Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes

Valentina M. Pugacheva ; Alexander E. Korotkov ; Eugene V. Korotkov

Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012) no. 2, pp. 461-475.

Résumé

This paper presents developed mathematical method for searching pair phase shifts of triplet periodicity. Such phase shifts could be a potential frameshifts in genes resulting the insertions of quite long DNA fragments. We developed software and checked if there are pair phase shifts of triplet periodicity in genes of 17 bacteria genomes. The results shows that there is about 1 percent of bacteria genes having pair phase shift of triplet periodicity in these 17 genoms. This paper also describes developed method for visualization of pair phase shifts of triplet periodicity and gives an examples of such shifts. Research results were partially confirmed by the search for aminoacids sequences similarities that had been made by alternative reading frames. The connection between pair phase shifts of triplet periodicity and frameshift in genes is disscussed.

Bibliographie

[1] Wei Q., Li L., Chen D. J. (eds.), DNA Repair, Genetic Instability, and Cancer, World Scientific, 2007

[2] Watson J. D., Levine M., Baker T. A., Gann A., Bell S. P., Molecular Biology of the Gene, Benjamin-Cummings Pub. Corp., 2007

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

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

[5] Kramer E. M., Su H.-J., Wu C.-C., Hu J.-M., “A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineageBMC”, Evolutionary Biology, 6 (2006), 30 | DOI

[6] States D. J., Botstein D., “Molecular sequence accuracy and the analysis of protein coding regions”, Proc. Natl. Acad. Sci., USA, 88 (1991), 5518–5522 | DOI

[7] Pearson W. R., Wood T., Zhang Z., Miller W., “Comparison of DNA sequences with protein sequences”, Genomics, 46 (1997), 24–36 | DOI

[8] Birney E., Thompson J., Gibson T., “PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames”, Nucl. Acids Res., 24 (1996), 2730–2739 | DOI

[9] Guan X., Uberbacher E. C., “Alignments of DNA and protein sequences containing frameshift errors”, Comput. Appl. Biosci., 12 (1996), 31–40

[10] Antonov I., Borodovsky M., “Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm”, J. Bioinform Comput Biol., 8:3, Jun. (2010), 535–51 | DOI | MR

[11] Kislyuk A., Lomsadze A., Lapidus A. L., Borodovsky M., “Frameshift detection in prokaryotic genomic sequences”, Int. J. Bioinform. Res. Appl., 5:4 (2009), 458–477 | DOI

[12] Fichant G. A., Quentin Y., “A frameshift error detection algorithm for DNA sequencing projects”, Nucleic Acids Res., 23 (1995), 2900–2908 | DOI

[13] Médigue C., Rose M., Viari A., Danchin A., “Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence”, Genome Res., 9 (1999), 1116–1127 | DOI

[14] Schiex T., Gouzy J., Moisan A., Oliveira Y. D., “FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences”, Nucleic Acids Res., 31 (2003), 3738–3741 | DOI

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

[16] 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

[17] Korotkov E. V., Korotkova M. A., “Study of the triplet periodicity phase shifts in genes”, Journal of Integrative Bioinformatics, 7 (2010), 131–141

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

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

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

[21] 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, Apr. 21 (1994), 413–414 | DOI

[22] 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, 2 (2005), 139–146 | DOI

[23] 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

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

[25] 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, 30:1–3, Oct. (1984), 157–166 | DOI

[26] Konopka A. K., “Sequences and codes: fundamentals of biomolecular cryptology”, Biocomputing: Informatics and genome projects, ed. Smith D., Academic Press, San Diego, CA, 1994, 119–174

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

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

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

[30] 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

[31] Korotkov E. V., Korotkova M. A., Frenkel F. E., Kudryashov N. A., “The Informational Concept of Searching for Periodicity in Symbol Sequences”, Molecular Biology, 37 (2003), 372–386 | DOI

[32] Suvorova Y. M., Rudenko V. M., Korotkov E. V., “Detection change points of triplet periodicity of gene”, Gene, 491 (2012), 58–64 | DOI

[33] Strauss B. S., “Frameshift mutation, microsatellites and mismatch repair”, Mutation Research, 437 (1999), 195–203 | DOI

[34] Korotkova M. A., Kudryashov N. A., Korotkov E. V., “An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity”, Genomics Proteomics Bioinformatics, 9 (2011), 158–170 | DOI