Publications

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
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
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
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
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
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
the many faces of protease-protein inhibitor interaction.	proteases and their natural protein inhibitors are among the most intensively studied protein-protein complexes. there are about 30 structurally distinct inhibitor families that are able to block serine, cysteine, metallo- and aspartyl proteases. the mechanisms of inhibition can be related to the catalytic mechanism of protease action or include a mechanism-unrelated steric blockage of the active site or its neighborhood. the structural elements that are responsible for the inhibition most often ...	2005	15775973
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
mechanisms of protein export across the bacterial outer membrane.		2005	15968039
unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression.	a major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. in vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. the widely used gene-to-phenotype approach involves the identification of altered niche-related phen ...	2005	15944455
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
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
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
bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion.	like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ...	2005	15757514
the 'permeome' of the malaria parasite: an overview of the membrane transport proteins of plasmodium falciparum.	the uptake of nutrients, expulsion of metabolic wastes and maintenance of ion homeostasis by the intraerythrocytic malaria parasite is mediated by membrane transport proteins. proteins of this type are also implicated in the phenomenon of antimalarial drug resistance. however, the initial annotation of the genome of the human malaria parasite plasmodium falciparum identified only a limited number of transporters, and no channels. in this study we have used a combination of bioinformatic approach ...	2005	15774027
structure and biochemical analysis of a secretin pilot protein.	the ability to translocate virulence proteins into host cells through a type iii secretion apparatus (ttss) is a hallmark of several gram-negative pathogens including shigella, salmonella, yersinia, pseudomonas, and enteropathogenic escherichia coli. in common with other types of bacterial secretion apparatus, the assembly of the ttss complex requires the preceding formation of its integral outer membrane secretin ring component. we have determined at 1.5 a the structure of mxim28-142, the shige ...	2005	15775974
functional insights from the distribution and role of homopeptide repeat-containing proteins.	expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ...	2005	15805494
lethal effect of the gliding arc discharges on erwinia spp.	to compare the decontamination performances of glidarc on strains of erwinia of industrial interest.	2005	15836472
autoinduction in erwinia amylovora: evidence of an acyl-homoserine lactone signal in the fire blight pathogen.	erwinia amylovora causes fire blight disease of apple, pear, and other members of the rosaceae. here we present the first evidence for autoinduction in e. amylovora and a role for an n-acyl-homoserine lactone (ahl)-type signal. two major plant virulence traits, production of extracellular polysaccharides (amylovoran and levan) and tolerance to free oxygen radicals, were controlled in a bacterial-cell-density-dependent manner. two standard autoinducer biosensors, agrobacterium tumefaciens ntl4 an ...	2005	15838048
three-dimensional structure of (1,4)-beta-d-mannan mannanohydrolase from tomato fruit.	the three-dimensional crystal structure of tomato (lycopersicon esculentum) beta-mannanase 4a (leman4a) has been determined to 1.5 a resolution. the enzyme adopts the (beta/alpha)(8) fold common to the members of glycohydrolase family gh5. the structure is comparable with those of the homologous trichoderma reesei and thermomonospora fusca beta-mannanases: there is a conserved three-stranded beta-sheet located near the n terminus that stacks against the central beta-barrel at the end opposite th ...	2005	15840830
structure of a full length psychrophilic cellulase from pseudoalteromonas haloplanktis revealed by x-ray diffraction and small angle x-ray scattering.	pseudoalteromonas haloplanktis is a psychrophilic gram-negative bacterium isolated in antarctica, that lives on organic remains of algae. this bacterium converts the cellulose, highly constitutive of algae, into an immediate nutritive form by biodegrading this biopolymer. to understand the mechanisms of cold adaptation of its enzymatic components, we studied the structural properties of an endoglucanase, cel5g, by complementary methods, x-ray crystallography and small angle x-ray scattering. usi ...	2005	15854656
imidazole antibiotics inhibit the nitric oxide dioxygenase function of microbial flavohemoglobin.	flavohemoglobins metabolize nitric oxide (no) to nitrate and protect bacteria and fungi from no-mediated damage, growth inhibition, and killing by no-releasing immune cells. antimicrobial imidazoles were tested for their ability to coordinate flavohemoglobin and inhibit its no dioxygenase (nod) function. miconazole, econazole, clotrimazole, and ketoconazole inhibited the nod activity of escherichia coli flavohemoglobin with apparent k(i) values of 80, 550, 1,300, and 5,000 nm, respectively. sacc ...	2005	15855504
