Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| bacillus subtilis gene cluster involved in calcium carbonate biomineralization. | calcium carbonate precipitation, a widespread phenomenon among bacteria, has been investigated due to its wide range of scientific and technological implications. nevertheless, little is known of the molecular mechanisms by which bacteria foster calcium carbonate mineralization. in our laboratory, we are studying calcite formation by bacillus subtilis, in order to identify genes involved in the biomineralization process. a previous screening of uv mutants and of more than one thousand mutants ob ... | 2007 | 17085570 |
| a mutant alpha-amylase with only part of the catalytic domain and its structural implication. | a truncated mutant alpha-amylase, xa-s2, was obtained from xanthomonas campestris wild type alpha-amylases (xa-wt) through random mutagenesis that contained 167 amino acid residues (approx 65% shorter than that of xa-wt). secondary structure prediction implied that xa-s2, would be unable to form the whole (beta/alpha)(8)-barrel catalytic domain and did not have the three conserved catalytic residues of wild type alpha-amylase, but it still displays the starch-hydrolyzing activity. xa-s2 was prep ... | 2007 | 17091385 |
| dynamic state of dna topology is essential for genome condensation in bacteria. | in bacteria, dps is one of the critical proteins to build up a condensed nucleoid in response to the environmental stresses. in this study, we found that the expression of dps and the nucleoid condensation was not simply correlated in escherichia coli, and that fis, which is an e. coli (gamma-proteobacteria)-specific nucleoid protein, interfered with the dps-dependent nucleoid condensation. atomic force microscopy and northern blot analyses indicated that the inhibitory effect of fis was due to ... | 2006 | 17093499 |
| expression, purification, and characterization of an aminopeptidase (xac2987) with broad specificity from xanthomonas axonopodis pv. citri. | we report here, the cloning, expression, and purification of a broad specificity aminopeptidase from xanthomonas campestris pv. citri in fusion with a hexa-histidine tag at the n-terminal portion of the protein to facilitate purification. the protein was expressed in the soluble fraction and could be purified in one step by imac, yielding approximately 50mg pure protein per liter of cells. we show that the protein is folded and presents aminopeptidase activity against synthetic substrates. also, ... | 2007 | 17110128 |
| effect of acidic electrolyzed water on the viability of bacterial and fungal plant pathogens and on bacterial spot disease of tomato. | acidic electrolyzed water (aew), known to have germicidal activity, was obtained after electrolysis of 0.045% aqueous solution of sodium chloride. freshly prepared aew (ph 2.3-2.6, oxidation-reduction potential 1007-1025 mv, and free active chlorine concentration 27-35 ppm) was tested in vitro and (or) on tomato foliage and seed surfaces for its effects on the viability of plant pathogen propagules that could be potential seed contaminants. foliar sprays of aew were tested against bacterial spot ... | 2006 | 17110959 |
| catalase (kata) and alkyl hydroperoxide reductase (ahpc) have compensatory roles in peroxide stress resistance and are required for survival, persistence, and nasal colonization in staphylococcus aureus. | oxidative-stress resistance in staphylococcus aureus is linked to metal ion homeostasis via several interacting regulators. in particular, perr controls the expression of a regulon of genes, many of which encode antioxidants. two perr regulon members, ahpc (alkylhydroperoxide reductase) and kata (catalase), show compensatory regulation, with independent and linked functions. an ahpc mutation leads to increased h2o2 resistance due to greater kata expression via relief of perr repression. moreover ... | 2007 | 17114262 |
| catalase (kata) and alkyl hydroperoxide reductase (ahpc) have compensatory roles in peroxide stress resistance and are required for survival, persistence, and nasal colonization in staphylococcus aureus. | oxidative-stress resistance in staphylococcus aureus is linked to metal ion homeostasis via several interacting regulators. in particular, perr controls the expression of a regulon of genes, many of which encode antioxidants. two perr regulon members, ahpc (alkylhydroperoxide reductase) and kata (catalase), show compensatory regulation, with independent and linked functions. an ahpc mutation leads to increased h2o2 resistance due to greater kata expression via relief of perr repression. moreover ... | 2007 | 17114262 |
| the transcription factors wrky11 and wrky17 act as negative regulators of basal resistance in arabidopsis thaliana. | transcription factors are believed to play a pivotal role in the activation and fine-tuning of plant defense responses, but little is known about the exact function of individual transcription factors in this process. we analyzed the role of the iid subfamily of wrky transcription factors in the regulation of basal resistance to pseudomonas syringae pv tomato (pst). the expression of four members of the subfamily was induced upon challenge with virulent and avirulent strains of pst. mutant analy ... | 2006 | 17114354 |
| solution structure of family 21 carbohydrate-binding module from rhizopus oryzae glucoamylase. | cbms (carbohydrate-binding modules) function independently to assist carbohydrate-active enzymes. family 21 cbms contain approx. 100 amino acid residues, and some members have starchbinding functions or glycogen-binding activities. we report here the first structure of a family 21 cbm from the sbd (starch-binding domain) of rhizopus oryzae glucoamylase (rocbm21) determined by nmr spectroscopy. this cbm has a beta-sandwich fold with an immunoglobulin-like structure. ligand-binding properties of r ... | 2007 | 17117925 |
| operon prediction for sequenced bacterial genomes without experimental information. | various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. in this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a bayesian hidden markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. the prediction algorithm performs as well ... | 2007 | 17122389 |
| operon prediction for sequenced bacterial genomes without experimental information. | various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. in this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a bayesian hidden markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. the prediction algorithm performs as well ... | 2007 | 17122389 |
