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Chapter 19 : Structure and Evolution of Genomes

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Abstract:

The existence of many informational proteins that are common to and and absent from is not only true for DNA replication, but also for translation, transcription, and RNA and protein processing. Many reviews have summarized insight from newly sequenced archaeal genomes and have usually focused on aspects of comparative genomics. This chapter focuses on the description of archaeal genomes and what can be learned from archaeal genomics about the mechanisms of genome evolution, and the history of the domain itself. Compared with , the number of completely sequenced archaeal genomes is much smaller. The larger genomes are from mesophilic archaea and contain a high proportion of genes recruited from bacteria by horizontal gene transfer (HGT). The chromosome terminus appears to be a hot spot of recombination in archaea, as it is in bacteria. This was clearly shown from a genome comparison of the two closely related species, and . Comparative genomics has shown that gene loss, gene duplication, and integration of foreign DNA are major forces shaping genome evolution. The continuous evolution of archaeal genomes by gene loss and acquisition is obvious from the comparative analyses of the proteomes of closely related species. In a recent study using unfolding simulation experiments to determine amino acid composition, the number of charged residues in hyperthermophiles was reported to be much greater than it would need to be for the stabilization. Ongoing metagenomics projects will continue to broaden the understanding of archaeal diversity and evolution.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19

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Figures

Image of Figure 1
Figure 1

(a) A schematic drawing of a DNA replication fork in and . The leading strand (thick line) is enriched in guanine residues or specific nucleotide words with respect to the lagging strand (thin line). (b) At the origin and terminus of DNA replication ( and , respectively) the leading strand becomes the lagging strand, and vice versa. (c) It is possible to localize the origin and terminus of DNA replication by scanning from an arbitrary position any complete genome sequence for either GC or specific word skews. Cumulative skews exhibit two inverted peaks on each side of the baseline, which correspond to the origin and terminus of replication.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Image of Figure 2
Figure 2

Graphs of cumulative skew and GC skew for and . Putative in both species are indicated by arrows.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Image of Figure 3
Figure 3

Marker frequency analysis. In a population of nonsynchronized cells, the copy number of a particular gene is directly proportional to its closeness to the origin of replication (). Boxes represent genes. Gene 1 is the closest to and the most represented.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Image of Figure 4
Figure 4

(A) A schematic view of the genome organization of the two closely related species and . Fragments E and F in the terminus region show a translocation between the two species, while fragment A, containing , and fragment C show an inversion. (B) Comparative BLAST-hit plot of the two genomes. (Adapted from reference with permission.)

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Figure 5

Schematic structure of a typical CRISPR.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Image of Figure 6
Figure 6

Cumulative transcription skew lines are smooth at fragments E, F, and C in , while they are disturbed in . (Adapted from reference with permission.)

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Figure 7

The percentage of various classes of amino acids in gene coding sequences from hyperthermophiles and mesophiles. Percentages were calculated for 9 fully sequenced hyperthermophilic and 53 mesophilic bacteria and archaea. Grey and black vertical bars indicate the mesophiles and the hyperthermophiles, respectively. The axis indicates percentages. CHA, charged; POL, polar; ALIPH, aliphatic; AROM, aromatic.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Figure 8

Unrooted maximum likelihood (ML) trees based on concatenation of 53 ribosomal proteins (A) and 12 RNA polymerase subunits and two transcription factors (B). Numbers at nodes are bootstrap values (BVs). The scale bars represent the number of changes per position for a unit branch length. Trees were produced by exhaustive searches performed by PROTML ( ). Branch lengths and likelihood values were calculated by TREE-PUZZLE (JJT model including a (-correction [8 categories of sites]) ( ). Numbers at nodes are bootstrap values computed with PUZZLEBOOT ( ) from 1,000 replications. Asterisks indicate constrained nodes (supported by BV = 100% in preliminary NJ and heuristic ML analyses). The names of groups showing incongruent positions between the two trees are in bold. (Adapted from reference with permission.)

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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Figure 9

An ideal tree of the based on recent phylogenetic analyses of large concatenated protein data sets.

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
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References

/content/book/10.1128/9781555815516.ch19
1. Adachi, J., and, M. Hasegawa. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1150.
2. Andersson, J. O.,, S. W. Sarchfield, and, A. J. Roger. 2005. Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol. Biol. Evol. 22:8590.
3. Aravind, L., and, E. V. Koonin. 1999. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27:46584670.
4. Atomi, H.,, R. Matsumi, and, T. Imanaka. 2004. Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol. 186:48294833.
5. Basak, S., and, T. C. Ghosh. 2005. On the origin of genomic adaptation at high temperature for prokaryotic organisms. Biochem. Biophys. Res. Commun. 330:629632.
6. Bentley, S. D.,, K. F. Chater,, A. M. Cerdeno-Tarraga,, G. L. Challis,, N. R. Thomson,, K. D. James,, D. E. Harris,, M. A. Quail,, H. Kieser,, D. Harper,, A. Bateman,, S. Brown,, G. Chandra,, C. W. Chen,, M. Collins,, A. Cronin,, A. Fraser,, A. Goble,, J. Hidalgo,, T. Hornsby,, S. Howarth,, C. H. Huang,, T. Kieser,, L. Larke,, L. Murphy,, K. Oliver,, S. O’Neil,, E. Rabbinowitsch,, M. A. Rajandream,, K. Rutherford,, S. Rutter,, K. Seeger,, D. Saunders,, S. Sharp,, R. Squares,, S. Squares,, K. Taylor,, T. Warren,, A. Wietzorrek,, J. Woodward,, B. G. Barrell,, J. Parkhill, and, D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141147.
7. Berezovsky, I. N., and, E. I. Shakhnovich. 2005. Physics and evolution of thermophilic adaptation. Proc. Natl. Acad. Sci. USA 102:1274212747.
8. Berquist, B. R., and, S. DasSarma. 2003. An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J. Bacteriol. 185:59595966.
9. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirk-patrick,, M. A. Goeden,, D. J. Rose,, B. Mau, and, Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
10. Brewer, B. J. 1988. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53:679686.
11. Brinkmann, H., and, H. Philippe. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:817825.
12. Brochier, C.,, P. Forterre, and, S. Gribaldo. 2005. An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5:36.
13. Brochier, C.,, P. Forterre, and, S. Gribaldo. 2004. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5:R17.
14. Brochier, C.,, S. Gribaldo,, Y. Zivanovic,, F. Confalonieri, and, P. Forterre. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6:R42.
15. Brügger, K.,, P. Redder,, Q. She,, F. Confalonieri,, Y. Zivanovic, and, R. A. Garrett. 2002. Mobile elements in archaeal genomes. FEMS Microbiol. Lett. 206:131141.
16. Brugger, K.,, E. Torarinsson,, P. Redder,, L. Chen, and, R. A. Garrett. 2004. Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements. Biochem. Soc. Trans. 32:179183.
17. 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, and, J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:10581073.
18. Caetano-Anolles, G., and, D. Caetano-Anolles. 2005. Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J. Mol. Evol. 60:484498.
19. Cambillau, C., and, J. M. Claverie. 2000. Structural and genomic correlates of hyperthermostability. J. Biol. Chem. 275:3238332386.
20. Cate, J. H.,, A. R. Gooding,, E. Podell,, K. Zhou,, B. L. Golden,, A. A. Szewczak,, C. E. Kundrot,, T. R. Cech, and, J. A. Doudna. 1996. RNA tertiary structure mediation by adenosine platforms. Science 273:16961699.
21. Cavicchioli, R.,, P. M. Curmi,, N. Saunders, and, T. Thomas. 2003. Pathogenic archaea: do they exist? Bioessays 25:11191128.
22. Charbonnier, F., and, P. Forterre. 1994. Comparison of plasmid DNA topology among mesophilic and thermophilic eu-bacteria and archaebacteria. J. Bacteriol. 176:12511259.
