Protozoan ALKBH8 oxygenases display both DNA repair and tRNA modification activities

PLoS One. 2014 Jun 10;9(6):e98729. doi: 10.1371/journal.pone.0098729. eCollection 2014.

Abstract

The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH1-8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity was previously demonstrated for one such protein. To further explore this apparent functional duality of the ALKBH8 proteins, we have here enzymatically characterized a panel of such proteins, originating from bacteria, protozoa and mimivirus. All the enzymes showed DNA repair activity in vitro, but, interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function different from that of their eukaryotic counterparts. The present study provides new insights on the function and evolution of the ALKBH8 family of proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agrobacterium tumefaciens / enzymology
  • Agrobacterium tumefaciens / genetics
  • Amino Acid Sequence
  • Computational Biology
  • DNA Damage
  • DNA Methylation
  • DNA Repair*
  • Dioxygenases / chemistry
  • Dioxygenases / genetics
  • Dioxygenases / metabolism*
  • Enzyme Activation
  • Humans
  • Molecular Sequence Data
  • Mutation
  • Protozoan Proteins / chemistry
  • Protozoan Proteins / genetics
  • Protozoan Proteins / metabolism*
  • RNA, Transfer / metabolism*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Alignment
  • tRNA Methyltransferases / chemistry
  • tRNA Methyltransferases / genetics
  • tRNA Methyltransferases / metabolism*

Substances

  • Protozoan Proteins
  • Recombinant Proteins
  • RNA, Transfer
  • Dioxygenases
  • tRNA Methyltransferases

Grants and funding

This work was supported by the Research Council of Norway; the Norwegian Cancer Society; the Polish-Norwegian Research Programme (PNRF-143-A1-1/07) and by Iceland, Liechtenstein and Norway by means of co-financing from the European Economic Area Financial Mechanism and the Norwegian Financial Mechanism as part of the Scholarship and Training Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.