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Ancient Paralogous Duplications and the Search for Archean Cells

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Book cover Self-Production of Supramolecular Structures

Part of the book series: NATO ASI Series ((ASIC,volume 446))

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Abstract

A detailed examination of traits common to the three cell lineages suggests that their last common ancestor was not an inmediate, direct descendant of the RNA world, but rather a complex cell comparable in many ways to modern prokaryotes. The phylogenetic analysis of sets of duplicated genes common to the three major branches of evolutionary trees provides insights into the characteristics of their cell-like ancestors, which appear to have been endowed with simpler metabolic abilities and a less complex replication apparatus. Such molecular explorations in the early stages of cell evolution may provide useful constraints that will aid in the design of experimental approaches to the understanding of the origin of the first self-sustaining, self-replicating biological systems.

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References

  • Achenbach-Richter L, Gupta R, Kandier KO, Woese CR. 1987. Were the original eubacteria thermophiles? System Appl hticrobiol 9:34–39.

    Article  CAS  Google Scholar 

  • Allison LA, Moyle M, Shales M, Ingles CJ. 1985. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42: 599–610.

    Article  CAS  Google Scholar 

  • Bachmann PA, Luisi PL, Lang J. 1992. Autocatalytic self replicating micelles as models for prebiotic structures. Nature 357:57–59.

    Article  CAS  Google Scholar 

  • Beckler GS, Reeve JN. 1986. Conservation of primary structure in the hisI gene of the archaebacterium Methanococcus vannielii, the eubacterium Escherichia coli, and the eucaryoteSaccharomyces cerevisiae. Mol Gen Genet 204:133–140.

    Article  CAS  Google Scholar 

  • Belozerskii AN. 1959. On the species specificity of the nucleic acids of bacteria. In: AI Oparin, AG Pasynskii, AE Braunshtein, TE Pavloskaya, eds., The Origin of Life on the Earth. New York: Pergamon Press, pp.322–331.

    Google Scholar 

  • Benachenhou-Lahfa N, Forterre P, Labedan B. 1993. Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J Mol Evol 36:335–346.

    Article  CAS  Google Scholar 

  • Benner SA, Cohen MA, Gonnet GH, Berkowitz DB, Johnsson KP. 1993. Reading the palimpsest: contemporary biochemical data and the RNA world. In: RF Gesteland, JF Atkins, eds. The RNA World. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, pp.27–70.

    Google Scholar 

  • Blanco L, Bernard A, Blasco MA, Salas M. 1991. A general structure for DNA-dependent DNA polymerases. Gene 100:27–38.

    Article  CAS  Google Scholar 

  • Brachet J. 1959. Les acides nucléiques et l’origine des protéines. In: AI Oparin, AG Pasynskii, AE Braunshtein, TE Pavloskaya, eds., The Origin of Life on the Earth. New York: Pergamon Press, pp.361–367.

    Google Scholar 

  • Chang YY, Cronan JE. 1988. Common ancestry of Escherichia colii pyruvate oxidase and the acetohydroxy acid synthases of the branched-chain amino acid biosynthetic pathways. J Bacteriol 170:3937–3945.

    CAS  Google Scholar 

  • Confalonieri F, Elie Ch, Nadal M, Bouthier de La Tour C, Forterre P, Duguet M. 1993. Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide. Proc Natl Acad Sci USA 90:4753–4758.

    Article  CAS  Google Scholar 

  • Danson MJ. 1988. Archaebacteria: The comparative enzymology of their central metabolic pathways. Adv Microbial Physiol 29: 165–231.

    Article  CAS  Google Scholar 

  • Darst SA, Kubalek EW, Kornberg RD. 1989. Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature 340:730–732.

    Article  CAS  Google Scholar 

  • Delarue M, Poch O, Tordo N, Moras D, Argos P. 1990. An attempt to unify the structure of polymerases. Protein Engineering 3:461–467.

    Article  CAS  Google Scholar 

  • Fani R, Lió P, Chiarelli I, Bazzicalupo M.1993. The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J Mol Evol:(In press).

    Google Scholar 

  • Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst Zool 19:127–113.

    Article  Google Scholar 

  • Forterre P, Benachenhou-Lahfa N, Confalonieri F, Duguet M, Elie Ch,Labedan B. 1993. The nature of the last universal ancestor and the root of the tree of life, still open questions. BioSystems 28: 15–32.

