Identification of mutations that decrease the stability of a fragment of Saccharomyces cerevisiae chromosome III lacking efficient replicators

Genetics

Volumn 177, Issue 3, 2007, Pages 1445-1458

  Theis, James F ^a   Dershowitz, Ann ^a   Irene, Carmela ^a   Maciariello, Clelia ^b   Tobin, Michael L ^a   Liberi, Giordano ^c   Tabrizifard, Sahba ^a,d   Korus, Malgorzata ^a   Fabiani, Lucia ^b   Newlon, Carol S ^a  

^a RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c UNIVERSITY OF MILAN   (Italy)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CELL DIVISION; CHROMOSOMAL INSTABILITY; CHROMOSOME 3; CHROMOSOME MUTATION; CHROMOSOME REPLICATION; DNA DAMAGE; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; YEAST;

ALLELES; CELL CYCLE PROTEINS; CHROMOSOMAL INSTABILITY; CHROMOSOMES, FUNGAL; DNA DAMAGE; DNA REPLICATION; DNA, FUNGAL; GENES, FUNGAL; MUTATION; PHENOTYPE; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 37249018464     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.074690     Document Type: Article

References (54)

1. ALLEN, J. B., Z. ZHOU, W. SIEDE, E. C. FRIEDBERG and S. J. ELLEDGE, 1994 The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev. 8: 2416-2428.
2. BELL, S. P., and B. STILLMAN, 1992 ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357: 128-134.
3. BRACHMANN, C. B., A. DAVIES, G. J. COST, E. CAPUTO, J. LI et al., 1998 Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132.
4. BREWER, B. J., and W. L. FANGMAN, 1987 The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463-471.
5. CAMPBELL, J. L., and C. S. NEWLON, 1991 Chromosomal DNA replication, pp. 41-146 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics, edited by J. R. BROACH, J. R. PRINGLE and E. JONES. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
6. CASPARI, T., J. M. MURRAY and A.M. CARR, 2002 Cdc2-cyclin B kinase activity links Crb2 and Rqh1-topoisomerase III. Genes Dev. 16: 1195-1208.
7. DEPAMPHILIS, M. L., 2006 DNA Replication and Human Disease. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. DERSHOWITZ, A., and C. S. NEWLON, 1993 The effect on chromosome stability of deleting replication origins. Mol. Cell. Biol. 13: 391-398.
9. DERSHOWITZ, A., M. SNYDER, M. SBIA, J.H. SKURNICK, L. Y. ONG et al., 2007 Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements. Mol. Cell. Biol. 27: 4652-4663.
10. DILLIN, A., and J. RINE, 1997 Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics 147: 1053-1062.
11. FENG, W., D. COLLINGWOOD, M. E. BOECK, L. A. FOX, G. M. ALVINO et al., 2006 Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat. Cell Biol. 8: 148-155.
12. FOIANI, M., F. MARINI, D. GAMBA, G. LUCCHINI and P. PLEVANI, 1994 The B subunit of the DNA polymerase alpha-primase complex in Saccharomyces cerevisiae executes an essential function at the initial stage of DNA replication. Mol. Cell. Biol. 14: 923-933.
13. FOIANI, M., A. PELLICIOLI, M. LOPES, C. LUCCA, M. FERRARI et al., 2000 DNA damage checkpoints and DNA replication controls in Saccharomyces cerevisiae. Mutat. Res. 451: 187-196.
14. FOX, C. A., S. LOO, A. DILLIN and J. RINE, 1995 The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication. Genes Dev. 9: 911-924.
15. GIAEVER, G., A. M. CHU, L. NI, C. CONNELLY, L. RILES et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
16. GILBERT, C. S., C. M. GREEN and N. F. LOWNDES, 2001 Budding yeast Rad9 is an ATP-dependent Rad53 activating machine. Mol. Cell 8: 129-136.
17. HIETER, P., C. MANN, M. SNYDER and R. W. DAVIS, 1985 Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell 40: 381-392.
18. HOGAN, E., and D. KOSHLAND, 1992 Addition of extra origins of replication to a minichromosome suppresses its mitotic loss in cdc6 and cdc14 mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 89: 3098-3102.
19. JI, H., D. P. MOORE, M. A. BLOMBERG, L. T. BRAITERMAN, D. F. VOYTAS et al., 1993 Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73: 1007-1018.
20. KELLY, T. J., and B. STILLMAN, 2006 Duplication of DNA in eukaryotic cells, pp. 1-29 in DNA Replication and Human Disease, edited by M. L. DEPAMPHILIS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
21. LEA, D., and C. COULSON, 1949 The distribution of numbers of mutants in bacterial population. J. Genet. 49: 264-285.
22. LIANG, C., M. WEINREICH and B. STILLMAN, 1995 ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome. Cell 81: 667-676.
23. LOPES, M., C. COTTA-RAMUSINO, A. PELLICIOLI, G. LIBERI, P. PLEVANI et al., 2001 The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412: 557-561.
24. MA, J. L., S. J. LEE, J. K. DUONG and D. F. STERN, 2006 Activation of the checkpoint kinase Rad53 by the phosphatidyl inositol kinase-like kinase Mec1. J. Biol. Chem. 281: 3954-3963.
25. MACALPINE, D. M., and S. P. BELL, 2005 A genomic view of eukaryotic DNA replication. Chromosome Res. 13: 309-326.
26. MELO, J., and D. TOCZYSKI, 2002 A unified view of the DNA-damage checkpoint. Curr. Opin. Cell Biol. 14: 237-245.
27. NIEDUSZYNSKI, C. A., Y. KNOX and A. D. DONALDSON, 2006 Genomewide identification of replication origins in yeast by comparative genomics. Genes Dev. 20: 1874-1879.
28. NIEDUSZYNSKI, C. A., S. HIRAGA, P. AK, C. J. BENHAM and A. D. DONALDSON, 2007 OriDB: a DNA replication origin database. Nucleic Acids Res. 35: D40-D46.
29. ORR-WEAVER, T. L., J. W. SZOSTAK and R. J. ROTHSTEIN, 1983 Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol. 101: 228-245.
30. PELLICIOLI, A., C. LUCCA, G. LIBERI, F. MARINI, M. LOPES et al., 1999 Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J. 18: 6561-6572.
31. POLOUMIENKO, A., A. DERSHOWITZ, J. DE and C. NEWLON, 2001 Completion of replicationmap of Saccharomyces cerevisiae chromosome III. Mol. Biol. Cell 12: 3317-3327.
32. RAGHURAMAN, M. K., E. A. WINZELER, D. COLLINGWOOD, S. HUNT, L. WODICKA et al., 2001 Replication dynamics of the yeast genome. Science 294: 115-121.
33. ROSE, M. D., F. WINSTON and P. HIETER, 1990 Methods in Yeast Genetics: A Laboratory Course Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. SANCHEZ, Y., B. A. DESANY, W. J. JONES, Q. LIU, B. WANG et al., 1996 Regulation of RAD53 by the ATM-like kinases MEC1 and TEL1 in yeast cell cycle checkpoint pathways. Science 271: 357-360.
35. SANTOCANALE, C., and J. F. DIFFLEY, 1998 A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 395: 615-618.
36. SANTOCANALE, C., K. SHARMA and J. F. DIFFLEY, 1999 Activation of dormant origins of DNA replication in budding yeast. Genes Dev. 13: 2360-2364.
37. SHIMADA, K., and S. M. GASSER, 2007 The origin recognition complex functions in sister-chromatid cohesion in Saccharomyces cerevisiae. Cell 128: 85-99.
38. SHIRAHIGE, K., Y. HORI, K. SHIRAISHI, M. YAMASHITA, K. TAKAHASHI et al., 1998 Regulation of DNA-replication origins during cell-cycle progression. Nature 395: 618-621.
39. SIKORSKI, R. S., and P. HIETER, 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
40. SIVAPRASAD, U., A. DUTTA and S. P. BELL, 2006 Assembly of prereplication complexes, pp. 63-88 in DNA Replication and Human Disease, edited by M. L. DEPAMPHILIS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. SOGO, J. M., M. LOPES and M. FOIANI, 2002 Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297: 599-602.
42. SPENCER, F., S. L. GERRING, C. CONNELLY and P. HIETER, 1990 Mitotic chromosome transmission fidelity mutants in Saccharomyces cerevisiae. Genetics 124: 237-249.
43. SUN, Z., D. S. FAY, F. MARINI, M. FOIANI and D. F. STERN, 1996 Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways. Genes Dev. 10: 395-406.
44. SWEENEY, F. D., F. YANG, A. CHI, J. SHABANOWITZ, D. F. HUNT et al., 2005 Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation. Curr. Biol. 15: 1364-1375.
45. THEIS, J. F., and C. S. NEWLON, 1994 Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function. Mol. Cell. Biol. 14: 7652-7659.
46. THEIS, J. F., and C. S. NEWLON, 2001 Two compound replication origins in Saccharomyces cerevisiae contain redundant origin recognition complex binding sites. Mol. Cell. Biol. 21: 2790-2801.
47. TOH, G. W., A. M. O'SHAUGHNESSY, S. JIMENO, I.M. DOBBIE, M. GRENON et al., 2006 Histone H2A phosphorylation and H3 methylation are required for a novel Rad9 DSB repair function following checkpoint activation. DNA Repair 5: 693-703.
48. VALLEN, E. A., M. A. HILLER, T. Y. SCHERSON and M. D. ROSE, 1992 Separate domains of KAR1 mediate distinct functions in mitosis and nuclear fusion. J. Cell Biol. 117: 1277-1287.
49. VAN BRABANT, A. J., C. D. BUCHANAN, E. CHARBONEAU, W. L. FANGMAN and B. J. BREWER, 2001 An origin-deficient yeast artificial chromosome triggers a cell cycle checkpoint. Mol. Cell 7: 705-713.
50. VUJCIC, M., C. A. MILLER and D. KOWALSKI, 1999 Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast. Mol. Cell. Biol. 19: 6098-6109.
51. WEINERT, T. A., and L. H. HARTWELL, 1990 Characterization of RAD9 of Saccharomyces cerevisiae and evidence that its function acts posttranslationally in cell cycle arrest after DNA damage. Mol. Cell. Biol. 10: 6554-6564.
52. WEINERT, T. A., G. L. KISER and L. H. HARTWELL, 1994 Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev. 8: 652-665.
53. WYRICK, J. J., J. G. APARICIO, T. CHEN, J. D. BARNETT, E. G. JENNINGS et al., 2001 Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294: 2357-2360.
54. XU, W., J. G. APARICIO, O. M. APARICIO and S. TAVARE, 2006 Genomewide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7: 276.