title: Birth and death of genes linked to chromosomal inversion.
abstract: 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.
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Furuta
authors.forename: Mikihiko
authors.initials: M
authors.lastname: Kawai
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.forename: Noriko
authors.initials: N
authors.lastname: Takahashi
authors.forename: Naofumi
authors.initials: N
authors.lastname: Handa
authors.forename: Takeshi
authors.initials: T
authors.lastname: Tsuru
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Masaru
authors.initials: M
authors.lastname: Yoshida
authors.forename: Takeshi
authors.initials: T
authors.lastname: Azuma
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.forename: Ichizo
authors.initials: I
authors.lastname: Kobayashi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D019457:Chromosome Breakage; D007446:Chromosome Inversion / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D005798:Genes, Bacterial / Q000235:genetics*; D016480:Helicobacter pylori / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011995:Recombination, Genetic
chemical_list: D001426:Bacterial Proteins