Publications

insertion sequence isecp1b is involved in expression and mobilization of a bla(ctx-m) beta-lactamase gene.	the genetic structures (ca. 10-kb dna fragment) surrounding the plasmid-borne extended-spectrum beta-lactamase bla(ctx-m-19) gene in a klebsiella pneumoniae clinical isolate were determined. this beta-lactamase gene was part of a 4,797-bp transposon inserted inside orf1 of tn1721. inside this transposon, bla(ctx-m-19) was bracketed upstream and downstream by insertion sequences ise cp1b and is903d, respectively, and further downstream by a truncated gene encoding an outer membrane protein for ir ...	2003	12936998
erwinia chrysanthemi tolc is involved in resistance to antimicrobial plant chemicals and is essential for phytopathogenesis.	tolc is the outer-membrane component of several multidrug resistance (mdr) efflux pumps and plays an important role in the survival and virulence of many gram-negative bacterial animal pathogens. we have identified and characterized the outer-membrane protein-encoding gene tolc in the bacterial plant pathogen erwinia chrysanthemi ec16. the gene was found to encode a 51-kda protein with 70% identity to its escherichia coli homologue. the e. chrysanthemi gene was able to functionally complement th ...	2003	13129948
staphostatins resemble lipocalins, not cystatins in fold.	staphostatins are the endogenous inhibitors of the major secreted cysteine proteases of staphylococcus aureus, the staphopains. here, we present the 1.4 a crystal structure of staphostatin b and show that the fold can be described as a fully closed, highly sheared eight-stranded beta-barrel. thus, staphostatin b is related to beta-barrel domains that are involved in the inhibition or regulation of proteases of various catalytic types and to the superfamily of lipocalins/cytosolic fatty acid bind ...	2003	14500882
mechanism of pseudomonas aeruginosa rhlr transcriptional regulation of the rhlab promoter.	pseudomonas aeruginosa contains two transcription regulators (lasr and rhlr) that, when complexed with their specific autoinducers (3-oxo-dodecanoyl-homoserine lactone and butanoyl-homoserine lactone, respectively) activate transcription of different virulence-associated traits. we studied the rhlr-dependent transcriptional regulation of the rhlab operon encoding rhamnosyltransferase 1, an enzyme involved in the synthesis of the surfactant monorhamnolipid, and showed that rhlr binds to a specifi ...	2003	14526008
the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons.	is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ...	2003	14563872
analysis of the corynebacterium diphtheriae dtxr regulon: identification of a putative siderophore synthesis and transport system that is similar to the yersinia high-pathogenicity island-encoded yersiniabactin synthesis and uptake system.	the diphtheria toxin repressor, dtxr, is a global iron-dependent regulatory protein in corynebacterium diphtheriae that controls gene expression by binding to 19-bp operator sequences. to further define the dtxr regulon in c. diphtheriae, a dtxr repressor titration assay (drta) was developed and used to identify 10 previously unknown dtxr binding sites. open reading frames downstream from seven of the newly identified dtxr binding sites are predicted to encode proteins associated with iron or he ...	2003	14617647
identification and characterization of genes required for biosynthesis and transport of the siderophore vibrioferrin in vibrio parahaemolyticus.	in response to low iron availability, vibrio parahaemolyticus synthesizes and secretes a polyhydroxycarboxylate-type siderophore vibrioferrin which is composed of 1 mol each of 2-ketoglutaric acid, l-alanine, ethanolamine, and citric acid. we have previously reported the cloning and characterization of the pvua gene, which encodes the 78-kda outer membrane receptor protein for ferric vibrioferrin. in this study, nine genes involved in the biosynthesis and transport of vibrioferrin have been iden ...	2003	14617658
the quorum sensing negative regulators esar and expr(ecc), homologues within the luxr family, retain the ability to function as activators of transcription.	most luxr homologues function as activators of transcription during the process of quorum sensing, but a few, including esar and expr(ecc), negatively impact gene expression. the luxr-activated luxi promoter and luxr binding site, the lux box, were used in artificial contexts to assess the potential for transcriptional activation and dna binding by esar and expr(ecc). although the acyl-homoserine lactone responsiveness of both proteins is the opposite of that shown by most luxr family members, e ...	2003	14617666
tomato pectin methylesterase: modeling, fluorescence, and inhibitor interaction studies-comparison with the bacterial (erwinia chrysanthemi) enzyme.	the molecular model of lycopersicon esculentum (tomato) pectin methylesterase (pme) was built by using the x-ray crystal structure of pme from the phytopathogenic bacterium erwinia chrysanthemi as a template. the overall structure and the position of catalytically important residues (asp132, asp 153, and arg 221, located at the bottom of the active site cleft) are conserved. instead, loop regions forming the walls of the catalytic site are much shorter and form a less deep cleft, as already reve ...	2003	14635125
molecular basis of bacterial outer membrane permeability revisited.	gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. this review summarizes the development in the field since ...	2003	14665678
hydrodynamic properties of oxidized extracellular polysaccharides from erwinia chrysanthemi spp.	the molecular weights of the native polysaccharides of erwinia chrysanthemi strains range from 1.8 to 7.1 x 10(6) and their hydrodynamic properties are those of polydisperse, polyanionic biopolymers with pseudoplastic, non-thixotropic flow characteristics in aqueous solutions. the effect on the hydrodynamic properties of the polysaccharides by adding carboxyl groups to increase the charge density is studied, with particular reference to their molecular weight (mw), viscosity and conformation. in ...	2003	14670735
the crystal structure of pectate lyase pel9a from erwinia chrysanthemi.	the "family 9 polysaccharide lyase" pectate lyase l (pel9a) from erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. pel9a has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family pel1a pectate lyases, and there is strong evidence for a common second calcium ion ...	2004	14670977
cloning of the pela gene from bacillus licheniformis 14a and biochemical characterization of recombinant, thermostable, high-alkaline pectate lyase.	the pectate lyase gene pela from alkaliphilic bacillus licheniformis strain 14a was cloned and sequenced. the nucleotide sequence corresponded to an open reading frame of 1,026 bp that codes for a 39 amino acid signal peptide and a mature protein with a molecular mass of 33,451 da. the mature pela showed significant homology to other pectate lyases belonging to polysaccharide lyase family 1, such as enzymes from different bacillus spp. and erwinia chrysanthemi. the pela gene was expressed in esc ...	2004	14673544
