Presence/Absence of Two Types of Z-DNA Binding Domains in the Genomes of Organisms from Archaea, Bacteria, and Eukaryotes and Its Implications — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Presence/Absence of Two Types of Z-DNA Binding Domains in the Genomes of Organisms from Archaea, Bacteria, and Eukaryotes and Its Implications
Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology, School of Health Sciences, Kanazawa University, Kanazawa, Japan
1 Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology, School of Health Sciences, Kanazawa University, Kanazawa, Japan
We conducted genome sequence analysis to examine the presence/absence of two types of Z-DNA binding domains in various organisms. We examined 68 organisms from archaea, 914 organisms from bacteria, and 199 organisms from eukaryotes. RecA protein from Escherichia coli has a Z-DNA binding domain and this protein promotes homologous recombination. All the organisms examined had this domain. This result indicated that this domain is essential for all the organisms. RNA editing enzyme, adenosine deaminase from human has another type of Z-DNA binding domain. This domain was observed in some organisms of archaea, bacteria, and eukaryotes. The presence/absence of Z-DNA binding domain in adenosine deaminase indicated that gain and loss of this domain had occurred in the process of evolution. The implication of presence and absence of this domain is discussed in this study.
KeywordsZ-DNA Binding DomainrecA ProteinAdenosine Deaminase Acting on RNAGenome Sequence Analysis
Rich, A., Nordheim, A. and Wang, A.H.-J. (1984) The Chemistry and Biology of Left-Handed Z-DNA. Annual Review of Biochemistry, 53, 791-846. https://doi.org/10.1146/annurev.bi.53.070184.004043
Nordheim, A., Tesser, P., Azorin, F., Kwon, Y.H., Möller A. and Rich, A. (1982) Isolation of Drosophila proteins That Bind Selectively to Left-Handed Z-DNA. Proceedings of the National Academy of Sciences of the United States of America, 79, 7729-7733. https://doi.org/10.1073/pnas.79.24.7729
Kuenzle, C.C., Heizmann, C.W., Hübscher, U., Hobi, R., Winkler, G.C. Jaeger, A.W. and Morgenegg, G. (1983) Chromatin Changes Accompanying Neuronal Differentiation. Cold Spring Harbor Symposia on Quantitative Biology, 48, 493-499. https://doi.org/10.1101/SQB.1983.048.01.054
Lafer, E.M., Sousa, R., Rosen, B., Hsu, A. and Rich, A. (1985) Isolation and Characterization of Z-DNA Binding Proteins from Wheat Germ. Biochemistry, 24, 5070-5076. https://doi.org/10.1021/bi00340a017
Gut, S.H., Bischoff, M., Hobi, R. and Kuenzle, C.C. (1987) Z-DNA-Binding Proteins from Bull Testis. Nucleic Acids Research, 15, 9691-9705. https://doi.org/10.1093/nar/15.23.9691
Blaho, J.A. and Wells, R.D. (1987) Left-Handed Z-DNA Binding by the recA Protein of Escherichia coli. The Journal of Biological Chemistry, 262, 6082-6088.
