The structure of selective dinucleotide interactions and periodicities in D melanogaster mtDNA
Biological Research - 2014
Tóm tắt
We found a strong selective 3-sites periodicity of deviations from randomness of the dinucleotide (DN) distribution, where both bases of DN were separated by 1, 2, K sites in prokaryotes and mtDNA. Three main aspects are studied. I) the specific 3 K-sites periodic structure of the 16 DN. II) to discard the possibility that the periodicity was produced by the highly nonrandom interactive association of contiguous bases, by studying the interaction of non-contiguous bases, the first one chosen each I sites and the second chosen J sites downstream. III) the difference between this selective periodicity of association (distance to randomness) of the four bases with the described fixed periodicities of base sequences. I) The 16 pairs presented a consistent periodicity in the strength of association of both bases of the pairs; the most deviated pairs are those where G and C are involved and the least deviated ones are those where A and T are involved. II) we found significant non-random interactions when the first nucleotide is chosen every I sites and the second J sites downstream until I = J = 76. III) we showed conclusive differences between these internucleotide association periodicities and sequence periodicities. This relational selective periodicity is different from sequence periodicities and indicates that any base strongly interacts with the bases of the residual genome; this interaction and periodicity is highly structured and systematic for every pair of bases. This interaction should be destroyed in few generations by recurrent mutation; it is only compatible with the Synthetic Theory of Evolution and agrees with the Wright’s adaptive landscape conception and evolution by shifting balanced adaptive peaks.
Từ khóa
Tài liệu tham khảo
Valenzuela CY: Foundational errors in the Neutral and Nearly-Neutral Theories of evolution in Relation to the Synthetic Theory. Is it necessary a new evolutionary paradigm? Biol Res 2013, 46: 101-119. 10.4067/S0716-97602013000200001
Valenzuela CY: Response by the author. Biol Res 2013, 46: 309.
Knoch TA, Göker M, Lohner R, Abuseiris A, Grosveld FG: Fine- structured multi-scaling long-range correlations in completely sequenced genomes-features, origin, and classification. Eur Biophys J 2009, 38: 757-779. 10.1007/s00249-009-0489-y
Valenzuela CY: Non-random pre-transcriptional evolution in HIV-1. Arefutation of the foundational conditions for neutral evolution. Genet Mol Biol 2009, 32: 159-169. 10.1590/S1415-47572009005000025
Valenzuela CY: Internucleotide correlation and nucleotide periodicity in Drosophila mtDNA: New evidence for panselective evolution. Biol Res 2010, 43: 497-502.
Valenzuela CY: Heterogeneous periodicity of drosophila mtDNA: new refutations of neutral and nearly neutral evolution. Biol Res 2011, 44: 283-293. 10.4067/S0716-97602011000300010
Valenzuela CY: Periodicidades e interacciones del DNA. El fin del neutralismo y del casi-neutralismo. In Darwin y la evolución. Edited by: Veloso A, Spotorno A. Santiago (Chile): Universitaria; 2012:189-295.
Valenzuela CY: Periodicidades genómicas y el fin del neutralismo. Proceedings of the XV Congreso Latinoamericano de Genética, 1 23rd edition. 2012, 15-16. J Basic Appl Genet
Solar H, Tobar S, Torres R, Valenzuela CY: Evolución molecular: Periodicidades en Archaea, Bacterias y Cromosoma 21 humano. In Proceedings of the XX Congreso de las Unidades de Investigación, 2° Año de Medicina, Facultad de Medicina. Santiago, Chile: Facultad de Medicina, Universidad de Chile; 2012:51.
Arques DG: Study of a perturbation in the coding periodicity. Math Biosci 1987, 86: 1-14. 10.1016/0025-5564(87)90060-5
Herzel H, Große I: Correlations in DNA sequences: the role of proteins coding segments. Phys Rev E 1997, 55: 800-810.
Korotkov EV, Korotkova MA, Tulko JS: Latent sequence periodicity of some oncogenes and DNA-binding protein genes. Comput Appl Biosci 1997, 13: 37-44.
