The ZDS1 and ZDS2 proteins require the Sir3p component of yeast silent chromatin to enhance the stability of short linear centromeric plasmids

Abstract.Yeast artificial chromosome (YAC) clones of Saccharomyces cerevisiae containing a centromere, origin of replication, two telomeres and a >50 kb insert of DNA are maintained as normal yeast chromosomes. However, short linear centromeric plasmids of 10–15 kb in size (short YACs) are missegregated at a much higher frequency than long YACs or 10–15 kb circular centromeric plasmids. A search for genes that stabilized short linear centromeric plasmids when present in multiple copies per cell uncovered ZDS1, which reduced the rate at which cells lost the short YAC, increased the fraction of cells that maintained the short YAC and decreased the number of short YACs per cell. Multiple copies of ZDS2, a homolog of ZDS1, had similar effects. Genes near yeast telomeres are transcriptionally silenced by the recruitment of proteins encoded by the SIR2, SIR3 and SIR4 genes (Sir2p, Sir3p and Sir4p). Multiple copies of ZDS1 and ZDS2 caused an increase in telomeric silencing. In addition, ZDS1 and ZDS2 both required the open reading frame encoding the N-terminal 174 amino acids of Sir3p to stabilize short YACs. Thus, the short YAC stability assay revealed a silencing-independent function for the Sir3p N-terminus. Two-hybrid analysis indicated that Zds1p and Zds2p interact with Sir2p, Sir3p, Sir4p or the yeast telomere binding protein Rap1p. Deletion of both ZDS1 and ZDS2 made short YACs, but not a 100 kb YAC, extremely unstable and also caused a 70 bp increase in the length of the telomeric TG1–3 repeats. These data indicate that short YACs can be stabilized by trans-acting factors and suggest that the proteins encoded by ZDS1 and ZDS2 alter short YAC stability by interacting with proteins that function at the telomere.

[1]  V. Zakian,et al.  Mitotic and meiotic stability of linear plasmids in yeast. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Broach,et al.  A yeast plasmid partitioning protein is a karyoskeletal component. , 1987, The Journal of biological chemistry.

[3]  L. Wetzel,et al.  Size threshold for Saccharomyces cerevisiae chromosomes: generation of telocentric chromosomes from an unstable minichromosome , 1986, Molecular and cellular biology.

[4]  R. Sternglanz,et al.  Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing , 1996, Nature.

[5]  M. Longtine,et al.  Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product , 1992, Molecular and cellular biology.

[6]  O. Ozier-Kalogeropoulos,et al.  A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[7]  Ronald W. Davis,et al.  Mitotic stability of yeast chromosomes: A colony color assay that measures nondisjunction and chromosome loss , 1985, Cell.

[8]  M. Grunstein,et al.  Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[9]  M. Dante,et al.  Multifunctional yeast high-copy-number shuttle vectors. , 1992, Gene.

[10]  M. Neff,et al.  A delay in the Saccharomyces cerevisiae cell cycle that is induced by a dicentric chromosome and dependent upon mitotic checkpoints , 1992, Molecular and cellular biology.

[11]  J. Berman,et al.  RLF2, a subunit of yeast chromatin assembly factor-I, is required for telomeric chromatin function in vivo. , 1997, Genes & development.

[12]  Barbara L. Billington,et al.  Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription , 1990, Cell.

[13]  S. Fields,et al.  The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. Hegemann,et al.  The centromere of budding yeast , 1993, BioEssays : news and reviews in molecular, cellular and developmental biology.

[15]  D. Burke,et al.  Checkpoint genes required to delay cell division in response to nocodazole respond to impaired kinetochore function in the yeast Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[16]  L. Guarente.  Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. , 1983, Methods in enzymology.

[17]  A. Lustig,et al.  Sir3p domains involved in the initiation of telomeric silencing in Saccharomyces cerevisiae. , 1998, Genetics.

[18]  A. Murray,et al.  Chromosome length controls mitotic chromosome segregation in yeast , 1986, Cell.

[19]  M. Grunstein,et al.  Spreading of transcriptional represser SIR3 from telomeric heterochromatin , 1996, Nature.

[20]  R. Wellinger,et al.  Evidence for a New Step in Telomere Maintenance , 1996, Cell.

[21]  D. Hirata,et al.  Role of calcineurin and Mpk1 in regulating the onset of mitosis in budding yeast , 1998, Nature.

[22]  R. Wellinger,et al.  Lack of positional requirements for autonomously replicating sequence elements on artificial yeast chromosomes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[23]  O. Aparicio,et al.  Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. , 1994, Genes & development.

[24]  S. Long,et al.  The Rhizobium meliloti groELc locus is required for regulation of early nod genes by the transcription activator NodD. , 1995, Genes & development.

[25]  T. Miki,et al.  Control of segregation of chromosomal DNA by sex factor F in Escherichia coli. Mutants of DNA gyrase subunit A suppress letD (ccdB) product growth inhibition. , 1992, Journal of molecular biology.

[26]  D. Stillman,et al.  Mutations in the homologous ZDS1 and ZDS2 genes affect cell cycle progression , 1996, Molecular and Cellular Biology.

[27]  J. Stavenhagen,et al.  Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae. , 1994, Genes & development.

[28]  B. Tye,et al.  The phenotype of the minichromosome maintenance mutant mcm3 is characteristic of mutants defective in DNA replication , 1990, Molecular and cellular biology.

[29]  A. Murray,et al.  Pedigree analysis of plasmid segregation in yeast , 1983, Cell.

[30]  J. Szostak,et al.  A mutant with a defect in telomere elongation leads to senescence in yeast , 1989, Cell.

[31]  K. Luo,et al.  SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. , 1997, Genes & development.

[32]  K. Runge,et al.  TEL2, an essential gene required for telomere length regulation and telomere position effect in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[33]  T. Silhavy,et al.  Multicopy suppression of cold-sensitive sec mutations in Escherichia coli , 1995, Journal of bacteriology.

[34]  A. Lustig,et al.  RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. , 1993, Genes & development.

[35]  D. Shore,et al.  Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length , 1990, Science.

[36]  M. Gotta,et al.  Functional Characterization of the N Terminus of Sir3p , 1998, Molecular and Cellular Biology.

[37]  K. Ito,et al.  Suppression of ftsH mutant phenotypes by overproduction of molecular chaperones , 1996, Journal of bacteriology.

[38]  A. Lustig,et al.  Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[39]  C. Ueguchi,et al.  Multicopy suppression: an approach to understanding intracellular functioning of the protein export system , 1992, Journal of bacteriology.

[40]  K Nasmyth,et al.  Control of the yeast cell cycle by the Cdc28 protein kinase. , 1993, Current opinion in cell biology.

[41]  C. Glover.  On the physiological role of casein kinase II in Saccharomyces cerevisiae. , 1998, Progress in nucleic acid research and molecular biology.

[42]  A. Lustig,et al.  C-terminal truncation of RAP1 results in the deregulation of telomere size, stability, and function in Saccharomyces cerevisiae , 1992, Molecular and cellular biology.

[43]  R. W. Davis,et al.  Centromeric DNA from Saccharomyces cerevisiae. , 1982, Journal of molecular biology.

[44]  D. Shore,et al.  A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. , 1992, Genes & development.

[45]  G. Gorbsky.  Cell cycle checkpoints: arresting progress in mitosis. , 1997, BioEssays : news and reviews in molecular, cellular and developmental biology.

[46]  David Botstein,et al.  Two differentially regulated mRNAs with different 5′ ends encode secreted and intracellular forms of yeast invertase , 1982, Cell.

[47]  M. Carlson,et al.  SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II , 1996, Molecular and cellular biology.

