Different biological species "broadcast" their DNAs at different (G + C)% "wavelengths"

Journal of Theoretical Biology

Volumn 178, Issue 4, 1996, Pages 405-417

  Forsdyke, D R ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; DNA BASE COMPOSITION; DNA SUPERCOILING; GENETIC RECOMBINATION; INFORMATION SCIENCE; PRIORITY JOURNAL; SPECIES DIFFERENCE;

ANIMALS; CYTOSINE; DNA; EVOLUTION; GUANOSINE; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 0029918528     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1996.0038     Document Type: Article

References (75)

1. AKASHI, H. (1994). Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. J. Mol. Evol. 136, 927-935.
2. ALFF-STEINBERGER, C. (1987). Codon usage in Homo sapiens: evidence for a coding pattern on the non-coding strand and evolutionary implications of dinucleotide discrimination. J. theor. Biol. 124, 89-95.
3. BARRAI, I., SCAPOLI, C., GAMBARI, R. & BRUGNOLI, F. (1991). Frequencies of codons in histones, tubulins and fibrinogen: bias due to interference between transcriptional signals and protein function. J. theor. Biol. 152, 405-426.
4. BERNARDI, G. & BERNARDI, G. (1986). Compositional constraints and genome evolution. J. Mol. Evol. 24, 1-11.
5. BERNARDI, G. (1989). The isochore organization of the human genome. Annu. Rev. Genet. 23, 637-661.
6. BERNSTEIN, C. & BERNSTEIN, H. (1991). Aging, Sex and DNA Repair. San Diego: Academic Press.
7. BIRD, A. P. (1980). DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8, 1499-1504.
8. BRANNAN, C. I., DEES, E. C., INGRAM, D. S. & TILGHMAN, S. M. (1990). The product of the H19 gene may function as an RNA. Mol. Cell. Biol. 10, 28-36.
9. BROCKDORFF, N., ASHWORTH, A., KAY, G. F., MCCABE, V. M., NORRIS, D. P., COOPER, P. J., et al. (1992). The product of the mouse Xist gene is a 15kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71, 515-526.
10. BRONSON, E. C. & ANDERSON, J. N. (1994). Nucleotide composition as a driving force in the evolution of retroviruses. J. Mol. Evol. 38, 506-532.
11. CHARGAFF, E. (1951). Structure and function of nucleic acids as cell constituents. Fed. Proc. 10, 654-659.
12. COYNE, J. A. (1992). Genetics and speciation. Nature 355, 511-515.
13. COX, E. C. & YANOFSKY, C. (1967). Altered base ratios in the DNA of an Echerichia coli mutator strain. Proc. Natl. Acad. Sci. U.S.A. 58, 1895-1902.
14. CRICK, F. (1971). General model for the chromosomes of higher organisms. Nature 234, 25-27.
15. DOBZHANSKY, T. (1936). Studies in hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics, 21, 113-135.
16. DOYLE, G. G. (1978). A general theory of chromosome pairing based on the palindromic DNA model of Sobell with modifications and amplification. J. theor. Biol. 70, 171-184.
17. EGUCHI, Y., ITOH, T. & TOMIZAWA, J. (1991). Antisense RNA. Annu. Rev. Biochem. 60, 631-652.
18. FILIPSKI, J. (1990). Evolution of DNA sequence. Contributions of mutational bias and selection to the origin of chromosomal compartments. Adv. Mutagenesis Res. 2, 1-54.
19. FORSDYKE, D. R. (1995a). Fine-tuning of intracellular protein concentrations, a collective protein function involved in aneuploid lethality, sex-determination and speciation? J. theor. Biol. 172, 335-345.
20. FORSDYKE, D. R. (1995b). A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol. Biol. Evol. 12, 949-958.
21. 2 genes. An application of FORS-D analysis. Mol. Biol. Evol. 12, 1157-1165.
22. FORSDYKE, D. R. (1995d). Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J. Mol. Evol. 41, 573-581.
23. FORSDYKE, D. R. (1995e). Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. J. Mol. Evol. 41, 1022-1037.
