Reconstructing the Last Universal Common Ancestor
There is general agreement that bacteria, archaea, and eukarya share common ancestry. However, tracing back extant lineages to reconstruct the ancestral gene set of the three domains has proven to be non-trivial, as there is little unambiguous signal this far back in time. In this chapter, I explain the basic principles behind reconstruction of the Last Universal Common Ancestor (LUCA) and summarise a few of the challenges associated with reconstruction. Finally, I consider whether a mid-resolution LUCA might be the most achievable goal, particularly from the perspective of the classes of chemistry available to early life.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Subscribe and save
Springer+ Basic
€32.70 /Month
- Get 10 units per month
- Download Article/Chapter or eBook
- 1 Unit = 1 Article or 1 Chapter
- Cancel anytime
Buy Now
Price includes VAT (France)
eBook EUR 117.69 Price includes VAT (France)
Softcover Book EUR 147.69 Price includes VAT (France)
Hardcover Book EUR 147.69 Price includes VAT (France)
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA’s (Last UCA) Lineage
Chapter © 2019
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor
Article Open access 18 July 2024
Concepts of the last eukaryotic common ancestor
Article 18 February 2019
References
- Andam, C.P., Williams, D., Gogarten, J.P.: Natural taxonomy in light of horizontal gene transfer. Biol. Philos. 25(4), 589–602 (2010) ArticleGoogle Scholar
- Beringer, M., Rodnina, M.V.: The ribosomal peptidyl transferase. Mol. Cell. 26(3), 311–321 (2007) ArticleGoogle Scholar
- Berkemer, S.J., McGlynn, S.E.: A new analysis of archaea-bacteria domain separation: variable phylogenetic distance and the tempo of early evolution. Mol. Biol. Evol. 37(8), 2332–2340 (2020) ArticleGoogle Scholar
- Boerlijst, M.C., Hogeweg, P.: Spiral wave structure in pre-biotic evolution: Hypercycles stable against parasites. Phys. D. 48(1), 17–28 (1991) ArticleMATHGoogle Scholar
- Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N., Gouy, M.: Parallel adaptations to high temperatures in the Archaean eon. Nature. 456(7224), 942–945 (2008) ArticleADSGoogle Scholar
- Brindefalk, B., Dessailly, B.H., Yeats, C., Orengo, C., Werner, F., Poole, A.M.: Evolutionary history of the TBP-domain superfamily. Nucleic Acids Res. 41(5), 2832–2845 (2013) ArticleGoogle Scholar
- Caetano-Anollés, G., Caetano-Anollés, D.: An evolutionarily structured universe of protein architecture. Genome Res. 13(7), 1563–1571 (2003) ArticleGoogle Scholar
- Caetano-Anollés, G., Kim, H.S., Mittenthal, J.E.: The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc. Natl. Acad. Sci. USA. 104(22), 9358–9363 (2007) ArticleADSGoogle Scholar
- Caetano-Anollés, G., Mittenthal, J.E., Caetano-Anollés, D., Kim, K.M.: A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity. Front. Genet. 5, 306 (2014) Google Scholar
- Cermakian, N., Cedergren, R.: Modified nucleotides always were: an evolutionary model. In: Grosjean, H., Benne, R. (eds.) Modification and Editing of RNA, pp. 535–541. ASM Press, Washington, DC (1998) Google Scholar
- Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B., Bork, P.: Toward automatic reconstruction of a highly resolved tree of life. Science. 311(5765), 1283–1287 (2006) ArticleADSGoogle Scholar
- Coleman, G.A., Pancost, R.D., Williams, T.A.: Investigating the origins of membrane phospholipid biosynthesis genes using outgroup-free rooting. Genome Biol. Evol. 11(3), 883–898 (2019) ArticleGoogle Scholar