the semi-phosphorylative entner-doudoroff pathway in hyperthermophilic archaea: a re-evaluation.	biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ed (entner-doudoroff) pathway generally proceeds via a non-phosphorylative variant. a key enzyme of the non-phosphorylating ed pathway of sulfolobus solfataricus, kdg (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. in the present study, a comparative genomics analysis is described that reveals conserved ed gene clusters in both thermoproteus tenax a ...	2005	15869466
production of autoinducer 2 in salmonella enterica serovar thompson contributes to its fitness in chickens but not on cilantro leaf surfaces.	food-borne illness caused by salmonella enterica has been linked traditionally to poultry products but is associated increasingly with fresh fruits and vegetables. we have investigated the role of the production of autoinducer 2 (ai-2) in the ability of s. enterica serovar thompson to colonize the chicken intestine and the cilantro phyllosphere. a mutant of s. enterica serovar thompson that is defective in ai-2 production was constructed by insertional mutagenesis of luxs. the population size of ...	2005	15870357
prevalence of pathogenicity island iicft073 genes among extraintestinal clinical isolates of escherichia coli.	uropathogenic escherichia coli is the most common cause of urinary tract infection (uti). cystitis in women is by far the most common uti; pyelonephritis in both sexes and prostatitis in men are more severe but are less frequent complaints. the ability of e. coli to cause uti is associated with specific virulence determinants, some of which are encoded on pathogenicity islands (pai). one such pai (pai iicft073), of the prototypical uropathogenic e. coli strain cft073, contains 116 open reading f ...	2005	15872276
iron-sulfur cluster biogenesis in chloroplasts. involvement of the scaffold protein cpisca.	the chloroplast contains many iron (fe)-sulfur (s) proteins for the processes of photosynthesis and nitrogen and s assimilation. although isolated chloroplasts are known to be able to synthesize their own fe-s clusters, the machinery involved is largely unknown. recently, a cysteine desulfurase was reported in arabidopsis (arabidopsis thaliana; atcpnifs) that likely provides the s for fe-s clusters. here, we describe an additional putative component of the plastid fe-s cluster assembly machinery ...	2005	15888686
bordetella alcs transporter functions in alcaligin siderophore export and is central to inducer sensing in positive regulation of alcaligin system gene expression.	bordetella pertussis and bordetella bronchiseptica, which are respiratory mucosal pathogens of mammals, produce and utilize the siderophore alcaligin to acquire iron in response to iron starvation. a predicted permease of the major facilitator superfamily class of membrane efflux pumps, alcs (synonyms, orfx and bcr), was reported to be encoded within the alcaligin gene cluster. in this study, alcs null mutants were found to be defective in growth under iron starvation conditions, in iron source ...	2005	15901687
novel molecular features of the fibrolytic intestinal bacterium fibrobacter intestinalis not shared with fibrobacter succinogenes as determined by suppressive subtractive hybridization.	suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium fibrobacter intestinalis dr7 not shared by fibrobacter succinogenes s85. subtractive clones from f. intestinalis were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. of these, 55 sequences were unique to f. intestinalis. the remaining contigs contained 764 genes with blastx simi ...	2005	15901698
1.6 a crystal structure of yter protein from bacillus subtilis, a predicted lyase.		2005	15906318
evolutionary relationships of three new species of enterobacteriaceae living as symbionts of aphids and other insects.	ecological studies on three bacterial lineages symbiotic in aphids have shown that they impose a variety of effects on their hosts, including resistance to parasitoids and tolerance to heat stress. phylogenetic analyses of partial sequences of gyrb and reca are consistent with previous analyses limited to 16s rrna gene sequences and yield improved confidence of the evolutionary relationships of these symbionts. all three symbionts are in the enterobacteriaceae. one of the symbionts, here given t ...	2005	15933033
involvement of bacterial quorum-sensing signals in spoilage of bean sprouts.	bacterial communication signals, acylated homoserine lactones (ahls), were extracted from samples of commercial bean sprouts undergoing soft-rot spoilage. bean sprouts produced in the laboratory did not undergo soft-rot spoilage and did not contain ahls or ahl-producing bacteria, although the bacterial population reached levels similar to those in the commercial sprouts, 10(8) to 10(9) cfu/g. ahl-producing bacteria (enterobacteriaceae and pseudomonads) were isolated from commercial sprouts, and ...	2005	15933035
role of xcpp in the functionality of the pseudomonas aeruginosa secreton.	in gram-negative bacteria, most signal-peptide-dependent exoproteins are secreted via the type ii secretion system (t2ss or secreton). in pseudomonas aeruginosa, t2ss consists of twelve xcp proteins (xcpa and xcpp to xcpz) thought to be organized as a multiproteic complex within the envelope. although well conserved, t2ss are known to be species-specific, namely for distant organisms, and this characteristic was thought to involve xcpp. to check which domain of xcpp could be involved in the spec ...	2005	15936176
