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Chapter 5 : Mechanisms of Genome Stability and Evolution †
Author:
Dennis W. Grogan1
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Affiliations:
1: Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006
Content Type: Monograph
Publication Year:
2007
Category: Microbial Genetics and Molecular Biology; Environmental Microbiology
Book DOI:
10.1128/9781555815516
Chapter DOI:
10.1128/9781555815516.ch5
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Mechanisms of Genome Stability and Evolution † , Page 1 of 2
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Abstract:
This chapter examines the ‘’natural genetics’’ of methanogenic, halophilic, and thermophilic archaea, progressing from the molecular scale to cells and finally to populations. The simplest reconciliation of observations would seem to be that the thermophilic and hyperthermophilic archaea have alternative molecular strategies that assume the function of classical MMR and NER systems but do not involve homologous proteins. In its most general sense, genetic recombination means the creation of new DNA sequences from existing sequences by processes involving strand exchange rather than error-prone synthesis. ‘’Illegitimate’’ recombination breaks and joins DNA sequences with negligible influence of the sequences involved. Limited migration elevates the importance of mutation and recombination in the evolution of natural populations. Testing hypothesis that archaea, or major archaeal groups will involve measuring molecular processes central to the survival, reproduction, and evolution of archaea and to the development of experimental tools for establishing gene function at the molecular level. Compared with bacteria and unicellular eucarya, archaea that have been analyzed in genetic terms have rather low rates of neutral mutation and high rates of recombination. This combination of properties would seem ideal for evolutionary adaptation. Combining computational genetic analyses of natural populations with experimental analyses of cultured archaea will help clarify how molecular mechanisms of archaea determine genetic properties and how genetic properties of archaea affect genome stability and evolution.
Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5
Key Concept Ranking
- Bacteria and Archaea
- 0.5554528
- Genetic Recombination
- 0.51193875
- DNA Synthesis
- 0.50994676
- Genetic Elements
- 0.5049552
- Transcription Start Site
- 0.49673802
- Holliday Junction Resolvase
- 0.45526806
0.5554528
Figures
Mechanisms of Genome Stability and Evolution†
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Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5
/content/10.1128/9781555815516.ch05.ch05fig01
Figure 1.
The five processes that drive genetic change in natural populations. Each horizontal line represents a distinct genotype (i.e., genome sequence) present in a hypothetical population of a microbial species as a function of time. New genotypes arise in this population by mutation, immigration from other populations, and recombination. Conversely, genotypes are eliminated randomly by drift, or according to functional properties determined by particular alleles, by selection. As a result of these natural processes, the genetic composition of the population changes irreversibly over time. For a comprehensive discussion, see Ridley (
88
).
10.1128/9781555815516/f0121-01_thmb.gif
10.1128/9781555815516/f0121-01.gif
Figure 1.
The five processes that drive genetic change in natural populations. Each horizontal line represents a distinct genotype (i.e., genome sequence) present in a hypothetical population of a microbial species as a function of time. New genotypes arise in this population by mutation, immigration from other populations, and recombination. Conversely, genotypes are eliminated randomly by drift, or according to functional properties determined by particular alleles, by selection. As a result of these natural processes, the genetic composition of the population changes irreversibly over time. For a comprehensive discussion, see Ridley ( 88 ).
Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5
/content/10.1128/9781555815516.ch05.ch05fig02
Figure 2.
Molecular strategies for coping with DNA damage. Schematic summary of the molecular events associated with damage reversal, damage excision, and damage tolerance. Abbreviations: AT, alkyl transfer; PR, photoreactivation; BER, base excision repair; NER, nucleotide excision repair; MMR, mismatch repair; TLS, trans-lesion synthesis; HR, homologous recombination. Some of the processes (HR, in particular) are shown greatly simplified; for comprehensive review, see Friedberg et al. (
26
).
10.1128/9781555815516/f0126-01_thmb.gif
10.1128/9781555815516/f0126-01.gif
Figure 2.
Molecular strategies for coping with DNA damage. Schematic summary of the molecular events associated with damage reversal, damage excision, and damage tolerance. Abbreviations: AT, alkyl transfer; PR, photoreactivation; BER, base excision repair; NER, nucleotide excision repair; MMR, mismatch repair; TLS, trans-lesion synthesis; HR, homologous recombination. Some of the processes (HR, in particular) are shown greatly simplified; for comprehensive review, see Friedberg et al. ( 26 ).
Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5
References
/content/book/10.1128/9781555815516.ch05
1.
Allers, T., and, M. Mevarech. 2005. Archaeal genetics—the third way. Nat. Rev. Genet. 6 : 58– 73.
2.
Beja, O.,, E. V. Koonin,, L. Aravind,, L. T. Taylor,, H. Seitz,, J. L. Stein,, D. C. Bensen,, R. A. Feldman,, R. V. Swanson, and, E. F. DeLong. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68 : 335– 345.
3.
Bertani, G. 1999. Transduction-like gene transfer in the methanogen Methanococcus voltae. J. Bacteriol. 181 : 2992– 3002.
4.
Bertani, G., and, L. Baresi. 1987. Genetic transformation in the methanogen Methanococcus voltae PS. J. Bacteriol. 169 : 2730– 2738.
5.
Blount, Z. D., and, D. W. Grogan. 2005. New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic archaea. Mol. Microbiol. 55 : 312– 325.
6.
Boudsocq, F.,, S. Iwai,, F. Hanaoka, and, R. Woodgate. 2001. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol Eta. Nucleic Acids Res. 29 : 4607– 4616.
7.
Brugger, K.,, P. Redder,, Q. She,, F. Confalonieri,, Y. Zivanovic, and, R. A. Garrett. 2002. Mobile elements in archaeal genomes. FEMS Microbiol. Lett. 206 : 131– 141.
8.
Burger, R. 1999. Evolution of genetic variability and the advantage of sex and recombination in changing environments. Genetics 153 : 1055– 1069.
9.
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 : 4992– 4999.
10.
Chung, J. H.,, M. J. Suh,, Y. I. Park,, J. A. Tainer, and, Y. S. Han. 2001. Repair activities of 8-oxoguanine DNA glycosylase from Archaeoglobus fulgidus, a hyperthermophilic archaeon. Mutat. Res. 486 : 99– 111.
11.
Claverys, J. P., and, S. A. Lacks. 1986. Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria. Microbiol. Rev. 50 : 133– 165.
12.
Conway, C.,, C. Proudfoot,, P. Burton,, J. D. Barry, and, R. McCulloch. 2002. Two pathways of homologous recombination in Trypanosoma brucei. Mol. Microbiol. 45 : 1687– 1700.
13.
Dillon, D., and, D. Stadler. 1994. Spontaneous mutation at the mtr locus in Neurospora: the molecular spectrum in wild-type and a mutator strain. Genetics 138 : 61– 74.
14.
DiRuggiero, J.,, N. Santangelo,, Z. Nackerdien,, J. Ravel, and, F. T. Robb. 1997. Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 179 : 4643– 4645.
15.
Drake, J. W.,, B. Charlesworth,, D. Charlesworth, and, J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148 : 1667– 1686.
16.
Drake, J. W., and, L. S. Ripley. 1994. Mutagenesis, p. 98– 124. In J. D. Karam,, J. W. Drake,, K. N. Kreuzer,, G. Mosig,, D. H. Hall,, F. A. Eiserling,, L. W. Black,, E. K. Spicer,, E. Kutter,, K. Carlson, and, E. S. Miller (ed.), Molecular Biology of Phage T4. ASM Press, Washington, D.C.
17.
Ehrlich, S. D.,, H. Bierne,, E. dʹAlencon,, D. Vilette,, M. Petra-novic,, P. Noirot, and, B. Michel. 1993. Mechanisms of illegitimate recombination. Gene 135 : 161– 166.
18.
Eisen, J. A., and, P. C. Hanawalt. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435 : 171– 213.
19.
Eiserling, F.,, A. Pushkin,, M. Gingery, and, G. Bertani. 1999. Bacteriophage-like particles associated with the gene transfer agent of Methanococcus voltae PS. J. Gen. Virol. 80(Pt 12) : 3305– 3308.
20.
Eker, A. P. M.,, L. Formenoy, and, L. E. A. De Wit. 1991. Photoreactivation in the extreme halophilic archaebacterium Halobacterium cutirubrum. Photochem. Photobiol. 53 : 643– 645.
21.
Escobar-Paramo, P.,, S. Ghosh, and, J. Diruggiero. 2005. Evidence for genetic drift in the diversification of a geographically isolated population of the hyperthermophilic archaeon Pyrococcus. Mol. Biol. Evol. 22 : 2297– 2303.
