Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Nov 25;19(22):6255–6262. doi: 10.1093/nar/19.22.6255

Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae.

S S Walker 1, A K Malik 1, S Eisenberg 1
PMCID: PMC329136  PMID: 1956786

Abstract

We have determined that ARS121 is an efficient origin of replication on chromosome X of Saccharomyces cerevisiae. This origin is comprised of at least three distinct functional domains. One of these domains is the ARS121 core sequence (approximately 35 bp-long), which is essential for origin activity. This essential core contains an 11 bp sequence resembling (2 bp mismatch) the ARS consensus. Another important domain is an enhancer of DNA replication, which binds the OBF1 protein. The third domain, ATR (A/T-rich, approximately 72 bp), is auxiliary and works in either orientation, but only when located 3' to the essential core. When fused to the ARS121 core both the enhancer and the ATR domain act synergistically to enhance the activity of the origin. Furthermore, when fused to the essential core sequences of heterologous ARSs, ARS1 and ARS307, the auxiliary domains also appeared to stimulate synergistically origin function. These results suggest that (i) in order to elicit maximal origin activity all three domains have to interact and (ii) activation of the essential core sequences at different origins of replication may share a common mechanism.

Full text

PDF
6255

Images in this article

Selected References

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

  1. Bouton A. H., Smith M. M. Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids. Mol Cell Biol. 1986 Jul;6(7):2354–2363. doi: 10.1128/mcb.6.7.2354. [DOI] [PMC free article] [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. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  13. Ferguson B. M., Brewer B. J., Reynolds A. E., Fangman W. L. A yeast origin of replication is activated late in S phase. Cell. 1991 May 3;65(3):507–515. doi: 10.1016/0092-8674(91)90468-e. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Francesconi S. C., Eisenberg S. The multifunctional protein OBF1 is phosphorylated at serine and threonine residues in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4089–4093. doi: 10.1073/pnas.88.10.4089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gibson S. I., Surosky R. T., Tye B. K. The phenotype of the minichromosome maintenance mutant mcm3 is characteristic of mutants defective in DNA replication. Mol Cell Biol. 1990 Nov;10(11):5707–5720. doi: 10.1128/mcb.10.11.5707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. Palzkill T. G., Oliver S. G., Newlon C. S. DNA sequence analysis of ARS elements from chromosome III of Saccharomyces cerevisiae: identification of a new conserved sequence. Nucleic Acids Res. 1986 Aug 11;14(15):6247–6264. doi: 10.1093/nar/14.15.6247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Sinha P., Chang V., Tye B. K. A mutant that affects the function of autonomously replicating sequences in yeast. J Mol Biol. 1986 Dec 20;192(4):805–814. doi: 10.1016/0022-2836(86)90030-6. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. Tschumper G., Carbon J. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene. 1980 Jul;10(2):157–166. doi: 10.1016/0378-1119(80)90133-x. [DOI] [PubMed] [Google Scholar]
  35. Umek R. M., Kowalski D. The DNA unwinding element in a yeast replication origin functions independently of easily unwound sequences present elsewhere on a plasmid. Nucleic Acids Res. 1990 Nov 25;18(22):6601–6605. doi: 10.1093/nar/18.22.6601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. 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]
  37. Umek R. M., Kowalski D. Thermal energy suppresses mutational defects in DNA unwinding at a yeast replication origin. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2486–2490. doi: 10.1073/pnas.87.7.2486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Van Houten J. V., Newlon C. S. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol. 1990 Aug;10(8):3917–3925. doi: 10.1128/mcb.10.8.3917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Walker S. S., Francesconi S. C., Eisenberg S. A DNA replication enhancer in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4665–4669. doi: 10.1073/pnas.87.12.4665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Williams J. F. Optimization strategies for the polymerase chain reaction. Biotechniques. 1989 Jul-Aug;7(7):762–769. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES