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Peer-reviewedCC BY 4.0Frontiers in Microbiology

Integrative multiomic characterization of the methylome and restriction-modification repertoire of Mycoplasma hyorhinis SK76

  • Elisabet Frutos-Grilo1
  • Matilde D’Angelo1
  • Miquel Anglada-Girotto1
  • Luis Serrano1,2,3
  1. 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology
  2. 2Universitat Pompeu Fabra (UPF)
  3. 3ICREA
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Abstract

Restriction-modification (R-M) systems are widespread in Mycoplasma species, contributing to defense against foreign DNA and epigenetic regulation. However, the limited genetic tractability of Mollicutes hinders the functional characterization of R-M systems. Here, we characterized the R-M repertoire of Mycoplasma hyorhinis SK76 by integrating comparative genomics, structural modeling, quantitative proteomics, and genome-wide methylome profiling. We found that SK76 encodes Type I, Type II and Type III R-M systems with some duplicated components. For Type I, HsdS2 was predicted to recognize a bipartite TA-N₆-ATC motif, which was detected as a secondary 6mA-associated methylation signature, whereas the remaining HsdS variants displayed features consistent with reduced functionality. Among the Type II R-M system, Mhy3 and its cognate endonuclease End3 were associated with the 5mC motif GATC, while the remaining predicted methyltransferases lacked both protein expression and corresponding methylation signatures. Regarding Type III, Mod1 was identified as the principal active adenine methyltransferase responsible for the asymmetric GGAT-centered methylation pattern, whereas additional Mod homologues likely represent phase-variable or conditionally regulated elements with limited activity. Overall, the functional methylome of M. hyorhinis represents only a subset of its genomic R-M repertoire, underscoring the value of integrating genomic, proteomic and methylome data to define active epigenetic systems.

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Cite

BibTeXRIS
BibTeX
@article{frutosgrilo2026integrative,
  title = {{Integrative multiomic characterization of the methylome and restriction-modification repertoire of Mycoplasma hyorhinis SK76}},
  author = {Elisabet Frutos-Grilo and Matilde D’Angelo and Miquel Anglada-Girotto and Luis Serrano},
  journal = {Frontiers in Microbiology},
  year = {2026},
  month = oct,
  doi = {10.3389/fmicb.2026.1950185},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1950185/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Integrative multiomic characterization of the methylome and restriction-modification repertoire of Mycoplasma hyorhinis SK76
AU  - Elisabet Frutos-Grilo
AU  - Matilde D’Angelo
AU  - Miquel Anglada-Girotto
AU  - Luis Serrano
PY  - 2026
DA  - 2026/10/22
JO  - Frontiers in Microbiology
DO  - 10.3389/fmicb.2026.1950185
UR  - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1950185/full
AB  - Restriction-modification (R-M) systems are widespread in Mycoplasma species, contributing to defense against foreign DNA and epigenetic regulation. However, the limited genetic tractability of Mollicutes hinders the functional characterization of R-M systems. Here, we characterized the R-M repertoire of Mycoplasma hyorhinis SK76 by integrating comparative genomics, structural modeling, quantitative proteomics, and genome-wide methylome profiling. We found that SK76 encodes Type I, Type II and Type III R-M systems with some duplicated components. For Type I, HsdS2 was predicted to recognize a bipartite TA-N₆-ATC motif, which was detected as a secondary 6mA-associated methylation signature, whereas the remaining HsdS variants displayed features consistent with reduced functionality. Among the Type II R-M system, Mhy3 and its cognate endonuclease End3 were associated with the 5mC motif GATC, while the remaining predicted methyltransferases lacked both protein expression and corresponding methylation signatures. Regarding Type III, Mod1 was identified as the principal active adenine methyltransferase responsible for the asymmetric GGAT-centered methylation pattern, whereas additional Mod homologues likely represent phase-variable or conditionally regulated elements with limited activity. Overall, the functional methylome of M. hyorhinis represents only a subset of its genomic R-M repertoire, underscoring the value of integrating genomic, proteomic and methylome data to define active epigenetic systems.
SN  - 1664-302X
ER  -