22.
Finlay, B. J. 2002. Global dispersal of free-living microbial eu-karyote species. Science 296 : 1061– 1063.
23.
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 hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles 1 : 36– 51.
24.
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 : 984– 989.
25.
Fogg, M. J.,, L. H. Pearl, and, B. A. Connolly. 2002. Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat. Struct. Biol. 9 : 922– 927.
26.
Friedberg, E. C.,, G. C. Walker, and, W. Siede. 1995. > DNA Repair and Mutagenesis. ASM Press, Washington, D.C.
27.
Gernhardt, P.,, O. Possot,, M. Foglino,, L. Sibold, and, A. Klein. 1990. Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol. Gen. Genet. 221 : 273– 279.
28.
Ghane, F., and, D. W. Grogan. 1998. Chromosomal marker exchange in the thermophilic archaeon Sulfolobus acidocaldarius: physiological and cellular aspects. Microbiology 144 : 1649– 1657.
29.
Glickman, B. W., and, L. S. Ripley. 1984. Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc. Natl. Acad. Sci. USA 81 : 512– 516.
30.
Goddard, M. R.,, H. C. Godfray, and, A. Burt. 2005. Sex increases the efficacy of natural selection in experimental yeast populations. Nature 434 : 636– 640.
31.
Greagg, M. A.,, M. J. Fogg,, G. Panayotou,, S. J. Evans,, B. A. Connolly, and, L. H. Pearl. 1999. A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc. Natl. Acad. Sci. USA 96 : 9045– 9050.
32.
Greene, C. N., and, S. Jinks-Robertson. 1997. Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol. Cell. Biol. 17 : 2844– 2850.
33.
Greve, B.,, S. Jensen,, K. Bruegger,, W. Zillig, and, R. Garrett. 2004. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1 : 231– 239.
34.
Grogan, D. W. 1996. Exchange of genetic markers at extremely high temperatures in the archaeon Sulfolobus acidocaldarius. J. Bacteriol. 178 : 3207– 3211.
35.
Grogan, D. W. 2004. Stability and repair of DNA in hyper-thermophilic Archaea. Curr. Issues Mol. Biol. 6 : 137– 144.
36.
Grogan, D. W.,, G. T. Carver, and, J. W. Drake. 2001. Genetic fidelity under harsh conditions: analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc. Natl. Acad. Sci. USA 98 : 7928– 7933.
37.
Grogan, D. W., and, J. E. Hansen. 2003. Molecular characteristics of spontaneous deletions in the hyperthermophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 185 : 1266– 1272.
38.
Halliday, J. A., and, B. W. Glickman. 1991. Mechanisms of spontaneous mutation in DNA repair-proficient Escherichia coli. Mutat. Res. 250 : 55– 71.
39.
Hansen, J. E.,, A. C. Dill, and, D. W. Grogan. 2005. Conjugational genetic exchange in the hyperthermophilic archaeon Sulfolobus acidocaldarius: intragenic recombination with minimal dependence on marker separation. J. Bacteriol. 187 : 805– 809.
40.
Hogrefe, H. H.,, C. J. Hansen,, B. R. Scott, and, K. B. Nielson. 2002. Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc. Natl. Acad. Sci. USA 99 : 596– 601.
41.
Ikeda, H.,, K. Shiraishi, and, Y. Ogata. 2004. Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli. Adv. Biophys. 38 : 3– 20.
42.
Jacobs, K. L., and, D. W. Grogan. 1997. Rates of spontaneous mutation in an archaeon from geothermal environments. J. Bacteriol. 179 : 3298– 3303.
43.
Jonuscheit, M.,, E. Martusewitsch,, K. M. Stedman, and, C. Schleper. 2003. A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol. Microbiol. 48 : 1241– 1252.
44.
Kawarabayasi, Y.,, Y. Hino,, H. Horikawa,, K. Jinno,, M. Takahashi,, M. Sekine,, S. Baba,, A. Ankai,, H. Kosugi,, A. Hosoyama,, S. Fukui,, Y. Nagai,, K. Nishijima,, R. Otsuka,, H. Nakazawa,, M. Takamiya,, Y. Kato,, T. Yoshizawa,, T. Tanaka,, Y. Kudoh,, J. Yamazaki,, N. Kushida,, A. Oguchi,, K. Aoki,, S. Masuda,, M. Yanagii,, M. Nishimura,, A. Yamagishi,, T. Oshima, and, H. Kikuchi. 2001. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 8 : 123– 140.