pseudomonas syringae type iii chaperones shco1, shcs1, and shcs2 facilitate translocation of their cognate effectors and can substitute for each other in the secretion of hopo1-1.	the pseudomonas syringae type iii secretion system (ttss) translocates effector proteins into plant cells. several p. syringae effectors require accessory proteins called type iii chaperones (ttcs) to be secreted via the ttss. we characterized the hopo1-1, hops1, and hops2 operons in p. syringae pv. tomato dc3000; these operons encode three homologous ttcs, shco1, shcs1, and shcs2. shco1, shcs1, and shcs2 facilitated the type iii secretion and/or translocation of their cognate effectors hopo1-1, ...	2005	15937188
cloning, expression and characterisation of erwinia carotovora l-asparaginase.	bacterial l-asparaginases (e.c. 3.5.1.1) have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia. l-asparaginase from erwinia carotovora ncyc 1526 (era) was cloned and expressed in e. coli. the enzyme was purified to homogeneity by a two-step procedure comprising cation-exchange chromatography and affinity chromatography on immobilised l-asparagine. the enzymatic properties of the recombinant enzyme were investigated and the kinetic parameters (k(m), k(ca ...	2005	15951039
epimerase active domain of pseudomonas aeruginosa algg, a protein that contains a right-handed beta-helix.	the polysaccharide alginate forms a protective capsule for pseudomonas aeruginosa during chronic pulmonary infections. the structure of alginate, a linear polymer of beta1-4-linked o-acetylated d-mannuronate (m) and l-guluronate (g), is important for its activity as a virulence factor. alginate structure is mediated by algg, a periplasmic c-5 mannuronan epimerase. algg also plays a role in protecting alginate from degradation by the periplasmic alginate lyase algl. here, we show that the c-termi ...	2005	15968068
flavohaemoglobin hmpx from erwinia chrysanthemi confers nitrosative stress tolerance and affects the plant hypersensitive reaction by intercepting nitric oxide produced by the host.	host cells respond to infection by generating nitric oxide (no) as a cytotoxic weapon to facilitate killing of invading microbes. bacterial flavohaemoglobins are well-known scavengers of no and play a crucial role in protecting animal pathogens from nitrosative stress during infection. erwinia chrysanthemi, which causes macerating diseases in a wide variety of plants, possesses a flavohaemoglobin (hmpx) whose function in plant pathogens has remained unclear. here we show that hmpx consumes no an ...	2005	15998309
siderophore-mediated upregulation of arabidopsis ferritin expression in response to erwinia chrysanthemi infection.	ferritins are multimeric iron storage proteins encoded by a four-member gene family in arabidopsis (atfer1-4). to investigate whether iron sequestration in ferritins is a part of an iron-withholding defense system induced in response to bacterial invasion, we used arabidopsis thaliana as a susceptible host for the pathogenic bacterium erwinia chrysanthemi. in this study, we used a t-dna insertion mutant line to show that the lack of a functional atfer1 gene resulted in an enhanced susceptibility ...	2005	15998312
ousb, a broad-specificity abc-type transporter from erwinia chrysanthemi, mediates uptake of glycine betaine and choline with a high affinity.	the ability of erwinia chrysanthemi to cope with environments of elevated osmolality is due in part to the transport and accumulation of osmoprotectants. in this study we have identified a high-affinity glycine betaine and choline transport system in e. chrysanthemi. by using a pool of tn5-b21 ousa mutants, we isolated a mutant that could grow in the presence of a toxic analogue of glycine betaine (benzyl-glycine betaine) at high osmolalities. this mutant was impaired in its ability to transport ...	2005	16000740
transfer of pectobacterium chrysanthemi (burkholder et al. 1953) brenner et al. 1973 and brenneria paradisiaca to the genus dickeya gen. nov. as dickeya chrysanthemi comb. nov. and dickeya paradisiaca comb. nov. and delineation of four novel species, dickeya dadantii sp. nov., dickeya dianthicola sp. nov., dickeya dieffenbachiae sp. nov. and dickeya zeae sp. nov.	a collection of 75 strains of pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of brenneria paradisiaca (cfbp 4178(t)) and pectobacterium cypripedii (cfbp 3613(t)) were studied by dna-dna hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16s rrna gene-based phylogenetic analyses. from analysis of 16s rrna gene sequences, it was deduced that p. chrysanthemi strains and b. paradisiaca cfbp 4178(t) formed a clade distinct from th ...	2005	16014461
mutation of the zinc-binding metalloprotease motif affects bacteroides fragilis toxin activity but does not affect propeptide processing.	to evaluate the role of the zinc-binding metalloprotease in bacteroides fragilis toxin (bft) processing and activity, the zinc-binding consensus sequences (h348, e349, h352, g355, h358, and m366) were mutated by site-directed-mutagenesis. our results indicated that single point mutations in the zinc-binding metalloprotease motif do not affect bft processing but do reduce or eliminate bft biologic activity in vitro.	2005	16041055
