Abstract

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.

中文翻译：

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通过进化时间和分类空间扩展“钠世界”

摘要

1986年，弗拉基米尔·斯库拉切夫（Vladimir Skulachev）和他的同事们用基于钠（Na）的生物能学为多种生物创造了“钠世界”一词。尽管那时只有很少的这种生物被发现，但是作者有深刻的洞察力指出：“利用Na循环的大量生物分类学表明这种新型的膜相关能量转导的普遍存在”。在这里，我们使用生物信息学的工具来追踪钠世界在进化时间和分类空间上的扩展。我们在原核基因组中搜索那些与不同生物利用ATP合成的Na电位相关的膜蛋白家族。除了已知的Na-易位子外，我们还发现了许多未知的蛋白质家族。它们中的大多数与所研究的蛋白质没有同源性。此外，我们追踪了许多新颖的古细菌和细菌进化枝中基于Na的能量学的存在，最近通过宏基因组学技术对其进行了鉴定。所获得的数据支持这样一种观点，即钠基能量学在演化过程中先于质子依赖的能量学，并在地球历史的前20亿年盛行，然后被大气氧化。因此，在原核生物中基于Na的能量学的全部能力仍未得到充分开发。由于Na转运系统获得了新功能，因此Sodium World得以扩展。具体而言，大多数类型的G蛋白偶联受体（GPCR）几乎都是由已知药物中的一半靶向的，它们似乎是由Na转运型微生物视紫红质演变而来的。因此，A类的GPCR具有人类基因组中的700个代表，在跨膜七螺旋束的中心保留了Na结合位点以及Na移位的能力。数学建模表明，A类GPCR可以利用跨膜Na电位的能量来提高其灵敏度和选择性。因此，GPCR是人类基因组编码的最大蛋白质家族，起源于钠世界，它鼓励探索其他依赖Na的真核生物酶。