24. FORSDYKE, D. R. (1996). Stem-loop potential in MHC genes: a new way of evaluating positive Darwinian selection. Immunogenetics 43, 182-189.
25. GILBERT, W. & GLYNIAS, M. (1993). On the ancient nature of introns. Gene 135, 137-144.
26. GRANTHAM, R. (1980). Workings of the genetic code. Trends Biochem. Sci. 5, 327-331.
27. GRANTHAM, R., GREENLAND, T., LOUAIL, S., MOUCHIROUD, D., PRATO, J. L., GOUY, M. & GAUTIER, C. (1985). Molecular evolution of viruses as seen by nucleic acid sequence study. Bull. Inst. Past. 83, 95-145.
28. GROSJEAN, H. & FIERS, W. (1982). Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18, 199-209.
29. HAWKINS, J. D. (1988). A survey of intron and exon lengths. Nucleic Acids Res. 16, 9853-9905.
30. HAWLEY, R. S. & ARBEL, T. (1993). Yeast genetics and the fall of the classical view of meiosis. Cell 72, 301-303.
31. HOLLIDAY, R. (1990). The history of heteroduplex DNA. BioEssays 12, 133-141.
32. IKEMURA, T. (1981). Correlation between the abundance of Echerichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol. 146, 1-21.
33. JOYCE, G. F. & ORGEL, L. E. (1993). Prospects for understanding the origin of the RNA world. In: The RNA World (Gesteland, R. F. & Atkins, J. F., eds) pp. 1-25. New York: Cold Spring Harbor Laboratory Press.
34. KAGAWA, Y., NOJIMA, H., NUKIWA, N., ISHIZUKA, M., NAKAJIMA, T., YASUHARA, Y., et al. (1984). High G + C content in the third letter of codons of an extreme thermophile. J. Biol. Chem. 259, 2956-2960.
35. KIMURA, M. (1989). The neutral theory of molecular evolution and the world view of the neutralists. Genome 31, 24-31.
36. KLECKNER, N., PADMORE, R. & BISHOP, D. K. (1991). Meiotic chromosome metabolism: one view. Cold Spring Harbour Symp. Quant. Biol. 56, 729-743.
37. KLECKNER, N. & WEINER, B. M. (1993). Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic and premeiotic cells. Cold Spring Harbor Symp. Quant. Biol. 58, 553-565.
38. KLEIN, S. (1994). Choose your partner: chromosome pairing in yeast meiosis. BioEssays 16, 869-871.
39. KURLAND, C. G. (1993). Major codon preference: theme and variation. Biochem. Soc. Trans. 21, 841-846.
40. LE, S.-Y. & MAIZEL, J. V. (1989). A method for assessing the statistical significance of RNA folding. J. theor. Biol. 138, 495-510.
41. Li, W. H. & GRAUR, D. (1991). Fundamentals of Molecular Evolution, pp. 77, Sunderland, MA: Sinauer Associates.
42. MEZA, L., ARAYA, A., LEON, G., KRAUSKOPF, M., SIDDIQUI, M. A. & GAREL, J. P. (1977). Specific alanine tRNA species associated with fibroin biosynthesis in the posterior silk-gland of Bombyx mori. FEBS. Lett. 77, 255-260.
43. MULLER, H. J. (1939). Reversibility in evolution considered from the standpoint of genetics. Biol. Rev. Camb. Philos. Soc. 14, 261-280.
44. MURCHIE, A. I. H., BOWATER, R., ABOUL-ELA, F. & LILLEY, D. M. J. (1992). Helix opening transitions in supercoiled DNA. Biochem. Biophys. Acta 1131, 1-15.
45. MUTO, A. & OSAWA, S. (1987). The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. U.S.A., 84, 166-169.
46. NICHOLS, B. P., BLUMENBERG, M. & YANOFSKY, C. (1981). Comparison of the nucleotide sequence of trpA and sequences immediately beyond the trp operon of Klebsiella aerogenes, Salmonella typhi, and Escherichia coli. Nucleic Acids Res. 9, 1743-1755.
47. NUSSINOV, R. (1982). Some indications for inverse DNA duplication. J. theor. Biol. 95, 783-793.
48. NUSSINOV, R. (1984). Doublet frequencies in evolutionarily distinct groups. Nucleic Acids Res. 12, 1749-1763.
49. OHTA, T. (1994). Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138, 1331-1337.
50. ORR, H. A. (1995). The population genetics of speciation: the evolution of hybrid incompatibility. Genetics 139, 1805-1813.
51. PRADHU, V. V. (1993). Symmetry observations in long nucleotide sequences. Nucleic Acids Res. 21, 2797-2800.
52. RADMAN, M. & WAGNER, R. (1993). Mismatch recognition in chromosomal interactions and speciation. Chromosoma 102, 369-373.
53. RAYSSIGUIER, C., THALER, D. & RADMAN, M. (1989). The barrier to recombination between Echerichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342, 396-401.
54. REED, K. M., BEUKEBOOM, L. W., EICKBUSH, D. G. & WERREN, J. H. (1994). Junction between repetitive DNAs on the PSR chromosome of Nasonia vitripennis: association of palindromes with recombination. J. Mol. Evol. 38, 352-362.
55. ROMANOVA, L. I., BLINOV, V. M., TOLSKAYA, E. A., VIKTOROVA, E. G., KOLESNIKOVA, M. S., GUSEVA, E. A. & AGOL, V. I. (1986). The primary structure of crossover regions of intertypic poliovirus recombinants: a model of recombination between RNA genomes. Virology 155, 202-213.
56. SALSER, W. (1978). Globin mRNA sequences: analysis of base pairing and evolutionary implications. Cold Spring Harb. Symp. Quant. Biol. 42, 985-1002.
57. SCHACHTEL, G. A., BUCHER, P., MORCARSKI, E. S., BLAISDELL, B. E. & KARLIN, S. (1991). Evidence for selective evolution of codon usage in conserved amino acid segments of human alpha-herpesvirus proteins. J. Mol. Evol. 33, 483-494.
58. SHANNON, C. E. (1948) The mathematical theory of communication. Bell Syst. Tech. J. 27, 397-423.
59. SHARP, P. M., STENICO, M., PEDEN, J. F. & LLOYD, A. T. (1993). Codon usage: mutational bias, translation selection, or both? Biochem. Soc. Trans. 21, 835-841.
60. SOBELL, H. M. (1972). Molecular mechanism for genetic recombination. Proc. Natl. Acad. Sci. U.S.A. 69, 2483-2487.
61. STOLTZFUS, A., SPENCER, D. F., ZUKER, M., LOGSDON, J. M. & DOOLITTLE, W. F. (1994). Testing the exon theory of genes: the evidence from protein structure. Science 265, 202-207.
62. SUEOKA, N. (1961). Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harbor Symp. Quant. Biol. 26, 35-43.
63. SUNG, P., REYNOLDS, P., PRAKASH, L. & PRAKASH, S. (1993). Purification and characterization of the Saccharomyces cerevisiae RAD1/RAD10 endonuclease. J. Biol. Chem. 268, 26391-26399.
64. SZOSTAK, J. W., ORR-WEAVER, T. L. & ROTHSTEIN, R. J. (1983). The double-strand-break repair model for recombination. Cell 33, 25-35.
65. TEMPLETON, A. R. (1989). The meaning of species and speciation: a genetic perspective. In: Speciation and its Consequences (Otte, D. & Endler, J. A., eds) pp. 3-27, Sunderland, MA: Sinauer Associates.
66. TOMIZAWA, J. (1984). Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38, 861-870.
67. TOMIZAWA, J. (1993). Evolution of functional structures of RNA. In: The RNA World (Gesteland, R. F. & Atkins, J. F., eds) pp. 419-445, New York: Cold Spring Harbor Laboratory Press.
68. WAGNER, R. E. & RADMAN, M. (1975). A mechanism for initiation of genetic recombination. Proc. Natl. Acad. Sci. U.S.A. 72, 3619-3622.
69. WANG, J. C., CARON, P. R. & KIM, R. A. (1990). The role of DNA topoisomerase in recombination and genome stability: a double-edged sword? Cell 62, 403-406.
70. WARD, G. K., MCKENZIE, R., ZANNIS-HADJOPOULOS, M. & PRICE, G. B. (1990). The dynamic distribution and quantification of DNA cruciforms in eukaryotic nuclei. Exp. Cell Res. 188, 235-246.
71. WATSON, J. D. & CRICK, F. H. C. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature 171, 964-967.
72. WEISMANN, A. (1892). Essays upon heredity and kindred biological problems, vol. 2. Oxford: Clarendon Press.
73. WOLFE, K. H. & SHARP, P. M. (1993). Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37, 441-456.
74. WYATT, G. R. (1952). The nucleic acids of some insect viruses. J. Gen. Physiol. 36, 201-205.
75. ZUKER, M. (1989). Computer prediction of RNA secondary structure. Meth. Enzym. 180, 262-289.