comparison of the complete genome sequences of pseudomonas syringae pv. syringae b728a and pv. tomato dc3000.	the complete genomic sequence of pseudomonas syringae pv. syringae b728a (pss b728a) has been determined and is compared with that of p. syringae pv. tomato dc3000 (pst dc3000). the two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and pst dc3000 having a more pronounced apoplastic growth habitat. the pss b728a ge ...	2005	16043691
the in situ observation of the temperature and pressure stability of recombinant aspergillus aculeatus pectin methylesterase with fourier transform ir spectroscopy reveals an unusual pressure stability of beta-helices.	the stability of recombinant aspergillus aculeatus pme (pectin methylesterase), an enzyme with high beta-helix content, was studied as a function of pressure and temperature. the conformational stability was monitored using ftir (fourier transform ir) spectroscopy whereas the functional enzyme stability was monitored by inactivation studies. protein unfolding followed by amorphous aggregation, which makes the process irreversible, was observed at temperatures above 50 degrees c. this could be co ...	2005	16050809
parallel beta-sheets and polar zippers in amyloid fibrils formed by residues 10-39 of the yeast prion protein ure2p.	we report the results of solid-state nuclear magnetic resonance (nmr) and atomic force microscopy measurements on amyloid fibrils formed by residues 10-39 of the yeast prion protein ure2p (ure2p(10)(-)(39)). measurements of intermolecular (13)c-(13)c nuclear magnetic dipole-dipole couplings indicate that ure2p(10)(-)(39) fibrils contain in-register parallel beta-sheets. measurements of intermolecular (15)n-(13)c dipole-dipole couplings, using a new solid-state nmr technique called dsq-redor, are ...	2005	16060675
the bacteriophage p1 hot gene product can substitute for the escherichia coli dna polymerase iii {theta} subunit.	the theta subunit (hole gene product) of escherichia coli dna polymerase (pol) iii holoenzyme is a tightly bound component of the polymerase core. within the core (alpha-epsilon-theta), the alpha and epsilon subunits carry the dna polymerase and 3' proofreading functions, respectively, while the precise function of theta is unclear. hole homologs are present in genomes of other enterobacteriae, suggestive of a conserved function. putative homologs have also been found in the genomes of bacteriop ...	2005	16077097
structure of bacterial extracellular polymeric substances at different ph values as determined by saxs.	extracellular polymeric substances (eps) play an important role in cell aggregation, cell adhesion, and biofilm formation, and protect cells from a hostile environment. the eps was isolated by trichloroacetic acid/ethanol extraction from broth culture of a marine bacterium isolate. the eps was composed of glucose and galactose as determined by hplc and tlc; the protein content was on average 15 +/- 5% of eps dry mass. the solution structure of eps at different values of ph was revealed by small- ...	2005	16085763
characterization of an unusual cold-active beta-glucosidase belonging to family 3 of the glycoside hydrolases from the psychrophilic isolate paenibacillus sp. strain c7.	we selected for spore-forming psychrophilic bacteria able to use lactose as a carbon source and one isolate, designated paenibacillus sp. strain c7, that was phylogenetically related to, but distinct from both paenibacillus macquariensis and paenibacillus antarcticus. some escherichia coli transformants obtained with genomic dna from this isolate hydrolyzed x-gal (5-bromo-4-chloro-3-indoyl-beta-d-galactopyranoside) only below 30 degrees c, an indication of cold-active beta-galactosidase activity ...	2005	16085807
mycosubtilin overproduction by bacillus subtilis bbg100 enhances the organism's antagonistic and biocontrol activities.	a bacillus subtilis derivative was obtained from strain atcc 6633 by replacement of the native promoter of the mycosubtilin operon by a constitutive promoter originating from the replication gene repu of the staphylococcus aureus plasmid pub110. the recombinant strain, designated bbg100, produced up to 15-fold more mycosubtilin than the wild type produced. the overproducing phenotype was related to enhancement of the antagonistic activities against several yeasts and pathogenic fungi. hemolytic ...	2005	16085851
elevated temperature enhances virulence of erwinia carotovora subsp. carotovora strain ec153 to plants and stimulates production of the quorum sensing signal, n-acyl homoserine lactone, and extracellular proteins.	erwinia carotovora subsp. atroseptica, e. carotovora subsp. betavasculorum, and e. carotovora subsp. carotovora produce high levels of extracellular enzymes, such as pectate lyase (pel), polygalacturonase (peh), cellulase (cel), and protease (prt), and the quorum-sensing signal n-acyl-homoserine lactone (ahl) at 28 degrees c. however, the production of these enzymes and ahl by these bacteria is severely inhibited during growth at elevated temperatures (31.2 degrees c for e. carotovora subsp. atr ...	2005	16085860
the family of serratia type pore forming toxins.	the serratia marcescens hemolysin represents the prototype of a growing family of pore forming toxins. the available bacterial genome sequences reveal serratia hemolysin homologues in additional species. however, only s. marcescens hemolysin has been studied in great molecular detail. this family of toxins has nothing in common with the pore forming toxins of e. coli type (rtx toxins), the staphylococcus aureus alpha-toxin or the thiol activated toxin of group a beta-hemolytic streptococci (stre ...	2005	16101433
identification of the mycobacterium tuberculosis suf machinery as the exclusive mycobacterial system of [fe-s] cluster assembly: evidence for its implication in the pathogen's survival.	the worldwide recrudescence of tuberculosis and widespread antibiotic resistance have strengthened the need for the rapid development of new antituberculous drugs targeting essential functions of its etiologic agent, mycobacterium tuberculosis. in our search for new targets, we found that the m. tuberculosis pps1 gene, which contains an intein coding sequence, belongs to a conserved locus of seven open reading frames. in silico analyses indicated that the mature pps1 protein is orthologous to th ...	2005	16109955
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
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
replication termination in escherichia coli: structure and antihelicase activity of the tus-ter complex.	the arrest of dna replication in escherichia coli is triggered by the encounter of a replisome with a tus protein-ter dna complex. a replication fork can pass through a tus-ter complex when traveling in one direction but not the other, and the chromosomal ter sites are oriented so replication forks can enter, but not exit, the terminus region. the tus-ter complex acts by blocking the action of the replicative dnab helicase, but details of the mechanism are uncertain. one proposed mechanism invol ...	2005	16148308
purification and characterization of the n-terminal domain of exea: a novel atpase involved in the type ii secretion pathway of aeromonas hydrophila.	aeromonas hydrophila secretes a number of degradative enzymes and toxins into the external milieu via the type ii secretory pathway or secreton. exea is an essential component of this system and is necessary for the localization and/or multimerization of the secretin exed. exea contains two sequence motifs characteristic of the walker superfamily of atpases. previous examination of substitution derivatives altered in these motifs suggested that atp binding or hydrolysis is required for exeab com ...	2005	16159770
role of conserved cysteines in mediating sulfur transfer from iscs to iscu.	the role of the three conserved cysteine residues on azotobacter vinelandii iscu in accepting sulfane sulfur and forming a covalent complex with iscs has been evaluated using electrospray-ionization mass spectrometry studies of variants involving individual cysteine-to-alanine substitutions. the results reveal that iscs can transfer sulfur to each of the three alanine-substituted forms of iscu to yield persulfide or polysulfide species, and formation of a heterodisulfide covalent complex between ...	2005	16165131
gene products of the hupghij operon are involved in maturation of the iron-sulfur subunit of the [nife] hydrogenase from rhizobium leguminosarum bv. viciae.	in the present study, we investigate the functions of the hupghij operon in the synthesis of an active [nife] hydrogenase in the legume endosymbiont rhizobium leguminosarum bv. viciae. these genes are clustered with 14 other genes including the hydrogenase structural genes hupsl. a set of isogenic mutants with in-frame deletions (deltahupg, deltahuph, deltahupi, and deltahupj) was generated and tested for hydrogenase activity in cultures grown at different oxygen concentrations (0.2 to 2.0%) and ...	2005	16199572
towards the identification of type ii secretion signals in a nonacylated variant of pullulanase from klebsiella oxytoca.	pullulanase (pula) from the gram-negative bacterium klebsiella oxytoca is a 116-kda surface-anchored lipoprotein of the isoamylase family that allows growth on branched maltodextrin polymers. pula is specifically secreted via a type ii secretion system. pelbsp-pula, a nonacylated variant of pula made by replacing the lipoprotein signal peptide (sp) with the signal peptide of pectate lyase pelb from erwinia chrysanthemi, was efficiently secreted into the medium. two 80-amino-acid regions of pula, ...	2005	16199575
role of the regulatory gene rira in the transcriptional response of sinorhizobium meliloti to iron limitation.	a regulatory network of sinorhizobium meliloti genes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rira) were analyzed by mutation and microarray analyses. a constructed s. meliloti rira mutant exhibited growth defects and enhanced h2o2 sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. to identify iron-responsive and rira-regulated s. meliloti genes, a transcriptome approach using whole-genome mic ...	2005	16204511
tol-pal proteins are critical cell envelope components of erwinia chrysanthemi affecting cell morphology and virulence.	the tol-pal genes are necessary for maintaining the outer-membrane integrity of gram-negative bacteria. these genes were first described in escherichia coli, and more recently in several other species. they are involved in the pathogenesis of e. coli, haemophilus ducreyi, vibrio cholerae and salmonella enterica. the role of the tol-pal genes in bacterial pathogenesis was investigated in the phytopathogenic enterobacterium erwinia chrysanthemi, assuming that this organism might be a good model fo ...	2005	16207916
nonnatural amino acid incorporation into the methionine 214 position of the metzincin pseudomonas aeruginosa alkaline protease.	the alkaline protease from pseudomonas aeruginosa (apra) is a member of the metzincin superfamily of metalloendoproteases. a key feature of these proteases is a conserved methionine-containing 1,4-tight beta turn at the base of the active site zinc binding region.	2005	16221305
