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Last universal common ancestor
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{{For|lowest common ancestors in graph theory and computer science|lowest common ancestor}}{{redirect|LUCA|other uses|Luca (disambiguation)}}{{update|date=January 2019}}{{evolutionary biology}}The last universal common ancestor (LUCA), also called the last universal ancestor (LUA), cenancestor, or (incorrectlyThere is a common misconception that definitions of LUCA and progenote are the same; however, progenote is defined as an organism “still in the process of evolving the relationship between genotype and phenotype”, and it is only hypothesed that LUCA is a progenote.JOURNAL, Gogarten, Johann Peter, Deamer, David, Is LUCA a thermophilic progenote?, Nature Microbiology, 1, 12, 25 November 2016, 16229, 10.1038/nmicrobiol.2016.229, 27886195, ) progenote, is the most recent population of organisms from which all organisms now living on Earth have a common descent.JOURNAL, Theobald DL, A formal test of the theory of universal common ancestry, Nature, 465, 7295, 219–22, May 2010, 20463738, 10.1038/nature09014, 2010Natur.465..219T, LUCA is the most recent common ancestor of all current life on Earth. LUCA is not thought to be the first living organism on Earth, but only one of many early organisms, whereas the others became extinct. While there is no specific fossil evidence of LUCA, it can be studied by comparing the genomes of its descendants, all organisms known to be living today. By this means, a 2016 study identified a set of 355 genes inferred to have been present in LUCA. This would imply it was already a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information between DNA, RNA, and proteins. However, some of those genes could have developed later and spread universally by horizontal gene transfer between archaea and bacteria.LUCA is estimated to have lived some 3.5 to 3.8 billion years ago in the Paleoarchean era,JOURNAL, Doolittle WF, February 2000, Uprooting the tree of life, Scientific American, 282, 2, 90–95, 2000SciAm.282b..90D, 10.1038/scientificamerican0200-90, 10710791, JOURNAL, Glansdorff N, Xu Y, Labedan B, 2008, The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner, Biology Direct, 3, 29, 10.1186/1745-6150-3-29, 2478661, 18613974, a few hundred million years after the earliest evidence of life on Earth, for which there are several candidates. Microbial mat fossils have been found in 3.48 billion-year-old sandstone from Western Australia,NEWS,weblink Oldest fossil found: Meet your microbial mom, Borenstein, Seth, 13 November 2013, 15 November 2013, Associated Press, JOURNAL, Noffke, N., Christian, D., Wacey, D., Hazen, R.M., December 2013, Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia, Astrobiology, 13, 12, 1103–24, 2013AsBio..13.1103N, 10.1089/ast.2013.1030, 3870916, 24205812, while biogenic graphite has been found in 3.7 billion-year-old metamorphized sedimentary rocks from Western Greenland.JOURNAL, Ohtomo, Yoko, Kakegawa, Takeshi, Ishida, Akizumi, Nagase, Toshiro, Rosing, Minik T., 2013, Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks, Nature Geoscience, 7, 1, 25–28, 2014NatGe...7...25O, 10.1038/ngeo2025, JOURNAL, Hassenkam, T., Andersson, M. P., Dalby, K. N., Mackenzie, D. M. A., Rosing, M. T., 2017, Elements of Eoarchean life trapped in mineral inclusions, Nature, 548, 7665, 78–81, 2017Natur.548...78H, 10.1038/nature23261, 28738409,weblink Recent studies have tentatively proposed evidence of life as early as 4.28 billion years ago.NEWS, Borenstein, Seth, Hints of life on what was thought to be desolate early Earth,weblink 19 October 2015, AP News, Associated Press, 9 October 2018, JOURNAL, Bell, Elizabeth A., Boehnke, Patrick, Harrison, T. Mark, Mao, Wendy L., 24 November 2015, Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon, Proceedings of the National Academy of Sciences of the United States of America, 112, 47, 14518–21, 2015PNAS..11214518B, 10.1073/pnas.1517557112, 1091-6490, 4664351, 26483481, JOURNAL, Dodd, Matthew S., Papineau, Dominic, Grenne, Tor, slack, John F., Rittner, Martin, Pirajno, Franco, O'Neil, Jonathan, Little, Crispin T. S., 2 March 2017, Evidence for early life in Earth's oldest hydrothermal vent precipitates,weblink Nature, 543, 7643, 60–64, 2017Natur.543...60D, 10.1038/nature21377, 28252057,weblink 10 February 2017, Charles Darwin proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859, saying, "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."{{Citation |last=Darwin |first=C. |year=1859 |title=The Origin of Species by Means of Natural Selection |page=490 |publisher=John Murray|title-link=The Origin of Species by Means of Natural Selection }} Later biologists have separated the problem of the origin of life from that of the LUCA.

