Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori

Hirokazu Yano, Md Zobaidul Alam, Emiko Rimbara, Tomoko F. Shibata, Masaki Fukuyo, Yoshikazu Furuta, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi

Research output: Contribution to journalArticlepeer-review

Abstract

Epigenetic DNA base methylation plays important roles in gene expression regulation. We here describe a gene expression regulation network consisting of many DNA methyltransferases each frequently changing its target sequence-specificity. Our object Helicobacter pylori, a bacterium responsible for most incidence of stomach cancer, carries a large and variable repertoire of sequence-specific DNA methyltransferases. By creating a dozen of single-gene knockout strains for the methyltransferases, we revealed that they form a network controlling methylome, transcriptome and adaptive phenotype sets. The methyltransferases interact with each other in a hierarchical way, sometimes regulated positively by one methyltransferase but negatively with another. Motility, oxidative stress tolerance and DNA damage repair are likewise regulated by multiple methyltransferases. Their regulation sometimes involves translation start and stop codons suggesting coupling of methylation, transcription and translation. The methyltransferases frequently change their sequence-specificity through gene conversion of their target recognition domain and switch their target sets to remodel the network. The emerging picture of a metamorphosing gene regulation network, or firework, consisting of epigenetic systems ever-changing their specificity in search for adaptation, provides a new paradigm in understanding global gene regulation and adaptive evolution.

Original languageEnglish
Article number1628
JournalFrontiers in Microbiology
Volume11
DOIs
Publication statusPublished - 2020 Jul 17

Keywords

  • DNA methylation
  • DNA methyltransferase
  • Pacbio
  • SMRT
  • epigenetics
  • epigenome
  • gastric cancer
  • methylome

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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