The last universal common ancestor ( LUCA) is the hypothesized common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya originated. The cell had a lipid bilayer; it possessed the genetic code and which translated from DNA or RNA to . Although the timing of the LUCA cannot be definitively constrained, most studies suggest that the LUCA existed by 3.5 billion years ago, and possibly as early as 4.3 billion years ago or earlier. The nature of this point or stage of divergence remains a topic of research.
All earlier forms of life preceding this divergence and all extant organisms are generally thought to share common ancestry. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported in preference to competing multiple-ancestry hypotheses. The first universal common ancestor (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.
Whether the genesis of falls before or after the LUCA–as well as the diversity of extant viruses and their hosts–remains a subject of investigation.
While no fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes its existence widely accepted by biochemists. Its characteristics can be inferred from shared features of modern genomes. These genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to mRNA to .
Historical background
The term "last universal common ancestor" or "LUCA" was first used in the 1990s for such a primordial organism.
Inferring LUCA's features
Biochemical mechanisms
The LUCA certainly had 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 DNA 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 . These were assembled from 20 free by translation of a messenger RNA via a mechanism of , , and a group of related proteins.
Although LUCA was likely not capable of sexual interaction, 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
The functionality of LUCA as well as evidence for the early evolution of membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes. As for the cell's 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 (or ion pumps). The cell multiplied by duplicating all its contents followed by cellular division. The cell used chemiosmosis to produce energy. It also Redox CO2 and oxidized H2 (methanogenesis or acetogenesis) via acetyl-Thioester.
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)".
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+ likely led to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It is 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 that it "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 (). 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".
A 2024 study suggests that LUCA's genome was similar in size to that of modern prokaryotes, coding for some 2,600 proteins; that it respired anaerobically, and was an acetogen; and that it had an early CRISPR-based anti-viral immune system.
An anaerobic thermophile
In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced Prokaryote 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, Carbon dioxide-fixing, Hydrogen-dependent with a Wood–Ljungdahl pathway (the reductive Acetyl-CoA pathway), Nitrogen-fixing and Thermophile. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms." The cofactors also reveal "dependence upon Transition metal, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, Corrin and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent Methylation." They show that Methanogen Clostridium were 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 Seabed. It is 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. Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the Abiogenesis took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.
Weiss and colleagues write that "Experiments ... demonstrate that ... acetyl-CoA pathway chemicals formate, methanol, Acetyl group 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.
Undersampled protein families
The presence of the energy-handling enzymes CODH/Acetyl-CoA synthase in LUCA could be compatible not only with being an autotroph but also with life as a mixotroph or heterotroph. Weiss et al. in 2018 replied that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.
A 2024 study directly estimated the order in which amino acids were added into the genetic code from early protein domain sequences. A total of 969 protein domains were classified as present in LUCA, including 101 domain sequences that dated back to the even-older pre-LUCA communities. 88% of the protein domains annotated as LUCA or pre-LUCA were confirmed by Moody et al. 2024, by being associated with proteins that are more than 50% likely to be present in LUCA. It found that amino acids that bind metals, and those that contain sulphur, came early in the genetic code. The study suggests that sulphur metabolism and catalysis involving metals were important elements of life at the time of LUCA.
Possibly a mesophile
The identification of thermophilic genes in the LUCA has been challenged, as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via horizontal gene transfer, as in Woese's 1998 hypothesis. For instance, the thermophile-specific topoisomerase, reverse gyrase, was initially attributed to LUCA before an exhaustive phylogenetic study revealed a more recent origin of this enzyme followed by extensive horizontal gene transfer. LUCA could have been a mesophile that fixed CO2 and relied on H2, and lived close to hydrothermal vents.
Further evidence that LUCA was Mesophile 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 phylogenetic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.
Evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.
Age
Root of the tree of life
In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g.). Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed. Presumably horizontal gene transfer has decreased with growing cell stability.
A modified version of the tree, based on several molecular studies, has its root between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota. A small minority of studies place the root in the domain bacteria, in the phylum Bacillota, or state that the phylum Chloroflexota (formerly Chloroflexi) is basal to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by Thomas Cavalier-Smith). Metagenomics analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea. With the later gene pool of LUCA's descendants, sharing a common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.
The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (as discussed by Wächtershäuser), Otto Kandler proposed a successive divergence of the three domains of life from a multiphenotypical population of Pre-cell, reached by gradual evolutionary improvements (cellularization). The phenotypically diverse pre-cells of this population were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time, the partition into three lines (the three domains) of life. Kandler's pre-cell theory is supported by Wächtershäuser. In 1998, Carl Woese, based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms. Other authors concur that there was a "complex collective genome" at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups; Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."
The theory of a universal common ancestry of life is widely accepted. In 2010, based on "the vast array of molecular sequences now available from all domains of life," D. L. Theobald published a "formal test" of universal common ancestry (UCA). This deals with the common descent of all extant terrestrial organisms, each being a genealogical descendant of a single species from the distant past. His formal test favoured the existence of a universal common ancestry over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles imply that all organisms do have a common ancestry.
A proposed non-cellular ancestor to LUCA is the First universal common ancestor (FUCA).
LUCA and viruses
Based on how viruses are currently distributed across the bacteria and archaea, the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts. Furthermore, extensive virus evolution seems to have preceded the LUCA, since the jelly-roll structure of capsid proteins is shared by RNA and DNA viruses across all three domains of life. LUCA's viruses were probably mainly dsDNA viruses in the groups called Duplodnaviria and Varidnaviria. Two other single-stranded DNA virus groups within the Monodnaviria, the Microviridae and the Tubulavirales, likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with RNA viruses directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.
LUCA might have been the ancestor to some viruses, as it might have had at least two descendants: LUCELLA, the Last Universal Cellular Ancestor, the ancestor to all cells, and the archaic virocell ancestor, the ancestor to large-to-medium-sized DNA virus. Viruses might have evolved before LUCA but after the First universal common ancestor (FUCA), according to the reduction hypothesis, where Giant virus evolved from primordial cells that became Parasitism.
See also
Notes
Further reading
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