Korotkov EV, Korotkova MA, Kudryashov NA: Information decomposition method to analyze symbolical sequences. Phys Lett A 2003, 312: 198-210. 10.1016/S0375-9601(03)00641-8
Korotkov EV, Korotkova MA, Frenkel FE, Kudryashov NA: The informational concept of searching for periodicity in symbol sequences. Mol Biol 2003, 37: 372-386. 10.1023/A:1024231109360
Chaley MA, Korotkov EV, Skryabin KG: Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples. DNA Res 1999, 6: 153-163. 10.1093/dnares/6.3.153
Fukushima A, Ikemura T, Kinouchi M, Oshima T, Kudo Y, Mori H, Kanaya S: Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 2002, 300: 203-211. 10.1016/S0378-1119(02)00850-8
Fukushima A, Ikemura T, Kanaya S: Comparative genome analysis focused on periodicity from prokaryote to higher eukaryote genomes based on power spectrum. J Comput Chem Jpn 2003, 2: 95-110. 10.2477/jccj.2.95
Takeuchi F, Futamura Y, Yoshikura H, Yamamoto K: Statistics of trinucleotides in coding sequences and evolution. J Theor Biol 2003, 222: 139-149. 10.1016/S0022-5193(03)00021-3
Turutina VP, Laskin AA, Kudryashov NA, Skryabin KG, Korotkov EV: Identification of amino acid latent periodicity within 94 protein families. J Comput Biol 2006, 13: 946-964. 10.1089/cmb.2006.13.946
Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J: A novel DNA sequence periodicity decodes nucleosome positioning. Nuc Ac Res 2008, 36: 6228-6236. 10.1093/nar/gkn626
Wang L, Stein LD: Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinformatics 2010, 11: 550-557. 10.1186/1471-2105-11-550
Korotkov EV, Korotkova MA: Study of the triplet periodicity phase shifts in genes. J Integr Bioinform 2010., 7(3): doi:10.2390/biecoll-jib-2010-131
Liu H, Lin S, Cai Z, Sun X: Role of 10–11 bp periodicities of eukaryotic sequence in nucleosome positioning. ByoSystems 2011, 105: 295-299. 10.1016/j.biosystems.2011.05.016
Zoltowski M: Insight into DNA periodicity by a single-channel sequence data approach. Proc IEEE Eng Med Biol Soc 2011, 2011: 2438-2441. doi:10.1109/IEMBS.2011.6090678
Kravatskaya GI, Kravatsky YV, Chechetkin VR, Tumanyan VG: Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling and transcription. Genomics 2011, 98: 223-231. 10.1016/j.ygeno.2011.06.006
Bettecken T, Frenkel Z, Trifonov EN: Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes. Genomics 2011, 12: 273-277.
Shah K, Krishnamachari A: On the origin of three base periodicity in genomes. BioSystems 2012, 107: 142-144. 10.1016/j.biosystems.2011.11.006
Chaley MA, Kutyrkin V: Profile-Statistical periodicity of DNA coding regions. DNA Res 2011, 18: 353-362. 10.1093/dnares/dsr023
Valenzuela CY, Flores SV, Cisternas J: Fixations of the HIV-1 env gene refute neutralism: new evidence for pan-selective evolution. Biol Res 2010, 43: 149-163.
Valenzuela CY, Santos JL: A model of complete random molecular evolution by recurrent mutation. Biol Res 1996, 29: 203-212.
Valenzuela CY: Non random DNA evolution. Biol Res 1997, 30: 117-123.
Valenzuela CY: Misconceptions and false expectations in neutral evolution. Biol Res 2000, 33: 187-195.
Valenzuela CY: A biotic big bang. In Fundamentals of Life. Edited by: Palyi G, Zucchi C, Caglioti L. Paris: Elsevier; 2002:197-202.
Valenzuela CY: Within selection. Rev Chil Hist Nat 2007, 80: 109-116.
Gatlin LL: Counter-examples to a neutralist hypothesis. J Mol Evol 1976, 7: 185-195. 10.1007/BF01731488
Jukes TH: Comments on counter-examples to a neutralist hypothesis. J Mol Evol 1976, 8: 295-297. 10.1007/BF01731002
Kimura M, Ohta T: Further comments on “counter-examples to a neutralist hipotesis”. J Mol Evol 1977, 9: 367-368. 10.1007/BF01796100
Krauss V, Eisenhardt C, Unger T: The genome of the stick insect Medauroidea extradentata is strongly methylated within genes and repetitive DNA. PLoS One 2009, 4(9):e7223. doi:10.1371/journal.pone.0007223 10.1371/journal.pone.0007223
Gou D, Rubalcava M, Sauer S, Mora-Bermudez F, Erdjument-Bromaje H, Tempst P, Kremmer E, Sauer F: SETDB1 is envolved in postembryonic DNA methylation and gene silencing in Drosophila . PLoS One 2010, 5(5):e10581. doi:10.1371/Journal. pone. 0010581 10.1371/journal.pone.0010581
Raddatz G, Guzzardo PM, Olova N, Fontappie MR, Rampp M, Schaefer M, Reik W, Hannon GJ, Lyko F: Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc Natl Acad Sci U S A 2013, 110: 8627-8631. 10.1073/pnas.1306723110
Drake JW: Rates of spontaneous mutation among RNA viruses. Proc Natl Acad Sci U S A 1993, 90: 4171-4175. 10.1073/pnas.90.9.4171
Drake JW: The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann N Y Acad Sci 1999, 870: 100-107. 10.1111/j.1749-6632.1999.tb08870.x
Drake JW, Charlesworth B, Charlesworth D, Crow JF: Rates of spontaneous mutation. Genetics 1998, 148: 1667-1686.