Evidence for an early prokaryotic endosymbiosis

Nature

Volumn 460, Issue 7258, 2009, Pages 967-971

  Lake, James A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OXYGEN;

ENDOSYMBIONT; EUKARYOTE; EVOLUTIONARY BIOLOGY; GENE FLOW; PROKARYOTE; PROTEIN; SYMBIOSIS; TAXONOMY;

ACTINOBACTERIA; ANTIQUITY; ARCHAEBACTERIUM; ATMOSPHERE; BACILLI; BACTERIAL MEMBRANE; CLOSTRIDIUM; CYTOARCHITECTURE; ENDOSYMBIONT; ENDOSYMBIOSIS; EUKARYOTE; EVOLUTION; GENOME; GRAM NEGATIVE BACTERIUM; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FAMILY; PROTEIN SYNTHESIS; SHORT SURVEY; TAXON;

ACTINOBACTERIA; CLOSTRIDIUM; ENDOCYTOSIS; EUKARYOTIC CELLS; EVOLUTION; GENE FLOW; MODELS, BIOLOGICAL; PHYLOGENY; PROKARYOTIC CELLS; SYMBIOSIS;

CLOSTRIDIUM; EUKARYOTA; NEGIBACTERIA; PROKARYOTA;

EID: 69149098846     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08183     Document Type: Short Survey

References (51)

