Health  Vol.3 No.9 , September 2011
In vitro examining the existing prognoses how TBP binds to TATA with SNP associated with human diseases
Abstract: We in vitro examined the existing prognoses of the dissociation constant, KD, between ТАТА- Binding Protein (TBP) and ТАТА box with single nucleotide polymorphism (SNP) associated with human diseases. Five SNPs of the genes for cytochrome P450 2A6 (associated with lung cancer), β-globin (associated with β-thalassemia), mannose binding lectin (associated with variable immunodeficiency), superoxide dismutase 1 (associated with amyotrophic lateral sclerosis) and triosephosphate isomerase (associated with anemia) fell within the range of –ln(KD;M/KD;WT) between –1.5 and –1 (here KD;WT and KD;M denote the normal ТАТА box and with SNP). The mea-surements using EMSA demonstrated that: 1) all the predictions stating that the affinity between ТВР and ТАТА boxes with SNPs would be reduced were correct; 2) the departures of three predictions from the measurements fell within the confidence interval; 3) all the predictions consistently underestimated actual mutational damage caused to ТАТА boxes with SNPs (a < 0.05; binomial law) and two of these predictions did so significantly (a < 0.05, Student’s t-test). This consistent underestimation seems to be associated with the damage to the context that modulates ТВP/ТАТА affinity, for example, the contact between the nucleosomal histone H3-Н4 dimer and the core promoter immediately near ТАТА boxes.
Cite this paper: nullDrachkova, I. , Ponomarenko, P. , Arshinova, T. , Ponomarenko, М. , Suslov, V. , Savinkova, L. and Kolchanov, N. (2011) In vitro examining the existing prognoses how TBP binds to TATA with SNP associated with human diseases. Health, 3, 577-583. doi: 10.4236/health.2011.39099.

[1]   Sherry, S.T., Ward, M. and Sirotkin, K. (1999) DbSNP database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Research, 9, 677-679.

[2]   Day, I.N. (2010) DbSNP in the detail and copy number complexities. Human Mutation, 31, 2-4. doi:10.1002/humu.21149

[3]   Batley, J. and Edwards, D. (2009) Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree. Methods in Molecular Biology, 537, 303-321. doi:10.1007/978-1-59745-251-9_15

[4]   Collaco, J.M. and Cutting, G.R. (2008) Update on gene modifiers in cystic fibrosis. Current Opinion in Pulmonary Medicine, 14, 559-566. doi:10.1097/MCP.0b013e3283121cdc

[5]   Faiger, H., Ivanchenko, M., Cohen, I. and Haran, T.E. (2006) TBP flanking sequences: Asymmetry of binding, long-range effects and consensus sequences. Nucleic Acids Research, 34, 104-119. doi:10.1093/nar/gkj414

[6]   Ponomarenko, P.M., Savinkova, L.K., Drachkova, I.A., Lysova, M.V., Arshinova, T.V., Ponomarenko, M.P. and Kolchanov, N.A. (2008) A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism. Doklady Biochemistry and Biophysics, 419, 88-92. doi:10.1134/S1607672908020117

[7]   Hahn, S., Buratowski, S., Sharp, P.A. and Guarente, L. (1989) Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and non nonconsensus DNA sequences. Proceedings of the National Academy of Sciences of USA, 86, 5718-5722. doi:10.1073/pnas.86.15.5718

[8]   Coleman, R.A. and Pugh, B.F. (1995) Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. The Journal of Biological Chemistry, 270, 13850-13859. doi:10.1074/jbc.270.23.13850

[9]   Bucher, P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. Journal of Molecular Biology, 212, 563-578. doi:10.1016/0022-2836(90)90223-9

[10]   Juo, Z.S., Chiu, T.K., Leiberman, P.M., Baikalov, I., Berk, A.J. and Dickerson, R.E. (1996) How proteins recognize the TATA box. Journal of Molecular Biology, 261, 239-254. doi:10.1006/jmbi.1996.0456

[11]   Powel, R., Parkhurst, K. and Parkhurst, L. (2002) Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters. The Journal of Biological Chemistry, 277, 7776-7784. doi:10.1074/jbc.M110147200

[12]   Savinkova, L.K., Drachkova, I.A., Ponomarenko, M.P., Lysova, M.V., Arshinova, T.V. and Kolchanov, N.A. (2007) Interaction between the recombinant TATA-binding protein and the TATA-boxes of the mammalian gene promoters. Ecological Genetics, 5, 44-49.

