| the sars-cov ferret model in an infection-challenge study. | phase i human clinical studies involving therapeutics for emerging and biodefense pathogens with low incidence, such as the severe acute respiratory syndrome coronavirus (sars-cov), requires at a minimum preclinical evaluation of efficacy in two well-characterized and robust animal models. thus, a ferret sars-cov model was evaluated over a period of 58 days following extensive optimization and characterization of the model in order to validate clinical, histopathological, virological and immunol ... | 2008 | 18234270 |
| in vitro activity of a novel antimicrobial agent, tg44, for treatment of helicobacter pylori infection. | due to concerns about the current therapeutic modalities for helicobacter pylori infection, e.g., the increased emergence of drug-resistant strains and the adverse reactions of drugs currently administered, there is a need to develop an anti-h. pylori agent with higher efficacy and less toxicity. the antibacterial activity of tg44, an anti-h. pylori agent with a novel structural formula, against 54 clinical isolates of h. pylori was examined and compared with those of amoxicillin (amx), clarithr ... | 2006 | 16940102 |
| population-associated differences between the phase variable lps biosynthetic genes of helicobacter pylori. | population structures are normally determined using genes under minimal functional selection. in this study we have assessed genes that are not always essential, show differences in alleles between strains, and are involved in the directly host-selectable phenotype of lps biosynthesis. | 2006 | 16981984 |
| iron-responsive repression of urease expression in helicobacter hepaticus is mediated by the transcriptional regulator fur. | persistent colonization of mucosal surfaces by bacteria in the mammalian host requires concerted expression of colonization factors, depending on the environmental conditions. helicobacter hepaticus is a urease-positive pathogen that colonizes the intestinal and hepatobiliary tracts of rodents. here it is reported that urease expression of h. hepaticus is iron repressed by the transcriptional regulator fur. iron restriction of growth medium resulted in a doubling of urease activity in wild-type ... | 2007 | 17101656 |
| characterization of a metal-independent cazy family 6 glycosyltransferase from bacteroides ovatus. | the myriad functions of complex carbohydrates include modulating interactions between bacteria and their eukaryotic hosts. in humans and other vertebrates, variations in the activity of glycosyltransferases of cazy family 6 generate antigenic variation between individuals and species that facilitates resistance to pathogens. the well characterized vertebrate glycosyltransferases of this family are multidomain membrane proteins with c-terminal catalytic domains. genes for proteins homologous with ... | 2009 | 19622749 |
| accelerated progression of gastritis to dysplasia in the pyloric antrum of tff2 -/- c57bl6 x sv129 helicobacter pylori-infected mice. | trefoil factor family 2 (tff2) is up-regulated in helicobacter spp.-infected gastric tissues of both humans and mice. to ascertain the biological effects of tff2 in vivo, tff2(-/-) c57bl/6 x sv129 and wild-type (wt) c57bl/6 x sv129 mice were orally infected with helicobacter pylori ss1. mice were evaluated for gastric h. pylori colonization, pathology, and cytokine profiles at 6 and 19 months post inoculation (pi). at 6 months pi, there was a significant difference (p < 0.05) for epithelial crit ... | 2007 | 17982128 |
| photodynamic therapy: a new antimicrobial approach to infectious disease? | photodynamic therapy (pdt) employs a non-toxic dye, termed a photosensitizer (ps), and low intensity visible light which, in the presence of oxygen, combine to produce cytotoxic species. pdt has the advantage of dual selectivity, in that the ps can be targeted to its destination cell or tissue and, in addition, the illumination can be spatially directed to the lesion. pdt has previously been used to kill pathogenic microorganisms in vitro, but its use to treat infections in animal models or pati ... | 2004 | 15122361 |
| random mutagenesis to identify novel helicobacter mustelae virulence factors. | helicobacter mustelae is a gastric pathogen of ferrets, where it causes disorders similar to those caused by helicobacter pylori in humans. the h. mustelae ferret model therefore has potential for the in vivo study of helicobacter pathogenesis in general. in this study a library of 500 individual h. mustelae mutants was generated using an in vitro random insertion mutagenesis technique. mutants were subsequently tested for motility and adherence, and 43 of the 500 mutants tested were found to be ... | 2007 | 17316371 |
| "candidatus helicobacter heilmannii" from a cynomolgus monkey induces gastric mucosa-associated lymphoid tissue lymphomas in c57bl/6 mice. | both helicobacter pylori and "candidatus helicobacter heilmannii" infections are associated with peptic ulcers, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue (malt) lymphomas. however, good animal models of h. pylori clinical diseases are rare. in this study, we aimed to establish an animal model of "candidatus helicobacter heilmannii" gastric malt lymphoma. we used a urease-positive gastric mucosal and mucus homogenate from a cynomolgus monkey maintained in c57bl/6 mouse ... | 2007 | 17194807 |
| "candidatus helicobacter heilmannii" from a cynomolgus monkey induces gastric mucosa-associated lymphoid tissue lymphomas in c57bl/6 mice. | both helicobacter pylori and "candidatus helicobacter heilmannii" infections are associated with peptic ulcers, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue (malt) lymphomas. however, good animal models of h. pylori clinical diseases are rare. in this study, we aimed to establish an animal model of "candidatus helicobacter heilmannii" gastric malt lymphoma. we used a urease-positive gastric mucosal and mucus homogenate from a cynomolgus monkey maintained in c57bl/6 mouse ... | 2007 | 17194807 |
| coupled amino acid deamidase-transport systems essential for helicobacter pylori colonization. | in addition to their classical roles as carbon or nitrogen sources, amino acids can be used for bacterial virulence, colonization, or stress resistance. we found that original deamidase-transport systems impact colonization by helicobacter pylori, a human pathogen associated with gastric pathologies, including adenocarcinoma. we demonstrated that l-asparaginase (hp-ansb) and gamma-glutamyltranspeptidase (hp-gammagt) are highly active periplasmic deamidases in h. pylori, producing ammonia and asp ... | 2010 | 20368342 |
