Molecular characterization and interstrain variability of pHPS1, a plasmid isolated from the Sydney strain (SS1) of Helicobacter pylori

The 5846-bp circular plasmid pHPS1 of Helicobacter pylori Sydney strain, SS1, was cloned, sequenced, and structurally characterized. The SS1 strain is widely used in animal studies of H. pylori infection. The sequence of pHPS1 revealed three open reading frames (ORFs), all of which are transcribed. Two ORFs encode putative plasmid replication proteins, RepA and RepB, similar to replicases resident on theta plasmids. In contrast, the function of ORF2 remains cryptic due to the absence of sequence similarity with any known protein in sequence databases. In addition, species specificity of these three coding regions was shown using DNA dot blot hybridization in 57 diverse clinical H. pylori isolates and 32 Helicobacter and Campylobacter strains. RepA appears to be the predominant plasmid replication protein of H. pylori and the deduced amino acid sequence was highly conserved (76-96%) in 8 H. pylori isolates, including SS1. RepB was detected in 3 H. pylori isolates examined in this study, 2 of which possess only the repB gene. Analysis of the protein sequences of these two replicases, together with previously characterized H. pylori plasmid replication proteins, supports the formation of a distinct class of H. pylori plasmid proteins. Moreover, comprehensive analysis of the whole genome sequence of H. pylori strain 26695, pHPS1, and other H. pylori plasmid sequences that are available revealed interesting insights as to the occurrence of plasmid-mediated recombination within H. pylori. Common regions between plasmids and chromosome sequences of H. pylori were identified in this study which could only have arisen by genetic recombination, thus providing the first line of evidence, albeit indirectly, of the contribution of H. pylori plasmids in generating an extensive genetic heterogeneity characteristic of this important gastroduodenal pathogen.     

Cloning and Characterization of a 22 kDa Outer-Membrane Protein (Omp22) from Helicobacter pylori

Helicobacter pylori is a causative agent of gastritis and peptic ulceration in humans. As the first step towards development of a vaccine against H. pylori infection, we have attempted to identify protective antigens. A potential target of vaccine development would be a H. pylori specific protein, which is surface-exposed and highly antigenic. We identified a 22 kDa outer-membrane protein (Omp22) from H. pylori, which was highly immunoreactive. By screening a H. pylori genomic DNA library with rabbit anti-H. pylori outer-membrane protein antibodies, the omp22 gene was cloned and 1.4 kb of the nucleotide sequence was determined. One open reading frame, encoding a 179-residue polypeptide, was identified and the amino acid sequence deduced showed homology with peptidoglycan-associated lipoproteins. The sequence was conserved among other H. pylori strains. Omp22 protein is expressed as a precursor polypeptide of 179 residues and undergoes lipid modification and cleavage of an 18 amino acid signal peptide to yield a mature protein. Omp22 protein in H. pylori as well as recombinant Omp22 protein expressed in E. coli was localized into the outer membrane and exposed on the cell surface. Omp22 may have the potential as a target antigen for the development of a H. pylori vaccine.     

Characterization of a plasmid from Helicobacter pylori encoding a replication protein common to plasmids in Gram-positive bacteria

A 1.5 kb cryptic plasmid was isolated from Helicobacter pylori. Low-stringency hybridization analysis using this plasmid as a DNA probe revealed base sequence homology with other plasmids in this species. Nucleotide sequence analysis identified an open reading frame encoding a putative polypeptide of 25 kDa. This protein showed marked amino acid sequence similarity to replication-initiation proteins commonly found in small plasmids endogenous to Gram-positive bacteria which replicate by the 'rolling-circle' mechanism. Sequence motifs corresponding to the origins-of-replication consensus sequences were found on this cryptic plasmid. DNA and oligonucleotide probes to these plasmid replication sequences were used in hybridization analysis to identify similar sequences in other H. pylori plasmids. We believe this is the first plasmid isolated from a Gram-negative bacterium to show replication determinants characteristic of the 'rolling-circle' group of plasmids from Gram-positive bacteria. The cloned plasmid will be used to develop a shuttle-vector for H. pylori.     

Essential role of Helicobacter pylori gamma-glutamyltranspeptidase for the colonization of the gastric mucosa of mice

Constitutive expression of gamma-glutamyltranspeptidase (GGT) activity is common to all Helicobacter pylori strains, and is used as a marker for identifying H. pylori isolates. Helicobacter pylori GGT was purified from sonicated extracts of H. pylori strain 85P by anion exchange chromatography. The N-terminal amino acid sequences of two of the generated endo-proteolysed peptides were determined, allowing the cloning and sequencing of the corresponding gene from a genomic H. pylori library. The H. pylori ggt gene consists of a 1681 basepair (bp) open reading frame encoding a protein with a signal sequence and a calculated molecular mass of 61 kDa. Escherichia coli clones harbouring the H. pylori ggt gene exhibited GGT activity at 37 degrees C, in contrast to E. coli host cells (MC1061, HB101), which were GGT negative at 37 degrees C. GGT activity was found to be constitutively expressed by similar genes in Helicobacter felis, Helicobacter canis, Helicobacter bilis, Helicobacter hepaticus and Helicobacter mustelae. Western immunoblots using rabbit antibodies raised against a His-tagged-GGT recombinant protein demonstrated that H. pylori GGT is synthesized in both H. pylori and E. coli as a pro-GGT that is processed into a large and a small subunit. Deletion of a 700 bp fragment within the GGT-encoding gene of a mouse-adapted H. pylori strain (SS1) resulted in mutants that were GGT negative yet grew normally in vitro. These mutants, however, were unable to colonize the gastric mucosa of mice when orally administered alone or together (co-infection) with the parental strain. These results demonstrate that H. pylori GGT activity has an essential role for the establishment of the infection in the mouse model, demonstrating for the first time a physiological role for a bacterial GGT enzyme.     

A positive assay for identification of cagA negative strains of Helicobacter pylori

A new PCR protocol was developed for the positive identification of cagA negative Helicobacter pylori strains. Amplification of a portion of the genome across the insertion point of the cag pathogenicity island (the ES-"empty site") generated a 106-bp fragment, which produces a positive signal for cagA negative strains. Combined with the results of the cagA assay, the signals for ES allowed the complete characterization of the patients' cagA status. DNA sequencing analysis confirmed the identity of the ES fragment. The new protocol and cagA assay were applied to 22 DNA preparations isolated from stools from H. pylori infected adult patients and to 21 DNA preparations isolated from stools from H. pylori infected children. The same analysis was also performed on nine colonies of H. pylori derived from gastric biopsies of nine of the adult patients. The total number of cagA positive cases from adult patients was 14 or 63.6% (11 mono- and 3 mixed) and of the cagA negative cases (or ES positive) was 9 or 40.9% (6 mono- and 3 mixed). Of the 21 stool DNA samples from children, 6 (28.6%) were cagA positive, 12 (57.1%) were cagA negative and 3 (14.3%) were positive for cagA and for the ES simultaneously. The proportions of mixed cagA positive and cagA negative H. pylori infections were almost equal in adults and children (13.6% and 14.3%, respectively). No reaction products of the proper fragment sizes for cagA or the empty site (ES) were obtained from any of the stool DNA samples of 10 H. pylori uninfected subjects (100% specificity). This noninvasive assay discriminates consistently cagA negative cases from cagA positive strains and from amplification failures. It can be a useful tool for clinical and epidemiological studies of H. pylori infection.     

Development of a PCR-based technique for detection of Helicobacter pylori

Abstract A primer-set was designed for specific detection of genes that encode for 16S rRNA of Helicobacter pylori , using direct polymerase chain reaction (PCR). The primers were selected in the hypervariable regions, derived from a complete small subunit 16S rRNA sequence of the reference strain H. pylori CCUG 17874. The primer-set amplified a 537 base pair (bp) sequence specifically from chromosomal H. pylori DNA. Amplification of purified chromosomal H. pylori DNA was achieved at concentrations as low as 1 femto gram (fg), equivalent to 5 bacteria. Furthermore, as few as 1 lysed H. pylori cell was detected by this PCR technique. The specificity of the primers was 100%, since purified chromosomal DNA was detected from all 32 various H. pylori isolates, whereas no other bacteria species were detected, whether related to Helicobacter or not. The 16S rDNA primers successfully detected H. pylori in antral biopsy specimens collected from infected patients.     

