Sequence permutations in the molecular evolution of DNA methyltransferases

Background DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic subdomain, and the target recognition domain (TRD), several classes of permutants have been proposed. The majority of known DNA MTases fall into the α, β, and γ classes. There is only one member of the ζ class known and no members of the δ and ε classes have been identified to date. Two mechanisms of permutation have been proposed: one involving gene duplication and in-frame fusion, and the other involving inter- and intragenic shuffling of gene segments. Results Two novel cases of sequence permutation in DNA MTases implicated in restriction-modification systems have been identified, which suggest that members of the δ and ζ classes (M.MwoI and M.TvoORF1413P, respectively) evolved from β-class MTases. This is the first identification of the δ-class MTase and the second known ζ-class MTase (the first ζ-class member among DNA:m4C and m6A-MTases). Conclusions Fragmentation of a DNA MTase gene may result from attack of nucleases, for instance when the RM system invades a new cell. Its reassembly into a functional form, the order of motifs notwithstanding, may be strongly selected for, if the cognate ENase gene remains active and poses a threat to the host's chromosome. The "cut-and-paste" mechanism is proposed for β-δ permutation, which is non-circular and involves relocation of one segment of a gene. The circular β-ζ permutation may be explained both by gene duplication or shuffling of gene fragments. These two mechanisms are not mutually exclusive and probably both played a role in the evolution of permuted DNA MTases.

[
  "009:25"
]

{
  "fn": "NIH",
  "@type": "vcard:Contact",
  "hasEmail": "mailto:info@nih.gov"
}

[
  {
    "@type": "dcat:Distribution",
    "title": "Official Government Data Source",
    "mediaType": "text/html",
    "description": "Visit the original government dataset for complete information, documentation, and data access.",
    "downloadURL": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102321/"
  }
]

[
  "dna-methyltransferases",
  "molecular-evolution",
  "nih",
  "restriction-modification",
  "sequence-permutation"
]

[
  "009:033"
]

{
  "name": "National Institutes of Health",
  "@type": "org:Organization"
}

[
  "NIH"
]