Sequence comparisons revealed that Ofd2 belongs to the AlkB family of dioxygenases

Furthermore, succinate formation by Ofd2 is stimulated by the presence of histones, and we find specific AZ 960 interactions between Ofd2 and histones. Ofd2 is categorized as an AlkB homolog; however, Ofd2 does not exhibit any AlkB-like DNA repair activity nor is the ofd22 mutant sensitized when exposed to DNA damaging agents. 2OG/Fe dioxygenases are involved in a wide range of biological processes and catalyze oxidation reactions in the presence of Fe by the use of oxygen and 2OG. Here, we show that Ofd2 from fission yeast mediates decarboxylation of 2OG in the absence of a primary substrate. This activity is dependent on Fe and an intact HXD/E…H motif, demonstrating that Ofd2 is a true 2OG and Fe dependent dioxygenase. E. coli AlkB, and also human ALKBH2 and ALKBH3, remove methyl damages from DNA and RNA bases, thereby restoring correct base pairing properties. We were not able to detect DNA repair activities for Ofd2, as previously observed. This result was supported by survival analysis of the ofd22 mutant, suggesting that Ofd2 is not a functional AlkB homolog. Further, ALKBH8 was recently shown to modify wobble nucleosides in certain tRNAs. However, nuclear localization of Ofd2 is in disagreement with a function of Ofd2 similar to ALKBH8, which is localized to the cytoplasm where tRNA modifications are carried out. Further, analysis of S. pombe tRNA have shown that the wobble nucleoside which is the product of ALKBH8 hydroxylation, is absent in fission yeast. However, the precursor 5-methoxycarbonylmethyluridine was identified and a tRNA methyltransferase, with homology to the methyltransferase domain of ALKBH8, is present in the S. pombe genome, demonstrating that at least parts of the tRNA modification apparatus found in higher eukaryotes is intact in fission yeast. Succinate formation by Ofd2 was stimulated when incubated with histones, especially H2A, suggesting that histones could be the prime substrate. However, despite thorough examination by MS, no change in modification pattern was detected. We speculate that another unknown biomolecule is the target for the oxidation reaction. If Ofd2 acts in a trans mode, one of the other histones in the nucleosome core could be the target molecule. Alternatively, additional proteins or cofactors might be necessary for the complete reaction to take place. Another class of 2OG/Fe dioxygenases, the JmjC family, was shown to possess histone demethylation activity by the use of the same mechanism as AlkB demethylation of DNA. In S. pombe, seven JmjC proteins have been identified and in humans about 30 which can be grouped into seven distinct subfamilies. The JmjC proteins have a very different sequence signature compared to AlkB and Ofd2 does not belong to this family. Hence, this is the first demonstration of an AlkB homolog that is stimulated by addition of protein and, moreover, that interacts with histones. Ofd2 was neither stimulated by recombinant histones nor in vitro synthesized peptides, probably suggesting that one or more specific histone modifications are required for the correct interaction to take place.

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