Genetic Markers of Genome Rearrangements in Helicobacter pylori

Helicobacter pylori exhibits a diverse genomic structure with high mutation and recombination rates. Various genetic elements function as drivers of this genomic diversity including genome rearrangements. Identifying the association of these elements with rearrangements can pave the way to understand its genome evolution. We analyzed the order of orthologous genes among 72 publicly available complete genomes to identify large genome rearrangements, and rearrangement breakpoints were compared with the positions of insertion sequences, genomic islands, and restriction modification genes. Comparison of the shared inversions revealed the conserved genomic elements across strains from different geographical locations. Some were region-specific and others were global, indicating that highly shared rearrangements and their markers were more ancestral than strain—or region—specific ones. The locations of genomic islands were an important factor for the occurrence of the rearrangements. Comparative genomics helps to evaluate the conservation of various elements contributing to the diversity across genomes.

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Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma

Pathogens ◽

10.3390/pathogens10030331 ◽

2021 ◽

Vol 10 (3) ◽

pp. 331

Author(s):

Montserrat Palau ◽

Núria Piqué ◽

M. José Ramírez-Lázaro ◽

Sergio Lario ◽

Xavier Calvet ◽

...

Keyword(s):

Helicobacter Pylori ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Virulence Factors ◽

Outer Membrane Proteins ◽

Whole Genome ◽

Flagellar Biosynthesis ◽

H Pylori ◽

Restriction Modification

Helicobacter pylori is a common pathogen associated with several severe digestive diseases. Although multiple virulence factors have been described, it is still unclear the role of virulence factors on H. pylori pathogenesis and disease progression. Whole genome sequencing could help to find genetic markers of virulence strains. In this work, we analyzed three complete genomes from isolates obtained at the same point in time from a stomach of a patient with adenocarcinoma, using multiple available bioinformatics tools. The genome analysis of the strains B508A-S1, B508A-T2A and B508A-T4 revealed that they were cagA, babA and sabB/hopO negative. The differences among the three genomes were mainly related to outer membrane proteins, methylases, restriction modification systems and flagellar biosynthesis proteins. The strain B508A-T2A was the only one presenting the genotype vacA s1, and had the most distinct genome as it exhibited fewer shared genes, higher number of unique genes, and more polymorphisms were found in this genome. With all the accumulated information, no significant differences were found among the isolates regarding virulence and origin of the isolates. Nevertheless, some B508A-T2A genome characteristics could be linked to the pathogenicity of H. pylori.

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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

Nucleic Acids Research ◽

10.1093/nar/gkn718 ◽

2008 ◽

Vol 36 (21) ◽

pp. 6893-6906 ◽

Cited By ~ 39

Author(s):

Olivier Humbert ◽

Nina R. Salama

Keyword(s):

Helicobacter Pylori ◽

Restriction Endonuclease ◽

Dna Methyltransferase ◽

Dna Uptake ◽

Modification System ◽

Exogenous Dna ◽

Restriction Modification System ◽

Restriction Modification

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Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction–modification genes with large genome polymorphisms

Gene ◽

10.1016/s0378-1119(00)00459-5 ◽

2000 ◽

Vol 259 (1-2) ◽

pp. 109-121 ◽

Cited By ~ 44

Author(s):

Akito Chinen ◽

Ikuo Uchiyama ◽

Ichizo Kobayashi

Keyword(s):

Genome Sequences ◽

Pyrococcus Horikoshii ◽

Large Genome ◽

Pyrococcus Abyssi ◽

Restriction Modification

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Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex

Molecular Microbiology ◽

10.1046/j.1365-2958.2001.02436.x ◽

2001 ◽

Vol 40 (4) ◽

pp. 932-940 ◽

Cited By ~ 36

Author(s):

N. Handa ◽

Y. Nakayama ◽

M. Sadykov ◽

I. Kobayashi

Keyword(s):

Genome Evolution ◽

Large Scale ◽

Genome Rearrangements ◽

Gene Complex ◽

Restriction Modification

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A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

PLoS ONE ◽

10.1371/journal.pone.0159419 ◽

2016 ◽

Vol 11 (8) ◽

pp. e0159419 ◽

Cited By ~ 10

Author(s):

Ikuo Uchiyama ◽

Jacob Albritton ◽

Masaki Fukuyo ◽

Kenji K. Kojima ◽

Koji Yahara ◽

...

Keyword(s):

Helicobacter Pylori ◽

Genome Analysis ◽

Genomic Islands ◽

Pan Genome ◽

Novel Approach

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Transcriptional Phase Variation of a Type III Restriction-Modification System in Helicobacter pylori

Journal of Bacteriology ◽

10.1128/jb.184.23.6615-6624.2002 ◽

2002 ◽

Vol 184 (23) ◽

pp. 6615-6623 ◽

Cited By ~ 61

Author(s):

Nicolette de Vries ◽

Dirk Duinsbergen ◽

Ernst J. Kuipers ◽

Raymond G. J. Pot ◽

Patricia Wiesenekker ◽

...

Keyword(s):

Helicobacter Pylori ◽

Phase Variation ◽

Transcriptional Level ◽

Length Variation ◽

Phase Variable ◽

Modification System ◽

Type Iii ◽

Restriction Modification System ◽

H Pylori ◽

Restriction Modification

ABSTRACT Phase variation is important in bacterial pathogenesis, since it generates antigenic variation for the evasion of immune responses and provides a strategy for quick adaptation to environmental changes. In this study, a Helicobacter pylori clone, designated MOD525, was identified that displayed phase-variable lacZ expression. The clone contained a transcriptional lacZ fusion in a putative type III DNA methyltransferase gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an operon-like structure with a putative type III restriction endonuclease gene (res, a homolog of the gene JHP1297), located directly upstream of it. This putative type III restriction-modification system was common in H. pylori, as it was present in 15 out of 16 clinical isolates. Phase variation of the mod gene occurred at the transcriptional level both in clone MOD525 and in the parental H. pylori strain 1061. Further analysis showed that the res gene also displayed transcriptional phase variation and that it was cotranscribed with the mod gene. A homopolymeric cytosine tract (C tract) was present in the 5′ coding region of the res gene. Length variation of this C tract caused the res open reading frame (ORF) to shift in and out of frame, switching the res gene on and off at the translational level. Surprisingly, the presence of an intact res ORF was positively correlated with active transcription of the downstream mod gene. Moreover, the C tract was required for the occurrence of transcriptional phase variation. Our finding that translation and transcription are linked during phase variation through slipped-strand mispairing is new for H. pylori.

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