Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa

Abstract

Background: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily in Metazoa is responsible for protein modification, nucleic acid repair and/or modification, and fatty acid metabolism.

Methods: Phylogenetic analysis, protein sequence similarity network (SSN) and other bioinformatics tools were used to analyze the evolutionary relationship and make functional inferences of Metazoa 2OG oxygenases.

Results: Sixty-four 2OG oxygenases have been previously found in Homo sapiens; they catalyze two reactions: hydroxylation and demethylation. Phylogenetic analyses indicated that enzymes with similar domain architecture are always clustered together, and the redox function can be performed by the 2OG oxygenase domain or Jumonji C (JmjC) domain, where the JmjC domain is always fused to other functional domains. We used the SSN to make functional inferences and to conduct distribution analysis of Metazoa 2OG oxygenases. >11,000 putative 2OG oxygenases across Metazoa could be assigned potential functions based on the SSN. The multiple sequence alignments showed that the residues binding iron are most highly conserved in both the 2OG oxygenase domain and JmjC domain. In contrast, the residues binding oxoglutarate are quite different in the two domains: the 2OG oxygenase domain tends to have an Arg/Lys at the C terminus, whereas the JmjC domain, an Asn/Lys residue in the middle region.

Conclusions: The results indicated that gene duplication and vertical gene transfer have played important roles in 2OG oxygenase evolution in Metazoa and clarified the difference between the 2OG oxygenase domain and JmjC domain.

General significance: These findings expand the understanding of the diversity, evolution, and functions of 2OG oxygenases.

Keywords: 2-oxoglutarate/Fe(II)-dependent oxygenase; Evolution; JmjC; Metazoa; Sequence similarity network.