[13]   Sokolenko, A.A., Sandomirski, I.I. and Savinkova, L.K. (1996) Interaction of yeast TATA-binding protein with promoters short sites. Molecular Biology, 30, 279-285.

[14]   Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S., Podkolodny, N.L., Savinkova, L.K., Kolchanov, N.A. and Overton, G.C. (1999) Identification of sequence dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics, 15, 687-703. doi:10.1093/bioinformatics/15.7.687

[15]   Delgadillo, R.F., Whittington, J.E., Parkhurst, L.K. and Parkhurst, L.J. (2009) The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism. Biochemistry, 48, 1801- 1809. doi:10.1021/bi8018724

[16]   Suslov, V.V., Ponomarenko, P.M., Efimov, V.M., Savinkova, L.K., Ponomarenko, M.P. and Kolchanov, N.A. (2010) SNPs in the HIV-1 TATA box and the AIDS pandemic. Journal of Bioinformatics and Computational Biology, 8, 607-625. doi:10.1142/S0219720010004677

[17]   Savinkova, L.K., Ponomarenko, M.P., Ponomarenko, P.M., Drachkova, I.A., Lysova, M.V., Arshinova, T.V. and Kolchanov, N.A. (2009) TATA box polymorphisms in human gene promoters and associated hereditary pathologies. Biochemistry, 74, 117-129. doi:10.1134/S0006297909020011

[18]   Suslov, V.V., Ponomarenko, P.M., Ponomarenko, M.P., Drachkova, I.A., Arshinova, T.V., Savinkova, L.K. and Kolchanov, N.A. (2010) TATA box polymorphisms in genes of commercial and laboratory animals and plants associated with selectively valuable traits. Russian Journal of Genetics, 46, 394-403. doi:10.1134/S1022795410040022

[19]   Ponomarenko, P.M., Ponomarenko, M.P., Drachkova, I.A., Lysova, M.V., Arshinova, T.V., Savinkova, L.K. and Kolchanov, N.A. (2009) Prognosis of affinity change of the TATA-binding protein to TATA-boxes upon polymorphisms of the human gene promoter TATA boxes. Molecular Biology (Mosc), 43, 512-520.

[20]   Peterson, M.G., Tanese, N., Pugh, B.F. and Tjian, R. (1990) Functional domains and upstream activation properties of cloned human TATA-binding protein. Science, 248, 1625-1630. doi:10.1126/science.2363050

[21]   Pugh, F. (1995) Purification of the human TATA-binding protein, TBP. Methods in Molecular Biology, 37, 359-367. doi:10.1385/0-89603-288-4:359

[22]   Drachkova, I.A., Lysova, M.V., Repkova, M.N., Prokuda, O.V., Sokolenko, A.A., Arshinova, T.V., Kobzev, V.F., Iamkovoi, V.I. and Savinkova, L.K. (2005) Interaction of proteins from general transcription complex RNA polymerase II with oligoribonucleotides. Molecular Biology, 39, 139-146.

[23]   Imbalzano, A.N., Kwon, H., Green, M.R. and Kingston, R.E. (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature, 370, 481-485. doi:10.1038/370481a0

[24]   Ioshikhes, I., Trifonov, E.N. and Zhang, M.Q. (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proceedings of the National Academy of Sciences of USA, 96, 2891-2895. doi:10.1073/pnas.96.6.2891

[25]   Richmond, T.J. and Davey, C.A. (2003) The structure of DNA in the nucleosome core. Nature, 423, 145-150. doi:10.1038/nature01595

[26]   Godde, J.S., Nakatani, Y. and Wolffe, A.P. (1995) The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA. Nucleic Acids Research, 23, 4557-4564. doi:10.1093/nar/23.22.4557

[27]   Kel, A.E., Kel-Margoulis, O.V., Babenko, V. and Wingender, E. (1999) Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. Journal of Molecular Biology, 288, 353-376. doi:10.1006/jmbi.1999.2684

[28]   Gunbin, K.V., Suslov, V.V. and Kolchanov, N.A. (2008) Molecular-genetic systems of development: Functional dynamics and molecular evolution. Biochemistry, 73, 219-230. doi:10.1134/S0006297908020144

[29]   Strunnikov, V.A. and Vyshinsky, I.M. (1991) Realization variation in silkworm. In: Problems in Genetics and the Theory of Evolution, Nauka, Novosibirsk, 99-114.