Production of a conserved adhesin by the human gastroduodenal pathogen Helicobacter pylori.

An adhesin protein with an approximate subunit molecular weight of 19,600 has been purified from the gastric pathogen Helicobacter pylori. The protein was loosely associated with the cell surface and was removed by gentle stirring or shearing. Released aggregates of the 19.6-kDa protein were removed from suspension by ultracentrifugation and separated from contaminating membranes by washing in 1.0% sodium dodecyl sulfate (SDS). The SDS-insoluble protein was purified further by Mono Q anion-exchange column chromatography. Electron microscopy of the purified adhesin demonstrated that it formed amorphous aggregates similar to the material attached to the bacterial cells and that the aggregates were morphologically distinct from typical fimbriae. Western blot (immunoblot) analysis with antiserum raised against the purified protein from one strain reacted with a protein with a similar subunit molecular weight present in all nine strains of H. pylori examined, but the protein was not present in other Helicobacter species examined. The N-terminal sequences of the 19.6-kDa protein purified from three different strains of H. pylori were identical for the first 28 amino acids, with the 10 amino-terminal residues showing limited sequence homology with the TcpA pilus protein of Vibrio cholerae. The H. pylori 19.6-kDa protein associated both with human and rabbit erythrocytes and with human buccal epithelial cells. Polystyrene microspheres coated with the protein agglutinated human, horse, and rabbit erythrocytes, suggesting that this protein species could mediate adhesion between H. pylori and eucaryotic cells. This ability to act as an adhesin may make this protein an important virulence factor for H. pylori and hence a potential target for a vaccine and therapy.     

Genetic diversity of Helicobacter pylori indexed with respect to clinical symptomatology, using a 16S rRNA and a species-specific DNA probe

DNA probes are described which identify group and fingerprint strains of the human gastric pathogen Helicobacter pylori , on the basis of well-defined band homologies. A 544 bp internal fragment of the 16S ribosomal RNA gene was generated by polymerase chain reaction (PCR) with primers derived from the Escherichia coli rRNA gene sequence. In genomic Southern blots this probe detected restriction site variation around these loci, generating simple but strain-specific molecular fingerprints. A small conserved chromosomal fragment of 1.2 kbp, Hps, species-specific for H. pylori , was obtained by cloning random Hind III fragments into pUC19. It was useful for dot-blot identification, and also separated isolates into one major and two minor groups. When results for these two probes were combined, a baseline characterization of genotype was obtained. A band-matching database of molecular fingerprints for the type strain and 63 clinical isolates of H. pylori from asymptomatic, ulcer and gastritis contexts is presented. No significant association between the genotypes at this level of definition and the associated clinical symptomatology of the isolates was detected.     

幽门螺杆菌东、西方株CagA的序列差异及其对胃癌细胞生长与凋亡的影响

【背景】幽门螺杆菌(Helicobacter pylori,H.pylori)是胃癌的主要致病因素,其分泌的细胞毒素相关基因A蛋白(Cytotoxin associated gene A,CagA)是目前已知唯一能被H.pylori注入胃上皮细胞并模拟细胞内蛋白发挥作用的癌蛋白,参与胃癌的发生发展。【目的】比较H.pylori东亚株和西方株CagA结构差异,初步探讨H.pylori-CagA对胃癌细胞增殖与凋亡的影响。【方法】对H.pylori东亚株和西方株CagA的核酸及氨基酸序列进行生物信息学分析,构建含东亚株和西方株cagA基因的真核表达载体,转染胃癌细胞AGS,用Western blot法检测CagA蛋白的表达,用CCK8法测定细胞的生长曲线,流式细胞术检测细胞凋亡。【结果】生物信息学分析发现H.pylori东亚、西方菌株CagA的核酸序列和氨基酸序列均存在特征性差异。构建了含东亚、西方菌株cagA基因的表达载体[命名为GZ7/cagA(东亚株)和26695/cagA(西方株)]。与空载体组比较,GZ7/cagA和26695/cagA转染组均表达CagA蛋白,两组比较表达量无显著性差异,GZ7/cagA转染组细胞生长显著增加,而26695/cagA转染组细胞生长显著降低(P0.05)。GZ7/cagA转染组、26695/cagA转染组细胞的凋亡率分别为7.23±0.96及9.17±1.40,均高于空载体组(5.03±0.63),差异有统计学意义(P0.05)。【结论】东亚株与西方株CagA之间有结构和功能的差异,东亚株CagA能促进细胞增殖,而西方株CagA却抑制细胞增殖,但两者均能促进细胞凋亡。     

Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori

Using transposon shuttle mutagenesis, we identified six Helicobacter pylori mutants from the NTUH-C1 strain that exhibited decreased adherence and cell elongation. Inverse polymerase chain reaction and DNA sequencing revealed that the same locus was interrupted in these six mutants. Nucleotide and amino acid sequences showed no homologies with H. pylori 26695 and J99 strains. This novel open reading frame contained 1617 base pairs. The amino acid sequence shared 24% identity with a putative nicking enzyme in Bacillus halodurans and 23 and 20% identity with type IIS restriction endonucleases PleI and MlyI, respectively. The purified protein, HpyC1I, showed endonuclease activity with the recognition and cleavage site 5'-CCATC(4/5)-3'. Two open reading frames were located upstream of the gene encoding HpyC1I. Together, HpyC1I and these two putative methyltransferases (M1.HpyC1I and M2.HpyC1I) function as a restriction-modification (R-M) system. The HpyC1I R-M genes were found in 9 of the 15 H. pylori strains tested. When compared with the full genome, significantly lower G + C content of HpyC1I R-M genes implied that these genes might have been acquired by horizontal gene transfer. Plasmid DNA transformation efficiencies and chromosomal DNA digestion assays demonstrated protection from HpyC1I digestion by the R-M system. In conclusion, we have identified a novel R-M system present in approximately 60% of H. pylori strains. Disruption of this R-M system results in cell elongation and susceptibility to HpyC1I digestion.     

Identification, characterization, and spatial localization of two flagellin species in Helicobacter pylori flagella.

Flagellar filaments were isolated from Helicobacter pylori by shearing, and flagellar proteins were further purified by a variety of techniques, including CsCl density gradient ultracentrifugation, pH 2.0 acid disassociation-neutral pH reassociation, and differential ultracentrifugation followed by molecular sieving with a Sephacryl S-500 column or Mono Q anion-exchange column, and purified to homogeneity by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transfer to an Immobilon membrane. Two flagellin species of pI 5.2 and with apparent subunit molecular weights (Mrs) of 57,000 and 56,000 were obtained. N-terminal amino acid analysis showed that the two H. pylori flagellin species were related to each other and shared sequence similarity with the N-terminal amino acid sequence of Campylobacter coli, Bacillus, Salmonella, and Caulobacter flagellins. Analysis of the amino acid composition of the predominant 56,000-Mr flagellin species isolated from two strains showed that it was comparable to the flagellins of other species. The minor 57,000-Mr flagellin species contained a higher content of proline. Immunoelectron microscopic studies with polyclonal monospecific H. pylori antiflagellin antiserum and monoclonal antibody (MAb) 72c showed that the two different-Mr flagellin species were located in different regions of the assembled flagellar filament. The minor 57,000-Mr species was located proximal to the hook, and the major 56,000-Mr flagellin composed the remainder of the filament. Western immunoblot analysis with polyclonal rabbit antisera raised against H. pylori or Campylobacter jejuni flagellins and MAb 72c showed that the 56,000-Mr flagellin carried sequences antigenetically cross-reactive with the 57,000-Mr H. pylori flagellin and the flagellins of Campylobacter species. This antigenic cross-reactivity did not extend to the flagellins of other gram-negative bacteria. The 56,000-Mr flagellin also carried H. pylori-specific sequences recognized by two additional MAbs. The epitopes for these MAbs were not surface exposed on the assembled inner flagellar filament of H. pylori but were readily detected by immunodot blot assay of sodium dodecyl sulfate-lysed cells of H. pylori, suggesting that this serological test could be a useful addition to those currently employed in the rapid identification of this important pathogen.     