insights into genome plasticity and pathogenicity of the plant pathogenic bacterium xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.	the gram-negative plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. this pathosystem has become a well-established model for studying bacterial infection strategies. here, we present the whole-genome sequence of the pepper-pathogenic xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-mb circular chromosome and four plasmids. th ...	2005	16237009
identification of erwinia amylovora genes induced during infection of immature pear tissue.	the enterobacterium erwinia amylovora is a devastating plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. in this study, we used a modified in vivo expression technology system to identify e. amylovora genes that are activated during infection of immature pear tissue, a process that requires the major pathogenicity factors of this organism. we identified 394 unique pear fruit-induced (pfi) genes on the basis of sequence similarity to known genes a ...	2005	16291682
structural basis for shikimate-binding specificity of helicobacter pylori shikimate kinase.	shikimate kinase (ec 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of atp. as the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, but not mammals, shikimate kinase represents an attractive target for the development of new antimicrobial agents, herbicides, and antiparasitic agents. here, we report the 1.8-angstroms crystal structure of helicobacter pylori shikimate kinase (hps ...	2005	16291688
a degenerate type iii secretion system from septicemic escherichia coli contributes to pathogenesis.	the type iii secretion system (t3ss) is an important virulence factor used by several gram-negative bacteria to deliver effector proteins which subvert host cellular processes. enterohemorrhagic escherichia coli o157 has a well-defined t3ss involved in attachment and effacement (ett1) and critical for virulence. a gene cluster potentially encoding an additional t3ss (ett2), which resembles the spi-1 system in salmonella enterica, was found in its genome sequence. the ett2 gene cluster has since ...	2005	16291689
identification of a twin-arginine translocation system in pseudomonas syringae pv. tomato dc3000 and its contribution to pathogenicity and fitness.	the bacterial plant pathogen pseudomonas syringae pv. tomato dc3000 (dc3000) causes disease in arabidopsis thaliana and tomato plants, and it elicits the hypersensitive response in nonhost plants such as nicotiana tabacum and nicotiana benthamiana. while these events chiefly depend upon the type iii protein secretion system and the effector proteins that this system translocates into plant cells, additional factors have been shown to contribute to dc3000 virulence and still many others are likel ...	2005	16321949
fermentation of 10% (w/v) sugar to d: (-)-lactate by engineered escherichia coli b.	derivatives of ethanologenic escherichia coli k011 were constructed for d: (-)-lactate production by deleting genes encoding competing pathways followed by metabolic evolution, a growth-based selection for mutants with improved performance. resulting strains, sz132 and sz186, contain native genes for sucrose utilization. no foreign genes are present in sz186. strain sz132 also contains a chromosomally integrated endoglucanase gene (erwinia chrysanthemi cely). strain sz132 produced over 1 mol lac ...	2005	16328986
alternative sigma factors and their roles in bacterial virulence.	sigma factors provide promoter recognition specificity to rna polymerase holoenzyme, contribute to dna strand separation, and then dissociate from the core enzyme following transcription initiation. as the regulon of a single sigma factor can be composed of hundreds of genes, sigma factors can provide effective mechanisms for simultaneously regulating expression of large numbers of prokaryotic genes. one newly emerging field is identification of the specific roles of alternative sigma factors in ...	2005	16339734
pectinmethylesterase from the rice weevil, sitophilus oryzae: cdna isolation and sequencing, genetic origin, and expression of the recombinant enzyme.	a cdna clone encoding pectinmethylesterase of the rice weevil, sitophilus oryzae (l.) has been isolated and sequenced. the cdna clone was expressed in cultured insect cells and active pectinmethylesterase was purified from the culture medium, thus confirming that the cdna encodes pectinmethylesterase. in situ hybridization indicated that the enzyme's transcript was present in the midgut. weevils treated with tetracycline so that they lack genes of known symbiotic organisms still contained the pe ...	2005	16341253
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
crystallization and preliminary crystallographic analysis of l-asparaginase from erwinia carotovora.	bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. however, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. in contrast, l-asparaginase from erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. recombinant er. carotovora l-asparaginase was crystallized in the ...	2005	16511054
pecs and pect coregulate the synthesis of hrpn and pectate lyases, two virulence determinants in erwinia chrysanthemi 3937.	erwinia chrysanthemi strain 3937 is a necrotrophic bacterial plant pathogen. pectinolytic enzymes and, in particular, pectate lyases play a key role in soft rot symptoms; however, the efficient colonization of plants by e. chrysanthemi requires additional factors. these factors include hrpn (harpin), a heat-stable, glycine-rich hydrophilic protein, which is secreted by the type iii secretion system. we investigated the expression of hrpn in e. chrysanthemi 3937 in various environmental condition ...	2005	16353555
