Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine

Genome Research

Volumn 10, Issue 2, 2000, Pages 228-236

  Lao, Perry J ^a   Forsdyke, Donald R ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GUANINE; MESSENGER RNA; PURINE; RNA;

ARTICLE; CODON; ENTROPY; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN STRUCTURE; RNA RNA HYBRIDIZATION; SEQUENCE ANALYSIS; THERMOPHILIC BACTERIUM; TRANSCRIPTION REGULATION;

ADENINE; BASE COMPOSITION; CYTOSINE NUCLEOTIDES; GENES, BACTERIAL; GUANINE; GUANINE NUCLEOTIDES; HEAT; METHANOCOCCUS; PURINES; REPLICATION ORIGIN; RNA, BACTERIAL; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS);

EID: 0034006790     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.2.228     Document Type: Article

References (38)

1. Ball, L.A. 1973. Secondary structure and coding potential of the coat protein gene of bacteriophage MS2. Nature 310: 207-211.
2. Bell, S.J. and D.R. Forsdyke. 1999a. Accounting units in DNA. J. Theor. Biol. 197: 51-61.
3. _. 1999b. Deviations from Chargaff's second parity rule correlate with direction of transcription. J. Theor. Biol. 197: 63-76.
4. Bell, S.J., Y.C. Chow, J.Y.K. Ho, and D.R. Forsdyke. 1998. Correlation of Chi orientation with transcription indicates a fundamental relationship between recombination and transcription. Gene 216: 285-292. [Correction 231: 213.]
5. 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 et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
6. Bronson, E.C. and J.N. Anderson. 1994. Nucleotide composition as a driving force in the evolution of retroviruses. J. Mol. Evol. 38: 506-532.
7. 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 et al. 1996. Complete genomic sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1072.
8. Cantor, C.R. and P.R. Schimmel. 1980. Statistical mechanics and kinetics of nucleic acid interactions. In Biophysical Chemistry, pp. 1183-1264. Freeman, San Francisco, CA.
9. Chargaff, E. 1979. How genetics got a chemical education. Ann. N.Y. Acad. Sci. 325: 345-360.
10. l switch genes in cultured T lymphocytes". Ph.D. thesis. Queen's University, Kingston, Ontario Canada.
11. Dang, K.D., P.B. Dutt, and D.R. Forsdyke. 1998. Chargaff difference analysis of the bithorax complex of Drosophila melanogaster. Biochem. Cell Biol. 76: 129-137.
12. Deckert, G., P.V. Warren, T. Gaasterland, W.G. Yong, A.L. Lenox, D.E. Graham, R. Overbeek, M.A. Snead, M. Keller, M. Aujay et al. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353-358.
13. Eguchi, Y., T. Itoh, and J. Tomizawa. 1991. Antisense RNA. Annu. Rev. Biochem. 60: 631-652.
14. Fire, A. 1999. RNA-triggered gene silencing. Trends Genet. 15: 358-363.
15. Fleischmann, R.D., M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, A.R. Kerlavage, C.J. Bult, J.F. Tomb, B.A. Dougherty, J.M. Merrick et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
16. Forsdyke, D.R. 1995. Entropy-driven protein self-aggregation as the basis for self/not-self discrimination in the crowded cytosol. J. Biol. Syst. 3: 273-287.
17. _. 1996. Different biological species "broadcast" their DNAs at different (C+G)% "wavelengths." J. Theor. Biol. 178: 405-417.
18. _. 1998. An alternative way of thinking about stem-loops in DNA. A case study of the G0S2 gene. J. Theor. Biol. 192: 489-504.
19. _. 1999a. Heat shock proteins as mediators of aggregation-induced "danger" signals: Implications of the slow evolutionary fine-tuning of sequences for the antigenicity of cancer cells. Cell Stress Chaperones 4: 205-210.
20. _. 1999b. The origin of species revisited. Queen's Q. 106: 112-133.
21. _. 1999c. Two levels of information in DNA. Relationship of Romanes' "intrinsic" variability of the reproductive system, and Bateson's "residue", to the species-dependent component of the base composition, (C+G)%. J. Theor. Biol. 201: 47-61.
22. Fraser, C.M., J.D. Gocayne, O. White, M.D. Adams, R.A. Clayton, R.D. Fleischmann, C.J. Bult, A.R. Kerlavage, G. Sutton, J.M. Kelley et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
23. Fulton, A.B. 1982. How crowded is the cytoplasm? Cell 30: 345-347.
24. Grantham, R. 1980. Workings of the genetic code. Trends Biochem. Sci. 5:327-331.
25. Himmelreich, R., H. Hilbert, H. Plagens, E. Pirkl, B.-C. Li, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24: 4420-4449.
26. Jaenicke, R. and G. Bohm. 1998. The stability of proteins in extreme environments. Curr. Opin. Struct. Biol. 8: 738-748.
27. Kagawa, Y., H. Nojima, N. Nukiwa, M. Ishizuka, T. Nakajima, T. Yasuhara, T. Tanaka, and T. Oshima. 1984. High guanine plus cytosine content in the third letter of codons of an extreme thermophile. J. Biol. Chem. 259: 2956-2960.
28. 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 et al. 1997. The complete genome sequence of the hyperthermophilic sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
29. Lauffer, M.A. 1975. Entropy-driven processes in biology. Springer-Verlag, New York, NY.
30. Lee, M.-A., M.E. Diamond, and J.L. Yates. 1999. Genetic evidence that EBNA-1 is needed for efficient stable latent infection by Epstein-Barr virus. J. Virol. 73: 2974-2982.
31. Lobry, J.R. 1996. Origin of replication of Mycoplasma genitalium. Science 272: 745-746.
32. Romanes, G.J. 1886. Physiological selection: an additional suggestion on the origin of species. J. Linn. Soc. (Zool.) 19: 337-411.
33. Smith, D.R., L.A. Doucette-Stamm, C, Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: Functional analysis and comparative genomics. J. Bacteriol. 179: 7135-7155.
34. Aγ fetal globin gene region. Cell 26: 345-353.
35. Sueoka, N. 1961. Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harbor Symp. Quant. Biol. 26: 35-43.
36. Szybalski, W., H. Kubinski, and O. Sheldrick. 1966. Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis. Cold Spring. Harbor Symp. Quant. Biol. 31: 123-127.
37. Turner, D.H. 1996. Thermodynamics of base pairing. Curr. Opin. Struct. Biol. 6: 299-304.
38. Zuckerkandl, E. 1986. Polite DNA: Functional density and functional compatibility in genomes. J. Mol. Evol. 24: 12-27.