Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

Kersulyte, Dangeruta; Lee, Woo Kon; Subramaniam, Dharmalingam; Anant, Shrikant; Herrera, Phabiola; Cabrera, Lilia; Balqui, Jacqueline; Barábas, O.; Kalia, Awdhesh; Gilman, Robert H.; Berg, Douglas E.

doi:10.1371/journal.pone.0006859

Cited by 86 publications

(145 citation statements)

References 57 publications

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“…Furthermore, protein families showing extensive gene gain and loss between species tend to have more members in DD than in PP and DF. Transposable elements and repeats are known agents for generating genome plasticity and diversification in prokaryotes and vertebrates (Bohne et al 2008;Kersulyte et al 2009), so they may have also contributed to increased morphological complexity in DD.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Heidel¹,

Lawal²,

Felder³

et al. 2011

Genome Res.

150

161

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Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF ) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of proteincoding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche-and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.[Supplemental material is available for this article.]The central and most fascinating problem in biology is how natural selection has acted on random changes in the genomes of individuals to generate the immense range and complexity of extinct and extant living forms. However, understanding the relationship between genotypic and phenotypic change on a genomewide scale is complicated by the large number of loci involved and the range of phenotypic change. Comparative genomics is the tool of choice to define common gene sets and the first occurrence of genetic changes that may have caused phenotypic innovation. Genetic manipulation of altered genes can then reveal whether the genomic change was causal to the phenotypic alteration.The social amoeba Dictyostelium discoideum (DD) is a widely used model system for studying a range of problems in cell and developmental biology and more recently the evolution of social behavior and multicellularity.

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Section: Discussionmentioning

confidence: 99%

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Heidel¹,

Lawal²,

Felder³

et al. 2011

Genome Res.

150

161

View full text Add to dashboard Cite

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“…Among other pairs of known inverted repeats in the H. pylori genomes (18,19), the repeat 8 pair showed inversion [inversions B1 (Shi470) and F (F16 and F32); Table S1]. Repeat 8 seems to have been lost after inversion B1 through insertion of conjugative transposonable element TnPZ (20) and secondary deletion events in Shi470 (Fig. S6).…”

Section: Linkage Of Changes In Number Ofmentioning

confidence: 99%

Birth and death of genes linked to chromosomal inversion

Furuta

Kawai

Yahara

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization. Helicobacter pylori , bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells.

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“…In contrast, however, XerT appears to cause cognate transposon insertion at and duplicate a specific 7 bp target sequence, which is found at many sites in a bacterial chromosome. 66 We look forward eagerly to detailed molecular analyses of the TnPZ transposition mechanism.…”

Section: Tn5 Transposition Mechanismmentioning

confidence: 99%

Julian Davies and the discovery of kanamycin resistance transposon Tn5

Berg

2016

J Antibiot

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This paper recounts some of my fond memories of a collaboration between Julian Davies and myself that started in 1974 in Geneva and that led to our serendipitous discovery of the bacterial kanamycin resistance transposon Tn5, and aspects of the lasting positive impact of our interaction and discovery on me and the community. Tn5 was one of the first antibiotic resistance transposons to be found. Its analysis over the ensuing decades provided valuable insights into mechanisms and control of transposition, and led to its use as a much-valued tool in diverse areas of molecular genetics, as also will be discussed here. The Journal of Antibiotics (2017) 70, 339-346; doi:10.1038/ja.2016.120; published online 12 October 2016 BACKGROUND It was wonderfully educational, productive and exciting for me to work with Julian Davies for a few years in the mid 1970s, doing experiments that led to the serendipitous discovery and initial characterizations of kanamycin resistance transposon Tn5 1 -one of the first and most useful of the many bacterial antibiotic resistance (AR) transposons that have been found. 2 I was inspired by Julian's knowledge of mechanisms of antibiotic action and resistance mechanisms, his creativity and clarity of thought and expression, as illustrated in his numerous papers, 3-6 and by his high energy, kindness and inventive good humor-traits that have enriched the lives and careers of many people over the years. Described here, in tribute to Julian and his special character, are my memories of a collaboration that led to Tn5's unexpected discovery, Tn5's properties, and some lasting impacts of our collaboration on the field and on me personally.We began interacting in 1974, soon after Julian arrived in Geneva to begin his sabbatical with Pierre Francois Spahr (Department of Molecular Biology of the University). 7 I was then in my fourth (final) year as Chargé de Recherche (senior postdoc) in Lucien Caro's group in the same department, studying λdv plasmids, often in collaboration with Grete Kellenberger-Gujer, also in Lucien's group 8-13 -and during these years, also hugely enjoying features in and out of the lab that have drawn researchers to Geneva for decades: a superb scientific atmosphere, year-round easy access to the exquisite Alps and Jura mountains, and the language, cuisine and culture of Geneva and vicinity. I had become intrigued the year before by Julian's ideas about origins and evolution of resistance genes, as described in his paper with Raoul Benveniste. 14 They advanced the then-novel theory that the types of bacteria that had provided life saving antibiotics were also the ancestral sources of AR genes that were becoming increasingly common in human and veterinary pathogens. Their inferences were

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Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

Cited by 86 publications

References 57 publications

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Birth and death of genes linked to chromosomal inversion

Julian Davies and the discovery of kanamycin resistance transposon Tn5

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