CTBP1/RBP1, a Saccharomyces cerevisiae protein which binds to T-rich single-stranded DNA containing the 11-bp core sequence of autonomously replicating sequence, is a poly(deoxypyrimidine)-binding protein

European Journal of Biochemistry

Volumn 238, Issue 1, 1996, Pages 38-47

  Ikeda, Masato ^a,b   Arai, Ken Ichi ^a   Masai, Hisao ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Glutathione S transferase fusion protein; Poly(deoxypyrimidine); Replication origin; RNA recognition motif; Single stranded DNA binding protein

Indexed keywords

SACCHAROMYCES CEREVISIAE;

DNA BINDING PROTEIN; HYBRID PROTEIN;

ARTICLE; BINDING AFFINITY; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA BINDING; DNA LIBRARY; DNA STRUCTURE; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; RNA BINDING; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

ALCOHOL OXIDOREDUCTASES; BASE SEQUENCE; BINDING SITES; BLOTTING, WESTERN; DNA REPLICATION; DNA, FUNGAL; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; FUNGAL PROTEINS; GLUTATHIONE TRANSFERASE; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PHOSPHOPROTEINS; PYRIMIDINES; RECOMBINANT FUSION PROTEINS; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUBSTRATE SPECIFICITY; THYMINE;

EID: 0029886067     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1996.0038q.x     Document Type: Article

References (62)

1. Adam, S. A., Nakagawa, T., Swanson, M. S., Woodruff, T. K. & Dreyfuss, G. (1986) mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence, Mol. Cell. Biol. 6, 2932-2943.
2. Bergemann, A. D. & Johnson, E. M. (1992) The HeLa Pur factor hinds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication, Mol. Cell. Biol. 12, 1257-1265.
3. Birney, E., Kumar, S. & Krainer, A. (1993) Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors, Nucleic Acids Res. 21, 5803-5816.
4. Burd, C. & Dreyfuss, G. (1994) Conserved structures and diversity of functions of RA-binding proteins, Science 265, 615-621.
5. Burd, C. G., Matunis, E. L. & Dreyfuss, G. (1991) The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities, Mol. Cell. Biol. 11, 3419-3424.
6. Brenner, C. & Fuller, R. S. (1992) Structural and enzymatic characterisation of a purified prohormone-processing enzyme: secreted soluble Kex2 protease, Proc. Natl Acad. Sci. USA 89, 922-926.
7. Brunel, F., Alzari, P. M., Ferrara, P. & Zakian, M. M. (1991) Cloning and sequencing of PYBP, a pyrimidine-rich specific single strand DNA-binding protein, Nucleic Acids Res. 19, 5237-5245.
8. Caceres, J. & Krainer, A. R. (1993) Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains, EMBO J. 12, 4715-4726.
9. Caddle, M. S., Lussier, R. H. & Heintz, N. H. (1990) CHO amplification origin, Mol. Cell. Biol. 211, 19-33.
10. Carmichael, E. P., Roome, J. M. & Wahl, A. F. (1993) Binding of a sequence-specific single-stranded DNA binding factor to the Simian Virus 40 core origin inverted repeat domain is cell cycle regulated, Mol. Cell. Biol. 13, 408-420.
11. Challberg, M. D. & Kelly, T. J. (1989) Animal virus DNA replication, Annn. Rev. Biochem. 58, 671-717.
12. Cockell, M., Frutiger, S., Hughes, G. J. & Gasser, S. M. (1994) The yeast protein encoded by PUB1 binds T-rich single-stranded DNA, Nucleic Acids Res. 22, 32-40.
13. Dignam, J. D., Lebovitz, R. M. & Roeder, R. G. (1983) Accurate transcription initiation by RNA polymerase 11 in a soluble extract from isolated mammalian nuclei, Nucleic Acids Res. 11, 1475-1489.
14. Donreiter, I., Erdile, L. F., Gilbert, I. U., von Winkler, D., Kelly, T. J. & Fanning, E. (1992) Interaction between DNA polymerase α primase and cellular replication protein A and SV40 T antigen, EMBO J. 11, 769-776.
15. Dunn, B. & Wobbe, C. R. (1993) Preparation of protein extracts from yeast, in Current Protocols in molecular biology (Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G. & Struhl, K., eds) unit 13, 13.
16. Dutta, A. (1993) Trans-plication factors? Current Biol. 3, 709-712.
17. Frangioni, J. V. & Neel, B. G. (1993) Solubilization and purification of enzymatically active glutathione S-transferase (pGEX) fusion proteins, Anal. Riochem. 210, 179-187.
18. Gorlach, M., Burd, C. G. & Dreyfuss, G. (1994) The determinant of RNA-binding specificity of heterogeneous nuclear ribonucleoprotein C proteins, J. Biol. Chem. 269, 23074-23078.
19. He, Z., Brinton, B. T., Greenblatt, J., Hassell, J. A. & Ingles, C. J. (1993) The transactivator protein VP16 and Ga14 bind replication factor A, Cell 73, 1223-1232.
20. Hofmann, J. F.-X. & Gasser, S. M. (1991) Identification and purification of a protein that binds the yeast ARS consensus sequence, Cell 64, 951-960.
21. Hoffman-Liebermann, B., Liebermann, D., Troutt, A., Kedes, L. H. & Cohen, S. N. (1986) Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo, Mol. Cell. Biol. 6, 3632-3642.
22. Jong, A. Y.-S., Michael, W. C., Gilbert, M., Oehm, A. & Campbell, J. L. (1987) Saccharomyces cerevisiae SSB1 protein and its relationship to nucleolar RNA-binding protein, Mol. Cell. Biol. 7, 2947-2955.
23. Kelly, R. C., Jensen, D. E. & von Hippel, P. H. (1976) DNA 'melting' proteins. IV. Fluorescence measurements of binding parameters for bacteriophage T4 gene 32-protein to mono-, oligo-, and polynucleotides, J. Biol. Chem. 251, 7240-7250.
24. Kenan, D. J., Query, C. C. & Keene, J. D. (1991) RNA recognition: towards identifying determinants of specificity, Trends Biochem Sci. 16, 214-220.
25. Kim, C., Snyder, R. O. & Wold, M. S. (1992) Binding properties of replication protein A from human and yeast cells, Mol. Cell. Biol. 12, 3050-3059.
26. Kornberg, A. & Baker, T. (1992) DNA replication, 2nd edn.
27. Krainer, A. R., Mayeda. A., Kozak, D. & Binns, G. (1991) Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators, Cell 66, 383-394.
28. Kumar, A., Casa-Finet, J. R., Luneau, C. J., Karpel, R. L., Merrill, B. M., Williams, K. R. & Wilson, S. H. (1990) Mammalian heterogeneous nuclear ribonucleoprotein A1: nucleic acid binding properties of the COOH-terminal domain, J. Biol. Chem. 265, 17094-17100.
29. Kuno, K., Murakami, S. & Kuno, S. (1990) Single-stranded-binding factor(s) which interact with ARS1 of Saccharomyces cerevisiae, Gene (Amst.) 5, 73-77.
30. Lee, F.-J. S. & Moss, J. (1993) An RNA binding protein gene (RBP1) of Saccharomyces cerevisiae encodes a putative glucose-responsive protein containing two RNA recognition motifs, J. Biol. Chem. 268, 15080-15087.
31. Li, R. & Botchan, M. R. (1993) The acidic transcriptional activation domains of VP16 and p53 bind the cellular replication protein A and stimulate in vitro BPV-1 DNA replication, Cell 73, 1223-1232.
32. Lohman, T. M. & Ferrari, M. E. (1994) Escherichia coli single-straned DNA binding protein: multiple DNA-binding modes and cooperativities, Annu. Rev. Biochem. 63, 527-570.
