Birth and death of genes linked to chromosomal inversion

PNAS January 6, 2011.

Yoshikazu Furuta, Mikihiko Kawaia, Koji Yahara, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi.

a:Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan;b:Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan;c:Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan;d:Graduate School of Medicine, Kurume University, Kurume, Fukuoka 830-0011, Japan;e:Fujitsu Kyushu Systems Ltd., Fukuoka, Fukuoka 814-8589, Japan;f:Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan;g:Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan;h:Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo 650-0017, Japan

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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