幽门螺杆菌CagA蛋白N端片段的表达、纯化及其与磷脂酰丝氨酸的亲和力检测

目的:表达和纯化幽门螺杆菌不同菌株的CagA蛋白N端片段,检测其与磷脂酰丝氨酸(PS)的相互作用及亲和力。方法:用PCR方法从幽门螺杆菌3个菌株中扩增出CagA蛋白N端基因,并连接到表达载体pET-28a上;转化大肠杆菌BL21,经IPTG诱导可溶性表达CagA蛋白N端880残基片段;经镍柱亲和纯化后,利用PLOA法检测CagA蛋白与PS的相互作用。结果:构建了3种幽门螺杆菌菌株cagA基因的原核表达质粒pET-28a/cagAJ99、pET-28a/cagA11637及pET-28a/cagASS1,并在大肠杆菌中获得可溶性表达,SDS-PAGE和Western印迹证实得到目标融合蛋白,亲和纯化得到高纯度CagA蛋白。PLOA结果表明,CagA蛋白与PS有明显的相互作用。结论:3种幽门螺杆菌菌株CagA蛋白与PS之间存在相互作用,且不同的CagA与PS有不同的亲和力。     

AP—PCR结合进化树分析在幽门螺杆菌地域起源特征研究中的价值

目的探讨随机引物PCR（Arbitrary primerPCR,AP—PCR）结合克隆测序及生物信息学分析等方法在研究幽门螺杆菌（Helicobacter pylori,Hpylori）菌株地域起源特征中的价值和意义。方法针对临床分离培养的Hpylori菌株的基因组DNA,采用一组10nt的寡核苷酸引物进行随机PCR扩增,选取相对保守的片段进行回收、克隆及测序,测序的基因序列提交GenBank数据库进行序列相似性的BLAST比对,收集BLAST比对得到的同源性较高不同地域来源螺杆菌的对应序列,用ClustalX软件进行排序,采用Mega4．0软件中的邻位相连法（Neighbor-joining）和最大简约法（Maximum—parsimony）进行进化树分析。结果随机引物扩增及筛选克隆测序得到的基因产物为NADH脱氢酶G和H亚单位的部分编码序列,与27株不同地域来源H．pylori及1株猫科动物来源螺杆菌菌株的同源性均高达90％以上,表明Hpylori中NADH脱氢酶基因序列为保守结构,进化树分析显示：采用AP．PCR方法得到的Hpylori临床菌株的基因序列,显示出东亚菌株来源的遗传特征,与具有东亚菌株特征的美洲秘鲁Sat464和Shi470菌株、韩国的52、51菌株、日本的1757菌株遗传距离较近,与南亚、欧洲菌株距离较远,与非洲的SouthAffica7菌株和猫科动物来源的Sheeba菌株的遗传距离最远。结论不仅某些特殊基因可以反映地域差异,随机定位相对保守的基因片段同样可以反映Hpylori的地域起源特征。AP—PCR、测序等技术方法与进化树分析相结合是探讨Hpylori地域起源特征的一种更为便捷有效的新方法。     

