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REVIEW: Expansion of the “Sodium World” through Evolutionary Time and Taxonomic Space

M. I. Kozlova1,2,a, I. M. Bushmakin3,b, J. D. Belyaeva3,c, D. N. Shalaeva1,d, D. V. Dibrova2,e, D. A. Cherepanov4,f, and A. Y. Mulkidjanian1,2,3,g*

1School of Physics, Osnabrueck University, 49069 Osnabrueck, Germany

2Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia

3School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia

4Semenov Institute of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia

* To whom correspondence should be addressed.

Received September 1, 2020; Revised September 27, 2020; Accepted September 27, 2020
In 1986, Vladimir Skulachev and his colleagues coined the term “Sodium World” for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that “the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions”. Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
KEY WORDS: bioenergetics, sodium transporter, sodium/potassium homeostasis, retinal-binding proteins, GPCR, agonist, comparative genomics, antibiotics, drug research

DOI: 10.1134/S0006297920120056