Early Vertebrate Evolution of the TATA-Binding Protein, TBP

Molecular Biology and Evolution

Volumn 20, Issue 11, 2003, Pages 1932-1939

  Bondareva, Alla A ^a   Schmidt, Edward E ^a  

^a NONE

Author keywords

Cyclostome; Minisatellite duplication; Polypeptide genesis; TFIID; Transcription

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; DNA MINISATELLITE; OLIGOPEPTIDE; TATA BINDING PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CYCLOSTOME; DNA MODIFICATION; DNA SEQUENCE; GENE DUPLICATION; GENETIC CONSERVATION; HAGFISH; LAMPREY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLACENTA; PROTEIN FUNCTION; SHARK; TRANSCRIPTION INITIATION; VERTEBRATE; ZEBRA FISH;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; EXONS; FISHES; GENE LIBRARY; INTRONS; MICE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PEPTIDES; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SPECIES SPECIFICITY; TATA-BOX BINDING PROTEIN;

ARCHAEA; BRANCHIOSTOMA LANCEOLATUM; CHONDRICHTHYES; DANIO RERIO; EUKARYOTA; HAGFISH; PETROMYZONTIDAE; PROKARYOTA; TETRAPODA; VERTEBRATA;

EID: 0242582324     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg205     Document Type: Article

References (47)

1. Ahearn, J. M. J., M. S. Bartolomei, M. L. West, L. J. Cisek, and J. L. Corden. 1987. Cloning and sequence analysis of the mouse genomic locus encoding the largest subunit of RNA polymerase II. J. Biol. Chem. 262:10695-10705.
2. Baker, C. V., and M. Bronner-Fraser. 1997. The origins of the neural crest. Part II: an evolutionary perspective. Mech. Dev. 69:13-29.
3. Bork, P. 1993. Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally? Proteins 17:363-374.
4. Comeron, J. M. 1995. A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41:1152-1159.
5. Delarbre, C., C. Gallut, V. Barriel, P. Janvier, and G. Gachelin. 2002. Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly. Mol. Phylogenet. Evol. 22:184-192.
6. de Souza, S., M., Long, and W. Gilbert. 1996. Introns and gene evolution. Genes Cells 1:493-505.
7. Dolle, P., M. Price, and D. Duboule. 1992. Expression of murine Dlx-1 homeobox gene during facial, ocular, and limb development. Differentiation 49:93-99.
8. Fowler, J., L. Vinall, and D. Swallow. 2001. Polymorphism of the human muc genes. Front. Biosci. 6:1207-1215.
9. Garcia-Castro, M. I., C. Marcelle, and M. Bronner-Fraser. 2002. Ectodermal Wnt function as a neural crest inducer. Science 297:848-851.
10. Gilbert, W., S. J. de Souza, and M. Long. 1997. Origin of genes. Proc. Natl. Acad. Sci. USA 94:7698-7703.
11. Heringa, J. 1998. Detection of internal repeats: how common are they? Curr. Opin. Struct. Biol. 8:338-345.
12. Hernandez, N. 1993. TBP, a universal eukaryotic transcription factor? Genes Dev. 7:1291-1308.
13. 2-microgolbulin-dependent interactions with the maternal immune system. Cell 110:43-54.
14. Hoshiyama, D., K. Kuma, and T. Miyata. 2001. Extremely reduced evolutionary rate of TATA-box binding protein in higher vertebrates and its evolutionary implications. Gene 280:169-173.
15. Janvier, P. 1999. Catching the first fish. Nature 402:21-22.
16. Kandil, E., C. Namikawa, M. Nonaka, A. S. Greenberg, M. F. Flajnik, T. Ishibashi, and M. Kasahara. 1996. Isolation of low molecular mass polypeptide complementary DNA clones from primitive vertebrates: implications for the origin of MHC class I-restricted antigen presentation. J. Immunol. 156:4245-4253.
17. Knecht, A. K., and M. Bronner-Fraser. 2002. Induction of the neural crest: a multigene process. Nat. Rev. Genet. 3:453-461.
18. Koide, R., S. Kobayashi, T. Shimohata, T. Ikeuchi, M. Maruyama, M. Saito, M. Yamada, H. Takahashi, and S. Tsuji. 1999. A neurological disease caused by an expanded CAG trinucleotide repeat in the TATA-binding protein gene: a new polyglutamine disease? Hum. Mol. Genet. 8:2047-2053.
19. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
20. Landschultz, W. H., P. F. Johnson, and S. L. McKnight. 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240:1759-1764.
21. Langeland, J. A., J. M. Tomsa, W. R. J. Jackman, and C. B. Kimmel. 1998. An amphioxus snail gene: expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo. Dev. Genes Evol. 208:569-577.
22. Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
23. Li, W. H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
24. Li, W. H., C. I. Wu, and C. C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
25. Lichtsteiner, S., and R. Tjian. 1993. Cloning and properties of the Caenorhabditis elegans TATA-box-binding protein. Proc. Natl. Acad. Sci. USA 90:9673-9677.
26. Long, M., S. J. de Souza, and W. Gilbert. 1995. Evolution of the intron-exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5:774-778.
27. Mosavi, L. K., D. L. J. Minor, and Z. Y. Peng. 2002. Consensus-derived structural determinants of the ankyrin repeat motif. Proc. Natl. Acad. Sci. USA 99:16029-16034.
28. Muhich, M. L., C. T. Iida, M. Horikoshi, R. G. Roeder, and C. S. Parker 1990. cDNA clone encoding Drosophila transcription factor TFIID. Proc. Natl. Acad. Sci. USA 87:9148-9152.
29. Nagata, T., T. Suzuki Y. Ohta, M. F. Flajnik, and M. Kasahara 2002. The leukocyte common antigen (CD45) of the Pacific hagfish, Eptatretus stoutii: implications for the primordial function of CD45. Immunogenetics 54:286-291.
30. Nakashima, K., I. Nobuhisa, M. Deshimaru, T. Ogawa, Y. Shimohigashi, Y. Fukumaki, M. Hattori, Y. Sakaki, S. Hattori, and M. Ohno. 1995. Structures of genes encoding TATA box-binding proteins from Trimeresurus gramineus and T. flavoviridis snakes. Gene 152:209-213.
31. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
32. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press, New York.
33. Neidert, A. H., V. Virupannavar, G. W. Hooker, and J. A. Langeland 2001. Lamprey Dlx genes and early vertebrate evolution. Proc. Natl. Acad. Sci. USA 98:1665-1670.
34. Ohbayashi, T., E. E. Schmidt, Y. Makino, T. Kishimoto, Y. Nabeshima, M. Muramatsu, and T. Tamura 1996. Promoter structure of the mouse TATA-binding protein (TBP) gene. Biochem. Biophys. Res. Commun. 225:275-280.
35. Pamilo, P., and N. O. Bianchi. 1993. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.
36. Rubinsztein, D. C., J. Leggo, T. J. Crow, L. E. DeLisi, C. Walsh, S. Jain, and E. S. Paykel. 1996. Analysis of polyglutamine-coding repeats in the TATA-binding protein in different human populations and in patients with schizophrenia and bipolar affective disorder. Am. J. Med. Genet. 67:495-498.
37. Schmidt, E. E., A. A. Bondareva, J. R. Radke, and M. R. Capecchi. 2003. Fundamental cellular processes do not require vertebrate-specific sequences in the TATA-binding protein. J. Biol. Chem. 278:6168-6174.
38. Shimada, M., T. Ohbayashi, M. Ishida, T. Nakadai, Y. Makino, T. Aoki, T. Kawata, T. Suzuki, Y. Matsuda, and T. Tamura. 1999. Analysis of the chicken TBP-like protein (tlp) gene: evidence for a striking conservation of vertebrate TLPs and for a close relationship between vertebrate tbp and tlp genes. Nucleic Acids Res. 27:3146-3152.
39. Simeone, A., E. Puelles, and D. Acampora. 2002. The Otx family. Curr. Opin. Genet. Dev. 12:409-415.
40. Sumita, K., Y. Makino, K. Katoh, T. Kishimoto, M. Muramatsu, K. Mikoshiba, and T. Tamura. 1993. Structure of a mammalian TBP (TATA-binding protein) gene: isolation of the mouse TBP genome. Nucleic Acids Res. 21:2769.
41. Tamura, T., K. Sumita, I. Fujino, A. Aoyama, M. Horikoshi, A. Hoffmann, R. G. Roeder, M. Muramatsu, and K. Mikoshiba. 1991. Striking homology of the 'variable' N-terminal as well as the 'conserved core' domains of the mouse and human TATA-factors (TFIID). Nucleic Acids Res. 19:3861-3865.
42. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight. Nucleic Acids Res. 22:4673-4680.
43. Tomsa, J. M., and J. A. Langeland. 1999. Otx expression during lamprey embryogenesis provides insights into the evolution of the vertebrate head and jaw. Dev. Biol. 207:26-37.
44. Vignali, R., S. Colombetti, G. Lupo, W. Zhang, S. Stachel, R. M. Harland, and G. Barsacchi. 2000. XOtx5b, a new member of the Otx gene family, may be involved in anterior and eye development in Xenopus laevius. Mech. Dev. 96:3-13.
45. Yamada, M., S. Tsuji, and H. Takahashi. 2000. Pathology of CAG repeat diseases. Neuropathology 20:319-325.
46. Yang, Z. 2001. Adaptive molecular evolution. Pp. 327-350 in D. Balding, M. Bishop, and C. Cannings, eds. Handbook of statistical genetics. Wiley, New York.
47. -. 2002. Inference of selection from multiple species alignments. Curr. Opin. Genet. Dev. 12:688-694