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

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. To investigate the evolutionary relationship and make functional inferences within th...

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Vydáno v:	Biochimica et biophysica acta. General subjects Ročník 1861; číslo 2; s. 323 - 334
Hlavní autoři:	Jia, Baolei, Jia, Xiaomeng, Kim, Kyung Hyun, Jeon, Che Ok
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Netherlands Elsevier B.V 01.02.2017
Témata:	2-Oxoglutarate/Fe(II)-dependent oxygenase bacteria Bacteria - metabolism bacterial proteins Binding Sites - physiology bioinformatics Catalysis coevolution Computational Biology - methods DNA Electron transfer Evolution Ferrous Compounds - metabolism horizontal gene transfer hydrophobicity Ketoglutaric Acids - metabolism messenger RNA Multi-domain proteins Oxidation-Reduction oxygenases Oxygenases - metabolism Peroxides - metabolism peroxiredoxin Peroxiredoxins - metabolism Protein Domains selection pressure sequence homology Sequence Homology, Amino Acid Sequence similarity network tyrosine Tyrosine - metabolism Electron transfer Evolution 2-Oxoglutarate/Fe(II)-dependent oxygenase Multi-domain proteins Sequence similarity network
ISSN:	0304-4165, 1872-8006
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Shrnutí:	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. 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. 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. 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. This work enables an expanded understanding of the diversity, evolution, and functions of bacterial 2OG oxygenases. •2OG oxygenases play diverse function such as biomolecular modification and synthesis.•Sequence similarity networks indicate that few 2OG oxygenases are experimentally defined.•Horizontal gene transfer plays an important role in 2OG oxygenase evolution.•Among the conserved amino acids, the primary substrates binding Tyr is not coevolved.•A Prx-2OG oxygenase catalyzes a straightforward electron transfer to degrade H2O2.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0304-4165 1872-8006
DOI:	10.1016/j.bbagen.2016.12.001