cytochrome p450 alkane hydroxylases of the cyp153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases.	several strains that grow on medium-chain-length alkanes and catalyze interesting hydroxylation and epoxidation reactions do not possess integral membrane nonheme iron alkane hydroxylases. using pcr, we show that most of these strains possess enzymes related to cyp153a1 and cyp153a6, cytochrome p450 enzymes that were characterized as alkane hydroxylases. a vector for the polycistronic coexpression of individual cyp153 genes with a ferredoxin gene and a ferredoxin reductase gene was constructed. ...	2006	16391025
a selc-associated genomic island of the extraintestinal avian pathogenic escherichia coli strain ben2908 is involved in carbohydrate uptake and virulence.	the complete nucleotide sequence and genetic organization of a new genomic island (agi-3) isolated from the extraintestinal avian pathogenic escherichia coli strain ben2908 is reported. this 49,600-bp island is inserted at the selc locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. agi-3 shows a mosaic structure of five modules. some of these modules are present in other e. coli strains and in other pathogenic bacter ...	2006	16428402
characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii.	the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ...	2006	16428406
calcium-regulated type iii secretion of yop proteins by an escherichia coli hha mutant carrying a yersinia pestis pcd1 virulence plasmid.	a series of four large deletions that removed a total of ca. 36 kb of dna from the ca. 70-kb yersinia pestis pcd1 virulence plasmid were constructed using lambda red-mediated recombination. escherichia coli hha deletion mutants carrying the virulence plasmid with the deletions expressed a functional calcium-regulated type iii secretion system. the e. coli hha/pcd1 system should facilitate molecular studies of the type iii secretion process.	2006	16428789
lbta and lbtb are required for production of the legionella pneumophila siderophore legiobactin.	under iron stress, legionella pneumophila secretes legiobactin, a nonclassical siderophore that is reactive in the chrome azurol s (cas) assay. here, we have optimized conditions for legiobactin expression, shown its biological activity, and identified two genes, lbta and lbtb, which are involved in legiobactin production. lbta appears to be iron repressed and encodes a protein that has significant homology with siderophore synthetases, and frga, a previously described iron-regulated protein of ...	2006	16452417
comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of atp-binding cassette transporters.	the transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. we integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. for functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cob ...	2006	16352848
disruption of n-acyl homoserine lactone-mediated cell signaling and iron acquisition in epiphytic bacteria by leaf surface compounds.	since n-acyl homoserine lactones (ahls) are key mediators of cell density-dependent regulation of traits involved in virulence and epiphytic fitness in gram-negative bacteria such as pseudomonas syringae, a variety of plant species were examined to determine their production of leaf surface compounds that could interact with these signaling systems. leaf washings of 17 of 52 plant species tested stimulated or inhibited ahl-dependent traits in at least one of the bacterial reporter strains used. ...	2006	16997987
pleiotropic role of quorum-sensing autoinducer 2 in photorhabdus luminescens.	bacterial virulence is an integrative process that may involve quorum sensing. in this work, we compared by global expression profiling the wild-type entomopathogenic photorhabdus luminescens subsp. laumondii tt01 to a luxs-deficient mutant unable to synthesize the type 2 quorum-sensing inducer ai-2. ai-2 was shown to regulate more than 300 targets involved in most compartments and metabolic pathways of the cell. ai-2 is located high in the hierarchy, as it controls the expression of several tra ...	2006	17021191
wtse, an avre-family effector protein from pantoea stewartii subsp. stewartii, causes disease-associated cell death in corn and requires a chaperone protein for stability.	the pathogenicity of pantoea stewartii subsp. stewartii to sweet corn and maize requires a hrp type iii secretion system. in this study, we genetically and functionally characterized a disease-specific (dsp) effector locus, composed of wtse and wtsf, that is adjacent to the hrp gene cluster. wtse, a member of the avre family of effector proteins, was essential for pathogenesis on corn and was complemented by dspa/e from erwinia amylovora. an intact c-terminus of wtse, which contained a putative ...	2006	17022173
characterization of xync from bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan.	secretion of xylanase activities by bacillus subtilis 168 supports the development of this well-defined genetic system for conversion of methylglucuronoxylan (megaxn [where n represents the number of xylose residues]) in the hemicellulose component of lignocellulosics to biobased products. in addition to the characterized glycosyl hydrolase family 11 (gh 11) endoxylanase designated xyna, b. subtilis 168 secretes a second endoxylanase as the translated product of the ynff gene. this sequence show ...	2006	17028274
