This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Brown, J. R.
Right arrow Articles by Doolittle, W. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Brown, J. R.
Right arrow Articles by Doolittle, W. F.

 Previous Article  |  Next Article 

Microbiol. Mol. Biol. Rev., Dec 1997, 456-502, Vol 61, No. 4
Copyright © 1997, American Society for Microbiology

Archaea and the prokaryote-to-eukaryote transition [In Process Citation]

JR Brown and WF Doolittle
Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada. James_R_Brown@sbphrd.com

Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.


This article has been cited by other articles:

  • Schoenfeld, T., Patterson, M., Richardson, P. M., Wommack, K. E., Young, M., Mead, D. (2008). Assembly of Viral Metagenomes from Yellowstone Hot Springs. Appl. Environ. Microbiol. 74: 4164-4174 [Abstract] [Full Text]  
  • Lin, Z., Nei, M., Ma, H. (2007). The origins and early evolution of DNA mismatch repair genes multiple horizontal gene transfers and co-evolution. Nucleic Acids Res 35: 7591-7603 [Abstract] [Full Text]  
  • Ono, Y., Sakai, A., Takechi, K., Takio, S., Takusagawa, M., Takano, H. (2007). NtPolI-like1 and NtPolI-like2, Bacterial DNA Polymerase I Homologs Isolated from BY-2 Cultured Tobacco Cells, Encode DNA Polymerases Engaged in DNA Replication in Both Plastids and Mitochondria. Plant Cell Physiol 48: 1679-1692 [Abstract] [Full Text]  
  • McGraw, A. P., Bevilacqua, P. C., Babitzke, P. (2007). TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region. RNA 13: 2020-2033 [Abstract] [Full Text]  
  • Liapounova, N. A., Hampl, V., Gordon, P. M. K., Sensen, C. W., Gedamu, L., Dacks, J. B. (2006). Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote Monocercomonoides. Eukaryot Cell 5: 2138-2146 [Abstract] [Full Text]  
  • Canfield, D. E, Rosing, M. T, Bjerrum, C. (2006). Early anaerobic metabolisms. Phil Trans R Soc B 361: 1819-1836 [Abstract] [Full Text]  
  • Boussau, B., Gouy, M. (2006). Efficient Likelihood Computations with Nonreversible Models of Evolution. Syst Biol 55: 756-768 [Abstract] [Full Text]  
  • Skophammer, R. G., Herbold, C. W., Rivera, M. C., Servin, J. A., Lake, J. A. (2006). Evidence that the Root of the Tree of Life Is Not within the Archaea. Mol Biol Evol 23: 1648-1651 [Abstract] [Full Text]  
  • Suchard, M. A., Redelings, B. D. (2006). BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22: 2047-2048 [Abstract] [Full Text]  
  • Robertson, D. L., Tartar, A. (2006). Evolution of Glutamine Synthetase in Heterokonts: Evidence for Endosymbiotic Gene Transfer and the Early Evolution of Photosynthesis. Mol Biol Evol 23: 1048-1055 [Abstract] [Full Text]  
  • Zhao, Y., Davis, R. E., Lee, I.-M. (2005). Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. Int. J. Syst. Evol. Microbiol. 55: 2131-2141 [Abstract] [Full Text]  
  • Makarova, K. S., Wolf, Y. I., Mekhedov, S. L., Mirkin, B. G., Koonin, E. V. (2005). Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 33: 4626-4638 [Abstract] [Full Text]  
  • Redelings, B. D., Suchard, M. A. (2005). Joint Bayesian Estimation of Alignment and Phylogeny. Syst Biol 54: 401-418 [Abstract] [Full Text]  
  • Simonson, A. B., Servin, J. A., Skophammer, R. G., Herbold, C. W., Rivera, M. C., Lake, J. A. (2005). Decoding the genomic tree of life. Proc. Natl. Acad. Sci. USA 102: 6608-6613 [Abstract] [Full Text]  
  • Cabello, P., Roldan, M. D., Moreno-Vivian, C. (2004). Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150: 3527-3546 [Abstract] [Full Text]  
  • Capaldi, S. A., Berger, J. M. (2004). Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus. Nucleic Acids Res 32: 4821-4832 [Abstract] [Full Text]  
  • Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F., Gelius-Dietrich, G., Henze, K., Kretschmann, E., Richly, E., Leister, D., Bryant, D., Steel, M. A., Lockhart, P. J., Penny, D., Martin, W. (2004). A Genome Phylogeny for Mitochondria Among {alpha}-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes. Mol Biol Evol 21: 1643-1660 [Abstract] [Full Text]  
  • Allers, T., Ngo, H.-P., Mevarech, M., Lloyd, R. G. (2004). Development of Additional Selectable Markers for the Halophilic Archaeon Haloferax volcanii Based on the leuB and trpA Genes. Appl. Environ. Microbiol. 70: 943-953 [Abstract] [Full Text]  
  • Qin, H., Lu, H. H. S., Wu, W. B., Li, W.-H. (2003). Evolution of the yeast protein interaction network. Proc. Natl. Acad. Sci. USA 100: 12820-12824 [Abstract] [Full Text]  
  • Xie, G., Keyhani, N. O., Bonner, C. A., Jensen, R. A. (2003). Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change. Microbiol. Mol. Biol. Rev. 67: 303-342 [Abstract] [Full Text]  
  • Daubin, V., Moran, N. A., Ochman, H. (2003). Phylogenetics and the Cohesion of Bacterial Genomes. Science 301: 829-832 [Abstract] [Full Text]  
  • Mourier, T., Jeffares, D. C. (2003). Eukaryotic Intron Loss. Science 300: 1393-1393 [Full Text]  
  • Harris, J. K., Kelley, S. T., Spiegelman, G. B., Pace, N. R. (2003). The Genetic Core of the Universal Ancestor. Genome Res 13: 407-412 [Abstract] [Full Text]  
  • Nanavati, D., Noll, K. M., Romano, A. H. (2002). Periplasmic maltose- and glucose-binding protein activities in cell-free extracts of Thermotoga maritima. Microbiology 148: 3531-3537 [Abstract] [Full Text]  
  • Lamanna, A. C., Gestwicki, J. E., Strong, L. E., Borchardt, S. L., Owen, R. M., Kiessling, L. L. (2002). Conserved Amplification of Chemotactic Responses through Chemoreceptor Interactions. J. Bacteriol. 184: 4981-4987 [Abstract] [Full Text]  
  • Griffiths, E., Gupta, R. S. (2002). Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces. Microbiology 148: 2541-2549 [Abstract] [Full Text]  
  • Woese, C. R. (2002). On the evolution of cells. Proc. Natl. Acad. Sci. USA 99: 8742-8747 [Abstract] [Full Text]  
  • Jardine, O., Gough, J., Chothia, C., Teichmann, S. A. (2002). Comparison of the Small Molecule Metabolic Enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Res 12: 916-929 [Abstract] [Full Text]  
  • Matte-Tailliez, O., Brochier, C., Forterre, P., Philippe, H. (2002). Archaeal Phylogeny Based on Ribosomal Proteins. Mol Biol Evol 19: 631-639 [Abstract] [Full Text]  
  • Anantharaman, V., Koonin, E. V., Aravind, L. (2002). Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 30: 1427-1464 [Abstract] [Full Text]  
  • Figge, R. M., Cerff, R. (2001). GAPDH Gene Diversity in Spirochetes: A Paradigm for Genetic Promiscuity. Mol Biol Evol 18: 2240-2249 [Abstract] [Full Text]  
  • Aravind, L., Dixit, V. M., Koonin, E. V. (2001). Apoptotic Molecular Machinery: Vastly Increased Complexity in Vertebrates Revealed by Genome Comparisons. Science 291: 1279-1284 [Abstract] [Full Text]  
  • Fosslien, E. (2001). Mitochondrial Medicine - Molecular Pathology of Defective Oxidative Phosphorylation. Annals of Clinical & Laboratory Science 31: 25-67 [Abstract] [Full Text]  
  • Kurland, C. G., Andersson, S. G. E. (2000). Origin and Evolution of the Mitochondrial Proteome. Microbiol. Mol. Biol. Rev. 64: 786-820 [Abstract] [Full Text]  
  • Koretke, K. K., Lupas, A. N., Warren, P. V., Rosenberg, M., Brown, J. R. (2000). Evolution of Two-Component Signal Transduction. Mol Biol Evol 17: 1956-1970 [Abstract] [Full Text]  
  • Gestwicki, J. E., Lamanna, A. C., Harshey, R. M., McCarter, L. L., Kiessling, L. L., Adler, J. (2000). Evolutionary Conservation of Methyl-Accepting Chemotaxis Protein Location in Bacteria and Archaea. J. Bacteriol. 182: 6499-6502 [Abstract] [Full Text]  
  • Wilding, E. I., Brown, J. R., Bryant, A. P., Chalker, A. F., Holmes, D. J., Ingraham, K. A., Iordanescu, S., So, C. Y., Rosenberg, M., Gwynn, M. N. (2000). Identification, Evolution, and Essentiality of the Mevalonate Pathway for Isopentenyl Diphosphate Biosynthesis in Gram-Positive Cocci. J. Bacteriol. 182: 4319-4327 [Abstract] [Full Text]  
  • Woese, C. R. (2000). Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA 97: 8392-8396 [Abstract] [Full Text]  
  • Grishin, N. V., Wolf, Y. I., Koonin, E. V. (2000). From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins. Genome Res 10: 991-1000 [Abstract] [Full Text]  
  • Hannaert, V., Brinkmann, H., Nowitzki, U., Lee, J. A., Albert, M.-A., Sensen, C. W., Gaasterland, T., M, M., Michels, P., Martin, W. (2000). Enolase from Trypanosoma brucei, from the Amitochondriate Protist Mastigamoeba balamuthi, and from the Chloroplast and Cytosol of Euglena gracilis: Pieces in the Evolutionary Puzzle of the Eukaryotic Glycolytic Pathway. Mol Biol Evol 17: 989-1000 [Abstract] [Full Text]  
  • Kirschvink, J. L., Gaidos, E. J., Bertani, L. E., Beukes, N. J., Gutzmer, J., Maepa, L. N., Steinberger, R. E. (2000). Paleoproterozoic snowball Earth: Extreme climatic and geochemical global change and its biological consequences. Proc. Natl. Acad. Sci. USA 97: 1400-1405 [Abstract] [Full Text]  
  • Gelfand, M. S., Koonin, E. V., Mironov, A. A. (2000). Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res 28: 695-705 [Abstract] [Full Text]  
  • Liaud, M.-F., Lichtl, C., Apt, K., Martin, W., Cerff, R. (2000). Compartment-Specific Isoforms of TPI and GAPDH are Imported into Diatom Mitochondria as a Fusion Protein: Evidence in Favor of a Mitochondrial Origin of the Eukaryotic Glycolytic Pathway. Mol Biol Evol 17: 213-223 [Abstract] [Full Text]  
  • Kluck, R. M., Esposti, M. D., Perkins, G., Renken, C., Kuwana, T., Bossy-Wetzel, E., Goldberg, M., Allen, T., Barber, M. J., Green, D. R., Newmeyer, D. D. (1999). The Pro-Apoptotic Proteins, Bid and Bax, Cause a Limited Permeabilization of the Mitochondrial Outer Membrane That Is Enhanced by Cytosol. JCB 147: 809-822 [Abstract] [Full Text]  
  • Willhoeft, U., Hamann, L., Tannich, E. (1999). A DNA Sequence Corresponding to the Gene Encoding Cysteine Proteinase 5 in Entamoeba histolytica Is Present and Positionally Conserved but Highly Degenerated in Entamoeba dispar. Infect. Immun. 67: 5925-5929 [Abstract] [Full Text]  
  • Kelman, Z., Pietrokovski, S., Hurwitz, J. (1999). Isolation and Characterization of a Split B-type DNA Polymerase from the Archaeon Methanobacterium thermoautotrophicum Delta H. J. Biol. Chem. 274: 28751-28761 [Abstract] [Full Text]  
  • Dale, H., Krebs, M. P. (1999). Membrane Insertion Kinetics of a Protein Domain In Vivo. THE BACTERIOOPSIN N TERMINUS INSERTS CO-TRANSLATIONALLY. J. Biol. Chem. 274: 22693-22698 [Abstract] [Full Text]  
  • Campbell, A., Mrazek, J., Karlin, S. (1999). Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl. Acad. Sci. USA 96: 9184-9189 [Abstract] [Full Text]  
  • Wolf, Y. I., Aravind, L., Grishin, N. V., Koonin, E. V. (1999). Evolution of Aminoacyl-tRNA Synthetases---Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events. Genome Res 9: 689-710 [Abstract] [Full Text]  
  • Macario, A. J. L., de Macario, E. C. (1999). The Archaeal Molecular Chaperone Machine: Peculiarities and Paradoxes. Genetics 152: 1277-1283 [Abstract] [Full Text]  
  • Makarova, K. S., Aravind, L., Galperin, M. Y., Grishin, N. V., Tatusov, R. L., Wolf, Y. I., Koonin, E. V. (1999). Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell. Genome Res 9: 608-628 [Abstract] [Full Text]  
  • Doolittle, W. F. (1999). Phylogenetic Classification and the Universal Tree. Science 284: 2124-2128 [Abstract] [Full Text]  
  • Reeve, J. N. (1999). Archaebacteria Then ... Archaes Now (Are There Really No Archaeal Pathogens?). J. Bacteriol. 181: 3613-3617 [Full Text]  
  • Tekaia, F., Lazcano, A., Dujon, B. (1999). The Genomic Tree as Revealed from Whole Proteome Comparisons. Genome Res 9: 550-557 [Abstract] [Full Text]  
  • Jain, R., Rivera, M. C., Lake, J. A. (1999). Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. USA 96: 3801-3806 [Abstract] [Full Text]  
  • Galtier, N., Tourasse, N., Gouy, M. (1999). A Nonhyperthermophilic Common Ancestor to Extant Life Forms. Science 283: 220-221 [Abstract] [Full Text]  
  • Gupta, R. S. (1998). Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol. Mol. Biol. Rev. 62: 1435-1491 [Abstract] [Full Text]  
  • Woese, C. (1998). The universal ancestor. Proc. Natl. Acad. Sci. USA 95: 6854-6859 [Abstract] [Full Text]  
  • Hashimoto, T., Sanchez, L. B., Shirakura, T., Muller, M., Hasegawa, M. (1998). Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. USA 95: 6860-6865 [Abstract] [Full Text]  
  • Wagner, M., Roger, A. J., Flax, J. L., Brusseau, G. A., Stahl, D. A. (1998). Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration. J. Bacteriol. 180: 2975-2982 [Abstract] [Full Text]  
  • Rivera, M. C., Jain, R., Moore, J. E., Lake, J. A. (1998). Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA 95: 6239-6244 [Abstract] [Full Text]  
  • Lecompte, O., Ripp, R., Puzos-Barbe, V., Duprat, S., Heilig, R., Dietrich, J., Thierry, J.-C., Poch, O. (2001). Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea. Genome Res 11: 981-993 [Abstract] [Full Text]  
  • Minambres, B., Olivera, E. R., Jensen, R. A., Luengo, J. M. (2000). A New Class of Glutamate Dehydrogenases (GDH). BIOCHEMICAL AND GENETIC CHARACTERIZATION OF THE FIRST MEMBER, THE AMP-REQUIRING NAD-SPECIFIC GDH OF STREPTOMYCES CLAVULIGERUS. J. Biol. Chem. 275: 39529-39542 [Abstract] [Full Text]  
  • Franzetti, B., Schoehn, G., Ebel, C., Gagnon, J., Ruigrok, R. W. H., Zaccai, G. (2001). Characterization of a Novel Complex from Halophilic Archaebacteria, Which Displays Chaperone-like Activities in Vitro. J. Biol. Chem. 276: 29906-29914 [Abstract] [Full Text]  
  • Giraldo, R., Diaz-Orejas, R. (2001). Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p). Proc. Natl. Acad. Sci. USA 98: 4938-4943 [Abstract] [Full Text]  
  • Chihade, J. W., Brown, J. R., Schimmel, P. R., Ribas de Pouplana, L. (2000). Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 97: 12153-12157 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»