from rhizomes of acorus gramineus.	an antifungal substance was isolated from the extract of acorus gramineus using various chromatographic procedures. the antibiotic was identified as beta-asarone, cis-2,4,5-trimethoxy-1-propenylbenzene, on the basis of the high-resolution ei-mass, nmr, and uv spectral data. beta-asarone completely inhibited mycelial growth of some plant pathogenic fungi, cladosporium cucumerinum,colletotrichum orbiculare, magnaporthe grisea, and pythium ultimum, in a range of 0.5-30 microg/ml. the growth of baci ...	2004	14969530
evidence for hrpxo-dependent expression of type ii secretory proteins in xanthomonas oryzae pv. oryzae.	xanthomonas oryzae pv. oryzae is a causal agent of bacterial leaf blight of rice. recently, an efficient hrp-inducing medium, xom2, was established for this bacterium. in this medium, more than 10 proteins were secreted from the wild-type strain of x. oryzae pv. oryzae. many of these proteins disappeared or decreased in amount in culture on xom2 when incubated with the strain that has a mutation in the hrp regulatory gene. interestingly, the secretory protein profile of a mutant lacking a type i ...	2004	14973015
genomic and genetic analysis of bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.	liu et al. recently described a group of related temperate bacteriophages that infect bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (liu et al., science 295: 2091-2094, 2002). tropism switching results from the introduction of single nucleotide substitutions at defined locations in the vr1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria ...	2004	14973019
transcriptional profiling of caulobacter crescentus during growth on complex and minimal media.	microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (pye) and minimal salts medium with glucose or xylose as the carbon source. nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. the differentially expressed genes included many encoding transport systems, most notably di ...	2004	14973021
identification and functional characterization of the lactococcus lactis rfb operon, required for dtdp-rhamnose biosynthesis.	dtdp-rhamnose is an important precursor of cell wall polysaccharides and rhamnose-containing exopolysaccharides (eps) in lactococcus lactis. we cloned the rfbacbd operon from l. lactis mg1363, which comprises four genes involved in dtdp-rhamnose biosynthesis. when expressed in escherichia coli, the lactococcal rfbacbd genes could sustain heterologous production of the shigella flexneri o antigen, providing evidence of their functionality. overproduction of the rfbac proteins in l. lactis resulte ...	2004	14973085
evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of paederus fuscipes beetles.	pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. it is used by apparently all members of the rove beetle genera paederus and paederidus as a chemical defense against predators. however, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. we have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-uncultu ...	2004	14973122
poplar peroxiredoxin q. a thioredoxin-linked chloroplast antioxidant functional in pathogen defense.	peroxiredoxins are ubiquitous thioredoxin- or glutaredoxin-dependent peroxidases, the function of which is to destroy peroxides. peroxiredoxin q, one of the four plant subtypes, is a homolog of the bacterial bacterioferritin comigratory proteins. we show here that the poplar (populus tremula x populus tremuloides) protein acts as a monomer with an intramolecular disulfide bridge between two conserved cysteines. a wide range of electron donors and substrates was tested. unlike type ii peroxiredox ...	2004	14976238
tetracycline and streptomycin resistance genes, transposons, and plasmids in salmonella enterica isolates from animals in italy.	fifty-eight multidrug-resistant salmonella enterica strains of 20 serotypes, isolated from animal sources in italy, were analyzed for tet(a) and stra-strb, conferring tetracycline and streptomycin resistance, respectively. the stra and strb genes were highly prevalent in salmonella strains of our collection, being detected in 84% of the streptomycin-resistant strains. in many strains, the stra and strb genes were linked to a particular tn5393-derivative transposon characterized by the presence o ...	2004	14982782
identification of a novel pathogen-induced gene encoding a leucine-rich repeat protein expressed in phloem cells of capsicum annuum.	the calrr1 gene, expressed in pepper leaves following infection by xanthomonas campestris pv. vesicatoria, encodes a secreted leucine-rich repeat (lrr) with five tandem repeats of a 24-amino-acid lrr motif. northern blot analyses revealed that calrr1 is not constitutively expressed in pepper plants, but is strongly induced upon the infection by x. campestris pv. vesicatoria, phytophthora capsici, colletotrichum coccodes and colletotrichum gloeosporioides on leaves. calrr1 was not systemically in ...	2004	14984927
