Phylogenomic analysis of type 1 NADH:Quinone oxidoreductase
- Authors: Novakovsky G.E.1, Dibrova D.V.2, Mulkidjanian A.Y.1,2,3
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Affiliations:
- Faculty of Bioengineering and Bioinformatics
- Belozersky Institute of Physico-Chemical Biology
- Department of Physics
- Issue: Vol 81, No 7 (2016)
- Pages: 770-784
- Section: Article
- URL: https://journals.rcsi.science/0006-2979/article/view/150960
- DOI: https://doi.org/10.1134/S0006297916070142
- ID: 150960
Cite item
Abstract
We performed phylogenomic analysis of the catalytic core of NADH:quinone oxidoreductases of type 1 (NDH-1). Analysis of phylogenetic trees, as constructed for the core subunits of NDH-1, revealed fundamental differences in their topologies. In the case of four putatively homologous ion-carrying membrane subunits, the trees for the NuoH and NuoN subunits contained separate archaeal clades, whereas subunits NuoL and NuoM were characterized by multiple archaeal clades spread among bacterial branches. Large, separate clades, which united sequences belonging to different archaeal subdomains, were also found for cytoplasmic subunits NuoD and NuoB, homologous to the large and small subunits of nickel-iron hydrogenases. A smaller such clade was also shown for subunit NuoC. Based on these data, we suggest that the ancestral NDH-1 complex could be present already at the stage of the Last Universal Cellular Ancestor (LUCA). Ancestral forms of membrane subunits NuoN and NuoH and cytoplasmic subunits NuoD, NuoB, and, perhaps NuoC, may have formed a membrane complex that operated as an ion-translocating membrane hydrogenase. After the complex attained the ability to reduce membrane quinones, gene duplications could yield the subunits NuoL and NuoM, which enabled translocation of additional ions.
About the authors
G. E. Novakovsky
Faculty of Bioengineering and Bioinformatics
Email: amulkid@uos.de
Russian Federation, Moscow, 119991
D. V. Dibrova
Belozersky Institute of Physico-Chemical Biology
Email: amulkid@uos.de
Russian Federation, Moscow, 119991
A. Y. Mulkidjanian
Faculty of Bioengineering and Bioinformatics; Belozersky Institute of Physico-Chemical Biology; Department of Physics
Author for correspondence.
Email: amulkid@uos.de
Russian Federation, Moscow, 119991; Moscow, 119991; Osnabrueck, 49069