JBiSE  Vol.3 No.9 , September 2010
Identification of the interactive region by the homology of the sequence spectrum
ABSTRACT
The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.

Cite this paper
nullNakahara, M. and Takeda, M. (2010) 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.
References
[1]   Takeda, M. and Nakahara, M. (2009) Structural features of the nucleotide sequences of genomes. Journal of Computer Aided Chemistry, 10, 38-52.

[2]   Nakahara, M. and Takeda, M. (2010) 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 Biomedical Science and Engineering, 3, 340-350.

[3]   Geli, V., Yang, M., Suda, K., Lustig, A. and Schatz, G. (1990) The MAS-encoded processing protease of yeast mitochondria. Overproduction and characterization of its two nonidentical subunits. Journal of Biological Chemistry, 265(31), 19216-19222.

[4]   West, A.H., Clark, D.J., Martin, J., Neupert, W., Hartl, F.U. and Horwich, A.L. (1992) Two related genes enco- ding extremely hydrophobic proteins suppress a lethal mutation in the yeast mitochondrial processing enhancing protein. Journal of Biological Chemistry, 267(34), 24625-24633.

[5]   Ito, A. (1999) Mitochondrial processing peptidase: multiple-site recognition of precursor proteins. Biochemical and Biophysical Research Communication, 265(3), 611- 616.

[6]   Nagao, Y., Kitada, S., Kojima, K., Toh, H., Kuhara, S., Ogishima, T. and Ito, A. (2000) Glycine-rich region of mitochondrial processing peptidase α-subunit is essential for binding and cleavage of the precursor proteins. Journal of Biological Chemistry, 275, 34552-34556.

[7]   Ogawa, N. and Oshima, Y. (1990) Functional domains of a positive regulatory protein, PHO4, for transcriptional control of the phosphatase region in Saccharomyces cerevisiae. Molecular and Cellular Biology, 10(5), 2224- 2236.

[8]   Okada, H. and Tohe, A. (1992) A novel mutation occurring in the PHO80 gene suppresses the PHO4c mutations of Saccharomyces cerevisiae. Current Genetics, 21(2), 95- 99.

[9]   Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science 292(5523), 1863-1876.

[10]   Baker, H.V. (1991) GCR1 of Saccharomyces cerevisiae encodes a DNA binding protein whose binding is abolished by mutations in the CTTCC sequence motif. Proce- eding National Academy of Sciences of the United States of America, 88(21), 9443-9447.

[11]   Uemura, H. and Jigami, Y. (1992) Role of GCR2 in transcriptional activation of yeast glycolytic genes. Molecular and Cellular Biology, 12(9), 3834-3842.

[12]   Deminoff, S.J., Tornow, J. and Santangelo, G.M. (1995) Unigenic evolution: A novel genetic method localizes a putative leucine zipper that mediate dimerization of the Saccharomyces cerevisiae regulator Gcr1p. Genetics, 141(4), 1263-1274.

[13]   Deminoff, S.J. and Santangelo, G.M. (2001) Rap1p req- uires Gcr1p and Gcr2p homodimers to activate ribosomal protein and glycolytic genes, respectively. Genetics, 158(1), 133-143.

[14]   Gourlay, C.W., Dewar, H., Warren, D.T., Costa, R., Satish, N. and Ayscough, K.R. (2003) An interaction be- tween Sla1p and Sla2p plays a role in regulating actin dyn- amics and endocytosis in budding yeast. Journal of Cell Science, 116(12), 2551-2564.

[15]   Liu, C., Yang, Z., Yang, J., Xia, Z., and Ao, S. (2000) Regulation of the yeast transcription factor PHO2 activity by phosphorylation. Journal of Biological Chemistry, 275(41), 31972-31978.

[16]   Yang, J. and Ao, S.Z. (1996) Interaction of the yeast PHO2 protein or its mutants with the PHO5 UAS in vitro. Sheng Wu Hua Xue Yu Sheng Wu Li Xue Bao (Shanhai) 28(3), 316-320.

[17]   Shimizu, T., Toumoto, A., Ihara, K., Shimizu, M., Kyo-goku, Y., Ogawa, N., Oshima, Y. and Hakoshima, T. (1997) Crystal structure of PHO4 bHLH domain-DNA complex: Flanking base recognition. EMBO Journal, 16(15), 4689-4697.

[18]   Bhoite, L.T. and Stillman, D.J. (1998) Residues in the Swi5 zinc finger protein that mediate cooperative DNA binding with the Pho2 homeodomain protein. Molecular and Cellular Biology, 18(11), 6436-6446.

[19]   Rodgers, A.J. and Wilse, M.C. (2000) Structure of the gammaepsilon complex of ATP synthase. Nature Structural Biology, 7(2000), 1051-1054.

[20]   Montgomery, G.C., Lesile, A.G. and Walker, J.E. (2000) The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution. Nature Structural Biology, 7(11), 1055-1061.

[21]   Tsumuraya, M., Furuike, S., Adachi, K., Kinoshita, K. jr. and Yoshida, M. (2009) Effect of ε subunit on the rotation of thermophilic Bacillus F1-ATPase. FEBS Letters, 583(7), 1121-1126.

[22]   Saccharomyce G.D (2010) (http://www.yeastgenome.org/).

[23]   Ding, W.V. and Johnston, S.A. (1997) The DNA binding and activation domains of Gal4p are sufficient for conveying its regulatory signals. Molecular and Cellular Biology, 17(5), 2538-2549.

[24]   Johnston, M. and Davis, R.W. (1984) Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Molecular and Cellular Biology, 4(11), 1440-1448.

[25]   Lorch, Y. and Kornberg, R.D. (1985) A region flanking the GAL7 gene and binding site for GAL4 protein as upstream activating sequences in yeast. Journal of Molecular Biology, 186(4), 821-824.

[26]   Tajima, M., Nogi, Y. and Fukazawa, T. (1986) Duplicate upstream activating sequences in the promoter region of the Saccharomyces cerevisiae GAL7 gene. Molecular and Cellular Biology, 6(1), 246-256.

[27]   Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Re- shetnikova, L., Clark, B.F. and Nyborg, J. (1995) Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science, 270(5241), 1464-1472.

[28]   Kataoka, T., Powers, S., McGill, C., Fasano, O., Strathern, J., Broach, J. and Wigler, M. (1984) Genetic analysis of yeast RAS1 and RAS2 genes. Cell, 37(2), 437- 445.

[29]   Mabuchi, T., Ichimura, Y., Takeda, M. and Douglas, M.G. (2000) ASC1/RAS2 suppresses the growth defect on glycerol caused by the atp1-2 mutation in the yeast Saccharomyces cerevisiae. Journal of Biological Chemistry, 275(14), 10492-10497.

 
 
Top