interaction between a geminivirus replication protein and the plant sumoylation system.	geminiviruses are small dna viruses that replicate in nuclei of infected plant cells after accumulation of host replication machinery. tomato golden mosaic virus (tgmv) and tomato yellow leaf curl sardinia virus (tylcsv) encode a protein, repac1 (or rep), that is essential for viral replication. rep/repac1 is an oligomeric protein that binds to double-stranded dna, catalyzes cleavage and ligation of single-stranded dna, and is sufficient for host induction. it also interacts with several host pr ...	2004	14990696
the pko2 linear plasmid prophage of klebsiella oxytoca.	temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only phages n15 and py54 are known to have a linear plasmid prophage with closed hairpin telomeres. we report here the complete nucleotide sequence of the 51,601-bp klebsiella oxytoca linear plasmid pko2, and we demonstrate experimentally that it is also a prophage. we call this bacteriophage phiko2. an analysis of the 64 predicted phiko2 genes indicate that it is a fairly close relative of phage n15; they share ...	2004	14996813
in vitro mutagenesis of xanthomonas campestris alpha-amylase gene by partially replacing deoxythymidine triphosphate with 5-bromo-2'-deoxyuridine-5'-triphosphate using a pcr technique.	three mutants of the wild type alpha-amylase gene from xanthomonas campestris pv. campestris 8004 were obtained using a pcr technique in which deoxythymidine triphosphate (dttp) was partially replaced by 5-bromo-2'-deoxyuridine-5'-triphosphate (brdutp), at an optimal dttp:brdutp ratio of 1000:1. of thre three mutants that were obtained and which were sequenced, one mutant with 40 times higher activity than the wild type alpha-amylase gene product was obtained by using primary pcr products as a t ...	2004	15000487
visualization of the phylogenetic content of five genomes using dekapentagonal maps.	the methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. if the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. analyses of genomes representing five photosynthetic ...	2004	15003123
[the gene wxca of xanthomonas campestris pv. campestris 8004 strain involved in eps yield].	xanthomonas campestris pv. campestris (xcc), the pathogenic agent of black rot disease in cruciferous plants, produces large amount of extracellular polysaccharide (eps), which has found wide applications in industry. for the great commercial value of the xanthan gum, many of the genes involved in eps biosynthesis have been cloned and the mechanism of eps biosynthesis also has been studied. in order to clone genes involved in eps biosynthesis, xcc wild-type strain 8004 was mutagenized with trans ...	2004	15968974
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
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
comparative genomics of gene-family size in closely related bacteria.	the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.	2004	15059260
organization of lin genes and is6100 among different strains of hexachlorocyclohexane-degrading sphingomonas paucimobilis: evidence for horizontal gene transfer.	the organization of lin genes and is6100 was studied in three strains of sphingomonas paucimobilis (b90a, sp+, and ut26) which degraded hexachlorocyclohexane (hch) isomers but which had been isolated at different geographical locations. dna-dna hybridization data revealed that most of the lin genes in these strains were associated with is6100, an insertion sequence classified in the is6 family and initially found in mycobacterium fortuitum. eleven, six, and five copies of is6100 were detected in ...	2004	15060023
characterization of the cis-acting regulatory element controlling hrpb-mediated activation of the type iii secretion system and effector genes in ralstonia solanacearum.	the ability of ralstonia solanacearum to cause disease on plants depends on its type iii secretion system (ttss) encoded by hrp genes. the expression of hrp genes and known ttss substrates is coordinately regulated by hrpb, a member of the arac family of transcriptional regulators. two hrpb-regulated promoters (hrpy and popabc) were characterized by deletion analysis, and the hrpb-dependent activation of these promoters was found to be conferred by a 25-nucleotide dna element, the hrp(ii) box (t ...	2004	15060033
fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy.	a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ...	2004	15060178
the oligopeptide permease (opp) of the plant pathogen xanthomonas axonopodis pv. citri.	the oligopeptide permease (opp), a protein-dependent abc transporter, has been found in the genome of xanthomonas axonopodis pv. citri ( xac), but not in xanthomonas campestris pv. campestris ( xcc). sequence analysis indicated that 4 opp genes ( oppa, oppb, oppc, oppd/f), located in a 33.8-kbp dna fragment present only in the xac genome, are arranged in an operon-like structure and share highest sequence similarities with streptomyces roseofulvus orthologs. nonetheless, analyses of the gc conte ...	2004	15060731
g-primer: greedy algorithm for selecting minimal primer set.	g-primer, a web-based primer design program, has been developed to compute a minimal primer set specifically annealed to all the open reading frames in a given microbial genome. this program has been successfully used in the microarray experiment for analyzing the expression of genes in the xanthomonas campestris genome. availability: it is available at http://mammoth.bii.a-star.edu.sg/gprimer/. its source code is available upon request.	2004	15073009
divergence and redundancy of 16s rrna sequences in genomes with multiple rrn operons.	the level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16s rrna-based methods. furthermore, the occurrence of widespread horizontal gene transfer (hgt) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. for this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16s rrna sequences were evaluated. bacterial genomes display up to 15 operons ...	2004	15090503
conserved glycines in the c terminus of minc proteins are implicated in their functionality as cell division inhibitors.	alignment of 36 minc sequences revealed four completely conserved c-terminal glycines. as minc inhibits cytokinesis in neisseria gonorrhoeae and escherichia coli, the functional importance of these glycines in n. gonorrhoeae minc (minc(ng)) and e. coli minc (minc(ec)) was investigated through amino acid substitution by using site-directed mutagenesis. each mutant was evaluated for its ability to arrest cell division and to interact with itself and mind. in contrast to overexpression of wild-type ...	2004	15090526
capsicum annuum tobacco mosaic virus-induced clone 1 expression perturbation alters the plant's response to ethylene and interferes with the redox homeostasis.	capsicum annuum tobacco mosaic virus (tmv)-induced clone 1 (catin1) gene was expressed early during incompatible interaction of hot pepper (caspsicum annuum) plants with tmv and xanthomonas campestris. rna-blot analysis showed that catin1 gene was expressed only in roots in untreated plants and induced mainly in leaf in response to ethylene, nacl, and methyl viologen but not by salicylic acid and methyl jasmonate. the ethylene dependence of catin1 induction upon tmv inoculation was demonstrated ...	2004	15107506
functional dissection of the xpsn (gspc) protein of the xanthomonas campestris pv. campestris type ii secretion machinery.	type ii secretion machinery is composed of 12 to 15 proteins for translocating extracellular proteins across the outer membrane. xpsl, xpsm, and xpsn are components of such machinery in the plant pathogen xanthomonas campestris pv. campestris. all are bitopic cytoplasmic-membrane proteins, each with a large c-terminal periplasmic domain. they have been demonstrated to form a dissociable ternary complex. by analyzing the c-terminally truncated xpsn and phoa fusions, we discovered that truncation ...	2004	15126454
evaluation of xanthan and highly substituted galactomannan from m. scabrella as a sustained release matrix.	a highly substituted galactomannan (g) from mimosa scabrella bentham (man:gal 1.1:1), isolated from the seeds of a brazilian leguminous tree and xanthan (x), an exopolysaccharide secreted by xanthomonas campestris (keltrol), were evaluated as a hydrophilic matrix system (xg) for controlled release (cr) of diclofenac sodium (ds) in tablets and capsules. the performance of xg (2:1) matrices containing 50 mg (a) or 100 mg (b) of ds was compared with a commercial cr product of ds. the drug release s ...	2004	15129986
the role of the jasmonate response in plant susceptibility to diverse pathogens with a range of lifestyles.	plants defend themselves against attack from insects and pathogens with various resistance strategies. the jasmonate and salicylate signaling pathways are two induced responses that protect plants against these attackers. knowledge of the range of organisms that are affected by each response is important for understanding how plants coordinate their defenses against multiple attackers and the generality of effect of different resistance mechanisms. the jasmonate response is known to protect plan ...	2004	15133157
bacterial signal transduction network in a genomic perspective.	bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. the complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. comparative studies revealed certain general trends in the organization of diverse signalling systems. these include (i) modular structure of signalling proteins; (ii) comm ...	2004	15142243
the pseudomonas syringae hopptov protein is secreted in culture and translocated into plant cells via the type iii protein secretion system in a manner dependent on the shcv type iii chaperone.	the bacterial plant pathogen pseudomonas syringae depends on a type iii protein secretion system and the effector proteins that it translocates into plant cells to cause disease and to elicit the defense-associated hypersensitive response on resistant plants. the availability of the p. syringae pv. tomato dc3000 genome sequence has resulted in the identification of many novel effectors. we identified the hopptov effector gene on the basis of its location next to a candidate type iii chaperone (t ...	2004	15150250