    Article  Google Scholar 

  • Forterre P, Bergerat A, Gadelle D, Elie C, Lorrspeich F, Confalonieri F, Duguet M, Holmes M, Dyall Smith M. 1994. Evolution of DNA topoisomerases and DNA polymerases: a perspective from Archaea. Syst Appl Microbiol:(ln press).

    Google Scholar 

  • Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole JR, Date T, Oshima T, Konishi J, Denda K, Yoshida M. 1989. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86:6661–6665.

    Article  CAS  Google Scholar 

  • Gupta RS, Singh B. 1992. Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model of the evolution of the HSP70 gene. J Bacteriol 174:4594–4605.

    CAS  Google Scholar 

  • Harvey PH, Pagel MD. 1991. The Comparative Method in Evolutionary Biology. Oxford: Oxford University Press.

    Google Scholar 

  • Hilario E, Gogarten JP. 1993. Horizontal transfer of ATPase genes: the tree of life becomes the net of life. BioSystems:(In press).

    Google Scholar 

  • Holm NG, ed. 1992. Marine Hydrothermal Systems and the Origin of Life. Dordrecht: Kluwer Academic Publ.

    Google Scholar 

  • Hong JI, Feng Q, Rotello V, Rebek, J Jr. 1992. Competition, cooperation, and mutation: improving a synthetic replicator by light irradiation. Science 255:848–850.

    Article  CAS  Google Scholar 

  • Ito J, Braithwaite DK. 1991. Compilation and alignment of DNA polymerase sequences. Nucleic Acid Res 19:4045–4057.

    Article  CAS  Google Scholar 

  • 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 86:9355–9359.

    Article  CAS  Google Scholar 

  • Iwasaki H, Ishino Y, Toh H, Nakata A, Shinagawa H. 1991. Escherichia coli DNA polymerase II is homologous to α-like DNA polymerases. Mol Gen Genet 226:24–33.

    Article  CAS  Google Scholar 

  • Jensen RA. 1976. Enzyme recruitment in evolution of new function. Ann Rev Microbiol 30:409–427.

    Article  CAS  Google Scholar 

  • Jordana X, Chatton B, Paz-Weisshaar M, Buhler JM, Cramer F, Ebel JP, Fasiolo F. 1987. Structure of the yeast valyl-tRNA synthetase gene (VASI) and the homology of its translated amino acid sequence with Escherichia coli isoleucyl-tRNA synthetase. J Biol Chem 262:7189–7194.

    CAS  Google Scholar 

  • Joyce GF, Schwartz AW, Miller SL, Orgel LE. 1987. The case for an ancestral genetic system involving simple analogues of the nucleotides. Proc Natl Acad Sci USA 84:4398–4402.

    Article  CAS  Google Scholar 

  • Kandier O. 1993. The early diversification of life. In: S. Bengtson, ed., Early Life on Earth: Nobel Symposium No. 84. New York: Columbia University Press. (In press).

    Google Scholar 

  • Kerschel L, Oesterhelt D. 1986. Pyruvate: ferrodoxin oxidoreductase new findings on an ancient enzyme. Trends Biochem Sci 7:371–374.

    Article  Google Scholar 

  • Klenk HP, Palm P, Lottspeich F, Zillig W. 1992. Component H of the DNA-dependent RNA polymerase of Archea is homologous to a subunit shared by the three eucaryal nuclear RNA polymerases. Proc Natl Acad Sci USA 89:407–410.

    Article  CAS  Google Scholar 

  • Klenow H, Hennington I. 1970. Selective elimination of the exonuclease activity of the DNA polymerase from E. coli B by a limited proteolysis. Proc Natl Acad Sci USA 65:168–175.

    Article  CAS  Google Scholar 

  • Kletzin A. 1992. Molecular characterization of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acid Res 20:5389–5396.

    Article  CAS  Google Scholar 

  • Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. 1992. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783–1790.

    Article  CAS  Google Scholar 

  • Kornberg A, Baker T. 1992. DNA Replication. San Francisco: Freeman Co.

    Google Scholar 

  • Kumada Y, Benson DR, Hillemannm D, Hosted TJ, Rochford DA, Thompson CJ, Wohlleben W, Tateno Y. 1993. Evolution of the glutamine synthase gene, one of the oldest existing and functioning genes. Proc Natl Acad Sci USA 90: 3009–3013.

    Article  CAS  Google Scholar 

  • Lam WL, Cohen A, Tsouluhas D, Doolittle WF. 1990. Genes for tryptophan biosynthesis in the archaebacterium Haloferax volcanii. Proc Natl Acad Sci USA 87:6614–6618.

    Article  CAS  Google Scholar 

  • Lazcano A. 1993a. The RNA world, its predecessors and descendants.In: S Bengtson ed., Early Life on Earth: Nobel Symposium No. 84. New York: Columbia University Press (In press).

    Google Scholar 

  • Lazcano A. 1993b. Biogenesis: Some like it very hot Science 260: 1154–1155.

    Article  CAS  Google Scholar 

  • Lazcano A. 1993c. The transition from non-living to living. In: S Bengtson ed., Early Life on Earth: Nobel Symposium No. 84. New York: Columbia University Press (In press).

    Google Scholar 

  • Lazcano A. 1994. The significance of ancient paralogous genes in the study of the early stages of microbial evolution. In: R Guerrer, C Pedrós-Alios, eds., Proceedings of the Sixth International Meeting on Microbial Ecology. Barcelona: Barcelona University Press (In press).

    Google Scholar 

  • Lazcano A, Díaz-Villagómez E, Mills T, Oró J. 1993. On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways. Adv Space Res (In press).

    Google Scholar 

  • Lazcano A, Fox GE, Oró J. 1992. Life before DNA: the origin and evolution of early Archean cells. In: R. P. Mortlock ed., The Evolution of Metabolic Function. Boca Raton: CRC Press, pp. 237–295.

    Google Scholar 

  • Lazcano A, Guerrero R, Margulis L, Oró L. 1988. The evolutionary transition from RNA to DNA on early cells. J Mol Evol 27: 283–290.

    Article  CAS  Google Scholar 

  • Lazcano A, Fastag J, Gariglio P, Ramirez C, Oró J. 1988. On the early evolution of RNA polymerase. J Mol Evol 27:365–376.

    Article  CAS  Google Scholar 

  • Lenard J. 1992. Mammalian hormones in microbial cells. Trends Biochem Sci 17: 147–150.

    Article  CAS  Google Scholar 

  • March PE, Inouye M. 1985. Characterization of the lep operon of Escherichia coli. J Biol Chem 260:7206–7213.

    CAS  Google Scholar 

  • Mathur EJ, Adams MWW, Callen WN, Cline JN. 1991. The DNA polymerase from the hyperthermophilic marine archaebacterium, Pyrococcus furiosus, shows sequence homology to a-like DNA polymerase. Nucleic Acid Res 19: 6952.

    Article  CAS  Google Scholar 

  • Miller SL, Bada JL. 1988. Submarine hot springs and the origin of life. Nature 334: 609–611.

    Article  Google Scholar 

  • Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA. 1985. Structure of the large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313:762–766.

    Article  CAS  Google Scholar 

  • Orgel LE. 1992. Molecular replication. Nature 358:203–209.

    Article  CAS  Google Scholar 

  • Oró J, Lazcano A. 1984. A minimal living system and the origin of a protocell. Adv Space Res 4:167–176.

    Article  Google Scholar 

  • Ouzonis C, Sander C. 1992. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell 71:189–190.

    Article  Google Scholar 

  • Pace NR. 1991. Origin of life -facing up to the physical setting. Cell 65:531–533.

    Article  CAS  Google Scholar 

  • Palenik B. 1992. Polymerase evolution and organism evolution. Curr Opinion Genet Develop 2:931–936.

    Article  CAS  Google Scholar 

  • Puhler G, Leffers H, Gropp F, Palm P, Klenk HP, Lottspeich F, Garrett RA, Zillig W. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc Natl Acad Sci USA 86:4569–4573.

    Article  CAS  Google Scholar 

  • Reichard P. 1993. From RNA to DNA, why so many ribonucleotide reductases? Science 260:1773–1777.

    Article  CAS  Google Scholar 

  • Richetti M, Buc H. 1993. E. coli DNA polymerase I as a reverse transcriptase. EMBO Jour 12:387–396.

    Google Scholar 

  • Schofield JP. 1993. Molecular studies on an ancient gene encoding for carbamoyl-phosphate synthetase. Clin Sci 84:119–128.

    CAS  Google Scholar 

  • Schopf JW. 1993. The oldest known records of life: Early Archean stromatolites, microfossils and organic matter. In: S. Bengtson, ed., Early Life on Earth: Nobel Symposium No. 84. New York: Columbia University Press (In press).

    Google Scholar 

  • Schwartz RM, Dayhoff MO. 1978. Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts. Science 199:395–403.

    Article  CAS  Google Scholar 

  • Segerer AH, Burograf S, Fiala G, Huber G, Huber R, Pley U, Stetter KO. 1993. Life in hot springs and hydrothermal vents. Orig Life Evol Bios 23:77–90.

    Article  CAS  Google Scholar 

  • Slesarev AI, Stetter KO, Lake JA, Geliert M, Krah A, Kozyavkin SA. 1993. DNA topoisomerase V is a a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote. 1993. Nature 364:735.

    Article  CAS  Google Scholar 

  • Steitz TA, Beese L, Breemont PS, Friedman JM, Sanderson MR. 1987. Structural studies of Klenow fragment: an enzyme with two active sites. Cold Spring Harbor Symp Quant Biol 52:465–471.

    Article  CAS  Google Scholar 

  • Stetter KO 1993. The lesson of archaebacteria. In: S. Bengtson, ed., Early Life on Earth: Nobel Symposium No. 84. New York: Columbia University Press (In press).

    Google Scholar 

  • Stevens PF. 1980. Evolutionary polarity of character states. Ann Rev Ecol Syst 11: 333–358.

    Article  Google Scholar 

  • Sousa R, Chung YJ, Rose JP, Wang BC. 1993. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature 364:593–599,

    Article  CAS  Google Scholar 

  • Takao M, Kobayashi T, Oikawa A, Yasui A. 1989. Tandem arrrangement of photolyase and Superoxide dismutase genes in Halobacterium halobium. J Bacteriol 171:6323–6329.

    CAS  Google Scholar 

  • Takao M, Oikawa A, Yasui A. 1990. Characterization of a Superoxide dismutase gene from the archaebacterium Methanobacterium thermoautotrophicum. Arch Biochem Biophys 283:210–216.

    Article  CAS  Google Scholar 

  • Tiboni O, Cammarano P, Sanangelantoni MA. 1993. Cloning and sequencing of the gene encoding glutamine synthase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archeal and bacterial glutamine synthase I sequences. J Bacteriol 175:2961–2969.

    CAS  Google Scholar 

  • Van Vliet F, Cunin R, Jacobs A, Piette J, Gigot D, Lawereys M, Piérard A, Glansdorff N. 1984. Evolutionary divergence of genes for ornithine and aspartate carbamoyl-transferases: complete sequence and mode of regulation of the Escherichia coli argF gene; comparison of argF with argI and pyr B. Nucleic Acid Res 12: 6277–6289.

    Google Scholar 

  • Wächtershäuser G. 1990. The case for the chemoautotrophic origins of life in an iron-sulfur world. Orig Life Evol Bios 20: 173–182.

    Article  Google Scholar 

  • Wheelis ML, Kandier O, Woese CR. 1992. On the nature of global classification. Proc Natl Acad Sci USA 89:2930–2934.

    Article  CAS  Google Scholar 

  • Woese CR. 1983. The primary lines of descent and the universal ancestor. In: DS Bendall, ed., Evolution from Molecules to Man. Cambridge: Cambridge University Press, pp.209–233.

    Google Scholar 

  • Woese CR1987. Bacterial evolution. Microbiol Rev 51:221–271.

    CAS  Google Scholar 

  • Woese CR, Fox GE. 1977. The concept of cellular evolution. J Mol Evol 10:1–6.

    Article  CAS  Google Scholar 

  • Woese CR, Kandier O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci USA 87:4576–4579.

    Article  CAS  Google Scholar 

  • Ycas M. 1974. On the earlier states of the biochemical system. J Theor Biol 44:145–160.

    Article  CAS  Google Scholar 

  • Yura T, Ishihama A. 1979. Genetics of bacterial RNA polymerases. Ann Rev Genet 13:59–97.

    Article  CAS  Google Scholar 

  • Zillig W, Schnabel R, Stetter KO. 1985. Archaebacteria and the origin of the eukaryotic cytoplasm. Curr Top Micrbiol Immunol 114: 1–8.

    Article  CAS  Google Scholar 

  • Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J Theor Biol 8:357–366.

    Article  CAS  Google Scholar 

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García-Meza, V., González-Rodríguez, A., Lazcano, A. (1994). Ancient Paralogous Duplications and the Search for Archean Cells. In: Fleischaker, G.R., Colonna, S., Luisi, P.L. (eds) Self-Production of Supramolecular Structures. NATO ASI Series, vol 446. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0754-9_19

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