[30]   Trut, L.N. (1997) D. K. Beliaev’s evolutionary concept—Ten years later. Russian Journal of Genetics, 33, 1060-1068.

[31]   De Jong, H. (2002) Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology, 9, 67-103. doi:10.1089/10665270252833208

[32]   Agalioti, T., Chen, G. and Thanos, D. (2002) Deciphering the transcriptional histone acetylation code for a human gene. Cell, 111, 381-392. doi:10.1016/S0092-8674(02)01077-2

[33]   Watanabe, M., Zingg, B.C. and Mohrenweiser, H.W. (1996) Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus. The American Journal of Human Genetics, 58, 308-316.

[34]   Koch, A., Melbye, M., S?rensen, P., Homoe, P., Madsen, H.O., Molbak, K. Hansen, C.H., Andersen, L.H., Hahn, G.W. and Garred, P. (2001) Acute respiratory tract infections and mannose-binding lectin insufficiency during early childhood. The Journal of the American Medical Association, 285, 1316-1321. doi:10.1001/jama.285.10.1316

[35]   Israels, J., Frakking, F.N., Kremer, L.C., Offringa, M., Kuijpers, T.W. and Van de Wetering, M.D. (2009) Mannose-binding lectin and infection risk in newborns: A systematic review. Archives in Disease in Childhood: Fetal & Neonatal Edition, 5, F452-F461.

[36]   Eisen, D.P. and Minchinton, R.M. (2003) Impact of mannose-binding lectin on susceptibility to infectious diseases. Clinical Infectious Diseases, 37, 1496-1505. doi:10.1086/379324

[37]   Verga Falzacappa, M.V., Segat, L., Puppini, B., Amoroso, A. and Crovella, S. (2004) Evolution of the mannose-binding lectin gene in primates. Genes & Immunity, 5, 653-661. doi:10.1038/sj.gene.6364140

[38]   Seyfarth, J., Garred, P. and Madsen, H.O. (2005) The “involution” of mannose-binding lectin. Human Molecular Genetics, 14, 2859-2869. doi:10.1093/hmg/ddi318

[39]   Cervera, A., Planas, A.M., Justicia, C., Urra, X., Jensenius, J.C., Torres, F., Lozano, F. and Chamorro, A. (2010) Genetically-defined deficiency of mannose-binding lectin is associated with protection after experimental stroke in mice and outcome in human stroke. PLoS ONE, 5, e8433. doi:10.1371/journal.pone.0008433

[40]   Sziller, I., Babula, O., Hupuczi, P., Nagy, B., Rigó, B., Szabó, G., Papp, Z., Linhares, I.M. and Witkin, S.S. (2007) Mannose-binding lectin (MBL) codon 54 gene polymorphism protects against development of pre-eclampsia, HELLP syndrome and pre-eclampsia-associated intrauterine growth restriction. Molecular Human Reproduction, 13, 281-285. doi:10.1093/molehr/gam003

[41]   Boldt, A.B., Culpi, L., Tsuneto, L.T., De Souza, R., Kun, J.F. and Petzl-Erler, M.L. (2006) Diversity of the MBL2 gene in various Brazilian populations and the case of selection at the mannose-binding lectin locus. Human Immunology, 67, 722-734. doi:10.1016/j.humimm.2006.05.009

[42]   Pitarque, M., Von Richter, O., Oke, B., Berkkan, H., Oscarson, M. and Ingelman-Sundberg, M. (2001) Identification of a single nucleotide polymorphism in the TATA box of the CYP2A6 gene: Impairment of its promoter activity. Biochemical and Biophysical Research Communications, 292, 455-460. doi:10.1006/bbrc.2001.4990

[43]   Fei, Y.J., Stoming, T.A., Efremov, G.D., Battacharia, R., Gonzalez-Redondo, J.M., Altay, C., Gurgey, A. and Huisman, T.H. (1988) Beta-thalassemia due to a T―A mutation within the ATA box. Biochemical and Biophysical Research Communications, 153, 741-747. doi:10.1016/S0006-291X(88)81157-4

[44]   Niemann, S., Broom, W.J. and Brown, R.H. Jr. (2007) Analysis of a genetic defect in the TATA box of the SOD1 gene in a patient with familial amyotrophic lateral sclerosis. Muscle & Nerve, 36, 704-707. doi:10.1002/mus.20855