Seema TRIVEDI, Satyawada Rama RAO, Hukam Singh GEHLOT

Nucleic acid stability in thermophilic prokaryotes: A review

60°C ve üzerindeki sıcaklıklarda, termofilik prokaryotlar (Archaea ve Eubacteria) farklı stratejiler uygularlar. Kodlayan dizinlerde CG içeriği, purin - purin ve pirimidin - pirimidinlerin nükleotiotid düzenlenmesi, nükleotidlerin metilasyonu, histon / histon benzeri proteinler, ters giraz, katyonlar v.b. stratejiler genoma termal kararlılık sağlarlar. DNA seviyesinde uygulanan stratejiler, doğal olarak, universal olmamasına rağmen, termofillerde RNA ya yansır. Artan purin yüklemesi (özellikle adenin), tercihli kodon kullanımı, post - transkripsiyonel modifikasyonlar termal kararlılığı sağlarlar. Bütün bu faktörler, tek olarak veya bir arada nükleik asitlere termal kararlılık sağlayabileceğinden durumdan duruma farklılık gösterebilirler.

Termofilik prokaryotlarda nükleik asit kararlılığı

In order to survive at temperatures of >60°C, thermophilic prokaryotes (Archaea and Eubacteria) have adopted different strategies. These strategies include high ÇG content in the coding sequences, nucleotide arrangement of purine-purine and pyrimidine-pyrimidine, methylation of nucleotides, histone/histone like proteins, reverse gyrase, cations, etc., also provide thermal stability to genome. Strategies adopted at the level of DNA are naturally, though not universally, reflected in RNA in thermophiles. Increased purine load (particularly of adenine), preferential codon usage, post-transcriptional modifications etc. provide thennal stability. All these factors may differ from taxa to taxa as no single or all the factors together can be universally attributed for providing thermal stability to nucleic acids.

