Chapter 4 : : Whose Sister Lineage?

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

: Whose Sister Lineage?, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap04-2.gif


Following a review of archaeal genomics, the author wishes to scrutinize the convenient though perhaps misleading construct that is organismic phylogeny. In so doing, the author will address theories of the origin of eukaryotes, theories which look to for answers, thanks to the (largely) accepted rooting of the tree of life in the bacterial branch. Interest in archaeal genomes, as judged by volume in the literature, has focused mainly on the extremely halophilic archaea. The genetic instability appears to be prevalent not only among members of the family but also among members of the order , though the insertion sequences responsible are apparently unrelated. Physical analysis of archaeal nucleoids lags behind the efforts of genetic characterization. Rooting of the tree, using anciently duplicated paralogous sequences further divided from Bacteria by positioning the root in the bacterial branch. The biological species will tend to restrict lateral transfers to specific groups. However, movement of genes from more distantly related organisms is not precluded, even between and . Specific genomes have subsets of these collections and typically possess a number of open reading frames not found anywhere else. Sequence evolution is responsible for the unmatched open reading frames, having erased the evidence of their homologies. Confounding things further are lateral genetic transfer and gene replacement, especially from extinct lineages. Comparative genomic analyses have begun, and they will undoubtedly transform the method of molecular evolutionary study.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4

Key Concept Ranking

Family B DNA Polymerase
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Eucaryal origin from the fusion of a bacterium with an archaeon ( ). The arrows indicate the two most important endosymbiotic events to occur since the origin of mitochondria and chloroplasts.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Eucaryal origin from the fusion of a gram-negative bacterium with an archaeon ( ). Although this modification of Fig. 1 helps to explain why are more closely related to gram-positive bacteria than to gram-negative bacteria, one must assume that a burst of evolutionary sequence change occurred shortly after the inception of and that early-branching are artifactually early branching (see text).

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Model of archaeal chimerism ( ) in which owe their metabolic similarity with to a large-scale lateral transfer of bacterial genes.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Fourth Domain model of eucaryal origins (right), based on the hypothesis that (E) are chimerae of (A) and an extinct (daggers) lineage of cytotrophs. If one trims the current phylogenetic tree (left) to the time in question (second from left), one suggests that the world supported an implausibly small microbial biodiversity, unless one accepts that other lineages existed (second from right) which have since gone extinct. Such a lineage may have engulfed an early archaeon, adopting its information processing mechanisms but retaining many of its own genes for fermentative metabolism.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5

Fourth Domain model, adjusted to take into account the sequence similarities among archaea, gram-positive bacteria, and cyanobacteria. Here, one must suppose that after the divergence of from gram-positive bacteria, redesigned their gene expression mechanisms, resulting in rapid sequence evolution. In this scenario, eucaryal genes are more closely related to archaeal genes or to gram-negative bacterial genes, since any affinity with gram-positive bacterial genes would be outweighed by the closer similarity to archaeal genes. is a gram-negative member of the gram-positive lineage, with the simplest of bacteriochlorophyll (BChl)-based photosynthetic apparatuses. + , addition of depth to the otherwise sheet-like murein sacculus; −, loss of the bacterial outer membrane, characteristic of gram-negative bacteria and believed to be ancestral ( ); AEexpr., invention of the archaeal-eucaryal style of gene expression and loss of peptidoglycan.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6

General model of the history of life, in which generic traits are largely inherited by descent except for common intraphyletic lateral genetic transfer—hence the thick branches—and occasional interphyletic lateral genetic transfer. The shaded bands represent contemporary gene pools, and the degree of shading indicates both the ease with which cross-kingdom exchanges might have occurred and the impact on all of extant life of such exchanges. The daggers indicate extinct lineages.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Amils, R.,, L. Ramírez,, J. L. Sanz,, I. Marín,, A. G. Pisabarro,, and D. Ureña. 1989. The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny. Can. J. Microbiol. 35:141147.
2. Antón, J.,, P. López-García,, J. P. Abad,, C. L. Smith,, and R. Amils. 1994. Alignment of genes and Swa I restriction sites to the Bam HI genomic map of Haloferax mediterranei. FEMS Microbiol. Lett. 117:5360.
3. Baldauf, S. L.,, J. D. Palmer,, and W. F. Doolittle. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93: 77497754.
4. Baumann, P.,, and S. P. Jackson. 1996. An archaebacterial homologue of the essential eubacterial cell division protein FtsZ. Proc. Natl. Acad. Sci. USA 93:67266730.
5. Bouthier de la Tour, C.,, C. Portemer,, M. Nadal,, K. O. Stetter,, P. Forterre,, and M. Duguet. 1990. Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria. J. Bacteriol. 172:68036808.
6. Bouthier de la Tour, C.,, C. Portemer,, R. Huber,, P. Forterre,, and M. Duguet. 1991. Reverse gyrase in thermophilic eubacteria.J. Bacteriol. 173:39213923.
7. Brendel, V.,, L. Brocchieri,, S. J. Sandler,, A. J. Clark,, and S. Karlin. 1997. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44:528541.
8. Brown, J. R.,, and W. F. Doolittle. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92:24412445.
9. Brown, J. R.,, and W. F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61:456502.
10. Bult, C. J.,, O. White,, G. J. Olsen,, L. Zhou,, R. D. Fleischmann,, G. G. Sutton,, J. A. Blake,, L. M. FitzGerald,, R. A. Clayton,, J. D. Gocayne,, A. R. Kerlavage,, B. A. Dougherty,, J.-F. Tomb,, M. D. Adams,, C. I. Reich,, R. Overbeek,, E. F. Kirkness,, K. G. Weinstock,, J. M. Merrick,, A. Glodek,, J. L. Scott,, N. S. M. Geoghagen,, J. F. Weidman,, J. L. Fuhrmann,, D. Nguyen,, T. R. Utter-back,, J. M. Kelley,, J. D. Peterson,, P. W. Sadow,, M. C. Hanna,, M. D. Cotton,, K. M. Roberts,, M. A. Hurst,, B. P. Kaine,, M. Bor-odovsky,, H.-P. Klenk,, C. M. Fräser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 10581073.
11. Cavalier-Smith, T. 1990. Microorganism megaevolution: integrating the fossil and living evidence. Rev. Micropaléontologie 33:145154.
12. Cavalier-Smith, T. 1992. Bacteria and eukaryotes. Nature 356:570.
13. Charlebois, R. L. 1996. The modern science of bacterial genomics. ASM News 62:255259.
14. Charlebois, R. L., 1999. Evolutionary origins of the haloarchaeal genome, p. 309317. In A. Oren (ed.), Microbiology and Biogeochemistry of Hypersaline Environments. CRC Press, Boca Raton, Fla..
15. Charlebois, R. L.,, and W. F. Doolittle,. 1989. Transposable elements and genome structure in halobacteria, p. 297307. In M. Howe, and D. Berg (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C..
16. Charlebois, R. L.,, and A. St. Jean. 1995. Supercoiling and map stability in the bacterial chromosome. J. Mol. Evol. 41:1523.
17. Charlebois, R. L.,, L. C. Schalkwyk,, J. D. Hofman,, and W. F. Doolittle. 1991. A detailed physical map and set of overlapping clones covering the genome of the archaebacterium Halqferax volcanii DS2 J. Mol. Biol. 222:509524.
18. Charlebois, R. L.,, T. Gaasterland,, M. A. Ragan,, W. F. Doolittle,, and C. W. Sensen. 1996. The Sulfolobus solfataricus P2 genome project. FEBS Lett. 389:8891. (Erratum, 398:343.).
19. Cohen, A.,, W. L. Lam,, R. L. Charlebois,, W. F. Doolittle,, and L. C. Schalkwyk. 1992. Localizing genes on the map of the genome of Halqferax volcanii, one of the Archaea. Proc. Natl. Acad. Sci. USA 89:16021606.
20. Confalonieri, F.,, C. Elie,, M. Nadal,, C. Bouthier de la Tour,, P. Forterre,, and M. Duguet. 1993. Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide. Proc. Natl. Acad. Sci. USA 90:47534757.
21. DasSarma, S. 1989. Mechanisms of genetic variability in Halobacterium halobium: the purple membrane and gas vesicle mutations. Can. J. Microbiol. 35:6572.