| protein homology network families reveal step-wise diversification of type iii and type iv secretion systems. | from the analysis of 251 prokaryotic genomes stored in public databases, the 761,260 deduced proteins were used to reconstruct a complete set of bacterial proteic families. using the new overlap algorithm, we have partitioned the protein homology network (phn), where the proteins are the nodes and the links represent homology relationships. the algorithm identifies the densely connected regions of the phn that define the families of homologous proteins, here called phn-families, recognizing the ... | 2006 | 17140285 |
| expression, crystallization and preliminary crystallographic studies of a novel bifunctional n-acetylglutamate synthase/kinase from xanthomonas campestris homologous to vertebrate n-acetylglutamate synthase. | a novel n-acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate n-acetylglutamate synthases was identified in xanthomonas campestris. the protein was overexpressed, purified and crystallized. the crystals belong to the hexagonal space group p6(2)22, with unit-cell parameters a = b = 134.60, c = 192.11 a, and diffract to about 3.0 a resolution. selenomethionine-substituted recombinant protein was produced and selenomethionine substitution w ... | 2006 | 17142901 |
| crystallization and preliminary x-ray analysis of xc1015, a histidine triad-like protein from xanthomonas campestris. | histidine-triad (hit) proteins are a superfamily of nucleotide hydrolases and transferases that contain a conserved hphi hphi hphi phi motif (where phi is a hydrophobic amino acid) and are found in a variety of organisms. in addition to binding to a variety of nucleotides, other biological functions of the hit superfamily proteins have been discovered and hit malfunction has been implicated in several human diseases. structural studies of hit superfamily proteins are thus of particular interest. ... | 2006 | 17142912 |
| evolution of enzymatic activities in the enolase superfamily: l-fuconate dehydratase from xanthomonas campestris. | many members of the mechanistically diverse enolase superfamily have unknown functions. in this report we use both genome (operon) context and screening of a library of acid sugars to assign the l-fuconate dehydratase (fucd) function to a member of the mandelate racemase (mr) subgroup of the superfamily encoded by the xanthomonas campestris pv. campestris str. atcc 33913 genome (gi:21233491). orthologues of fucd are found in both bacteria and eukaryotes, the latter including the rts beta protein ... | 2006 | 17144652 |
| coverage of whole proteome by structural genomics observed through protein homology modeling database. | we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ... | 2006 | 17146617 |
| role of a novel pathogen-induced pepper c3-h-c4 type ring-finger protein gene, carfpi, in disease susceptibility and osmotic stress tolerance. | limited information is available about the roles of ring-finger proteins in plant defense. a pepper carfp1 encoding the c3-h-c4 type ring-finger protein that physically interacted with the basic pr-1 protein cabpr1 was isolated from pepper leaves infected by xanthomonas campestris pv. vesicatoria. the carfp1 protein has vwfa domain, and n-terminal serine-rich and c-terminal cysteine-rich regions. the carfp1 transcripts accumulated earlier than did those of the basic pr-1 gene cabpr1 during the i ... | 2007 | 17149652 |
| the hd-gyp domain, cyclic di-gmp signaling, and bacterial virulence to plants. | cyclic di-gmp is an almost ubiquitous second messenger in bacteria that was first described as an allosteric activator of cellulose synthase but is now known to regulate a range of functions, including virulence in human and animal pathogens. two protein domains, ggdef and eal, are implicated in the synthesis and degradation, respectively, of cyclic di-gmp. these domains are widely distributed in bacteria, including plant pathogens. the majority of proteins with ggdef and eal domains contain add ... | 2006 | 17153922 |
| hpar, a putative marr family transcriptional regulator, is positively controlled by hrpg and hrpx and involved in the pathogenesis, hypersensitive response, and extracellular protease production of xanthomonas campestris pathovar campestris. | the marr family of transcriptional regulators of bacteria are involved in the regulation of many cellular processes, including pathogenesis. in this work, we have demonstrated genetically that hpar (hpa, hrp associated), which encodes a putative marr family regulator, is involved in the hypersensitive response (hr), pathogenicity, and extracellular protease production of the phytopathogenic bacterium xanthomonas campestris pathovar campestris. a mutation in hpar resulted in complete loss of viru ... | 2007 | 17158655 |
| hpar, a putative marr family transcriptional regulator, is positively controlled by hrpg and hrpx and involved in the pathogenesis, hypersensitive response, and extracellular protease production of xanthomonas campestris pathovar campestris. | the marr family of transcriptional regulators of bacteria are involved in the regulation of many cellular processes, including pathogenesis. in this work, we have demonstrated genetically that hpar (hpa, hrp associated), which encodes a putative marr family regulator, is involved in the hypersensitive response (hr), pathogenicity, and extracellular protease production of the phytopathogenic bacterium xanthomonas campestris pathovar campestris. a mutation in hpar resulted in complete loss of viru ... | 2007 | 17158655 |
| messing with bacterial quorum sensing. | quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. interestingly, eukaryotes produce quorum-sensing-interfering (qsi) compo ... | 2006 | 17158701 |
| stimulus perception in bacterial signal-transducing histidine kinases. | two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. they consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. they can be identifi ... | 2006 | 17158704 |
| mutations in alternative carbon utilization pathways in candida albicans attenuate virulence and confer pleiotropic phenotypes. | the interaction between candida albicans and cells of the innate immune system is a key determinant of disease progression. transcriptional profiling has revealed that c. albicans has a complex response to phagocytosis, much of which is similar to carbon starvation. this suggests that nutrient limitation is a significant stress in vivo, and we have shown that glyoxylate cycle mutants are less virulent in mice. to examine whether other aspects of carbon metabolism are important in vivo during an ... | 2007 | 17158734 |
| mutations in alternative carbon utilization pathways in candida albicans attenuate virulence and confer pleiotropic phenotypes. | the interaction between candida albicans and cells of the innate immune system is a key determinant of disease progression. transcriptional profiling has revealed that c. albicans has a complex response to phagocytosis, much of which is similar to carbon starvation. this suggests that nutrient limitation is a significant stress in vivo, and we have shown that glyoxylate cycle mutants are less virulent in mice. to examine whether other aspects of carbon metabolism are important in vivo during an ... | 2007 | 17158734 |
| synergistic stimulation of epse atp hydrolysis by epsl and acidic phospholipids. | epse is a cytoplasmic component of the type ii secretion system in vibrio cholerae. through atp hydrolysis and an interaction with the cytoplasmic membrane protein epsl, epse supports secretion of cholera toxin across the outer membrane. in this study, we have determined the effect of the cytoplasmic domain of epsl (cyto-epsl) and purified phospholipids on the atpase activity of epse. acidic phospholipids, specifically cardiolipin, bound the copurified epse/cyto-epsl complex and stimulated its a ... | 2007 | 17159897 |
| synergistic stimulation of epse atp hydrolysis by epsl and acidic phospholipids. | epse is a cytoplasmic component of the type ii secretion system in vibrio cholerae. through atp hydrolysis and an interaction with the cytoplasmic membrane protein epsl, epse supports secretion of cholera toxin across the outer membrane. in this study, we have determined the effect of the cytoplasmic domain of epsl (cyto-epsl) and purified phospholipids on the atpase activity of epse. acidic phospholipids, specifically cardiolipin, bound the copurified epse/cyto-epsl complex and stimulated its a ... | 2007 | 17159897 |
| identification of quantitative trait loci for resistance to xanthomonas campestris pv. campestris in brassica rapa. | resistance to six known races of black rot in crucifers caused by xanthomonas campestris pv. campestris (pammel) dowson is absent or very rare in brassica oleracea (c genome). however, race specific and broad-spectrum resistance (to type strains of all six races) does appear to occur frequently in other brassica genomes including b. rapa (a genome). here, we report the genetics of broad spectrum resistance in the b. rapa chinese cabbage accession b162, using qtl analysis of resistance to races 1 ... | 2007 | 17160671 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| high precision multi-genome scale reannotation of enzyme function by eficaz. | the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction. | 2006 | 17166279 |
| functional analysis of pilt from the toxic cyanobacterium microcystis aeruginosa pcc 7806. | the evolution of the microcystin toxin gene cluster in phylogenetically distant cyanobacteria has been attributed to recombination, inactivation, and deletion events, although gene transfer may also be involved. since the microcystin-producing microcystis aeruginosa pcc 7806 is naturally transformable, we have initiated the characterization of its type iv pilus system, involved in dna uptake in many bacteria, to provide a physiological focus for the influence of gene transfer in microcystin evol ... | 2007 | 17172325 |
| functional analysis of pilt from the toxic cyanobacterium microcystis aeruginosa pcc 7806. | the evolution of the microcystin toxin gene cluster in phylogenetically distant cyanobacteria has been attributed to recombination, inactivation, and deletion events, although gene transfer may also be involved. since the microcystin-producing microcystis aeruginosa pcc 7806 is naturally transformable, we have initiated the characterization of its type iv pilus system, involved in dna uptake in many bacteria, to provide a physiological focus for the influence of gene transfer in microcystin evol ... | 2007 | 17172325 |
| the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole. | we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ... | 2007 | 17172338 |
| the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole. | we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ... | 2007 | 17172338 |
| insights on the evolution of trehalose biosynthesis. | the compatible solute trehalose is a non-reducing disaccharide, which accumulates upon heat, cold or osmotic stress. it was commonly accepted that trehalose is only present in extremophiles or cryptobiotic organisms. however, in recent years it has been shown that although higher plants do not accumulate trehalose at significant levels they have actively transcribed genes encoding the corresponding biosynthetic enzymes. | 2006 | 17178000 |
| preliminary x-ray analysis of xc5848, a hypothetical orfan protein with an sm-like motif from xanthomonas campestris. | xc5848, a hypothetical protein from the pathogenic bacterium xanthomonas campestris that causes black rot, has been chosen as a potential target for the discovery of novel folds. it is unique to the xanthomonas genus and has significant sequence identity mainly to corresponding proteins from the xanthomonas genus. in this paper, the cloning, overexpression, purification and crystallization of the xc5848 protein are reported. the xc5848 crystals diffracted to a resolution of at least 1.68 a. they ... | 2007 | 17183169 |
| preliminary x-ray analysis of xc5848, a hypothetical orfan protein with an sm-like motif from xanthomonas campestris. | xc5848, a hypothetical protein from the pathogenic bacterium xanthomonas campestris that causes black rot, has been chosen as a potential target for the discovery of novel folds. it is unique to the xanthomonas genus and has significant sequence identity mainly to corresponding proteins from the xanthomonas genus. in this paper, the cloning, overexpression, purification and crystallization of the xc5848 protein are reported. the xc5848 crystals diffracted to a resolution of at least 1.68 a. they ... | 2007 | 17183169 |
| sporulating bacteria prefers predation to cannibalism in mixed cultures. | predatory behavior, a property associated with ecosystems, is not commonly observed in microorganisms. however, cannibalistic tendencies have been observed in microorganisms under stress. for example, pure culture of bacillus subtilis exhibits cannibalism under nutrient limitation. it has been proposed that a fraction of cells in the population produce spo0a, a regulatory protein that is responsible for delaying sporulation. cells containing spo0a would produce a killing factor by activating skf ... | 2007 | 17184776 |
| the alternative sigma factor sigmah is required for toxin gene expression by bacillus anthracis. | expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated co(2), and the trans-acting positive regulator atxa. in addition to these requirements, toxin gene expression is under growth phase regulation. the transition state regulator abrb represses atxa expression to influence toxin synthesis. during the late exponential phase of growth, when abrb levels begin to decrease, toxin synthesis increases. here we report that t ... | 2007 | 17189374 |
