Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer

Mol Microbiol. 2008 Jan;67(2):323-35. doi: 10.1111/j.1365-2958.2007.06047.x. Epub 2007 Dec 7.


The Pyrococcus abyssi genome displays two genes possibly coding for S-adenosyl-l-methionine-dependent RNA(uracil, C5)-methyltransferases (PAB0719 and PAB0760). Their amino acid sequences are more closely related to Escherichia coli RumA catalysing the formation of 5-methyluridine (m(5)U)-1939 in 23S rRNA than to E. coli TrmA (tRNA methyltransferase A) methylating uridine-54 in tRNA. Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ancestor of Thermococcales and Nanoarchaea. This transfer event was followed by a duplication event in Thermococcales leading to two closely related genes. None of the gene products of the two P. abyssi paralogues catalyses in vitro the formation of m(5)U in a P. abyssi rRNA fragment homologous to the bacterial RumA substrate. Instead, PAB0719 enzyme (renamed (Pab)TrmU54) displays an identical specificity to TrmA, as it catalyses the in vitro formation of m(5)U-54 in tRNA. Thus, during evolution, at least one of the two P. abyssi RumA-type enzymes has changed of target specificity. This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / classification
  • Archaea / enzymology*
  • Archaea / genetics*
  • Bacteria / genetics
  • Bacterial Proteins / genetics*
  • Base Sequence
  • Computational Biology
  • Conserved Sequence
  • Evolution, Molecular
  • Gene Transfer, Horizontal*
  • Genome, Archaeal
  • Iron / metabolism
  • Magnesium / metabolism
  • Methylation
  • Molecular Sequence Data
  • Nanoarchaeota / genetics
  • Phylogeny
  • Pyrococcus abyssi / genetics
  • RNA, Transfer / metabolism
  • Recombinant Fusion Proteins / isolation & purification
  • Recombinant Fusion Proteins / metabolism
  • Sulfur / metabolism
  • Thermococcales / genetics
  • Uracil / metabolism
  • Uridine / metabolism
  • tRNA Methyltransferases / genetics*
  • tRNA Methyltransferases / metabolism


  • Bacterial Proteins
  • Recombinant Fusion Proteins
  • RumA protein, Bacteria
  • Uracil
  • Sulfur
  • RNA, Transfer
  • Iron
  • tRNA Methyltransferases
  • Magnesium
  • Uridine