Skip to main content
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1986 Jul;6(7):2354–2363. doi: 10.1128/mcb.6.7.2354

Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids.

A H Bouton, M M Smith
PMCID: PMC367788  PMID: 3023929

Abstract

An autonomously replicating segment, ARS, is located 293 base pairs downstream from the histone H4 gene at the copy-I H3-H4 locus. The sequences needed for autonomous replication were defined by deletion analysis to include an ARS consensus sequence and an additional 3'-flanking region. External deletions into the 3'-flanking yeast sequences resulted in a loss of replication function. However, disruptions of the required 3'-flanking domain by either 10-base-pair linker-scanning substitutions or larger internal deletions did not impair autonomous replication. Thus, replication is dependent upon a flanking chromosome domain, but not an exact DNA sequence. The extent of the yeast sequences required in the 3'-flanking domain is variable depending on the nature of neighboring plasmid vector sequences. That is, there are certain vector sequences that prohibit replication when they are placed too close to the ARS consensus. These results suggest that the functional 3'-flanking domain of the H4 ARS is a specific DNA or chromatin structure or both.

Full text

PDF
2354

Selected References

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

  1. Beggs J. D. Transformation of yeast by a replicating hybrid plasmid. Nature. 1978 Sep 14;275(5676):104–109. doi: 10.1038/275104a0. [DOI] [PubMed] [Google Scholar]
  2. Botstein D., Falco S. C., Stewart S. E., Brennan M., Scherer S., Stinchcomb D. T., Struhl K., Davis R. W. Sterile host yeasts (SHY): a eukaryotic system of biological containment for recombinant DNA experiments. Gene. 1979 Dec;8(1):17–24. doi: 10.1016/0378-1119(79)90004-0. [DOI] [PubMed] [Google Scholar]
  3. Breunig K. D., Mackedonski V., Hollenberg C. P. Transcription of the bacterial beta-lactamase gene in Saccharomyces cerevisiae. Gene. 1982 Nov;20(1):1–10. doi: 10.1016/0378-1119(82)90082-8. [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. 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]
  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. Dawes I. W., Carter B. L. Nitrosoguanidine mutagenesis during nuclear and mitochondrial gene replication. Nature. 1974 Aug 30;250(5469):709–712. doi: 10.1038/250709a0. [DOI] [PubMed] [Google Scholar]
  8. Fagrelius T. J., Livingston D. M. Location of DNAase I sensitive cleavage sites in the yeast 2 micron plasmid DNA chromosome. J Mol Biol. 1984 Feb 15;173(1):1–13. doi: 10.1016/0022-2836(84)90400-5. [DOI] [PubMed] [Google Scholar]
  9. Fangman W. L., Hice R. H., Chlebowicz-Sledziewska E. ARS replication during the yeast S phase. Cell. 1983 Mar;32(3):831–838. doi: 10.1016/0092-8674(83)90069-7. [DOI] [PubMed] [Google Scholar]
  10. Hieter P., Mann C., Snyder M., Davis R. W. Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell. 1985 Feb;40(2):381–392. doi: 10.1016/0092-8674(85)90152-7. [DOI] [PubMed] [Google Scholar]
  11. Hinnen A., Hicks J. B., Fink G. R. Transformation of yeast. Proc Natl Acad Sci U S A. 1978 Apr;75(4):1929–1933. doi: 10.1073/pnas.75.4.1929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Jongstra J., Reudelhuber T. L., Oudet P., Benoist C., Chae C. B., Jeltsch J. M., Mathis D. J., Chambon P. Induction of altered chromatin structures by simian virus 40 enhancer and promoter elements. Nature. 1984 Feb 23;307(5953):708–714. doi: 10.1038/307708a0. [DOI] [PubMed] [Google Scholar]
  13. Kearsey S. Analysis of sequences conferring autonomous replication in baker's yeast. EMBO J. 1983;2(9):1571–1575. doi: 10.1002/j.1460-2075.1983.tb01626.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Kingsman A. J., Clarke L., Mortimer R. K., Carbon J. Replication in Saccharomyces cerevisiae of plasmid pBR313 carrying DNA from the yeast trpl region. Gene. 1979 Oct;7(2):141–152. doi: 10.1016/0378-1119(79)90029-5. [DOI] [PubMed] [Google Scholar]
  16. Koshland D., Kent J. C., Hartwell L. H. Genetic analysis of the mitotic transmission of minichromosomes. Cell. 1985 Feb;40(2):393–403. doi: 10.1016/0092-8674(85)90153-9. [DOI] [PubMed] [Google Scholar]