| the alternative sigma factor sigmah is required for toxin gene expression by bacillus anthracis. | expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated co(2), and the trans-acting positive regulator atxa. in addition to these requirements, toxin gene expression is under growth phase regulation. the transition state regulator abrb represses atxa expression to influence toxin synthesis. during the late exponential phase of growth, when abrb levels begin to decrease, toxin synthesis increases. here we report that t ... | 2007 | 17189374 |
| type iii effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race. | the concept of the coevolutionary arms race holds a central position in our understanding of pathogen-host interactions. here we identify the molecular mechanisms and follow the stepwise progression of an arms race in a natural system. we show how the evolution and function of the hopz family of type iii secreted effector proteins carried by the plant pathogen pseudomonas syringae are influenced by a coevolutionary arms race between pathogen and host. we surveyed 96 isolates of p. syringae and i ... | 2006 | 17194219 |
| molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. | tryptophan 2,3-dioxygenase (tdo) and indoleamine 2,3-dioxygenase (ido) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. here, we report extensive structural and biochemical studies of the xanthomonas campestris tdo and a related protein so4414 from shewanella oneidensis, including the structure at 1.6-a resolution of the catalytically active, ferrous form of tdo in a binary complex with the substrate l-trp. the carboxylate and ammonium moieties of try ... | 2007 | 17197414 |
| molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. | tryptophan 2,3-dioxygenase (tdo) and indoleamine 2,3-dioxygenase (ido) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. here, we report extensive structural and biochemical studies of the xanthomonas campestris tdo and a related protein so4414 from shewanella oneidensis, including the structure at 1.6-a resolution of the catalytically active, ferrous form of tdo in a binary complex with the substrate l-trp. the carboxylate and ammonium moieties of try ... | 2007 | 17197414 |
| structural analysis of xanthomonas xopd provides insights into substrate specificity of ubiquitin-like protein proteases. | xopd (xanthomonas outer protein d), a type iii secreted effector from xanthomonas campestris pv. vesicatoria, is a desumoylating enzyme with strict specificity for its plant small ubiquitin-like modifier (sumo) substrates. based on sumo sequence alignments and peptidase assays with various plant, yeast, and mammalian sumos, we identified residues in sumo that contribute to xopd/sumo recognition. further predictions regarding the enzyme/substrate specificity were made by solving the xopd crystal ... | 2007 | 17204475 |
| natural variation in partial resistance to pseudomonas syringae is controlled by two major qtls in arabidopsis thaliana. | low-level, partial resistance is pre-eminent in natural populations, however, the mechanisms underlying this form of resistance are still poorly understood. | 2006 | 17205127 |
| characterization of isxax1, a novel insertion sequence restricted to xanthomonas axonopodis pv. phaseoli (variants fuscans and non-fuscans) and xanthomonas axonopodis pv. vesicatoria. | isxax1 is a novel insertion sequence belonging to the is256 and mutator families. dot blot, southern blot, and pcr analyses revealed that isxax1 is restricted to xanthomonas axonopodis pv. phaseoli (variants fuscans and non-fuscans) and x. axonopodis pv. vesicatoria strains. directed aflp also showed that a high degree of polymorphism is associated with isxax1 insertion in these strains. | 2007 | 17209062 |
| characterization of tdp-4-keto-6-deoxy-d-glucose-3,4-ketoisomerase from the d-mycaminose biosynthetic pathway of streptomyces fradiae: in vitro activity and substrate specificity studies. | deoxysugars are critical structural elements for the bioactivity of many natural products. ongoing work on elucidating a variety of deoxysugar biosynthetic pathways has paved the way for manipulation of these pathways for the generation of structurally diverse glycosylated natural products. in the course of this work, the biosynthesis of d-mycaminose in the tylosin pathway of streptomyces fradiae was investigated. attempts to reconstitute the entire mycaminose biosynthetic machinery in a heterol ... | 2007 | 17209568 |
| the rbmbcdef gene cluster modulates development of rugose colony morphology and biofilm formation in vibrio cholerae. | vibrio cholerae, the causative agent of cholera, can undergo phenotypic variation generating rugose and smooth variants. the rugose variant forms corrugated colonies and well-developed biofilms and exhibits increased levels of resistance to several environmental stresses. many of these phenotypes are mediated in part by increased expression of the vps genes, which are organized into vps-i and vps-ii coding regions, separated by an intergenic region. in this study, we generated in-frame deletions ... | 2007 | 17220218 |
| the lipopolysaccharide of sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant medicago truncatula. | in the establishment of symbiosis between medicago truncatula and the nitrogen-fixing bacterium sinorhizobium meliloti, the lipopolysaccharide (lps) of the microsymbiont plays an important role as a signal molecule. it has been shown in cell cultures that the lps is able to suppress an elicitor-induced oxidative burst. to investigate the effect of s. meliloti lps on defense-associated gene expression, a microarray experiment was performed. for evaluation of the m. truncatula microarray datasets, ... | 2007 | 17220366 |
| a fermentation system designed to independently evaluate mixing and/or oxygen tension effects in microbial processes: development, application and performance. | in order to evaluate the independent effects of hydrodynamic conditions and/or oxygen tension on culture physiology and productivity, a fermentation system designed to control dissolved oxygen at constant power drawn (p/v) was developed. the system included a fully instrumented 14 l bioreactor coupled to a pc for data acquisition and control. power drawn was measured (using a commercial torquemeter coupled to the shaft) and maintained constant by varying the agitation speed; while gas blending w ... | 2007 | 17225992 |
