Advertisement

Astrobiology pp 91-103 | Cite as

The Common Ancestor of All Modern Life

  • Satoshi AkanumaEmail author
Chapter

Abstract

All modern organisms on Earth share a common mechanism for replication and expression of genetic material. Given the complexity of the genetic mechanism, it seems unlikely that the same construct developed independently in different organisms. Therefore, a reasonable hypothesis is that all modern organisms on Earth are descendants of a single common ancestral organism, and the common ancestor already had the basic genetic mechanism found in modern organisms. A phylogenetic tree that illustrates the evolutionary paths of organisms also shows that all existing organisms originate from a single root that is located between the last common archaeal and bacterial ancestors. Recently published articles on the universal ancestor suggest that it was an anaerobic autotroph dependent on H2 and CO2 from geochemical sources and surrounded by a cell membrane similar to those found in modern bacteria and eukaryotes. In contrast to conflicting conclusions of in silico studies on the environmental temperature of the universal ancestor, reconstruction of ancestral protein sequences and characterization of their properties in vitro suggest that the universal ancestor was a thermophile or hyperthermophile that thrived at a very high temperature. Future research may continue to revise these predictions of features associated with the universal ancestor.

Keywords

Anaerobic autotroph Ancestral sequence reconstruction Cell membrane Single ancestry Thermophilicity 

References

  1. Achenbach-Richter L, Gupta R, Zillig W, Woese CR (1988) Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution. Syst Appl Microbiol 10:231–240CrossRefGoogle Scholar
  2. Akanuma S (2017) Characterization of reconstructed ancestral proteins suggests a change in temperature of the ancient biosphere. Life (Basel, Switzerland) 7(3). doi: https://doi.org/10.3390/life7030033 CrossRefGoogle Scholar
  3. Akanuma S, Nakajima Y, Yokobori S, Kimura M, Nemoto N, Mase T, Miyazono K, Tanokura M, Yamagishi A (2013a) Experimental evidence for the thermophilicity of ancestral life. Proc Natl Acad Sci USA 110(27):11067–11072.  https://doi.org/10.1073/pnas.1308215110 CrossRefPubMedGoogle Scholar
  4. Akanuma S, Yokobori S, Yamagishi A (2013b) Comparative genomics of thermophilic bacteria and archaea. In: Satyanarayana T, Litterchild J, Kawarabayasi Y (eds) Thermophilic microbes in environmental and industrial biotechnology. Springer, Dordrecht, pp 331–349CrossRefGoogle Scholar
  5. Akanuma S, Yokobori S, Nakajima Y, Bessho M, Yamagishi A (2015) Robustness of predictions of extremely thermally stable proteins in ancient organisms. Evol Intl J Org Evol 69(11):2954–2962.  https://doi.org/10.1111/evo.12779 CrossRefGoogle Scholar
  6. Bell EA, Boehnke P, Harrison TM, Mao WL (2015) Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. Proc Natl Acad Sci USA 112(47):14518–14521.  https://doi.org/10.1073/pnas.1517557112 CrossRefPubMedGoogle Scholar
  7. Blanquart S, Lartillot N (2008) A site- and time-heterogeneous model of amino acid replacement. Mol Biol Evol 25(5):842–858.  https://doi.org/10.1093/molbev/msn018 CrossRefGoogle Scholar
  8. Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M (2008) Parallel adaptations to high temperatures in the Archaean eon. Nature 456(7224):942–945.  https://doi.org/10.1038/nature07393 CrossRefPubMedGoogle Scholar
  9. Brooks DJ, Fresco JR, Singh M (2004) A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics (Oxford, England) 20(14):2251–2257.  https://doi.org/10.1093/bioinformatics/bth235 CrossRefGoogle Scholar
  10. Brown JR, Doolittle WF (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92(7):2441–2445CrossRefGoogle Scholar
  11. Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM (2013) Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 8(12):e84300.  https://doi.org/10.1371/journal.pone.0084300 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Cavalier-Smith T (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52(Pt 1):7–76.  https://doi.org/10.1099/00207713-52-1-7 CrossRefPubMedGoogle Scholar
  13. Cavalier-Smith T (2006a) Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond Ser B Biol Sci 361(1470):969–1006.  https://doi.org/10.1098/rstb.2006.1842 CrossRefGoogle Scholar
  14. Cavalier-Smith T (2006b) Rooting the tree of life by transition analyses. Biol Direct 1:19.  https://doi.org/10.1186/1745-6150-1-19 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Cavalier-Smith T (2010) Deep phylogeny, ancestral groups and the four ages of life. Philos Trans R Soc Lond Ser B Biol Sci 365(1537):111–132.  https://doi.org/10.1098/rstb.2009.0161 CrossRefGoogle Scholar
  16. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science (New York, NY) 311(5765):1283–1287.  https://doi.org/10.1126/science.1123061 CrossRefGoogle Scholar
  17. Cleaves HJ 2nd (2010) The origin of the biologically coded amino acids. J Theor Biol 263(4):490–498.  https://doi.org/10.1016/j.jtbi.2009.12.014 CrossRefPubMedGoogle Scholar
  18. Cornish-Bowden A, Cardenas ML (2017) Life before LUCA. J Theor Biol.  https://doi.org/10.1016/j.jtbi.2017.05.023 CrossRefGoogle Scholar
  19. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM (2008) The archaebacterial origin of eukaryotes. Proc Natl Acad Sci USA 105(51):20356–20361.  https://doi.org/10.1073/pnas.0810647105 CrossRefPubMedGoogle Scholar
  20. Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. Murray, LondonGoogle Scholar
  21. Di Giulio M (2000) The universal ancestor lived in a thermophilic or hyperthermophilic environment. J Theor Biol 203(3):203–213.  https://doi.org/10.1006/jtbi.2000.1086 CrossRefPubMedGoogle Scholar
  22. Di Giulio M (2003) The universal ancestor and the ancestor of bacteria were hyperthermophiles. J Mol Evol 57(6):721–730.  https://doi.org/10.1007/s00239-003-2522-6 CrossRefPubMedGoogle Scholar
  23. Di Giulio M (2006) The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA). J Theor Biol 240(3):343–352.  https://doi.org/10.1016/j.jtbi.2005.09.023 CrossRefPubMedGoogle Scholar
  24. Dibrova DV, Galperin MY, Mulkidjanian AY (2014) Phylogenomic reconstruction of archaeal fatty acid metabolism. Environ Microbiol 16(4):907–918.  https://doi.org/10.1111/1462-2920.12359 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Dodd MS, Papineau D, Grenne T, Slack JF, Rittner M, Pirajno F, O’Neil J, Little CT (2017) Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 543(7643):60–64.  https://doi.org/10.1038/nature21377 CrossRefPubMedGoogle Scholar