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
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
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
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
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
plant-microbe interactions: identification of epiphytic bacteria and their ability to alter leaf surface permeability.	bacteria were either isolated from leaf surfaces of hedera helix or obtained from a culture collection in order to analyse their effect on barrier properties of isolated hedera and prunus laurocerasus cuticles. on the basis of the 16s rdna sequences the genera of the six bacterial isolates from hedera were identified as pseudomonas sp., stenotrophomonas sp. and achromobacter. water permeability of cuticles isolated from h. helix was measured before and after inoculation with the six bacterial st ...	2005	15819920
molecular properties of the xanthomonas avrrxv effector and global transcriptional changes determined by its expression in resistant tomato plants.	the xanthomonas campestris pv. vesicatoria avirulence gene avrrxv specifies resistance on the tomato line hawaii 7998 by interacting with three nondominant plant resistance genes. avrrxv molecular properties that impinge on its avirulence activity were characterized and transcriptional changes caused by avrrxv expression in resistant tomato plants were extensively examined. avrrxv localized predominantly to the cytoplasm and possibly in association with plasma and nuclear membranes in both resis ...	2005	15828682
identification of a new quorum-sensing-controlled virulence factor in erwinia carotovora subsp. atroseptica secreted via the type ii targeting pathway.	two-dimensional polyacrylamide gel electrophoresis of the secreted proteins of erwinia carotovora subsp. atroseptica revealed a low-abundance protein that was identified by mass spectrometry as a homologue of a xanthomonas campestris avirulence protein with unknown function. the predicted svx protein has an n-terminal signal sequence and zinc binding-region signature, and the mature protein is post-translationally modified. a 2d difference gel electrophoresis (dige) showed that the protein is se ...	2005	15828685
three prochlorococcus cyanophage genomes: signature features and ecological interpretations.	the oceanic cyanobacteria prochlorococcus are globally important, ecologically diverse primary producers. it is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. here we present an analysis of genomes from three prochlorococcus phages: a podovirus and two myoviruses. the morphology, overall genome features, and gene content of these phages suggest that they are quite similar to t7-like (p-ssp7) and t4-like (p-ssm2 and p-ssm4) ph ...	2005	15828858
novel roles of ohrr-ohr in xanthomonas sensing, metabolism, and physiological adaptive response to lipid hydroperoxide.	lipid hydroperoxides are highly toxic to biological systems. here, the xanthomonas campestris pv. phaseoli sensing and protective systems against linoleic hydroperoxide (looh) were investigated by examining the phenotypes, biochemical and regulatory characteristics of various xanthomonas mutants in known peroxide resistance pathways. analysis of looh resistance levels indicates that both alkyl hydroperoxide reductase (ahpc) and organic hydroperoxide resistance enzyme (ohr) have important and non ...	2005	15838057
spoilage of vegetable crops by bacteria and fungi and related health hazards.	after harvest, vegetables are often spoiled by a wide variety of microorganisms including many bacterial and fungal species. the most common bacterial agents are erwinia carotovora, pseudomonas spp., corynebacterium, xanthomonas campestris, and lactic acid bacteria with e. carotovora being the most common, attacking virtually every vegetable type. fungi commonly causing spoilage of fresh vegetables are botrytis cinerea, various species of the genera alternaria, aspergillus, cladosporium, colleto ...	2005	15839403
synthesis and characterization of novel 6-fluoro-4-piperidinyl-1,2-benzisoxazole amides and 6-fluoro-chroman-2-carboxamides: antimicrobial studies.	novel derivatives of 6-fluoro-4-piperidinyl-1,2-benzisoxazole amides 4(i-vi) were obtained by the condensation of different acid chlorides with 6-fluoro-3-piperidin-4yl-benzo[d]isoxazole. also, 6-fluoro-chroman-2-carboxamides 6(i-iii) were synthesized by using nebulic acid chloride with different amines in presence of triethylamine as acid scavenger and dichloroethane as solvent. the synthesized compounds were characterized by ir, 1h nmr, and chn analysis. these molecules were evaluated for thei ...	2005	15846867
antisense suppression of a (+)-delta-cadinene synthase gene in cotton prevents the induction of this defense response gene during bacterial blight infection but not its constitutive expression.	in cotton (gossypium hirsutum) the enzyme (+)-delta-cadinene synthase (cdns) catalyzes the first committed step in the biosynthesis of cadinane-type sesquiterpenes, such as gossypol, that provide constitutive and inducible protection against pests and diseases. a cotton cdna clone encoding cdns (cdn1-c4) was isolated from developing embryos and functionally characterized. southern analysis showed that cdns genes belong to a large multigene family, of which five genomic clones were studied, inclu ...	2005	15849309
characterization of a recombinant type ii 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from helicobacter pylori.	dah7p (3-deoxy-d-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (pep) and d-erythrose 4-phosphate (e4p) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. previous work has identified two families of dah7p synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type i paralogues from escherichia coli ...	2005	15853768
biofilm formation and sloughing in serratia marcescens are controlled by quorum sensing and nutrient cues.	we describe here a role for quorum sensing in the detachment, or sloughing, of serratia marcescens filamentous biofilms, and we show that nutrient conditions affect the biofilm morphotype. under reduced carbon or nitrogen conditions, s. marcescens formed a classical biofilm consisting of microcolonies. the filamentous biofilm could be converted to a microcolony-type biofilm by switching the medium after establishment of the biofilm. similarly, when initially grown as a microcolony biofilm, s. ma ...	2005	15866935
bacillus subtilis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase revisited: resolution of two long-standing enigmas.	the mono/bifunctional and metallo/non-metallo properties of bacillus subtilis dahps (3-deoxy-d-arabino-heptulosonate 7-phosphate synthase) have been controversial for several decades. the present study investigated the dahpss from both the b. subtilis parent marburg strain and the derivative strain 168 in detail and clarified the above two long-standing questions. the dahpss from the parent and the derivative 168 strains have identical sequence and are both bifunctional enzymes with a cm (choris ...	2005	15869469
reduced genetic variation occurs among genes of the highly clonal plant pathogen xanthomonas axonopodis pv. vesicatoria, including the effector gene avrbs2.	the bacterial plant pathogen xanthomonas axonopodis pv. vesicatoria, also known as xanthomonas campestris pv. vesicatoria group a, is the causal agent of bacterial spot in pepper and tomato. in order to test different models that may explain the coevolution of avrbs2 with its host plants, we sequenced avrbs2 and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55 x. axonopodis pv. vesicatoria strains collected from diseased peppers. we found an extreme lack of genetic va ...	2005	15870329
the unique glutathione reductase from xanthomonas campestris: gene expression and enzyme characterization.	the glutathione reductase gene, gor, was cloned from the plant pathogen xanthomonas campestris pv. phaseoli. its gene expression and enzyme characteristics were found to be different from those of previously studied homologues. northern blot hybridization, promoter-lacz fusion, and enzyme assay experiments revealed that its expression, unlike in escherichia coli, is oxyr-independent and constitutive upon oxidative stress conditions. the deduced amino acid sequence shows a unique nadph binding mo ...	2005	15883020
genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes.	bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (phx) genes and several genomic properties. there is a striking difference in the status of phx ribosomal protein (rp) genes where the archaeal genome generally encodes more rp genes and fewer phx rps compared with bacterial genomes. the increase in rps in archaea and eukaryotes compared with that in bacteria may reflect a more complex set of interactions in archaea and eukaryotes in regulating tr ...	2005	15883367
an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus.	dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ...	2005	15886391
bacteriophage control of foodborne bacteriat.	bacteriophages are measurable components of the natural microflora in the food production continuum from the farm to the retail outlet. phages are remarkably stable in these environments and are readily recovered from soil, sewage, water, farm and processing plant effluents, feces, and retail foods. purified high-titer phage lysates have been used for the species-specific control of bacteria during the pre- and postharvest phases of food production and storage. for example, the inhibition of the ...	2005	15895751
comparative and functional genomic analyses of the pathogenicity of phytopathogen xanthomonas campestris pv. campestris.	xanthomonas campestris pathovar campestris (xcc) is the causative agent of crucifer black rot disease, which causes severe losses in agricultural yield world-wide. this bacterium is a model organism for studying plant-bacteria interactions. we sequenced the complete genome of xcc 8004 (5,148,708 bp), which is highly conserved relative to that of xcc atcc 33913. comparative genomics analysis indicated that, in addition to a significant genomic-scale rearrangement cross the replication axis betwee ...	2005	15899963