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Last universal common ancestor

(Redirected fromLUCA)
"LUCA" redirects here. For other uses, seeLuca.

Thelast universal common ancestor(LUCA) is the hypothesized common ancestralcellfrom which thethree domains of life,theBacteria,theArchaea,and theEukaryaoriginated. The cell had alipid bilayer;it possessed thegenetic codeandribosomeswhichtranslatedfromDNAorRNAtoproteins.The LUCA probably existed at latest 3.6 billion years ago, and possibly as early as 4.3 billion years ago[2]or earlier. The nature of this point or stage of divergence remains a topic of research.

Phylogenetic treelinking all major groups of living organisms, namely theBacteria,Archaea,andEukarya,as proposed by Woese et al 1990,[1]with the last universal common ancestor (LUCA) shown at the root

All earlier forms of life preceding this divergence and all extant organisms are generally thought to sharecommon ancestry.On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported versus competing multiple-ancestry hypotheses. Thefirst universal common ancestor(FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.

Whether the genesis ofvirusesfalls 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 fromshared features of modern genomes.These genes describe a complex life form with manyco-adaptedfeatures, includingtranscriptionandtranslationmechanisms to convert information fromDNAtomRNAtoproteins.

Historical background

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Further information:Tree of life (biology)
Atree of life,like this one fromCharles Darwin's notebooksc. July 1837,implies a single common ancestor at its root (labelled "1" ).

Aphylogenetic treedirectly portrays the idea ofevolutionbydescent from a single ancestor.[3]An early tree of life was sketched byJean-Baptiste Lamarckin hisPhilosophie zoologiquein 1809.[4][5]Charles Darwinmore famously proposed the theory of universal common descent through an evolutionary process in his bookOn the Origin of Speciesin 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."[6]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...

— [6]

The term "last universal common ancestor" or "LUCA" was first used in the 1990s for such a primordial organism.[7][8][9]

Inferring LUCA's features

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An anaerobic thermophile

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Further information:Phylogenetic bracketing
A direct way to infer LUCA'sgenomewould be to find genes common to all surviving descendants, but little can be learnt by this approach, as there are only about 30 such genes. They are mostly forribosomeproteins, proving that LUCA had thegenetic code.Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.[10]
Three ways to infer genes present in LUCA: universal presence, presence in both theBacterialandArchaeandomains, and presence in twophylain both domains. The first yields as stated only about 30 genes; the second, some 11,000 withlateral 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.[10]

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequencedprokaryoticgenomes representing manyphylogenetic 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 aWood–Ljungdahl pathway(the reductiveacetyl-coenzyme Apathway),N2-fixing andthermophilic.LUCA's biochemistry was replete withFeSclusters andradicalreaction mechanisms. "[11]Thecofactorsalso reveal "dependence upontransition metals,flavins,S-adenosyl methionine,coenzyme A,ferredoxin,molybdopterin,corrinsandselenium.Its genetic code requirednucleosidemodifications and S-adenosylmethionine-dependentmethylations."[11]They show thatmethanogenicclostridiawerebasal, near the root of the phylogenetic tree,in the 355 protein lineages examined, and that the LUCA may therefore have inhabited an anaerobichydrothermal ventsetting in a geochemically active environment rich in H2,CO2,and iron, whereoceanwater interacted with hotmagmabeneath theocean floor.[11]It is even inferred that LUCA also grew from H2and CO2via the reverse incomplete Krebs cycle.[12]Other metabolic pathways inferred in LUCA are thepentose phosphate pathway,glycolysis,andgluconeogenesis.[13]Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that theorigin of lifetook place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.[14]

While the gross anatomy of the LUCA can be reconstructed only with much uncertainty, itsbiochemical mechanismscan be described in some detail, based on the "universal" properties currently shared by all independently living organisms on Earth.[15]

LUCA systems and environment, including theWood–Ljungdahl or reductive acetyl–CoA pathwaytofix carbon,and most likelyDNAcomplete with thegenetic codeandenzymestoreplicateit,transcribe it to RNA,andtranslate it to proteins.

The LUCA certainly hadgenesand agenetic code.[10]Its genetic material was most likely DNA,[15]so that it lived after theRNA world.[a][18]The DNA was kept double-stranded by anenzyme,DNA polymerase,which recognises the structure and directionality of DNA.[19]The integrity of the DNA was maintained by a group ofrepairenzymes includingDNA topoisomerase.[20]If the genetic code was based ondual-stranded DNA,it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependentRNA polymeraseusing nucleotides similar to those of DNA.[15]It had multipleDNA-binding proteins,such as histone-fold proteins.[21]The genetic code was expressed intoproteins.These were assembled from 20 freeamino acidsbytranslationof amessenger RNAvia a mechanism ofribosomes,transfer RNAs,and a group of related proteins.[15]

LUCA was likely capable ofsexual interactionin the sense that adaptive gene functions were present that promoted the transfer of DNA between individuals of the population to facilitategenetic recombination.Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as theRecAprotein in bacteria, the RadA protein in archaea, and theRad51andDmc1proteins in eukaryota.[22]

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.[23]As for the cell's gross structure, it contained a water-basedcytoplasmeffectively enclosed by alipid bilayermembrane; it was capable of reproducing by cell division.[15]It tended to excludesodiumand concentratepotassiumby means of specificion transporters(or ion pumps). The cell multiplied by duplicating all its contents followed bycellular division.The cell usedchemiosmosisto produce energy. It alsoreducedCO2and oxidized H2(methanogenesisoracetogenesis) viaacetyl-thioesters.[24][25]

Byphylogenetic 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 ofDNAfloating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of thethree-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]

The LUCA used theWood–Ljungdahl or reductive acetyl–CoA pathwaytofix carbon,if it was anautotroph,or torespire anaerobically,if it was aheterotroph.

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,acetylmoieties, and evenpyruvatearise spontaneously... from CO2,native metals, and water ", a combination present in hydrothermal vents.[10]

An experiment shows that Zn2+,Cr3+,and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called thereverse Krebs cyclein acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.[26]

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 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".[27]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".[10]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 theorigin of life".[28]

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 anacetogen;and that it had an earlyCAS-based anti-viral immune system.[29]

Alternative interpretations

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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. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributingconvergenceor horizontal gene transfer events to vertical descent; on the other hand, it risks 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, andPO3−
4which would imply a terrestrialhot springhabitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated toautotrophy(the ability of an organism to create its ownorganic matter), suggesting that the LUCA had aheterotrophiclifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.[30]Nick Laneargues that Na+/H+antiporters could readily explain the low concentration of Na+in the LUCA and its descendants.

The presence of the energy-handling enzymesCODH/acetyl-coenzyme Asynthase in LUCA could be compatible not only with being anautotrophbut also with life as amixotrophorheterotroph.[31]Weiss et al. 2018 reply that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.[10]

Evidence that LUCA was mesophilic

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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.[32][33][14]

The identification of thermophilic genes in the LUCA has been criticized,[34]as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these viahorizontal gene transfer,as in Woese's 1998 hypothesis.[35]For instance, the thermophile-specific topoisomerase,reverse gyrase,was initially attributed to LUCA[11]before an exhaustive phylogenetic study revealed a more recent origin of this enzyme followed by extensive horizontal gene transfer.[36]LUCA could have been a mesophile that fixed CO2and relied on H2,and lived close to hydrothermal vents.[37]

Further evidence that LUCA wasmesophiliccomes 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.[38]According to phylogentic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.[14]

Finally, 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.[39]

Age

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Further information:Abiogenesis

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 thePaleoarchean,[40]a few hundred million years before theearliest fossil evidence of life,for which candidates range in age from 3.48 to 4.28 billion years ago.[41][42][43][44][45]This placed the origin of the first forms of life shortly after theLate Heavy Bombardmentwhich was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied amolecular clockmodel to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment (making the LUCA over 3.9 billion years ago).[46]A 2022 study suggested an age of around 3.6-4.2 billion years for the LUCA.[47]A 2024 study suggested that the LUCA lived around 4.2 billion years ago (with a confidence interval of 4.09–4.33 billion years ago).[29]

Root of the tree of life

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2005tree of lifeshowinghorizontal gene transfersbetween branches including (coloured lines) thesymbiogenesisofplastidsandmitochondria."Horizontal gene transfer and how it has impacted the evolution of life is presented through a web connecting bifurcating branches that complicate, yet do not erase, the tree of life".[48]
For branching of bacteria phyla, seeBacterial phyla.

In 1990, a novel concept of thetree of lifewas presented, dividing the living world into three stems, classified as the domainsBacteria,Archaea,Eukarya.[1][49][50][51]It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form".[1]This tree and its rooting became the subject of debate.[49][b]

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.[53][48]). 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.[48]Presumably horizontal gene transfer has decreased with growing cell stability.[54]

A modified version of the tree, based on several molecular studies, has its root between amonophyleticdomainBacteriaand acladeformed byArchaeaandEukaryota.[53]A small minority of studies place the root in the domain bacteria, in the phylumBacillota,[55]or state that the phylumChloroflexota(formerly Chloroflexi) isbasalto a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed byThomas Cavalier-Smith).[56]Metagenomicanalyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea.[57][58][59]With the later gene pool of LUCA's descendants, sharing a common framework of theAT/GC ruleand the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.[60]

The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (sensuWächtershäuser),Otto Kandlerproposed a successive divergence of the three domains of life[1]from a multiphenotypicalpopulationofpre-cells,reached by gradual evolutionary improvements (cellularization).[61][62][63]These phenotypically diverse pre-cells 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.[64][65]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 throughhorizontal gene transferamong an ancient community of organisms.[66]Other authors concur that there was a "complex collective genome"[67]at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups;[67]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."[68]

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,"[69]D. L. Theobald published a "formal test"of universal common ancestry (UCA). This deals with thecommon descentof 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.[70]

A proposed, earlier, non-cellular ancestor to LUCA is theFirst universal common ancestor(FUCA).[71][72]FUCA would therefore be the ancestor to every modern cell as well as ancient, now-extinct cellular lineages not descendant of LUCA. FUCA is assumed to have had other descendants than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have beenhorizontally transferredinto the genome of early descendants of LUCA.[60]

LUCA and viruses

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Theorigin of virusesremains disputed. Since viruses need host cells for their replication, it is likely that they emergedaftertheformation of cells.Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life.[51]There are different hypotheses for the origins of viruses, for instance an early viral origin from theRNA worldor a later viral origin fromselfish DNA.[51]

Based on how viruses are currently distributed across thebacteriaandarchaea,the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts.[73]Furthermore, extensive virus evolution seems to have preceded the LUCA, since thejelly-roll structureofcapsidproteins is shared by RNA and DNA viruses across all three domains of life.[74][75]LUCA's viruses were probably mainly dsDNA viruses in the groups calledDuplodnaviriaandVaridnaviria.Two othersingle-stranded DNA virusgroups within theMonodnaviria,theMicroviridaeand theTubulavirales,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 withRNA virusesdirectly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.[73]

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-sizedDNA viruses.[76]Viruses might have evolved before LUCA but after theFirst universal common ancestor(FUCA), according to the reduction hypothesis, wheregiant virusesevolved from primordial cells that becameparasitic.[60]

See also

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Notes

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  1. ^Other studies propose that LUCA may have been defined wholly throughRNA,[16]consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.[17]
  2. ^One debate dealt with a formercladistichypothesis: The tree could not be ascribed a root in the usual algorithmic way, because that would require anoutgroupfor reference. In the case of the universal tree, no outgroup would exist. The cladistic method was used "to root the purple bacteria, for example. But establishing a root for the universal tree of life, the branching order among the primary urkingdoms, was another matter entirely."[52]

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