| a novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium hydrogenobacter thermophilus tk-6. | glutamate synthases are classified according to their specificities for electron donors. ferredoxin-dependent glutamate synthases had been found only in plants and cyanobacteria, whereas many bacteria have nadph-dependent glutamate synthases. in this study, hydrogenobacter thermophilus, a hydrogen-oxidizing chemoautotrophic bacterium, was shown to possess a ferredoxin-dependent glutamate synthase like those of phototrophs. this is the first observation, to our knowledge, of a ferredoxin-dependen ... | 2007 | 17237175 |
| functional characterization of the initiation enzyme of s-layer glycoprotein glycan biosynthesis in geobacillus stearothermophilus nrs 2004/3a. | the glycan chain of the s-layer glycoprotein of geobacillus stearothermophilus nrs 2004/3a is composed of repeating units [-->2)-alpha-l-rhap-(1-->3)-beta-l-rhap-(1-->2)-alpha-l-rhap-(1-->], with a 2-o-methyl modification of the terminal trisaccharide at the nonreducing end of the glycan chain, a core saccharide composed of two or three alpha-l-rhamnose residues, and a beta-d-galactose residue as a linker to the s-layer protein. in this study, we report the biochemical characterization of wsap o ... | 2007 | 17237178 |
| cyclic di-gmp signalling in the virulence and environmental adaptation of xanthomonas campestris. | cyclic di-gmp is a second messenger with a role in regulation of a range of cellular functions in diverse bacteria including the virulence of pathogens. cellular levels of cyclic di-gmp are controlled through synthesis, catalysed by the ggdef protein domain, and degradation by eal or hd-gyp domains. here we report a comprehensive study of cyclic di-gmp signalling in bacterial disease in which we examine the contribution of all proteins with ggdef, eal or hd-gyp domains to virulence and virulence ... | 2007 | 17241199 |
| chromosome-encoded narrow-spectrum ambler class a beta-lactamase gil-1 from citrobacter gillenii. | a novel beta-lactamase gene was cloned from the whole-cell dna of an enterobacterial citrobacter gillenii reference strain that displayed a weak narrow-spectrum beta-lactam-resistant phenotype and was expressed in escherichia coli. it encoded a clavulanic acid-inhibited ambler class a beta-lactamase, gil-1, with a pi value of 7.5 and a molecular mass of ca. 29 kda. gil-1 had the highest percent amino acid sequence identity with tem-1 and shv-1, 77%, and 67%, respectively, and only 46%, 31%, and ... | 2007 | 17242148 |
| requirement of a mip-like gene for virulence in the phytopathogenic bacterium xanthomonas campestris pv. campestris. | macrophage infectivity potentiators (mips) are fkbp domain-containing proteins reported as virulence factors in several human pathogens, such as members of genera legionella, salmonella and chlamydia. the putative peptidylprolyl cis-trans isomerase (ppiase) encoded by xc2699 of the plant bacterial pathogen xanthomonas campestris pv. campestris 8004 exhibits a 49% similarity at the amino-acid level to the mip protein of legionella pneumophila. this mip-like gene, xc2699, was overexpressed in esch ... | 2007 | 17249419 |
| factors affecting survival of bacteriophage on tomato leaf surfaces. | the ability of bacteriophage to persist in the phyllosphere for extended periods is limited by many factors, including sunlight irradiation, especially in the uv zone, temperature, desiccation, and exposure to copper bactericides. the effects of these factors on persistence of phage and formulated phage (phage mixed with skim milk) were evaluated. in field studies, copper caused significant phage reduction if applied on the day of phage application but not if applied 4 or 7 days in advance. sunl ... | 2007 | 17259361 |
| erythromycin resistance-conferring plasmid prsb105, isolated from a sewage treatment plant, harbors a new macrolide resistance determinant, an integron-containing tn402-like element, and a large region of unknown function. | the erythromycin resistance plasmid prsb105 was previously isolated from an activated sludge bacterial community of a municipal wastewater treatment plant. compilation of the complete prsb105 nucleotide sequence revealed that the plasmid is 57,137 bp in size and has a mean g+c content of 56.66 mol%. the prsb105 backbone is composed of two different replication and/or partitioning modules and a functional mobilization region encoding the mobilization genes mobcde and mobba. the first replicon (re ... | 2007 | 17261525 |
| phylogenetic signal and functional categories in proteobacteria genomes. | a comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. in this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods. | 2007 | 17288580 |
| a ptha homolog from xanthomonas axonopodis pv. citri responsible for host-specific suppression of virulence. | strains of the plant-pathogenic bacterium xanthomonas axonopodis pv. citri are differentiated into two groups with respect to aggressiveness (normal and weak) on citrus grandis cultivars but not on other citrus species such as citrus sinensis. random mutagenesis using the transposon tn5 in x. axonopodis pv. citri strain kc21, which showed weak aggressiveness on a c. grandis cultivar, was used to isolate mutant kc21t46, which regained a normal level of aggressiveness on the cultivar. the gene ina ... | 2007 | 17293422 |
| a complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in rhodobacter sphaeroides. | bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. approximately 40 proteins are required for the assembly and functionality of this structure. rhodobacter sphaeroides has two flagellar systems. one of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. in this work we found th ... | 2007 | 17293429 |
| the mtmmpl1 early nodulin is a novel member of the matrix metalloendoproteinase family with a role in medicago truncatula infection by sinorhizobium meliloti. | we show here that mtmmpl1, a medicago truncatula nodulin gene previously identified by transcriptomics, represents a novel and specific marker for root and nodule infection by sinorhizobium meliloti. this was established by determining the spatial pattern of mtmmpl1 expression and evaluating gene activation in the context of various plant and bacterial symbiotic mutant interactions. the mtmmpl1 protein is the first nodulin shown to belong to the large matrix metalloendoproteinase (mmp) family. w ... | 2007 | 17293436 |
| a conserved carboxylesterase is a suppressor of avrbst-elicited resistance in arabidopsis. | avrbst is a type iii effector from xanthomonas campestris pv vesicatoria that is translocated into plant cells during infection. avrbst is predicted to encode a cys protease that targets intracellular host proteins. to dissect avrbst function and recognition in arabidopsis thaliana, 71 ecotypes were screened to identify lines that elicit an avrbst-dependent hypersensitive response (hr) after xanthomonas campestris pv campestris (xcc) infection. the hr was observed only in the pi-0 ecotype infect ... | 2007 | 17293566 |
| characterization of a putative xylella fastidiosa diffusible signal factor by hrgc-ei-ms. | xylella fastidiosa (x.f.) is a plant pathogen with high levels of genomic similarity to xanthomonas campestris pv. campestris (x.c.c.). it has been shown that x. fastidiosa synthesizes a putative diffusible signal factor (x.f.-dsf) that activates regulation of pathogenicity factor (rpf) genes in a x.c.c. reporter system, which might be involved in the regulation of pathogenesis associated genes as in x.c.c., as well as in quorum-sensing. the nature of the x.f.-dsf is not known, whereas the x.c.c ... | 2007 | 17295415 |
| pseudomonas syringae pv. tomato hijacks the arabidopsis abscisic acid signalling pathway to cause disease. | we have found that a major target for effectors secreted by pseudomonas syringae is the abscisic acid (aba) signalling pathway. microarray data identified a prominent group of effector-induced genes that were associated with aba biosynthesis and also responses to this plant hormone. genes upregulated by effector delivery share a 42% overlap with aba-responsive genes and are also components of networks induced by osmotic stress and drought. strongly induced were nced3, encoding a key enzyme of ab ... | 2007 | 17304219 |
| benzoic acid-degrading bacteria from the intestinal tract of macrotermes michaelseni sjöstedt. | the intestinal tracts of termites host a wide variety of microbial symbionts, which have been implicated in degradative processes. in this study, a fungus-cultivating termite, macrotermes michaelseni was found to harbor 2.2 x 10(6) bacterial cells per ml of gut homogenates capable of degrading benzoic acid. two benzoic acid degrading bacteria were isolated from the highest dilution of gut homogenates in oxic media with benzoic acid as the sole carbon source. isolate cbc was related to stenotroph ... | 2007 | 17304624 |
| plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. | tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ... | 2007 | 17311090 |
| sensitive and specific detection of xanthomonas campestris pv. vesicatoria by pcr using pathovar-specific primers based on rhs family gene sequences. | the present study describes pcr assay to detect bacterial spot caused by xanthomonas campestris pv. vesicatoria in pepper and tomato. one set of pcr primer was developed to amplify gene required for an rhs family gene homologous to rhsa, cell envelope biogenesis, outer membrane. only a pcr product of a 517bp was produced in pcr reaction with the xanthomonas campestris pv. vesicatoria (xcvf/xcvr) primer set. a specific, and highly sensitive and rapid pcr assay for the detection of x. campestris p ... | 2009 | 17317128 |
| a novel locus involved in extracellular polysaccharide production and virulence of xanthomonas campestris pathovar campestris. | xanthomonas campestris pathovar campestris (xcc) is the causal agent of black rot disease in cruciferous plants. the extracellular polysaccharide (eps) produced by xcc is an important pathogenicity factor and also has a range of industrial uses. in preliminary work a number of transposon-mediated insertion mutants in xcc with defects in eps production were identified. here, one of these mutated loci was investigated in detail. six orfs within the locus (orfs xc3811-3816) were disrupted by plasmi ... | 2007 | 17322194 |
| proteomic analysis of a non-virulent mutant of the phytopathogenic bacterium erwinia chrysanthemi deficient in osmoregulated periplasmic glucans: change in protein expression is not restricted to the envelope, but affects general metabolism. | osmoregulated periplasmic glucans (opgs) are general constituents of the envelope of gram-negative bacteria. they are required for full virulence of bacterial phytopathogens such as pseudomonas syringae, xanthomonas campestris and erwinia chrysanthemi. e. chrysanthemi is a pectinolytic gamma-proteobacterium that causes soft rot disease on a wide range of plant species. in addition to the loss of virulence, opg mutants exhibit a pleiotropic phenotype that affects motility, bile-salt resistance, e ... | 2007 | 17322196 |
| mutations blocking side chain assembly, polymerization, or transport of a wzy-dependent streptococcus pneumoniae capsule are lethal in the absence of suppressor mutations and can affect polymer transfer to the cell wall. | extracellular polysaccharides of many bacteria are synthesized by the wzy polymerase-dependent mechanism, where long-chain polymers are assembled from undecaprenyl-phosphate-linked repeat units on the outer face of the cytoplasmic membrane. in gram-positive bacteria, wzy-dependent capsules remain largely cell associated via membrane and peptidoglycan linkages. like many wzy-dependent capsules, the streptococcus pneumoniae serotype 2 capsule is branched. in this study, we found that deletions of ... | 2007 | 17322316 |
| structural and evolutionary bioinformatics of the spout superfamily of methyltransferases. | spout methyltransferases (mtases) are a large class of s-adenosyl-l-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. in 2001, when no crystal structures were available for any of these proteins, anantharaman, koonin, and aravind identified homology between spou and trmd mtases and defined the spout superfamily. since then, multiple crystal structures of knotted mtases have been solved and numerous new homologous sequences appeared in the dat ... | 2007 | 17338813 |
| surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms. | major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. the enzyme n-acetylglutamate synthase (nags), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from archaea. in many bacteria, shorter proteins related to the gcn5-related n-acetyltransferase family appear to acet ... | 2007 | 17347518 |
| impairment of cellulose synthases required for arabidopsis secondary cell wall formation enhances disease resistance. | cellulose is synthesized by cellulose synthases (cesas) contained in plasma membrane-localized complexes. in arabidopsis thaliana, three types of cesa subunits (cesa4/irregular xylem5 [irx5], cesa7/irx3, and cesa8/irx1) are required for secondary cell wall formation. we report that mutations in these proteins conferred enhanced resistance to the soil-borne bacterium ralstonia solanacearum and the necrotrophic fungus plectosphaerella cucumerina. by contrast, susceptibility to these pathogens was ... | 2007 | 17351116 |
| transcription activation mediated by a cyclic amp receptor protein from thermus thermophilus hb8. | the extremely thermophilic bacterium thermus thermophilus hb8, which belongs to the phylum deinococcus-thermus, has an open reading frame encoding a protein belonging to the cyclic amp (camp) receptor protein (crp) family present in many bacteria. the protein named t. thermophilus crp is highly homologous to the crp family proteins from the phyla firmicutes, actinobacteria, and cyanobacteria, and it forms a homodimer and interacts with camp. crp mrna and intracellular camp were detected in this ... | 2007 | 17369302 |
| cowpea chloroplastic atp synthase is the source of multiple plant defense elicitors during insect herbivory. | in cowpea (vigna unguiculata), fall armyworm (spodoptera frugiperda) herbivory and oral secretions (os) elicit phytohormone production and volatile emission due to inceptin [vu-in; (+)icdingvcvda(-)], a peptide derived from chloroplastic atp synthase gamma-subunit (catpc) proteins. elicitor-induced plant volatiles can function as attractants for natural enemies of insect herbivores. we hypothesized that inceptins are gut proteolysis products and that larval os should contain a mixture of related ... | 2007 | 17369425 |
| a glimpse of streptococcal toxic shock syndrome from comparative genomics of s. suis 2 chinese isolates. | streptococcus suis serotype 2 (ss2) is an important zoonotic pathogen, causing more than 200 cases of severe human infection worldwide, with the hallmarks of meningitis, septicemia, arthritis, etc. very recently, ss2 has been recognized as an etiological agent for streptococcal toxic shock syndrome (stss), which was originally associated with streptococcus pyogenes (gas) in streptococci. however, the molecular mechanisms underlying stss are poorly understood. | 2007 | 17375201 |
| the power of phylogenetic approaches to detect horizontally transferred genes. | horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. high genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? the answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred ge ... | 2007 | 17376230 |
| xanthomonas campestris cell-cell communication involves a putative nucleotide receptor protein clp and a hierarchical signalling network. | the bacterial pathogen xanthomonas campestris pv. campestris co-ordinates virulence factor production and biofilm dispersal through a diffusible signal factor (dsf)-mediated cell-cell communication mechanism. the rpfc/rpfg two-component system plays a key role in dsf signal transduction and appears to modulate downstream dsf regulon by changing intracellular content of cyclic dimeric gmp (c-di-gmp), an unusual nucleotide second messenger. here we show that clp, a conserved global regulator showi ... | 2007 | 17378922 |
| type iii effector activation via nucleotide binding, phosphorylation, and host target interaction. | the pseudomonas syringae type iii effector protein avirulence protein b (avrb) is delivered into plant cells, where it targets the arabidopsis rin4 protein (resistance to pseudomonas maculicula protein 1 [rpm1]-interacting protein). rin4 is a regulator of basal host defense responses. targeting of rin4 by avrb is recognized by the host rpm1 nucleotide-binding leucine-rich repeat disease resistance protein, leading to accelerated defense responses, cessation of pathogen growth, and hypersensitive ... | 2007 | 17397263 |
| transcriptional regulatory network discovery via multiple method integration: application to e. coli k12. | transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ... | 2007 | 17397539 |
| natural origin biodegradable systems in tissue engineering and regenerative medicine: present status and some moving trends. | the fields of tissue engineering and regenerative medicine aim at promoting the regeneration of tissues or replacing failing or malfunctioning organs, by means of combining a scaffold/support material, adequate cells and bioactive molecules. different materials have been proposed to be used as both three-dimensional porous scaffolds and hydrogel matrices for distinct tissue engineering strategies. among them, polymers of natural origin are one of the most attractive options, mainly due to their ... | 2007 | 17412675 |
| arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots. | in natural ecosystems, the roots of many plants exist in association with arbuscular mycorrhizal (am) fungi, and the resulting symbiosis has profound effects on the plant. the most frequently documented response is an increase in phosphorus nutrition; however, other effects have been noted, including increased resistance to abiotic and biotic stresses. here we used a 16,000-feature oligonucleotide array and real-time quantitative rt-pcr to explore transcriptional changes triggered in medicago tr ... | 2007 | 17419842 |
| a novel bifunctional n-acetylglutamate synthase-kinase from xanthomonas campestris that is closely related to mammalian n-acetylglutamate synthase. | in microorganisms and plants, the first two reactions of arginine biosynthesis are catalyzed by n-acetylglutamate synthase (nags) and n-acetylglutamate kinase (nagk). in mammals, nags produces an essential activator of carbamylphosphate synthetase i, the first enzyme of the urea cycle, and no functional nagk homolog has been found. unlike the other urea cycle enzymes, whose bacterial counterparts could be readily identified by their sequence conservation with arginine biosynthetic enzymes, mamma ... | 2007 | 17425781 |
| branchclust: a phylogenetic algorithm for selecting gene families. | automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ... | 2007 | 17425803 |
| a tale of two oxidation states: bacterial colonization of arsenic-rich environments. | microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ... | 2007 | 17432936 |
| isolation and characterization of a xanthan-degrading microbacterium sp. strain xt11 from garden soil. | isolation and characterization of the xanthan-degrading microbacterium sp. xt11. | 2007 | 17448171 |
| the flik protein and flagellar hook-length control. | the bacterial flagellum is a highly complex prokaryotic organelle. it is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two-component systems. part of the flagellum is a type iii secretion system, and it is via this structure that flagellar components are exported. the assem ... | 2007 | 17456739 |
| diffusible signal factor-dependent cell-cell signaling and virulence in the nosocomial pathogen stenotrophomonas maltophilia. | the genome of stenotrophomonas maltophilia encodes a cell-cell signaling system that is highly related to the diffusible signal factor (dsf)-dependent system of the phytopathogen xanthomonas campestris. here we show that in s. maltophilia, dsf signaling controls factors contributing to the virulence and antibiotic resistance of this important nosocomial pathogen. | 2007 | 17468254 |
| repeat domain diversity of avrbs3-like genes in ralstonia solanacearum strains and association with host preferences in the field. | genes homologous to avrbs3 of xanthomonas were detected in 309 strains of ralstonia solanacearum biovars 3, 4, and 5 but not biovar 1 or 2. a statistically significant association between the originating plant species and internal repeats of the gene was found. sequences of repeats and variation between nearly clonal strains revealed evidence of frequent recombination. | 2007 | 17468277 |
