title: Helicobacter Pylori's plasticity zones are novel transposable elements.
abstract: BACKGROUND
  Genes present in only certain strains of a bacterial species can strongly affect cellular phenotypes and evolutionary potentials. One segment that seemed particularly rich in strain-specific genes was found by comparing the first two sequenced Helicobacter pylori genomes (strains 26695 and J99) and was named a "plasticity zone".
  
  
  RESULTS
  We studied the nature and evolution of plasticity zones by sequencing them in five more Helicobacter strains, determining their locations in additional strains, and identifying them in recently released genome sequences. They occurred as discrete units, inserted at numerous chromosomal sites, and were usually flanked by direct repeats of 5'AAGAATG, a sequence generally also present in one copy at unoccupied sites in other strains. This showed that plasticity zones are transposable elements, to be called TnPZs. Each full length TnPZ contained a cluster of type IV protein secretion genes (tfs3), a tyrosine recombinase family gene ("xerT"), and a large (>or=2800 codon) orf encoding a protein with helicase and DNA methylase domains, plus additional orfs with no homology to genes of known function. Several TnPZ types were found that differed in gene arrangement or DNA sequence. Our analysis also indicated that the first-identified plasticity zones (in strains 26695 and J99) are complex mosaics of TnPZ remnants, formed by multiple TnPZ insertions, and spontaneous and transposable element mediated deletions. Tests using laboratory-generated deletions showed that TnPZs are not essential for viability, but identified one TnPZ that contributed quantitatively to bacterial growth during mouse infection and another that affected synthesis of proinflammatory cytokines in cell culture.
  
  
  CONCLUSIONS
  We propose that plasticity zone genes are contained in conjugative transposons (TnPZs) or remnants of them, that TnPZ insertion is mediated by XerT recombinase, and that some TnPZ genes affect bacterial phenotypes and fitness.
authors.affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors.forename: Dangeruta
authors.initials: D
authors.lastname: Kersulyte
authors.forename: Wookon
authors.initials: W
authors.lastname: Lee
authors.forename: Dharmalingam
authors.initials: D
authors.lastname: Subramaniam
authors.forename: Shrikant
authors.initials: S
authors.lastname: Anant
authors.forename: Phabiola
authors.initials: P
authors.lastname: Herrera
authors.forename: Lilia
authors.initials: L
authors.lastname: Cabrera
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Balqui
authors.forename: Orsolya
authors.initials: O
authors.lastname: Barabas
authors.forename: Awdhesh
authors.initials: A
authors.lastname: Kalia
authors.forename: Robert H
authors.initials: RH
authors.lastname: Gilman
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Berg
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D016207:Cytokines / Q000378:metabolism; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000032:analysis; D017353:Gene Deletion; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics* / Q000502:physiology*; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D016207:Cytokines; D004251:DNA Transposable Elements; D004269:DNA, Bacterial