[48]  F. Spencer,et al.  Abnormal kinetochore structure activates the spindle assembly checkpoint in budding yeast. , 1996, Molecular biology of the cell.

[49]  H. Scherthan,et al.  The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae , 1996, The Journal of cell biology.

[50]  A. Murray,et al.  Aberrantly segregating centromeres activate the spindle assembly checkpoint in budding yeast , 1996, The Journal of cell biology.

[51]  M. Grunstein,et al.  A search for proteins that interact genetically with histone H3 and H4 amino termini uncovers novel regulators of the Swe1 kinase in Saccharomyces cerevisiae. , 1996, Genes & development.

[52]  R. Wellinger,et al.  yces Tehwes Acquire Single-St- TG1-3 Tails Late in S Phase , 1993 .

[53]  S. Shuman,et al.  Multicopy suppressors of temperature-sensitive mutations of yeast mRNA capping enzyme. , 1996, Gene expression.

[54]  R. R. Meyer,et al.  Suppression of the Escherichia coli ssb-1 mutation by an allele of groEL. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[55]  L. Hartwell,et al.  Genetic analysis of the mitotic transmission of minichromosomes , 1985, Cell.

[56]  S. Gasser,et al.  Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold , 1988, Cell.

[57]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[58]  R. Larossa,et al.  Demonstration by genetic suppression of interaction of GroE products with many proteins , 1989, Nature.

[59]  V. Zakian,et al.  Extra telomeres, but not internal tracts of telomeric DNA, reduce transcriptional repression at Saccharomyces telomeres. , 1995, Genetics.

[60]  E. Bi,et al.  ZDS1 and ZDS2, genes whose products may regulate Cdc42p in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

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

[62]  J. Rine,et al.  Replication and segregation of plasmids containing cis-acting regulatory sites of silent mating-type genes in Saccharomyces cerevisiae are controlled by the SIR genes , 1987, Molecular and cellular biology.

[63]  P. Laine,et al.  Interaction of the heat shock protein GroEL of Escherichia coli with single-stranded DNA-binding protein: suppression of ssb-113 by groEL46 , 1992, Journal of bacteriology.

[64]  C. Newlon.  Yeast chromosome replication and segregation , 1988, Microbiological reviews.

[65]  Oscar M. Aparicio,et al.  Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae , 1991, Cell.

[66]  D. Kupfer,et al.  Replication and segregation of an unstable plasmid in yeast. , 1982, Plasmid.

[67]  D. Stillman,et al.  Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[68]  D. Shore,et al.  Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. , 1994, Genes & development.

[69]  P. Nurse,et al.  Identification of fission yeast nuclear markers using random polypeptide fusions with green fluorescent protein. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Andreas Hecht,et al.  Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: A molecular model for the formation of heterochromatin in yeast , 1995, Cell.

[71]  A. Lustig,et al.  Mechanisms of silencing in Saccharomyces cerevisiae. , 1998, Current opinion in genetics & development.

[72]  K. Runge,et al.  Introduction of extra telomeric DNA sequences into Saccharomyces cerevisiae results in telomere elongation , 1989, Molecular and cellular biology.

[73]  A. Wolf,et al.  RAP1 protein interacts with yeast telomeres in vivo: Overproduction alters telomere structure and decreases chromosome stability , 1990, Cell.

[74]  S. Shuman,et al.  Effects of deletion mutations in the yeast Ces1 protein on cell growth and morphology and on high copy suppression of mutations in mRNA capping enzyme and translation initiation factor 4A. , 1998, Nucleic acids research.

[75]  R. Kornberg,et al.  Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein , 1988, Molecular and cellular biology.

[76]  Sanjay K. Chhablani,et al.  Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. , 1993, Genes & development.

[77]  D. Shore,et al.  A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. , 1997, Genes & development.

[78]  T. Petes,et al.  Identification of yeast mutants with altered telomere structure. , 1986, Proceedings of the National Academy of Sciences of the United States of America.