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The archaea also use a unique form of electron transport in methanogenesis (Schafer 2004). The viral SF3 superfamily (Leitão 2015) helicase tree shows variants active on both RNA and SNA substrates, consistent with an origin in the RNA era (Caprari et al. Supporting the notion of subunits, a beta-chain of ATP synthase is homologous to a hepatic lipoprotein receptor (Martinez et al. Fig 1b2: Left: Rotary action of ATPsynthase, shown centre. Right: Evolutionary tree of viral RNAhelicase includes forms active in both RNA and single and double-stranded DNA viruses (Caprari et al. Respiratory electron transport occurs in both aerobic and anaerobic organisms and the terminal oxidases, iron-sulphur proteins and flavin-binding polypeptides all show evolutionary trees reaching back to the common ancestor of the three domains, implying terminal oxidases predate oxygenic photosynthesis.The extremely ancient origin of the rhodopsin family of heptahelical receptors can be seen from the ultra-primitive archael photosynthesis in Halobacteria, which relies on direct coupling between photo-stimulated chemiosmotic H-dependent ATPsynthase universal to the chemiosmotic coupling of electron transport to ATP production is a rotary motor which appears to have evolved from two separate subunits, one of which has been proposed to be a helicase (Doering et al. Hexameric helicases are found both in the SF3 superfamily in viruses (Hickman & Dyda 2005) and the MCM helicases are critical to replication forks in diverse organisms from humans to archaea (Fletcher et al. The fact that many components of archaeal electron transport are significantly different in structure from those of bacteria implies these evolved separately and that archaeal electron transport is not simply a more recent result of horizontal transfer (Schafer 2004).

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The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of biological diversity.

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).

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).

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.It also strives to be a fully up-to-date scientfic account of the discovery process for which we all owe a vote of thanks to the many researchers whose work is illustrated and cited in this extensive review article. The transition to enclosed cells is likely to have been in an active iron-sulphur reaction phase still present in living cells and associated with sodium-proton anti-porters activating ATP (Lane and Martin 2012, Lane 2009b), leading in turn to electron transport and some of the most ancient proteins, such as ferredoxin, The universal common ancestor of the three domains of life may have thus been a proton-pumping membranous interface from which archaea and bacteria emerged as free-living adaptions.Following a phase of biogenesis possibly emerging directly from cosmic symmetry-breaking (King 1978, 2004), based on spontaneous prebiotic RNA synthesis (Powner et. 2009, 2010) recent research suggests that the last universal common ancestor (LUCA) of all life on the planet may have arisen before the first cells, from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic acidified iron-rich ocean (Martin and Russel 2003) in which differential dynamics in membranous micropores in the vents managed to concentrate polypeptides and polynucleotides to biologically sustainable levels (Baaske et. This is suggested by fundamental differences in their cell walls and other details of evolutionary relationships among some of the oldest genes.In particular, in the evolution of the aminoacyl-t RNA synthetases (aa RS), coupling an amino acid to its respective t-RNA, analysis of genetic trees shows that there have been multiple horizontal transfer of such genes, including some from putative sister species of LUCA, in a similar manner to the introgression of Neanderthal DNA into One intriguing indication of the state of genetic translation in LUCA is the incorporation of selenocysteine into the genetic code.Selenoenzymes which contain selenocysteine as a genetically translated amino acid are essential to the three domains of life and source back to LUCA, despite the fact that the 21st coded amino acid selenocysteine could not be fitted into the genetic code.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).