| roles of his-rich hpn and hpn-like proteins in helicobacter pylori nickel physiology. | individual gene-targeted hpn and hpn-like mutants and a mutant with mutations in both hpn genes were more sensitive to nickel, cobalt, and cadmium toxicity than was the parent strain, with the hpn-like strain showing the most metal sensitivity of the two individual his-rich protein mutants. the mutant strains contained up to eightfold more urease activity than the parent under nickel-deficient conditions, and the parent strain was able to achieve mutant strain activity levels by nickel supplemen ... | 2007 | 17384182 |
| chemotactic control of the two flagellar systems of rhodobacter sphaeroides is mediated by different sets of chey and flim proteins. | rhodobacter sphaeroides expresses two different flagellar systems, a subpolar flagellum (fla1) and multiple polar flagella (fla2). these structures are encoded by different sets of flagellar genes. the chemotactic control of the subpolar flagellum (fla1) is mediated by three of the six different chey proteins (chey6, chey4, or chey3). we show evidence that chey1, chey2, and chey5 control the chemotactic behavior mediated by fla2 flagella and that rsp6099 encodes the fla2 flim protein. | 2007 | 17890312 |
| helicobacter pylori represses proton pump expression and inhibits acid secretion in human gastric mucosa. | helicobacter pylori infection of gastric mucosa causes gastritis and transient hypochlorhydria, which may provoke emergence of a mucosal precancer phenotype; h pylori strains containing a cag pathogenicity island (pai) augment cancer risk. acid secretion is mediated by the catalytic alpha subunit of parietal cell h,k-atpase (hkalpha). in ags gastric epithelial cells, h pylori induces nuclear factor-kappab (nf-kappab) binding to and repression of transfected hkalpha promoter activity. this study ... | 2010 | 20581234 |
| crystal structure and functional insight of hp0420-homolog from helicobacter felis. | helicobacter pylori infect more than half of the world's population and are considered a cause of peptic ulcer disease and gastric cancer. recently, hypothetical gene hp0421 was identified in h. pylori as a cholesterol alpha-glucosyltransferase, which is required to synthesize cholesteryl glucosides, essential cell wall components of the bacteria. in the same gene-cluster, hp0420 was co-identified, whose function remains unknown. here we report the crystal structure of hp0420-homolog of h. felis ... | 2010 | 20302842 |
| experimental helicobacter marmotae infection in a/j mice causes enterohepatic disease. | helicobacter marmotae has been identified in the inflamed livers of eastern woodchucks (marmota monax) infected with woodchuck hepatitis virus (whv), as well as from the livers of whv-negative woodchucks. because the majority of whv-positive woodchucks with hepatic tumours were culture or pcr positive for this helicobacter, and whv-negative woodchucks with h. marmotae had hepatitis, the bacterium may have a role in tumour promotion related to chronic inflammation. in this study, the type strain ... | 2010 | 20616187 |
| relevance of muc1 mucin variable number of tandem repeats polymorphism in h pylori adhesion to gastric epithelial cells. | to evaluate the influence of muc1 mucin variable number of tandem repeats (vntr) variability on h pylori adhesion to gastric cells. | 2008 | 18322957 |
| characterization of nikr-responsive promoters of urease and metal transport genes of helicobacter mustelae. | the nikr protein is a nickel-responsive regulator, which in the gastric pathogen helicobacter pylori controls expression of nickel-transporters and the nickel-cofactored urease acid resistance determinant. although nikr-dna interaction has been well studied, the helicobacter nikr operator site remains poorly defined. in this study we have identified the nikr operators in the promoters of two inversely nickel-regulated urease operons (ureab and urea2b2) in the ferret pathogen helicobacter mustela ... | 2010 | 19894125 |
| H. pylori vaccines: Why we still don't have any. | Helicobacter pylori was appreciated as the major cause of peptic ulcers about 30 years ago and the most significant etiological agent in gastric cancer in the mid-1990s. Since that time, progress in the development of a preventive or therapeutic H. pylori vaccine has been relatively slow. The impediments to rapid advances in the field include a luke-warm enthusiasm among clinicians, research scientists, and public health authorities concerning the need for a vaccine, rudimentary understanding of ... | 2011 | 22048119 |
| gastric helicobacter species as a cause of feline gastric lymphoma: a viable hypothesis. | gastric helicobacter spp. are associated with chronic inflammation and neoplastic transformation in humans as well as domestic and laboratory species. the present study examined the association of helicobacter heilmannii (hhe) infection in pet cats with feline gastric mucosa associated lymphoid tissue (malt) lymphoma. tissues were collected via gastric biopsy or at necropsy from 47 pet cats with clinical signs of gastrointestinal disease, including vomiting and inappetance, and classified as gas ... | 2008 | 18387674 |
| identification of nine sequence types of the 16s rrna genes of campylobacter jejuni subsp. jejuni isolated from broilers. | campylobacter is the most commonly reported bacterial cause of enteritis in humans in the eu member states and other industrialized countries. one significant source of infection is broilers and consumption of undercooked broiler meat. campylobacter jejuni is the campylobacter sp. predominantly found in infected humans and colonized broilers. sequence analysis of the 16s rrna gene is very useful for identification of bacteria to genus and species level. the objectives in this study were to deter ... | 2008 | 18492293 |
| cystic renal disease in the domestic ferret. | cystic renal diseases in domestic ferrets are a common anecdotal finding but have received scant systematic assessment. we performed a 17-y, case-control retrospective analysis of the medical records of 97 ferrets housed at our institution between 1987 and 2004, to determine the prevalence and morphotypes of cystic renal diseases in this species. histologic sections stained with hematoxylin and eosin, masson trichrome, or periodic acid-schiff were evaluated by a comparative pathologist, and stat ... | 2008 | 18524174 |
| inverse nickel-responsive regulation of two urease enzymes in the gastric pathogen helicobacter mustelae. | the acidic gastric environment of mammals can be chronically colonized by pathogenic helicobacter species, which use the nickel-dependent urea-degrading enzyme urease to confer acid resistance. nickel availability in the mammal host is low, being mostly restricted to vegetarian dietary sources, and thus helicobacter species colonizing carnivores may be subjected to episodes of nickel deficiency and associated acid sensitivity. the aim of this study was to investigate how these helicobacter speci ... | 2008 | 18564183 |
| cd25+ t cells induce helicobacter pylori-specific cd25- t-cell anergy but are not required to maintain persistent hyporesponsiveness. | the gastric pathogen helicobacter pylori infects over half the world's population. the lifelong infection induces gastric inflammation but the host fails to generate protective immunity. to study the lack of protective h. pylori immunity, cd4(+)cd25(+) t(reg) cells were investigated for their ability to down-regulate h. pylori-specific cd4(+)cd25(-) cells in a murine model. cd25(-) lymphocytes from infected mice were hyporesponsive to antigenic stimulation in vitro even in the absence of cd25(+) ... | 2008 | 19003932 |
| carbohydrate-dependent defense mechanisms against helicobacter pylori infection. | helicobacter pylori is a gram-negative bacterium that infects over 50% of the world's population. this organism causes various gastric diseases such as chronic gastritis, peptic ulcer, and gastric cancer. h. pylori possesses lipopolysaccharide, which shares structural similarity to lewis blood group antigens in gastric mucosa. such antigenic mimicry could result in immune tolerance against antigens of this pathogen. on the other hand, h. pylori colonize gastric mucosa by utilizing adhesins, whic ... | 2009 | 19149511 |
| an outer membrane receptor of neisseria meningitidis involved in zinc acquisition with vaccine potential. | since the concentration of free iron in the human host is low, efficient iron-acquisition mechanisms constitute important virulence factors for pathogenic bacteria. in gram-negative bacteria, tonb-dependent outer membrane receptors are implicated in iron acquisition. it is far less clear how other metals that are also scarce in the human host are transported across the bacterial outer membrane. with the aim of identifying novel vaccine candidates, we characterized in this study a hitherto unknow ... | 2010 | 20617164 |
| a commensal helicobacter sp. of the rodent intestinal flora activates tlr2 and nod1 responses in epithelial cells. | helicobacter spp. represent a proportionately small but significant component of the normal intestinal microflora of animal hosts. several of these intestinal helicobacter spp. are known to induce colitis in mouse models, yet the mechanisms by which these bacteria induce intestinal inflammation are poorly understood. to address this question, we performed in vitro co-culture experiments with mouse and human epithelial cell lines stimulated with a selection of helicobacter spp., including known p ... | 2009 | 19401779 |
| the helicobacter pylori anti-sigma factor flgm is predominantly cytoplasmic and cooperates with the flagellar basal body protein flha. | helicobacter pylori requires flagellar motility and orientation to persist actively in its habitat. a particular feature of flagella in most helicobacter species including h. pylori is a membraneous flagellar sheath. the anti-sigma factor flgm of h. pylori is unusual, since it lacks an n-terminal domain present in other flgm homologs, e.g., flgm of salmonella spp., whose regulatory function is intimately coupled to its secretion through the flagellar type iii secretion system. the aim of the pre ... | 2009 | 19465658 |
| comparative genomics and proteomics of helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. | helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. h. mustelae remains the only helicobacter other than h. pylori that causes gastric ulceration and cancer in its natural host. to improve understanding of h. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the h. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. | 2010 | 20219135 |
| nonprimate animal models of h. pylori infection. | ever since the realization that helicobacter pylori was intimately associated with the development of gastritis and peptic ulcer disease in humans, there has been a need for a simple animal model in which modes of pathogenicity, transmission, immunization, and chemotherapeutic intervention can be evaluated. whereas small animals such as mice and rats are particularly well suited as experimental hosts for many infections, early studies suggested that h. pylori had a very narrow host range that di ... | 1997 | 21351037 |
| evaluation of 16s rrna gene-based pcr assays for genus-level identification of helicobacter species. | the inclusivity, exclusivity, and detection limit of six 16s rrna gene-based helicobacter genus-specific pcr assays were examined. five out of six assays were 100% inclusive, but the tests varied considerably in their exclusivity (9.1 to 95.5%). the clinical detection limit varied between 10(3) and 1 viable bacterial cell per reaction mixture. | 2008 | 18337392 |
| enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities? | changes in bacterial populations termed "dysbiosis" are thought central to ulcerative colitis (uc) pathogenesis. in particular, the possibility that novel helicobacter organisms play a role in human uc has been debated but not comprehensively investigated. the aim of this study was to develop a molecular approach to investigate the presence of helicobacter organisms in adults with and without uc. | 2011 | 21383845 |
| morphologic, genetic, and biochemical characterization of helicobacter magdeburgensis, a novel species isolated from the intestine of laboratory mice. | the presence of enterohepatic helicobacter species (ehs) is commonly noted in mouse colonies. these infections often remain unrecognized but can cause severe health complications or more subtle host immune perturbations and therefore can confound the results of animal experiments. the aim of this study was to isolate and characterize a putative novel ehs that has previously been detected by pcr screening of specific-pathogen-free mice. | 2010 | 21083746 |