22. Dawkins, R. 1976 The Selfish Gene. Oxford University Press, Oxford, United Kingdom.
23. Deckert, G.,, P. V. Warren,, T. Gaasterland,, W. G. Young,, A. L. Lenox,, D. E. Graham,, R. Overbeek,, M. A. Snead,, M. Keller,, M. Aujay,, R. Huber,, R. A. Feldman,, J. M. Short,, G.J. Olsen,, and R. V. Swanson. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353358.
24. Dennis, P. P.,, and L. C. Shimmin. 1997. Evolutionary divergence and salinity-mediated selection in halophilic archaea. Microbiol. Mol. Biol. Rev. 61:90104.
25. Doolittle, R. F. 1995. The origins and evolution of eukaryotic proteins. Phil. Trans. R. Soc. Lond. B 349:235240.
26. Doolittle, R. F. 1998. Microbial genomes opened up. Nature 392:339342.
27. Doolittle, R. F.,, D.-F. Feng,, S. Tsang,, G. Cho,, and E. Little. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470477.
28. Doolittle, W. F.,, and J. R. Brown. 1994. Tempo, mode, the progenote, and the universal root. Proc. Natl. Acad. Sci. USA 91:67216728.
29. Ebert, K.,, and W. Goebel. 1985. Conserved and variable regions in the chromosomal and extrachromosomal DNA of halobacteria. Mol. Gen. Genet. 200:96102.
30. Ebert, K.,, W. Goebel,, and F. Pfeifer. 1984. Homologies between heterogeneous extrachromosomal DNA populations of Halobacterium halobium and four new halobacterial isolates. Mol. Gen. Genet. 194:9197.
31. Edgell, D. R.,, and W. F. Doolittle. 1997. Archaebacterial genomics: the complete genomic sequence of Methanococcus jannaschii. Bioessays 19:14.
32. Edgell, D. R.,, H.-P. Klenk,, and W. F. Doolittle. 1997. Gene duplications in evolution of archaeal family B DNA polymerases. J. Bacteriol. 179:26322640.
33. Fitch, W. M.,, and K. Upper. 1987. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp. Quant. Biol 52: 759767.
34. Fitz-Gibbon, S.,, A. J. Choi,, J. H. Miller,, K. O. Stetter,, M. I. Simon,, R. Swanson,, and U.-J. Kim. 1997. A fosmid-based genomic map and identification of 474 genes of the hyper-thermophilic archaeon Pyrobaculum aerophilum. Extremophiles 1:3651.
35. Forterre, P., 1992. New hypotheses about the origins of viruses, prokaryotes and eukaryotes, p. 221234. In I. K. Trân Thanh Vân,, J. C. Mounolou,, J. Schneider,, and C. McKay (ed.), Frontiers of Life. Éditions Frontieres, Gif-sur-Yvette, France.
36. Forterre, P. 1995. Thermoreduction, a hypothesis for the origin of prokaryotes. C. R. Acad. Sci. III 318:415422.
37. Forterre, P.,, N. Benachenhou-Lahfa,, F. Confalonieri,, M. Duguet,, C. Elie,, and B. Labedan. 1993. The nature of the last universal ancestor and the root of the tree of life, still open questions. BioSystems 28:1532.
38. Forterre, P.,, F. Confalonieri,, F. Charbonnier,, and M. Duguet. 1995. Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive. Orig. Life Evol. Biosph. 25:235249.
39. Forterre, P.,, A. Bergerat,, and P. LopezGarcia. 1996. The unique DNA topology and DNA topoisomerases of hyperthermophilic Archaea. FEMS Microbiol. Rev. 18:237248.
39a.. Fortier, A.,, and R. L. Charlebois. Unpublished data.
40. Fox, G. E.,, L. J. Magrum,, W. E. Balch,, R. S. Wolfe,, and C. R. Woese. 1977. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc. Natl. Acad. Sci. USA 74:45374541.
41. Fox, G. E.,, E. Stackebrandt,, R. B. Hespell,, J. Gibson,, J. Maniloff,, T. A. Dyer,, R. S. Wolfe,, W. E. Balch,, R. S. Tanner,, L. J. Magrum,, L. B. Zablen,, R. Blakemore,, R. Gupta,, L. Bönen,, B. J. Lewis,, D. A. Stahl,, K. R. Luehrsen,, K. N. Chen,, and C. R. Woese. 1980. The phylogeny of prokaryotes. Science 209:457463.
42. Fujiwara, S.,, S. Okuyama,, and T. Imanaka. 1996. The world of archaea: genome analysis, evolution and thermostable enzymes. Gene 179: 165170.
42a.. Gaasterland, T.,, and M. A. Ragan. 1998. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics 3:199217.
43. Gambacorta, A.,, A. Trincone,, B. Nicolaus,, L. Lama,, and M. De Rosa. 1994. Unique features of lipids of Archaea. Syst. Appl. Microbiol. 16:518527.
44. Gogarten, J. P.,, H. Kibak,, P. Dittrich,, L. Taiz,, E. J. Bowman,, B. J. Bowman,, M. F. Manolson,, R. J. Poole,, T. Date,, T. Oshima,, J. Konishi,, K. Denda,, and M. Yoshida. 1989. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl Acad. Sci. USA 86:66616665.
45. Golding, G. B.,, and R. S. Gupta. 1995. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol Biol Evol. 12: 16.
46. Gray, M. W.,, and W. F. Doolittle. 1982. Has the endosymbiont hypothesis been proven? Microbiol Rev. 46:142.
47. Grayling, R. A.,, K. Sandman,, and J. N. Reeve. 1994. Archaeal DNA binding proteins and chromosome structure. Syst. Appl Microbiol. 16:582590.
48. Gribaldo, S.,, V. Lumia,, R. Creti,, E. Conway de Macario,, A. Sanangelantoni,, and P. Cammarano. 1999. Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol. 181:434443.
49. Gupta, R. 1984. Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol Chem. 259:94619471.
50. Gupta, R.,, J. M. Lanter,, and C. R. Woese. 1983. Sequence of the 16S ribosomal RNA from Halobacterium volcanii, an archaebacterium. Science 221:656659.
51. Gupta, R. S. 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62:14351491.
52. Gupta, R. S.,, and G. B. Golding. 1993. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J. Mol. Evol. 37:573582.
53. Gupta, R. S.,, and B. Singh. 1994. Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr. Biol. 4:11041114.
54. Gupta, R. S.,, K. Aitken,, M. Falah,, and B. Singh. 1994. Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 91:28952899.
55. Gutiérrez, M. C.,, M. T. García,, A. Ventosa,, J. J. Nieto,, and F. Ruiz-Berraquero. 1986. Occurrence of megaplasmids in halobacteria. J. Appl. Bacteriol. 61:6771.
56. Hackett, N. R.,, Y. Bobovnikova,, and N. Heyrovska. 1994. Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium. J. Bacteriol. 176:77117718.
57. Hilpert, R.,, J. Winter,, W. Hammes,, and O. Kandier. 1981. The sensitivity of archaebacteria to antibiotics. Zentbl. Bakteriol. Hyg. Abt. 1 Orig. C 2:1120.
58. Itaya, M. 1995. An estimation of minimal genome size required for life. FEBS Lett. 262: 257260.
59. Iwabe, N.,, K. Kuma,, M. Hasegawa,, S. Osawa,, and T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86: 93559359.
60. Kandier, O. 1994. Cell wall biochemistry and the three-domain concept of life. Syst. Appl. Microbiol. 16:501509.
61. Karawabayasi, Y.,, M. Sawada,, H. Horikawa,, Y. Haikawa,, Y. Hino,, S. Yamamoto,, M. Sekine,, S. Baba,, H. Kosugi,, A. Hosoyama,, Y. Nagai,, M. Sakai,, K. Ogura,, R. Otsuka,, H. Nakazawa,, M. Takamiya,, Y. Ohfuku,, T. Funahashi,, T. Tanaka,, Y. Kudoh,, J. Yamazaki,, N. Kushida,, A. Oguchi,, K. Aoki,, and H. Kikuchi. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:5576.