crystallization of the pectate lyase peli from erwinia chrysanthemi and sad phasing of a gold derivative.	the pectate lyase peli is involved in the degradation of plant tissues by the phytopathogenic bacterium erwinia chrysanthemi. it has been crystallized from a solution containing peg 550 in the space group p2(1), with unit-cell parameters a = 61.6, b = 70.7, c = 73.4 a, beta = 112.8 degrees. crystals diffract to 1.45 a using synchrotron radiation. sad phases have been computed from a gold-derivative crystal at the wavelength of maximum absorption (l(iii) edge).	2004	14684926
role of siderophore biosynthesis in virulence of staphylococcus aureus: identification and characterization of genes involved in production of a siderophore.	molecular determinants underlying the production of siderophores in the human and animal pathogen staphylococcus aureus and the contribution of siderophore production to the virulence of this bacterium have, until now, remained undefined. here, we show that s. aureus strains rn6390 and newman produce siderophore when the cells are starved for iron. we further identified and characterized a nine-gene, iron-regulated operon, designated sbn and situated between sirabc and gale on the s. aureus chro ...	2004	14688077
legionella pneumophila type ii protein secretion promotes virulence in the a/j mouse model of legionnaires' disease pneumonia.	legionella pneumophila, the gram-negative agent of legionnaires' disease, possesses type iv pili and a type ii protein secretion (lsp) system, both of which are dependent upon the pild prepilin peptidase. by analyzing multiple pild mutants and various types of lsp mutants as well as performing trans-complementation of these mutants, we have confirmed that pild and type ii secretion genes are required for l. pneumophila infection of both amoebae and human macrophages. based upon a complete analys ...	2004	14688110
an evolutionary hot spot: the pngr234b replicon of rhizobium sp. strain ngr234.	rhizobium sp. strain ngr234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. since the overall organization of the ngr234 genome is strikingly similar to that of the narrow-host-range symbiont rhizobium meliloti strain 1021 (also known as sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? study of the early symbiotic genes of both bacteria (carried by the syma plasmids) did not provide obvious answers. yet, bo ...	2004	14702322
pseudomonas syringae type iii secretion system targeting signals and novel effectors studied with a cya translocation reporter.	pseudomonas syringae pv. tomato strain dc3000 is a pathogen of tomato and arabidopsis: the hrp-hrc-encoded type iii secretion system (ttss), which injects bacterial effector proteins (primarily called hop or avr proteins) into plant cells, is required for pathogenicity. in addition to being regulated by the hrpl alternative sigma factor, most avr or hop genes encode proteins with n termini that have several characteristic features, including (i) a high percentage of ser residues, (ii) an aliphat ...	2004	14702323
the nifl-nifa system: a multidomain transcriptional regulatory complex that integrates environmental signals.		2004	14729684
automated correction of genome sequence errors.	by using information from an assembly of a genome, a new program called autoeditor significantly improves base calling accuracy over that achieved by previous algorithms. this in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. we describe the algorithm and its application in a large set of recent genome sequencing projects. the number of erroneous base calls in these projects was reduced by 80%. in an analysis of over ...	2004	14744981
the sufr gene (sll0088 in synechocystis sp. strain pcc 6803) functions as a repressor of the sufbcds operon in iron-sulfur cluster biogenesis in cyanobacteria.	the suf operon is composed of four genes (sufb, sufc, sufd, and sufs) and is highly conserved in the genomes of cyanobacteria. open reading frame sll0088 in synechocystis sp. strain pcc 6803 is located near the 5' end of the suf operon but is transcribed in the direction opposite that of the suf operon. we previously reported the isolation of two independent suppressor strains of c14s(psac) that mapped to sll0088 and restored photoautotrophic growth. the protein encoded by sll0088 has two signif ...	2004	14761990
norm, an erwinia amylovora multidrug efflux pump involved in in vitro competition with other epiphytic bacteria.	blossoms are important sites of infection for erwinia amylovora, the causal agent of fire blight of rosaceous plants. before entering the tissue, the pathogen colonizes the stigmatic surface and has to compete for space and nutrient resources within the epiphytic community. several epiphytes are capable of synthesizing antibiotics with which they antagonize phytopathogenic bacteria. here, we report that a multidrug efflux transporter, designated norm, of e. amylovora confers tolerance to the tox ...	2004	14766544
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
analysis of erwinia chrysanthemi ec16 pele::uida, pell::uida, and hrpn::uida mutants reveals strain-specific atypical regulation of the hrp type iii secretion system.	the plant pathogen erwinia chrysanthemi produces a variety of factors that have been implicated in its ability to cause soft-rot diseases in various hosts. these include hrpn, a harpin secreted by the hrp type iii secretion system; pele, one of several major pectate lyase isozymes secreted by the type ii system; and pell, one of several secondary pels secreted by the type ii system. we investigated these factors in e. chrysanthemi ec16 with respect to the effects of medium composition and growth ...	2004	14964532
the phop-phoq two-component regulatory system of photorhabdus luminescens is essential for virulence in insects.	photorhabdus luminescens is a symbiont of entomopathogenic nematodes. analysis of the genome sequence of this organism revealed a homologue of phop-phoq, a two-component system associated with virulence in intracellular bacterial pathogens. this organism was shown to respond to the availability of environmental magnesium. a mutant with a knockout mutation in the regulatory component of this system (phop) had no obvious growth defect. it was, however, more motile and more sensitive to antimicrobi ...	2004	14973084
the rhas activator controls the erwinia chrysanthemi 3937 genes rhin, rhit and rhie involved in rhamnogalacturonan catabolism.	erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. the linear regions of pectin are composed of an acidic sugar, d-galacturonic acid. the ramified regions of pectin also include neutral sugars, and are rich in l-rhamnose residues. e. chrysanthemi is able to degrade these polysaccharides, polygalacturonate and rhamnogalacturonate. in e. chrysanthemi, the production of pectinases acting on linear regions is induced in the pre ...	2004	14982630
novel chromosomally encoded multidrug efflux transporter mdea in staphylococcus aureus.	antibiotic efflux is an important mechanism of resistance in pathogenic bacteria. here we describe the identification and characterization of a novel chromosomally encoded multidrug resistance efflux protein in staphylococcus aureus, mdea (multidrug efflux a). mdea was identified from screening an s. aureus open reading frame expression library for resistance to antibiotic compounds. when overexpressed, mdea confers resistance on s. aureus to a range of quaternary ammonium compounds and antibiot ...	2004	14982783
molecular cloning of a cytosolic ascorbate peroxidase cdna from cell cultures of sweet potato and its expression in response to stress.	a cdna encoding a cytosolic ascorbate peroxidase (apx), swapx1, was isolated from cell cultures of sweet potato ( ipomoea batatas) by cdna library screening, and its expression in the context of various environmental stresses was investigated. swapx1 contains an orf of 250 amino acids (27.5 kda) encoding a protein with a pi value of 5.32. the swapx1 orf does not code for a transit peptide, suggesting that the product is a cytosolic isoform. rna blot analysis showed that swapx1 gene is expressed ...	2004	14986108
systematic analysis, by the yeast two-hybrid, of protein interaction between components of the type ii secretory machinery of erwinia chrysanthemi.	type ii systems allow for the secretion of numerous enzymes and toxins in several gram-negative pathogens. in erwinia chrysanthemi, 14 out proteins are necessary for building the type ii apparatus. we performed a systematic two-hybrid analysis to test interactions between the periplasmic regions of the out proteins. results obtained using this approach suggested that outj (a pseudopilin) was able to interact with (i) outd, the outer membrane secretin, (ii) outi, mainly located in the periplasm, ...	2004	14990257
regulation of escherichia coli hemolysin e expression by h-ns and salmonella slya.	the escherichia coli hlye gene (also known as clya or shea) codes for a novel pore-forming toxin. previous work has shown that the global transcription factors fnr and crp positively regulate hlye expression by binding at the same site. here in vivo transcription studies reveal that fnr occupies the hlye promoter more frequently than crp, providing a mechanism for the moderate upregulation of hlye expression in response to two distinct environmental signals (oxygen and glucose starvation). it ha ...	2004	14996792
methionine sulfoxide reductases protect ffh from oxidative damages in escherichia coli.	in proteins, methionine residues are primary targets for oxidation. methionine oxidation is reversed by methionine sulfoxide reductases a and b, a class of highly conserved enzymes. ffh protein, a component of the ubiquitous signal recognition particle, contains a methionine-rich domain, interacting with a small 4.5s rna. in vitro analyses reported here show that: (i) oxidized ffh is unable to bind 4.5s rna, (ii) oxidized ffh contains methionine sulfoxide residues, (iii) oxidized ffh is a substr ...	2004	15057280
identification of streptococcus thermophilus cnrz368 genes involved in defense against superoxide stress.	to better understand the defense mechanism of streptococcus thermophilus against superoxide stress, molecular analysis of 10 menadione-sensitive mutants, obtained by insertional mutagenesis, was undertaken. this analysis allowed the identification of 10 genes that, with respect to their putative functions, were classified into five categories: (i) those involved in cell wall metabolism, (ii) those involved in exopolysaccharide translocation, (iii) those involved in rna modification, (iv) those i ...	2004	15066816
identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium microbulbifer degradans.	polyserine linkers (psls) are interdomain, serine-rich sequences found in modular proteins. though common among eukaryotes, their presence in prokaryotic enzymes is limited. we identified 46 extracellular proteins involved in complex carbohydrate degradation from microbulbifer degradans that contain psls that separate carbohydrate-binding domains or catalytic domains from other binding domains. in nine m. degradans proteins, psls also separated amino-terminal lipoprotein acylation sites from the ...	2004	15075401
the crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway.	filamentous hemagglutinin (fha), the major 230-kda adhesin of the whooping cough agent bordetella pertussis, is one of the most efficiently secreted proteins in gram-negative bacteria. fha is secreted by means of the two-partner secretion (tps) pathway. several important human, animal, and plant pathogens also secrete adhesins and other virulence factors by using this mode of secretion. a tps system is composed of two separate proteins, with tpsa the secreted protein and tpsb its associated spec ...	2004	15079085
cloning and characterization of the gene encoding the major cell-associated phospholipase a of legionella pneumophila, plab, exhibiting hemolytic activity.	legionella pneumophila, the causative agent of legionnaires' disease, is an intracellular pathogen of amoebae, macrophages, and epithelial cells. the pathology of legionella infections involves alveolar cell destruction, and several proteins of l. pneumophila are known to contribute to this ability. by screening a genomic library of l. pneumophila, we found an additional l. pneumophila gene, plab, which coded for a hemolytic activity and contained a lipase consensus motif in its deduced protein ...	2004	15102773
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
genomic diversity of erwinia carotovora subsp. carotovora and its correlation with virulence.	we used genetic and biochemical methods to examine the genomic diversity of the enterobacterial plant pathogen erwinia carotovora subsp. carotovora. the results obtained with each method showed that e. carotovora subsp. carotovora strains isolated from one ecological niche, potato plants, are surprisingly diverse compared to related pathogens. a comparison of 23 partial mdh sequences revealed a maximum pairwise difference of 10.49% and an average pairwise difference of 2.13%, values which are mu ...	2004	15128563
negative cross-communication among wheat rhizosphere bacteria: effect on antibiotic production by the biological control bacterium pseudomonas aureofaciens 30-84.	phenazine antibiotic production in the biological control bacterium pseudomonas aureofaciens 30-84 is regulated in part via the phzr/phzi n-acyl homoserine lactone (ahl) system. previous work showed that a subpopulation of the wheat rhizosphere community positively affected phenazine gene expression in strain 30-84 via ahl signals (e. a. pierson, d. w. wood, j. a. cannon, f. m. blachere, and l. s. pierson iii, mol. plant-microbe interact. 11:1078-1084, 1998). in the present work, a second subpop ...	2004	15128573
identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin e3.	colicin e3 is a cytotoxic ribonuclease that specifically cleaves 16s rrna at the ribosomal a-site to abolish protein synthesis in sensitive escherichia coli cells. we have performed extensive mutagenesis of the 96-residue colicin e3 cytotoxic domain (e3 rrnase), assayed mutant colicins for in vivo cytotoxicity, and tested the corresponding e3 rrnase domains for their ability to inactivate ribosome function in vitro. from 21 alanine mutants, we identified five positions where mutation resulted in ...	2004	15133158
definition of a consensus dna-binding site for pecs, a global regulator of virulence gene expression in erwinia chrysanthemi and identification of new members of the pecs regulon.	in erwinia chrysanthemi, production of pectic enzymes is modulated by a complex network involving several regulators. one of them, pecs, which belongs to the marr family, also controls the synthesis of various other virulence factors, such as cellulases and indigoidine. here, the pecs consensus-binding site is defined by combining a systematic evolution of ligands by an exponential enrichment approach and mutational analyses. the consensus consists of a 23-base pair palindromic-like sequence (c( ...	2004	15140891
methionine sulfoxide reductase a (msra) deficiency affects the survival of mycobacterium smegmatis within macrophages.	methionine sulfoxide reductase a (msra) is an antioxidant repair enzyme which reduces oxidized methionine to methionine. since oxidation of methionine in proteins impairs their function, an absence of msra leads to abnormalities in different organisms, including alterations in the adherence patterns and in vivo survival of certain pathogenic bacteria. to understand the role of msra in intracellular survival of bacteria, we disrupted the gene encoding msra in mycobacterium smegmatis through homol ...	2004	15150247
modifying an immunogenic epitope on a therapeutic protein: a step towards an improved system for antibody-directed enzyme prodrug therapy (adept).	carboxypeptidase g2 (cp) is a bacterial enzyme, which is targeted to tumours by an antitumour antibody for local prodrug activation in antibody-directed enzyme prodrug therapy (adept). repeated cycles of adept are desirable but are hampered by human antibody response to cp (haca). to address this, we aimed to identify and modify clinically important immunogenic sites on mfecp, a recombinant fusion protein of cp with mfe-23, a single chain fv (scfv) antibody. a discontinuous conformational epitop ...	2004	15162148
identification of mdod, an mdog paralog which encodes a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures.	osmoregulated periplasmic glucans (opgs) of escherichia coli are anionic and highly branched oligosaccharides that accumulate in the periplasmic space in response to low osmolarity of the medium. the glucan length, ranging from 5 to 12 glucose residues, is under strict control. two genes that form an operon, mdogh, govern glucose backbone synthesis. the new gene mdod, which appears to be a paralog of mdog, was characterized in this study. cassette inactivation of mdod resulted in production of o ...	2004	15175282
atnap7 is a plastidic sufc-like atp-binding cassette/atpase essential for arabidopsis embryogenesis.	in bacteria, yeast, and mammals, iron-sulfur (fe-s) cluster-containing proteins are involved in numerous processes including electron transfer, metabolic reactions, sensing, signaling, and regulation of gene expression. in humans, iron-storage diseases such as x-linked sideroblastic anemia and ataxia are caused by defects in fe-s cluster availability. the biogenesis of fe-s clusters involves several pathways, and in bacteria, the sufabcdse operon has been shown to play a vital role in fe-s bioge ...	2004	15184673
inducible defense mechanism against nitric oxide in candida albicans.	the yeast candida albicans is an opportunistic pathogen that threatens patients with compromised immune systems. immune cell defenses against c. albicans are complex but typically involve the production of reactive oxygen species and nitrogen radicals such as nitric oxide (no) that damage the yeast or inhibit its growth. whether candida defends itself against no and the molecules responsible for this defense have yet to be determined. the defense against no in various bacteria and the yeast sacc ...	2004	15189992
differential expression of 10 sweetpotato peroxidase genes in response to bacterial pathogen, pectobacterium chrysanthemi.	to understand the function of each peroxidase (pod, ec 1.11.1.7) in terms of biotic stress, changes in pod specific activity and expression of 10 pod genes were investigated in four cultivars of sweetpotato (ipomoea batatas) after infection with pectobacterium chrysanthemi. pod specific activity (units mg(-1) protein) increased from 16 h after inoculation (hai) in three varieties. pod activities of two cultivars, shinwhangmi and white star, reached a maximum level at 24 hai by about three times ...	2004	15191750
the erwinia chrysanthemi ec16 hrp/hrc gene cluster encodes an active hrp type iii secretion system that is flanked by virulence genes functionally unrelated to the hrp system.	erwinia chrysanthemi is a host-promiscuous plant pathogen that possesses a type iii secretion system (ttss) similar to that of the host-specific pathogens e. amylovora and pseudomonas syringae. the regions flanking the ttss-encoding hrp/hrc gene clusters in the latter pathogens encode various ttss-secreted proteins. dna sequencing of the complete e. chrysanthemi hrp/hrc gene cluster and approximately 12 kb of the flanking regions (beyond the previously characterized heca adhesin gene in the left ...	2004	15195947
carbohydrate-binding modules: fine-tuning polysaccharide recognition.	the enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. in order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic cbms (carbohydrate-bind ...	2004	15214846
structure and hydrodynamic properties of the extracellular polysaccharide from a mutant strain (ra3w) of erwinia chrysanthemi ra3.	the structure of the extracellular polysaccharide (eps) produced by erwinia chrysanthemi strain ra3w, a mutant strain of e. chrysanthemi ra3, has been determined using low pressure size-exclusion and anion-exchange chromatographies, high ph anion-exchange chromatography, glycosyl linkage analysis, and 1d 1h nmr spectroscopy. the polysaccharide is structurally similar, if not identical, to the family of eps produced by such as e. chrysanthemi strains ech9, ech9sm6, and sr260. the molecular weight ...	2004	15261600
a type ii protein secretory pathway required for levansucrase secretion by gluconacetobacter diazotrophicus.	the endophytic diazotroph gluconacetobacter diazotrophicus secretes a constitutively expressed levansucrase (lsda, ec 2.4.1.10) to utilize plant sucrose. lsda, unlike other extracellular levansucrases from gram-negative bacteria, is transported to the periplasm by a signal-peptide-dependent pathway. we identified an unusually organized gene cluster encoding at least the components lsdg, -o, -e, -f, -h, -i, -j, -l, -m, -n, and -d of a type ii secretory system required for lsda translocation acros ...	2004	15262940
cloning serratia entomophila antifeeding genes--a putative defective prophage active against the grass grub costelytra zealandica.	serratia entomophila and serratia proteamaculans (enterobacteriaceae) cause amber disease in the grass grub costelytra zealandica (coleoptera: scarabaeidae), an important pasture pest in new zealand. larval disease symptoms include cessation of feeding, clearance of the gut, amber coloration, and eventual death. a 155-kb plasmid, padap, carries the genes sepa, sepb, and sepc, which are essential for production of amber disease symptoms. transposon insertions in any of the sep genes in padap abol ...	2004	15262948
genome sequence of the enterobacterial phytopathogen erwinia carotovora subsp. atroseptica and characterization of virulence factors.	the bacterial family enterobacteriaceae is notable for its well studied human pathogens, including salmonella, yersinia, shigella, and escherichia spp. however, it also contains several plant pathogens. we report the genome sequence of a plant pathogenic enterobacterium, erwinia carotovora subsp. atroseptica (eca) strain scri1043, the causative agent of soft rot and blackleg potato diseases. approximately 33% of eca genes are not shared with sequenced enterobacterial human pathogens, including s ...	2004	15263089
kinetic and structural optimization to catalysis at low temperatures in a psychrophilic cellulase from the antarctic bacterium pseudoalteromonas haloplanktis.	the cold-adapted cellulase celg has been purified from the culture supernatant of the antarctic bacterium pseudoalteromonas haloplanktis and the gene coding for this enzyme has been cloned, sequenced and expressed in escherichia coli. this cellulase is composed of three structurally and functionally distinct regions: an n-terminal catalytic domain belonging to glycosidase family 5 and a c-terminal cellulose-binding domain belonging to carbohydrate-binding module family 5. the linker of 107 resid ...	2004	15287848
role of the pilot protein yscw in the biogenesis of the yscc secretin in yersinia enterocolitica.	the yscc secretin is a major component of the type iii protein secretion system of yersinia enterocolitica and forms an oligomeric structure in the outer membrane. in a mutant lacking the outer membrane lipoprotein yscw, secretion is strongly reduced, and it has been proposed that yscw plays a role in the biogenesis of the secretin. to study the interaction between the secretin and this putative pilot protein, yscc and yscw were produced in trans in a y. enterocolitica strain lacking all other c ...	2004	15292137
erwinia chrysanthemi o antigen is required for betaine osmoprotection in high-salt media.	cellular components necessary for osmoprotection are poorly known. in this study we show that o antigen is specifically required for the effectiveness of betaines as osmoprotectants for erwinia chrysanthemi in saline media. the phenotype is correlated with the inability of rfb mutant strains to maintain a high accumulation level of betaines in hypersaline media.	2004	15292161
salt-inducible multidrug efflux pump protein in the moderately halophilic bacterium chromohalobacter sp.	it has been known that halophilic bacteria often show natural resistance to antibiotics, dyes, and toxic metal ions, but the mechanism and regulation of this resistance have remained unexplained. we have addressed this question by identifying the gene responsible for multidrug resistance. a spontaneous ofloxacin-resistant mutant derived from the moderately halophilic bacterium chromohalobacter sp. strain 160 showed a two- to fourfold increased resistance to structurally diverse compounds, such a ...	2004	15294769
purification and characterization of chitosanase from bacillus sp. strain kctc 0377bp and its application for the production of chitosan oligosaccharides.	for the enzymatic production of chitosan oligosaccharides from chitosan, a chitosanase-producing bacterium, bacillus sp. strain kctc 0377bp, was isolated from soil. the bacterium constitutively produced chitosanase in a culture medium without chitosan as an inducer. the production of chitosanase was increased from 1.2 u/ml in a minimal chitosan medium to 100 u/ml by optimizing the culture conditions. the chitosanase was purified from a culture supernatant by using cm-toyopearl column chromatogra ...	2004	15294781
crystallization and preliminary x-ray crystallographic analysis of shikimate kinase from erwinia chrysanthemi.	shikimate kinase from erwinia chrysanthemi, overexpressed in escherichia coli has been crystallized by the vapour-diffusion method using sodium chloride as a precipitant. mass spectrometry was used to confirm the purity of the shikimate kinase and dynamic light scattering was used to assess conditions for the monodispersity of the enzyme. the crystals are tetragonal, space group p4(1)2(1)2 or enantiomorph with cell dimensions a = b = 108.5 and c = 92.8 a (at 100 k). native crystals diffract to b ...	1997	15299895
crystallization of xylanase from erwinia chrysanthemi: influence of heat and polymeric substrate.	xylanase from the bacterial plant pathogen erwinia chrysanthemi (e.c. 3.2.1.8), expressed in e. coli, has been crystallized for x-ray diffraction analysis both in the presence and the absence of its polymeric substrate 4-o-methyl glucuronoxylan. in all cases it was found that the quality, time of appearance, and reproducibility of both the native and complex crystals were significantly enhanced by heating of the protein to 323 k prior to dispensing the crystallization trials. crystals of the nat ...	1997	15299927
crystallization of cytochrome b562 from erwinia chrysanthemi.	cytochrome b(562) from erwinia chrysanthemi has been crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate as the precipitant. x-ray precession photographs show that the crystals formed belong to either of the enantiomorphic space groups p4(1)2(1)2 or p4(3)2(1)2 with the cell parameters a = b = 98.6 and c = 62.7 a. estimation of the crystal density and consideration of the possible values for v(m) indicate that there is either a dimer or trimer in the asymmetric unit. ...	1997	15299955
comparison of atpase-encoding type iii secretion system hrcn genes in biocontrol fluorescent pseudomonads and in phytopathogenic proteobacteria.	type iii protein secretion systems play a key role in the virulence of many pathogenic proteobacteria, but they also occur in nonpathogenic, plant-associated bacteria. certain type iii protein secretion genes (e.g., hrcc) have been found in pseudomonas sp. strain sbw25 (and other biocontrol pseudomonads), but other type iii protein secretion genes, such as the atpase-encoding gene hrcn, have not been found. using both colony hybridization and a pcr approach, we show here that hrcn is nevertheles ...	2004	15345390
identification of specific in vivo-induced (ivi) genes in yersinia ruckeri and analysis of ruckerbactin, a catecholate siderophore iron acquisition system.	this work reports the utilization of an in vivo expression technology system to identify in vivo-induced (ivi) genes in yersinia ruckeri after determination of the conditions needed for its selection in fish. fourteen clones were selected, and the cloned dna fragments were analyzed after partial sequencing. in addition to sequences with no significant similarity, homology with genes encoding proteins putatively involved in two-component and type iv secretion systems, adherence, specific metaboli ...	2004	15345400
genetic elucidation of nitric oxide signaling in incompatible plant-pathogen interactions.	recent experiments indicate that nitric oxide (no) plays a pivotal role in disease resistance and several other physiological processes in plants. however, most of the current information about the function of no in plants is based on pharmacological studies, and additional approaches are therefore required to ascertain the role of no as an important signaling molecule in plants. we have expressed a bacterial nitric oxide dioxygenase (nod) in arabidopsis plants and/or avirulent pseudomonas syrin ...	2004	15347797
phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion.	comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. this process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial dna. many prophages from bacterial pathogens encode virulence factors. two situations can be distinguished: vibrio cholerae, shiga toxin-producing escherichia coli, corynebacterium diphtheriae, and clostridium botulinum depend on a specific p ...	2004	15353570
the secretome of the plant pathogenic bacterium erwinia chrysanthemi.	erwinia chrysanthemi causes soft-rot diseases of many plants by secreting a battery of enzymes which degrade the plant cell walls. we initiated a proteomic analysis to create a reference map of the e. chrysanthemi secretome. extracellular proteins were isolated from e. chrysanthemi culture supernatants and resolved by two-dimensional electrophoresis. by analysis of mutants, western blotting, and matrix-assisted laser desorption/ionization-time of flight (maldi-tof) 55 spots representing 25 uniqu ...	2004	15378709
genome-wide identification of plant-upregulated genes of erwinia chrysanthemi 3937 using a gfp-based ivet leaf array.	a green fluorescent protein-based in vivo expression technology leaf array was used to identify genes in erwinia chrysanthemi 3937 that were specifically upregulated in plants compared with growth in a laboratory culture medium. of 10,000 e. chrysanthemi 3937 clones, 61 were confirmed as plant upregulated. on the basis of sequence similarity, these were recognized with probable functions in metabolism (20%), information transfer (15%), regulation (11%), transport (11%), cell processes (11%), and ...	2004	15384490
transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium thermotoga maritima.	thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees c. a whole-genome cdna microarray was used to examine differential expression patterns between biofilm and planktonic populations. mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the ge ...	2004	15466556
variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice.	in animal pathogenic bacteria, horizontal gene transfer events (hgt) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (lps). as a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. since lps is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. although lps has been suggested as a ...	2004	15473911
glutamine, glutamate, and alpha-glucosylglycerate are the major osmotic solutes accumulated by erwinia chrysanthemi strain 3937.	erwinia chrysanthemi is a phytopathogenic soil enterobacterium closely related to escherichia coli. both species respond to hyperosmotic pressure and to external added osmoprotectants in a similar way. unexpectedly, the pools of endogenous osmolytes show different compositions. instead of the commonly accumulated glutamate and trehalose, e. chrysanthemi strain 3937 promotes the accumulation of glutamine and alpha-glucosylglycerate, which is a new osmolyte for enterobacteria, together with glutam ...	2004	15528516
comparative genomics of the kdgr regulon in erwinia chrysanthemi 3937 and other gamma-proteobacteria.	in the plant-pathogenic enterobacterium erwinia chrysanthemi, almost all known genes involved in pectin catabolism are controlled by the transcriptional regulator kdgr. in this study, the comparative genomics approach was used to analyse the kdgr regulon in completely sequenced genomes of eight enterobacteria, including erw. chrysanthemi, and two vibrio species. application of a signal recognition procedure complemented by operon structure and protein sequence analysis allowed identification of ...	2004	15528647
crystal structure of jun a 1, the major cedar pollen allergen from juniperus ashei, reveals a parallel beta-helical core.	pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the northern hemisphere. we report the first crystal structure of a cedar allergen, jun a 1, from the pollen of the mountain cedar juniperus ashei (cupressaceae). the core of the structure consists primarily of a parallel beta-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms. four ige epitopes mapped to the surfa ...	2004	15539389
crystal structure of jun a 1, the major cedar pollen allergen from juniperus ashei, reveals a parallel beta-helical core.	pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the northern hemisphere. we report the first crystal structure of a cedar allergen, jun a 1, from the pollen of the mountain cedar juniperus ashei (cupressaceae). the core of the structure consists primarily of a parallel beta-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms. four ige epitopes mapped to the surfa ...	2004	15539389
ralstonia solanacearum iron scavenging by the siderophore staphyloferrin b is controlled by phca, the global virulence regulator.	phca is a transcriptional regulator that activates expression of multiple virulence genes in the plant pathogen ralstonia solanacearum. relative to their wild-type parents, phca mutants overproduced iron-scavenging activity detected with chrome azurol s siderophore detection medium. transposon mutagenesis of strain aw1-pc (phca1) generated strain gb6, which was siderophore negative but retained weak iron-scavenging activity. the ssd gene inactivated in gb6 encodes a protein similar to group iv a ...	2004	15547261
