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A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an

Nils Birkholz1,2, Simon A Jackson1,2,3, Robert D Fagerlund1,2,3

  • 1Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.

Nucleic Acids Research
|March 14, 2022
PubMed

Insights

Bacteria use DNA methylation for defence, but this study reveals a conflict between two systems in Pectobacterium carotovorum. One system silences the other via DNA methylation, preventing lethal competition.

Area of Science:

  • Bacterial epigenetics
  • Molecular biology
  • Microbial defence mechanisms

Background:

  • Epigenetic DNA methylation is crucial for bacterial gene regulation and distinguishing self from foreign DNA.
  • Restriction-modification (RM) systems and solitary restriction endonucleases (REases) are mobile defence systems that impact horizontal gene transfer.
  • The interaction between mobile defence systems and pre-existing host defences is not well understood.

Purpose of the Study:

  • To investigate the epigenetic interactions between RM systems and methylation-dependent REases in Pectobacterium carotovorum.
  • To elucidate the mechanism of co-existence between competing defence systems within a bacterial cell.

Main Methods:

  • Comparative genome analysis
  • Investigating the PcaRCI RM system and the methylation-dependent PcaRCII REase in Pectobacterium carotovorum RC5297.
  • Studying epigenetic silencing via promoter methylation.

Main Results:

  • The PcaRCI RM system protects against foreign DNA but its methylation motif is targeted by PcaRCII.
  • PcaRCI MTase epigenetically silences the PcaRCII-encoding gene through promoter methylation.
  • Comparative genomics suggests PcaRCII was silenced after PcaRCI establishment.

Conclusions:

  • This study reveals an epigenetic conflict and intracellular competition between bacterial defence systems.
  • RM systems exhibit "selfishness" by silencing competing defence mechanisms.
  • Epigenetic regulation plays a key role in managing the co-existence of multiple defence systems in bacteria.

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