23. Chen, L.,, K. Brugger,, M. Skovgaard,, P. Redder,, Q. She,, E. Torarinsson,, B. Greve,, M. Awayez,, A. Zibat,, H. P. Klenk, and, R. A. Garrett. 2005. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J. Bacteriol. 187:49924999.
24. Chinen, A.,, I. Uchiyama, and, I. Kobayashi. 2000. Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 259:109121.
25. Ciaramella, M.,, A. Napoli, and, M. Rossi. 2005. Another extreme genome: how to live at pH 0. Trends Microbiol. 13:4951.
26. Cohen, G. N.,, V. Barbe,, D. Flament,, M. Galperin,, R. Heilig,, O. Lecompte,, O. Poch,, D. Prieur,, J. Querellou,, R. Ripp,, J. C. Thierry,, J. Van der Oost,, J. Weissenbach,, Y. Zivanovic, and, P. Forterre. 2003. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47:14951512.
27. Constantinesco, F.,, P. Forterre,, E. V. Koonin,, L. Aravind, and, C. Elie. 2004. A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Nucleic Acids Res. 32:14391447.
28. Cubonova, L.,, K. Sandman,, S. J. Hallam,, E. F. Delong, and, J. N. Reeve. 2005. Histones in crenarchaea. J. Bacteriol. 187:54825485.
29. Daubin, V.,, M. Gouy, and, G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12:10801090.
30. Delsuc, E,, H. Brinkmann, and, H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361375.
31. Deppenmeier, U.,, A. Johann,, T. Hartsch,, R. Merkl,, R. A. Schmitz,, R. Martinez-Arias,, A. Henne,, A. Wiezer,, S. Baumer,, C. Jacobi,, H. Bruggemann,, T. Lienard,, A. Christmann,, M. Bomeke,, S. Steckel,, A. Bhattacharyya,, A. Lykidis,, R. Overbeek,, H. P. Klenk,, R. P. Gunsalus,, H. J. Fritz, and, G. Gotts-chalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453461.
32. Diruggiero, J.,, D. Dunn,, D. L. Maeder,, R. Holley-Shanks,, J. Chatard,, R. Horlacher,, F. T. Robb,, W. Boos, and, R. B. Weiss. 2000. Evidence of recent lateral gene transfer among hyperthermophilic archaea. Mol. Microbiol. 38:684693.
33. Fitz-Gibbon, S. T,, H. Ladner,, U. J. Kim,, K. O. Stetter,, M. I. Simon, and, J. H. Miller. 2002. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 99:984989.
34. Forterre, P. 2002. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 18:236237.
35. Forterre, P. 1997. Archaea: what can we learn from their sequences? Curr. Opin. Genet. Dev. 7:764670.
36. Forterre, P. 1995. Thermoreduction, a hypothesis for the origin of prokaryotes. C. R. Acad. Sci. Ser. III 318:415422.
37. Forterre, P.,, C. Bouthier De La Tour,, H. Philippe, and, M. Duguet. 2000. Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet. 16:152154.
38. Frank, A. C., and, J. R. Lobry. 1999. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:6577.
39. Fukui, T,, H. Atomi,, X. Kanai,, R. Matsumi,, S. Fujiwara, and, T. Imanaka. 2005. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15:352363.
40. Futterer, O.,, A. Angelov,, H. Liesegang,, G. Gottschalk,, C. Schleper,, B. Schepers,, C. Dock,, G. Antranikian, and, W. Liebl. 2004. Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc. Natl. Acad. Sci. USA 101:90919096.
41. Gadelle, D.,, J. Filee,, C. Buhler, and, P. Forterre. 2003. Phylogenomics of type II DNA topoisomerases. Bioessays 25:232242.
42. Galagan, J. E.,, C. Nusbaum,, A. Roy,, M. G Endrizzi,, P. Macdonald,, W. FitzHugh,, S. Calvo,, R. Engels,, S. Smirnov,, D. Atnoor,, A. Brown,, N. Allen,, J. Naylor,, N. Stange-Thomann,, K. DeArellano,, R. Johnson,, L. Linton,, P. McEwan,, K. Mc-Kernan,, J. Talamas,, A. Tirrell,, W. Ye,, A. Zimmer,, R. D. Barber,, I. Cann,, D. E. Graham,, D. A. Grahame,, A. M. Guss,, R. Hed-derich,, C. Ingram-Smith,, H. C. Kuettner,, J. A. Krzycki,, J. A. Leigh,, W. Li,, J. Liu,, B. Mukhopadhyay,, J. N. Reeve,, K. Smith,, T. A. Springer,, L. A. Umayam,, O. White,, R. H. White,, E. Conway de Macario,, J. G. Ferry,, K. E. Jarrell,, H. Jing,, A. J. Macario,, I. Paulsen,, M. Pritchett,, K. R. Sowers,, R. V. Swanson,, S. H. Zinder,, E. Lander,, W W. Metcalf, and, B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532542.
43. Galtier, N., and, J. R. Lobry. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44:632636.
44. Grabowski, B., and, Z. Kelman. 2003. Archeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57:487516.
45. Guipaud, O.,, E. Marguet,, K. M. Noll,, C. B. de la Tour, and, P. Forterre. 1997. Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga mar-itima. Proc. Natl. Acad. Sci. USA 94:1060610611.
46. Haney, P. J.,, J. H. Badger,, G. L. Buldak,, C. I. Reich,, C. R. Woese, and, G. J. Olsen. 1999. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA 96:35783583.
47. Haring, M.,, X. Peng,, K. Brugger,, R. Rachel,, K. O. Stetter,, R. A. Garrett, and, D. Prangishvili. 2004. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323:233242.
48. Hendrickson, E. L.,, R. Kaul,, Y. Zhou,, D. Bovee,, P. Chapman,, J. Chung,, E. Conway de Macario,, J. A. Dodsworth,, W. Gillett,, D. E. Graham,, M. Hackett,, A. K. Haydock,, A. Kang,, M. L. Land,, R. Levy,, T. J. Lie,, T. A. Major,, B. C. Moore,, I. Porat,, A. Palmeiri,, G. Rouse,, C. Saenphimmachak,, D. Soll,, S. Van Dien,, T. Wang,, W. B. Whitman,, Q. Xia,, Y. Zhang,, F. W. Larimer,, M. V. Olson, and, J. A. Leigh. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186:69566969.
49. Herzel, H.,, O. Weiss, and, E. N. Trifonov. 1998. Sequence periodicity in complete genomes of archaea suggests positive supercoiling. J. Biomol. Struct. Dyn. 16:341345.
50. Hickey, D. A., and, G. A. Singer. 2004. Genomic and pro-teomic adaptations to growth at high temperature. Genome Biol. 5:117.
51. Holder, M. E., and, A. J. Roger. 2002. A shell-script program called “puzzleboot” that allows the analysis of multiple data sets with PUZZLE even though PUZZLE lacks the “M” option of many PHYLIP programs. http://hades.biochem.dal.ca/Rogerlab/Software/software.html#puzzleboot.
52. Jansen, R.,, J. D. van Embden,, W. Gaastra, and, L. M. Schouls. 2002. Identification of a novel family of sequence repeats among prokaryotes. Omics 6:2333.
53. Kampmann, M., and, D. Stock. 2004. Reverse gyrase has heat-protective DNA chaperone activity independent of su-percoiling. Nucleic Acids Res. 32:35373545.
54. Kennedy, S. P.,, W. V. Ng,, S. L. Salzberg,, L. Hood, and, S. Das-Sarma. 2001. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11:16411650.
55. Koonin, E. V.,, Y. I. Wolf, and, L. Aravind. 2001. Prediction of the archaeal exosome and its connections with the pro-teasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11:240252.
56. Lake, J. A.,, E. Henderson,, M. Oakes, and, M. W. Clark. 1984. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl. Acad. Sci. USA 81:37863790.
57. Lambros, R. J.,, J. R. Mortimer, and, D. R. Forsdyke. 2003. Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 7:443450.
58. Lao, P. J., and, D. R. Forsdyke. 2000. Thermophilic bacteria strictly obey Szybalski’s transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res. 10:228236.
59. Lecompte, O.,, R. Ripp,, J. C. Thierry,, D. Moras, and, O. Poch. 2002. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res. 30:53825390.
60. Lewis, P. J. 2001. Bacterial chromosome segregation. Microbiology 147:519526.
61. Lobry, J. R. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13:660605.
62. Londei, P. 2005. Evolution of translational initiation: new insights from the archaea. FEMS Microbiol. Rev. 29:185200.
63. Lopez, P.,, H. Philippe,, H. Myllykallio, and, P. Forterre. 1999. Identification of putative chromosomal origins of replication in Archaea. Mol. Microbiol. 32:883886.
64. Lopez-Garcia, P.,, C. Brochier,, D. Moreira, and, F. Rodriguez-Valera. 2004. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ. Microbiol. 6:1934.
65. Lopez-Garcia, P.,, P. Forterre,, J. van der Oost, and, G. Erauso. 2000. Plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled. J. Bacteriol. 182:49985000.
66. Lundgren, M.,, A. Andersson,, L. Chen,, P. Nilsson, and, R. Bernander. 2004. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc. Natl. Acad. Sci. USA 101:70467051.
67. Luscombe, N. M.,, D. Greenbaum, and, M. Gerstein. 2001. What is bioinformatics? A proposed definition and overview of the field. Methods Inf. Med. 40:346358.
68. Lynn, D. J.,, G. A. Singer, and, D. A. Hickey. 2002. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30:42724277.
69. Maeder, D. L.,, R. B. Weiss,, D. M. Dunn,, J. L. Cherry,, J. M. Gonzalez,, J. DiRuggiero, and, F. T. Robb. 1999. Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics 152:12991305.
70. Maisnier-Patin, S.,, L. Malandrin,, N. K. Birkeland, and, R. Bernander. 2002. Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii. Mol. Microbiol. 45:14431450.
71. Makarova, K. S.,, L. Aravind,, M. Y. Galperin,, N. V. Grishin,, R. L. Tatusov,, Y. I. Wolf, and, E. V. Koonin. 1999. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9:608628.
72. Makarova, K. S.,, L. Aravind,, N. V. Grishin,, I. B. Rogozin, and, E. V. Koonin. 2002. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30:482496.
73. Makarova, K. S., and, E. V. Koonin. 2003. Comparative genomics of Archaea: how much have we learned in six years, and what’s next? Genome Biol. 4:115.
74. Makarova, K. S., and, E. V. Koonin. 2005. Evolutionary and functional genomics of the Archaea. Curr. Opin. Microbiol. 117:5267.
75. Makarova, K. S.,, Y. I. Wolf, and, E. V. Koonin. 2003. Potential genomic determinants of hyperthermophily. Trends Genet. 19:172176.
76. Makino, S., and, M. Suzuki. 2001. Bacterial genomic reorganization upon DNA replication. Science 292:803.
77. Marguet, E., and, P. Forterre. 1994. DNA stability at temperatures typical for hyperthermophiles. Nucleic Acids Res. 22:16811686.
78. Marguet, E., and, P. Forterre. 1998. Protection of DNA by salts against thermodegradation at temperatures typical for hyperthermophiles. Extremophiles 2:115122.
79. Marguet, E., and, P. Forterre. 2001. Stability and manipulation of DNA at extreme temperatures. Methods Enzymol. 334:205115.
80. Matsunaga, F.,, P. Forterre,, Y. Ishino, and, H. Myllykallio. 2001. In vivo interactions of archaeal Cdc6/Orc1 and mini-chromosome maintenance proteins with the replication origin. Proc. Natl. Acad. Sci. USA 98:1115211157.
81. Matte-Tailliez, O.,, Y. Zivanovic, and, P. Forterre. 2000. Mining archaeal proteomes for eukaryotic proteins with novel functions: the PACE case. Trends Genet. 16:533536.
82. McLean, M. J.,, K. H. Wolfe, and, K. M. Devine. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:691696.
83. Mojica, F. J.,, C. Diez-Villasenor,, J. Garcia-Martinez, and, E. Soria. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174182.
84. Mojica, F. J.,, C. Diez-Villasenor,, E. Soria, and, G. Juez. 2000. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36:2446.
85. Mojica, F. J.,, C. Ferrer,, G. Juez, and, F. Rodriguez-Valera. 1995. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 17:8593.
86. Mrazek, J., and, S. Karlin. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95:37203725.
87. Myllykallio, H.,, P. Lopez,, P. Lopez-Garcia,, R. Heilig,, W. Saurin,, Y. Zivanovic,, H. Philippe, and, P. Forterre. 2000. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288:22122215.
88. Napoli, A.,, A. Valenti,, V. Salerno,, M. Nadal,, F. Garnier,, M. Rossi, and, M. Ciaramella. 2004. Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus sol-fataricus. J. Biol. Chem. 279:3319233198.
89. Nelson, K. E.,, R. A. Clayton,, S. R. Gill,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, W. C. Nelson,, K. A. Ketchum,, L. McDonald,, T. R. Utterback,, J. A. Malek,, K. D. Linher,, M. M. Garrett,, A. M. Stewart,, M. D. Cotton,, M. S. Pratt,, C. A. Phillips,, D. Richardson,, J. Heidelberg,, G. G. Sutton,, R. D. Fleischmann,, J. A. Eisen, and, C. M. Fraser. 1999. Evidence for lateral gene transfer between Ar-chaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323329.
90. Ng, W. V.,, S. P. Kennedy,, G. G. Mahairas,, B. Berquist,, M. Pan,, H. D. Shukla,, S. R. Lasky,, N. S. Baliga,, V. Thorsson,, J. Sbrogna,, S. Swartzell,, D. Weir,, J. Hall,, T. A. Dahl,, R. Welti,, Y. A. Goo,, B. Leithauser,, K. Keller,, R. Cruz,, M. J. Danson,, D. W. Hough,, D. G. Maddocks,, P. E. Jablonski,, M. P. Krebs,, C. M. Angevine,, H. Dale,, T. A. Isenbarger,, R. F. Peck,, M. Pohlschroder,, J. L. Spudich,, K. H. Jung,, M. Alam,, T. Freitas,, S. Hou,, C. J. Daniels,, P. P. Dennis,, A. D. Omer,, H. Ebhardt,, T. M. Lowe,, P. Liang,, M. Riley,, L. Hood, and, S. DasSarma. 2000. Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. USA. 97:1217612181.
91. Olsen, G. J., and, C. R. Woese. 1997. Archaeal genomics: an overview. Cell 89:991994.
92. Opalka, N.,, M. Chlenov,, P. Chacon,, W. J. Rice,, W. Wriggers, and, S. A. Darst. 2003. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114:335345.
93. Paz, A.,, D. Mester,, I. Baca,, E. Nevo, and, A. Korol. 2004. Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc. Natl. Acad. Sci. USA 101:29512956.
94. Peng, X.,, K. Brugger,, B. Shen,, L. Chen,, Q. She, and, R. A. Garrett. 2003. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J. Bacteriol. 185:24102417.
95. Pietrokovski, S. 2001. Intein spread and extinction in evolution. Trends Genet. 17:465472.
96. Poole, A.,, D. Jeffares, and, D. Penny. 1999. Early evolution: prokaryotes, the new kids on the block. Bioessays 21:880889.
97. Pourcel, C.,, G. Salvignol, and, G. Vergnaud. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151:653663.
98. Querol, E.,, J. A. Perez-Pons, and, A. Mozo-Villarias. 1996. Analysis of protein conformational characteristics related to thermostability. Protein Eng. 9:265271.
99. Robinson, N. P.,, I. Dionne,, M. Lundgren,, V. L. Marsh,, R. Bernander, and, S. D. Bell. 2004. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus sol-fataricus. Cell 116:2538.
100. Rocha, E. P. 2004. Order and disorder in bacterial genomes. Curr. Opin. Microbiol. 7:519527.
101. Rocha, E. P. 2004. The replication-related organization of bacterial genomes. Microbiology 150:16091627.
102. Rocha, E. P., and, A. Danchin. 2003. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat. Genet. 34:377378.
103. Rocha, E. P., and, A. Danchin. 2001. Ongoing evolution of strand composition in bacterial genomes. Mol. Biol. Evol. 18:17891799.
104. Saunders, N. F.,, T. Thomas,, P. M. Curmi,, J. S. Mattick,, E. Kuczek,, R. Slade,, J. Davis,, P. D. Franzmann,, D. Boone,, K. Rusterholtz,, R. Feldman,, C. Gates,, S. Bench,, K. Sowers,, K. Kadner,, A. Aerts,, P. Dehal,, C. Detter,, T. Glavina,, S. Lucas,, P. Richardson,, F. Larimer,, L. Hauser,, M. Land, and, R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methano-genium frigidum and Methanococcoides burtonii. Genome Res. 13:15801588.
105. Schieg, P., and, H. Herzel. 2004. Periodicities of 10–11bp as indicators of the supercoiled state of genomic DNA. J. Mol. Biol. 343:891901.
106. Schmidt, H. A.,, K. Strimmer,, M. Vingron, and, A. von Hae-seler. 2002. TREE-PUZZLE: maximum likelihood phyloge-netic analysis using quartets and parallel computing. Bio-informatics 18:502504.
107. She, Q.,, R. K. Singh,, F. Confalonieri,, Y. Zivanovic,, G. Allard,, M. J. Awayez,, C. C. Chan-Weiher,, I. G. Clausen,, B. A. Curtis,, A. De Moors,, G. Erauso,, C. Fletcher,, P. M. Gordon,, I. Heikamp-de Jong,, A. C. Jeffries,, C. J. Kozera,, N. Medina,, X. Peng,, H. P. Thi-Ngoc,, P. Redder,, M. E. Schenk,, C. Theri-ault,, N. Tolstrup,, R. L. Charlebois,, W. F. Doolittle,, M. Duguet,, T. Gaasterland,, R. A. Garrett,, M. A. Ragan,, C. W. Sensen, and, J. Van der Oost. 2001. The complete genome of the crenarchaeon Sulfolobus sol-fataricus P2. Proc. Natl. Acad. Sci. USA 98:78357840.
108. Singer, G. A., and, D. A. Hickey. 2003. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317:3947.
109. Slesarev, A. I.,, K. V. Mezhevaya,, K. S. Makarova,, N. N. Polushin,, O. V. Shcherbinina,, V. V. Shakhova,, G. I. Belova,, L. Aravind,, D. A. Natale,, I. B. Rogozin,, R. L. Tatusov,, Y. I. Wolf,, K. O. Stetter,, A. G. Malykh,, E. V. Koonin, and, S. A. Kozyavkin. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:46444649.
110. Shure, K., and, J. M. Claverie. 2003. Genomic correlates of hyperthermostability, an update. J. Biol. Chem. 278:1719817202.
111. Tillier, E. R., and, R. A. Collins. 2000. Genome rearrangement by replication-directed translocation. Nat. Genet. 26:195197.
112. Vieille, C., and, G. J. Zeikus. 2001. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 65:143.
113. Waters, E.,, M. J. Hohn,, I. Ahel,, D. E. Graham,, M. D. Adams,, M. Barnstead,, K. Y. Beeson,, L. Bibbs,, R. Bolanos,, M. Keller,, K. Kretz,, X. Lin,, E. Mathur,, J. Ni,, M. Podar,, T. Richardson,, G. G. Sutton,, M. Simon,, D. Soll,, K. O. Stetter,, J. M. Short, and, M. Noordewier. 2003. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 100:1298412988.
114. White, M. F., and, S. D. Bell. 2002. Holding it together: chromatin in the Archaea. Trends Genet. 18:621626.
115. Wiezer, A., and, R. Merkl. 2005. A comparative categorization of gene flux in diverse microbial species. Genomics 86:462475.
116. Woese, C. R.,, O. Kandler, 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.
117. Zhang, J. 1999. Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16:868875.
118. Zhang, R., and, C. T. Zhang. 2005. Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 1:335346.
119. Zhang, R., and, C. T. Zhang. 2004. Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii. Extremophiles 8:253258.
120. Zivanovic, Y.,, P. Lopez,, H. Philippe, and, P. Forterre. 2002. Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30:19021910.

Tables

Generic image for table
Table 1.

Complete and in-progress archaeal genomes in public databases

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
Generic image for table
Table 2.

Archaeal genomes in progress in public databases

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19
Generic image for table
Table 3.

Complete archael genome replication origin identification

Citation: Forterre P, Zivanovic Y, Gribaldo S. 2007. Structure and Evolution of Genomes, p 411-433. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch19

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