61a.. Karawabayasi, Y.,, M. Sawada,, H. Horikawa,, Y. Haikawa,, Y. Hino,, S. Yamamoto,, M. Sekine,, S. Baba,, H. Kosugi,, A. Hosoyama,, Y. Nagai,, M. Sakai,, K. Ogura,, R. Otsuka,, H. Nakazawa,, M. Takamiya,, Y. Ohfuku,, T. Funahashi,, T. Tanaka,, Y. Kudoh,, J. Yamazaki,, N. Kushida,, A. Oguchi,, K. Aoki,, and H. Kikuchi. 1998. complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 (supplement). DNA Res. 5:147155.
62. Keeling, P. J.,, and W. F. Doolittle. 1995. Archaea: narrowing the gap between prokaryotes and eukaryotes. Proc. Natl. Acad. Sci. USA 92: 57615764.
63. Keeling, P. J.,, R. L. Charlebois,, and W. F. Doolittle. 1994. Archaebacterial genomes: eubacterial form and eukaryotic content. Curr. Opin. Genet. Dev. 4:816822.
64. Klenk, H.-P.,, P. Palm,, and W. Zillig. 1994. DNA-dependent RNA polymerases as phylogenetic marker molecules. Syst. Appl. Microbiol. 16:638647.
65. Klenk, H.-P.,, R. A. Clayton,, J.-F. Tomb,, O. White,, K. E. Nelson,, K. A. Ketchum,, R. J. Dodson,, M. Gwinn,, E. K. Hickey,, J. D. Peterson,, D. L. Richardson,, A. R. Kerlavage,, D. E. Graham,, N. C. Kyrpides,, R. D. Fleischmann,, J. Quackenbush,, N. H. Lee,, G. G. Sutton,, S. Gill,, E. F. Kirkness,, B. A. Dougherty,, K. McKenney,, M. D. Adams,, B. Loftus,, S. Peterson,, C. I. Reich,, L. K. McNeil,, J. H. Badger,, A. Glodek,, L. Zhou,, R. Overbeek,, J. D. Gocayne,, J. F. Weidman,, L. McDonald,, T. Utterback,, M. D. Cotton,, T. Spriggs,, P. Artiach,, B. P. Kaine,, S. M. Sykes,, P. W. Sadow,, K. P. D'Andrea,, C. Bowman,, C. Fujii,, S. A. Garland,, T. M. Mason,, G. J. Olsen,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic sulphate-reducing archaeon Archaeoglobus fulgidus. Nature (London) 390:364370.
66. Kolstø, A.-B. 1997. Dynamic bacterial genome organization. Mol. Microbiol. 24:241248.
67. Kondo, S.,, A. Yamagishi,, and T. Oshima. 1993. A physical map of the sulfur-dependent archaebacterium Sulfolobus acidocaldarius 7 chromosome. J. Bacteriol. 175:15321536.
68. Koonin, E. V.,, A. R. Mushegian,, M. Y. Galperin,, and D. R. Walker. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol 25:619637.
69. Lan, R.,, and P. R. Reeves. 1996. Gene transfer is a major factor in bacterial evolution. Mol Biol Evol 13:4755.
70. Langer, D.,, J. Hain,, P. Thuriaux,, and W. Zillig. 1995. Transcription in Archaea: similarity to that in Eucarya. Proc. Natl Acad. Sci. USA 92: 57685772.
71. Lawrence, J. G.,, and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol Evol 44:383397.
72. Lawson, F. S.,, R. L. Charlebois,, and J. R. Dillon. 1996. Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life. Mol. Biol. Evol. 13:970977.
73. LefFers, H.,, J. Kjems,, L. Østergaard,, N. Larsen,, and R. A. Garrett. 1987. Evolutionary relationships amongst archaebacteria. A comparative study of 23S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen. J. Mol Biol. 195:4361.
74. López-García, P.,, J. P. Abad,, C. Smith,, and R. Amils. 1992. Genomic organization of the halophilic archaeon Haloferax mediterranei: physical map of the chromosome. Nucleic Acids Res. 20: 24592464.
75. López-García, P.,, A. St. Jean,, R. Amils,, and R. L. Charlebois. 1995. Genomic stability in the archaea Haloferax volcanii and Haloferax mediterranei. J. Bacteriol. 177:14051408.
