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Fig 1c2: Left: Evolutionary tree of selenophosphate synthetase (Romero et al. Centre: SECIS hairpins of archaea (A), bacteria (B) and corresponding eukaryote variants (C, D) (Moldave ed 2006).
Top right: Tertiary structure of SECIS showing highly conserved regions (hot) (Walczak et al. Lower right: SECIS acts as an RNA-enzyme to attach the selenocysteine t-RNA to the nascent protein (click to enlarge).
It is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher Eucaryotes, plants, animals and fungi, but Protista, Eubacteria and Archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself.
The notion of a tree of evolution veertically down te generations has become complicated by evidence for promiscuous horizontal gene transfer and for genetic symbiosis at the root of the eucaryote tree.
SECIS is an unusual hairpin loop structure which has varying forms in archaea and prokaryotes with both forms appearing in eucaryotes, but they have a common feature of a highly conserved hairpin loop forming an RNA translational catalyst, which literally takes over some of the ribosomal RNA function, binding to the selenocysteine t-RNA and coupling selenocysteine to the nascent protein chain, as shown in fig 1c2.
It is clear that this unique piece of genetic software engineering evolved in LUCA because the wobble positions of three other essential amino acid t-RNAs, lysine, glutamine and glutamic acid (those with two wobble positions XAA-XAG, the fourth set being amber and ochre stop codons), all depend on a modified 2-seleno-uridine base to function and this has to be generated from selenophosphate, which in turn is generated by selenophosphate synthetase.
This article is a fully referenced research review to overview progress in unraveling the details of the evolutionary Tree of Life, from life's first occurrence in the RNA-era, to humanity's emergence and diversification, through migration and intermarriage.
The evolutionary tree of life is our immortal progenitor, not just of ourselves, but of all the species with which we co-depend, so we need to both understand it and protect it for the future generations.
As shown above left, this enzyme has an evolutionary tree extending back to LUCA confirming the obvious - that the genetic code cannot exist without the 21st software engineered amino acid selenocysteine!
In a ground-breaking project to identify genes that can illuminate the biology of LUCA, a team associated with Martin, (Weiss et al.
Fig 1b3: Evolutionary trees for two components of the electron transport chain, Fe-S proteins (left) and flavin-binding polypeptides (right archaea lower right Homo sapiens upper left), span the three domains of life (Schafer et al. It has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct DNA replication enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed RNA-DNA metabolism based on reverse transcriptase, pinpointing it to the latter phases of the RNA era (Leipe et. The validity of the RNA-era concept and the capacity for RNAs to be both replicating informational and active ribo-enzymes is emphasized by the continuing dependence of the ribosome on r RNA rather than the protein components demonstrated by the 3D realizations of the two subunits in fig 1c1, which show that the r RNA molecules are still carrying out the central task of protein assembly with only minor modification due to the 'chaperoning' proteins, despite 3.8 billion years of evolution. (2002) have found that the amino acids used in sections of genes common to life which are believed to originate with LUCA show amino acid distributions reflecting the relative abundance of such amino acids in primitive synthesis, indicating that the first translational genes used the amino acids which were spontaneously available, consistent with my original hypothesis on origin of the genetic code in Biocosmology.
A specfic model of the evolution of the ribosome envisages that the smaller subunit which binds to and moves along the m RNA began first as an RNA-based RNA helicase which was essential to avoid the RNA era ending in non-replicating double stranded hairpins (Zenkin 2012).