• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of molcellbPermissionsJournals.ASM.orgJournalMCB ArticleJournal InfoAuthorsReviewers
Mol Cell Biol. Nov 1994; 14(11): 7643–7651.
PMCID: PMC359300

Functional conservation of multiple elements in yeast chromosomal replicators.

Abstract

Replicators that control the initiation of DNA replication in the chromosomes of Saccharomyces cerevisiae retain their function when cloned into plasmids, where they are commonly referred to as autonomously replicating sequences (ARSs). Previous studies of the structure of ARS1 in both plasmid and chromosome contexts have shown that it contains one essential DNA element, A, that includes a match to the ARS consensus sequence (ACS), and three additional elements, B1, B2, and B3, that are also important for ARS function. Elements A and B3 are bound by a candidate initiator protein called the origin recognition complex and ARS-binding factor 1, respectively. Although the A and B3 elements have been found in other ARSs, sequence comparisons among ARSs have failed to identify B1- and B2-like elements. To assess the generality of the modular nature of yeast replicators, linker substitution mutagenesis of another yeast chromosomal replicator, ARS307, was performed. Three DNA sequence elements were identified in ARS307, and they were demonstrated to be functionally equivalent to the A, B1, and B2 elements present in ARS1. Despite the lack of DNA sequence similarity, the B1 and B2 elements at each ARS were functionally conserved. Single-base substitutions in the core of the ARS1 B1 and B2 elements identified critical nucleotides required for the function of the B1 element. In contrast, no single-point mutations were found to affect B2 function. The results suggest that multiple DNA sequence elements might be a general and conserved feature of replicator sequences in S. cerevisiae.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.7M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Amati B, Gasser SM. Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeasts. Mol Cell Biol. 1990 Oct;10(10):5442–5454. [PMC free article] [PubMed]
  • Bell SP, Kobayashi R, Stillman B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science. 1993 Dec 17;262(5141):1844–1849. [PubMed]
  • 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]
  • Brewer BJ, Fangman WL. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987 Nov 6;51(3):463–471. [PubMed]
  • Broach JR, Li YY, Feldman J, Jayaram M, Abraham J, Nasmyth KA, Hicks JB. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. [PubMed]
  • Buchman AR, Kimmerly WJ, Rine J, Kornberg RD. 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. [PMC free article] [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]
  • 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, Cocker JH. Protein-DNA interactions at a yeast replication origin. Nature. 1992 May 14;357(6374):169–172. [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]
  • 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]
  • Eisenberg S, Civalier C, Tye BK. 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. [PMC free article] [PubMed]
  • Estes HG, Robinson BS, Eisenberg S. At least three distinct proteins are necessary for the reconstitution of a specific multiprotein complex at a eukaryotic chromosomal origin of replication. Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11156–11160. [PMC free article] [PubMed]
  • Foss M, McNally FJ, Laurenson P, Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. [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]
  • Holmes SG, Smith MM. Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain. Mol Cell Biol. 1989 Dec;9(12):5464–5472. [PMC free article] [PubMed]
  • Hsiao CL, Carbon J. High-frequency transformation of yeast by plasmids containing the cloned yeast ARG4 gene. Proc Natl Acad Sci U S A. 1979 Aug;76(8):3829–3833. [PMC free article] [PubMed]
  • Huang RY, Kowalski D. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 1993 Dec;12(12):4521–4531. [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]
  • Kearsey S. Structural requirements for the function of a yeast chromosomal replicator. Cell. 1984 May;37(1):299–307. [PubMed]
  • Kunkel TA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. [PMC free article] [PubMed]
  • Li JJ, Herskowitz I. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science. 1993 Dec 17;262(5141):1870–1874. [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]
  • Marahrens Y, Stillman B. Replicator dominance in a eukaryotic chromosome. EMBO J. 1994 Jul 15;13(14):3395–3400. [PMC free article] [PubMed]
  • McKnight SL, Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. [PubMed]
  • Micklem G, Rowley A, Harwood J, Nasmyth K, Diffley JF. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature. 1993 Nov 4;366(6450):87–89. [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]
  • Natale DA, Umek RM, Kowalski D. Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res. 1993 Feb 11;21(3):555–560. [PMC free article] [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]
  • Palzkill TG, Oliver SG, Newlon CS. 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. [PMC free article] [PubMed]
  • Rhode PR, Sweder KS, Oegema KF, Campbell JL. The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev. 1989 Dec;3(12A):1926–1939. [PubMed]
  • Rivier DH, Rine J. An origin of DNA replication and a transcription silencer require a common element. Science. 1992 May 1;256(5057):659–663. [PubMed]
  • Rowley A, Dowell SJ, Diffley JF. Recent developments in the initiation of chromosomal DNA replication: a complex picture emerges. Biochim Biophys Acta. 1994 Apr 6;1217(3):239–256. [PubMed]
  • Stillman B. DNA replication. Replicator renaissance. Nature. 1993 Dec 9;366(6455):506–507. [PubMed]
  • Stillman B. Initiation of chromosomal DNA replication in eukaryotes. Lessons from lambda. J Biol Chem. 1994 Mar 11;269(10):7047–7050. [PubMed]
  • Stinchcomb DT, Struhl K, Davis RW. Isolation and characterisation of a yeast chromosomal replicator. Nature. 1979 Nov 1;282(5734):39–43. [PubMed]
  • Theis JF, Newlon CS. Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function. Mol Cell Biol. 1994 Nov;14(11):7652–7659. [PMC free article] [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]
  • 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]
  • 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, 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]

Articles from Molecular and Cellular Biology are provided here courtesy of American Society for Microbiology (ASM)

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...