Skip to main content

Molecular Biology and the Reconstruction of Microbial Phylogenies: Des Liaisons Dangereuses?

  • Conference paper
Astrobiology

Abstract

Only half-a-century after the DNA double chain model was first suggested, molecular biology has become one of the most provocative, rapidly developing fields of of scientific research, that has led not only to tantalizing new findings on processes and mechanisms at the molecular level, but also to major conceptual revolutions in life sciences. Is there any hope of developing methodological approaches and theoretical frameworks not only to make sense of the overwhelming growing body of data that this relatively new field is producing, but also to use them to develop a more integrative, truly multidisciplinaiy understanding of biological phenomena? As Peter Bowler wrote a few years ago, Charles Darwin and his followers were accutely aware that “evolutionism’s strength as a theory came fom its ability to make sense out of a vast range of otherwise meaningless facts” (Bowler, 1990). This situation has not changed. Evolutionary biology may be in a state of major turmoil, but its unifying powers have not diminished at all. In fact, they probably represent one of the most promising possibilities of overcoming the perils of reductionism that have plagued molecular biology since its inception.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Achenbach-Richter, L., Gupta, R., Stetter., K. O., and Woese, C. R. (1987) Were the original eubacteria thermophiles? System. Appl. Microbiol. 9, 34–39.

    Article  CAS  Google Scholar 

  • Bhattacharjee, J. K. (1985) β-aminoadipate pathway for the biosynthesis of lysine in lower eukaryotes, CRC Crit. Rev. Microbiol. 12, 131–151.

    Article  CAS  Google Scholar 

  • Bowler, P. J. (1990) Charles Darwin, The man and his influence, Basil Blackwell, Oxford.

    Google Scholar 

  • Confalonieri, F., Elie, C., Nadal, M., Bouthier de la Tour, C., Forterre, P., and 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  PubMed  CAS  Google Scholar 

  • DeLey, J. (1968) Molecular biology and bacterial phylogeny, in T. Dobzhansky,. K. Hecht, and W. C. Steere (eds), Evolutionary Biology, Appleton-Century-Crofts, New York, pp. 104–156.

    Google Scholar 

  • Doolittle, W. F. (1999) Phylogenetic classification and the universal tree, Science 284, 2124–2128.

    Article  PubMed  CAS  Google Scholar 

  • Doolittle, W. F. and Brown, J. R. (1994) Tempo, mode, the progenote and the universal root, Proc. Natl. Acad. Sci. USA 91,6721–6728.

    Article  PubMed  CAS  Google Scholar 

  • Donoghue, M. J. (1992) Homology, in E. Fox Keller and E. A. Lloyd (eds), Keywords in Evolutionary Biology, Harvard University Press, Cambridge, pp. 170–179.

    Google Scholar 

  • Fitch, W. M. (1970) Distinguishing homologous from analogous proteins, Syst. Zool. 19, 99–113.

    Article  PubMed  CAS  Google Scholar 

  • Fitch, W. M. and Upper, K. (1987) The phylogeny of tRNA sequences provides evidence of ambiguity reduction in the origin of the genetic code, Cold Spring Harbor Symp. Quant. Biol. 52, 759–767.

    Article  PubMed  CAS  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 

  • Galtier,, N., Tourasse, N., and Gouy, M. (1999) A nonhyperthermophilic common ancestor to extant life forms, Science 283, 220–221.

    Article  PubMed  CAS  Google Scholar 

  • García-Meza, V., González-Rodríguez, A, and Lazcano, A. (1995) Ancient paralogous duplications and the search for Archean cells, in G. R. Fleischaker, S. Colonna, and P. L. Luisi (eds), Self-Reproduction of Supramolecular Structures, from synthetic structures to models of minimalliving systems, Klüwer, Amsterdam, pp. 231–246.

    Google Scholar 

  • Germont, A., Phillipe, H., and Le Guyader, H. (1997) Evidence for the loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae, Mol Biochem. Parasitol. 8, 159–168.

    Article  Google Scholar 

  • Gogarten-Boekels, M. and Gogarten, J. P. (1994) The effects of heavy meteorite bombardment on the early evolution of life —a new look at the molecular record, Origins of Life and Evol. Biosph. 25, 78–83.

    Google Scholar 

  • Gogarten, J. P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E. J., Bowman, B. J., Manolson, M. L., Poole, J., Date, T., Oshima, Konishi, L., Denda, K., and Yoshida, M. (1989) Evolution of the vacuolar H+-ATPase, implications for the origin of eukayotes, Proc. Natl. Acad. Sci. USA 86, 6661–6665.