| using the ralstonia solanacearum tat secretome to identify bacterial wilt virulence factors. | to identify secreted virulence factors involved in bacterial wilt disease caused by the phytopathogen ralstonia solanacearum, we mutated tatc, a key component of the twin-arginine translocation (tat) secretion system. the r. solanacearum tatc mutation was pleiotropic; its phenotypes included defects in cell division, nitrate utilization, polygalacturonase activity, membrane stability, and growth in plant tissue. bioinformatic analysis of the r. solanacearum strain gmi1000 genome predicted that t ... | 2007 | 17468289 |
| transcriptional profiling of bacillus anthracis during infection of host macrophages. | the interaction between bacillus anthracis and the mammalian phagocyte is one of the central stages in the progression of inhalational anthrax, and it is commonly believed that the host cell plays a key role in facilitating germination and dissemination of inhaled b. anthracis spores. given this, a detailed definition of the survival strategies used by b. anthracis within the phagocyte is critical for our understanding of anthrax. in this study, we report the first genome-wide analysis of b. ant ... | 2007 | 17470545 |
| tomato mitogen-activated protein kinases lempk1, lempk2, and lempk3 are activated during the cf-4/avr4-induced hypersensitive response and have distinct phosphorylation specificities. | tomato (solanum lycopersicum) plants with the cf-4 resistance gene recognize strains of the pathogenic fungus cladosporium fulvum that secrete the avirulence protein avr4. transgenic tomato seedlings coexpressing cf-4 and avr4 mount a hypersensitive response (hr) at 20 degrees c, which is suppressed at 33 degrees c. within 120 min after a shift from 33 degrees c to 20 degrees c, tomato mitogen-activated protein (map) kinase (lempk) activity increases in cf-4/avr4 seedlings. searching tomato geno ... | 2007 | 17478632 |
| roles of cyclic diguanylate in the regulation of bacterial pathogenesis. | cyclic diguanylate (c-di-gmp) is a bacterial second messenger of growing recognition involved in the regulation of a number of complex physiological processes. this review describes the biosynthesis and hydrolysis of c-di-gmp and several mechanisms of regulation of c-di-gmp metabolism. the contribution of c-di-gmp to regulating biofilm formation and motility, processes that affect pathogenesis of many bacteria, is described, as is c-di-gmp regulation of virulence gene expression. finally, ways i ... | 2007 | 17480182 |
| the copper-inducible cin operon encodes an unusual methionine-rich azurin-like protein and a pre-q0 reductase in pseudomonas putida kt2440. | the genome sequences of several pseudomonads have revealed a gene cluster containing genes for a two-component heavy metal histidine sensor kinase and response regulator upstream of cina and cinq, which we show herein to encode a copper-containing azurin-like protein and a pre-q(0) reductase, respectively. in the presence of copper, pseudomonas putida kt2440 produces the cina and cinq proteins from a bicistronic mrna. uv-visible spectra of cina show features at 439, 581, and 719 nm, which is typ ... | 2007 | 17483220 |
| simple sequence repeats in prokaryotic genomes. | simple sequence repeats (ssrs) in dna sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general dna sequences. they are variable in length because of slip-strand mutations and may also affect local structure of the dna molecule or the encoded proteins. long ssrs (lssrs) are common in eukaryotes but rare in most prokaryotes. in pathogens, ssrs can enhance antigenic variance of the pathogen populati ... | 2007 | 17485665 |
| a novel restriction-modification system from xanthomonas campestris pv. vesicatoria encodes a m4c-methyltransferase and a nonfunctional restriction endonuclease. | a novel restriction-modification (r-m) system, designated as xveiirm, from chromosomal dna of the xanthomonas campestris pv. vesicatoria strain 7-1 (xcv7-1) was cloned and characterized. the xveiirm genes involved in this r-m system are aligned in a tail-to-tail orientation and overlapped by 12 base pairs. xveii methyltransferase gene could encode a 299-amino acid protein (m.xveii) with an estimated mass of 33.7 kda and was classified to be a member of beta-class of m4c-mtase. m.xveii methylates ... | 2007 | 17488332 |
| characterization of agrobacterium tumefaciens dna ligases c and d. | agrobacterium tumefaciens encodes a single nad+-dependent dna ligase and six putative atp-dependent ligases. two of the ligases are homologs of ligd, a bacterial enzyme that catalyzes end-healing and end-sealing steps during nonhomologous end joining (nhej). agrobacterium ligd1 and atuligd2 are composed of a central ligase domain fused to a c-terminal polymerase-like (pol) domain and an n-terminal 3'-phosphoesterase (pe) module. both ligd proteins seal dna nicks, albeit inefficiently. the ligd2 ... | 2007 | 17488851 |
| a complex thiolate switch regulates the bacillus subtilis organic peroxide sensor ohrr. | oxidation of protein thiolates is central to numerous redox-regulated processes. bacillus subtilis ohrr is an organic peroxide sensor that represses expression of an inducible peroxiredoxin, ohra. here, we present evidence that oxidation of the sole cysteine residue in ohrr leads to a sulfenic acid-containing intermediate that retains dna-binding activity: further reaction to generate either a mixed disulfide (s-thiolation) or a protein sulfenamide (sulfenyl-amide) derivative is essential for de ... | 2007 | 17502599 |
| refinement of the xanthomonas campestris pv. vesicatoria hrpd and hrpe operon structure. | the plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria possesses a type iii secretion (t3s) system which is encoded in the 23-kb hypersensitive response and pathogenicity (hrp) gene cluster. the t3s system is essential for pathogenicity in susceptible hosts and the induction of the hypersensitive response in resistant plants. in this study, we revisited the operon structure of the right part of the hrp gene cluster. based on complementation experiments of transposon insertions and ... | 2007 | 17506333 |
| genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis. | genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and sirnas. an artificial neural network (ann) is a machine learning technique that can effectively process complex and high noise data. here, anns are applied to process the unique subsequence distribution for prediction of specific oligos. | 2007 | 17518996 |