[molecular identification and genetic diversity in konnyaku's soft rot bacteria].	the soft rot bacteria erwinia are an important pathogens of konnyaku and other ornamental plants. thirty-three strains were isolated from soft-rotted konnyaku and other ornamental plants. according to the characteristics of pathogenicity and culture character on semi selective medium (crystal violet pectate, cvp), most of strains tested caused rotten symptom in tubers and stems of konnyaku, and characteristic deep cavities were formed on cvp. to amplify 16s-23s rdna intergenic transcribed spacer ...	2006	17037047
nps6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes.	nps6, encoding a nonribosomal peptide synthetase, is a virulence determinant in the maize (zea mays) pathogen cochliobolus heterostrophus and is involved in tolerance to h(2)o(2). deletion of nps6 orthologs in the rice (oryza sativa) pathogen, cochliobolus miyabeanus, the wheat (triticum aestivum) pathogen, fusarium graminearum, and the arabidopsis thaliana pathogen, alternaria brassicicola, resulted in reduced virulence and hypersensitivity to h(2)o(2). introduction of the nps6 ortholog from th ...	2006	17056706
bacterial outer membrane secretin puld assembles and inserts into the inner membrane in the absence of its pilotin.	dodecamerization and insertion of the outer membrane secretin puld is entirely determined by the c-terminal half of the polypeptide (puld-cs). in the absence of its cognate chaperone puls, puld-cs and puld mislocalize to the inner membrane, from which they are extractable with detergents but not urea. electron microscopy of puld-cs purified from the inner membrane revealed apparently normal dodecameric complexes. electron microscopy of puld-cs and puld in inner membrane vesicles revealed inserte ...	2006	17082772
the symbiosis regulator rscs controls the syp gene locus, biofilm formation and symbiotic aggregation by vibrio fischeri.	successful colonization of a eukaryotic host by a microbe involves complex microbe-microbe and microbe-host interactions. previously, we identified in vibrio fischeri a putative sensor kinase, rscs, required for initiating symbiotic colonization of its squid host euprymna scolopes. here, we analysed the role of rscs by isolating an allele, rscs1, with increased activity. multicopy rscs1 activated transcription of genes within the recently identified symbiosis polysaccharide (syp) cluster. wild-t ...	2006	17087775
isolation and characterization of acid-tolerant, thermophilic bacteria for effective fermentation of biomass-derived sugars to lactic acid.	biomass-derived sugars, such as glucose, xylose, and other minor sugars, can be readily fermented to fuel ethanol and commodity chemicals by the appropriate microbes. due to the differences in the optimum conditions for the activity of the fungal cellulases that are required for depolymerization of cellulose to fermentable sugars and the growth and fermentation characteristics of the current industrial microbes, simultaneous saccharification and fermentation (ssf) of cellulose is envisioned at c ...	2006	16672461
characterization of the siderophore of francisella tularensis and role of fsla in siderophore production.	we determined that lvs and schu s4 strains of the human pathogen francisella tularensis express a siderophore when grown under iron-limiting conditions. we purified this siderophore by conventional column chromatography and high-pressure liquid chromatography and used mass spectrometric analysis to demonstrate that it is structurally similar to the polycarboxylate siderophore rhizoferrin. the siderophore promoted the growth of lvs and schu s4 strains in iron-limiting media. we identified a poten ...	2006	16707671
the synchrony phenotype persists after elimination of multiple gatc sites from the dnaa promoter of escherichia coli.	to examine whether methylation of the gatc sites present in the dnaa promoter region is responsible for the strict temporal coordination of initiation events at oric as measured by the synchrony of initiation, we introduced point mutations eliminating three (tgw1) and five (tgw2) of the six gatc sites present in the dnaa promoter region. all of the strains containing these mutations, including the one with five gatc sites eliminated, initiated chromosomal replication synchronously.	2006	16740964
the role of several multidrug resistance systems in erwinia chrysanthemi pathogenesis.	the role of several multidrug resistance (mdr) systems in the pathogenicity of erwinia chrysanthemi 3937 was analyzed. using the blast algorithm, we have identified several mdr systems in the e. chrysanthemi genome and selected two acridine resistance (acr)-like systems, two emr-like systems, and one member of the major facilitator super-family family to characterize. we generated mutants in genes encoding for these systems and analyzed the virulence of the mutant strains in different hosts and ...	2006	16776294
the brucella abortus cyclic beta-1,2-glucan virulence factor is substituted with o-ester-linked succinyl residues.	brucella periplasmic cyclic beta-1,2-glucan plays an important role during bacterium-host interaction. nuclear magnetic resonance spectrometry analysis, thin-layer chromatography, and deae-sephadex chromatography were used to characterize brucella abortus cyclic glucan. in the present study, we report that a fraction of b. abortus cyclic beta-1,2-glucan is substituted with succinyl residues, which confer anionic character on the cyclic beta-1,2-glucan. the oligosaccharide backbone is substituted ...	2006	16816173