    Article  PubMed  CAS  Google Scholar 

  • Gupta, R. S. and Golding, G. B. (1993) Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes, J. Mol Evol. 37, 573–582.

    Article  PubMed  CAS  Google Scholar 

  • Harvey, R. B. (1924) Enzymes of thermal algae, Science 60, 481–482.

    Article  PubMed  CAS  Google Scholar 

  • Holm, N. G., ed., (1992) Marine Hydrothermal Systems and the Origin of Life, Klüwer Academic Publ., Dordrecht.

    Book  Google Scholar 

  • Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., and 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  PubMed  CAS  Google Scholar 

  • Jensen, R. A. (1976) Enzyme recruitment in the evolution of new function, Ann. Rev. Microbiol. 30, 409–425.

    Article  CAS  Google Scholar 

  • Kaine, B. P., Mehr, I. J., and Woese, C. R. (1994) The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription, Proc. Natl. Acad. Sci. USA 91, 3854–3856.

    Article  PubMed  CAS  Google Scholar 

  • Kandier, O. (1994) The early diversification of life, in S. Bengtson (ed), Early Life on Earth, Nobel Symposium No. 84, Columbia University Press, New York, pp. 124–131.

    Google Scholar 

  • Keefe, A. D., Lazcano, A and Miller, S. L. (1994) Evolution of the biosynthesis of the branched-chain amino acids, Origins of Life and Evol. Biosph. 25, 99–110.

    Article  Google Scholar 

  • Lazcano, A (1993) Biogenesis, some like it very hot, Science 260, 1154–1155.

    Article  PubMed  CAS  Google Scholar 

  • Lazcano, A (1994) The transition from non-living to living, in S. Bengtson (ed), Early Life on Earth, Nobel Symposium No. 84, Columbia University Press, New York, pp. 60–69.

    Google Scholar 

  • Lazcano, A. (1995) Cellular evolution during the early Archaean: what happended between the progenote and the cenanestor? Microbiologia SEM 11, 1–13.

    Google Scholar 

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

    Google Scholar 

  • Lazcano, A and Miller, S. L. (1994) How long did it take for life to begin and evolve to cyanobacteria? Jour. Mol. Evol. 39, 546–554.

    Article  CAS  Google Scholar 

  • Lazcano, A and Miller, S. L. (1996) The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time, Cell 85, 793–798.

    Article  PubMed  CAS  Google Scholar 

  • Margulis, L. (1993) Symbiosis in Cell Evolution, W. H. Freeman, New York.

    Google Scholar 

  • Margulis, L. and Guerrero, R. (1991) Kingdoms in turmoil, New Scientist 132, 46–50.

    Google Scholar 

  • Mayr, E. (1990) A natural system of organisms, Nature 348, 491.

    Article  Google Scholar 

  • Miller, S. L. and Bada, J. L. (1988) Submarine hot springs and the origin of life, Nature 334, 609–611.

    Article  PubMed  CAS  Google Scholar 

  • Müller, M. (1988) Energy metabolism of protozoa without mitochondria, Ann. Rev. Microbiol. 42, 465–488.

    Article  Google Scholar 

  • Nuttall, G. H. F. (1904) Blood Immunity and Blood Relationship: a demonstration of certain blood-relationships amongst animals by means of the precipitation test for blood, Cambridge University Press, Cambridge.

    Google Scholar 

  • Oparin, A. I. (1938) The Origin of Life, MacMillan, New York.

    Google Scholar 

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

    Article  Google Scholar 

  • Patterson, C. (1988) Homology in classical and molecular biology, Mol. Biol. Evol. 5, 603–625.

    PubMed  CAS  Google Scholar 

  • Pisani, F.M., De Martino, C., and Rossi, M. (1992) A DNA polymerase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA polymerases. Nucleic Acid Res. 20, 2711–2716.

    Article  PubMed  CAS  Google Scholar 

  • Reeck, G. R., de Häen, C., Teller, D. C., Doolittle, R. F., Fitch, W., Dickerson, R. E., Chambon, P., McLachlan, A. D., Margottasti, E., Jukes, T. H., and Zuckerkandl, E. (1987) “Homology” in proteins and nucleic acids, a terminology muddle and a way out of it, Cell 50, 667.

    Article  PubMed  CAS  Google Scholar 

  • Rivera, M. C. and Lake, J. A. (1992) Evidence that eukaryotes and eocyte prokaryotes are inmediate relatives, Science 257, 74–76.

    Article  PubMed  CAS  Google Scholar 

  • Schwartz, M. and Dayhoff, M. O. (1978) Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts, Science 199,395–403.

    Article  PubMed  CAS  Google Scholar 

  • Sidow, A. and Bowman, B. H. (1991) Molecular phylogeny, Current Opinion Genet. Develop. 1, 451–456.

    Article  CAS  Google Scholar 

  • Sleep, N. H., Zahnle, K. J., Kastings, J. F., and Morowitz, H. J. (1989) Annihilation of ecosystems by large asteroid impacts on the early Earth, Nature 342, 139–142.

    Article  PubMed  CAS  Google Scholar 

  • Snel, B., Bork, P., and Huynen, M. A (1999) Genome phylogeny based on gene content, Nature Genetics 21, 108–110.

    Article  PubMed  CAS  Google Scholar 

  • Sogin, M. L. (1994) The origin of eukaryotes and evolution into major kingdoms, in S. Bengtson (ed), Early Life on Earth, Nobel Symposium No. 84, Columbia University Press, New York, pp. 181–192.

    Google Scholar 

  • Stark, G. R., and Wahl, G. M. (1984) Gene amplification, Ann. Rev. Biochem. 53, 447–491.

    Article  PubMed  CAS  Google Scholar 

  • Stetter, K. O. (1994) The lesson of archaebacteria, in S. Bengtson (ed), Early Life on Earth, Nobel Symposium No. 84, Columbia University Press, New York, pp. 114–122.

    Google Scholar 

  • Tekaia, F. and Dujon, B. (1999) Pervasiveness of gene conservation and persistence of duplicates in cellular genomes, J. Mol Evol. 49, 591–600.

    Article  PubMed  CAS  Google Scholar 

  • Tekaia, F., Lazcano, A., and Dujon, B. (1999) The genomic tree as revealed from whole proteome comparisons, Genome Research 9, 550–557.

    PubMed  CAS  Google Scholar 

  • Wächtershäuser, G. (1990) The case for the chemoautotrophic origins of life in an iron-sulfur world, Origins of Life Evol Biosph. 20, 173–182.

    Article  Google Scholar 

  • Wallace, D. C. and Morowitz, N. H. (1973) Genome size and evolution, Chromosoma 40, 121–126.

    Article  PubMed  CAS  Google Scholar 

  • Wheelis, M. L., Kandier, O., and Woese, C. R. (1992) On the nature of global classification, Proc. Natl. Acad. Sci. USA 89, 2930–2934.

    Article  PubMed  CAS  Google Scholar 

  • Woese, C. R. (1987) Bacterial evolution, Microbiol. Reviews 51, 221–271.

    CAS  Google Scholar 

  • Woese, C. R. (1993) The archaea, their history and significance, in M. Kates, D. J. Kushner, and A. T. Matheson (eds), The Biochemistry of the Archaea (Archaebarteria), Elsevier Science Publishers, Amsterdam, pp. vii–xxix.

    Chapter  Google Scholar 

  • Woese, C. R. and Fox, G. E. (1977) The concept of cellular evolution, Jour. Mol. Evol. 10, 1–6.

    Article  CAS  Google Scholar 

  • Woese, C. R., Kandier, O., and Wheelis, M. L. (1990) Towards a natural system of organisms, proposal for the domains Archaea, Bacteria, and Eucarya, Proc. Natl. Acad. Sci. USA 87, 4576–4579.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Young, D. (1992) The Discovery of Evolution, Natural History Museum Publications, Cambridge.

    Google Scholar 

  • Zuckerkandl, E. and Pauling, L. (1965) Molecules as documents of evolutionary history, J. Theoret. Biol. 8, 357–366.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Science+Business Media Dordrecht

About this paper

Cite this paper

Becerra, A., Silva, E., Lloret, L., Islas, S., Velasco, A.M., Lazcano, A. (2000). Molecular Biology and the Reconstruction of Microbial Phylogenies: Des Liaisons Dangereuses?. In: Chela-Flores, J., Lemarchand, G.A., Oró, J. (eds) Astrobiology. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4313-4_11

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-4313-4_11

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5865-0

  • Online ISBN: 978-94-011-4313-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics