Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1990 Jun;87(12):4665–4669. doi: 10.1073/pnas.87.12.4665

A DNA replication enhancer in Saccharomyces cerevisiae.

S S Walker 1, S C Francesconi 1, S Eisenberg 1
PMCID: PMC54177  PMID: 2191298

Abstract

We have dissected the autonomously replicating sequence ARS121 using site-directed in vitro mutagenesis. Three domains important for origin function were identified; one of these is essential and contains an 11-base-pair sequence resembling the canonical ARS core consensus; the second region, deletion of which affects the efficiency of the origin, is located 3' to the T-rich strand of the essential sequence and encompasses several elements with near matches to the ARS core consensus; the third region, containing two OBF1 DNA-binding sites and located 5' to the essential sequence, also affects the efficiency of the ARS. Here we demonstrate that a synthetic OBF1 DNA-binding site can substitute for the entire third domain in origin function. A dimer of the synthetic binding site, fused to a truncated origin containing only domains one and two, restored the origin activity to the levels of the wild-type ARS. The stimulation of origin function by the synthetic binding site was relatively orientation independent and could occur at distances as far as 1 kilobase upstream to the essential domain. Based on these results we conclude that the OBF1 DNA-binding site is an enhancer of DNA replication. We suggest that the DNA-binding site and the OBF1 protein are involved in the regulation of the activation of nuclear origins of replication in Saccharomyces cerevisiae.

Full text

PDF
4665

Images in this article

4667Image
on p.4667

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bramhill D., Kornberg A. A model for initiation at origins of DNA replication. Cell. 1988 Sep 23;54(7):915–918. doi: 10.1016/0092-8674(88)90102-x. [DOI] [PubMed] [Google Scholar]
  2. Brand A. H., Micklem G., Nasmyth K. A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. Cell. 1987 Dec 4;51(5):709–719. doi: 10.1016/0092-8674(87)90094-8. [DOI] [PubMed] [Google Scholar]
  3. Brewer B. J., Fangman W. L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987 Nov 6;51(3):463–471. doi: 10.1016/0092-8674(87)90642-8. [DOI] [PubMed] [Google Scholar]
  4. Broach J. R., Li Y. Y., Feldman J., Jayaram M., Abraham J., Nasmyth K. A., Hicks J. B. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. doi: 10.1101/sqb.1983.047.01.132. [DOI] [PubMed] [Google Scholar]
  5. Buchman A. R., Kimmerly W. J., Rine J., Kornberg R. D. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jan;8(1):210–225. doi: 10.1128/mcb.8.1.210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Burke W., Fangman W. L. Temporal order in yeast chromosome replication. Cell. 1975 Jul;5(3):263–269. doi: 10.1016/0092-8674(75)90101-4. [DOI] [PubMed] [Google Scholar]
  7. Celniker S. E., Sweder K., Srienc F., Bailey J. E., Campbell J. L. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol Cell Biol. 1984 Nov;4(11):2455–2466. doi: 10.1128/mcb.4.11.2455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chan C. S., Tye B. K. Autonomously replicating sequences in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6329–6333. doi: 10.1073/pnas.77.11.6329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cheng L., Kelly T. J. Transcriptional activator nuclear factor I stimulates the replication of SV40 minichromosomes in vivo and in vitro. Cell. 1989 Nov 3;59(3):541–551. doi: 10.1016/0092-8674(89)90037-8. [DOI] [PubMed] [Google Scholar]
  10. Diffley J. F., Stillman B. Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2120–2124. doi: 10.1073/pnas.85.7.2120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Diffley J. F., Stillman B. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science. 1989 Nov 24;246(4933):1034–1038. doi: 10.1126/science.2511628. [DOI] [PubMed] [Google Scholar]
  12. Dorsman J. C., van Heeswijk W. C., Grivell L. A. Identification of two factors which bind to the upstream sequences of a number of nuclear genes coding for mitochondrial proteins and to genetic elements important for cell division in yeast. Nucleic Acids Res. 1988 Aug 11;16(15):7287–7301. doi: 10.1093/nar/16.15.7287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Eisenberg S., Civalier C., Tye B. K. Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences. Proc Natl Acad Sci U S A. 1988 Feb;85(3):743–746. doi: 10.1073/pnas.85.3.743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Eisenberg S., Francesconi S. C., Civalier C., Walker S. S. Purification of DNA-binding proteins by site-specific DNA affinity chromatography. Methods Enzymol. 1990;182:521–529. doi: 10.1016/0076-6879(90)82041-y. [DOI] [PubMed] [Google Scholar]
  15. Fletcher C., Heintz N., Roeder R. G. Purification and characterization of OTF-1, a transcription factor regulating cell cycle expression of a human histone H2b gene. Cell. 1987 Dec 4;51(5):773–781. doi: 10.1016/0092-8674(87)90100-0. [DOI] [PubMed] [Google Scholar]
  16. Francesconi S. C., Eisenberg S. Purification and characterization of OBF1: a Saccharomyces cerevisiae protein that binds to autonomously replicating sequences. Mol Cell Biol. 1989 Jul;9(7):2906–2913. doi: 10.1128/mcb.9.7.2906. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Goel A., Pearlman R. E. Transposable element-mediated enhancement of gene expression in Saccharomyces cerevisiae involves sequence-specific binding of a trans-acting factor. Mol Cell Biol. 1988 Jun;8(6):2572–2580. doi: 10.1128/mcb.8.6.2572. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Halfter H., Kavety B., Vandekerckhove J., Kiefer F., Gallwitz D. Sequence, expression and mutational analysis of BAF1, a transcriptional activator and ARS1-binding protein of the yeast Saccharomyces cerevisiae. EMBO J. 1989 Dec 20;8(13):4265–4272. doi: 10.1002/j.1460-2075.1989.tb08612.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Halfter H., Müller U., Winnacker E. L., Gallwitz D. Isolation and DNA-binding characteristics of a protein involved in transcription activation of two divergently transcribed, essential yeast genes. EMBO J. 1989 Oct;8(10):3029–3037. doi: 10.1002/j.1460-2075.1989.tb08453.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hamil K. G., Nam H. G., Fried H. M. Constitutive transcription of yeast ribosomal protein gene TCM1 is promoted by uncommon cis- and trans-acting elements. Mol Cell Biol. 1988 Oct;8(10):4328–4341. doi: 10.1128/mcb.8.10.4328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Holmes S. G., Smith M. M. Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain. Mol Cell Biol. 1989 Dec;9(12):5464–5472. doi: 10.1128/mcb.9.12.5464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Huberman J. A., Spotila L. D., Nawotka K. A., el-Assouli S. M., Davis L. R. The in vivo replication origin of the yeast 2 microns plasmid. Cell. 1987 Nov 6;51(3):473–481. doi: 10.1016/0092-8674(87)90643-x. [DOI] [PubMed] [Google Scholar]
  23. Huberman J. A., Zhu J. G., Davis L. R., Newlon C. S. Close association of a DNA replication origin and an ARS element on chromosome III of the yeast, Saccharomyces cerevisiae. Nucleic Acids Res. 1988 Jul 25;16(14A):6373–6384. doi: 10.1093/nar/16.14.6373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kearsey S. Structural requirements for the function of a yeast chromosomal replicator. Cell. 1984 May;37(1):299–307. doi: 10.1016/0092-8674(84)90326-x. [DOI] [PubMed] [Google Scholar]
  26. Kemler I., Schreiber E., Müller M. M., Matthias P., Schaffner W. Octamer transcription factors bind to two different sequence motifs of the immunoglobulin heavy chain promoter. EMBO J. 1989 Jul;8(7):2001–2008. doi: 10.1002/j.1460-2075.1989.tb03607.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kimmerly W., Buchman A., Kornberg R., Rine J. Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeast silencer. EMBO J. 1988 Jul;7(7):2241–2253. doi: 10.1002/j.1460-2075.1988.tb03064.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Linskens M. H., Huberman J. A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4927–4935. doi: 10.1128/mcb.8.11.4927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Maine G. T., Sinha P., Tye B. K. Mutants of S. cerevisiae defective in the maintenance of minichromosomes. Genetics. 1984 Mar;106(3):365–385. doi: 10.1093/genetics/106.3.365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Marczynski G. T., Jaehning J. A. A transcription map of a yeast centromere plasmid: unexpected transcripts and altered gene expression. Nucleic Acids Res. 1985 Dec 9;13(23):8487–8506. doi: 10.1093/nar/13.23.8487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Newlon C. S. Yeast chromosome replication and segregation. Microbiol Rev. 1988 Dec;52(4):568–601. doi: 10.1128/mr.52.4.568-601.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Palzkill T. G., Newlon C. S. A yeast replication origin consists of multiple copies of a small conserved sequence. Cell. 1988 May 6;53(3):441–450. doi: 10.1016/0092-8674(88)90164-x. [DOI] [PubMed] [Google Scholar]
  34. Poellinger L., Roeder R. G. Octamer transcription factors 1 and 2 each bind to two different functional elements in the immunoglobulin heavy-chain promoter. Mol Cell Biol. 1989 Feb;9(2):747–756. doi: 10.1128/mcb.9.2.747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Ptashne M. Gene regulation by proteins acting nearby and at a distance. Nature. 1986 Aug 21;322(6081):697–701. doi: 10.1038/322697a0. [DOI] [PubMed] [Google Scholar]
  36. Rhode P. R., Sweder K. S., Oegema K. F., Campbell J. L. The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev. 1989 Dec;3(12A):1926–1939. doi: 10.1101/gad.3.12a.1926. [DOI] [PubMed] [Google Scholar]
  37. Saffer L. D., Miller O. L., Jr Electron microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol Cell Biol. 1986 Apr;6(4):1148–1157. doi: 10.1128/mcb.6.4.1148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Shore D., Stillman D. J., Brand A. H., Nasmyth K. A. Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication. EMBO J. 1987 Feb;6(2):461–467. doi: 10.1002/j.1460-2075.1987.tb04776.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Singh H., Sen R., Baltimore D., Sharp P. A. A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes. Nature. 1986 Jan 9;319(6049):154–158. doi: 10.1038/319154a0. [DOI] [PubMed] [Google Scholar]
  41. Snyder M., Buchman A. R., Davis R. W. Bent DNA at a yeast autonomously replicating sequence. Nature. 1986 Nov 6;324(6092):87–89. doi: 10.1038/324087a0. [DOI] [PubMed] [Google Scholar]
  42. Snyder M., Sapolsky R. J., Davis R. W. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol. 1988 May;8(5):2184–2194. doi: 10.1128/mcb.8.5.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Srienc F., Bailey J. E., Campbell J. L. Effect of ARS1 mutations on chromosome stability in Saccharomyces cerevisiae. Mol Cell Biol. 1985 Jul;5(7):1676–1684. doi: 10.1128/mcb.5.7.1676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Staudt L. M., Singh H., Sen R., Wirth T., Sharp P. A., Baltimore D. A lymphoid-specific protein binding to the octamer motif of immunoglobulin genes. Nature. 1986 Oct 16;323(6089):640–643. doi: 10.1038/323640a0. [DOI] [PubMed] [Google Scholar]
  45. Stinchcomb D. T., Struhl K., Davis R. W. Isolation and characterisation of a yeast chromosomal replicator. Nature. 1979 Nov 1;282(5734):39–43. doi: 10.1038/282039a0. [DOI] [PubMed] [Google Scholar]
  46. Strich R., Woontner M., Scott J. F. Mutations in ARS1 increase the rate of simple loss of plasmids in Saccharomyces cerevisiae. Yeast. 1986 Sep;2(3):169–178. doi: 10.1002/yea.320020305. [DOI] [PubMed] [Google Scholar]
  47. Sturm R., Baumruker T., Franza B. R., Jr, Herr W. A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer. Genes Dev. 1987 Dec;1(10):1147–1160. doi: 10.1101/gad.1.10.1147. [DOI] [PubMed] [Google Scholar]
  48. Sweder K. S., Rhode P. R., Campbell J. L. Purification and characterization of proteins that bind to yeast ARSs. J Biol Chem. 1988 Nov 25;263(33):17270–17277. [PubMed] [Google Scholar]
  49. Szostak J. W., Wu R. Insertion of a genetic marker into the ribosomal DNA of yeast. Plasmid. 1979 Oct;2(4):536–554. doi: 10.1016/0147-619x(79)90053-2. [DOI] [PubMed] [Google Scholar]
  50. Umek R. M., Kowalski D. The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell. 1988 Feb 26;52(4):559–567. doi: 10.1016/0092-8674(88)90469-2. [DOI] [PubMed] [Google Scholar]
  51. Walker S. S., Francesconi S. C., Tye B. K., Eisenberg S. The OBF1 protein and its DNA-binding site are important for the function of an autonomously replicating sequence in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Jul;9(7):2914–2921. doi: 10.1128/mcb.9.7.2914. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES