Editing Last universal common ancestor (section)

=== Biochemical mechanisms ===

While the anatomy of the LUCA cannot be reconstructed with certainty, its [[Metabolic pathway|biochemical mechanisms]] can be deduced and described in some detail, based on properties shared by currently living organisms as well as genetic analysis.<ref name="Wächtershäuser 1998">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1 |bibcode=1998SyApM..21N1475W }}</ref>

The LUCA certainly had [[gene]]s and a [[genetic code]].<ref name="Weiss Preiner Xavier 2018">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref> Its genetic material was most likely DNA,<ref name="Wächtershäuser 1998"/> so that it lived after the [[RNA world]].{{efn|Other studies propose that LUCA may have been defined wholly through [[RNA]],<ref>{{cite magazine |url=https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |title=Life began with a planetary mega-organism |last=Marshall |first=Michael |magazine=[[New Scientist]] |access-date=31 July 2016 |archive-url=https://web.archive.org/web/20160725170104/https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |archive-date=25 July 2016 |df=dmy-all |url-status=live}}</ref> consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |author1-link=Eugene V. Koonin |last2=Martin |first2=William F. |author2-link=William F. Martin |date=1 December 2005 |df=dmy-all |title=On the origin of genomes and cells within inorganic compartments |journal=Trends in Genetics |volume=21 |issue=12 |pages=647–654 |doi=10.1016/j.tig.2005.09.006 |pmid=16223546 |pmc=7172762 }}</ref>}}<ref name="PiP">{{cite journal |last=Garwood |first=Russell J. |title=Patterns In Palaeontology: The first 3 billion years of evolution |year=2012 |journal=Palaeontology Online |volume=2 |issue=11 |pages=1–14 |url=http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |access-date=June 25, 2015 |archive-url=https://web.archive.org/web/20150626104131/http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |archive-date=June 26, 2015 |url-status=live }}</ref> The DNA was kept double-stranded by an [[enzyme]], [[DNA polymerase]], which recognises the structure and directionality of DNA.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |author1-link=Eugene V. Koonin |last2=Krupovic |first2=M. |last3=Ishino |first3=S. |last4=Ishino |first4=Y. |title=The replication machinery of LUCA: common origin of DNA replication and transcription. |journal=BMC Biology |date=2020 |volume=18 |issue=1 |pages=61 |doi=10.1186/s12915-020-00800-9 |pmid=32517760 |pmc=7281927 |doi-access=free }}</ref> The integrity of the DNA was maintained by a group of [[DNA repair|repair]] enzymes including [[DNA topoisomerase]].<ref>{{Cite journal |last1=Ahmad |first1=Muzammil |last2=Xu |first2=Dongyi |last3=Wang |first3=Weidong |date=2017-05-23 |df=dmy-all |title=Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life |journal=RNA Biology |volume=14 |issue=7 |pages=854–864 |doi=10.1080/15476286.2017.1330741 |pmc=5546716 |pmid=28534707 }}</ref> If the genetic code was based on [[Nucleic acid double helix|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<!--, with the exception that the DNA nucleotide [[thymidine]] was replaced by [[uridine]] in RNA-->.<ref name="Wächtershäuser 1998"/> It had multiple [[DNA-binding protein]]s, such as histone-fold proteins.<ref>{{Cite journal |last1=Lupas |first1=Andrei N. |last2=Alva |first2=Vikram |year=2018 |title=Histones predate the split between bacteria and archaea |journal=Bioinformatics |volume=35 |issue=14 |pages=2349–2353 |doi=10.1093/bioinformatics/bty1000 |pmid=30520969}}</ref> The genetic code was expressed into [[protein]]s. These were assembled from 20 free [[amino acid]]s by [[Translation (biology)|translation]] of a [[messenger RNA]] via a mechanism of [[ribosome]]s, [[transfer RNA]]s, and a group of related proteins.<ref name="Wächtershäuser 1998"/>

Although LUCA was likely not capable of [[sexual reproduction|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 [[RecA]] protein in bacteria, the RadA protein in archaea, and the [[RAD51|Rad51]] and [[DMC1 (gene)|Dmc1]] proteins in eukaryota.<ref>Bernstein, H., Bernstein, C. (2017). Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis. In: Witzany, G. (eds) Biocommunication of Archaea. Springer, Cham. https://doi.org/10.1007/978-3-319-65536-9_7 {{Webarchive|url=https://web.archive.org/web/20240223213424/https://link.springer.com/chapter/10.1007/978-3-319-65536-9_7 |date=23 February 2024 }}</ref>

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.<ref>{{Cite journal |last1=Gogarten |first1=Johann Peter |last2=Taiz |first2=Lincoln |date=1992 |title=Evolution of proton pumping ATPases: Rooting the tree of life |url=http://dx.doi.org/10.1007/bf00039176 |journal=Photosynthesis Research |volume=33 |issue=2 |pages=137–146 |doi=10.1007/bf00039176 |pmid=24408574 |bibcode=1992PhoRe..33..137G |s2cid=20013957 |issn=0166-8595 |access-date=4 December 2023 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223213452/https://link.springer.com/article/10.1007/BF00039176 |url-status=live }}</ref> 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.<ref name="Wächtershäuser 1998"/> It tended to exclude [[sodium]] and concentrate [[potassium]] by means of specific [[Ion transporter|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 [[Redox|reduced]] CO<sub>2</sub> and oxidized H<sub>2</sub> ([[methanogenesis]] or [[acetogenesis]]) via [[acetyl]]-[[Thioester|thioesters]].<ref>{{cite journal |last1=Martin |first1=W. |last2=Russell |first2=M. J. |date=October 2007 |title=On the origin of biochemistry at an alkaline hydrothermal vent |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=362 |issue=1486 |pages=1887–1925 |doi=10.1098/rstb.2006.1881 |pmc=2442388 |pmid=17255002}}</ref><ref>{{cite journal |last1=Lane |first1=Nick |author1-link=Nick Lane |last2=Allen |first2=J. F. |last3=Martin |first3=William |author3-link=William F. Martin |date=April 2010 |title=How did LUCA make a living? Chemiosmosis in the origin of life |journal=BioEssays |volume=32 |issue=4 |pages=271–280 |doi=10.1002/bies.200900131 |pmid=20108228}}</ref>

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)".<ref name="Woese Kandler Wheelis 1990">{{cite journal |last1=Woese |first1=C.R. |author1-link=Carl Woese |last2=Kandler |first2=O. |author-link2=Otto Kandler |last3=Wheelis |first3=M.L. |author-link3=Mark Wheelis |date=June 1990 |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=PNAS |volume=87 |issue=12 |pages=4576–4579 |bibcode=1990PNAS...87.4576W |doi=10.1073/pnas.87.12.4576 |doi-access=free |pmc=54159 |pmid=2112744}}</ref> 

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<sup>+</sup>/H<sup>+</sup> 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".<ref name="Sojo Pomiankowski Lane 20142">{{Cite journal |last1=Sojo |first1=Víctor |last2=Pomiankowski |first2=Andrew |last3=Lane |first3=Nick |author3-link=Nick Lane |date=2014-08-12 |title=A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria |journal=PLOS Biology |volume=12 |issue=8 |pages=e1001926 |doi=10.1371/journal.pbio.1001926 |pmc=4130499 |pmid=25116890 |doi-access=free}}</ref> 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".<ref name="Weiss Preiner Xavier 2018"/> It is likely that the permeable membrane of LUCA was composed of archaeal lipids ([[isoprenoids]]) and bacterial lipids ([[Fatty acid|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]]".<ref name="Jordan Nee Lane 20192">{{Cite journal |last1=Jordan |first1=S. F. |last2=Nee |first2=E. |last3=Lane |first3=Nick |author3-link=Nick Lane |date=18 October 2019 |title=Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide |journal=Interface Focus |volume=9 |issue=6 |doi=10.1098/rsfs.2019.0067 |pmc=6802135 |pmid=31641436}}{{Creative Commons text attribution notice|cc=by4|from this source=yes}}</ref>

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|CAS]]-based anti-viral immune system.<ref name="Moody et al 2024"/>