Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

Luo, Cheng-Hung; Chiou, Pei-Yu; Yang, Chiou-Ying; Lin, Ning

doi:10.1128/jvi.00446-12

Cited by 46 publications

(55 citation statements)

References 48 publications

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“…Several bacteriophages (phages) of H. pylori have been reported (4,5,9,12). In general, phages are considered to contribute to bacterial evolution and may affect host features, such as biological behavior, pathogenesis, or adaptation, via their possible roles in horizontal gene transfer and bacteria-phage antagonistic coevolution (4,5,7).…”

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confidence: 99%

“…In general, phages are considered to contribute to bacterial evolution and may affect host features, such as biological behavior, pathogenesis, or adaptation, via their possible roles in horizontal gene transfer and bacteria-phage antagonistic coevolution (4,5,7). In this study, to extend our understanding not only of the H. pylori phages themselves but also of the process of coevolution of H. pylori and its phages, phages KHP30 and KHP40 were isolated from the culture supernatants of East Asian-type isolates from Japanese patients living in distinct geographic regions, and their complete genomic sequences were determined.…”

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Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

Uchiyama

Takeuchi

Kato

et al. 2012

J Virol

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Helicobacter pylori causes peptic ulcers and gastric cancer, which lead to significantly higher morbidity in Japan than elsewhere in the world. As bacteriophage (phage) and host bacteria coevolve, the study of H. pylori phages is important to extend understanding of the evolution and pathogenesis of H. pylori. Here we report two complete genome sequences of H. pylori phages KHP30 and KHP40, which were released spontaneously from the most pathogenic East Asian-type isolates from Japanese patients. Helicobacter pylori, a Gram-negative spiral bacterium, colonizes the human stomach and infects approximately 50% of the global population (2, 10). Infection can cause chronic inflammation, which may progress to peptic ulceration, atrophic gastritis, or gastric cancer (8). There is a significant correlation between the H. pylori strain type and the incidence of gastric cancer. In particular, the East Asian-type strain of H. pylori is the individual strain most likely to cause gastric cancer (10).Several bacteriophages (phages) of H. pylori have been reported (4, 5, 9, 12). In general, phages are considered to contribute to bacterial evolution and may affect host features, such as biological behavior, pathogenesis, or adaptation, via their possible roles in horizontal gene transfer and bacteria-phage antagonistic coevolution (4, 5, 7). In this study, to extend our understanding not only of the H. pylori phages themselves but also of the process of coevolution of H. pylori and its phages, phages KHP30 and KHP40 were isolated from the culture supernatants of East Asian-type isolates from Japanese patients living in distinct geographic regions, and their complete genomic sequences were determined.The genomic DNA of the phages was isolated from phage particles that had been purified by CsCl density gradient ultracentrifugation, essentially as described elsewhere (11). The genomic sequences were determined with a primer walking method using an ABI Prism 3100-Avant genetic analyzer (Applied Biosystems, Foster City, CA), and both strands were sequenced. The genome sequences of phages KHP30 and KHP40 were circularly connected. Whole-genome PCR scanning also validated our sequencing results. A BLASTN analysis was conducted between the genome sequences of phages KHP30 and KHP40. Open reading frames (ORFs) were predicted using Prodigal and GeneMark.hmm with heuristic models (1, 3) and were then manually confirmed with reference to the ribosomal binding site sequences. The conserved protein domains were analyzed using the NCBI Conserved Domain Database (6).The complete DNA sequencing of phages KHP30 and KHP40 revealed that their genomes consist of 26,215 bp (GϩC, 35.8%) and 26,449 bp (GϩC, 35.8%), respectively. A comparison of the genomic sequences of KHP30 and KHP40 with BLASTN indicated a high level of sequence similarity (total score, 3.540e Ϫ 04; query coverage, 96%; E value, 0.0). Moreover, 30 and 32 ORFs were inferred in phages KHP30 and KHP40, respectively. A genomic analysis of KHP30 and KHP40 predicted an integrase (ORF2 in ...

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confidence: 99%

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confidence: 99%

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

Uchiyama

Takeuchi

Kato

et al. 2012

J Virol

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“…In fact, an evolutionary link between a prophage and differentiation in B. subtilis has been suggested, howeverthe underlying mechanisms and associated factors are still not fully understood (Lewis et al, 1998;Luo et al, 2012). Besides this, the mutations shifting the balance from lysogeny to lysis have also been suggested as a cause of autoplaque phenomenon (Bednarz et al, 2014).…”

Section: Issn: 2319-7706 Volume 6 Number 9 (2017) Pp 32-46mentioning

confidence: 99%

“…In fact, in some bacteria, the autoplaque forming phages show a narrow host range and serve as a vehicle to specifically drive genetic diversification of the bacterial host (Luo et al, 2012). Further, the release of DNA due to autolysis serves as a raw material to drive transformation and evolution of bacterial population and minimize the accumulation of damages DNA or mutations (Redfield, 1988).…”

Section: Issn: 2319-7706 Volume 6 Number 9 (2017) Pp 32-46mentioning

confidence: 99%

Prevalence of Autoplaque Phenomenon in Bacterial Communities from Spatially Heterogeneous Environment of an Abandoned Mine

Karmakar¹,

Sharma²

2017

Int.J.Curr.Microbiol.App.Sci

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“…This diversity can be attributed to altered DNA repair, elevated mutation rates, high frequency of intraspecific recombination, chromosomal DNA transfer events from other species, incorporation of naked DNA from the environment, plasmid mobilization, and integration of acquired DNA in the so-called plasticity zones [4,[8][9][10]. In addition, the presence of phages has been described for several H. pylori strains, acting as another source of bacterial diversity and evolution [11][12][13][14][15]. Using newly developed bioinformatics programs, recent comparative studies of 29 complete genome sequences of strains from different parts of the world revealed a high-resolution picture of the H. pylori population structure as well as the extent and direction of genetic flux between subgroups of the bacterium [16].…”

Section: Introductionmentioning

confidence: 99%

DNA transfer in the gastric pathogen Helicobacter pylori

Fernández-González

Backert

2014

J Gastroenterol

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The gastric pathogen Helicobacter pylori is one of the most genetically diverse bacteria. Recombination and DNA transfer contribute to its genetic variability and enhance host adaptation. Among the strategies described to increase genetic diversity in bacteria, DNA transfer by conjugation is one of the best characterized. Using this mechanism, a fragment of DNA from a donor cell can be transferred to a recipient, always mediated by a conjugative nucleoprotein complex, which is evolutionarily related to type IV secretion systems (T4SSs). Interestingly, the H. pylori chromosomes can encode up to four T4SSs, including the cagPAI, comB, tfs3, and tfs4 genes, some of which are known to promote chronic H. pylori infection. The T4SS encoded by the cagPAI mediates the injection of the effector protein CagA and proinflammatory signaling, and the comB system is involved in DNA uptake from the environment. However, the role of tfs3 and tfs4 is not yet clear. The presence of a functional XerD tyrosine recombinase and 5 0 AAAGAATG-3 0 border sequences as well as two putative conjugative relaxases (Rlx1 and Rlx2), a coupling protein (TraG), and a chromosomal region carrying a putative origin of transfer (oriT) suggest the existence of a DNA transfer apparatus in tfs4. Moreover, a conjugation-like DNA transfer mechanism in H. pylori has already been described in vitro, but whether this occurs in vivo is still unknown. Some extrachromosomal plasmids and phages are also present in various H. pylori strains. Genetic exchange among plasmids and chromosomes, and involved DNA mobilization events, could explain part of H. pylori's genetic diversity. Here, we review our knowledge about the possible DNA transfer mechanisms in H. pylori and its implications in bacterial adaptation to the host environment.

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Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

Abstract: Helicobacter pyloriis a common human pathogen that has been identified to be carcinogenic. This study isolated the temperate bacteriophage 1961P from the lysate of a clinical strain ofH. pyloriisolated in Taiwan. The bacteriophage has an ico… Show more

Cited by 46 publications

References 48 publications

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

Prevalence of Autoplaque Phenomenon in Bacterial Communities from Spatially Heterogeneous Environment of an Abandoned Mine

DNA transfer in the gastric pathogen Helicobacter pylori

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