atp-binding cassette transporters are targets for the development of antibacterial vaccines and therapies.		2004	15557595
[genetic regulation of pathogenicity and virulence factors in bacteria erwinia carotovora subsp. atroseptica: identification of kdud gene].	a mutant that cannot utilize pectin substances of plant cell walls was obtained via insertion of mini-mini-tn5xyle transposon into the chromosome of phytopathogenic bacteria erwinia carotovora subsp. atroseptica. the inability of mutant cells to utilize these substrates was caused by a failure to accomplish the catabolism of unsaturated digalacturonic acid (uda). study of enzymatic activities has established that mutant bacteria lost the ability to produce 2,5-diketo-3-deoxygluconate dehydrogena ...	2004	15559145
[genetic regulation of pathogenicity and virulence factors in bacteria erwinia carotovora subsp. atroseptica: phenotypic characteristic of bacteria with the mutant kdud gene].	in contrast to the closely related bacteria erwinia chrysanthemi, bacteria erwinia carotovora subsp. atroseptica produce lower levels of main pathogenicity and virulence factors (pectate lyases, cellulases, and proteases) in the presence of pectins. this effect was shown to be connected with the accumulation of the intermediate product of intracellular degradation of these substances, 2,5-diketo-3-deoxygluconate (dk2). the presence of dk2 in the culture broth of mutant bacteria, connected to its ...	2004	15559146
the biosynthesis of udp-galacturonic acid in plants. functional cloning and characterization of arabidopsis udp-d-glucuronic acid 4-epimerase.	udp-glca 4-epimerase (uglcae) catalyzes the epimerization of udp-alpha-d-glucuronic acid (udp-glca) to udp-alpha-d-galacturonic acid (udp-gala). udp-gala is a precursor for the synthesis of numerous cell-surface polysaccharides in bacteria and plants. using a biochemical screen, a gene encoding atuglcae1 in arabidopsis (arabidopsis thaliana) was identified and the recombinant enzyme biochemically characterized. the gene belongs to a small gene family composed of six isoforms. all members of the ...	2004	15563616
analysis of bgl operon structure and characterization of beta-glucosidase from pectobacterium carotovorum subsp. carotovorum ly34.	a putative bgl operon of pectobacterium carotovorum subsp. carotovorum ly34 (pcc ly34) was isolated. sequence analysis of the 5,557 bp cloned dna fragment (accession no. ay542524) showed three open reading frames (bglt, bglp, and bglb) predicted to encode 287, 633, and 468 amino acid proteins respectively. bglt and bglp orfs show high similarity to that of the pectobacterium chrysanthemi arbg antiterminator and arbf permease respectively. also, the latter contains most residues important for pho ...	2004	15564664
comparison of proteolytic activities produced by entomopathogenic photorhabdus bacteria: strain- and phase-dependent heterogeneity in composition and activity of four enzymes.	twenty strains (including eight phase variant pairs) of nematode-symbiotic and insect-pathogenic photorhabdus bacteria were examined for the production of proteolytic enzymes by using a combination of several methods, including gelatin liquefaction, zymography coupled to native and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and activity measurement with two chromogen substrate types. four protease activities (approximately 74, approximately 55, approximately 54, and approximately ...	2004	15574931
involvement of sirabc in iron-siderophore import in staphylococcus aureus.	staphylococcus aureus sira was previously identified as a lipoprotein, and sirb and sirc are thought to encode the transmembrane domains of an abc transporter. sir proteins show similarity to iron-siderophore transporters in several bacteria. here, we show that the iron-regulated sirabc operon is divergently transcribed from the sbn operon that encodes enzymes involved in the synthesis of staphylobactin, a recently described siderophore produced by s. aureus. mutation of either sira or sirb incr ...	2004	15576785
type v protein secretion pathway: the autotransporter story.	gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. to overcome this barrier, bacteria have developed several systems for protein secretion. the type v secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type vc or at-2 family of proteins. since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the adv ...	2004	15590781
process of protein transport by the type iii secretion system.	the type iii secretion system (ttss) of gram-negative bacteria is responsible for delivering bacterial proteins, termed effectors, from the bacterial cytosol directly into the interior of host cells. the ttss is expressed predominantly by pathogenic bacteria and is usually used to introduce deleterious effectors into host cells. while biochemical activities of effectors vary widely, the ttss apparatus used to deliver these effectors is conserved and shows functional complementarity for secretion ...	2004	15590783
identification of two new genes involved in diazotrophic growth via the alternative fe-only nitrogenase in the phototrophic purple bacterium rhodobacter capsulatus.	growth of rhodobacter capsulatus with molecular dinitrogen as the sole n source via the alternative fe-only nitrogenase requires all seven gene products of the anfhdgk-1-2-3 operon. in contrast to mutant strains carrying lesions in the structural genes of nitrogenase (anfh, anfd, anfg, and anfk), strains defective for either anf1, anf2, or anf3 are still able to reduce the artificial substrate acetylene, although with diminished activity. to obtain further information on the role of anf1, we scr ...	2005	15601692
atnap1 represents an atypical sufb protein in arabidopsis plastids.	the assembly of iron-sulfur (fe-s) clusters involves several pathways and in prokaryotes the mobilization of the sulfur (suf) system is paramount for fe-s biogenesis and repair during oxidative stress. the prokaryotic suf system consists of six proteins: sufc is an abc/atpase that forms a complex with sufb and sufd, sufa acts as a scaffold protein, and sufe and sufs are involved in sulfur mobilization from cysteine. despite the importance of fe-s proteins in higher plant plastids, little is know ...	2004	15611066
atnap1 represents an atypical sufb protein in arabidopsis plastids.	the assembly of iron-sulfur (fe-s) clusters involves several pathways and in prokaryotes the mobilization of the sulfur (suf) system is paramount for fe-s biogenesis and repair during oxidative stress. the prokaryotic suf system consists of six proteins: sufc is an abc/atpase that forms a complex with sufb and sufd, sufa acts as a scaffold protein, and sufe and sufs are involved in sulfur mobilization from cysteine. despite the importance of fe-s proteins in higher plant plastids, little is know ...	2004	15611066
erwinia chrysanthemi requires a second iron transport route dependent of the siderophore achromobactin for extracellular growth and plant infection.	full virulence of the pectinolytic enterobacterium erwinia chrysanthemi strain 3937 depends on the production in planta of the catechol-type siderophore chrysobactin. under iron-limited conditions, e. chrysanthemi synthesizes a second siderophore called achromobactin belonging to the hydroxy/carboxylate class of siderophore. in this study, we cloned and functionally characterized a 13 kb long operon comprising seven genes required for the biosynthesis (acs) and extracellular release (yhca) of ac ...	2005	15612933
a mutation in the sap operon attenuates survival of nontypeable haemophilus influenzae in a chinchilla model of otitis media.	bacteria have evolved strategies to resist killing by antimicrobial peptides (aps), important effectors of innate immunity. the sap (sensitivity to antimicrobial peptides) operon confers resistance to ap-mediated killing of salmonella. we have recently shown that sapa gene expression is upregulated in the middle ear in a chinchilla model of nontypeable haemophilus influenzae (nthi)-induced otitis media. based on these findings, we constructed an nthi strain containing a lux reporter plasmid driv ...	2005	15618200
the erwinia chrysanthemi type iii secretion system is required for multicellular behavior.	enterobacterial animal pathogens exhibit aggregative multicellular behavior, which is manifested as pellicles on the culture surface and biofilms at the surface-liquid-air interface. pellicle formation behavior requires production of extracellular polysaccharide, cellulose, and protein filaments, known as curli. protein filaments analogous to curli are formed by many protein secretion systems, including the type iii secretion system (ttss). here, we demonstrate that erwinia chrysanthemi, which d ...	2005	15629935
a clp gene homologue belonging to the crp gene family globally regulates lytic enzyme production, antimicrobial activity, and biological control activity expressed by lysobacter enzymogenes strain c3.	lysobacter enzymogenes strain c3, a biological control agent for plant diseases, produces multiple extracellular hydrolytic enzymes and displays antimicrobial activity against various fungal and oomycetous species. however, little is known about the regulation of these enzymes or their roles in antimicrobial activity and biocontrol. a study was undertaken to identify mutants of strain c3 affected in extracellular enzyme production and to evaluate their biocontrol efficacy. a single mini-tn5-lacz ...	2005	15640196
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096
construction of minimum size cellulase (cel5z) from pectobacterium chrysanthemi py35 by removal of the c-terminal region.	pectobacterium chrysanthemi py35 secretes the endoglucanase cel5z, an enzyme of the glycoside hydrolase family 5. cel5z is a 426 amino acid, signal peptide (sp)-containing protein composed of two domains: a large n-terminal catalytic domain (cd; 291 amino acids) and a small c-terminal cellulose binding domain (cbd; 62 amino acids). these two domains are separated by a 30 amino acid linker region (lr). a truncated cel5z gene was constructed with the addition of a nonsense mutation that removes th ...	2005	15666145
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
mutations of ousa alter the virulence of erwinia chrysanthemi.	a negative correlation was observed between the aggressiveness of several erwinia chrysanthemi strains on potato tuber and their osmotic tolerance. the disruption of the ousa gene encoding the major osmoprotectant uptake system highly enhanced bacterial virulence on potato tubers. the ousa disruption also increased the maceration efficiency on potato tubers under anaerobic conditions. in the absence of oxygen, pectate lyase (pel) production was significantly higher in the tissue macerated with t ...	2005	15720084
structural basis for the interaction between pectin methylesterase and a specific inhibitor protein.	pectin, one of the main components of the plant cell wall, is secreted in a highly methyl-esterified form and subsequently deesterified in muro by pectin methylesterases (pmes). in many developmental processes, pmes are regulated by either differential expression or posttranslational control by protein inhibitors (pmeis). pmeis are typically active against plant pmes and ineffective against microbial enzymes. here, we describe the three-dimensional structure of the complex between the most abund ...	2005	15722470
a sequence-based identification of the genes detected by probesets on the affymetrix u133 plus 2.0 array.	one of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. we believe that this is largely the result of poor gene identification. we re-identified the probesets on the affymetrix u133 plus 2.0 genechip array. this identification was based on the sequence of the probes and the sequence of the human genome. using the blast program, we matched probes with documented a ...	2005	15722477
hosa, a member of the slya family, regulates motility in enteropathogenic escherichia coli.	in enteropathogenic and enterohemorraghic escherichia coli (epec and ehec), two members of the slya family of transcriptional regulators have been identified as slya. western blot analysis of the wild type and the corresponding hosa and slya deletion mutants indicated that slya and hosa are distinct proteins whose expression is not interdependent. of 27 different e. coli strains (epec, ehec, enteroinvasive, enteroaggregative, uropathogenic, and commensal) examined, 14 were positive for both gene ...	2005	15731069
function and expression of an n-acetylneuraminic acid-inducible outer membrane channel in escherichia coli.	the escherichia coli yjha (renamed nanc) gene encodes a protein of the kdgm family of outer membrane-specific channels. it is transcribed divergently from fimb, a gene involved in the site-specific inversion of the region controlling transcription of the fimbrial structural genes but is separated from it by one of the largest intergenic regions in e. coli. we show that nanc expression is induced by n-acetylneuraminic acid and modulated by n-acetylglucosamine. this regulation occurs via the nanr ...	2005	15743943
role of the phop-phoq system in the virulence of erwinia chrysanthemi strain 3937: involvement in sensitivity to plant antimicrobial peptides, survival at acid hh, and regulation of pectolytic enzymes.	erwinia chrysanthemi is a phytopathogenic bacterium that causes soft-rot diseases in a broad number of crops. the phop-phoq system is a key factor in pathogenicity of several bacteria and is involved in the bacterial resistance to different factors, including acid stress. since e. chrysanthemi is confronted by acid ph during pathogenesis, we have studied the role of this system in the virulence of this bacterium. in this work, we have isolated and characterized the phop and phoq mutants of e. ch ...	2005	15743964
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