| mua (hp0868) is a nickel-binding protein that modulates urease activity in helicobacter pylori. | abstract a novel mechanism aimed at controlling urease expression in helicobacter pylori in the presence of ample nickel is described. higher urease activities were observed in an hp0868 mutant (than in the wild type) in cells supplemented with nickel, suggesting that the hp0868 protein (herein named mua for modulator of urease activity) represses urease activity when nickel concentrations are ample. the increase in urease activity in the δmua mutant was linked to an increase in urease transcrip ... | 2011 | 21505055 |
| the complete genome sequence and analysis of the epsilonproteobacterium arcobacter butzleri. | arcobacter butzleri is a member of the epsilon subdivision of the proteobacteria and a close taxonomic relative of established pathogens, such as campylobacter jejuni and helicobacter pylori. here we present the complete genome sequence of the human clinical isolate, a. butzleri strain rm4018. | 2007 | 18159241 |
| residues in a conserved {alpha}-helical segment are required for cleavage but not secretion of an e. coli serine protease autotransporter passenger domain. | autotransporters are a superfamily of virulence factors produced by gram-negative bacteria that are comprised of an n-terminal extracellular domain ("passenger domain") and a c-terminal β barrel domain ("β domain") that resides in the outer membrane (om). the β domain promotes the translocation of the passenger domain across the om by an unknown mechanism. available evidence indicates that an α-helical segment that spans the passenger domain-β domain junction is embedded inside the β domain at a ... | 2011 | 21642456 |
| genome sequence of helicobacter suis supports its role in gastric pathology. | abstract: helicobacter (h.) suis has been associated with chronic gastritis and ulcers of the pars oesophagea in pigs, and with gastritis, peptic ulcer disease and gastric mucosa-associated lymphoid tissue lymphoma in humans. in order to obtain better insight into the genes involved in pathogenicity and in the specific adaptation to the gastric environment of h. suis, a genome analysis was performed of two h. suis strains isolated from the gastric mucosa of swine. homologs of the vast majority o ... | 2011 | 21414191 |
| change is good: variations in common biological mechanisms in the epsilonproteobacterial genera campylobacter and helicobacter. | microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. the epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. some epsilonproteobacteria, such as campylobacter jejuni and helicobacter pylori, are common pathogens of humans tha ... | 2011 | 21372321 |
| rapid identification and quantification of campylobacter coli and campylobacter jejuni by real-time pcr in pure cultures and in complex samples. | abstract: background: campylobacter spp., especially campylobacter jejuni (c. jejuni) and campylobacter coli (c. coli), are recognized as the leading human foodborne pathogens in developed countries. livestock animals carrying campylobacter pose an important risk for human contamination. pigs are known to be frequently colonized with campylobacter, especially c. coli, and to excrete high numbers of this pathogen in their faeces. molecular tools, notably real-time pcr, provide an effective, rapid ... | 2011 | 21600037 |
| an abc-type cobalt transport system is essential for growth of sinorhizobium melilotiat trace metal concentrations. | we report expression and mutant phenotypes for a gene cluster in sinorhizobium meliloti, designated cbtjkl, that has been shown to encode an abc-type cobalt transport system. transcription of cbtjklinitiated 384 nucleotides upstream from the cbtjtranslation start codon, and the resulting 5' region contained a putative b(12)riboswitch. expression of the cbtjklgenes appeared to be controlled by (cobalt-loaded) cobalamin interacting at the b(12)riboswitch, since (i) a putative b(12)riboswitch was l ... | 2011 | 21725018 |
| asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes. | the terms "proteolytic enzyme" and "peptidase" have been treated as synonymous, and all proteolytic enzymes have been considered to be hydrolases (ec 3.4). however, the recent discovery of proteins that cleave themselves at asparagine residues indicates that not all peptide bond cleavage occurs by hydrolysis. these self-cleaving proteins include the tsh protein precursor of escherichia coli, in which the large c-terminal propeptide acts as an autotransporter; certain viral coat proteins; and pro ... | 2011 | 21832066 |
| Function of UreB in Klebsiella aerogenes urease. | Urease from Klebsiella aerogenes is composed of three subunits (UreA-UreB-UreC) that assemble into a (UreABC)(3) quaternary structure. UreC harbors the dinuclear nickel active site, whereas the functions of UreA and UreB remain unknown. UreD and UreF accessory proteins previously were suggested to reposition UreB and increase the level of exposure of the nascent urease active site, thus facilitating metallocenter assembly. In this study, cells were engineered to separately produce (UreAC)(3) or ... | 2011 | 21939280 |
| rcnb is a periplasmic protein essential for maintaining intracellular ni and co concentrations in escherichia coli. | nickel and cobalt are both essential trace elements that are toxic when present in excess. the main resistance mechanism that bacteria use to overcome this toxicity is the efflux of these cations out of the cytoplasm. rnd (resistance-nodulation-cell division)- and mfs (major facilitator superfamily)-type efflux systems are known to export either nickel or cobalt. the rcna efflux pump, which belongs to a unique family, is responsible for the detoxification of ni and co in escherichia coli. in thi ... | 2011 | 21665978 |
| iron-containing urease in a pathogenic bacterium. | helicobacter mustelae, a gastric pathogen of ferrets, synthesizes a distinct iron-dependent urease in addition to its archetypical nickel-containing enzyme. the iron-urease is oxygen-labile, with the inactive protein exhibiting a methemerythrin-like electronic spectrum. significantly, incubation of the oxidized protein with dithionite under anaerobic conditions leads to restoration of activity and bleaching of the spectrum. structural analysis of the oxidized species reveals a dinuclear iron met ... | 2011 | 21788478 |
| Apoprotein isolation and activation, and vibrational structure of the Helicobacter mustelae iron urease. | The micro aerophilic pathogen Helicobacter mustelae synthesizes an oxygen-labile, iron-containing urease (UreA2B2) in addition to its standard nickel-containing enzyme (UreAB). An apoprotein form of the iron urease was prepared from ureA2B2-expressing recombinant Escherichia coli cells that were grown in minimal medium. Temperature-dependent circular dichroism measurements of holoprotein and apoprotein demonstrate an enhancement of thermal stability associated with the UreA2B2 metallocenter. In ... | 2011 | 22196017 |
| mapping the regulon of vibrio cholerae ferric uptake regulator expands its known network of gene regulation. | chip coupled with next-generation sequencing (chip-seq) has revolutionized whole-genome mapping of dna-binding protein sites. although chip-seq rapidly gained support in eukaryotic systems, it remains underused in the mapping of bacterial transcriptional regulator-binding sites. using the virulence-required iron-responsive ferric uptake regulator (fur), we report a simple, broadly applicable chip-seq method in the pathogen vibrio cholerae. combining our chip-seq results with available microarray ... | 2011 | 21750152 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| biosynthesis of the urease metallocenter. | metalloenzymes often require elaborate metallocenter assembly systems to create functional active sites. the medically important dinuclear nickel enzyme urease provides an excellent model for studying metallocenter assembly. nickel is inserted into the urease active site in a gtp-dependent process with the assistance of ured/ureh, uree, uref, and ureg. these accessory proteins orchestrate apoprotein activation by delivering the appropriate metal, facilitating protein conformational changes, and ... | 2013 | 23539618 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| an abc transporter and a tonb ortholog contribute to helicobacter mustelae nickel and cobalt acquisition. | the genomes of helicobacter species colonizing the mammalian gastric mucosa (like helicobacter pylori) contain a large number of genes annotated as iron acquisition genes but only few nickel acquisition genes, which contrasts with the central position of nickel in the urease-mediated acid resistance of these gastric pathogens. in this study we have investigated the predicted iron and nickel acquisition systems of the ferret pathogen helicobacter mustelae. the expression of the outer membrane pro ... | 2010 | 20643857 |
| surreptitious manipulation of the human host by helicobacter pylori. | microbial pathogens contribute to the development of more than 1 million cases of cancer per year. gastric adenocarcinoma is the second leading cause of cancer-related death in the world, and gastritis induced by helicobacter pylori is the strongest known risk factor for this malignancy. h. pylori colonizes the stomach for years, not days or weeks, as is usually the case for bacterial pathogens and it always induces inflammation; however, only a fraction of colonized individuals ever develop dis ... | 2010 | 20976041 |
| Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. | ABSTRACT: | 2011 | 22039924 |
| interplay of metal ions and urease. | urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. several mechanisms of urease catalysis have been proposed on the basis of enzyme crystal structures, model complexes, and computational efforts, but the precise steps in catalysis and the requirement of nickel versus other metals remain unclear. purified bacterial urease is partially activated ... | 2009 | 20046957 |
| family 6 glycosyltransferases in vertebrates and bacteria: inactivation and horizontal gene transfer may enhance mutualism between vertebrates and bacteria. | glycosyltransferases (gts) control the synthesis and structures of glycans. inactivation and intense allelic variation in members of the gt6 family generate species-specific and individual variations in carbohydrate structures, including histo-blood group oligosaccharides, resulting in anti-glycan antibodies that target glycan-decorated pathogens. gt6 genes are ubiquitous in vertebrates but are otherwise rare, existing in a few bacteria, one protozoan, and cyanophages, suggesting lateral gene tr ... | 2010 | 20870714 |
| enhancement of biocontrol efficacy of pichia carribbica to postharvest diseases of strawberries by addition of trehalose to the growth medium. | the effects of trehalose on the antagonistic activity of pichia caribbica against rhizopus decay and gray mold decay of strawberries and the possible mechanisms involved were investigated. the proteomic analysis and comparison of p. carribbica in response to trehalose was analyzed based on two-dimensional gel electrophoresis. the antagonistic activity of p. carribbica harvested from the culture media of nydb amended with trehalose at 0.5% was improved greatly compared with that without trehalose ... | 2012 | 22489189 |
| the polar and lateral flagella from plesiomonas shigelloides are glycosylated with legionaminic acid. | plesiomonas shigelloides is the unique member of the enterobacteriaceae family able to produce polar flagella when grow in liquid medium and lateral flagella when grown in solid or semisolid media. in this study on p. shigelloides 302-73 strain, we found two different gene clusters, one exclusively for the lateral flagella biosynthesis and the other one containing the biosynthetic polar flagella genes with additional putative glycosylation genes. p. shigelloides is the first enterobacteriaceae w ... | 2015 | 26167161 |
| rapid detection of the chlamydiaceae and other families in the order chlamydiales: three pcr tests. | few identification methods will rapidly or specifically detect all bacteria in the order chlamydiales, family chlamydiaceae. in this study, three pcr tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. two tests exclusively recognized the chlamydiaceae: a multiplex test targeting the ompa gene and the rrna intergenic spacer and a taqman test targeting the 23s ribosomal dna. the multiplex test was able to detect as few as 200 inclusion ... | 1999 | 9986815 |
| xer recombinase and genome integrity in helicobacter pylori, a pathogen without topoisomerase iv. | in the model organism e. coli, recombination mediated by the related xerc and xerd recombinases complexed with the ftsk translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. computational genome analysis of helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerh) and its cognate dif site (difh). here we show that recombination between directly repeated difh sit ... | 2012 | 22511919 |
| evolution of the selenoproteome in helicobacter pylori and epsilonproteobacteria. | by competing for the acquisition of essential nutrients, helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. although the h. pylori genome apparently encodes selenocysteine synthase (sela, hp1513), a key pyridoxal phosphate (plp)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. we analyzed the evol ... | 2015 | 26342139 |
| complete genome sequence of helicobacter cinaedi strain pagu611, isolated in a case of human bacteremia. | we report the complete genome sequence of helicobacter cinaedi strain pagu611, isolated in a case of human bacteremia. the pagu611 genome comprises a 2,078,348-bp chromosome and a 23,054-bp plasmid. the chromosome contains a unique genomic island, encoding a type vi secretion system and clustered regularly interspaced short palindromic repeat (crispr) loci. | 2012 | 22740670 |
| identification and characterization of a lipopolysaccharide α,2,3-sialyltransferase from the human pathogen helicobacter bizzozeronii. | terminal sialic acid in the lipopolysaccharides (lpss) of mucosal pathogens is an important virulence factor. here we report the characterization of a helicobacter sialyltransferase involved in the biosynthesis of sialylated lps in helicobacter bizzozeronii, the only non-pylori gastric helicobacter species isolated from humans thus far. starting from the genome sequences of canine and human strains, we identified potential sialyltransferases downstream of three genes involved in the biosynthesis ... | 2012 | 22408169 |
| Apoprotein isolation and activation, and vibrational structure of the Helicobacter mustelae iron urease. | The micro aerophilic pathogen Helicobacter mustelae synthesizes an oxygen-labile, iron-containing urease (UreA2B2) in addition to its standard nickel-containing enzyme (UreAB). An apoprotein form of the iron urease was prepared from ureA2B2-expressing recombinant Escherichia coli cells that were grown in minimal medium. Temperature-dependent circular dichroism measurements of holoprotein and apoprotein demonstrate an enhancement of thermal stability associated with the UreA2B2 metallocenter. In ... | 2011 | 22196017 |
| ankyrin domains across the tree of life. | ankyrin (ank) repeats are one of the most common amino acid sequence motifs that mediate interactions between proteins of myriad sizes, shapes and functions. we assess their widespread abundance in bacteria and archaea for the first time and demonstrate in bacteria that lifestyle, rather than phylogenetic history, is a predictor of ank repeat abundance. unrelated organisms that forge facultative and obligate symbioses with eukaryotes show enrichment for ank repeats in comparison to free-living b ... | 2014 | 24688847 |
| bacterial urease and its role in long-lasting human diseases. | urease is a virulence factor found in various pathogenic bacteria. it is essential in colonization of a host organism and in maintenance of bacterial cells in tissues. due to its enzymatic activity, urease has a toxic effect on human cells. the presence of ureolytic activity is an important marker of a number of bacterial infections. urease is also an immunogenic protein and is recognized by antibodies present in human sera. the presence of such antibodies is connected with progress of several l ... | 2012 | 23305365 |
| the complex methylome of the human gastric pathogen helicobacter pylori. | the genome of helicobacter pylori is remarkable for its large number of restriction-modification (r-m) systems, and strain-specific diversity in r-m systems has been suggested to limit natural transformation, the major driving force of genetic diversification in h. pylori. we have determined the comprehensive methylomes of two h. pylori strains at single base resolution, using single molecule real-time (smrt®) sequencing. for strains 26695 and j99-r3, 17 and 22 methylated sequence motifs were id ... | 2013 | 24302578 |
| crossroads between bacterial and mammalian glycosyltransferases. | bacterial glycosyltransferases (gt) often synthesize the same glycan linkages as mammalian gt; yet, they usually have very little sequence identity. nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. thus, bacterial gt can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. a comparison is made here between mammalian and bacterial enzymes t ... | 2014 | 25368613 |
| a variable homopolymeric g-repeat defines small rna-mediated posttranscriptional regulation of a chemotaxis receptor in helicobacter pylori. | phase variation of hypermutable simple sequence repeats (ssrs) is a widespread and stochastic mechanism to generate phenotypic variation within a population and thereby contributes to host adaptation of bacterial pathogens. although several examples of ssrs that affect transcription or coding potential have been reported, we now show that a ssr also impacts small rna-mediated posttranscriptional regulation. based on in vitro and in vivo analyses, we demonstrate that a variable homopolymeric g-re ... | 2014 | 24474799 |
| characterization in helicobacter pylori of a nickel transporter essential for colonization that was acquired during evolution by gastric helicobacter species. | metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. in particular, nickel is a virulence determinant for the human gastric pathogen helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [nife] hydrogenase. to import nickel despite its scarcity in the human body, h. pylori requires efficient uptake mechanisms that are only partially defined. indeed, alternative ways of nickel entry were predicted to exis ... | 2016 | 27923069 |
| diagnosis of genus helicobacter through a hemi-nested pcr assay of 16s rrna. | the present study aimed to establish a genus-specific pcr-based assay to detect helicobacters using 16s rrna gene as the target template. we designed the hemi-nested primers based on sequences of 16s rrna gene of 34 types of helicobacter species. the inclusivity, sensitivity, and specificity of the pcr assay using these primers were examined in three different models, comprising feces simulated samples, blab/c mice infection model and clinic patients samples. the detection sensitivity of helicob ... | 2016 | 27275113 |
| molecular identification of helicobacter dna in human gastric adenocarcinoma tissues using helicobacter species-specific 16s rrna pcr amplification and pyrosequencing analysis. | helicobacter pylori (h. pylori) is a microaerophilic gram-negative bacterium known to be associated with chronic gastritis, peptic ulcer and gastric adenocarcinoma. in the present study, the presence of helicobacter dna was investigated using a helicobacter species-specific 16s rrna pcr amplification and pyrosequencing analysis in 51 resected gastric adenocarcinomas. dna was extracted from paraffin-embedded tissues of resected gastric adenocarcinomas. pcr primers were designed to amplify the 133 ... | 2010 | 22966342 |
| virulence functions of autotransporter proteins. | | 2001 | 11179284 |
| sequence divergence and conservation in genomes of helicobacter cetorum strains from a dolphin and a whale. | strains of helicobacter cetorum have been cultured from several marine mammals and have been found to be closely related in 16 s rdna sequence to the human gastric pathogen h. pylori, but their genomes were not characterized further. | 2013 | 24358262 |
| evolution of helicobacter: acquisition by gastric species of two histidine-rich proteins essential for colonization. | metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. virulence of the human gastric pathogen helicobacter pylori is dependent on nickel, cofactor of two enzymes essential for in vivo colonization, urease and [nife] hydrogenase. we found that two small paralogous nickel-binding proteins with high content in histidine (hpn and hpn-2) play a central role in maintaining non-toxic intracellular ... | 2015 | 26641249 |
| rapid identification and subtyping of helicobacter cinaedi strains by intact-cell mass spectrometry profiling with the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. | helicobacter cinaedi infection is recognized as an increasingly important emerging disease in humans. although h. cinaedi-like strains have been isolated from a variety of animals, it is difficult to identify particular isolates due to their unusual phenotypic profiles and the limited number of biochemical tests for detecting helicobacters. moreover, analyses of the 16s rrna gene sequences are also limited due to the high levels of similarity among closely related helicobacters. this study was c ... | 2014 | 24153128 |
| mouse models of gastric cancer. | animal models have greatly enriched our understanding of the molecular mechanisms of numerous types of cancers. gastric cancer is one of the most common cancers worldwide, with a poor prognosis and high incidence of drug-resistance. however, most inbred strains of mice have proven resistant to gastric carcinogenesis. to establish useful models which mimic human gastric cancer phenotypes, investigators have utilized animals infected with helicobacter species and treated with carcinogens. in addit ... | 2013 | 24216700 |
| common themes and unique proteins for the uptake and trafficking of nickel, a metal essential for the virulence of helicobacter pylori. | nickel is a virulence determinant for the human gastric pathogen helicobacter pylori. indeed, h. pylori possesses two nickel-enzymes that are essential for in vivo colonization, [nife] hydrogenase and urease, an abundant virulence factor that contains 24 nickel ions per active complex. because of these two enzymes, survival of h. pylori relies on an important supply of nickel, implying a tight control of its distribution and storage. in this review, we will present the pathways of activation of ... | 2013 | 24367767 |
| nitrate and periplasmic nitrate reductases. | the nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. in this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. many bacteria readily reduce nitrate to nit ... | 2014 | 24141308 |
| inverse regulation of fe- and ni-containing sod genes by a fur family regulator nur through small rna processed from 3'utr of the sodf mrna. | superoxide dismutases (sods) are widely distributed enzymes that convert superoxides to hydrogen peroxide and molecular oxygen, using various metals as cofactors. many actinobacteria contain genes for both ni-containing (sodn) and fe-containing (sodf) sods. in streptomyces coelicolor, expression of the sodf and sodn genes is inversely regulated by nickel-specific nur, a fur-family regulator. with sufficient nickel, nur directly represses sodf transcription, while inducing sodn indirectly. bioinf ... | 2013 | 24234448 |
| inverse regulation of fe- and ni-containing sod genes by a fur family regulator nur through small rna processed from 3'utr of the sodf mrna. | superoxide dismutases (sods) are widely distributed enzymes that convert superoxides to hydrogen peroxide and molecular oxygen, using various metals as cofactors. many actinobacteria contain genes for both ni-containing (sodn) and fe-containing (sodf) sods. in streptomyces coelicolor, expression of the sodf and sodn genes is inversely regulated by nickel-specific nur, a fur-family regulator. with sufficient nickel, nur directly represses sodf transcription, while inducing sodn indirectly. bioinf ... | 2013 | 24234448 |
| nickel-dependent metalloenzymes. | this review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase i, acireductone dioxygenase, urease, superoxide dismutase, [nife]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme a synthase/decarbonylase, methyl-coenzyme m reductase, and lactate racemase. these enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more com ... | 2013 | 24036122 |
| nickel-dependent metalloenzymes. | this review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase i, acireductone dioxygenase, urease, superoxide dismutase, [nife]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme a synthase/decarbonylase, methyl-coenzyme m reductase, and lactate racemase. these enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more com ... | 2013 | 24036122 |
| factors required for activation of urease as a virulence determinant in cryptococcus neoformans. | urease in cryptococcus neoformans plays an important role in fungal dissemination to the brain and causing meningoencephalitis. although urea is not required for synthesis of apourease encoded by ure1, the available nitrogen source affected the expression of ure1 as well as the level of the enzyme activity. activation of the apoenzyme requires three accessory proteins, ure4, ure6, and ure7, which are homologs of the bacterial urease accessory proteins ured, uref, and ureg, respectively. a yeast ... | 2013 | 23653445 |
| protein complexes are under evolutionary selection to assemble via ordered pathways. | is the order in which proteins assemble into complexes important for biological function? here, we seek to address this by searching for evidence of evolutionary selection for ordered protein complex assembly. first, we experimentally characterize the assembly pathways of several heteromeric complexes and show that they can be simply predicted from their three-dimensional structures. then, by mapping gene fusion events identified from fully sequenced genomes onto protein complex assembly pathway ... | 2013 | 23582331 |
| helicobacter hepaticus nikr controls urease and hydrogenase activities via the nikabde and hh0418 putative nickel import proteins. | helicobacter hepaticus open reading frame hh0352 was identified as a nickel-responsive regulator nikr. the gene was disrupted by insertion of an erythromycin resistance cassette. the h. hepaticus nikr mutant had five- to sixfold higher urease activity and at least twofold greater hydrogenase activity than the wild-type strain. however, the urease apo-protein levels were similar in both the wild-type and the mutant, suggesting the increase in urease activity in the mutant was due to enhanced ni-m ... | 2013 | 23139401 |
| new diagnostic strategies for detection of helicobacter pylori infection in pediatric patients. | helicobacter pylori (h pylori) is a common chronic bacterial infection that is an important cause of peptic ulcer disease and gastroduodenal disease in children. h pylori is also associated with extragastric manifestations, including growth reduction, iron-deficiency anemia, and idiopathic thrombocytopenic purpura. current guidelines recommend endoscopy with biopsy for the definitive demonstration of h pylori infection. in contrast to serology, the fecal antigen test and the urea breath test pro ... | 2014 | 26491414 |
| andrographolide sodium bisulphite-induced inactivation of urease: inhibitory potency, kinetics and mechanism. | the inhibitory effect of andrographolide sodium bisulphite (asb) on jack bean urease (jbu) and helicobacter pylori urease (hpu) was performed to elucidate the inhibitory potency, kinetics and mechanism of inhibition in 20 mm phosphate buffer, ph 7.0, 2 mm edta, 25 °c. | 2015 | 26179287 |
| the tracrrna and cas9 families of type ii crispr-cas immunity systems. | crispr-cas is a rapidly evolving rna-mediated adaptive immune system that protects bacteria and archaea against mobile genetic elements. the system relies on the activity of short mature crispr rnas (crrnas) that guide cas protein(s) to silence invading nucleic acids. a set of crispr-cas, type ii, requires a trans-activating small rna, tracrrna, for maturation of precursor crrna (pre-crrna) and interference with invading sequences. following co-processing of tracrrna and pre-crrna by rnase iii, ... | 2013 | 23563642 |
| the complex methylome of the human gastric pathogen helicobacter pylori. | the genome of helicobacter pylori is remarkable for its large number of restriction-modification (r-m) systems, and strain-specific diversity in r-m systems has been suggested to limit natural transformation, the major driving force of genetic diversification in h. pylori. we have determined the comprehensive methylomes of two h. pylori strains at single base resolution, using single molecule real-time (smrt®) sequencing. for strains 26695 and j99-r3, 17 and 22 methylated sequence motifs were id ... | 2013 | 24302578 |
| enterohepatic helicobacter species as a potential causative factor in inflammatory bowel disease: a meta-analysis. | the helicobacter species in the gut microbiota comprise helicobacter pylori (h pylori) and enterohepatic helicobacter species (ehs), which can colonize the intestinal mucosa. however, it is unclear whether ehs are associated with inflammatory bowel disease (ibd). therefore, we conducted this meta-analysis to examine the association between ehs and ibd.pubmed, scopus, cochrane library, and web of science databases, as well as abstracts from conference proceedings were searched to identify studies ... | 2015 | 26559250 |
| role of the alpha-helical linker of the c-terminal translocator in the biogenesis of the serine protease subfamily of autotransporters. | autotransporters are secreted virulence factors that comprise three domains: an n-terminal signal peptide, an internal passenger domain, and a c-terminal beta-domain. the mechanism of passenger translocation across the outer membrane remains undefined, with four models having been proposed: the "hairpin," the "threading," the "multimeric," and the "omp85 (yaet)" models. in an attempt to understand autotransporter biogenesis, we screened the sequences of the serine protease subfamily of autotrans ... | 2006 | 16926387 |
| gastric and enterohepatic non-helicobacter pylori helicobacters. | a substantial number of reports published in the last year have contributed to a better understanding of both human and animal infection with non-helicobacter pylori helicobacter species (nhph). gastric infection of humans with helicobacter suis and helicobacter felis as well as unidentified nhph has been described to cause a chronic gastritis and a variety of clinical symptoms, whereas enterohepatic nhph, including helicobacter cinaedi, helicobacter bilis, and helicobacter canis, have been repo ... | 2013 | 24011248 |
| elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation. | microorganisms play a dominant role in the biogeochemical cycling of nutrients. they are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. limitations for specific elements, either fleetin ... | 2012 | 22633059 |
| helicobacter spp. other than h. pylori. | significant advances have been made over the last 12 months in the understanding of the biology of non-h. pylori helicobacter species (nhph). several studies have investigated the association between nhph and human disease, including crohn's disease, lithiasis, liver disease, coronary disease, gastritis, and pyoderma gangrenosum-like ulcers. novel helicobacter taxa were identified in new vertebrate hosts, and new methodologies in the fields of identification of helicobacter spp. and evaluation o ... | 2012 | 22958157 |
| the gyra encoded gene: a pertinent marker for the phylogenetic revision of helicobacter genus. | phylogeny of epsilonproteobacteria is based on sequencing of the 16s rrna gene. however, this gene is not sufficiently discriminatory in helicobacter species and alternative markers would be useful. in this study, the 16s rrna, gyra, hsp60, gyrb, and urea-ureb gene sequences, as well as gyra, hsp60 and gyrb protein sequences were analyzed as tools to support helicobacter species phylogeny: 72 helicobacter strains, belonging to 41 species of which 36 are validated species, were included. results ... | 2016 | 26829999 |