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comparative analysis of prophage-like elements in helicobacter sp. genomes.prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. information on helicobacter sp. prophages remains scarce. in this study, sixteen prophages were identified and analyzed in detail. eight of them are described for the first time. based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. phylogenetic relationships of cluster a helicobacter ...201627169002
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 ...201627275113
plant proteins are smaller because they are encoded by fewer exons than animal proteins.protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. we found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. while eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. proteins unique to plants are ∼81aa s ...201627998811
how old are bacterial pathogens?only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. the global genetic diversity of helicobacter pylori, which infects human stomachs, parallels that of its human host. the time to the most recent common ancestor (tmrca) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence withi ...201627534956
pattern recognition on read positioning in next generation sequencing.the usefulness and the utility of the next generation sequencing (ngs) technology are based on the assumption that the dna or cdna cleavage required to generate short sequence reads is random. several previous reports suggest the existence of sequencing bias of ngs reads. to address this question in greater detail, we analyze ngs data from four organisms with different gc content, plasmodium falciparum (19.39%), arabidopsis thaliana (36.03%), homo sapiens (40.91%) and streptomyces coelicolor (72 ...201627299343
mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids.in the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of dna or rna sequences. fluorescence in situ hybridization (fish) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. to achieve the expected accuracy in detection, fish probes should have high binding affinity towards their complementary strands and discrim ...201525840566
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 ...201526641249
dormant phages of helicobacter pylori reveal distinct populations in europe.prophages of helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. however, their role in the diversity of h. pylori strains is unknown. we demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between european populations, and that h. pylori prophages and their host bacteria share a complex evolutionary history. by comparing the phylogenetic trees of two prophage genes (integra ...201526387443
pathology in captive wild felids at german zoological gardens.this retrospective study provides an overview on spontaneous diseases occurring in 38 captive wild felids submitted for necropsy by german zoological gardens between 2004 and 2013. species included 18 tigers, 8 leopards, 7 lions, 3 cheetahs and 2 cougars with an age ranging from 0.5 to 22 years. renal lesions, predominantly tubular alterations (intra-tubular concrements, tubular degeneration, necrosis, intra-tubular cellular debris, proteinaceous casts, dilated tubuli) followed by interstitial ( ...201526086731
complete genome sequences of two helicobacter pylori strains from a canadian arctic aboriginal community.we report here the complete genome sequences of two amerind helicobacter pylori strains from aklavik, northwest territories, canada. one strain contains extra iron-cofactored urease genes and ~140 rearrangements in its chromosome relative to other described strains (typically differing from one another by <10 rearrangements), suggesting that it represents a novel lineage of h. pylori.201525883278
recombinant bacillus subtilis spores elicit th1/th17-polarized immune response in a murine model of helicobacter pylori vaccination.current progress in research on vaccines against helicobacter pylori emphasizes the significance of eliciting the th1/th17-polarized immune response. such polarization can be achieved by selection of appropriate antigen and adjuvant. in this study, we wanted to check the polarization of the immune response elicited by ureb protein of helicobacter acinonychis delivered by recombinant bacillus subtilis spores upon oral immunization. b. subtilis spores presenting fragment of ureb protein and able t ...201525779639
comparative genomics and genome biology of invasive campylobacter jejuni.campylobacter jejuni is a major pathogen in bacterial gastroenteritis worldwide and can cause bacteremia in severe cases. c. jejuni is highly structured into clonal lineages of which the st677cc lineage has been overrepresented among c. jejuni isolates derived from blood. in this study, we characterized the genomes of 31 c. jejuni blood isolates and 24 faecal isolates belonging to st677cc in order to study the genome biology related to c. jejuni invasiveness. we combined the genome analyses with ...201526603914
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 ...201526342139
transmission of the pabi family of restriction dna glycosylase genes: mobility and long-term inheritance.r.pabi is an exceptional restriction enzyme that functions as a dna glycosylase. the enzyme excises an unmethylated base from its recognition sequence to generate apurinic/apyrimidinic (ap) sites, and also displays ap lyase activity, cleaving the dna backbone at the ap site to generate the 3'-phospho alpha, beta-unsaturated aldehyde end in addition to the 5'-phosphate end. the resulting ends are difficult to religate with dna ligase. the enzyme was originally isolated in pyrococcus, a hypertherm ...201526481899
