2016/07/01 by G. E. Novakovsky, Gherman Novakovsky, D. V. Dibrova +3
Biochemistry, Genetics and Molecular Biology · Environmental Science · #ATP Synthase and ATPases Research #Biochemistry #Biology #Clade #Cytoplasm #Enzyme #Gene #Genetics #Hydrogenase #Membrane #Membrane protein #Membrane topology #Microbial Fuel Cells and Bioremediation #Photosynthetic Processes and Mechanisms #Phylogenetic tree #Protein subunit
paper · doi:10.1134/s0006297916070142
crossref issued 2016/07/01 · crossref published 2016/07/01 · crossref published-print 2016/07/01 · openalex publication_date 2016/07/01 · crossref created 2016/07/12 · crossref published-online 2016/07/13 · openalex created_date 2025/10/10 · crossref deposited 2026/03/16 · crossref indexed 2026/07/24 · openalex updated_date 2026/08/06
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.