Two Compound Replication Origins in Saccharomyces cerevisiae Contain Redundant Origin Recognition Complex Binding Sites

ABSTRACT While many of the proteins involved in the initiation of DNA replication are conserved between yeasts and metazoans, the structure of the replication origins themselves has appeared to be different. As typified by ARS1, replication origins inSaccharomyces cerevisiae are <150 bp long and have a simple modular structure, consisting of a single binding site for the origin recognition complex, the replication initiator protein, and one or more accessory sequences. DNA replication initiates from a discrete site. While the important sequences are currently less well defined, metazoan origins appear to be different. These origins are large and appear to be composed of multiple, redundant elements, and replication initiates throughout zones as large as 55 kb. In this report, we characterize two S. cerevisiae replication origins, ARS101 and ARS310, which differ from the paradigm. These origins contain multiple, redundant binding sites for the origin recognition complex. Each binding site must be altered to abolish origin function, while the alteration of a single binding site is sufficient to inactivate ARS1. This redundant structure may be similar to that seen in metazoan origins.

[1]  H. Masukata,et al.  Clustered Adenine/Thymine Stretches Are Essential for Function of a Fission Yeast Replication Origin , 1999, Molecular and Cellular Biology.

[2]  Marija Vujcic,et al.  Activation of Silent Replication Origins at Autonomously Replicating Sequence Elements near the HML Locus in Budding Yeast , 1999, Molecular and Cellular Biology.

[3]  C. Newlon,et al.  DNA sequence and functional analysis of homologous ARS elements of Saccharomyces cerevisiae and S. carlsbergensis. , 1999, Genetics.

[4]  C. Fox,et al.  A role for a replicator dominance mechanism in silencing , 1999, The EMBO journal.

[5]  C. Newlon,et al.  Conservation of ARS elements and chromosomal DNA replication origins on chromosomes III of Saccharomyces cerevisiae and S. carlsbergensis. , 1999, Genetics.

[6]  S. Gerbi,et al.  Chromosomal ARS1 has a single leading strand start site. , 1999, Molecular cell.

[7]  R. Chuang,et al.  The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. H. Rivier,et al.  Identification of a Compound Origin of Replication at theHMR-E Locus in Saccharomyces cerevisiae * , 1999, The Journal of Biological Chemistry.

[9]  M. DePamphilis Replication origins in metazoan chromosomes: fact or fiction? , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  P. Dijkwel,et al.  Distal sequences, but not ori-beta/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin. , 1998, Molecular cell.

[11]  J. Huberman,et al.  Multiple Orientation-Dependent, Synergistically Interacting, Similar Domains in the Ribosomal DNA Replication Origin of the Fission Yeast, Schizosaccharomyces pombe , 1998, Molecular and Cellular Biology.

[12]  M. DePamphilis,et al.  Identification of Primary Initiation Sites for DNA Replication in the Hamster Dihydrofolate Reductase Gene Initiation Zone , 1998, Molecular and Cellular Biology.

[13]  D. Gilbert,et al.  Replication origins in yeast versus metazoa: separation of the haves and the have nots. , 1998, Current opinion in genetics & development.

[14]  S. Gerbi,et al.  Discrete start sites for DNA synthesis in the yeast ARS1 origin. , 1998, Science.

[15]  S. Bell,et al.  Architecture of the yeast origin recognition complex bound to origins of DNA replication , 1997, Molecular and cellular biology.

[16]  S. Gerbi,et al.  Replication initiation point mapping. , 1997, Methods.

[17]  H Yoshikawa,et al.  The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI , 1997, Genes to cells : devoted to molecular & cellular mechanisms.

[18]  W. L. Fangman,et al.  Replication profile of Saccharomyces cerevisiae chromosome VI , 1997, Genes to cells : devoted to molecular & cellular mechanisms.

[19]  C. Newlon,et al.  The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Lin,et al.  Functional equivalency and diversity of cis-acting elements among yeast replication origins , 1997, Molecular and cellular biology.

[21]  S. Bell,et al.  Coordinate Binding of ATP and Origin DNA Regulates the ATPase Activity of the Origin Recognition Complex , 1997, Cell.

[22]  C. Newlon,et al.  DNA Replication Fork Pause Sites Dependent on Transcription , 1996, Science.

[23]  I. Todorov,et al.  Large, complex modular structure of a fission yeast DNA replication origin , 1996, Current Biology.

[24]  D. Kowalski,et al.  Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome. , 1996, Nucleic acids research.

[25]  T. Kelly,et al.  Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. , 1995, The EMBO journal.

[26]  P. Dijkwel,et al.  The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites , 1995, Molecular and cellular biology.

[27]  J. Diffley,et al.  Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC. , 1995, The EMBO journal.

[28]  B. Stillman,et al.  The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[29]  P. Richterich,et al.  Cytosine specific DNA sequencing with hydrogen peroxide. , 1995, Nucleic acids research.

[30]  B. J. Brewer,et al.  Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. , 1995, Methods in enzymology.

[31]  C. Newlon,et al.  Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function , 1994, Molecular and cellular biology.

[32]  B. Stillman,et al.  Functional conservation of multiple elements in yeast chromosomal replicators , 1994, Molecular and cellular biology.

[33]  J. Huberman,et al.  Three ARS elements contribute to the ura4 replication origin region in the fission yeast, Schizosaccharomyces pombe. , 1994, The EMBO journal.

[34]  B. Stillman,et al.  Replicator dominance in a eukaryotic chromosome. , 1994, The EMBO journal.

[35]  K. Matsumoto,et al.  Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region , 1994, Molecular and cellular biology.

[36]  M. Marinus,et al.  The dam and dcm strains of Escherichia coli--a review. , 1994, Gene.

[37]  W. L. Fangman,et al.  Initiation preference at a yeast origin of replication. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[38]  C. Newlon,et al.  A physical comparison of chromosome III in six strains of Saccharomyces cerevisiae , 1994, Yeast.

[39]  W. L. Fangman,et al.  Initiation at closely spaced replication origins in a yeast chromosome. , 1993, Science.

[40]  H Yoshikawa,et al.  Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[41]  C. Newlon,et al.  The effect on chromosome stability of deleting replication origins , 1993, Molecular and cellular biology.

[42]  C. Newlon,et al.  Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae. , 1993, Cold Spring Harbor symposia on quantitative biology.

[43]  Bruce Stillman,et al.  ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex , 1992, Nature.

[44]  B. Stillman,et al.  A yeast chromosomal origin of DNA replication defined by multiple functional elements. , 1992, Science.

[45]  S. Eisenberg,et al.  Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae. , 1991, Nucleic acids research.

[46]  C. Newlon,et al.  Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins , 1991, Molecular and cellular biology.

[47]  C. Newlon,et al.  Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements. , 1991, Genetics.

[48]  P. Dijkwel,et al.  Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix , 1991, Molecular and cellular biology.

[49]  T. Kunkel,et al.  Efficient site-directed mutagenesis using uracil-containing DNA. , 1991, Methods in enzymology.

[50]  L. Guarente,et al.  High-efficiency transformation of yeast by electroporation. , 1991, Methods in enzymology.

[51]  L. Vassilev,et al.  Identification of an origin of bidirectional DNA replication in mammalian chromosomes , 1990, Cell.

[52]  C. Newlon,et al.  Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III , 1990, Molecular and cellular biology.

[53]  L. Mullenders,et al.  Replication forks are associated with the nuclear matrix. , 1990, Nucleic acids research.

[54]  H. Cedar,et al.  Mapping replication units in animal cells , 1989, Cell.

[55]  R. Sikorski,et al.  A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.

[56]  S. Ho,et al.  Site-directed mutagenesis by overlap extension using the polymerase chain reaction. , 1989, Gene.

[57]  C. Newlon,et al.  A yeast replication origin consists of multiple copies of a small conserved sequence , 1988, Cell.

[58]  W. L. Fangman,et al.  The localization of replication origins on ARS plasmids in S. cerevisiae , 1987, Cell.

[59]  G. Natsoulis,et al.  5-Fluoroorotic acid as a selective agent in yeast molecular genetics. , 1987, Methods in enzymology.

[60]  C. Newlon,et al.  DNA sequence analysis of ARS elements from chromosome III of Saccharomyces cerevisiae: identification of a new conserved sequence. , 1986, Nucleic acids research.

[61]  M. Smith,et al.  Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids , 1986, Molecular and cellular biology.

[62]  J. Hamlin,et al.  An amplified chromosomal sequence that includes the gene for dihydrofolate reductase initiates replication within specific restriction fragments. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[63]  J. Carbon,et al.  High-frequency transformation of yeast by plasmids containing the cloned yeast ARG4 gene. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[64]  R. W. Davis,et al.  High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. , 1979, Proceedings of the National Academy of Sciences of the United States of America.