Skip to main content

The indefinable term ‘prokaryote’ and the polyphyletic origin of genes

Journal of Genetics volume 96, pages 393–397 (2017)Cite this article

Abstract

An analysis has been performed on implications existing between the presence/absence of the evolutionary stage of the prokaryote, that is to say, the presence/absence of common characteristics between archaea and bacteria, and the monophyletic/polyphyletic origin of genes of proteins. Thereafter, a theorem stating that: ‘the polyphyletic origin of proteins would imply the absence of common characteristics between bacteria and archaea and therefore the lack of the evolutionary stage of the prokaryote, and vice versa that the indefinable prokaryote stage implies a polyphyletic origin of proteins’, has been made and validated. The conclusion is that given the absence of truth in common characteristics between archaea and bacteria, the origin of genes of proteins should have been polyphyletic.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1

References

  • Aravind I., Walkers D. R. and Koonin E. K. 1999 Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27, 1223–1242.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Branciamore S. and Di Giulio M. 2011 The presence in tRNA molecule sequences of the double hairpin, an evolutionary stage through which the origin of this molecule is thought to have passed. J. Mol. Evol. 72, 352–363.

    CAS  Article  PubMed  Google Scholar 

  • Di Giulio M. 1999 The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2000 The universal ancestor lived in a thermophilic or hyperthermophilic environment. J. Theor. Biol.  203, 203–213.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2001 The non-universality of the genetic code: the universal ancestor was a progenote. J. Theor. Biol. 209, 345–349.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2004 The origin of the tRNA molecule: implications for the origin of protein synthesis. J. Theor. Biol. 226, 89–93.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2005 The ocean abysses witnessed the origin of the genetic code. Gene 346, 7–12.

  • Di Giulio M. 2006a Nanoarchaeum equitans is a living fossil. J. Theor. Biol. 242, 257–260.

  • Di Giulio M. 2006b 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, 343–352.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2008a The origin of genes could be polyphyletic. Gene 426, 39–46.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2008b The split genes of Nanoarchaeum equitans are an ancestral character. Gene 421, 20–26.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2008c Permuted tRNA genes of Cyanidioschyzon merolae, the origin of the tRNA molecule and the root of the Eukarya domain. J. Theor. Biol. 253, 587–592.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2008d Split genes, ancestral genes. In Prebiotic evolution and astrobiology (ed. J. Tze-Fei Wong and A. Lazcano), chapter 13. Landes Bioscience Publisher, Texas, USA.

  • Di Giulio M. 2008e Transfer RNA genes in pieces are an ancestral character.  EMBO Rep. 9, 820.

    Article  PubMed  PubMed Central  Google Scholar 

  • Di Giulio M. 2009a A comparison among the models proposed to explain the origin of the tRNA molecule: a synthesis. J. Mol. Evol.  69, 1–9.

    CAS  Article  PubMed  Google Scholar 

  • Di Giulio M. 2009b Formal proof that the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character. J. Mol. Evol. 69, 505–511.

    CAS  Article  PubMed  Google Scholar 

  • Di Giulio M. 2011 The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes. J. Mol. Evol. 72, 119–126.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2012a The origin of the tRNA molecule: independent data favor a specific model of its evolution. Biochimie 94, 1464–1466.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2012b The ‘recently’ split transfer RNA genes may be close to merging the two halves of the tRNA rather than having just separated them. J. Theor. Biol. 310, 1–2.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2013a A polyphyletic model for the origin of tRNAs has more support than a monophyletic model. J. Theor. Biol. 318, 124–128.

    Article  PubMed  Google Scholar 

  • Di Giulio M. 2013b Is Nanoarchaeum equitans a paleokaryote? J. Biol. Res. 19, 83–88.

    Google Scholar 

  • Di Giulio M. 2014 The split genes of Nanoarchaeum equitans have not originated in its lineage and have been merged in another Nanoarchaeota: a reply to Podar et al. J. Theor. Biol. 349, 167–169.

  • Di Giulio M. 2015 The non-biological meaning of the term “prokaryote” and its implications. J. Mol. Evol. 80, 98–101.

    Article  PubMed  Google Scholar 

  • Dolan M. F. and Margulis L. 2007 Advances in biology reveal truth about prokaryotes. Nature 445, 21.

    CAS  Article  PubMed  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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Doolittle W. F. and Zhaxybayeva O. 2009 On the origin of the prokaryotic species. Genome Res. 19, 744–756.

    CAS  Article  PubMed  Google Scholar 

  • Doolittle W. F. and Zhaxybayeva O. 2013 What is a prokaryote? In The prokaryotes—prokaryotic biology and symbiotic associations (ed. E. Rosenberg et al.), pp. 21–37. Springer, Heidelberg, Germany.

  • Forterre P. 2000 Three RNA cells for ribosomal lineages and three DNA virus to replicate their genomes: a hypothesis for the origin of cellular domain. Proc. Natl. Acad. Sci. USA 103, 3669–3674.

    Article  Google Scholar 

  • Forterre P. 2005 The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie 87, 793–803.

    CAS  Article  PubMed  Google Scholar 

  • Fox-Keller E. 2010 The mirage of a space between nature and nurture. Duke Univesity Press, Durham, USA.

    Book  Google Scholar 

  • Leipe D. D., Aravind L. and Koonin E. V. 1999 Did DNA replication evolve twice independently? Nucleic Acids Res. 27, 3389–3401.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Lupas A. N., Ponting C. P. and Russell R. B. 2001 On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol.  134, 191–203.

    CAS  Article  PubMed  Google Scholar 

  • Martin W. and Koonin E. V. 2006 A positive definition of prokaryotes. Nature 442, 868.

    CAS  Article  PubMed  Google Scholar 

  • Mat W. K., Xue H. and Wong J. T. 2008 The genomics of LUCA. Front Biosci.  3, 5605–5613.

    Article  Google Scholar 

  • Mushegian A. R. and Koonin E. V. 1996 A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93, 10268–10273.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ouzounis C. and Kyrpides N. 1996 The emergence of major cellular processes in evolution. FEBS Lett.  390, 119–123.

    CAS  Article  PubMed  Google Scholar 

  • Ouzounis C. A., Kunin V., Darzentas N. and Goldovsky L. 2006 A minimal estimate for the gene content of the last universal common ancestor. Res. Microbiol.  157, 57–68.

    CAS  Article  PubMed  Google Scholar 

  • Pace N. R. 2006 Time for a change. Nature 441, 289.

    CAS  Article  PubMed  Google Scholar 

  • Pace N. R. 2009 Rebuttal: the modern concept of prokaryote. J. Bacteriol.  191, 2006–2007.

  • Poole A. M. and Logan D. T. 2005 Modern mRNA proofreading and repair: clues that the last universal ancestor possessed an RNA genome? Mol. Biol. Evol.  22, 1444–1455.

    CAS  Article  PubMed  Google Scholar 

  • Sapp R. 2006 Two faces of the prokaryote concept. Intern. Microbiol.  9, 163–172.

    CAS  Google Scholar 

  • Spang A., Saw J. H., Jørgensen S. L., Zaremba-Niedzwiedzka K., Martijn J. et al. 2015 Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Tuller T., Birin H., Gophna U., Kupiec M. and Ruppin E. 2010 Reconstruction ancestral gene content by coevolution. Genome Res. 20, 122–132.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Whitman W. B. 2009 The modern concept of the procaryote. J. Bacteriol.  191, 2000–2005.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Williams T. A., Foster P. G., Nye T. M., Cox C. J. and Embley T. M. 2012 A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. R. Soc. London B 279, 4870–4879.

  • Williams T. A., Foster P. G., Cox C. J. and Embley T. M. 2013 An archaeal origin of, eukaryotes supports only two primary domains of life. Nature 504, 231–236.

  • Woese C. R. 1987 Bacterial evolution. Microbiol. Res. 51, 221–271.

    CAS  Google Scholar 

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

Download references

Acknowledgements

This work was carried out in the Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic, during my stay in this university, financed by the short-term mobility programme of the National Research Council, Italy. I would like to thank Prof Jaroslav Flegr for discussions and cordial hospitality.

Author information

Affiliations

  1. Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino, 111, 80131 , Naples, Italy

    Massimo Di Giulio

Authors
  1. Massimo Di Giulio
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Massimo Di Giulio.

Additional information

Di Giulio M. 2017 The indefinable term ‘prokaryote’ and the polyphyletic origin of genes. J. Genet. 96, xx–xx

Corresponding editor: Rajiva Raman

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Di Giulio, M. The indefinable term ‘prokaryote’ and the polyphyletic origin of genes. J Genet 96, 393–397 (2017). https://doi.org/10.1007/s12041-017-0775-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-017-0775-x

Keywords

  • progenote
  • last universal common ancestor
  • evolutionary stages
  • early evolution of life