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Structural features of the nucleotide sequences of virus and organelle genomes

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DOI: 10.4236/jbise.2011.411089    4,112 Downloads   7,468 Views   Citations
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ABSTRACT

The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P (L) (the probability of the base-distribution at L), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

Takeda, M. (2011) Structural features of the nucleotide sequences of virus and organelle genomes. Journal of Biomedical Science and Engineering, 4, 719-733. doi: 10.4236/jbise.2011.411089.

References

[1] Watson, J.D. and Crick, F.H.C. (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature (London), 171, 964-967. doi:10.1038/171964b0
[2] Chargaff, E. (1953) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experimentia, 6, 201-240. doi:10.1007/BF02173653
[3] Franklin, R.E. and Gosling, R.G. (1953) Molecular configuration in sodium thymonucleate. Nature, 171, 740- 741. doi:10.1038/171740a0
[4] Feughelman, M., Langridge, R., Wilkins, M.H.F., Barclay, R.K. and Hamilton, L.D. (1955) Molecular structure of Deoxyribose nucleic acid and nucleoprotein. Nature, 175, 834-838. doi:10.1038/175834a0
[5] Karkas, J.D., Rudner, R. and Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands. II. Template functions and composition as determined by transcription by RNA polymerase. Proceeding National Academy of Sciences of the United States of America, 60, 915-920. doi:10.1073/pnas.60.3.915
[6] Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley. A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A.3rd and Smith, H.O. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium. Science, 319, 1215-1220. doi:10.1126/science.1151721
[7] NCBI genome data base. (2011). http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome
[8] The Sanger Institute. (2011). http://www.sanger.ac.uk
[9] Saccharomyces Genome Database, (2011). http://www.yeastgenome.org/
[10] Crick, F.H.C. (1968) The origin of genetic code. Journal of Molecular Biology, 38, 367-379. doi:10.1016/0022-2836(68)90392-6
[11] Takeda, M. and Nakahara, M. (2009) Structural Features of the nucleotide Sequences of Genomes. Journal of Computer Aided Chemistry, 10, 38-52. doi:10.2751/jcac.10.38
[12] Bernardi, G. and Bernardi, G. (1986) Compositional constraints and genome evolution. Journal of Molecular Evolution, 24, 1-11. doi:10.1007/BF02099946
[13] Le, S-Y. and Maizei, J.V. (1986) A method for assessing the statistical significances of RNA folding. Journal of Theoretical Biology, 138, 495-510. doi:10.1016/S0022-5193(89)80047-5
[14] Prabhu, V.V. (1993) Symmetry observations in long nucleotide sequence. Nucleic Acids Research, 21, 2797- 2800. doi:10.1093/nar/21.12.2797
[15] Forsdyke, D.R. (1995a) A stem-loop “kissing” model for the initiation of recombination and the origin of intron. Molecular Biology of Evolution, 12, 949-958.
[16] Forsdyke, D.R. (1995b) Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. Journal of Molecular Evolution, 41, 1022-1037. doi:10.1007/BF00173184
[17] Searls, D.B. and Murphy, K. (1995) Automatic-theoretic model of mutation and alignment. Proceedings of the 3rd International Conference on Intelligent Systems Molecular Biology, 3, 341-349.
[18] Stern, L., Allison, L., Coppel, R.L. and Dix, T.I. (2001) Discovering patterns in Plasmodium falciparum genomic DNA. Molecular and Biochemical Parasitology, 112, 71-77.
[19] Kanaya, S., Kinouchi, M., Abe, T., Kudo, Y., Yamada, Y., Nishi, T., Mori, H. and Ikemura, T. (2001) Analysis of codon usage diversity of bacterial genes with a self- organizing map (SOM): Characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene, 276, 89-99. doi:10.1016/S0378-1119(01)00673-4
[20] Baisnee, P.-F., Hampson, S. and Baldi, P. (2002) Why are complementary DNA strands symmetric? Bioinformatics, 18, 1021-1033. doi:10.1093/bioinformatics/18.8.1021
[21] Chen, L. and Zhao, H. (2005) Negative correlation between compositional symmetries and local recombination rates. Bioinformatics, 21, 3951-3958. doi:10.1093/bioinformatics/bti651
[22] Albrecht-Buehler, G. (2006). Asymptotically increasing compliance of genomes with Chargaff’s second parity rules through inversions and inverted transpositions. Proceeding National Academy of Sciences of the United States of America, 103, 17828-17833. doi:10.1073/pnas.0605553103
[23] Knoch, T.A., G?ker, M., Lohner, R., Abuseiris, A. and Grosveld, F.G. (2009) Fine-structures multi-scaling long- range correlations in completely sequenced genomes- features, origin, and classification. European Biophysical Journal, 38, 757-779. doi:10.1007/s00249-009-0489-y
[24] Chor, B., Horn, D., Goldman, N., Levy, Y. and Massingham, T. (2009) Genomic DNA k-mer spectra: Models and modalities. Genome Biology, 10, R108.
[25] Mattick, J.S. (2004) RNA regulation: A new genetics? Nature Review Genetics, 5, 316-323. doi:10.1038/nrg1321
[26] Haber, J.E. and Leung, W.Y. (1996) Lack of chromosome territoriality in yeast: promiscuous rejoining of broken chromosome ends. Proceeding National Academy of Sciences of the United States of America, 93, 13949-13954. doi:10.1073/pnas.93.24.13949
[27] Rowley, J.D. (2001) Chromosomal translocations; dangerous liaisons revisited. Nature Review Cancer, 1, 245- 250. doi:10.1038/35106108
[28] Meaburn, K.J., Misteli, T. and Soutoglou, E. (2007) Spatial genome organization in the formation of chromosomal translocations. Seminars in Cancer Biology, 17, 80- 90. doi:10.1016/j.semcancer.2006.10.008
[29] Webb, C.F., Das, C., Eneff, K. and Tucker, P.W. (1991) Identification of a matrix-associated region 5’ of an immunoglobulin heavy chain variable region gene. Molecular and. Cellular Biology, 11, 5206-5211.
[30] West, A.G., Gaszner, M. and Felsenfeld, G. (2002) Insulators: many functions, many mechanisms. Genes and Development, 16, 271-288. doi:10.1101/gad.954702
[31] Levine, M. and Tjian, R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151. doi:10.1038/nature01763
[32] Lai, E.C., Roegiers, F., Qin, X., Jan, Y.N. and Rubin, G.M. (2005) The ubiquitin ligase Drosophila Mind bomb promotes Notch signaling by regulating the localization and activity of Serrate and Delta. Development, 132, 2319-2332. doi:10.1242/dev.01825
[33] Martens, J.A., Wu, P.Y. and Winston, F. (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes and Develoment, 19, 2695-2704. doi:10.1101/gad.1367605
[34] Taft, R.J., Pheasant, M. and Mattick, J.S. (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays. 29, 288-299. doi:10.1002/bies.20544
[35] Nakahara, M. and Takeda, M. (2010a). Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome—A new method for analysis of genome structure. Journal of Biomedical Science and Engineering, 3, 340-350. doi:10.4236/jbise.2010.34047
[36] Nakahara, M. and Takeda, M. (2010b). Identification of the interactive region by the homology of the sequence spectrum. Journal of Biomedical Science and Engineering, 3, 868-883. doi:10.4236/jbise.2010.39117
[37] Parisi, G. and Frisch, U. (1985) In: Ghil, N., Benzi, R., and Parisi, G., Eds., Turbulence and predictability of geophysical flows and climatic dynamics. North Holland, Amsterdam, 84-87.
[38] Halsey, T.C. Jensen, M.H., Kadanoff, L.P., Procaccia, I. and Shraiman, B. (1986) Fractal measure and their singularities: The characterization of strange sets. Physical Review A, 33, 1141-1151. doi:10.1103/PhysRevA.33.1141
[39] MIPS data. (2010). The yeast genome project. http://www.mips.biochem.mpg.de/
[40] Grantham, R. (1980) Working of the genetic code. Trends in Biochemical Sciences (TIBS), 5, 327-331. doi:10.1016/0968-0004(80)90143-7
[41] Cohen, W.D. and Gardner, R.S. (1959) Viral theory and endosymbiosis. http://www.psychoneuroendocrinology.com/symbiosis.pdf.
[42] Lynn, S. (1967) On the origin of mitosing cells. Journal of Theoretical Biology, 14, 255–274
[43] Blanchard, J.L. and Lynch, M. (2000) Organellar genes: why do they end up in the nucleus? Trends in Geneicst. 16, 315-320. doi:10.1016/S0168-9525(00)02053-9
[44] Peng, C.K., Buldrev, S.V., Goldberger, A.L., Havlin, S., Sciortino, M., Simons, M. and Stanley, H.E. (1992) Long-range correlations in nucleotide sequences. Nature, 356, 168-170. doi:10.1038/356168a0
[45] Voss, R.F. (1992) Evolution of long-range fractal correlation and 1/f noise in DNA base sequences. Physical Review Letters, 68, 3805-3809. doi:10.1103/PhysRevLett.68.3805
[46] Bains, W. (1993) Local self-similarity of sequence in mammalian nuclear DNA is modulated by a 180 bp periodicity. Journal of Theoretical Biology, 161, 137-143. doi:10.1006/jtbi.1993.1046
[47] Weinberger, E.D. and Stadler, P.F. (1993) Why some fitness landscapes are fractal. Journal of Theoretical Biology, 163, 255-275. doi:10.1006/jtbi.1993.1120
[48] Crick, F.H.C. (1971) General model for the chromosomes of higher organisms. Nature, 234, 25-27. doi:10.1038/234025a0
[49] Crick, F.H.C, Wang, J.C. and Bauer, W.R. (1979) Is DNA really a double helix? Journal of Molecular Biology, 129, 449-461. doi:10.1016/0022-2836(79)90506-0

  
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