Chromosoma

, Volume 103, Issue 6, pp 414–422 | Cite as

Comparison of the two major ARS elements of the ura4 replication origin region with other ARS elements in the fission yeast, Schizosaccharomyces pombe

  • Jiguang Zhu
  • Deborah L. Carlson
  • Dharani D. Dubey
  • Karuna Sharma
  • Joel A. Huberman
Original Articles

Abstract

We have previously peported that the replication orgin region located near the ura4 gene on chromosome III of the fission yeast, Schizosaccharomyces pombe, contains three closely spaced origins, each associated with an autonomously replicating sequence (ARS) element. Here we report the nucleotide sequences of two of these ARS elements, ars3002 and ars3003. The two ARS elements are located on either side of a transcribed 1.5 kb open reading frame. Like 11 other S. pombe ARS elements whose sequences have previously been determined in other laboratories, the 2 new ARS elements are unusually A+T-rich. All 13 ARS elements contain easily unwound stretches of DNA. Each of the ARS elements contains numerous copies, at a higher than expected frequency, of short stretches of A+T-rich DNA in which most of the Ts are on one strand and most of the As are on the complementary strand. We discuss the potential significance for ARS function of these multiple asymmetric A+T-rich sequences.

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References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410Google Scholar
  2. Amati B, Gasser SM (1990) Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeasts. Mol Cell Biol 10:5442–5454Google Scholar
  3. Amati BB, Gasser SM (1988) Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54:967–978Google Scholar
  4. Barker DG, White JHM, Johnston LH (1987) Molecular characterisation of the DNA ligase gene, CDC17, from the fission yeast Schizosaccharomyces pombe. Eur J Biochem 162:659–667Google Scholar
  5. Bell SP, Stillman B (1992) ATP dependent recognition of eukaryotic orgins of DNA replication by a multi-protein complex. Nature 357:128–134Google Scholar
  6. Breslauer KJ, Frank R, Blöcker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83:3746–3750Google Scholar
  7. Brewer BJ, Fangman WL (1987) The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463–471Google Scholar
  8. Campbell JL, Newlon CS (1991) Chromosomal DNA replication. In: Broach JR, Pringle JR, Jones EW (eds) The molecular biology and cellular biology of the yeast Saccharomyces: genome dynamics, protein synthesis, and energetics. (Cold Spring Harbor monograph series 1) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 41–146Google Scholar
  9. Deshpande AM, Newlon CS (1992) The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae. Mol Cell Biol 12:4305–4313Google Scholar
  10. Dubey DD, Zhu J, Carlson DL, Sharma K, Huberman JA (1994) Three ARS elements contribute to the ura4 replication origin region in the fission yeast, Schizosaccharomyces pombe. EMBO J 13:3638–3647Google Scholar
  11. Eckdahl TT, Anderson JN (1990) Conserved DNA structures in origins of replication. Nucleic Acids Res 18:1609–1612Google Scholar
  12. Gasser SM, Laemmli UK (1986) Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521–530Google Scholar
  13. Grimm C, Kohli J (1988) Observations on integrative transformation in Schizosaccharomyces pombe. Mol Gen Genet 215:87–93Google Scholar
  14. Grimm C, Kohli J, Murray J, Maundrell K (1988) Genetic engineering of Schizosaccharomyces pombe: a system for gene disruption and replacement using the ura4 gene as a selectable marker. Mol Gen Genet 215:81–86Google Scholar
  15. Heyer W-D, Sipiczki M, Kohli J (1986) Replicating plasmids in Schizosaccharomyces pombe: Improvement of symmetric segregation by a new genetic element. Mol Cell Biol 6:80–89Google Scholar
  16. Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272Google Scholar
  17. Huang R-Y, Kowalski D (1993) A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J 12:4521–4531Google Scholar
  18. Huberman JA, Spotila LD, Nawotka KA, El-Assouli SM, Davis LR (1987) The in vivo replication origin of the yeast 2 μm plasmid. Cell 51:473–481Google Scholar
  19. Jacob F, Brenner S, Cuzin F (1963) On the regulation of DNA replication in bacteria. Cold Spring Harbor Symp Quant Biol 28:329–348Google Scholar
  20. Johnston LH, Barker DG (1987) Characterisation of an autonomously replicating sequence from the fission yeast Schizosaccharomyces pombe. Mol Gen Genet 207:161–164Google Scholar
  21. Luehrsen KR, Pearlman RE, Pata J, Orias E (1988) Comparison of Tetrahymena ARS sequence function in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Curr Genet 14:225–233Google Scholar
  22. Marahrens Y, Stillman B (1992) A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817–823Google Scholar
  23. Maundrell K, Wright APH, Piper M, Shall S (1985) Evaluation of heterologous ARS activity in S. cerevisiae using cloned DNA from S. pombe. Nucleic Acids Res 13:3711–3722Google Scholar
  24. Maundrell K, Hutchison A, Shall S (1988) Sequence analysis of ARS elements in fission yeast. EMBO J 7:2203–2209Google Scholar
  25. Moreno S, Klar A, Nurse P (1991) Molecular genetic analysis of fission yeast. Methods Enzymol 194:795–823Google Scholar
  26. Natale DA, Schubert AE, Kowalski D (1992) DNA helical stability accounts for mutational defects in a yeast replication origin. Proc Natl Acad Sci USA 89:2654–2658Google Scholar
  27. Natale DA, Umek RM, Kowalski D (1993) Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res 21:555–560Google Scholar
  28. Nelson HCM, Finch JT, Luisi BF, Klug A (1987) The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature 330:221–226Google Scholar
  29. Pardoll DM, Vogelstein B, Coffey DS (1980) A fixed site of DNA replication in eucaryotic cells. Cell 19:527–536Google Scholar
  30. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444–2448Google Scholar
  31. Razin SV, Kekelidze MG, Lukanidin EM, Scherrer K, Georgiev GP (1986) Replication origins are attached to the nuclear skeleton. Nucleic Acids Res 14:8189–8207Google Scholar
  32. Rivier DH, Rine J (1992) An origin of DNA replication and a transcription silencer require a common element. Science 256:659–663Google Scholar
  33. Saito Y, Laemmli UK (1994) Metaphase chromosome structure: bands arise from a differential folding path of the highly AT-rich scaffold. Cell 76:609–622Google Scholar
  34. Sakaguchi J, Yamamoto M (1982) Cloned ura1 locus of Schizosaccharomyces pombe propagates autonomously in this yeast assuming a polymeric form. Proc Natl Acad Sci USA 79:7819–7823Google Scholar
  35. Sakai K, Sakaguchi J, Yamamoto M (1984) High-frequency co-transformation by copolymerization of plasmids in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol 4:651–656Google Scholar
  36. Snyder M, Buchman AR, Davis RW (1986) Bent DNA at a yeast autonomously replicating sequence. Nature 324:87–89Google Scholar
  37. Umek RM, Kowalski D (1988) The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell 52:559–567Google Scholar
  38. Umek RM, Kowalski D (1990) Thermal energy suppresses mutational defects in DNA unwinding at a yeast replication origin. Proc Natl Acad Sci USA 87:2486–2490Google Scholar
  39. Walker SS, Malik AK, Eisenberg S (1991) Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae. Nucleic Acids Res 19:6255–6262Google Scholar
  40. Wright APH, Maundrell K, Shall S (1986) Transformation of Schizosaccharomyces pombe by non-homologous, unstable integration of plasmids in the genome. Curr Genet 10:503–508Google Scholar
  41. Zhu J, Brun C, Kurooka H, Yanagida M, Huberman JA (1992) Identification and characterization of a complex chromosomal replication origin in Schizosaccharomyces pombe. Chromosoma 102:S7-S16Google Scholar

Copyright information

© Springer-Verlag 1994

Authors and Affiliations

  • Jiguang Zhu
    • 1
  • Deborah L. Carlson
    • 1
  • Dharani D. Dubey
    • 1
  • Karuna Sharma
    • 1
  • Joel A. Huberman
    • 1
  1. 1.Department of Molecular and Cellular BiologyRoswell Park Cancer InstituteBuffaloUSA
  2. 2.Department of NeurosurgeryBrigham & Women's HospitalBostonUSA

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