New systems for replicating DNA in vitro

Current Opinion in Cell Biology

Volumn 10, Issue 3, 1998, Pages 304-310

  Pasero, Philippe ^a   Gasser, Susan M ^a  

^a SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; CELL CYCLE; CELL CYCLE G1 PHASE; CELL CYCLE S PHASE; CELL FUSION; CELL NUCLEUS MEMBRANE; DNA REPLICATION; DNA REPLICATION ORIGIN; EUKARYOTE; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; REVIEW; XENOPUS; YEAST;

ANIMALIA; EUKARYOTA; VERTEBRATA; XENOPUS;

EID: 0031805473     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0955-0674(98)80004-5     Document Type: Article

References (60)

1. Rao PN, Johnson RT. Mammalian cell fusion: studies on the regulation of DNA synthesis and mitosis. Nature. 225:1970;159-164.
2. Coverley D, Laskey RA. Regulation of eukaryotic DNA replication. Annu Rev Biochem. 63:1994;745-776.
3. Blow JJ. Chromosome replication in Xenopus egg extracts. Hames BD, Glover DM. Eukaryotic DNA replication. 1996;143-165 IRL Press, Oxford.
4. Nasmyth K. At the heart of the budding yeast cell cycle. Trends Genet. 12:1996;405-412.
5. 1 nuclei with recombinant Cyclin A/Cdk2 or Cyclin E/Cdk2, confirming the role of these two complexes in the initiation of DNA replication.
6. Dutta A, Bell SP. Initiation of DNA replication in eukaryotic cells. Ann Rev Cell Dev Biol. 13:1997;293-332.
7. Jallepalli PV, Kelly TJ. Cyclin-dependent kinase and initiation at eukaryotic origins: a replication switch? Curr Opin Cell Biol. 9:1997;358-363.
8. 2, but cannot recruit MCMs, unless Cdks are inactivated. The licensing of yeast origins by MCMs is therefore regulated by two mechanisms, the occupancy of the origins by Cdc6p and Cdk activity.
9. 1. In S phase, the interaction of Cdc45p and MCMs with non-origin sequences, similar to DNA polymerase epsilon, suggests that these proteins are present at the replication fork.
10. 1 in a Cdc6p dependent way. Once loaded, however, MCMs remain bound to chromatin even after extraction of ORC or CDC6p.
11. 2 and early M phase when origins are in a post-RC state. Moreover, it shows that cdc6-3, a new gain-of-function dominant mutant, can bypass the Cdk inhibition of rereplication.
12. Coleman TR, Carpenter PB, Dunphy WG. The Xenopus Cdc6 protein is essential for the initiation of a single round of DNA replication in cell-free extracts. Cell. 87:1996;53-63.
13. Romanowski P, Madine MA, Rowles A, Blow JJ, Laskey RA. The Xenopus origin recognition complex is essential for DNA replication and MCM binding to chromatin. Curr Biol. 6:1996;1416-1425.
14. Rowles A, Chong JP, Brown L, Howell M, Evan GI, Blow JJ. Interaction between the origin recognition complex and the replication licensing system in Xenopus. Cell. 87:1996;287-296.
15. Sato N, Arai K, Masai H. Human and Xenopus cDNAs encoding budding yeast Cdc7-related kinases: in vitro phosphorylation of MCM subunits by a putative human homologue of Cdc7. of special interest EMBO J. 16:1997;4340-4351 This paper reports the cloning of Cdc7-related kinases from human and Xenopus. The human protein phosphorylates Mcm2p and Mcm3p in vitro.
16. Leatherwood J, Lopez-Girona A, Russell P. Interaction of Cdc2 and Cdc18 with a fission yeast ORC2-like protein. Nature. 379:1996;360-363.
17. Elsasser S, Lou F, Wang B, Campbell JL, Jong A. Interaction between yeast Cdc6 protein and B-type cyclin/Cdc28 kinases. Mol Biol Cell. 7:1996;1723-1735.
18. Brown GW, Jallepalli PV, Huneycutt BJ, Kelly TJ. Interaction of the S phase regulator cdc18 with cyclin-dependent kinase in fission yeast. of special interest Proc Natl Acad Sci USA. 94:1997;6142-6147 The Cdc6p homolog Cdc18p copurifies with active cyclin B/Cdk complex, suggesting an interaction of this complex with the pre-RC.
19. 1/S transition, in a Cdc2p dependent way. Overexpression of a constitutively hypophosphorylated form of Cdc18p leads to rereplication, which is consistent with the idea that this protein is targeted to degradation through phosphorylation.
20. 2.
21. 1, and gets simultaneously phosphorylated and displaced from chromatin upon entry into S phase.
22. Dalton S, Hopwood B. Characterization of Cdc47p-minichromosome maintenance complexes in Saccharomyces cerevisiae: Identification of Cdc45p as a subunit. of special interest Mol Cell Biol. 17:1997;5867-5875 This paper shows that Mcm3p, Mcm5p and Mcm7p can be immunoprecipitated in large and heterogeneous complexes. Mcm5p and Mcm7p form a stable complex throughout the cell cycle, and their replication-defective forms do not bind each other. Cdc45p is also bound to a subfraction of these MCM complexes.
23. Kubota Y, Mimura S, Nishimoto S, Masuda T, Nojima H, Takisawa H. Licensing of DNA replication by a multi-protein complex of MCM/P1 proteins in Xenopus eggs. EMBO J. 16:1997;3320-3331.
24. Thommes P, Kubota Y, Takisawa H, Blow JJ. The RLF-M component of the replication licensing system forms complexes containing all six MCM/P1 polypeptides. of special interest EMBO J. 16:1997;3312-3319 This paper and Kubota 1997 [23] show that Xenopus MCMs bind chromatin coordinately before S phase and are all essential for initiation. They form a physical complex containing all the six members of the MCM family.