Jaworski, A., Hsieh, W.-T., Blaho, J.A., Larson, J.E. and Wells, R.D. (1987) Left-Handed DNA in Vivo. Science, 238, 773-777. https://doi.org/10.1126/science.3313728
Kitayama, S., Matsumura, O. and Masuda, S. (1988) Isolation of a DNA-Binding Protein from Deinococcus radiodurans Having an Affinity for a Z-Form Polynucleotide. The Journal of Biochemistry, 104, 127-130. https://doi.org/10.1093/oxfordjournals.jbchem.a122407
Herbert, A.G., Spitzner, J.R., Lowenhaupt, K. and Rich, A (1993) Z-DNA Binding Protein from Chicken Blood Nuclei. Proceedings of the National Academy of Sciences of the United States of America, 90, 3339-3342. https://doi.org/10.1073/pnas.90.8.3339
Herbert, A., Alfken, J., Kim, Y.-G., Mian, I.S., Nishikura, K. and Rich, A (1997) A Z-DNA Binding Domain Present in the Human Editing Enzyme, Double-Stranded RNA Adenosine Deaminase. Proceedings of the National Academy of Sciences of the United States of America, 94, 8421-8426. https://doi.org/10.1073/pnas.94.16.8421
Schwartz, T., Rould, M.A., Lowenhaupt, K., Herbert, A. and Rich, A. (1999) Crystal Structure of the Zβ Domain of the Human Editing Enzyme ADAR1 Bound to Left-Handed Z-DNA. Science, 284, 1841-1845. https://doi.org/10.1126/science.284.5421.1841
Schade, M., Turner, C.J., Kühne, R., Schmieder, P., Lowenhaupt, K., Herbert, A., Rich, A. and Oschkinat, H. (1999) The Solution Structure of the Zβ Domain of the Human RNA Editing Enzyme ADAR1 Reveals a Prepositioned Binding Surface for Z-DNA. Proceedings of the National Academy of Sciences of the United States of America, 96, 12465-12470. https://doi.org/10.1073/pnas.96.22.12465
Kim, H.-E, Ahn, H.-C., Lee, Y.-M., Lee, E.-H., Seo, Y.-J., Kim, Y.-G., Kim, K.K., Choi, B.-S. and Lee, J.-H. (2011) The Zβ Domain of Human DAI Binds to Z-DNA via a Novel B-Z Transition Pathway. FEBS Letters, 585, 772-778. https://doi.org/10.1016/j.febslet.2011.01.043
Kim, K., Khayrutdinov, B.I., Lee, C.-K., Cheong, H.-K., Kang, S.W., Park, H., Lee, S., Kim, Y.-G., Jee, J., Rich, A., Kim, K.K. and Jeon, Y.H. (2011) Solution Structure of the Zβ Domain of Human DNA-Dependent Activator of IFN-Regulatory Factors and Its Binding Modes to B- and Z-DNAs. Proceedings of the National Academy of Sciences of the United States of America, 108, 6921-6926. https://doi.org/10.1073/pnas.1014898107
Story, R.M., Weber, I.T. and Steitz, T.A. (1992) The Structure of the E. coli recA Protein Monomer and Polymer. Nature, 355, 318-325. https://doi.org/10.1038/355318a0
Oh, D.-B., Kim, Y.-G. and Rich, A. (2002) Z-DNA-Binding Proteins Can Act as Potent Effectors of Gene Expression in Vivo. Proceedings of the National Academy of Sciences of the United States of America, 99, 16666-16671. https://doi.org/10.1073/pnas.262672699
Kawabata, T., Fukuchi, S., Homma, K., Ota, M., Araki, J., Ito, T., Ichiyoshi, N. and Nishikawa, K. (2002) GTOP: A Database of Protein Structures Predicted from Genome Sequences. Nucleic Acids Research, 30, 294-298. https://doi.org/10.1093/nar/30.1.294
Fukuchi, S., Homma, K., Sakamoto, S., Sugawara, H., Tateno, Y., Gojobori, T. and Nishikawa, K. (2009) The GTOP Database in 2009: Updated Content and Novel Features to Expand and Deepen Insights into Protein Structures and Functions. Nucleic Acids Research, 37, D333-D337. https://doi.org/10.1093/nar/gkn855
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Research, 28, 235-242. https://doi.org/10.1093/nar/28.1.235
Westbrook, J., Feng, Z., Jain, S., Bhat, T.N., Thanki, N., Ravichandran, V., Gilliland, G.L., Bluhm, W.F., Weissig, H., Greer, D.S., Bourne, P.E. and Berman, H.M. (2002) The Protein Data Bank: Unifying the Archive. Nucleic Acids Research, 30, 245-248. https://doi.org/10.1093/nar/30.1.245
Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology, 247, 536-540. https://doi.org/10.1016/S0022-2836(05)80134-2
Bairoch, A. and Apweiler, R. (2000) The SWISS-PROT Protein Sequence Database and Its Supplement TrEMBL in 2000. Nucleic Acids Research, 28, 45-48. https://doi.org/10.1093/nar/28.1.45
Woese, C.R. and Fox, G.E. (1977) Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 74, 5088-5090. https://doi.org/10.1073/pnas.74.11.5088
Muller, F., Brissac, T., Le Bris, N., Felbeck, H. and Gros, O. (2010) First Description of Giant Archaea (Thaumarchaeota) Associated with Putative Bacterial Ectosymbionts in a Sulfidic Marine Habitat. Environmental Microbiology, 12, 2371-2383. https://doi.org/10.1111/j.1462-2920.2010.02309.x
Gupta, R.S. (1998) Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationship among Archaebacteria, Eubacteria, and Eukaryotes. Microbiology and Molecular Biology Reviews, 62, 1435-1491.
Nishikura K. (2010) Functions and Regulations of RNA Editing by ADAR Deaminases. Annual Review of Biochemistry, 79, 321-349. https://doi.org/10.1146/annurev-biochem-060208-105251
Samuel, C.E. (2011) Adenosine Deaminases Acting on RNA (ADARs) Are Both Antiviral and Proviral Dependent upon the Virus. Virology, 411, 180-193. https://doi.org/10.1016/j.virol.2010.12.004
Tonkin, L.A., Saccomanno, L., Morse, D.P., Brodigan, T., Krause, M. and Bass, B.L. (2002) RNA Editing by ADARs Is Important for Normal Behavior in Caenorhabditis elegans. The EMBO Journal, 21, 6025-6035. https://doi.org/10.1093/emboj/cdf607
Palladino, M.J., Keegan, L.P., O’Connell, M.A. and Reenan, R.A. (2000) dADAR, a Drosophila Double-Stranded RNA-Specific Adenosine Deaminase Is Highly Developmentally Regulated and Is Itself a Target for RNA Editing. RNA, 6, 1004-1018. https://doi.org/10.1017/S1355838200000248
Palavicini, J.P., O’Connell, M.A. and Rosenthal, J.J.C. (2009) An Extra Double-Stranded RNA Binding Domain Confers High Activity to a Squid RNA Editing Enzyme. RNA, 15, 1208-1218. https://doi.org/10.1261/rna.1471209
Savva, Y.A., Rieder, L.E. and Reenan, R.A. (2012) The ADAR Protein Family. Genome Biology, 13, 252. https://doi.org/10.1186/gb-2012-13-12-252
Köhler, M., Burnashev, N., Sakmann, B. and Seeburg, P.H. (1993) Determinants of Ca2+ Permeability in Both TM1 and TM2 of High Affinity Kainite Receptor Channels: Diversity by RNA Editing. Neuron, 10, 491-500. https://doi.org/10.1016/0896-6273(93)90336-P
Burns, C.M., Chu, H., Rueter, S.M., Hutchinson, L.K., Canton, H., Sanders-Bush, E. and Emeson, R.B. (1997) Regulation of Seletonin-2C Receptor G-Protein Coupling by RNA Editing. Nature, 387, 303-308. https://doi.org/10.1038/387303a0
Ochman, H., Lawrence, J.G. and Groisman, E.A. (2000) Lateral Gene Transfer and the Nature of Bacterial Innovation. Nature, 405, 299-304. https://doi.org/10.1038/35012500
Ochman, H., Lerat, E. and Daubin, V. (2005) Examining Bacterial Species under the Specter of Gene Transfer and Exchange. Proceedings of the National Academy of Sciences of the United States of America, 102, 6595-6599. https://doi.org/10.1073/pnas.0502035102
Ravenhall, M., Skunca, N., Lassalle, F. and Dessimoz, C. (2015) Inferring Horizontal Gene Transfer. PLoS Computational Biology, 11, e1004095. https://doi.org/10.1371/journal.pcbi.1004095