  17. Kunkel G. R., Martinson H. G. Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981 Dec 21;9(24):6869–6888. doi: 10.1093/nar/9.24.6869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Livingston D. M. A sequence of the yeast 2 micron DNA plasmid chromosome near the origin of replication is exposed to restriction endonuclease digestion. J Mol Biol. 1982 Sep 25;160(3):397–410. doi: 10.1016/0022-2836(82)90304-7. [DOI] [PubMed] [Google Scholar]
  19. Long C. M., Brajkovich C. M., Scott J. F. Alternative model for chromatin organization of the Saccharomyces cerevisiae chromosomal DNA plasmid TRP1 RI circle (YARp1). Mol Cell Biol. 1985 Nov;5(11):3124–3130. doi: 10.1128/mcb.5.11.3124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McKnight S. L. Functional relationships between transcriptional control signals of the thymidine kinase gene of herpes simplex virus. Cell. 1982 Dec;31(2 Pt 1):355–365. doi: 10.1016/0092-8674(82)90129-5. [DOI] [PubMed] [Google Scholar]
  21. McKnight S. L., Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. doi: 10.1126/science.6283634. [DOI] [PubMed] [Google Scholar]
  22. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Murray A. W., Szostak J. W. Pedigree analysis of plasmid segregation in yeast. Cell. 1983 Oct;34(3):961–970. doi: 10.1016/0092-8674(83)90553-6. [DOI] [PubMed] [Google Scholar]
  24. Murray N. E., Bruce S. A., Murray K. Molecular cloning of the DNA ligase gene from bacteriophage T4. II. Amplification and preparation of the gene product. J Mol Biol. 1979 Aug 15;132(3):493–505. doi: 10.1016/0022-2836(79)90271-7. [DOI] [PubMed] [Google Scholar]
  25. Prunell A. Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT). EMBO J. 1982;1(2):173–179. doi: 10.1002/j.1460-2075.1982.tb01143.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Saragosti S., Moyne G., Yaniv M. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell. 1980 May;20(1):65–73. doi: 10.1016/0092-8674(80)90235-4. [DOI] [PubMed] [Google Scholar]
  28. Smith M. M., Andrésson O. S. DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins. J Mol Biol. 1983 Sep 25;169(3):663–690. doi: 10.1016/s0022-2836(83)80164-8. [DOI] [PubMed] [Google Scholar]
  29. Smith M. M., Murray K. Yeast H3 and H4 histone messenger RNAs are transcribed from two non-allelic gene sets. J Mol Biol. 1983 Sep 25;169(3):641–661. doi: 10.1016/s0022-2836(83)80163-6. [DOI] [PubMed] [Google Scholar]
  30. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. St John T. P., Scherer S., McDonell M. W., Davis R. W. Deletion analysis of the Saccharomyces GAL gene cluster. Transcription from three promoters. J Mol Biol. 1981 Oct 25;152(2):317–334. doi: 10.1016/0022-2836(81)90245-x. [DOI] [PubMed] [Google Scholar]
  33. Thoma F., Bergman L. W., Simpson R. T. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J Mol Biol. 1984 Aug 25;177(4):715–733. doi: 10.1016/0022-2836(84)90046-9. [DOI] [PubMed] [Google Scholar]
  34. Thoma F., Simpson R. T. Local protein-DNA interactions may determine nucleosome positions on yeast plasmids. Nature. 1985 May 16;315(6016):250–252. doi: 10.1038/315250a0. [DOI] [PubMed] [Google Scholar]
  35. Varshavsky A. J., Sundin O. H., Bohn M. J. SV40 viral minichromosome: preferential exposure of the origin of replication as probed by restriction endonucleases. Nucleic Acids Res. 1978 Oct;5(10):3469–3477. doi: 10.1093/nar/5.10.3469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Veit B. E., Fangman W. L. Chromatin organization of the Saccharomyces cerevisiae 2 microns plasmid depends on plasmid-encoded products. Mol Cell Biol. 1985 Sep;5(9):2190–2196. doi: 10.1128/mcb.5.9.2190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Williamson D. H. The yeast ARS element, six years on: a progress report. Yeast. 1985 Sep;1(1):1–14. doi: 10.1002/yea.320010102. [DOI] [PubMed] [Google Scholar]
  38. Zakian V. A., Kupfer D. M. Replication and segregation of an unstable plasmid in yeast. Plasmid. 1982 Jul;8(1):15–28. doi: 10.1016/0147-619x(82)90037-3. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES