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Type II restriction modification system in Ureaplasma parvum OMC-P162 strain

Heng Ning Wu1, Yukiko Nakura1, Michinobu Yoshimura1

  • 1Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi City, Osaka, Japan.

Plos One
|October 17, 2018
PubMed

Insights

Ureaplasma parvum serovar 3 strain OMC-P162 possesses a novel type II restriction-modification system. Genes UPV_229 and UPV_230 encode a DNA methyltransferase and an endonuclease (UpaP162) that modifies the CATG sequence.

Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Ureaplasma parvum is a common human commensal and opportunistic pathogen.
  • Serovar 3 strains have been associated with various clinical conditions, including preterm birth.
  • Understanding the genomic features of Ureaplasma strains is crucial for elucidating their pathogenic mechanisms.

Purpose of the Study:

  • To sequence and analyze the complete genome of Ureaplasma parvum serovar 3 strain OMC-P162, isolated from a preterm placenta.
  • To identify unique genes and potential functional elements within the OMC-P162 genome.
  • To investigate the presence and activity of restriction-modification systems in this strain.

Main Methods:

  • Whole-genome sequencing of Ureaplasma parvum OMC-P162.
  • Comparative genomic analysis with other serovar 3 strains.
  • Bioinformatic prediction of gene function and operon structures.
  • Recombinant protein expression and enzymatic activity assays (endonuclease and methyltransferase).
  • DNA modification analysis (m4C, m6A, m5C).

Main Results:

  • The complete genome of Ureaplasma parvum serovar 3 strain OMC-P162 was sequenced.
  • Ten unique genes were identified in OMC-P162, including UPV_229 and UPV_230, forming an operon.
  • The UPV_230 gene product, UpaP162, demonstrated endonuclease activity, specifically recognizing and cutting the CATG sequence.
  • The UPV_229 gene product inhibited UpaP162 activity, suggesting a DNA methyltransferase function.
  • The genome analysis revealed N4-methylcytosine (m4C) and N6-methyladenine (m6A) modifications, but not 5-methylocytosine (m5C).

Conclusions:

  • The UPV_229 and UPV_230 genes constitute a type II restriction-modification system in Ureaplasma parvum OMC-P162.
  • This system, involving the endonuclease UpaP162, likely plays a role in the strain's biology and interaction with host environments.
  • Further research is warranted to understand the prevalence and functional significance of this system in Ureaplasma pathogenesis.

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