1. Margulis, L. Origin of the Eukaryotic Ceils (Yale Univ. Press, 1970).
2. Margulis, L. Symbiosis in Cell Evolution (Freeman and Company, 1981).
3. Lake, J. A. & Rivera, M. C. Was the nucleus the first endosymbiont? Proc. Natl Acad. Sci. USA 91, 2880-2881 (1994).
4. Martin, W. & Muller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37-41 (1998).
5. Lang, B. F. & Gray, M. W. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33, 351-397 (1999).
6. Poole, A., Jeffares, D. & Penny, D. Early evolution: prokaryotes, the new kids on the block. Bioessays 21, 880-889 (1999).
7. Keeling, P. J. & Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nature Rev. Genet. 9, 605-614 (2008).
8. Archibald, J. M. & Keeling, P. J. Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genef. 18, 577-584 (2002).
9. Syvanen, M. & Kado, C. I. (eds) Horizontal Gene Transfer (Chapman and Hall, 1998).
10. Jain, R., Rivera, M. C., Moore, J. E. & Lake, J. A. Horizontal gene transfer in microbial genome evolution. Theor. Popul. Biol. 61, 489-495 (2002).
11. Bowler, C., Karl, D. M. & Colwell, R. R. Microbial oceanography in a sea of opportunity. Nature 459, 180-184 (2009).
12. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
13. DeLong, E. F. The microbial ocean from genomes to biomes. Nature 459, 200-206 (2009).
14. von Dohlen, C. D., Kohler, S., Alsop, S. T. & McManus, W. R. Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412, 433-436 (2001).
15. Froestl, J. & Overmann, J. Phylogenetic affiliation of the bacteria that constitute phototrophic consortia. Arch. Microbiol. 174, 50-58 (2000).
16. Wanner, G., Vogl, K. & Overmann, J. Ultrastructural characterization of the prokaryotic symbiosis in "Chiorochromatium aggregatum". J. Bacteriol. 190, 3721-3730 (2008).
17. Hilario, E. & Gogarten, J. P. Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 31, 111-119 (1993).
18. Dagan, T. & Martin, W. The tree of one percent. Genome Biol. 7, 1181-1187 (2006).
19. Jain, R., Rivera, M. C., Moore, J. E. & Lake, J. A. Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20, 1598-1602 (2003).
20. Rivera, M. C. & Lake, J. A. The ring of life: evidence for a genome fusion origin of eukaryotes. Nature 431, 152-155 (2004).
21. Konstantinidis, K. T. & Tiedje, J. M. Towards a genome-based taxonomy for prokaryotes. J. Bacterioi. 187, 6258-6264 (2005).
22. Sorek, R. et al. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449-1452 (2007).
23. Doolittle, W. F. Phylogenetic classification and the universal tree. Science 284, 2124-2128 (1999).
24. Mclnerney, J. O. & Pisani, D. Paradigm for life. Science 318, 1390-1391 (2007).
25. Martin, W. & Embley, T. M. Early evolution comes full circle. Nature 431, 134-136 (2004).
26. Ohno, M. et al. Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth. Int. J. Syst. Evol. Microbiol. 50, 1829-1832 (2000).
27. Garrity, G. & Holt, J. G. in Sergey's Manual of Systematic Bacteriology (eds Boone, D. & Castenholz, R. W.) 119-141 (Springer, 2001).
28. Wu, M. et al. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 1, 563-574 (2005).
29. Lake, J. A., Servin, J. A., Herbold, C. W. & Skophammer, R. G. Evidence for a new root of the tree of life. Syst Biol. 57, 835-843 (2008).
30. Skophammer, R. G., Herbold, C. W., Rivera, M., Servin, J. A. & Lake, J. A. Evidence that the root of the tree of life is not within the Archaea. Mol. Biol. Evol. 23, 1648-1651 (2006).
31. Lake, J. A., Herbold, C. W., Rivera, M. C., Servin, J. A. & Skophammer, R. G. Rooting the tree of life using non-ubiquitous genes. Mol. Biol. Evol. 24, 130-136 (2007).
32. Skophammer, R. G., Servin, J. A., Herbold, C. W. & Lake, J. A. Evidence for a Gram positive, eubacterial root of the tree of life. Mol. Biol. Evol. 24, 1761-1768 (2007).
33. Ueda, K. et al. Genome sequence of Symbiobacterium thermophiium, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res. 32, 4937-4944 (2004).
34. Boone, D. & Castenholz, R. W. (eds) Sergey's Manual of Systematic Bacteriology 2nd edn Vol. 1, The Archaea and the Deep Branching and Phototrophic Bacteria (ed. Garrity, G. M.) (Springer, 2001).
35. Wilkinson, M., Mclnerney, J. O., Hirt, R. P., Foster, P. G. & Embley, T. M. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Ecol. Evol. 22, 114-115 (2007).
36. Stanier, R. Y., Adelberg, E. A. & Ingraham, J. L. The Microbial World (Prentice-Hall, 1976).
37. Gupta, R. S. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62, 1435-1491 (1998).
38. Lake, J. A. Reconstructing evolutionary graphs: 3D parsimony. Mol. Biol. Evol. 25, 1677-1682 (2008).
39. Lake, J. A. & Rivera, M. C. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21, 681-690 (2004).
40. Lake, J. A. Calculating the probability of multitaxon evolutionary trees-bootstrappers gambit. Proc. Natl Acad. Sci. USA 92, 9662-9666 (1995).
41. Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801-3806 (1999).
42. Gest, H. & Favinger, J. L. Heiiobacterium chiorum gen. nov. sp. nov., an anoxygenic brownish-green photosynthetic bacterium containing a new form of bacteriochlorophyll. Arch. Microbiol. 136, 11-16 (1983).
43. Raymond, J., Zhaxybayeva, O., Gogarten, J. P., Gerdes, S. Y. & Blankenship, R. E. Whole-genome analysis of photosynthetic prokaryotes. Science 298, 1616-1620 (2002).
44. 2 or formate uptake. Appl. Environ. Microbiol. 55, 1735-1741 (1989).
45. Overmann, J. & Schubert, K. Phototropic consortia: model systems for symbiotic interrelations between prokaryotes. Arch. Microbiol. 177, 201-208 (2002).
46. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004).
47. Margulis, L. in Genomes in Flux (eds Gogarten, M. Olendzenski, L & Gogarten, J. P.) (Humana, in the press).
48. Fischer, W. W. Life before the rise of oxygen. Nature 455, 1051-1052 (2008).
49. Rasmussen, B., Fletcher, I. R., Brocks, J. J. & Kilburn, M. R. Reassessing the first appearance of eukaryotes and cyanobacteria. Nature 455, 1101-1104 (2008).
50. Ventura, G. T. et al. Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere. Proc. Natl Acad. Sci. USA 104, 14260-14265 (2007).
51. Servin, J. A., Herbold, C. W., Skophammer, R. G. & Lake, J. A. Evidence excluding the root of the tree of life from the Actinobacteria. Mol. Biol. Evol. 25, 1-4 (2008).