33. Masai, H. & Arai, K. (1993) Replication and transcription on single-stranded DNA templates: proteins that specifically recognize single-stranded DNA sequences with a higher order structure, Mol. Biol. (Life Sci. Adv.) 13, 19-37.
34. Manor, H., Rao, B. S. & Martin, R. G. (1988) Abundance and degree of dispersion of genomic d(GA)/(TC)n sequences, J. Mol. Evol. 27, 96-101.
35. Meissner, P. S., Sisk, W. P. & Berman, M. L. (1987) Bacteriophage lambda cloning system for the construction of directional cDNA libraries, Proc. Natl Acad. Sci. USA 84, 4171-4175.
36. Mizusawa, S. & Gottesman, S. (1983) Protein degradation in Escherichia coli: The Ion gene controls the stability of sulA protein, Proc. Natl Acad. Sci. USA 80, 358-362.
37. Nagai, K., Oubridge, C., Ito, N., Avis, J. & Evans, P. (1995) The RNP domain: a sequence-specific RNA binding domain involved in processing and transport of RNA, Trend Biochem. Sci. 20, 235-240.
38. Newlon, C. S. (1988) Yeast chromosome replication and segregation, Microbiol. Rev. 52, 568-601.
39. Nietfeld, W., Mentzel, H. & Pieler, T. (1990) The Xenopus laevis poly(A) binding protein is composed of multiple functionally independent RNA binding domains, EMBO J. 9, 3699-3705.
40. Nomoto, S., Nakayama, N., Arai, K. & Matsumoto, K. (1990) Regulation of the yeast pheromone response pathway by G protein subunits, EMBO J. 9, 691-696.
41. Oubridge, C., Ito, N., Evans, P., Teo, C.-H. & Nagai, K. (1994) Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin, Nature 372, 432-438.
42. Plazkill, T. G. & Newlon, C. S. (1988) A yeast replication origin consists of multiple copies of a small conserved sequence, Cell 53, 441-450.
43. Sachs, A. B., Bond, M. W. & Kornberg, R. D. (1986) A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression, Cell 45, 827-835.
44. Scherly, D., Boelens, W., Dathan, N. A., van Venrooij, W. J. & Mattaj, I. W. (1990) Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B and their cognate RNAs, Nature 345, 502-506.
45. Schmidt, A. M. A., Herterich, S. U. & Krauss, G. (1991) A single-stranded DNA binding protein from S. cerevisiae specifically recognizes the T-rich strand of the core sequence of ARS elements and discriminates against mutant sequences, EMBO J. 10, 981-985.
46. Shirahige, K., Iwasaki, T., Rashid, M. B., Ogasawara, N. & Yoshikawa, H. (1993) Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae, Mol. Cell. Biol. 13, 5043-5056.
47. Smith, D. B. & Johnson, K. S. (1988) Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase, Gene (Amst.) 6, 731-740.
48. Stillman, B. (1989) Initiation of eukaryotic DNA replication in vitro, Annu. Rev. Cell Biol. 5, 197-245.
49. Sun, W. & Godson, G. N. (1993) Binding and phasing of Escherichia coli single-stranded DNA-binding protein by the secondary structure of phage G4 origin of complementary DNA strand synthesis (G4oric), J. Biol. Chem. 268, 8026-8039.
50. Swanson, M. S. & Dreyfuss, G. (1988a) Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities, Mol. Cell. Biol. 8, 2237-2241.
51. Swanson, M. S. & Dreyfuss, G. (1988b) RNA binding specificity of hnRNP proteins: a subset bind to the 3′ end of introns, EMBO J. 7, 3519-3529.
52. Tzfati, Y., Abeliovich, H., Kapeller, I. & Shiomai, J. (1992) A single-stranded DNA-binding protein from Crithidia fasciculata recognizes the nucleotide sequence at the origin of replication of kinetoplast DNA minicircles, Proc. Natl Acad. Sci. USA 89, 6891-6895.
53. Umek, R. M. & Kowalski, D. (1988) The ease of DNA unwinding as a determinant of initiation at yeast replication origins, Cell 52, 559-567.
54. Umek, R. M., Liskens, M. H. K., Kowalski, D. & Huberman, J. A. (1989) New beginnings in studies of eukaryotic DNA replication origins, Biochim. Biophys. Acta 1007, 1-14.
55. van Houten, J. V. & Newton, C. S. (1990) Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III, Mol. Cell. Biol. 10, 3917-3925.
56. Weinerb, A., Collier, D. A., Birshtein, B. K. & Wells, R. D. (1990) Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange, J. Biol. Chem. 265, 1352-1359.
57. Wells, R. D., Collier, D. A., Hanvey, J. C., Shimizu, M. & Wohlrab, F. (1988) The chemistry and biology of unusual DNA structures adopted by oligopurine/oligopyrimidine sequences, FASEB J. 2, 2939-2949.
58. Yamazoe, M., Shirahige, K., Rashid, M. B., Kaneko, Y., Nakayama, T., Ogasawara, N. & Yoshikawa, H. (1994) A protein which binds preferentially to single-stranded core sequence of autonomously replicating sequence is essential for respiratory function in mitochondria of Saccharomyces cerevisiae, J. Biol. Chem. 269, 15244-15252.
59. Yokota, T., Arai, K. & Kaziro, Y. (1979) Studies on 30S ribosomal protein S1 from E. coli. I. Purification and physiochemical properties, J. Biochem (Tokyo) 86, 1725-1737.
60. Zahler, A. M., Lane, W. S., Stolk, J. A. & Roth, M. B. (1992) SR proteins: a conserved family of pre-mRNA splicing factors, Genes & Dev. 6, 837-847.
61. Zamore, P. D., Patton, J. G. & Green, M. R. (1992) Cloning and domain structure of the mammalian splicing factor U2AF, Nature 355, 609-614.
62. Zeidler, R., Hobert, O., Johannes, L., Faulhammer, H. & Kraus, G. (1993) Characterization of two novel single-stranded DNA-specific autonomously replicating sequence-binding protein from Saccharomyces cerevisiae, one of which is adenylosuccinate synthetase, J. Biol. Chem. 268, 20191-20197.