76. López-García, P.,, R. Amils,, and J. Anton. 1996. Sizing chromosomes and megaplasmids in haloarchaea. Microbiology 142:14231428.
77. Lurz, R.,, M. Grote,, J. Dijk,, R. Reinhardt,, and B. Dobrinski. 1986. Electron microscopic study of DNA complexes with proteins from the archaebacterium Sulfolobus acidocaldarius. EMBOJ. 5:37153721.
78. Mai, V. Q.,, X. Chen,, R. Hong,, and L. Huang. 1998. Small abundant DNA binding proteins from the thermoacidophilic archaeon Sulfolobus shibatae constrain negative DNA supercoils. J. Bacteriol. 180:25602563.
79. Margulis, L. 1996. Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl Acad. Sci. USA 93:10711076.
80. Martin, W.,, and M. Müller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392: 3741.
81. Mayr, E. 1990. A natural system of organisms. Nature 348:491.
82. McCloskey, J. A. 1986. Nucleoside modification in archaebacterial transfer RNA. Syst. Appl. Microbiol. 7:246252.
83. Moore, R. L.,, and B. J. McCarthy. 1969. Characterization of the deoxyribonucleic acid of various strains of halophilic bacteria. J. Bacteriol. 99:248254.
84. Mushegian, A. R.,, and E. V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93:1026810273.
85. Ng, W.-L. V.,, S. A. Ciufo,, T. M. Smith,, R. E. Bumgarner,, D. Baskin,, J. Faust,, B. Hall,, C. Loretz,, J. Seto,, J. Slagel,, L. Hood,, and S. DasSarma. 1998. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res. 8: 11311141.
86. Noll, K. M. 1989. Chromosome map of the thermophilic archaebacterium Thermococcus celer. J. Bacteriol. 171:67206725.
87. Olsen, G. J.,, and C. R. Woese. 1997. Archaeal genomes: an overview. Cell 89:991994.
88. Pfeifer, F. 1986. Insertion elements and genome organization of Halobacterium halobium. Syst. Appl. Microbiol. 7:3640.
89. Pfeifer, F.,, and M. Betlach. 1985. Genome organization in Halobacterium halobium: a 70 kb island of more (AT) rich DNA in the chromosome. Mol. Gen. Genet. 198:449455.
90. Pfeifer, F.,, G. Weidinger,, and W. Goebel. 1981. Characterization of plasmids in halobacteria. J. Bacteriol. 145:369374.
91. Pfeifer, F.,, G. Weidinger,, and W. Goebel. 1981. Genetic variability in Halobacterium halobium. J. Bacteriol 145:375381.
92. Pfeifer, F.,, K. Ebert,, G. Weidinger,, and W. Goebel. 1982. Structure and functions of chromosomal and extrachromosomal DNA in halobacteria. Zentbl. Bakteriol. Hyg. Abt. 1 Orig. C 3:110119.
93. Pfeifer, F.,, U. Blaseio,, and P. Ghahraman. 1988. Dynamic plasmid populations in Halobacterium halobium. J. Bacteriol. 170:37183724.
94. Pfeifer, F.,, U. BlaScio,, and M. Home. 1989. Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants. Can. J. Microbiol 35:96100.
95. Pfeifer, F.,, J. Griffig,, and D. Oesterhelt. 1993. The fdx gene encoding the [2Fe-2S] ferredoxin of Halobacterium salinarium (H. halobium). Mol Gen. Genet. 239:6671.
96. Poplawski, A.,, and R. Bernander. 1997. Nucleoid structure and distribution in thermophilic Archaea. J. Bacteriol 179:76257630.
97. Reeve, J. N.,, J. Nölling,, R. M. Morgan,, and D. R. Smith. 1997. Methanogenesis: genes, genomes, and who's on first? J. Bacteriol. 179: 59755986.
98. Rivera, M. C.,, and J. A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:7476.
99. Ronimus, R. S.,, and D. R. Musgrave. 1995. A comparison of the DNA binding properties of histone-like proteins derived from representatives of the two kingdoms of the Archaea. FEMS Microbiol. Lett. 134:7984.
100. Ronimus, R. S.,, and D. R. Musgrave. 1996. A gene, han 1A, encoding an archaeal histone-like protein from the Thermococcus species AN1: homology with eukaryal histone consensus sequences and the implications for delineation of the histone fold. Biochim. Biophys. Acta 1307:17.
101. Schleper, C.,, R. Röder,, T. Singer,, and W. Zillig. 1994. An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous β-galactosidase gene. Mol. Gen. Genet. 243:9196.
102. Sensen, C. W.,, H.-P. Klenk,, R. K. Singh,, G. Allard,, C. C.-Y. Chan,, Q. Y. Liu,, S. L. Penny,, F. Young,, M. E. Schenk,, T. Gaasterland,, W. F. Doolittle,, M. A. Ragan,, and R. L. Charlebois. 1996. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol. Microbiol. 22:175191.
103. Sitzmann, J.,, and A. Klein. 1991. Physical and genetic map of the Methanococcus voltae chromosome. Mol. Microbiol. 5:505513.
104. Smith, D. R.,, L. A. Doucette-Stamm,, C. Deloughery,, H. Lee,, J. Dubois,, T. Aldredge,, R. Bashirzadeh,, D. Blakely,, R. Cook,, K. Gilbert,, D. Harrison,, L. Hoang,, P. Keagle,, W. Lumm,, P. Pothier,, D. Qiu,, R. Spadafora,, R. Vicaire,, Y. Wang,, J. Wierzbowski,, R. Gibson,, N. Jiwani,, A. Caruso,, D. Bush,, H. Safer,, D. Patwell,, S. Prabhakar,, S. McDougall,, G. Shimer,, A. Goyal,, S. Pietrokovski,, G. M. Church,, C. J. Daniels,, J.-I. Mao,, P. Rice,, J. Nölling,, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum δ H: functional analysis and comparative genomics. J. Bacteriol. 179:71357155.
105. Smith, M. W.,, D.-F. Feng,, and R. F. Doolittle. 1992. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17:489493.
106. Sogin, M. L. 1991. Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1:457463.
107. Stettler, R.,, and T. Leisinger. 1992. Physical map of the Methanobacterium thermoautotrophicum Marburg chromosome. J. Bacteriol. 174:72277234.
108. Stettler, R.,, G. Erauso,, and T. Leisinger. 1995. Physical and genetic map of the Methanobacterium wolfei genome and its comparison with the updated genomic map of Methanobacterium thermoautotrophicum Marburg. Arch. Microbiol. 163:205210.
109. St. Jean, A.,, and R. L. Charlebois. 1996. Comparative genomic analysis of the Haloferax volcanii DS2 and Halobacterium salinarium GRB contig maps reveals extensive rearrangement. J. Bacteriol. 178:38603868.
109a.. St. Jean, A.,, and R. L. Charlebois. Unpublished data.
110. St. Jean, A.,, B. A. Trieselmann,, and R. L. Charlebois. 1994. Physical map and set of overlapping cosmid clones representing the genome of the archaeon Halobacterium sp. GRB. Nucleic Acids Res. 22:14761483.
111. Takayanagi, S.,, S. Morimura,, H. Kusaoke,, Y. Yokoyama,, K. Kano,, and M. Shioda. 1992. Chromosomal structure of the halophilic archaebacterium Halobacterium salinarium. J. Bacteriol. 174:72077216.
112. Tchelet, R.,, and M. Mevarech. 1994. Interspecies genetic transfer in halophilic archaebacteria. Syst. Appl. Microbiol. 16:578581.
113. Walsby, A. E. 1994. Gas vesicles. Microbiol Rev. 58:94144.
114. Weidinger, G.,, G. Klotz,, and W. Goebel. 1979. A large plasmid from Halobacterium halobium carrying genetic information for gas vacuole formation. Plasmid 2:377386.
115. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221271.
116. Woese, C. R. 1998. The universal ancestor. Proc. Natl. Acad. Sci. USA 95:68546859.
117. Woese, C. R.,, and G. E. Fox. 1977. The concept of cellular evolution. J. Mol. Evol. 10: 16.
118. Woese, C. R.,, and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:50885090.
119. Woese, C. R.,, O. Kandier,, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:45764579.
120. Zillig, W. 1991. Comparative biochemistry of Archaea and Bacteria. Curr. Opin. Genet. Dev. 1:544551.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error