Last universal common ancestor

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A 1990 phylogenetic tree linking all major groups of living organisms to the LUCA, based on ribosomal RNA sequence data.[1]

The last universal common ancestor (LUCA) is the most recent population of organisms from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. The LUCA is not thought to be the first life on Earth, but rather the latest that is ancestral to all current existing life.

While there is no specific fossil evidence of the LUCA, it can be studied by comparing the genomes of all modern organisms, its descendants. The genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to RNA to proteins. The LUCA probably lived in the high-temperature water of deep sea vents near ocean-floor magma flows. The LUCA may have lived as much as 4.5 billion years ago, during the Hadean.

Historical background[edit]

A tree of life, like this one from Charles Darwin's notebooks c. July 1837, implies a single common ancestor at its root.

An early tree of life was sketched by Jean-Baptiste Lamarck in his Philosophie zoologique in 1809.[2][3] Charles Darwin more famously proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859: "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed."[4] Patrick Forterre was the first to use the term "Last Universal Common Ancestor", or "LUCA", in a 1999 paper.[5][6]

In On the Origin of Species, Darwin twice states that he presumed there had been only one progenitor for all life forms. In the summary he writes "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed."[7] The last sentence of the book begins with a restatement of the hypothesis: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one..."[7] In 1924, Alexander Oparin further proposed that the origin of life was a chemical process kickstarted by some energy source.[8]

Inferring LUCA's features[edit]

Inferring LUCA's genome. Genes common to most surviving descendants could be ancestral.[9]

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes of various phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results "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."[10][9][11] The results are rather specific: they show that methanogenic clostridia was a basal clade in the 355 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.[10]

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.[12][13][14][15]

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.

Its genetic code was likely based on DNA,[16] so that it lived after the RNA world.[a] If DNA was present, it was composed exclusively of the four modern-day nucleotides: deoxyadenosine, deoxycytidine, deoxythymidine, and deoxyguanosine. The DNA was kept double-stranded by a template-dependent enzyme, DNA polymerase, which was recently proposed to belong to the family D.[19] The integrity of the DNA benefited from a group of maintenance and repair enzymes including DNA topoisomerase.[20] If the genetic code was DNA-based, it was expressed via single-stranded RNA intermediates. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA, with the exception that the DNA nucleotide thymidine was replaced by uridine in RNA.[12][13][14] It had multiple DNA-binding proteins, such as histone-fold proteins.[21]

The genetic code was expressed into proteins. These were assembled from free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins. The ribosomes were composed of two subunits, a big 50S and a small 30S. Each ribosomal subunit was composed of a core of ribosomal RNA surrounded by ribosomal proteins. Both types of RNA molecules (ribosomal and transfer RNAs) played an important role in the catalytic activity of the ribosomes. Only 20 amino acids were used, only in L-isomers, to the exclusion of countless other amino acids. ATP served as an energy intermediate. Several hundred protein enzymes catalyzed chemical reactions to extract energy from fats, sugars, and amino acids, and to synthesize fats, sugars, amino acids, and nucleic acid bases through various chemical pathways.[12][13][14]

The cell contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane. 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.[12][13][14] The cell used chemiosmosis to produce energy. It also reduced CO2 and oxidized H2 (methanogenesis or acetogenesis) via acetyl-thioesters.[22][23]

The LUCA probably lived in the high-temperature conditions found in deep sea vents caused by ocean water interacting with magma beneath the ocean floor.[10] By phylogenetic bracketing, analysis of the presumed LUCA's offspring groups, it 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)".[1]

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. Experiments show that acetyl-CoA pathway chemicals such as formate, methanol, acetyl entities, and pyruvate all arise spontaneously in the presence of water, carbon dioxide, and native metals, as occurs in hydrothermal vents.[24]

Age[edit]

Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.5 to 3.8 billion years ago in the Paleoarchean,[25][26] a few hundred million years before the earliest fossil evidence of life, for which candidates range in age from 3.48 to 4.28 billion years ago.[27][28][29][30][31] A 2018 study from the University of Bristol, applying a molecular clock model, places the LUCA shortly after 4.5 billion years ago, within the Hadean.[32] It is often assumed that the LUCA (and the origin of life more generally) cannot have existed prior to the formation of the moon,[32][33][34] which, according to the Giant Impact Hypothesis, would have rendered Earth uninhabitable, melting or vaporising its surface.[35]

Hypotheses[edit]

2005 tree of life showing horizontal gene transfers between branches, giving rise to an interconnected network rather than a tree[36]

When the LUCA was first proposed, cladograms based on genetic distance between living cells indicated that Archaea split early from the rest of living things. This was inferred from the fact that the archaeans known at that time were highly resistant to environmental extremes such as high salinity, temperature or acidity, leading some scientists to suggest that the LUCA evolved in areas like the deep ocean vents, where such extremes prevail today. Archaea, however, were later discovered in less hostile environments, and are now believed to be more closely related to the Eukaryota than to the Bacteria.[37][38]

In 2010, based on "the vast array of molecular sequences now available from all domains of life,"[39] a formal test of universal common ancestry was published.[40] The formal test favoured the existence of a universal common ancestor over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles make it overwhelmingly likely that all organisms do have a single common ancestor. It is extremely unlikely that organisms that had descended from separate incidents of cell-formation would be able to complete a horizontal gene transfer without garbling each other's genes, converting them into noncoding segments. Further, many more amino acids are chemically possible than the 22 found in protein molecules. These lines of chemical evidence, incorporated into the formal statistical test, point to a single cell having been the LUCA. While the test overwhelmingly favoured the existence of a single LUCA, this does not imply that the LUCA was ever alone: Instead, it was one of many early microbes,[40] but the only one whose descendants survived beyond the Paleoarchean.[41]

With the later gene pool of the 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. In 1988, Carl Woese 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.[42]

There is evidence that both archaea and bacteria have reduced their genomes through evolution, suggesting that the LUCA could have been more complex than some modern prokaryotes; Bayesian phylogenetic comparisons imply that LUCA's phenotype was indeed complex.[43]

In rare cases, gene linkage has been identified predating the LUCA, as with the F-ATPase genes.[44]

Location of the root[edit]

The most commonly accepted tree of life, based on several molecular studies, has its root between a monophyletic domain bacteria and a clade formed by Archaea and Eukaryota.[45][46][47][48][49] A small minority of studies place the root in the domain bacteria, in the phylum Bacillota,[50] 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).[51]

Martin's 2016 findings could mean that life on Earth originated in such hydrothermal vents, but it is also possible that life was restricted to such locations at some later time, perhaps by the Late Heavy Bombardment.[10] The identification of these genes as being present in the LUCA has also been criticized, as they may simply represent later genes that migrated via horizontal gene transfers between archaea and bacteria.[52] Further, the presence of 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.[53]

LUCA's viruses[edit]

Based on the extant distribution of viruses across the two primary domains of life, bacteria and archaea, the LUCA could have been associated with a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea;[54] further, 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.[55][56] This ancestral virome was likely dominated by dsDNA viruses from the realms Duplodnaviria and Varidnaviria. In addition, two groups of single-stranded DNA viruses (realm Monodnaviria), namely Microviridae and Tubulavirales, can be traced to the last bacterial common ancestor (LBCA), whereas spindle-shaped viruses most likely infected the last archaeal common ancestor (LACA). The possibility that these virus groups were present in the LUCA virome but were subsequently lost in one of the two primary domains cannot be dismissed. By contrast, RNA viruses do not appear to have been a prominent part of the LUCA virome, even though straightforward thinking might have envisaged the LUCA virome as a domain of RNA viruses descending from the primordial RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been largely supplanted by the more efficient DNA virosphere.[54]

See also[edit]

Footnotes[edit]

  1. ^ However, other studies propose that LUCA may have been defined wholly through RNA,[17] consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.[18]

References[edit]

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