- Copley, S.D.: Moonlighting is mainstream: paradigm adjustment required. BioEssays. 34(7), 578–588 (2012) ArticleGoogle Scholar
- Dagan, T., Martin, W.: The tree of one percent. Genome Biol. 7(10), 118 (2006) ArticleGoogle Scholar
- Dagan, T., Roettger, M., Bryant, D., Martin, W.: Genome networks root the tree of life between prokaryotic domains. Genome Biol. Evol. 2, 379–392 (2010) ArticleGoogle Scholar
- Doolittle, W.F.: Phylogenetic classification and the universal tree. Science. 284(5423), 2124–2129 (1999) ArticleGoogle Scholar
- Doolittle, W.F.: W. Ford Doolittle. Curr. Biol. 14(5), R176–R177 (2004) ArticleGoogle Scholar
- Forterre, P.: Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol. 33(3), 457–465 (1999) ArticleGoogle Scholar
- Forterre, P.: Genomics and early cellular evolution. The origin of the DNA world. C. R. Acad. Sci. III. 324(12), 1067–1076 (2001) ArticleGoogle Scholar
- Forterre, P.: The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol. 5(5), 525–532 (2002) ArticleGoogle Scholar
- Forterre, P.: The universal tree of life: an update. Front. Microbiol. 6, 717 (2015) ArticleGoogle Scholar
- Forterre, P., Grosjean, H.: The Interplay Between RNA and DNA Modifications: Back to the RNA World. Molecular Biology Intelligence Unit Landes Bioscience. Springer, Austin, TX (2009) Google Scholar
- Forterre, P., Philippe, H.: Where is the root of the universal tree of life? BioEssays. 21(10), 871–879 (1999) ArticleGoogle Scholar
- Forterre, P., Filée, J., Myllykallio, H.: Origin and evolution of DNA and DNA replication machineries. In: de Pouplana, L.R. (ed.) The Genetic Code and the Origin of Life. Landes Bioscience, Georgetown, TX (2004) Google Scholar
- Fullmer, M.S., Soucy, S.M., Gogarten, J.P.: The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis. Front. Microbiol. 6, 728 (2015) ArticleGoogle Scholar
- Galtier, N., Tourasse, N., Gouy, M.: A nonhyperthermophilic common ancestor to extant life forms. Science. 283(5399), 220–221 (1999) ArticleGoogle Scholar
- Gardner, P.P., Bateman, A., Poole, A.M.: SnoPatrol: how many snoRNA genes are there? J. Biol. 9(1), 4 (2010) ArticleGoogle Scholar
- Gaspin, C., Cavaille, J., Erauso, G., Bachellerie, J.P.: Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J. Mol. Biol. 297(4), 895–906 (2000) ArticleGoogle Scholar
- Glansdorff, N., Xu, Y., Labedan, B.: The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol. Direct. 3, 29 (2008) ArticleGoogle Scholar
- Gogarten, J.P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E.J., Bowman, B.J., et al.: Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA. 86(17), 6661–6665 (1989) ArticleADSGoogle Scholar
- Goldman, A.D., Baross, J.A., Samudrala, R.: The enzymatic and metabolic capabilities of early life. PLoS One. 7(9), e39912 (2012) ArticleADSGoogle Scholar
- Goldman, A.D., Bernhard, T.M., Dolzhenko, E., Landweber, L.F.: LUCApedia: a database for the study of ancient life. Nucleic Acids Res. 41(Database issue), D1079–D1082 (2013) Google Scholar
- Gribaldo, S., Brochier-Armanet, C.: Evolutionary relationships between archaea and eukaryotes. Nat. Ecol. Evol. 4(1), 20–21 (2020) ArticleGoogle Scholar
- Gribaldo, S., Poole, A.M., Daubin, V., Forterre, P., Brochier-Armanet, C.: The origin of eukaryotes and their relationship with the archaea: are we at a phylogenomic impasse? Nat. Rev. Microbiol. 8(10), 743–752 (2010) ArticleGoogle Scholar
- Hacker, J., Carniel, E.: Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2(5), 376–381 (2001) ArticleGoogle Scholar
- Harris, J.K., Kelley, S.T., Spiegelman, G.B., Pace, N.R.: The genetic core of the universal ancestor. Genome Res. 13, 407–412 (2003) ArticleGoogle Scholar
- Hoeppner, M.P., Poole, A.M.: Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evol. Biol. 12, 183 (2012) ArticleGoogle Scholar
- Hoeppner, M.P., Gardner, P.P., Poole, A.M.: Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput. Biol. 8(11), e1002752 (2012) ArticleADSGoogle Scholar
- Hogeweg, P., Takeuchi, N.: Multilevel selection in models of prebiotic evolution: compartments and spatial self-organization. Orig. Life Evol. Biosph. 33(4–5), 375–403 (2003) ArticleADSGoogle Scholar
- Illergård, K., Ardell, D.H., Elofsson, A.: Structure is three to ten times more conserved than sequence: a study of structural response in protein cores. Proteins. 77(3), 499–508 (2009) ArticleGoogle Scholar
- Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., Miyata, T.: Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA. 86(23), 9355–9359 (1989) ArticleADSGoogle Scholar
- Jain, R., Rivera, M.C., Lake, J.A.: Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA. 96(7), 3801–3806 (1999) ArticleADSGoogle Scholar
- Jeffares, D.C., Poole, A.M., Penny, D.: Relics from the RNA world. J. Mol. Evol. 46(1), 18–36 (1998) ArticleADSGoogle Scholar
- Jékely, G.: Did the last common ancestor have a biological membrane? Biol. Direct. 1, 35 (2006) ArticleGoogle Scholar
- Jensen, R.A.: Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409–425 (1976) ArticleGoogle Scholar
- Kim, K.M., Caetano-Anollés, G.: Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol. Biol. Evol. 27(7), 1710–1733 (2010) ArticleGoogle Scholar
- King, T.H., Liu, B., McCully, R.R., Fournier, M.J.: Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol. Cell. 11(2), 425–435 (2003) ArticleGoogle Scholar
- Koonin, E.V.: Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1(2), 127 (2003) ArticleMathSciNetGoogle Scholar
- Koonin, E.V., Martin, W.: On the origin of genomes and cells within inorganic compartments. Trends Genet. 21(12), 647–654 (2005) ArticleGoogle Scholar
- Koonin, E.V., Mushegian, A.R., Bork, P.: Non-orthologous gene displacement. Trends Genet. 12(9), 334–336 (1996) ArticleGoogle Scholar
- Koumandou, V.L., Wickstead, B., Ginger, M.L., van der Giezen, M., Dacks, J.B., Field, M.C.: Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48(4), 373–396 (2013) ArticleGoogle Scholar
- Kyrpides, N., Overbeek, R., Ouzounis, C.: Universal protein families and the functional content of the last universal common ancestor. J. Mol. Evol. 49(4), 413–423 (1999) ArticleADSGoogle Scholar
- Lafontaine, D.L., Tollervey, D.: Birth of the snoRNPs: the evolution of the modification-guide snoRNAs. Trends Biochem. Sci. 23(10), 383–388 (1998) ArticleGoogle Scholar
- Lapierre, P., Gogarten, J.P.: Estimating the size of the bacterial pan-genome. Trends Genet. 25(3), 107–110 (2009) ArticleGoogle Scholar
- Lawrence, J.G., Roth, J.R.: Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics. 143(4), 1843–1860 (1996) ArticleGoogle Scholar
- Leipe, D.D., Aravind, L., Koonin, E.V.: Did DNA replication evolve twice independently? Nucleic Acids Res. 27(17), 3389–3401 (1999) ArticleGoogle Scholar
- Lindgreen, S., Umu, S.U., Lai, A.S., Eldai, H., Liu, W., McGimpsey, S., et al.: Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput. Biol. 10(10), e1003907 (2014) ArticleGoogle Scholar
- Lundin, D., Gribaldo, S., Torrents, E., Sjöberg, B.M., Poole, A.M.: Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evol. Biol. 10, 383 (2010) ArticleGoogle Scholar
- Lundin, D., Poole, A.M., Sjöberg, B.M., Hogbom, M.: Use of structural phylogenetic networks for classification of the ferritin-like superfamily. J. Biol. Chem. 287(24), 20565–20575 (2012) ArticleGoogle Scholar
- Malik, A.J., Poole, A.M., Allison, J.R.: Structural phylogenetics with confidence. Mol. Biol. Evol. 37(9), 2711–2726 (2020) ArticleGoogle Scholar
- Myllykallio, H., Lipowski, G., Leduc, D., Filee, J., Forterre, P., Liebl, U.: An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 297(5578), 105–107 (2002) ArticleADSGoogle Scholar
- Neumann, N., Lundin, D., Poole, A.M.: Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS One. 5(10), e13241 (2010) ArticleADSGoogle Scholar
- O’Brien, P.J., Herschlag, D.: Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6(4), R91–R105 (1999) ArticleGoogle Scholar
- Ofengand, J., Bakin, A.: Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266(2), 246–268 (1997) ArticleGoogle Scholar
- Omer, A.D., Lowe, T.M., Russell, A.G., Ebhardt, H., Eddy, S.R., Dennis, P.P.: Homologs of small nucleolar RNAs in archaea. Science. 288(5465), 517–522 (2000) ArticleADSGoogle Scholar
- Penny, D., Poole, A.: The nature of the last universal common ancestor. Curr. Opin. Genet. Dev. 9(6), 672–677 (1999) ArticleGoogle Scholar
- Penny, D., Hoeppner, M.P., Poole, A.M., Jeffares, D.C.: An overview of the introns-first theory. J. Mol. Evol. 69(5), 527–540 (2009) ArticleADSGoogle Scholar
- Peretó, J., López-García, P., Moreira, D.: Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem. Sci. 29(9), 469–477 (2004) ArticleGoogle Scholar
- Poole, A.M.: Getting from an RNA world to modern cells just got a little easier. BioEssays. 28(2), 105–108 (2006) ArticleGoogle Scholar
- Poole, A.M.: Horizontal gene transfer and the earliest stages of the evolution of life. Res. Microbiol. 160(7), 473–480 (2009) ArticleGoogle Scholar
- Poole, A.M., Logan, D.T.: Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol. Biol. Evol. 22(6), 1444–1455 (2005) ArticleGoogle Scholar
- Poole, A.M., Jeffares, D.C., Penny, D.: The path from the RNA world. J. Mol. Evol. 46(1), 1–17 (1998) ArticleADSGoogle Scholar
- Poole, A., Penny, D., Sjöberg, B.M.: Confounded cytosine! Tinkering and the evolution of DNA. Nat. Rev. Mol. Cell Biol. 2(2), 147–151 (2001) ArticleGoogle Scholar
- Poole, A.M., Phillips, M.J., Penny, D.: Prokaryote and eukaryote evolvability. Biosystems. 69(2–3), 163–185 (2003) ArticleGoogle Scholar
- Poole, A.M., Lundin, D., Rytkönen, K.T.: The evolution of early cellular systems viewed through the lens of biological interactions. Front. Microbiol. 6, 1144 (2015) ArticleGoogle Scholar
- Raymann, K., Brochier-Armanet, C., Gribaldo, S.: The two-domain tree of life is linked to a new root for the archaea. Proc. Natl. Acad. Sci. USA. 112(21), 6670–6675 (2015) ArticleADSGoogle Scholar
- Rivera, M.C., Jain, R., Moore, J.E., Lake, J.A.: Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA. 95(11), 6239–6244 (1998) ArticleADSGoogle Scholar
- Shimada, H., Yamagishi, A.: Stability of heterochiral hybrid membrane made of bacterial sn-G3P lipids and archaeal sn-G1P lipids. Biochemistry. 50(19), 4114–4120 (2011) ArticleGoogle Scholar