45.
Kiener, A.,, R. Gall,, T. Rechsteiner, and, T. Leisinger. 1985. Photoreactivation in Methanobacterium thermoautotrophicum. Arch. Microbiol. 143 : 147– 150.
46.
Kiener, A.,, I. Husain,, A. Sancar, and, C. Walsh. 1989. Purification and properties of Methanobacterium thermoautotrophicum DNA photolyase. J. Biol. Chem. 264 : 13880– 13887.
47.
Koch, A. L. 1982. Mutation and growth rates from Luria-Delbruck fluctuation tests. Mutat. Res. 95 : 129– 143.
48.
Kokoska, R. J.,, K. Bebenek,, F. Boudsocq,, R. Woodgate, and, T. A. Kunkel. 2002. Low fidelity DNA synthesis by a Y family DNA polymerase due to misalignment in the active site. J. Biol. Chem. 277 : 19633– 19638.
49.
Komori, K.,, T. Miyata,, J. DiRuggiero,, R. Holley-Shanks,, I. Hayashi,, I. K. Cann,, K. Mayanagi,, H. Shinagawa, and, Y. Ishino. 2000. Both RadA and RadB are involved in homologous recombination in Pyrococcus furiosus. J. Biol. Chem. 275 : 33782– 33790.
50.
Koulis, A.,, D. A. Cowan,, L. H. Pearl, and, R. Savva. 1996. Uracil-DNA glycosylase activities in hyperthermophilic microorganisms. FEMS Microbiol. Lett. 143 : 267– 271.
51.
Kreuzer, K. N. 2005. Interplay between DNA replication and recombination in prokaryotes. Annu. Rev. Microbiol. 59 : 43– 67.
52.
Kunz, B. A.,, X. L. Kang, and, L. Kohalmi. 1991. The yeast rad18 mutator specifically increases G.C—T.A transversions without reducing correction of G-A or C-T mismatches to G.C pairs. Mol. Cell. Biol. 11 : 218– 225.
53.
Kurosawa, N., and, D.W. Grogan. 2005. Homologous recombination of exogenous DNA with the Sulfolobus acidocaldar-ius genome: properties and uses. FEMS Lett. 253 : 141– 149.
54.
Lang, A. S., and, J. T. Beatty. 2001. The gene transfer agent of Rhodobacter capsulatus and “constitutive transduction” in prokaryotes. Arch. Microbiol. 175 : 241– 249.
55.
Lasken, R. S.,, D. M. Schuster, and, A. Rashtchian. 1996. Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J. Biol. Chem. 271 : 17692– 17696.
56.
Leclere, M. M.,, M. Nishioka,, T. Yuasa,, S. Fujiwara,, M. Takagi, and, T. Imanaka. 1998. The O 6-methylguanine-DNA methyltransferase from the hyperthermophilic archaeon Pyrococcus sp. KOD1: a thermostable repair enzyme. Mol. Gen. Genet. 258 : 69– 77.
57.
Lee, G. S.,, E. A. Savage,, R. G. Ritzel, and, R. C. von Borstel. 1988. The base-alteration spectrum of spontaneous and ultraviolet radiation-induced forward mutations in the URA3 locus of Saccharomyces cerevisiae. Mol. Gen. Genet. 214 : 396– 404.
58.
Levin, B. R., and, C. T. Bergstrom. 2000. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. USA 97 : 6981– 6985.
59.
Ling, H.,, F. Boudsocq,, R. Woodgate, and, W. Yang. 2001. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107 : 91– 102.
60.
Liu, J.,, B. He,, H. Qing, and, Y. W. Kow. 2000. A deoxyinosine specific endonuclease from hyperthermophile, Archaeoglobus fulgidus: a homolog of Escherichia coli endonuclease V. Mutat. Res. 461 : 169– 177.
61.
Lundblad, V.,, A. F. Taylor,, G. R. Smith, and, N. Kleckner. 1984. Unusual alleles of recB and recC stimulate excision of inverted repeat transposons Tn10 and Tn5. Proc. Natl. Acad. Sci. USA 81 : 824– 828.
62.
Mahillon, J., and, M. Chandler. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62 : 725– 774.
63.
Reference deleted.
64.
Mao, E. F.,, L. Lane,, J. Lee, and, J. H. Miller. 1997. Proliferation of mutators in A cell population. J. Bacteriol. 179 : 417– 422.
65.
Martusewitsch, E.,, C. W. Sensen, and, C. Schleper. 2000. High spontaneous mutation rate in the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by transposable elements. J. Bacteriol. 182 : 2574– 2581.
66.
Matsunaga, F.,, C. Norais,, P. Forterre, and, H. Myllykallio. 2003. Identification of short ʹeukaryoticʹ Okazaki fragments synthesized from a prokaryotic replication origin. EMBO Rep. 4 : 154– 158.
67.
McCready, S. 1996. The repair of ultraviolet light-induced DNA damage in the halophilic archaebacteria, Halobacterium cutirubrum, Halobacterium halobium and Haloferax volcanii. Mutat. Res. 364 : 25– 32.
68.
McCready, S., and, L. Marcello. 2003. Repair of UV damage in Halobacterium salinarum. Biochem. Soc. Trans. 31 : 694– 698.
69.
McIlwraith, M. J.,, D. R. Hall,, A. Z. Stasiak,, A. Stasiak,, D. B. Wigley, and, S. C. West. 2001. RadA protein from Ar-chaeoglobus fulgidus forms rings, nucleoprotein filaments and catalyses homologous recombination. Nucleic Acids Res. 29 : 4509– 4517.
70.
Meile, L.,, P. Abendschein, and, T. Leisinger. 1990. Transduction in the archaebacterium Methanobacterium thermoau-totrophicum Marburg. J. Bacteriol. 172 : 3507– 3508.
71.
Mevarech, M., and, R. Werczberger. 1985. Genetic transfer in Halobacterium volcanii. J. Bacteriol. 162 : 461– 462.
72.
Muskhelishvili, G.,, P. Palm, and, W. Zillig. 1993. SSV1-encoded site-specific recombination system in Sulfolobus shi-batae. Mol. Gen. Genet. 237 : 334– 342.
73.
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 solfataricus. J. Biol. Chem. 279 : 33192– 33198.
74.
Ogrunc, M.,, D. F. Becker,, S. W. Ragsdale, and, A. Sancar. 1998. Nucleotide excision repair in the third kingdom. J. Bacteriol. 180 : 5796– 5798.
75.
Oosumi, T.,, B. Garlick, and, W. R. Belknap. 1996. Identification of putative nonautonomous transposable elements associated with several transposon families in Caenorhabditis elegans. J. Mol. Evol. 43 : 11– 18.
76.
Papke, R. T.,, J. E. Koenig,, F. Rodriguez-Valera, and, W. F. Doolittle. 2004. Frequent recombination in a saltern population of Halorubrum. Science 306 : 1928– 1929.
77.
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 : 2951– 2956.
78.
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 : 2410– 2417.
79.
Petursdottir, S. K.,, G. O. Hreggvidsson,, M. S. Da Costa, and, J. K. Kristjansson. 2000. Genetic diversity analysis of Rhodothermus reflects geographical origin of the isolates. Extre-mophiles 4 : 267– 274.
80.
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 : 449– 455.
81.
Pfeifer, F.,, M. Betlach,, R. Martienssen,, J. Friedman, and, H. W. Boyer. 1983. Transposable elements of Halobacterium halobium. Mol. Gen. Genet. 191 : 182– 188.
82.
Pfeifer, F., and, U. Blaseio. 1989. Insertion elements and deletion formation in a halophilic archaebacterium. J. Bacteriol. 171 : 5135– 5140.
83.
Prakash, S., and, L. Prakash. 2000. Nucleotide excision repair in yeast. Mutat. Res. 451 : 13– 24.
84.
Redder, P.,, Q. She, and, R. A. Garrett. 2001. Non-autonomous mobile elements in the crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 306 : 1– 6.
85.
Reddy, M., and, J. Gowrishankar. 1997. Identification and characterization of ssb and uup mutants with increased frequency of precise excision of transposon Tn10 derivatives: nucleotide sequence of uup in Escherichia coli. J. Bacteriol. 179 : 2892– 2899.
86.
Reilly, M. S., and, D. W. Grogan. 2002. Biological effects of DNA damage in the hyperthermophilic archaeon Sulfolobus acidocaldarius. FEMS Microbiol. Lett. 208 : 29– 34.
87.
Reiter, W. D.,, P. Palm, and, S. Yeats. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17 : 1907– 1914.
88.
Ridley, M. 2004. Natural selection and genetic drift in molecular evolution, p. 156– 193. In Evolution, 3rd ed. Blackwell Science Ltd., Malden, Mass.
89.
Roberts, J., and, M. F. White. 2005. An archaeal endonuclease displays key properties of both eukaryal XPF-ERCC1 and Mus81. J. Biol. Chem. 280 : 5924– 5928.
90.
Roberts, M. S., and, F. M. Cohan. 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49 : 1081– 1094.
91.
Rose, M., and, F. Winston. 1984. Identification of a Ty insertion within the coding sequence of the S. cerevisiae URA3 gene. Mol. Gen. Genet. 193 : 557– 560.
92.
Sandler, S. J.,, P. Hugenholtz,, C. Schleper,, E. F. DeLong,, N. R. Pace, and, A. J. Clark. 1999. Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J. Bacteriol. 181 : 907– 915.
93.
Sapienza, C., and, W. F. Doolittle. 1982. Unusual physical organization of the Halobacterium genome. Nature 295 : 384– 389.
94.
Sapienza, C.,, M. R. Rose, and, W. F. Doolittle. 1982. High-frequency genomic rearrangements involving archaebacterial repeat sequence elements. Nature 299 : 182– 185.
95.
Sartori, A. A., and, J. Jiricny. 2003. Enzymology of base excision repair in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Biol. Chem. 278 : 24563– 24576.
96.
Sato, T.,, T. Fukui,, H. Atomi, and, T. Imanaka. 2003. Targeted gene disruption by homologous recombination in the hyper-thermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185 : 210– 220.
97.
Scheerer, J. B., and, G. M. Adair. 1994. Homology dependence of targeted recombination at the Chinese hamster APRT locus. Mol. Cell. Biol. 14 : 6663– 6673.
98.
Scheller, J.,, A. Schurer,, C. Rudolph,, S. Hettwer, and, W. Kramer. 2000. MPH1, a yeast gene encoding a DEAH protein, plays a role in protection of the genome from spontaneous and chemically induced damage. Genetics 155 : 1069– 1081.
99.
Schleper, C.,, E. F. DeLong,, C. M. Preston,, R. A. Feldman,, K. Y. Wu, and, R. V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180 : 5003– 5009.
100.
Schleper, C.,, I. Holz,, D. Janekovic,, J. Murphy, and, W. Zillig. 1995. A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J. Bacteriol. 177 : 4417– 4426.
101.
Schmidt, K. J.,, K. E. Beck, and, D. W. Grogan. 1999. UV stimulation of chromosomal marker exchange in Sulfolobus acidocaldarius: implications for DNA repair, conjugation and homologous recombination at extremely high temperatures. Genetics 152 : 1407– 1415.
102.
Seitz, E. M., and, S. C. Kowalczykowski. 2000. The DNA binding and pairing preferences of the archaeal RadA protein demonstrate a universal characteristic of DNA strand exchange proteins. Mol. Microbiol. 37 : 555– 560.
103.
Serre, M. C.,, C. Letzelter,, J. R. Garel, and, M. Duguet. 2002. Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase. J. Biol. Chem. 277 : 16758– 16767.
104.
She, Q.,, B. Shen, and, L. Chen. 2004. Archaeal integrases and mechanisms of gene capture. Biochem. Soc. Trans. 32 : 222– 226.
105.
She, Q.,, R. K. Singh,, F. Confalonieri,, Y. Zivanovic,, G. Allard, and, 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. Theriault,, 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 cren-archaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98 : 7835– 7840.
106.
Shen, P., and, H. V. Huang. 1986. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112 : 441– 457.
107.
Shuttleworth, G.,, M. J. Fogg,, M. R. Kurpiewski,, L. Jen-Jacobson, and, B. A. Connolly. 2004. Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. J. Mol. Biol. 337 : 621– 634.
108.
Silvian, L. F.,, E. A. Toth,, P. Pham,, M. F. Goodman, and, T. Ellenberger. 2001. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat. Struct. Biol. 8 : 984– 989.
109.
Simon, H. M.,, C. E. Jahn,, L. T. Bergerud,, M. K. Sliwinski,, P. J. Weimer,, D. K. Willis, and, R. M. Goodman. 2005. Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl. Environ. Microbiol. 71 : 4751– 4760.
110.