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Aravind L, Walker DR and Koonin EV. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27: 1223-42, 1999.
Arcus VL, Backbro K, Roos A, Daniel EL and Baker EN. Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. J Biol Chem. 279: 16471-16478, 2004.
Bailey KA, Marc F, Sandman K and Reeve JN. Both DNA and histone fold sequences contribute to archaeal nucleosome stability. J Biol Chem. 277: 9293-9301, 2002.
Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J and Yang H. A complete sequence of the T. tengcongensis genome. Genome Res. 12: 689-700, 2002.
Belova GI, Prasad R, Kozyavkin SA, Lake JA, Wilson SH and Slesarev AI. A typeIB topoisomerase with DNA repair activities. Proc Natl Acad Sci.(USA), 98: 6015–6020, 2001.
Brown JW, Haas ES and Pace NR. Characterization of ribonuclease P RNAs from thermophilic bacteria. Nucleic Acids Res. 3: 671-679, 1993.
Bujinicki JM and Radlinsks M. Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin. Nucleic Acids Res. 22: 4501- 4509, 1999.
Di Ruggiero J, Santangelo N, Nackerdien Z, Ravel J and Robb FT. Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 179: 4643- 4645, 1997.
Doolittle RF. Of Archaea and Eo: What's in a name? Proc Natl Acad Sci.(USA), 92: 2421-2423, 1995.
Edmonds CG, Crain PF, Gupta R, Hashizume T, Hocart CH, Kowalak JA, Pomerantz SC, Stetter KO and McCloskey JA Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J Bacteriol. 173: 3138-48, 1991.
Ehrlich M, Gama-Sosa MA, Carreira LH, Ljungdahl LG, Kuo KC and Gehrke CW. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5- methylcytosine, and N6-methyladenine. Nucleic Acids Res. 13: 1399-1412, 1985.
Fitz-Gibbon ST, Ladner H, Kim U, Stetter KO, Simon MI and Miller JH. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci. (USA), 99: 984–989, 2002.
Futterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G and Liebl W. Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci. (USA), 101: 9091–9096, 2004.
Galtier N, Tourasse N and Gouy M. Anonhyperthermophilic common ancestor to extant life forms. Science, 283: 220-221, 1999.
Gorgan DW. Hyperthermophiles and the problem of DNA instability. Molec Microbiol. 28: 1043–1049, 1998. Gorgan DW. The question of DNA repair in hyperthermophilic Archaea. Trends in Microbiology, 8: 179- 184, 2000.
Gorgan DW. Stability and Repair of DNA in Hyperthermophilic Archaea. Curr. Issues Mol. Biol. 6: 000- 000, 2004.
Haas BJ, Sandigursky M, Tainer JA, Franklin WA and Cunningham RP. Purification and characterization of Thermotoga maritima endonuclease IV, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase. J Bacteriol. 181: 2834-2839, 1999.
Kawashima T, Amano A, Koike A, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto K, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K and Suzuki M. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma canium. Proc Natl Acad Sci. (USA), 97: 14257-14262, 2000.
Klein RJ, Misulovin Z and Eddy SR. Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci. (USA), 99: 7542-7547, 2002.
Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B and Venter JC et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature, 390: 364–370, 1997.
Kowalak JA, Dalluge JJ, McCloskey JA and Stetter KO. The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry, 33: 7869-7876, 1994.
Kreil DP and Ouzounis CA. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res. 29: 1608-1615, 2001. Lao PJ and Forsdyke DR. Thermophilic bacteria strictly obey Szybalski’s transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res. 10: 228-236, 2000.
Lobry LR and Chessel D. Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J. Appl. Genet. 44: 235-261, 2003.
Lynn DJ, Singer GA and Hickey DA. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30: 4272-4277, 2002.
Makarova KS, Aravind L, Grishin NV, Rogozin IB and Koonin EV. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30: 482-496, 2002.
Makarova KS and Koonin EV. Comparative genomics of Archaea: how much have we learned in six years, and what’s next? Genome Biol. 4: 115, 2003.
McDonald JH, Grasso AM and Rejto LK. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol Biol. Evol. 16: 1785-90, 1999.
Musgrave D, Forterre P and Slesarev A. Negative constrained DNA supercoiling in archaeal nucleosomes. Mol Microbiol. 35: 341-349, 2000.
Nakashima H, Fukuchi S and Nishikawa K. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biol. Chem. 133: 507-513, 2003.
Napoli A, Kvaratskelia M, White MF, Rossi M and Ciaramella M. A novel member of the bacterial-archaeal regulator family is a nonspecific dna-binding protein and induces positive supercoiling. J Biol. Chem. 27614: 10745-10752, 2001.
Paz A, Mester D, Baca I, Nevo E and Korol A. Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc Natl Acad Sci. (USA), 101: 2951-6, 2004.
Peak MJ, Robb FT and Peak JG. Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 177: 6316-6318, 1995.
Sandigursky M and Franklin WA. Thermostable uracil-DNA glycosylase from Thermostoga maritima a member of a novel class of DNA repair enzymes. Curr Biol. 9: 531- 534, 1999.
Sandman K, Grayling RA, Dobrinski B, Lurz R and Reeve JN. Growth-phase-dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc Natl Acad Sci. (USA), 91: 12624-12628, 1994.
Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M and Cavicchioli R. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13: 1580-1588, 2003.
Singer GA and Hickey DA. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene, 317: 39-47, 2003.
Skorvaga M, Raven NDH and Margison GP. Thermostable archaeal O6-alkylguanine-DNA alkyltransferases. Proc Natl Acad Sci. (USA), 95: 6711-6715, 1998.
Stepanov VG and Nyborg J. Thermal stability of aminoacyltRNAs in aqueous solutions. Extremophiles, 6: 485-490, 2002.
Watanabe M, Matsuo M, Tanaka S, Akimoto H, Asahi S, Nishimura S, Katze JR, Hashizume T, Crain PF, McCloskey JA and Okada N. Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to Archaeal tRNA, proceeds via a pathway involving base replacement on the trna polynucleotide chain. J. Biol. Chem. 272: 20146–20151, 1997.
Weng L, Feng Y, Ji X, Cao S, Kosugi Y and Matsui I. Recombinant expression and characterization of an extremely hyperthermophilic archaeal histone from Pyrococcus horikoshii OT3. Protein Expr Purif. 33: 145-152, 2004.
White MF. Archaeal DNA repair: paradigms and puzzles. Biochem. Soc. Trans. 31: 690-3, 2003.
Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms: Proposal for the domain Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci. (USA), 87: 4576-4579, 1990.
Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC and Miller JH. Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J Bacteriol. 82: 1272-9, 2000.
Yokoyama S, Watanabe K and Miyazawa T. Dynamic structures and functions of transfer ribonucleic acids from extreme thermophiles. Adv. Biophys. 23: 115-147, 1987.
Zlatanova J. Archaeal chromatin: virtual or real? Proc Natl Acad Sci. (USA), 94: 12251-12254, 1997.