- Shutt, T.E., Gray, M.W.: Bacteriophage origins of mitochondrial replication and transcription proteins. Trends Genet. 22(2), 90–95 (2006) ArticleGoogle Scholar
- Skophammer, R.G., Servin, J.A., Herbold, C.W., Lake, J.A.: Evidence for a gram-positive, eubacterial root of the tree of life. Mol. Biol. Evol. 24(8), 1761–1768 (2007) ArticleGoogle Scholar
- Snel, B., Bork, P., Huynen, M.A.: Genome phylogeny based on gene content. Nat. Genet. 21(1), 108–110 (1999) ArticleGoogle Scholar
- Soo, V.W., Hanson-Manful, P., Patrick, W.M.: Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc. Natl. Acad. Sci. USA. 108(4), 1484–1489 (2011) ArticleADSGoogle Scholar
- Spang, A., Saw, J.H., Jorgensen, S.L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A.E., et al.: Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 521(7551), 173–179 (2015) ArticleADSGoogle Scholar
- Stern, A., Mayrose, I., Penn, O., Shaul, S., Gophna, U., Pupko, T.: An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst. Biol. 59(2), 212–225 (2010) ArticleGoogle Scholar
- Szathmáry, E., Demeter, L.: Group selection of early replicators and the origin of life. J. Theor. Biol. 128(4), 463–486 (1987) ArticleADSGoogle Scholar
- Vetsigian, K., Woese, C., Goldenfeld, N.: Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA. 103(28), 10696–10701 (2006) ArticleADSGoogle Scholar
- Villanueva, L., von Meijenfeldt, F.A.B., Westbye, A.B., Yadav, S., Hopmans, E.C., Dutilh, B.E., et al.: Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids. ISME J. 15, 168–182 (2020) ArticleGoogle Scholar
- Warner, J.R., McIntosh, K.B.: How common are extraribosomal functions of ribosomal proteins? Mol. Cell. 34(1), 3–11 (2009) ArticleGoogle Scholar
- Weiss, M.C., Sousa, F.L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S., et al.: The physiology and habitat of the last universal common ancestor. Nat. Microbiol. 1(9), 16116 (2016) ArticleGoogle Scholar
- White 3rd., H.B.: Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7(2), 101–104 (1976) ArticleADSGoogle Scholar
- Williams, T.A., Cox, C.J., Foster, P.G., Szollosi, G.J., Embley, T.M.: Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol. Evol. 4(1), 138–147 (2020) ArticleGoogle Scholar
- Woese, C.: The universal ancestor. Proc. Natl. Acad. Sci. USA. 95(12), 6854–6859 (1998) ArticleADSGoogle Scholar
- Woese, C.R., Fox, G.E.: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA. 74(11), 5088–5090 (1977) ArticleADSGoogle Scholar
- Woese, C.R., Kandler, O., Wheelis, M.L.: Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc. Natl. Acad. Sci. USA. 87(12), 4576–4579 (1990) ArticleADSGoogle Scholar
- Wool, I.G.: Extraribosomal functions of ribosomal proteins. Trends Biochem. Sci. 21(5), 164–165 (1996) ArticleGoogle Scholar
- Zaremba-Niedzwiedzka, K., Caceres, E.F., Saw, J.H., Backstrom, D., Juzokaite, L., Vancaester, E., et al.: Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 541(7637), 353–358 (2017) ArticleADSGoogle Scholar
- Zintzaras, E., Santos, M., Szathmáry, E.: “Living” under the challenge of information decay: the stochastic corrector model vs. hypercycles. J. Theor. Biol. 217(2), 167–181 (2002) ArticleMathSciNetADSGoogle Scholar
Author information
Authors and Affiliations
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand Anthony M. Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand Anthony M. Poole
- Te Ao Mārama Centre for Fundamental Inquiry, University of Auckland, Auckland, New Zealand Anthony M. Poole
- Anthony M. Poole