Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization.
Decoding of closely related genomes is now revealing the process of population evolution. In bacteria, population divergence appears associated with a unique set of sequence-specific epigenetic DNA methylation systems, often within restriction-modification (RM) systems. They might define a unique gene expression pattern and limit genetic flux between lineages in population divergence. We addressed the contribution of methylation systems to population diversification in panmictic bacterial species, Helicobacter pylori, which shows an interconnected population structure through frequent mutual recombination. We analyzed complete genome sequences of 28 strains collected in Fukui, Japan. Their nucleotide sequences are closely related although fine-scale analyses revealed two subgroups likely reflecting human subpopulations. Their sequences are tightly connected by homologous recombination. Our extensive analysis of RM systems revealed an extreme variability in DNA methyltransferases, especially in their target recognition domains. Their diversity was, however, not immediately related to the genome sequence diversity, except for very closely related strains. An interesting exception is a hybrid strain, which likely has conserved the methylation gene repertoire from one parent but diversified in sequence by massive acquisition of fragmentary DNA sequences from the other parent. Our results demonstrate how a bacterial population can be extremely divergent in epigenetics and yet homogenized in sequence.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan Institute of Medical Science, University of Tokyo, Tokyo, Japan Genetic Information Research Institute, Los Altos, CA Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Kenji K
KK
Kojima
Institute of Medical Science, University of Tokyo, Tokyo, Japan Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Yoshikazu
Y
Furuta
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan Institute of Medical Science, University of Tokyo, Tokyo, Japan Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
Koji
K
Yahara
Institute of Medical Science, University of Tokyo, Tokyo, Japan Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Masaki
M
Fukuyo
Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan.
Yuh
Y
Shiwa
Division of Gastroenterology, Department of Internal Medicine, Graduate School of Medicine, Kobe University, Kobe, Japan.
Shin
S
Nishiumi
Division of Gastroenterology, Department of Internal Medicine, Graduate School of Medicine, Kobe University, Kobe, Japan.
Masaru
M
Yoshida
Division of Gastroenterology, Department of Internal Medicine, Graduate School of Medicine, Kobe University, Kobe, Japan.
Takeshi
T
Azuma
Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan.
Hirofumi
H
Yoshikawa
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan Institute of Medical Science, University of Tokyo, Tokyo, Japan Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan ikobaya@ims.u-tokyo.ac.jp zat14430@nifty.com.
Ichizo
I
Kobayashi
D001483:Base Sequence; D005075:Biological Evolution; D019175:DNA Methylation; D015254:DNA Modification Methylases; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D015254:DNA Modification Methylases
epigenetics; genome evolution; inversion; restriction–modification