  26. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science (New York, NY) 284(5423):2124–2129CrossRefGoogle Scholar
  27. Doolittle WF, Brown JR (1994) Tempo, mode, the progenote, and the universal root. Proc Natl Acad Sci USA 91(15):6721–6728CrossRefGoogle Scholar
  28. Edwards RJ, Shields DC (2004) GASP: gapped ancestral sequence prediction for proteins. BMC Bioinforma 5:123.  https://doi.org/10.1186/1471-2105-5-123 CrossRefGoogle Scholar
  29. Feng DF, Cho G, Doolittle RF (1997) Determining divergence times with a protein clock: update and reevaluation. Proc Natl Acad Sci USA 94(24):13028–13033CrossRefGoogle Scholar
  30. Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci USA 103(10):3669–3674.  https://doi.org/10.1073/pnas.0510333103 CrossRefPubMedGoogle Scholar
  31. Fournier GP, Andam CP, Alm EJ, Gogarten JP (2011) Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig Life Evol Biosph J Int Soc Study Orig Life 41(6):621–632.  https://doi.org/10.1007/s11084-011-9261-2 CrossRefGoogle Scholar
  32. Fournier GP, Andam CP, Gogarten JP (2015) Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol 15:70.  https://doi.org/10.1186/s12862-015-0350-0 CrossRefPubMedPubMedCentralGoogle Scholar
  33. Furukawa R, Nakagawa M, Kuroyanagi T, Yokobori SI, Yamagishi A (2017) Quest for ancestors of eukaryal cells based on phylogenetic analyses of aminoacyl-tRNA synthetases. J Mol Evol 84(1):51–66.  https://doi.org/10.1007/s00239-016-9768-2 CrossRefPubMedGoogle Scholar
  34. Galtier N, Tourasse N, Gouy M (1999) A nonhyperthermophilic common ancestor to extant life forms. Science (New York, NY) 283(5399):220–221CrossRefGoogle Scholar
  35. Gaucher EA, Thomson JM, Burgan MF, Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(6955):285–288.  https://doi.org/10.1038/nature01977 CrossRefPubMedGoogle Scholar
  36. Gaucher EA, Govindarajan S, Ganesh OK (2008) Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451(7179):704–707.  https://doi.org/10.1038/nature06510 CrossRefPubMedGoogle Scholar
  37. Gaucher EA, Kratzer JT, Randall RN (2010) Deep phylogeny – how a tree can help characterize early life on Earth. Cold Spring Harb Perspect Biol 2(1):a002238.  https://doi.org/10.1101/cshperspect.a002238 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole RJ, Date T, Oshima T et al (1989) Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86(17):6661–6665CrossRefGoogle Scholar
  39. Groussin M, Hobbs JK, Szollosi GJ, Gribaldo S, Arcus VL, Gouy M (2015) Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Mol Biol Evol 32(1):13–22.  https://doi.org/10.1093/molbev/msu305 CrossRefPubMedGoogle Scholar
  40. Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13(3):407–412.  https://doi.org/10.1101/gr.652803 CrossRefPubMedPubMedCentralGoogle Scholar
  41. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86(23):9355–9359CrossRefGoogle Scholar
  42. Kandler O (1995) Cell wall biochemistry in Archaea and its phylogenetic implications. J Biol Phys 20(1):165–169.  https://doi.org/10.1007/bf00700433 CrossRefGoogle Scholar
  43. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780.  https://doi.org/10.1093/molbev/mst010 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Lake JA, Servin JA, Herbold CW, Skophammer RG (2008) Evidence for a new root of the tree of life. Syst Biol 57(6):835–843.  https://doi.org/10.1080/10635150802555933 CrossRefPubMedGoogle Scholar
  45. Lake JA, Skophammer RG, Herbold CW, Servin JA (2009) Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond Ser B Biol Sci 364(1527):2177–2185.  https://doi.org/10.1098/rstb.2009.0035 CrossRefGoogle Scholar
  46. Longo LM, Lee J, Blaber M (2013) Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proc Natl Acad Sci USA 110(6):2135–2139.  https://doi.org/10.1073/pnas.1219530110 CrossRefPubMedGoogle Scholar
  47. Merkl R, Sterner R (2016) Ancestral protein reconstruction: techniques and applications. Biol Chem 397(1):1–21.  https://doi.org/10.1515/hsz-2015-0158 CrossRefPubMedGoogle Scholar
  48. Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science (New York, NY) 117(3046):528–529CrossRefGoogle Scholar
  49. Miyazaki J, Nakaya S, Suzuki T, Tamakoshi M, Oshima T, Yamagishi A (2001) Ancestral residues stabilizing 3-isopropylmalate dehydrogenase of an extreme thermophile: experimental evidence supporting the thermophilic common ancestor hypothesis. J Biochem 129(5):777–782CrossRefGoogle Scholar
  50. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93(19):10268–10273CrossRefGoogle Scholar
  51. Nisbet EG, Sleep NH (2001) The habitat and nature of early life. Nature 409(6823):1083–1091.  https://doi.org/10.1038/35059210 CrossRefPubMedGoogle Scholar
