Study of Completed Archaeal Genomes and Proteomes: Hypothesis of Strong Mutational AT Pressure Existed in Their Common Predecessor

Genomics, Proteomics and Bioinformatics

Volumn 8, Issue 1, 2010, Pages 22-32

  Khrustalev, Vladislav V ^a   Barkovsky, Eugene V ^a  

^a BELARUSIAN STATE MEDICAL UNIVERSITY   (Belarus)

Author keywords

3GC; archaea; arginine; entropy; G+C; mutational pressure

Indexed keywords

ALANINE; ARGININE; CYTOSINE; GLUTAMINE; HISTIDINE; ISOLEUCINE; LYSINE;

AMINO ACID BLOOD LEVEL; ANALYTICAL ERROR; ARCHAEAL GENOME; ARCHEAN; ARTICLE; CODON USAGE; CONTROLLED STUDY; ENTROPY; GENE MUTATION; GENETIC ALGORITHM; HALOARCULA MARISMORTUI; HALOBACTERIUM; HALOQUADRATUM WALSBYI; MATHEMATICAL ANALYSIS; MUTATIONAL ANALYSIS; NATRONOBACTERIUM PHARAONIS; NONHUMAN; PROTEOMICS; SEQUENCE ANALYSIS; SULFOLOBUS SOLFATARICUS;

AMINO ACIDS; ARCHAEA; BASE COMPOSITION; CODON; GENOME; GENOME, ARCHAEAL; MUTATION; PROTEOME;

ARCHAEA; HALOQUADRATUM WALSBYI;

EID: 77951692183     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(10)60003-4     Document Type: Article

References (19)

1. Nakamura Y., et al. Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28 (2000) 292
2. Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85 (1988) 2653-2657
3. Sueoka N. Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses. Gene 300 (2002) 141-154
4. Khrustalev V.V., and Barkovsky E.V. An in-silico study of alphaherpesviruses ICP0 genes: positive selection or strong mutational GC-pressure?. IUBMB Life 60 (2008) 456-460
5. Gros L., et al. Enzymology of the repair of free radicals-induced DNA damage. Oncogene 21 (2002) 8905-8925
6. Yoon J.H., et al. Human thymine DNA glycosylase (TDG) and methyl-CpG-binding protein 4 (MBD4) excise thymine glycol (Tg) from a Tg:G mispair. Nucleic Acids Res. 31 (2003) 5399-5404
7. Moe A., et al. Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V. Nucleic Acids Res. 31 (2003) 3893-3900
8. Khrustalev V.V., and Barkovsky E.V. Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses. Comput. Biol. Chem. 33 (2009) 295-302
9. Khrustalev V.V., and Barkovsky E.V. Main pathways of proteome simplification in alphaherpesviruses under the influence of the strong mutational GC-pressure. J. Proteomics Bioinform. 2 (2009) 88-96
10. Fukuchi S., et al. Unique amino acid composition of proteins in halophilic bacteria. J. Mol. Biol. 327 (2003) 347-357
11. Saleh M., et al. Indicators from archaeal secre-tomes. Microbiol Res. 165 (2008) 1-10
12. Bolhuis H., et al. The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7 (2006) 169
13. Falb M., et al. Metabolism of halophilic archaea. Extremophiles 12 (2008) 177-196
14. Cuadros-Orellana S., et al. Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J. 1 (2007) 235-245
15. Khrustalev V.V., and Barkovsky E.V. Levels of CpG and GpC dinucleotides in coding districts of archaeal genomes. Proceedings of the Conference on Computational Phylogenetics and Molecular Systematics 2007 (2007), KMK Scientific Press, Moscow, Russia 354-357
16. Maeder D.L., et al. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J. Bacteriol. 188 (2006) 7922-7931
17. Galagan J.E., et al. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12 (2002) 532-542
18. Khrustalev, V. V. and Barkovsky, E.V. 2009. Common predecessor's effect in archaeal genomes and proteomes. In Proceedings of the Fourth Moscow Conference on Computational Molecular Biology, pp. 163-164. Moscow, Russia.
19. Brown J.R., and Doolittle W.F. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61 (1997) 456-502