Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria

Abstract

Background: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites.

Methods: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily.

Results: The network based on experimentally characterized 2OG oxygenases reflects functional clustering. Networks based on all of the bacterial 2OG oxygenases from the Interpro database indicate that only few proteins in this superfamily are functionally defined. The uneven distribution of the enzymes supports the hypothesis that horizontal gene transfer plays an important role in 2OG oxygenase evolution. A hydrophobic tyrosine residue binding the primary substrates at the N-termini is conserved. At the C-termini, the iron-binding, oxoglutarate-binding, and hydrophobic motifs are conserved and coevolved. Considering the proteins in the family are largely unexplored, we annotated them by the Pfam database and hundreds of novel and multi-domain proteins are discovered. Among them, a two-domain protein containing an N-terminal peroxiredoxin domain and a C-terminal 2OG oxygenase domain was characterized enzymatically. The results show that the enzyme could catalyze the reduction of peroxide using 2-oxoglutarate as an electron donor.

Conclusions: Our observations suggest relatively low evolutionary pressure on the bacterial 2OG oxygenases and a straightforward electron transfer pathway catalyzed by the two-domain 2OG oxygenase.

General significance: This work enables an expanded understanding of the diversity, evolution, and functions of bacterial 2OG oxygenases.

Keywords: 2-Oxoglutarate/Fe(II)-dependent oxygenase; Electron transfer; Evolution; Multi-domain proteins; Sequence similarity network.