A universal and constant rate of gene content change traces pangenome flux to LUCA.

Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC).

The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third.

Molecular oxygen is a stable diradical. All O-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O started accumulating on Earth 2.

Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life.

Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO to organic compounds, provided that suitable catalysts are present.

The Moon-Forming Impact and the Autotrophic Origin of Life.

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis.

Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA).

Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, Δ, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of Δ across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H, CO, NH, HS and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (Δ ≤ 0 kJ⋅mol) at pH 7-10 and 80-100°C under nonequilibrium conditions with H replacing biochemical reductants.

Pyrophosphate and Irreversibility in Evolution, or why PP Is Not an Energy Currency and why Nature Chose Triphosphates.

The possible evolutionary significance of pyrophosphate (PP) has been discussed since the early 1960s. Lipmann suggested that PP could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PP vectorializes metabolism because ubiquitous pyrophosphatases render PP forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H, CO, and NH.

The metabolic network of the last bacterial common ancestor.

Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites.

Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.

The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA.

The Autotrophic Core: An Ancient Network of 404 Reactions Converts H, CO, and NH into Amino Acids, Bases, and Cofactors.

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H, CO, and ammonia (NH) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment.