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Mol Cell Biol. 1993 Aug; 13(8): 5043–5056.
PMCID: PMC360155

Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae.

Abstract

We have reported the isolation of linking clones of HindIII and EcoRI fragments, altogether spanning a 230-kb continuous stretch of chromosome VI. The presence or absence of autonomously replicating sequence (ARS) activities in all of these fragments has been determined by using ARS searching vectors containing CEN4. Nine ARS fragments were identified, and their positions were mapped on the chromosome. Structures essential for and/or stimulative to ARS activity were determined for the ARS fragments by deletions and mutations. The organization of functional elements composed of core and stimulative sequences was found to be variable. Single core sequences were identified in eight of nine ARSs. The remaining ARS (ARS603) essential element is composed of two core-like sequences. The lengths of 3'- and 5'-flanking stimulative sequences required for the full activity of ARSs varied from ARS to ARS. Five ARSs required more than 100 bp of the 3'-flanking sequence as stimulative sequences, while not more than 79 bp of the 3' sequence was required by the other three ARSs. In addition, five ARSs had stimulative sequences varying from 127 to 312 bp in the 5'-flanking region of the core sequence. In general, these stimulative activities were correlated with low local delta Gs of unwinding, suggesting that the low local delta G of an ARS is an important element for determining the efficiency of initiation of replication of ARS plasmids.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bell SP, Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. [PubMed]
  • Bouton AH, Smith MM. Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids. Mol Cell Biol. 1986 Jul;6(7):2354–2363. [PMC free article] [PubMed]
  • Brand AH, 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. [PubMed]
  • Celniker SE, Sweder K, Srienc F, Bailey JE, Campbell JL. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol Cell Biol. 1984 Nov;4(11):2455–2466. [PMC free article] [PubMed]
  • Chan CS, Tye BK. Autonomously replicating sequences in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6329–6333. [PMC free article] [PubMed]
  • Deshpande AM, Newlon CS. The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Oct;12(10):4305–4313. [PMC free article] [PubMed]
  • Diffley JF, 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. [PMC free article] [PubMed]
  • Dower WJ, Miller JF, Ragsdale CW. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 1988 Jul 11;16(13):6127–6145. [PMC free article] [PubMed]
  • Dubey DD, Davis LR, Greenfeder SA, Ong LY, Zhu JG, Broach JR, Newlon CS, Huberman JA. Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins. Mol Cell Biol. 1991 Oct;11(10):5346–5355. [PMC free article] [PubMed]
  • Fangman WL, Hice RH, Chlebowicz-Sledziewska E. ARS replication during the yeast S phase. Cell. 1983 Mar;32(3):831–838. [PubMed]
  • Feldman JB, Hicks JB, Broach JR. Identification of sites required for repression of a silent mating type locus in yeast. J Mol Biol. 1984 Oct 5;178(4):815–834. [PubMed]
  • Ferguson BM, Brewer BJ, Reynolds AE, Fangman WL. A yeast origin of replication is activated late in S phase. Cell. 1991 May 3;65(3):507–515. [PubMed]
  • Gietz RD, Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. [PubMed]
  • Greenfeder SA, Newlon CS. A replication map of a 61-kb circular derivative of Saccharomyces cerevisiae chromosome III. Mol Biol Cell. 1992 Sep;3(9):999–1013. [PMC free article] [PubMed]
  • Huberman JA, Zhu JG, Davis LR, Newlon CS. 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. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Iwasaki T, Shirahige K, Yoshikawa H, Ogasawara N. The direct cloning of the yeast genome using the gap-filling method and the complete physical mapping of Saccharomyces cerevisiae chromosome VI. Gene. 1991 Dec 20;109(1):81–87. [PubMed]
  • Kearsey S. Structural requirements for the function of a yeast chromosomal replicator. Cell. 1984 May;37(1):299–307. [PubMed]
  • Kowalski D, Eddy MJ. The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 1989 Dec 20;8(13):4335–4344. [PMC free article] [PubMed]
  • Linskens MH, Huberman JA. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4927–4935. [PMC free article] [PubMed]
  • Mann C, Davis RW. Meiotic disjunction of circular minichromosomes in yeast does not require DNA homology. Proc Natl Acad Sci U S A. 1986 Aug;83(16):6017–6019. [PMC free article] [PubMed]
  • Marahrens Y, Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science. 1992 Feb 14;255(5046):817–823. [PubMed]
  • McCarroll RM, Fangman WL. Time of replication of yeast centromeres and telomeres. Cell. 1988 Aug 12;54(4):505–513. [PubMed]
  • Murray AW, Szostak JW. Pedigree analysis of plasmid segregation in yeast. Cell. 1983 Oct;34(3):961–970. [PubMed]
  • Natale DA, Schubert AE, Kowalski D. DNA helical stability accounts for mutational defects in a yeast replication origin. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2654–2658. [PMC free article] [PubMed]
  • Newlon CS. Yeast chromosome replication and segregation. Microbiol Rev. 1988 Dec;52(4):568–601. [PMC free article] [PubMed]
  • Newlon CS, Lipchitz LR, Collins I, Deshpande A, Devenish RJ, Green RP, Klein HL, Palzkill TG, Ren RB, Synn S, et al. Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements. Genetics. 1991 Oct;129(2):343–357. [PMC free article] [PubMed]
  • Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, et al. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. [PubMed]
  • Palzkill TG, Newlon CS. A yeast replication origin consists of multiple copies of a small conserved sequence. Cell. 1988 May 6;53(3):441–450. [PubMed]
  • Petes TD, Newlon CS, Byers B, Fangman WL. Yeast chromosomal DNA: size, structure, and replication. Cold Spring Harb Symp Quant Biol. 1974;38:9–16. [PubMed]
  • Rivin CJ, Fangman WL. Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae. J Cell Biol. 1980 Apr;85(1):108–115. [PMC free article] [PubMed]
  • Simpson RT. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature. 1990 Jan 25;343(6256):387–389. [PubMed]
  • Skryabin KG, Eldarov MA, Larionov VL, Bayev AA, Klootwijk J, de Regt VC, Veldman GM, Planta RJ, Georgiev OI, Hadjiolov AA. Structure and function of the nontranscribed spacer regions of yeast rDNA. Nucleic Acids Res. 1984 Mar 26;12(6):2955–2968. [PMC free article] [PubMed]
  • Srienc F, Bailey JE, Campbell JL. Effect of ARS1 mutations on chromosome stability in Saccharomyces cerevisiae. Mol Cell Biol. 1985 Jul;5(7):1676–1684. [PMC free article] [PubMed]
  • Sweder KS, Rhode PR, Campbell JL. Purification and characterization of proteins that bind to yeast ARSs. J Biol Chem. 1988 Nov 25;263(33):17270–17277. [PubMed]
  • 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. [PubMed]
  • Umek RM, Kowalski D. The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell. 1988 Feb 26;52(4):559–567. [PubMed]
  • Umek RM, 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. [PMC free article] [PubMed]
  • Umek RM, Linskens MH, Kowalski D, Huberman JA. New beginnings in studies of eukaryotic DNA replication origins. Biochim Biophys Acta. 1989 Jan 23;1007(1):1–14. [PubMed]
  • Van Houten JV, Newlon CS. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol. 1990 Aug;10(8):3917–3925. [PMC free article] [PubMed]
  • Verdier JM. Regulatory DNA-binding proteins in yeast: an overview. Yeast. 1990 Jul-Aug;6(4):271–297. [PubMed]
  • Walker SS, Francesconi SC, Eisenberg S. A DNA replication enhancer in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4665–4669. [PMC free article] [PubMed]
  • Walker SS, Francesconi SC, Tye BK, 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. [PMC free article] [PubMed]
  • Walker SS, Malik AK, Eisenberg S. Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae. Nucleic Acids Res. 1991 Nov 25;19(22):6255–6262. [PMC free article] [PubMed]
  • Yoshikawa A, Isono K. Construction of an ordered clone bank and systematic analysis of the whole transcripts of chromosome VI of Saccharomyces cerevisiae. Nucleic Acids Res. 1991 Mar 25;19(6):1189–1195. [PMC free article] [PubMed]
  • Zhu J, Newlon CS, Huberman JA. Localization of a DNA replication origin and termination zone on chromosome III of Saccharomyces cerevisiae. Mol Cell Biol. 1992 Oct;12(10):4733–4741. [PMC free article] [PubMed]

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