Singer, B. S.,, L. Gold,, P. Gauss, and, D. H. Doherty. 1982. Determination of the amount of homology required for recombination in bacteriophage T4. Cell 31 : 25– 33.
111.
Skorvaga, M.,, N. D. Raven, and, G. P. Margison. 1998. Thermostable archaeal O 6-alkylguanine-DNA alkyltransferases. Proc. Natl. Acad. Sci. USA 95 : 6711– 6715.
112.
Smith, G. R. 2001. Homologous recombination near and far from DNA breaks: alternative roles and contrasting views. Annu. Rev. Genet. 35 : 243– 274.
113.
Smith, J. M.,, E. J. Feil, and, N. H. Smith. 2000. Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays 22 : 1115– 1122.
114.
Sugawara, N.,, G. Ira, and, J. E. Haber. 2000. DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair. Mol. Cell. Biol. 20 : 5300– 5309.
115.
Surtees, J. A.,, J. L. Argueso, and, E. Alani. 2004. Mismatch repair proteins: key regulators of genetic recombination. Cyto-genet. Genome Res. 107 : 146– 159.
116.
Tchelet, R., and, M. Mevarech. 1994. Interspecies genetic transfer in halophilic archaebacteria. Syst. Appl. Microbiol. 16 : 578– 581.
117.
Tippin, B.,, P. Pham, and, M. F. Goodman. 2004. Error-prone replication for better or worse. Trends Microbiol. 12 : 288– 295.
118.
Tyson, G. W.,, J. Chapman,, P. Hugenholtz,, E. E. Allen,, R. J. Ram,, P. M. Richardson,, V. V. Solovyev,, E. M. Rubin,, D. S. Rokhsar, and, J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428 : 37– 43.
119.
Whitaker, R. J.,, D. W. Grogan, and, J. W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301 : 976– 978.
120.
Whitaker, R. J.,, D. W. Grogan, and, J. W. Taylor. 2005. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus ʹislandicus.ʹ. Mol. Biol. Evol. 22 : 2354– 2361.
121.
Wilkins, B. M. 1995. Gene transfer by bacterial conjugation: diversity of systems and functional specializations, p. 59– 88. In S. Baumberg,, J. P. W. Young,, E. M. H. Wellington, and, J. R. Saunders (ed.), Population Genetics of Bacteria, vol. 1. Cambridge University Press, Cambridge, United Kingdom.
122.
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 : 4576– 4579.
123.
Wood, E. R.,, F. Ghane, and, D. W. Grogan. 1997. Genetic responses of the thermophilic archaeon Sulfolobus acidocaldarius to short-wavelength UV light. J. Bacteriol. 179 : 5693– 5698.
124.
Woods, W. G., and, M. L. Dyall-Smith. 1997. Construction and analysis of a recombination-deficient (radA) mutant of Haloferax volcanii. Mol. Microbiol. 23 : 791– 797.
125.
Worrell, V. E.,, D. P. Nagle, Jr.,, D. McCarthy, and, A. Eisen-braun. 1988. Genetic transformation system in the archaebacterium Methanobacterium thermoautotrophicum Marburg. J. Bacteriol. 170 : 653– 656.
126.
Worthington, P.,, V. Hoang,, F. Perez-Pomares, and, P. Blum. 2003. Targeted disruption of the alpha-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 185 : 482– 488.
127.
Yonemasu, R.,, S. J. McCready,, J. M. Murray,, F. Osman,, M. Takao,, K. Yamamoto,, A. R. Lehmann, and, A. Yasui. 1997. Characterization of the alternative excision repair pathway of UV-damaged DNA in Schizosaccharomyces pombe. Nucleic Acids Res. 25 : 1553– 1558.
Tables
Mechanisms of Genome Stability and Evolution†
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Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5
/content/10.1128/9781555815516.ch05.ch05tab01
Table 1.
Comparison of mutational spectra across the three domains
a
/content/10.1128/9781555815516.ch05.ch05tab02
Table 2.
Representation of major DNA repair pathways in microbial genomes
a
/content/10.1128/9781555815516.ch05.ch05tab03
Table 3.
Distinct types of genetic recombination
Table 3.
Distinct types of genetic recombination
Citation:
Grogan D.
2007.
Mechanisms of Genome Stability and Evolution
†
,
p 120-138.
In
Cavicchioli R (ed),
Archaea.
ASM Press, Washington, DC.
doi: 10.1128/9781555815516.ch5