Restriction–modification systems may be associated with <i>Helicobacter pylori</i> virulence

Ando, Takafumi; Ishiguro, Kazuhiro; Watanabe, Osamu; Miyake, Nobuyuki; Kato, Tsuyoshi; Hibi, Satoshi; Mimura, Shunya; Nakamura, Masanao; Miyahara, Ryoji; Ohmiya, Naoki; Niwa, Yasumasa; Goto, Hidemi

doi:10.1111/j.1440-1746.2009.06211.x

Cited by 13 publications

(15 citation statements)

References 48 publications

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“…That the deletions did not impair growth suggests H. pylori does not have alternative uses for DNA restriction other than for controlling incoming DNA. This contrasts with the subversion of methylases in introduced R-M systems that may provide regulatory functions for the host cells (2,8,41,46). Considering that DNA methylation potentially affects bacterial cell cycle, DNA replication, repair, and mutation rates (23,40,41), the phenotypes we observed suggest that the targeted deletion of the RE genes most likely does not affect transcription of the adjacent DNA methylases.…”

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confidence: 48%

“…The transformation mixture then was harvested and placed in 1.0 ml of PBS, and 100-l 10-fold serial dilutions were plated onto either TSA plates or BA plates containing 10% NBCS and suitable antibiotics. The plates were incubated for 4 days at 37°C in 5% CO 2 , and the total transformation frequency was determined by the number of colonies on selective plates divided by the total CFU on nonselective media. In each transformation experiment, H. pylori strains with no DNA added also were tested in parallel as negative controls; no colonies were seen in any case.…”

Section: Figurementioning

confidence: 99%

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Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Zhang

2012

J Bacteriol

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Restriction-modification (RM) systems are important for bacteria to limit foreign DNA invasion. The naturally competent bacterium Helicobacter pylori has highly diverse strain-specific type II systems. To evaluate the roles of strain-specific restriction in H. pylori natural transformation, a markerless type II restriction endonuclease-deficient (REd) mutant was constructed. We deleted the genes encoding all four active type II restriction endonucleases in H. pylori strain 26695 using sacB-mediated counterselection. Transformation by donor DNA with exogenous cassettes methylated by Escherichia coli was substantially (1.7 and 2.0 log 10 for cat and aphA, respectively) increased in the REd strain. There also was significantly increased transformation of the REd strain by donor DNA from other H. pylori strains, to an extent corresponding to their shared type II R-M system strain specificity with 26695. Comparison of the REd and wild-type strains indicates that restriction did not affect the length of DNA fragment integration during natural transformation. There also were no differentials in cell growth or susceptibility to DNA damage. In total, the data indicate that the type II REd mutant has enhanced competence with no loss of growth or repair facility compared to the wild type, facilitating H. pylori mutant construction and other genetic engineering.

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confidence: 48%

Section: Figurementioning

confidence: 99%

Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Zhang

2012

J Bacteriol

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“…DNA adenine methylation was known to regulate the expression of some virulence genes in bacteria including H.pylori [17, 18, 33]. Inhibitors of DNA adenine methylation may have a broad antimicrobial action by targeting DNA adenine methyltransferase.…”

Section: Discussionmentioning

confidence: 99%

“…H. pylori 26695, for example, has 23 R-M systems [20]. Methyltransferases were suggested to be involved in H. pylori pathogenicity [33]. M1.HpyAVI is a DNA adenine MTase that belongs to the type II R-M system.…”

Section: Introductionmentioning

confidence: 99%

Biochemical and structural characterization of a DNA N6-adenine methyltransferase fromHelicobacter pylori

Liu

et al. 2016

Oncotarget

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DNA N6-methyladenine modification plays an important role in regulating a variety of biological functions in bacteria. However, the mechanism of sequence-specific recognition in N6-methyladenine modification remains elusive. M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. Taken together, our data revealed the structural basis underlying DNA N6-adenine methyltransferase substrate promiscuity.

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“…For example, H. pylori encodes a variety of restriction-modification (R-M) systems as a defense strategy against invasion by foreign DNA such as that of phages [65]. To circumvent R-M systems, an alternative method for DNA exchange might be transfer by conjugation.…”

Section: Evidence For Multiple Pathways Of Plasmid Transfer In H Pylorimentioning

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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Restriction–modification systems may be associated with Helicobacter pylori virulence

Cited by 13 publications

References 48 publications

Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Biochemical and structural characterization of a DNA N6-adenine methyltransferase fromHelicobacter pylori

DNA transfer in the gastric pathogen Helicobacter pylori

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