Features

{{further information|Phylogenetic bracketing}}By analysis of the presumed LUCA's offspring groups, the LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell, like modern bacteria. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. However, Carl Woese et al., who first proposed the currently-used three domain system based on an analysis of ribosomal RNA (rRNA) sequences of bacteria, archaea, and eukaryotes, 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)".JOURNAL, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,weblink Proceedings of the National Academy of Sciences, 1990, 0027-8424, 2112744, 4576–79, 87, 12, 10.1073/pnas.87.12.4576, C. R., Woese, O., Kandler, M. L., Wheelis, 54159, 1990PNAS...87.4576W, While the gross anatomy of LUCA can only be reconstructed with much uncertainty, its biochemical mechanisms can be described in some detail, based on the properties currently shared by all independently living organisms on Earth.JOURNAL, Wächtershäuser, Günter, 1998, Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment, Systematic and Applied Microbiology, 21, 4, 473–74, IN1, 475–77, 10.1016/S0723-2020(98)80058-1, WEB,weblink What is Life?, Michael, Gregory, Clinton College, yes,weblink 2007-12-13, JOURNAL, Pace NR, The universal nature of biochemistry, Proceedings of the National Academy of Sciences of the United States of America, 98, 3, 805–08, January 2001, 11158550, 33372, 2001PNAS...98..805P, 10.1073/pnas.98.3.805, JOURNAL, Wächtershäuser, G., From pre-cells to Eukarya – a tale of two lipids, Molecular Microbiology, 47, 1, 13–22, January 2003, 12492850, 10.1046/j.1365-2958.2003.03267.x, The genetic code was likely based on DNA,JOURNAL, Patterns In Palaeontology: The first 3 billion years of evolution, Russell J., Garwood, 2012, Palaeontology Online, 2, 11, 1–14,weblink June 25, 2015, with multiple DNA-binding proteins, such as histone-fold proteins,JOURNAL, Lupas, Andrei N., Alva, Vikram, Histones predate the split between bacteria and archaea,weblink Bioinformatics, en, 10.1093/bioinformatics/bty1000, being traced back to LUCA. However, other studies propose that LUCA may have been defined wholly through RNA,WEB, Michael, Marshall, Life began with a planetary mega-organism,weblink
, New Scientist, consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.JOURNAL, Koonin, Eugene V., Martin, William, 2005-12-01, On the origin of genomes and cells within inorganic compartments,weblink Trends in Genetics, 21, 12, 647–654, 10.1016/j.tig.2005.09.006, 0168-9525, If DNA was present, it was composed exclusively of four nucleotides: deoxyadenosine, deoxycytidine, deoxythymidine, and deoxyguanosine. The DNA was kept double-stranded by a template-dependent enzyme, DNA polymerase. The integrity of the DNA benefited from a group of maintenance and repair enzymes including DNA topoisomerase.JOURNAL, Ahmad, Muzammil, Xu, Dongyi, Wang, Weidong, 2017-05-23, Type IA topoisomerases can be “magicians” for both DNA and RNA in all domains of life,weblink RNA Biology, 14, 7, 854–864, 10.1080/15476286.2017.1330741, 1547-6286, 5546716, 28534707, If the code was DNA-based, its genetic code 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.
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.The cell contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane. The cell 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.JOURNAL, Martin, W., Russell, M.J., On the origin of biochemistry at an alkaline hydrothermal vent, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 362, 1486, 1887–925, October 2007, 17255002, 2442388, 10.1098/rstb.2006.1881, JOURNAL, Lane, N., Allen, J.F., Martin, W., How did LUCA make a living? Chemiosmosis in the origin of life, BioEssays, 32, 4, 271–80, April 2010, 20108228, 10.1002/bies.200900131, 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.NEWS,weblink Meet Luca, the Ancestor of All Living Things, Wade, Nicholas, 2016-07-25, The New York Times, 0362-4331, 26 July 2016,

Hypotheses

File:Phylogenetic tree.svg|right|thumb|upright=1.5|A 1990 (phylogenetic tree]] linking all major groups of living organisms to the LUCA (the black trunk at the bottom), based on ribosomal RNA sequence data.JOURNAL, Woese, C.R., Kandler, O., Wheelis, M.L., Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proceedings of the National Academy of Sciences of the United States of America, 87, 12, 4576–79, June 1990, 2112744, 54159, 10.1073/pnas.87.12.4576, 1990PNAS...87.4576W, )In 1859, Charles Darwin published On the Origin of Species in which he twice stated the hypothesis that there was only one progenitor for all life forms. In the summation he states, "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."Darwin, Charles. On the Origin of Species. London: John Murray, Albermarle Street. 1859. pp. 484, 490. The very last sentence 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..."When the LUCA was hypothesized, cladograms based on genetic distance between living cells indicated that Archaea split early from the rest of life. 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, although many details are still unknown.JOURNAL, Xie, Q., Wang, Y., Lin, J., Qin, Y., Wang, Y., Bu, W., Potential key bases of ribosomal RNA to kingdom-specific spectra of antibiotic susceptibility and the possible archaeal origin of eukaryotes, PLoS ONE, 7, 1, e29468, 2012, 22247777, 3256160, 10.1371/journal.pone.0029468, 2012PLoSO...729468X, JOURNAL, Yutin, N., Makarova K.S., Mekhedov S.L., Wolf, Y.I., Koonin, E.V., The deep archaeal roots of eukaryotes, Molecular Biology and Evolution, 25, 8, 1619–30, August 2008, 18463089, 2464739, 10.1093/molbev/msn108, File:Tree Of Life (with horizontal gene transfer).svg|thumb|upright=1.1|left|2005 tree of life showing horizontal gene transfers between branches, giving rise to an interconnected network rather than a plain hierarchy]]In 2010, based on "the vast array of molecular sequences now available from all domains of life,"JOURNAL, Steel, M., Penny, D., Origins of life: Common ancestry put to the test, Nature, 465, 7295, 168–69, May 2010, 20463725, 10.1038/465168a, 2010Natur.465..168S, a formal test of universal common ancestry was published. The formal test favored 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 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 twenty found in modern 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 favored the existence of a single LUCA, this does not imply that the LUCA was ever alone: instead, it was one of many early microbes but the only one whose descendents survived beyond the Paleoarchean Era.JOURNAL, Egel, Richard, Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life, Life, March 2012, 2, 1, 170–212, 10.3390/life2010170, 4187143, 25382122, With the later gene pool of the LUCA's descendants, with their common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have been feasible and could have been very common.In an earlier hypothesis, Carl Woese (1988) had proposed that: (1) no individual organism can be considered a LUCA, and (2) the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.JOURNAL, Woese C, The universal ancestor, Proceedings of the National Academy of Sciences of the United States of America, 95, 12, 6854–59, June 1998, 9618502, 22660, 10.1073/pnas.95.12.6854, 1998PNAS...95.6854W, While the results described by Theobald (2010) and Saey (2010) demonstrate the existence of a single LUCA, Woese's argument can still be applied to Ur-organisms (initial products of abiogenesis) before the LUCA. At the beginnings of life, ancestry was not as linear as it is today because the genetic code had not evolved.BOOK, The Major Transitions in Evolution, Maynard Smith, John, John Maynard Smith, Eörs, Szathmáry, Eörs Szathmáry, Oxford University Press, 1995, Oxford, England, 978-0-19-850294-4,weblink {{page needed|date=June 2014}} Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. However, the LUCA lived after the origin of the genetic code and at least some rudimentary early form of molecular proofreading.

Location of the root

File:Reduktiver Acetyl-CoA-Weg.png|thumb|upright=1.4|The LUCA used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon.]]{{for|branching of Bacteria phyla|Bacterial phyla}}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.Brown, J. R., and W. F. Doolittle. 1995. “Root of the Universal Tree of Life Based on Ancient Aminoacyl-tRNA Synthetase Gene Duplications.” Proc Natl Acad Sci USA 92 (7): 2441–45. PMID 7708661Gogarten, J. P., H. Kibak, P. Dittrich, L. Taiz, E. J. Bowman, B. J. Bowman, M. F. Manolson, et al. 1989. “Evolution of the Vacuolar H+-ATPase: Implications for the Origin of Eukaryotes.” Proc Natl Acad Sci USA 86 (17): 6661–65. PMID 2528146JOURNAL, Gogarten, J.P., Taiz, L., 1992, Evolution of Proton Pumping ATPases: Rooting the Tree of Life, Photosynthesis Research, 33, 2, 137–46, 10.1007/BF00039176, 24408574, Gribaldo, S, and P Cammarano. 1998. “The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery.” Journal of Molecular Evolution 47 (5): 508–16. PMID: 9797401Iwabe, Naoyuki, Kei-Ichi Kuma, Masami Hasegawa, Syozo Osawa, Takashi Miyata Source, Masami Hasegawat, Syozo Osawat, and Takashi Miyata. 1989. “Evolutionary Relationship of Archaebacteria, Eubacteria, and Eukaryotes Inferred from Phylogenetic Trees of Duplicated Genes.” Proc Natl Acad Sci USA 86 (86): 9355–59. PMID 2531898BOOK, David R., Boone, Richard W., Castenholz, George M., Garrity, The Archaea and the Deeply Branching and Phototrophic Bacteria, Bergey's Manual of Systematic Bacteriology, 978-0-387-21609-6,weblink 10.1007/978-0-387-21609-6, Springer, 2001, {{page needed|date=June 2014}} However, a very small minority of studies place the root in the domain Bacteria, either in the phylum FirmicutesJOURNAL, Valas, R.E., Bourne, P.E., The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon, Biology Direct, 6, 16, 2011, 21356104, 3056875, 10.1186/1745-6150-6-16, or state that the phylum Chloroflexi is basal to a clade with Archaea and Eukaryotes and the rest of Bacteria (as proposed by Thomas Cavalier-Smith).JOURNAL, Cavalier-Smith T, Rooting the tree of life by transition analyses, Biology Direct, 1, 19, 2006, 16834776, 1586193, 10.1186/1745-6150-1-19, Ground-breaking research by William F. Martin (2016) 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.""The physiology and habitat of the last universal common ancestor" by Madeline C. Weiss, FilipaL.Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi and William F. Martin (July 25, 2016) (Nature Microbiology 16116 | {{Doi|10.1038/NMICROBIOL.2016.116}}Nick Lane: The Vital Question – Energy, Evolution, and the Origins of Complex Life, WW Norton, 2015, {{ISBN|978-0-393-08881-6}}Joseph F. Sutherland: on The Origin Of Tha Bacteria And The Archaea, auf B.C vom 16. August 2014 The results are "quite specific":NEWS, Wade, Nicholas, Meet Luca, the Ancestor of All Living Things,weblink 25 July 2016, The New York Times, 8 October 2018, 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. These 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. The identification of these genes as being present in LUCA has also been criticized, as they may simply represent later genes which migrated via horizontal gene transfers between archaea and bacteria.JOURNAL, Gogarten, Johann Peter, Deamer, David, Is LUCA a thermophilic progenote?, Nature Microbiology, 1, 12, 2016, 16229, 10.1038/nmicrobiol.2016.229, 27886195,

See also

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Remark

References

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External links

{{Origin of life}}{{Evolution}}

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