Transposable Element IS
            <i>Hp608</i>
            of
            <i>Helicobacter pylori</i>
            : Nonrandom Geographic Distribution, Functional Organization, and Insertion Specificity

Kersulyte, Dangeruta; Velapatiño, Billie; Dailide, Giedrius; Mukhopadhyay, Asish K.; Ito, Yoshiyuki; Cahuayme, Lizbeth; Parkinson, Alan J.; Gilman, Robert H.; Berg, Douglas E.

doi:10.1128/jb.184.4.992-1002.2002

Cited by 77 publications

(123 citation statements)

References 34 publications

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“…This study began with subtractive hybridization (as in [37,38]) to find genes or alleles that differed markedly between representative Japanese versus Western strains. One recovered clone contained a fragment of gene hp0519.…”

Section: Results/discussion H Pylori Slr Gene Familymentioning

confidence: 99%

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

et al. 2005

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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 are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such ''Sel1-like repeat'' (SLR) genes (''slr genes''). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, d N /d S ¼ x . 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (x J . 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.

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Section: Results/discussion H Pylori Slr Gene Familymentioning

confidence: 99%

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

et al. 2005

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“…The mechanism of transposition of the recently discovered IS200/IS605 insertion sequence family greatly differs from systems already described, in particular those using DDE transposase catalysis (55). The best-studied representative of this family, IS608, was originally identified in Helicobacter pylori (81). It presents at its ends short palindromes recognized as hairpins by the TnpA transposase.…”

Section: Hairpins and Recombinationmentioning

confidence: 97%

Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes

Bikard

Loot

Baharoglu

et al. 2010

Microbiol Mol Biol Rev

171

151

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SUMMARY Structured forms of DNA with intrastrand pairing are generated in several cellular processes and are involved in biological functions. These structures may arise on single-stranded DNA (ssDNA) produced during replication, bacterial conjugation, natural transformation, or viral infections. Furthermore, negatively supercoiled DNA can extrude inverted repeats as hairpins in structures called cruciforms. Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements. More recently, they were shown to be used as recombination sites. Many of these functions are found on mobile genetic elements likely to be single stranded, including viruses, plasmids, transposons, and integrons, thus giving some clues as to the manner in which they might have evolved. We review here, with special focus on prokaryotes, the functions in which DNA secondary structures play a role and the cellular processes giving rise to them. Finally, we attempt to shed light on the selective pressures leading to the acquisition of functions for DNA secondary structures.

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“…Rather, the transposase mediates DNA-DNA interactions involving base-pairing between two ssDNA regions, and this directs the appropriate scissile phosphate into the active site. This same mechanism also ensures site-specificity of integration, which precisely targets either a tetra-or pentanucleotide sequence (164,165).…”

Section: Huh Transposases (I) Transposon End Recognitionmentioning

confidence: 99%

Mechanisms of DNA Transposition

Hickman

Dyda

2015

Microbiol Spectr

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DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.In this chapter, we provide an overview of the fundamental concepts of DNA transposition mechanisms. Our aim is to emphasize basic themes and, in this effort, we will focus on specific illustrative cases rather than attempt an exhaustive review of the literature. We hope that the selected references will point the curious reader towards the landmark studies in the field as well as some of the most exciting recent results. We also direct the reader to other recent reviews (1-3).DNA transposases are enyzmes that move discrete segments of DNA called transposons from one location in the genome (often called the donor site) to a new site without using RNA intermediates. DNA transposases are usually encoded by the mobile element itself (in which case they are "autonomous" transposons). However, some transposons are missing a self-encoded transposase yet have ends that can be recognized by a transposase encoded somewhere else in the genome, and thus are "non-autonomous" (Siguier et al., this volume). Although logic suggests that all DNA transposons are moved by transposases, the term was originally reserved for those enzymes that do not require significant regions of homology between any part of the transposon and the sites to which they are moved, the so-called target (or insertion or integration) sites. As biology is not always neat and tidy, transposases can exhibit a spectrum of homology requirements and vagaries of terminology have arisen such that certain transposases are sometimes referred to as "resolvases" or by the generic term "recombinases".From a mechanistic perspective, t...

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Transposable Element IS Hp608 of Helicobacter pylori : Nonrandom Geographic Distribution, Functional Organization, and Insertion Specificity

Cited by 77 publications

References 34 publications

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes

Mechanisms of DNA Transposition

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