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Synthesis of prebiotic molecules

Condensation reactions likely played major roles in the synthesis of the first biotic molecules including early peptides and nucleic acids. However, reactions that lead to elongation of peptides and nucleic acids are both endergonic and requires activation. In fact, condensation reactions would be required at multiple steps in RNA oligomerization: the condensation of nucleobase and pentose, nucleoside phosphorylation, and nucleotide polymerization.

${\ce {2 Glycine <=> diglycine + H2O}}$

${\ce {Adenosine + HPO4^2- <=> AMP^2- + H2 O}}$

At room temperature and neutral pH, the thermodynamic requirement for aqueous peptide synthesis (first equation above) is 3.5 kcal/mol; the energy needed to synthesize adenosine monophosphate (second equation) is 2.7 kcal/mol.

Plausible condensing agents for early life

Fortunately, both carbon-nitrogen based and phosphorus based condensing agents would likely have been available in prebiotic environments to facilitate the bonds formed in these reactions. These condensing agents include cyanamide, dicyandiamide, and urea. Cyanamide is likely to have been generated through the production of limestone in a prebiotic environment, and easily forms its dimer, dicyandiamide and under mild conditions, in the presence of phosphate salt, can hydrolyze to urea. In addition to serving as a precursor for important biomolecules (purines, pyrimidines, and nucleotide precursors), it can serve as a condensing agent for various condensation reactions relevant to the Origin of Life, including dipeptides and nucleotides.

Condensed phosphates may also serve as condensing agents in prebiotic synthesis reactions.

Inferring LUCA's features

LUCA as an anaerobic thermophile

Further information: Phylogenetic bracketing

A direct way to infer LUCA's genome would be to find genes common to all surviving descendants. Unfortunately, there are only about 30 such genes, mostly for ribosome proteins, proving that LUCA had the genetic code. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.

Three ways to infer genes present in LUCA: universal presence, presence in both the Bacterial and Archaean domains, and presence in two phyla in both domains. The first yields as stated only about 30 genes; the second, some 11,000 with lateral gene transfer (LGT) very likely; the third, 355 genes probably in LUCA, since they were found in at least two phyla in both domains, making LGT an unlikely explanation.

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes representing many phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms." The cofactors also reveal "dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." They show that methanogenic clostridia was basal, near the root of the phylogenetic tree, in the 355 protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂, and iron, where ocean water interacted with hot magma beneath the ocean floor. It's even inferred that LUCA also grew from H₂ and CO₂ via the reverse incomplete Krebs cycle. Other metabolic pathways inferred in LUCA are the pentose phosphate pathway, glycolysis, and gluconeogenesis.

While the gross anatomy of the LUCA can only be reconstructed with much uncertainty, its biochemical mechanisms can be described in some detail, based on the "universal" properties currently shared by all independently living organisms on Earth.

LUCA systems and environment, including the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, and most likely DNA complete with the genetic code and enzymes to replicate it, transcribe it to RNA, and translate it to proteins.

The LUCA certainly had genes and a genetic code. Its genetic material was most likely DNA, so that it lived after the RNA world. The DNA was kept double-stranded by an enzyme, DNA polymerase, which recognises the structure and directionality of DNA. The integrity of the DNA was maintained by a group of repair enzymes including DNA topoisomerase. If the genetic code was based on dual-stranded DNA, it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA. It had multiple DNA-binding proteins, such as histone-fold proteins. The genetic code was expressed into proteins. These were assembled from 20 free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins.

The LUCA was likely capable of sexual interaction in the sense that adaptive gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate genetic recombination. Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the RecA protein in bacteria, the RadA protein in archaea, and the Rad51 and Dmc1 proteins in eukaryota.

The functionality of LUCA as well as evidence for the early evolution membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes. As for the cell's gross structure, it contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane; it was capable of reproducing by cell division. It tended to exclude sodium and concentrate potassium by means of specific ion transporters (or ion pumps). The cell multiplied by duplicating all its contents followed by cellular division. The cell used chemiosmosis to produce energy. It also reduced CO₂ and oxidized H₂ (methanogenesis or acetogenesis) via acetyl-thioesters.

By phylogenetic bracketing, analysis of the presumed LUCA's offspring groups, LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of the three-domain system, Carl Woese, stated that in its genetic machinery, the LUCA would have been a "simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".

The LUCA used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, if it was an autotroph, or to respire anaerobically, if it was a heterotroph.

An alternative to the search for "universal" traits is to use genome analysis to identify phylogenetically ancient genes. This gives a picture of a LUCA that could live in a geochemically harsh environment and is like modern prokaryotes. Analysis of biochemical pathways implies the same sort of chemistry as does phylogenetic analysis. Weiss and colleagues write that "Experiments ... demonstrate that ... acetyl-CoA pathway [chemicals used in anaerobic respiration] formate, methanol, acetyl moieties, and even pyruvate arise spontaneously ... from CO₂, native metals, and water", a combination present in hydrothermal vents.

An experiment shows that Zn²⁺, Cr³⁺, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the reverse Krebs cycle in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.

Because both bacteria and archaea have differences in the structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na⁺/H⁺ antiporters likely lead to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It's stated that "The late and independent evolution of glycolysis but not gluconeogenesis is entirely consistent with LUCA being powered by natural proton gradients across leaky membranes. Several discordant traits are likely to be linked to the late evolution of cell membranes, notably the cell wall, whose synthesis depends on the membrane and DNA replication". Although LUCA likely had DNA, it is unknown if it could replicate DNA and is suggested to "might just have been a chemically stable repository for RNA-based replication". It is likely that the permeable membrane of LUCA was composed of archaeal lipids (isoprenoids) and bacterial lipids (fatty acids). Isoprenoids would have enhanced stabilization of LUCA's membrane in the surrounding extreme habitat. Nick Lane and coauthors state that "The advantages and disadvantages of incorporating isoprenoids into cell membranes in different microenvironments may have driven membrane divergence, with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".

While UV light between 200-280 nm (at the time, unprotected by the ozone layer) would have been damaging to nucleotides at the surface, it is likely that LUCA existed in a UV environment because of the prevalence of photolyase across the tree of life. Photolyase uses UV to drive photoreactivation, a that works to repair damage from radiation, caused by UV.

Alternative interpretations

Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. Attempts to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016) risk, on the one hand, misattributing convergence or horizontal gene transfer events to vertical descent and, on the other hand, misattributing potential LUCA gene families as horizontal gene transfer events.

A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K⁺-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K⁺/Na⁺ ratio, NH⁺
₄, Fe²⁺, CO²⁺, Ni²⁺, Mg²⁺, Mn²⁺, Zn²⁺, pyrophosphate, and PO³⁻
₄ which would imply a terrestrial hot spring habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to autotrophy (the ability of an organism to create its own organic matter), suggesting that the LUCA had a heterotrophic lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment. Nick Lane argues that Na⁺/H⁺ antiporters could readily explain the low concentration of Na⁺ in the LUCA and its descendants.

The presence of the energy-handling enzymes CODH/acetyl-coenzyme A synthase in LUCA could be compatible not only with being an autotroph but also with life as a mixotroph or heterotroph. Weiss et al. 2018 reply that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.

Evidence for a mesophilic LUCA

Several lines of evidence now suggest that LUCA was non-thermophilic.

The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result they occur more frequently in the rRNA of thermophiles; however this is not seen in LUCA's reconstructed rRNA.

The identification of thermophilic genes in the LUCA has been criticized, as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via horizontal gene transfers, as in Woese's 1998 hypothesis. LUCA could have been a mesophile that fixed CO₂ and relied on H₂, and lived close to hydrothermal vents.

Further evidence of a mesophilic LUCA comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature. According to phylogentic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.

Finally, evidence that Bacteria and Archaea–Eukaryota both independently underwent phases of increased and subsequently decreased thermo-tolerance, suggests a post-LUCA environmental climate shift that affected both populations and explains the seeming genetic pervasiveness of thermo-tolerant genetics.