Phase shifts of the triplet periodicity in DNA sequences of genes

E. V. Korotkov ; V. M. Rudenko

Matematičeskaâ biologiâ i bioinformatika, Tome 4 (2009) no. 2, pp. 66-80.

Résumé

Triplet periodicity is a well known property of the coding DNA sequences. But recently researches have shown that about 20% (122829) sequences from data bank KEGG (release 29) have not triplet periodicity without insertion/deletions on statistically significant level. The goal of this work was to show that the absence of triplet periodicity could be explained by shift of the open reading frame. To finding shifts of the open reading frame we suggest a new mathematical method based on calculation a measure of similarity between triplet periodicity types before and after the position of hypothetical open reading frame shift. Using developed method it was found 4724 sequences with possible open reading frame shifts. We assume that in these cases deletions and insertions were the cause of formation the new open reading frame and destruct the triplet periodicity. Revealed sequences were coded in amino acids sequences using current and ancient open reading frame. Ancient frames were obtained using shift information. 243 amino acids sequences, which were obtained by ancient reading frames, have similarities with proteins from Swiss-prot data bank. It confirms our assumption about possibility of genes evolution by open reading frame shifts.

Bibliographie

[1] Fickett J. W., “Predictive methods using nucleotide sequences”, Methods Biochem. Anal., 39 (1998), 231–245 | DOI

[2] Staden R., “Staden: statistical and structural analysis of nucleotide sequences”, Methods Mol. Biol., 25 (1994), 69–77

[3] Baxevanis A. D., “Predictive methods using DNA sequences”, Methods Biochem. Anal., 43 (2001), 233–252 | DOI

[4] Gutierrez G., Oliver J. L., Marin A., “On the origin of the periodicity of three in protein coding DNA sequences”, J. Theor. Biol., 167:4 (1994), 413–441 | DOI

[5] Gao J., Qi Y., Cao Y., Tung W. W., “Protein coding sequence identification by simultaneously characterizing the periodic and random features of DNA sequences”, Journal of Biomedicine and Biotechnology, 2005:2 (2005), 139–146 | DOI

[6] Yin C., Yau S. S., “Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence”, Journal of Theoretical Biology, 247 (2007), 687–694 | DOI | MR

[7] Eskesen S. T., Eskesen F. N., Kinghorn B., Ruvinsky A., “Periodicity of DNA in exons”, BMC Molecular Biology, 5:12 (2004)

[8] Bibb M. J., Findlay P. R., Johnson M. W., “The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences”, Gene, 30 (1984), 157–166 | DOI

[9] Konopka A. K., “Sequences and codes: fundamentals of biomolecular cryptology.”, Biocomputing: Informatics and genome projects, eds. Smith D., Academic Press, San Diego, 119–174

[10] Frenkel F. E., Korotkov E. V., “Classification analysis of triplet periodicity in protein-coding regions of genes”, Gene, 421 (2008), 52–60 | DOI

[11] Trifonov E. N., “Elucidating sequence codes: three codes for evolution”, Ann NY Acad. Sci., 870 (1999), 330–338 | DOI

[12] Eigen M., Winkler-Oswatitsch R., “Transfer-RNA: the early adaptor”, Naturwissenschaften, 68 (1981), 217–228 | DOI

[13] Zoltowski M., “Is DNA Code Periodicity Only Due to CUF – Codons Usage Frequency?”, Conf. Proc. IEEE Eng. Med. Biol. Soc., 1 (2007), 1383–1386

[14] Antezana M. A., Kreitman M., “The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences”, J. Mol. Evol., 49:1 (1999), 36–43 | DOI | MR

[15] Issac B., Singh H., Kaur H., Raghava G. P. S., “Locating probable genes using Fourier transform approach”, Bioinformatics, 18:1 (2002), 196–197 | DOI

[16] Tiwari S., Ramachandran S., Bhattacharya A., Bhattacharya S., Ramaswamy R., “Prediction of probable genes by Fourier analysis of genomic sequences”, Comput. Appl. Biosci., 13:3 (1997), 263–270

[17] Azad R. K., Borodovsky M., “Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory”, Briefings in bioinformatics, 5:2 (2004), 118–130 | DOI

[18] Henderson J., Salzberg S., Fasman K. H., “Finding genes in DNA with a Hidden Markov Model”, J. Comput. Biol., 4 (1997), 127–141 | DOI

[19] Snyder E. E., Stormo G. D., “Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks”, Nucl. Acids Res., 21 (1993), 607–613 | DOI

[20] Thomas A., Skolnick M. H., “A probabilistic model for detecting coding regions in DNA sequences”, IMA J. Math. Appl. Med. Biol., 11:3 (1994), 149–160 | DOI | Zbl

[21] Korotkov E. V., Korotkova M. A., Frenkel F. E., Kudryashov N. A., “Information approach for search of periodicity of symbolical sequences”, Molek. Biol., 37 (2003), 372–386 | DOI

[22] Korotkov E. V., Korotkova M. A., Kudryashov N. A., “Information decomposition method for analysis of symbolical sequences”, Physical Letters A, 312 (2003), 198–210 | DOI | MR | Zbl

[23] Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., Kanehisa M., “KEGG: Kyoto Encyclopedia of Genes and Genomes”, Nucl. Acids Res., 27 (1999), 29–34 | DOI

[24] Frenkel F. E., Korotkov E. V., “Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes”, DNA Res., 16 (2009), 105–114 | DOI

[25] Okamura K., Feuk L., Marquès-Bonet T., Navarro A., Scherer S. W., “Frequent appearance of novel protein-coding sequences by frameshift translation”, Genomics, 88 (2006), 690–697 | DOI

[26] Raes J., Van de Peer Y., “Functional divergence of proteins through frameshift mutations”, Trends Genet., 21 (2005), 428–431 | DOI

[27] Kramer E. M., Huei-Jiun Su, Cheng-Chiang Wu, Jer-Ming Hu., “A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage”, BMC Evolutionary Biology, 6:30 (2006)

[28] Kullback S., Information Theory and Statistics, Wiley, New York, 1959 | MR | Zbl

[29] Mir, Moscow, 1967 | Zbl

[30] “UniProt Consortium. The Universal Protein Resource (UniProt)”, Nucl. Acids Res., 35 (2007), 193–197

[31] Needleman S. B., Wunsch C. D., “A general method applicable to the search for similarities in the amino acid sequence of two proteins”, J. Mol. Biol., 48:3 (1970), 443–453 | DOI

[32] Altschul S. F. et al., “Basic local alignment search tool”, J. Mol. Biol., 215:3 (1990), 403–410

[33] Bollenbach T., Vetsigian K., Kishony R., “Evolution and multilevel optimization of the genetic code”, Genome Res., 17:4 (2007), 405–412 | DOI