  52. Nutman AP, Bennett VC, Friend CR, Van Kranendonk MJ, Chivas AR (2016) Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures. Nature 537(7621):535–538.  https://doi.org/10.1038/nature19355 CrossRefPubMedGoogle Scholar
  53. Pace NR (1991) Origin of life – facing up to the physical setting. Cell 65(4):531–533CrossRefGoogle Scholar
  54. Pereto J, Lopez-Garcia P, Moreira D (2004) Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem Sci 29(9):469–477.  https://doi.org/10.1016/j.tibs.2004.07.002 CrossRefPubMedGoogle Scholar
  55. Philip GK, Freeland SJ (2011) Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology 11(3):235–240.  https://doi.org/10.1089/ast.2010.0567 CrossRefPubMedGoogle Scholar
  56. Randau L, Munch R, Hohn MJ, Jahn D, Soll D (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433(7025):537–541.  https://doi.org/10.1038/nature03233 CrossRefPubMedGoogle Scholar
  57. Raymann K, Brochier-Armanet C, Gribaldo S (2015) The two-domain tree of life is linked to a new root for the Archaea. Proc Natl Acad Sci USA 112(21):6670–6675.  https://doi.org/10.1073/pnas.1420858112 CrossRefPubMedGoogle Scholar
  58. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431–437.  https://doi.org/10.1038/nature12352 CrossRefGoogle Scholar
  59. Rivera MC, Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science (New York, NY) 257(5066):74–76CrossRefGoogle Scholar
  60. Rosing MT (1999) 13C-depleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from West Greenland. Science (New York, NY) 283(5402):674–676CrossRefGoogle Scholar
  61. Schopf JW (1993) Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science (New York, NY) 260:640–646CrossRefGoogle Scholar
  62. Shen Y, Buick R, Canfield DE (2001) Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410(6824):77–81.  https://doi.org/10.1038/35065071 CrossRefGoogle Scholar
  63. Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A (2007) Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus. J Mol Biol 369(4):1060–1069.  https://doi.org/10.1016/j.jmb.2007.04.001 CrossRefPubMedGoogle Scholar
  64. Stetter KO (2006) Hyperthermophiles in the history of life. Philos Trans R Soc Lond Ser B Biol Sci 361(1474):1837–1842.; discussion 1842–1833.  https://doi.org/10.1098/rstb.2006.1907 CrossRefGoogle Scholar
  65. Theobald DL (2010) A formal test of the theory of universal common ancestry. Nature 465(7295):219–222.  https://doi.org/10.1038/nature09014 CrossRefPubMedGoogle Scholar
  66. Thornton JW (2004) Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 5(5):366–375.  https://doi.org/10.1038/nrg1324 CrossRefPubMedGoogle Scholar
  67. Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y (2006) Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440(7083):516–519.  https://doi.org/10.1038/nature04584 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Wacey D, McLoughlin N, Green OR, Parnell J, Stoakes CA, Brasier MD (2006) The ~3.4 billion-year-old Strelley Pool Sandstone: a new window into early life on Earth. Int J Astrobiol 5(04):333.  https://doi.org/10.1017/s1473550406003466 CrossRefGoogle Scholar
  69. Watanabe K, Ohkuri T, Yokobori S, Yamagishi A (2006) Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree. J Mol Biol 355(4):664–674.  https://doi.org/10.1016/j.jmb.2005.10.011 CrossRefPubMedGoogle Scholar
  70. Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF (2016) The physiology and habitat of the last universal common ancestor. Nat Microbiol 1(9):16116.  https://doi.org/10.1038/nmicrobiol.2016.116 CrossRefPubMedGoogle Scholar
  71. Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504(7479):231–236.  https://doi.org/10.1038/nature12779 CrossRefPubMedGoogle Scholar
  72. Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271PubMedPubMedCentralGoogle Scholar
  73. Woese CR, Fox GE (1977) The concept of cellular evolution. J Mol Evol 10(1):1–6CrossRefGoogle Scholar
  74. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87(12):4576–4579CrossRefGoogle Scholar
  75. Yamagishi A, Kon T, Takahashi G, Oshima T (1998) From the common ancestor of all living organisms to protoeukaryotic cell. In: Wiegel J, Adams MWW (eds) Thermophiles: the keys to molecular evolution and the origin of life? Taylor & Francis, LondonGoogle Scholar
  76. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci CABIOS 13(5):555–556PubMedGoogle Scholar
  77. Yokobori SI, Nakajima Y, Akanuma S, Yamagishi A (2016) Birth of archaeal cells: molecular phylogenetic analyses of G1P dehydrogenase, G3P dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having G1P polar lipids. Archaea (Vancouver, BC) 2016:1802675.  https://doi.org/10.1155/2016/1802675 CrossRefGoogle Scholar
  78. Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV (2008) The deep archaeal roots of eukaryotes. Mol Biol Evol 25(8):1619–1630.  https://doi.org/10.1093/molbev/msn108 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Faculty of Human SciencesWaseda UniversityTokorozawaJapan

Personalised recommendations