Short DNA fragments without sequence similarity are initiation sites for replication in the chromosome of the yeast Yarrowia lipolytica

Molecular Biology of the Cell

Volumn 10, Issue 3, 1999, Pages 757-769

  Vernis, Laurence ^a   Chasles, Marion ^a   Pasero, Philippe ^a   Lepingle, Andrée ^a   Gaillardin, Claude ^a   Fournier, Philippe ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA;

ARTICLE; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; GENE ACTIVITY; GENE ISOLATION; GENE MAPPING; GENE STRUCTURE; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; YARROWIA LIPOLYTICA;

EUKARYOTA; FUNGI; MYXOGASTRIA; SACCHAROMYCES CEREVISIAE; YARROWIA LIPOLYTICA;

EID: 0032911199     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.10.3.757     Document Type: Article

References (74)

1. Amati, B.B., and Gasser, S.M. (1988). Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54, 967-978.
2. Amati, B., Pick, L., Laroche, T., and Gasser, S.M. (1990). Nuclear scaffold attachment stimulates, but is not essential for ARS activity in Saccharomyces cerevisiae: analysis of the Drosophila ftz SAR. EMBO J. 9, 4007-4016.
3. Barth, G., and Gaillardin, C. (1996). Yarrowia lipolytica. In: Nonconventional Yeasts in Biotechnology: A Handbook, ed. K. Wolf, Springer-Verlag: Heidelberg, 313-388.
4. Bénard, M., Lagnel, C., Pallotta, D., and Pierron, G. (1996). Mapping of a replication origin within the promoter region of two unlinked, abundantly transcribed actin genes of Physarum polycephalum. Mol. Cell. Biol. 16, 968-976.
5. Bénard, M., Lagnel, C., and Pierron, G. (1995). Site-specific initiation of DNA replication within the nontranscribed spacer of Physarum rDNA. Nucleic Acids Res. 23, 1447-1453.
6. Bergemann, A.D., and Johnson, E.M. (1992). The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication. Mol. Cell. Biol. 12, 1257-1265.
7. Bielinsky, A.K., and Gerbi, S.A. (1998). Discrete Start Sites for DNA Synthesis in the Yeast ARS1 Origin. Science 279, 95-98.
8. Bolshoy, A., McNamara, P., Harrington, R.E., and Trifonov, E.N. (1991). Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88, 2312-2316.
9. Breslauer, K.J., Franck, R., Blöcker, H., and Marky, L.A. (1986). Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746-3750.
10. Brun, C., Dang, Q., and Miassod, R. (1990). Studies of an 800-kb DNA stretch of the Drosophila X chromosome: comapping of a subclass of scaffold-attached regions with sequences able to replicate autonomously in Saccharomyces cerevisiae. Mol. Cell. Biol. 10, 5455-5463.
11. Burhans, W.C., and Huberman, J.A. (1994). DNA replication origins in animal cells: a question of context? Science 263, 639-640.
12. Burhans, W.S., Vassilev, L.T., Caddle, M.S., Heintz, N.H., DePamphilis, M.L. (1990). Identification of an origin of bidirectional DNA replication in mammalian chromosomes. Cell 62, 955-965.
13. Caddle, M.S., and Calos, M.P. (1994). Specific initiation at an origin of replication from Schizosaccharomyces pombe. Mol. Cell. Biol. 14, 1796-1805.
14. Casarégola, S., Feynerol, C., Diez, M., Fournier, P., and Gaillardin, C. (1997). Genomic organization of the yeast Yarrowia lipolytica. Chromosoma 106, 380-390.
15. Cook, P.R. (1991). The nucleoskeleton and the topology of replication. Cell 66, 627-635.
16. DePamphilis, M. L. (1996). Origins of DNA replication. In: DNA Replication in Eukaryotic Cells, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 45-86.
17. Dhar, S.K., Chardhury, N.R., Mittal, V., Bhattacharya, A., and Bhatracharya, S. (1996). Replication initiates at multiple dispersed sites in the ribosomal DNA plasmid of the protozoan parasite Entamoeba histolytica. Mol. Cell. Biol. 16, 2314-2324.
18. Diffley, J.F., Cocker, J.H., Dowell, S.J., and Rowley, A. (1994). Two steps in the assembly of complexes at yeast replication origins in vivo. Cell 78, 303-316.
19. Diffley, J.F., Cocker, J.H., Dowell, S.J., Harwood, J., and Rowley, A. (1995). Stepwise assembly of initiation complexes at budding yeast replication origins during the cell cycle. J. Cell Sci. Suppl. 19, 67-72.
20. Diffley, J.F.X. (1996). Once and only once upon a time: specifying and regulating origins of DNA replication in eukaryotic cells. Genes Dev. 10, 2819-2830.
21. Dijkwel, P.A., Vaughn, J.P., and Hamlin, J.L. (1994). Replication initiation sites are distributed widely in the amplified CHO dihydrofolate reductase domain. Nucleic Acids Res. 22, 4989-4996.
22. Dobbs, D.L., Shaiu, W.L., and Benbow, R.M. (1994). Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA. Nucleic Acids Res. 22, 2479-2489.
23. Du, C., Sanzgiri, R.P., Shaiu, W-L., Choi, J-K., Hou, Z., Benbow, R.M., and Dobbs, D.L. (1995). Modular structural elements in the replication origin region of Tetrahymena rDNA. Nucleic Acids Res. 23, 1766-1774.
24. Dubey, D.D., Kim, S.M., Todorov, I.T., and Huberman, J.A. (1996). Large, complex modular structure of a fission yeast DNA replication origin. Curr. Biol. 6, 467-473.
25. Dubey, D.D., Zhu, J.G., Carlson, D.L., Sharma, K., and Huberman, J.A. (1994). Three ARS elements contribute to the ura4 replication origin region in the fission yeast, Schizosaccharomyces pombe. EMBO J. 13, 3638-3647.
26. Eckdahl, T.T., and Anderson, J.N. (1987). Computer modelling of DNA structures involved in chromosome maintenance. Nucleic Acids Res. 15, 8530-8545.
27. Eckdahl, T.T., and Anderson, J.N. (1990). Conserved DNA structures in origins of replication. Nucleic Acids Res. 18, 1609-1612.
28. Fabiani, L., Frontali, L., and Newlon, C.S. (1996). Identification of an essential core element and stimulatory sequences in a Kluyveromyces lactis ARS element, KARS101. Mol. Microbiol. 19, 757-766.
29. Fournier, P., Abbas, A., Chasles, M., Kudla, B., Ogrydziak, D.M., Yaver, D., Xuan, J-W., Peito, A., Ribet, A-M., Feynerol, C., He, F., and Gaillardin, C. (1993). Colocalizatlon of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica. Proc. Natl. Acad. Sci. USA 90, 4912-4916.
30. Fournier, P., Gaillardin, C., Persuy, M.A., Klootwijk, J., and van Heerikhuizen, H. (1986). Heterogeneity in the ribosomal family of the yeast Yarrowia lipolytica: genomic organization and segregation studies. Gene 42, 273-282.
31. Fournier, P., Guyaneux, L., Chasles, M., and Gaillardin, C. (1991). Scarcity of ARS sequences isolated in a morphogenesis mutant of the yeast Yarrowia lipolytica. Yeast 7, 25-36.
32. Huberman, J.A. (1994). Analysis of DNA replication origins and directions by two-dimensional gel electrophoresis. In: The Cell Cycle: A Practical Approach, ed. P. Fantes and R.F. Brooks, Oxford, UK: Oxford University Press, 213-234.
33. Hyrien, O., Maric, C., and Lucas, I. (1997). Role of nuclear architecture in the initiation of eukaryotic DNA replication. Biochimie 79, 541-548.
34. Hyrien, O., Maric, C., and Méchali, M. (1995). Transition in specification of embryonic metazoan DNA replication origins. Science 270, 994-997.
35. Jallepalli, P.V., and Kelly, T.J. (1997). Cyclin-dependent kinase and initiation at eukaryotic origins: a replication switch? Curr. Opin. Cell Biol. 9, 358-363.
36. Larner, J.M., Lee, H., and Hamlin, J.L. (1997). S phase damage sensing checkpoints in mammalian cells. Cancer Surv. 29, 25-45.
37. Lawlis, S.J., Keezer, S.M., Wu, J-R., and Gilbert, D.M. (1996). Chromosome architecture can dictate site-specific initiation of DNA replication in Xenopus egg extracts. J. Cell Biol. 135, 1207-1218.
38. Lee, D.G., and Bell, S.P. (1997). Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol. Cell. Biol. 17, 7159-7168.
39. Lin, S., and Kowalski, D. (1997). Functional equivalency and diversity of cis-acting elements among yeast replication origins. Mol. Cell. Biol. 17, 5473-5484.
40. Linskens, M.H., and Huberman, J.A. (1988). Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8, 4927-4935.
41. Marahrens, Y., and Stillman, B. (1992). A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255, 817-823.
42. Marilley, M., and Pasero, P. (1996). Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. Nucleic Acids Res. 24, 2204-2211.
43. Matsuoka, M., Matsubara, M., Daidoh, H., Imanaka, T., Uchida, K., and Aiba, S. (1993). Analysis of regions essential for the function of chromosomal replicator sequences from Yarrowia lipolytica. Mol. Gen. Genet. 237, 327-333.
44. Maundrell, K., Hutchinson, A., and Shall, S. (1988). Sequence analysis of ARS elements in fission yeast. EMBO J. 7, 2203-2209.
45. Maundrell, K., Wright, A.P.H., Piper, M., and Shall, S. (1985). Evaluation of heterologous ARS activity in S. cerevisiae using cloned DNA from S. pombe. Nucleic Acids Res. 13, 3711-3722.
46. Natale, D.A., Umek, R.M., and Kowalski, D. (1993). Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res. 21, 555-560.
47. Newlon, C.S., Collins, I., Dershowitz, A., Deshpande, A.M., Greenfeder, S.A., Ong, L.Y., and Theis, J.F. (1993). Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 58, 415-423.
48. Newlon, C.S., and Theis, J.F. (1993). The structure and function of yeast ARS elements. Curr. Opin. Genet. Dev. 3, 752-758.
49. Pasero, P., Braguglia, D., and Gasser, S.M. (1997). ORC-dependent and origin-specific initiation of DNA replication at defined foci in isolated yeast nuclei. Genes Dev. 11, 1504-1518.
50. Pasero, P., Sjakste, N., Blettry, C., Got, C., and Marilley, M. (1993). Long-range organization and sequence-directed curvature of Xenopus laevis satellite 1 DNA. Nucleic Acids Res. 21, 4703-4710.
51. Razin, S.V., Vassetzky, Y.S., and Hancock, R. (1991). Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin. Biochem. Biophys. Res. Commun. 177, 265-270.
52. Roberge, M., and Gasser, S.M. (1992). DNA loops: structural and functional properties of scaffold-attached regions. Mol. Microbiol. 6, 419-423.
53. Rowles, A, and Blow, J. (1997). Chromatin proteins involved in the initiation of DNA replication. Curr. Opin. Genet. Dev. 7, 152-157.
54. Rowley, A., Cocker, J.H., Harwood, J., and Diffley, J.F. (1995). Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC. EMBO J. 14, 2631-2641.
55. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
56. Sanchez, J.A., Kim, S-M., and Huberman, J.A. (1998a). Ribosomal DNA replication in the fission yeast, Schizosaccharomyces pombe. Exp. Cell Res. 238, 220-230.
57. Sanchez, J.P., Murakami, Y., Huberman, J.A., and Hunvitz, J. (1998b). Isolation, characterization, and molecular cloning of a protein (Abp2) that binds to a Schizosaccharomyces pombe origin of replication (ars3002). Mol. Cell. Biol. 18, 1670-1681.
58. Schmid-Berger, N., Schmid, B., and Barth, G. (1994). Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica. J. Bacteriol. 176, 2477-2482.
59. Shinomiya, T., and Ina, S. (1994). Mapping an initiation region of DNA replication at a single-copy chromosomal locus in Drosophila melanogaster cells by two-dimensional gel methods and PCR-mediated nascent-strand analysis: multiple replication origins in a broad zone. Mol. Cell. Biol. 14, 7394-7403.
60. Snyder, M., Buchman, A.R., and Davis, R.W. (1986). Bent DNA at a yeast autonomously replicating sequence. Nature 324, 87-89.
61. Tanaka, T., Knapp, D., and Nasmyth, K. (1997). Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell 90, 649-660.
62. Theis, J.F., and Newlon, C.S. (1997). The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl. Acad. Sci. USA 94, 10786-10791.
63. Trifonov, E.N. (1991). DNA in profile. Trends Biochem. Sci. 16, 467-470.
64. Umek, R.M., and Kowalski, D. (1988). The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell 52, 559-567.
65. van Heerikhuizen, H., Ykema, A., Klootwijk, J., Gaillardin, C., Ballas, C., and Fournier, P. (1985). Heterogeneity in the rRNA genes of the yeast Yarrowia lipolytica: cloning and analysis of two size classes of repeats. Gene 39, 213-222.
66. Vernis, L., Abbas, A., Chasles, M., Gaillardin, C.M., Brun, C., Huberman, J.A., and Fournier, P. (1997). An origin and a centromere are both needed to establish a replicative plasmid in the yeast Yarrowia lipolytica. Mol. Cell. Biol. 17, 1995-2004.
67. Vita-Pearlman, V.J., Gunaratne, P.H., and Chinault, A.C. (1993). Analysis of a replication initiation sequence from the adenosine deaminase region of the mouse genome. Mol. Cell. Biol. 13, 5931-5942.
68. Wesolowski, M., Algeri, A., and Fukuhara, H. (1981). Gene organization of the mitochondrial DNA of yeasts: Kluyveromyces lactis and Saccharromycopsis lipolytica. Curr. Genet. 3 157-162.
69. Williams, J.S., Eckdahl, T.T., and Anderson, J.N. (1988). Bent DNA functions as a replication enhancer in Saccharomyces cerevisiae. Mol. Cell. Biol. 8, 2763-2769.
70. Wohlgemuth, J.G., Bulboaca, G.H., Moghadam, M., Caddle, M.S., and Calos, M.P. (1994). Physical mapping of origins of replication in the fission yeast Schizosaccharomyces pombe. Mol. Biol. Cell 5, 839-849.
71. Xuan, J.W., Fournier, P., and Gaillardin, C. (1988). Cloning of the LYS5 gene encoding saccharopine dehydrogenase from the yeast Yarrowia lipolytica by targeted integration. Curr. Genet. 24, 19-21.
72. Zhu, J.G., Carlson, D.L., Dubey, D.D., Sharma, K., and Huberman, J.A. (1994). Comparison of the two major ARS elements of the ura4 replication origin region with other ARS elements in the fission yeast, Schizosaccharomyces pombe. Chromosoma 103, 414-422.
73. Zimmermann, M., and Fournier, P. (1996). Electrophoretic karyotyping of yeasts. In: Nonconventional Yeasts in Biotechnology: A Handbook, ed. K. Wolf, Springer-Verlag: Heidelberg, 101-116.
74. Zweifel, S.G., and Fangrnan, W.L. (1990). Creation of ARS activity in yeast through iteration of nonfunctional sequences. Yeast 6, 179-186.