幽门螺杆菌Cag-PAI hp0525基因的克隆表达及其重组蛋白HP0525对SGC-7901细胞增殖的影响

目的：由于文献报道幽门螺杆菌（Helicobacter pylori）是产生胃溃疡和胃癌的致病菌之一,一个重要的影响因素是由cag致病岛编码的四型分泌系统。Hp0525是Cag致病岛中重要成分,是一种内膜蛋白ATPase。而幽门螺杆菌中Cag蛋白的表达以及Cag PAI编码的各自蛋白功能研究得还很少,为进一步研究幽门螺杆菌的致病机制和研发幽门螺杆菌诊断试剂盒及疫苗,特克隆幽门螺杆菌NCTC 11637hp0525 (caga) 基因,并对其进行测序,构建原核重组质粒,表达HP0525蛋白,初步研究其对SGC-7901细胞增殖的影响。方法：应用PCR技术从H.pylori基因组DNA中扩增hp0525编码基因片段,克隆至pMD18-T载体后,再将其定向插入pET-30a载体中,双酶切鉴定筛选阳性克隆,以DNA自动分析仪进行序列测定。测序分析正确后,经IPTG诱导表达,表达蛋白以Ni2＋-NTA柱进行纯化,并经Western blot和MALDI-TOF鉴定,透析除盐后的蛋白,通过免疫新西兰大白兔和抗体效价的测定,纯化的蛋白作用于SGC-7901细胞,用MTT法检测蛋白对细胞增殖的影响。结果：成功克隆hp0525基因,全长993bp,编码330个氨基酸,与GenBank 公布的其他H.pylori菌株基因序列的核苷酸同源性为97%~99%。工程菌诱导后SDS-PAGE显示新生表达蛋白带,相对分子质量为36 000,与预期一致,经Ni2＋-NTA柱纯化后可获得纯度为98％重组蛋白。蛋白作用于SGC-7901细胞后,结果呈现一定量的时间和剂量依赖性。它是一种ATPase,通过测定具有一定的活性。活性为4.40IU/ml结论：成功克隆hp0525基因,并在大肠杆菌BL21中表达,经过镍柱纯化后得到纯度较高的蛋白, MTT法来检测出重组蛋白抑制细胞增殖;同时具有一定的酶活力,为进一步研究其生物学功能奠定了基础。     

Purification of the novel endonuclease, Hpy188I, and cloning of its restriction-modification genes reveal evidence of its horizontal transfer to the Helicobacter pylori genome

We have isolated a novel restriction endonuclease, Hpy188I, from Helicobacter pylori strain J188. Hpy188I recognizes the unique sequence, TCNGA, and cleaves the DNA between nucleotides N and G in its recognition sequence to generate a one-base 3' overhang. Cloning and sequence analysis of the Hpy188I modification gene in strain J188 reveal that hpy188IM has a 1299-base pair (bp) open reading frame (ORF) encoding a 432-amino acid product. The predicted protein sequence of M.Hpy188I contains conserved motifs typical of aminomethyltransferases, and Western blotting indicates that it is an N-6 adenine methyltransferase. Downstream of hpy188IM is a 513-bp ORF encoding a 170-amino acid product, that has a 41-bp overlap with hpy188IM. The predicted protein sequence from this ORF matches the amino acid sequence obtained from purified Hpy188I, indicating that it encodes the endonuclease. The Hpy188I R-M genes are not present in either strain of H. pylori that has been completely sequenced but are found in two of 11 H. pylori strains tested. The significantly lower G + C content of the Hpy188I R-M genes implies that they have been introduced relatively recently during the evolution of the H. pylori genome.     

Specific and sensitive detection of H. pylori in biological specimens by real-time RT-PCR and in situ hybridization

PCR detection of H. pylori in biological specimens is rendered difficult by the extensive polymorphism of H. pylori genes and the suppressed expression of some genes in many strains. The goal of the present study was to (1) define a domain of the 16S rRNA sequence that is both highly conserved among H. pylori strains and also specific to the species, and (2) to develop and validate specific and sensitive molecular methods for the detection of H. pylori. We used a combination of in silico and molecular approaches to achieve sensitive and specific detection of H. pylori in biologic media. We sequenced two isolates from patients living in different continents and demonstrated that a 546-bp domain of the H. pylori 16S rRNA sequence was conserved in those strains and in published sequences. Within this conserved sequence, we defined a 229-bp domain that is 100% homologous in most H. pylori strains available in GenBank and also is specific for H. pylori. This sub-domain was then used to design (1) a set of high quality RT-PCR primers and probe that encompassed a 76-bp sequence and included at least two mismatches with other Helicobacter sp. 16S rRNA; and (2) in situ hybridization antisense probes. The sensitivity and specificity of the approaches were then demonstrated by using gastric biopsy specimens from patients and rhesus monkeys. This H. pylori-specific region of the 16S rRNA sequence is highly conserved among most H. pylori strains and allows specific detection, identification, and quantification of this bacterium in biological specimens.