innate endogenous adjuvants prime to desirable immune responses via mucosal routes.vaccination is an effective strategy to prevent infectious or immune related diseases, which has made remarkable contribution in human history. recently increasing attentions have been paid to mucosal vaccination due to its multiple advantages over conventional ways. subunit or peptide antigens are more reasonable immunogens for mucosal vaccination than live or attenuated pathogens, however adjuvants are required to augment the immune responses. many mucosal adjuvants have been developed to prim ...201425503634
innate endogenous adjuvants prime to desirable immune responses via mucosal routes.vaccination is an effective strategy to prevent infectious or immune related diseases, which has made remarkable contribution in human history. recently increasing attentions have been paid to mucosal vaccination due to its multiple advantages over conventional ways. subunit or peptide antigens are more reasonable immunogens for mucosal vaccination than live or attenuated pathogens, however adjuvants are required to augment the immune responses. many mucosal adjuvants have been developed to prim ...201425503634
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 ...201424474799
mucosal adjuvant activity of il-2 presenting spores of bacillus subtilis in a murine model of helicobacter pylori vaccination.the endospores of bacillus subtilis are now widely used as a platform for presentation of heterologous proteins and due to their safety record and high resistance to harsh environmental conditions can be considered as potential vehicles for oral vaccination. in this research we show that recombinant b. subtilis spores presenting a fragment of the helicobacter acinonychis ureb protein and expressing the ureb gene under vegetative promoter elicit a strong cellular immune response in orally immuniz ...201424743850
a system of vectors for bacillus subtilis spore surface display.bacterial spores have been utilized as platforms for protein display. the best studied display systems are based on bacillus subtilis spores in which several coat proteins have successfully been used as anchors for heterologous protein. increasing knowledge about spore coat structure enables selection of new anchor proteins such as cotz and cgea. here we describe a system of vectors for display of proteins on the surface of b. subtilis spores.201424568122
draft genome sequence of strain x47-2al, a feline helicobacter pylori isolate.helicobacter pylori is a human-specific pathogen that exclusively inhabits the human gastric mucosa. however, occasionally, humans transmit h. pylori to susceptible animal hosts bred in colonies. here, we report the genome sequence of strain x47-2al, isolated from a domestic cat and used in anti-h. pylori immunization studies.201324356847
sequencing error correction without a reference genome.next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. identifying sequencing errors from true biological variants is a challenging task. for organisms without a reference genome this difficulty is even more challenging.201324350580
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.201324358262
helicobacter pylori genomic microevolution during naturally occurring transmission between adults.the human gastric pathogen helicobacter pylori is usually acquired during childhood and, in the absence of treatment, chronic infection persists through most of the host's life. however, the frequency and importance of h. pylori transmission between adults is underestimated. here we sequenced the complete genomes of h. pylori strains that were transmitted between spouses and analysed the genomic changes. similar to h. pylori from chronic infection, a significantly high proportion of the determin ...201324340004
genome sequences of three hpafrica2 strains of helicobacter pylori.we present the genome sequences of three hpafrica2 strains of helicobacter pylori, which are postulated to have evolved in isolation for many millennia in people of san ethnicity. although previously considered to be ancestral to helicobacter acinonychis, the hpafrica2 strains differ markedly from h. acinonychis in their gene arrangement. these data provide new insights into helicobacter evolution.201324072860
comparison of the complete genome sequence of two closely related isolates of 'candidatus phytoplasma australiense' reveals genome plasticity.'candidatus phytoplasma australiense' is associated with at least nine diseases in australia and new zealand. the impact of this phytoplasma is considerable, both economically and environmentally. the genome of a nz isolate was sequenced in an effort to understand its pathogenicity and ecology. comparison with a closely related australian isolate enabled us to examine mechanisms of genomic rearrangement.201323915186
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 ...201323539618
new stable anchor protein and peptide linker suitable for successful spore surface display in b. subtilis.in last decade spores have been successfully used as a surface display platform. various peptides or proteins were displayed this way as functional enzymes or antigens. nearly all attempts involved use of three coat proteins: cotb, cotc or cotg. increasing knowledge of the structure of the spore coat allowed us to propose the use of other proteins whose localization in the spore envelope has been determined. we also propose the application of a new linker suitable for building fusion proteins.201323448318
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 ...201324302578
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 ...201324302578
electron microscopic, genetic and protein expression analyses of helicobacter acinonychis strains from a bengal tiger.colonization by helicobacter species is commonly noted in many mammals. these infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. the aim of this study was to isolate and characterize putative novel helicobacter spp. from bengal tigers in thailand. morphological investigation (gram-staining and electron microscopy) and genetic studies (16srrna, 23srrna, flagellin, urease and prophage gene analyses, rapd dna fingerprinting and ...201323940723
pseudomonas fluorescens-like bacteria from the stomach: a microbiological and molecular study.to characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases.201323466902
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 ...201222408169
characterization of α2,3- and α2,6-sialyltransferases from helicobacter acinonychis.genome sequence data were used to clone and express two sialyltransferase enzymes of the gt-42 family from helicobacter acinonychis atcc 51104, a gastric disease isolate from cheetahs. the deposited genome sequence for these genes contains a large number of tandem repeat sequences in each of them: hac1267 (rqkele)(15) and hac1268 (eekllefkni)(13). we obtained two clones with different numbers of repeat sequences for the hac1267 gene homolog and a single clone for the hac1268 gene homolog. both g ...201222504533
outer membrane biogenesis in escherichia coli, neisseria meningitidis, and helicobacter pylori: paradigm deviations in h. pylori.the bacterial pathogen helicobacter pylori is capable of colonizing the gastric mucosa of the human stomach using a variety of factors associated with or secreted from its outer membrane (om). lipopolysaccharide (lps) and numerous om proteins have been shown to be involved in adhesion and immune stimulation/evasion. many of these factors are essential for colonization and/or pathogenesis in a variety of animal models. despite this wide array of potential targets present on the bacterial surface, ...201222919621
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 ...201222511919
optimizing hybrid assembly of next-generation sequence data from enterococcus faecium: a microbe with highly divergent genome.sequencing of bacterial genomes became an essential approach to study pathogen virulence and the phylogenetic relationship among close related strains. bacterium enterococcus faecium emerged as an important nosocomial pathogen that were often associated with resistance to common antibiotics in hospitals. with highly divergent gene contents, it presented a challenge to the next generation sequencing (ngs) technologies featuring high-throughput and shorter read-length. this study was designed to i ...201223282199
in silico evolutionary analysis of helicobacter pylori outer membrane phospholipase a (ompla).in the past decade, researchers have proposed that the plda gene for outer membrane phospholipase a (ompla) is important for bacterial colonization of the human gastric ventricle. several conserved helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. the current study will shed light on the importance of the plda gene in h. pylori. in silico sequence analysis will be used to investigate whether ...201222974200
origin of the diversity in dna recognition domains in phasevarion associated moda genes of pathogenic neisseria and haemophilus influenzae.phase variable restriction-modification (r-m) systems have been identified in a range of pathogenic bacteria. in some it has been demonstrated that the random switching of the mod (dna methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). moda of neisseria and haemophilus influenzae contain a highly variable, dna recognition domain (drd) that defines the target sequence that is modified by methylation and is used to ...201222457715
gastric helicobacter spp. infection in captive neotropical brazilian feline.ten captive neotropical brazilian feline were submitted to gastroscopic examination and samples of gastric mucosa from fundus, corpus and pyloric antrum were evaluated for the presence of helicobacter species. warthin-starry (ws) staining and pcr assay with species-specific primers and enzymatic cleavage were applied for bacterial detection and identification. histological lesions were evaluated by haematoxylin and eosin staining. all animals showed normal gross aspect of gastric mucosa. helicob ...201124031634
horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. while there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. we analyzed closely related prokaryote strains or species with small genomes (helicobacter, neisseria, stre ...201121298028
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 ...201121372321
new implications on genomic adaptation derived from the helicobacter pylori genome comparison.helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. it evolved with its particular characteristics for biological adaptation. because several h. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.201121387011
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 ...201121505055
comparing de novo genome assembly: the long and short of it.recent advances in dna sequencing technology and their focal role in genome wide association studies (gwas) have rekindled a growing interest in the whole-genome sequence assembly (wgsa) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. and yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. no commonly accepted and standardized method for comparison exists yet. even worse ...201121559467
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 ...201121788478
recombination and dna repair in helicobacter pylori.all organisms have pathways that repair the genome, ensuring their survival and that of their progeny. but these pathways also serve to diversify the genome, causing changes at the nucleotide, whole gene, and genome structure levels. sequencing of bacteria has revealed wide allelic diversity and differences in gene content within the same species, highlighting the importance of understanding pathways of recombination and dna repair. the human stomach pathogen helicobacter pylori is an excellent ...201121682641
genome sequencing reveals a phage in helicobacter pylori.helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. genomic analysis of several strains has revealed an extensive h. pylori pan-genome, likely to grow as more genomes are sampled. here we describe the draft genome sequence (63 contigs; 26× mean coverage) of h. pylori strain b45, isolated from a patient with gastric mucosa-associa ...201122086490
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:201122039924
helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis.helicobacter pylori is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. in its co-evolution with humans, a streamlining of the h. pylori genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. bioinformatic analysis revealed that h. pylori lacks the enzymatic machinery for de novo production of inosine monophosphate (imp), the first purine nucleot ...201122194455
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is stric ...201122003381
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 ...201124710297
genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ...201020071371
detection of atypical cultivable canine gastric helicobacter strain and its biochemical and morphological characters in naturally infected dogs.helicobacter-like organisms are frequently found in canine stomachs, but the relationship between such organisms and gastric pathology has not been established. however, some such organisms have zoonotic importance. the aims of this study were to evaluate the morphological and biochemical characteristics of cultivable canine gastric helicobacter-like organisms (ghlos) in pets and stray dogs and their prevalence in these two groups of dogs. specimens were taken by gastroscopy from 30 clinically h ...201019486497
the helicobacter pylori groes cochaperonin hspa functions as a specialized nickel chaperone and sequestration protein through its unique c-terminal extension.the transition metal nickel plays a central role in the human gastric pathogen helicobacter pylori because it is required for two enzymes indispensable for colonization, the nickel metalloenzyme urease and [nife] hydrogenase. to sustain nickel availability for these metalloenzymes while providing protection from the metal's harmful effects, h. pylori is equipped with several specific nickel-binding proteins. among these, h. pylori possesses a particular chaperone, hspa, that is a homolog of the ...201020061471
in helicobacter pylori, luxs is a key enzyme in cysteine provision through a reverse transsulfuration pathway.in many bacteria, luxs functions as a quorum-sensing molecule synthase. however, it also has a second, more central metabolic function in the activated methyl cycle (amc), which generates the s-adenosylmethionine required by methyltransferases and recycles the product via methionine. helicobacter pylori lacks an enzyme catalyzing homocysteine-to-methionine conversion, rendering the amc incomplete and thus making any metabolic role of h. pylori luxs (luxs(hp)) unclear. interestingly, luxs(hp) is ...201020061483
expression and display of urea of helicobacter acinonychis on the surface of bacillus subtilis spores.the bacterial endospore (spore) has recently been proposed as a new surface display system. antigens and enzymes have been successfully exposed on the surface layers of the bacillus subtilis spore, but only in a few cases the efficiency of expression and the effective surface display and have been determined. we used this heterologous expression system to produce the a subunit of the urease of the animal pathogen helicobater acinonychis. ureases are multi-subunit enzymes with a central role in t ...201020082702
simple sequence repeats in helicobacter canadensis and their role in phase variable expression and c-terminal sequence switching.helicobacter canadensis is an emerging human pathogen and zoonotic agent. the genome of h. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts.201020105305
decoupling environment-dependent and independent genetic robustness across bacterial species.the evolutionary origins of genetic robustness are still under debate: it may arise as a consequence of requirements imposed by varying environmental conditions, due to intrinsic factors such as metabolic requirements, or directly due to an adaptive selection in favor of genes that allow a species to endure genetic perturbations. stratifying the individual effects of each origin requires one to study the pertaining evolutionary forces across many species under diverse conditions. here we conduct ...201020195496
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.201020219135
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 ...201020368342
whole genome assembly of a natto production strain bacillus subtilis natto from very short read data.bacillus subtilis natto is closely related to the laboratory standard strain b. subtilis marburg 168, and functions as a starter for the production of the traditional japanese food "natto" made from soybeans. although re-sequencing whole genomes of several laboratory domesticated b. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, b. subtilis natto, from very short read data is more challe ...201020398357
identification of helicobacter spp. in bile and gallbladder tissue of patients with symptomatic gallbladder disease.this experimental study was designed to determine if helicobacter spp. contribute to benign gallbladder disease using polymerase chain reaction (pcr) methods.201020495657
sequencing, annotation, and comparative genome analysis of the gerbil-adapted helicobacter pylori strain b8.the mongolian gerbils are a good model to mimic the helicobacter pylori-associated pathogenesis of the human stomach. in the current study the gerbil-adapted strain b8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain b128.201020507619
from array-based hybridization of helicobacter pylori isolates to the complete genome sequence of an isolate associated with malt lymphoma.helicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. to determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach.201020537153
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 ...201020643857
mutagenesis of conserved amino acids of helicobacter pylori fur reveals residues important for function.the ferric uptake regulator (fur) of the medically important pathogen helicobacter pylori is unique in that it has been shown to function as a repressor both in the presence of an fe2+ cofactor and in its apo (non-fe2+-bound) form. however, virtually nothing is known concerning the amino acid residues that are important for fur functioning. therefore, mutations in six conserved amino acid residues of h. pylori fur were constructed and analyzed for their impact on both iron-bound and apo repressi ...201020644138
molecular phylogeny and functional genomics of beta-galactoside alpha2,6-sialyltransferases that explain ubiquitous expression of st6gal1 gene in amniotes.sialyltransferases are key enzymes in the biosynthesis of sialoglycoconjugates that catalyze the transfer of sialic residue from its activated form to an oligosaccharidic acceptor. β-galactoside α2,6-sialyltransferases st6gal i and st6gal ii are the two unique members of the st6gal family described in higher vertebrates. the availability of genome sequences enabled the identification of more distantly related invertebrates' st6gal gene sequences and allowed us to propose a scenario of their evol ...201020855889
molecular evolution of the helicobacter pylori vacuolating toxin gene vaca.helicobacter pylori is a genetically diverse organism that is adapted for colonization of the human stomach. all strains contain a gene encoding a secreted, pore-forming toxin known as vaca. genetic variation at this locus could be under strong selection as h. pylori adapts to the host immune response, colonizes new human hosts, or inhabits different host environments. here, we analyze the molecular evolution of vaca. phylogenetic reconstructions indicate the subdivision of vaca sequences into t ...201020870762
nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics.the ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. here we evaluate the microbial biota in healthy mule deer (odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cdna libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node rna enriched for polyadenylated rna and sequenced using ...201020976145
quake: quality-aware detection and correction of sequencing errors.we introduce quake, a program to detect and correct errors in dna sequencing reads. using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, quake achieves the highest accuracy on realistically simulated reads. we further demonstrate substantial improvements in de novo assembly and snp detection after using quake. quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from ...201021114842
vitamin b(6) is required for full motility and virulence in helicobacter pylori.despite recent advances in our understanding of how helicobacter pylori causes disease, the factors that allow this pathogen to persist in the stomach have not yet been fully characterized. to identify new virulence factors in h. pylori, we generated low-infectivity variants of a mouse-colonizing h. pylori strain using the classical technique of in vitro attenuation. the resulting variants and their highly infectious progenitor bacteria were then analyzed by global gene expression profiling. the ...201021151756
prediction of type iii secretion signals in genomes of gram-negative bacteria.pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. the type iii secretion system represents such a mechanism. proteins transported via this pathway ("effector proteins") have to be distinguished from all other proteins that are not exported from the bacterial cell. although a special targeting signal at the n-terminal end of effector proteins has bee ...200919526054
impact of chromatin structures on dna processing for genomic analyses.chromatin has an impact on recombination, repair, replication, and evolution of dna. here we report that chromatin structure also affects laboratory dna manipulation in ways that distort the results of chromatin immunoprecipitation (chip) experiments. we initially discovered this effect at the saccharomyces cerevisiae hmr locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. using input samples from chip-seq studies, we detected a similar bias through ...200919693276
the dif/xer recombination systems in proteobacteria.in e. coli, 10 to 15% of growing bacteria produce dimeric chromosomes during dna replication. these dimers are resolved by xerc and xerd, two tyrosine recombinases that target the 28-nucleotide motif (dif) associated with the chromosome's replication terminus. in streptococci and lactococci, an alternative system is composed of a unique, xer-like recombinase (xers) genetically linked to a dif-like motif (dif(sl)) located at the replication terminus. preliminary observations have suggested that t ...200919727445
geographic distribution of methyltransferases of helicobacter pylori: evidence of human host population isolation and migration.helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. this ubiquitous association between h. pylori and humans is thought to be present since the origin of modern humans. the h. pylori genome encodes for an exceptional number of restriction and modifications (r-m) systems. to evaluate if r-m systems are an adequate tool to determine the geographic distribution of h. pylori strains, we typed 221 strains from africa, america, asia, and ...200919737407
evaluation of a new test, genotype helicodr, for molecular detection of antibiotic resistance in helicobacter pylori.the eradication rate of helicobacter pylori by standard therapy is decreasing due to antibiotic resistance, mainly to clarithromycin. our aim was to provide a new molecular test to guide the treatment of new and relapsed cases. we first studied 126 h. pylori strains for phenotypic (mic) and genotypic resistance to clarithromycin (rrl mutation) and levofloxacin (gyra mutation) and then developed a dna strip genotyping test on the basis of the correlation results and literature data. clinical stra ...200919759218
functional analysis of the helicobacter pylori flagellar switch proteins.helicobacter pylori uses flagellum-mediated chemotaxis to promote infection. bacterial flagella change rotational direction by changing the state of the flagellar motor via a subcomplex referred to as the switch. intriguingly, the h. pylori genome encodes four switch complex proteins, flim, flin, fliy, and flig, instead of the more typical three of escherichia coli or bacillus subtilis. our goal was to examine whether and how all four switch proteins participate in flagellation. previous work de ...200919767432
a study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (chargaff's second parity rule).chargaff's rule of intra-strand parity (isp) between complementary mono/oligonucleotides in chromosomes is well established in the scientific literature. although a large numbers of papers have been published citing works and discussions on isp in the genomic era, scientists are yet to find all the factors responsible for such a universal phenomenon in the chromosomes. in the present work, we have tried to address the issue from a new perspective, which is a parallel feature to isp. the composit ...200919861381
examination of genome homogeneity in prokaryotes using genomic signatures.dna word frequencies, normalized for genomic at content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a "genomic signature." the genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled dna. genomic signatures can also be used to search for horizontally transferred dna or dna regions subjected to special selection forces. thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. the fact ...200919956556
molecular evolution of multisubunit rna polymerases: sequence analysis.transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ...200919895820
molecular evolution of multisubunit rna polymerases: sequence analysis.transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ...200919895820
unsupervised statistical clustering of environmental shotgun sequences.the development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. while previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed.200919799776
de novo assembly using low-coverage short read sequence data from the rice pathogen pseudomonas syringae pv. oryzae.we developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. by combining data generated from 454 life sciences (roche) and illumina (formerly known as solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. we applied this method to two isolates of the phytopathogenic bacteria pseudomonas syringae. seque ...200919015323
structural analysis of the dna-binding domain of the helicobacter pylori response regulator arsr.the helicobacter pylori arss-arsr two-component signal transduction system, comprised of a sensor histidine kinase (arss) and a response regulator (arsr), allows the bacteria to regulate gene expression in response to acidic ph. we expressed and purified the full-length arsr protein and the dna-binding domain of arsr (arsr-dbd), and we analyzed the tertiary structure of the arsr-dbd using solution nuclear magnetic resonance (nmr) methods. both the full-length arsr and the arsr-dbd behaved as mon ...200919117956
failure to detect helicobacter pylori dna in drinking and environmental water in dhaka, bangladesh, using highly sensitive real-time pcr assays.the main transmission pathway of helicobacter pylori has not been determined, but several reports have described detection of h. pylori dna in drinking and environmental water, suggesting that h. pylori may be waterborne. to address this possibility, we developed, tested, and optimized two complementary h. pylori-specific real-time pcr assays for quantification of h. pylori dna in water. the minimum detection level of the assays including collection procedures and dna extraction was shown to be ...200919304824
pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus campylobacter.an open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. the genus campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. we estimate the campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core gen ...200919304960
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 ...200919401779
synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes.comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (ni). comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in ni among taxa. a low level of nonsynonym ...200818667439
the human gastric pathogen helicobacter pylori has a potential acetone carboxylase that enhances its ability to colonize mice.helicobacter pylori colonizes the human stomach and is the etiological agent of peptic ulcer disease. all three h. pylori strains that have been sequenced to date contain a potential operon whose products share homology with the subunits of acetone carboxylase (encoded by acxabc) from xanthobacter autotrophicus strain py2 and rhodobacter capsulatus strain b10. acetone carboxylase catalyzes the conversion of acetone to acetoacetate. genes upstream of the putative acxabc operon encode enzymes that ...200818215283
de novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.novel high-throughput dna sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. however, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. this study focuses on the illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. we ...200818332092
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.200818337392
substantial biases in ultra-short read data sets from high-throughput dna sequencing.novel sequencing technologies permit the rapid production of large sequence data sets. these technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. we generated and analyzed two illumina 1g ultra-short read data sets, i.e. 2.8 million 27mer reads from a beta vulgaris genomic clone and 12.3 million 36mers from the helicobacter acinonychis genome. we found that error rates range from 0.3% at the beginn ...200818660515
role of the helicobacter hepaticus flagellar sigma factor flia in gene regulation and murine colonization.the enterohepatic helicobacter species helicobacter hepaticus colonizes the murine intestinal and hepatobiliary tract and is associated with chronic intestinal inflammation, gall stone formation, hepatitis, and hepatocellular carcinoma. thus far, the role of h. hepaticus motility and flagella in intestinal colonization is unknown. in other, closely related bacteria, late flagellar genes are mainly regulated by the sigma factor flia (sigma(28)). we investigated the function of the h. hepaticus fl ...200818689480
the helicobacter pylori hpyaxii restriction-modification system limits exogenous dna uptake by targeting gtac sites but shows asymmetric conservation of the dna methyltransferase and restriction endonuclease components.the naturally competent organism helicobacter pylori encodes a large number of restriction-modification (r-m) systems that consist of a restriction endonuclease and a dna methyltransferase. r-m systems are not only believed to limit dna exchange among bacteria but may also have other cellular functions. we report a previously uncharacterized h. pylori type ii r-m system, m.hpyaxii/r.hpyaxii. we show that this system targets gtac sites, which are rare in the h. pylori chromosome but numerous in r ...200818978016
conjugative transfer of chromosomally encoded antibiotic resistance from helicobacter pylori to campylobacter jejuni.many strains of helicobacter pylori are naturally competent for transformation and able to transfer chromosomal dna among different isolates using a conjugation-like mechanism. in this study, we sought to determine whether h. pylori can transfer dna into campylobacter jejuni, a closely related species of the campylobacterales group. to monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsl gene of h. pylori was used. mating o ...200717135441
conjugative transfer of chromosomally encoded antibiotic resistance from helicobacter pylori to campylobacter jejuni.many strains of helicobacter pylori are naturally competent for transformation and able to transfer chromosomal dna among different isolates using a conjugation-like mechanism. in this study, we sought to determine whether h. pylori can transfer dna into campylobacter jejuni, a closely related species of the campylobacterales group. to monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsl gene of h. pylori was used. mating o ...200717135441
evidence for type iii restriction and modification systems in mycoplasma pulmonis.mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type iii restriction and modification (r-m) enzymes. transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of r-m activity. genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.200717209015
plasmids and rickettsial evolution: insight from rickettsia felis.the genome sequence of rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of r. felis as either typhus group (tg) or spotted fever group (sfg) rickettsiae. most intriguing was the first report from rickettsiae of a conjugative plasmid (prf) that contains 68 putative open reading frames, several of which are predicted to enc ...200717342200
development and application of a novel peptide nucleic acid probe for the specific detection of helicobacter pylori in gastric biopsy specimens.in this work, a fluorescence in situ hybridization (fish) method for the rapid detection of helicobacter pylori using a novel peptide nucleic acid (pna) probe is reported. laboratory testing with several different bacterial species, including other helicobacter spp., has shown that this probe is highly specific for h. pylori strains. in addition, the pna fish method has been successfully adapted for detection of the pathogen in paraffin-embedded gastric biopsy specimens.200717609326
helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic sel1-like genes.geographic partitioning is postulated to foster divergence of helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. h. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. sequenced h. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that ...200717696605
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