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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.
Among proteins encoded in sequenced prokaryotic genomes, they sought those that: (1) are present in at least two higher taxa of bacteria and archaea, and (2) its tree should recover bacterial and archaeal monophyly.
Although it has been suggested that glycolysis evolved before ion pumping and electron transport (Alberts et al.
2002, Koonin 2003), respiratory electron transport is universal to the three domains of life including eucaryote mitochondria and chloroplasts and both bacteria and archaea (Schafer et al. Among the archaea, halobacteria still use a form of photosynthesis generating ATP from H antiporters to generate ion gradients, and their membrane proteins, such as the ATP synthase, are compatible with gradients of sodium ions or protons (Lane and Martin 2012, Yong 2012).
I have updated and amended this several times as new research has clarified specific parts of the trunk and branches.
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.
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).Terminal oxidases belonging to oxygen, nitrate, sulfate, and sulfur respiratory pathways have been sequenced in members of both bacteria and archaea including cytochrome oxidase, nitrate reductase, adenylylsulfate reductase, sulfite reductase, and polysulfide reductase which can likewise be assigned to LUCA (Castresana & Moreira 1999).Similar considerations apply to ferredoxins, one of the most ancient coded proteins (Fitch & Bruschi 1987, Hall, Cammack & Rao 1974). To get a characterization of LUCA at the point it diversified into the three domains of life Archaea, Eucaryotes and Bacteria, one cannot rely on nucleotide gene sequences because these would have mutated beyond recognition, but amino acid sequences mutate more slowly because neutral mutations leave the amino acid sequence fixed and the tertiary folded structure of a protein is even more strongly conserved.This initial tree forms a good representation of the evolution of higher plants and fungi, so the remainder of the article will examine the tortuous route from the last common ancestor, through the eucaryotes to metazoa, and ultimately to humanity, language and culture.This article seeks to be a real time account of the discovery processes showing us in ever-incteasing detail, the nature of the tree and its many tangled interactions, both at the genetic and organismic level. 2009), giving rise to the RNA era, while at the same time providing a free energy source based on proton transport across membranous microcellular interfaces resulting from fatty acids also being concentrated above their critical aggregate concentration.An ingenious piece of genetic software engineering evolved in which the amber stop codon UAG is overridden if the m-RNA possesses a motif called SECIS (selenocysteine insertion sequence).