25. Ishimi Y. A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex. of special interest J Biol Chem. 272:1997;24508-24513 A complex of three MCM proteins (Mcm4, 6 and 7) purified from HeLa cells displays an ATP-dependent 3′ to 5′ helicase activity in vitro. This activity is consistent with the presence of a conserved ATPase motif in these proteins. The low processivity of this complex makes it unlikely that this is the helicase acting at the DNA replication fork. The low processivity could reflect the absence of a cofactor that stimulates helicase activity in vivo. Alternatively, this complex could be involved in the unwinding of the origin through its interaction with ORC.
26. Hua XH, Newport J. Identification of a preinitiation step in DNA replication that is independent of Origin Recognition Complex and Cdc6, but dependent on Cdk2. of special interest J Cell Biol. 140:1998;271-281 After assembly of MCMs into the preinitiation complex, Cdc6p seems to be removed from chromatin in a Cyclin E / Cdk2 dependent way. Moreover, once MCMs are loaded, ORC can also be displaced from chromatin without affecting initiation. These results suggest that ORC and Cdc6 are not be involved in the final steps of the initiation process in Xenopus egg extracts.
27. Ishimi Y, Ichinose S, Omori A, Sato K, Kimura H. Binding of human minichromosome maintenance proteins with histone H3. J Biol Chem. 271:1996;24115-24122.
28. 1/S transition, promoting their dissociation from chromatin.
29. Lei M, Kawasaki Y, Young MR, Kihara M, Sugino A, Tye BK. Mcm2 is a target of regulation by Cdc7-Dbf4 during the initiation of DNA synthesis. of special interest Genes Dev. 11:1997;3365-3374 Identification of a new allele, dbf4-6, as a second site suppressor of mcm2-1. The complex Cdc7-Dbf4 interacts physically with Mcm2p and phosphorylates Mcm2, 3, 4 and 6 in vitro. The in vivo phosphorylation of Mcm2p is impaired in the absence of Cdc7p activity. Taken together, these data suggest that the phosphorylation of some MCMs by Cdc7p is a critical step in the initiation of DNA replication.
30. Bousset K, Diffley JF. The Cdc7 protein kinase is required for origin firing during S phase. of outstanding interest Genes Dev. 12:1998;480-490 See annotation for reference [31].
31. Donaldson AD, Fangman WL, Brewer BJ. Cdc7 is required throughout the yeast S phase to activate replication origins. of outstanding interest Genes Dev. 12:1998;491-501 This paper and Bousset 1998 [30] show that Cdc7p is not a general regulator of S phase but plays a more direct role in the firing of replication origins. It is required for the activation of the late-firing origins after a hydroxyurea block.
32. Diffley JF, Cocker JH, Dowell SJ, Rowley A. Two steps in the assembly of complexes at yeast replication origins in vivo. Cell. 78:1994;303-316.
33. 2- or M-phase nuclei replicate in the presence of an S-phase nuclear extract. Finally, biotin-dUTP is incorporated into genomic DNA at discrete subnuclear foci, indicating that replication origins are clustered in yeast, as they are in higher eukaryotes.
34. Bielinsky AK, Gerbi SA. Discrete start sites for DNA synthesis in the yeast ARS1 origin. of outstanding interest Science. 279:1998;95-98 This paper describes the mapping of the initiation site at ARS1, using a new technique that allows the detection of initiation sites at the nucleotide level. The SV40 virus origin of DNA replication was first used to prove the validity of the approach. When applied to ARS1, a transition from continuous to discontinuous DNA synthesis was mapped within an 18 base pair region close to the B1 element of the origin. This region corresponds to the DNase 1 hypersensitive site that appears upon ORC binding.
35. 1/S transition.
36. Lee DG, Bell SP. Architecture of the yeast origin recognition complex bound to origins of DNA replication. of special interest Mol Cell Biol. 17:1997;7159-7168 This paper shows that the coordinate action of Orc1-5p, but not Orc6p, is required for DNA binding. Residues of several ARS elements involved in ORC interaction were mapped to the ARS consensus sequences and the B1 element. In the case of ARS1, interactions were also mapped to the B2 element and an ORC-induced bending of the molecule was detected.
37. Walter J, Newport JW. Regulation of replicon size in Xenopus egg extracts. of special interest Science. 275:1997;993-995 In Xenopus egg extracts, the length of the S phase increases when increasing concentrations of nuclei are used. The elongation rate is the same over a wide range of nuclei concentration, suggesting that the size of replicons increases with the number of nuclei. Because ORC is not stochiometrically limiting in the reaction, an other still unidentified factor may control how many origins fire every cell cycle.
38. Newport J, Yan H. Organization of DNA into foci during replication. Curr Opin Cell Biol. 8:1996;365-368.
39. Zou L, Mitchell J, Stillman B. CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication. of special interest Mol Cell Biol. 17:1997;553-563 This paper describes the cloning and the characterization of Cdc45p, a protein that interacts with all the MCMs involved in replication. Cold sensitive cdc45-1 mutant cells are defective for initiation of DNA replication at the nonpermissive temperature.
40. 1/S transition. The pre-RC is stable in cdc45-1 mutant arrested at the restrictive temperature. Temperature shift experiments suggest that Cdc45p and Cdc7-Dbf4 could act together to trigger initiation.
41. Merchant AM, Kawasaki Y, Chen Y, Lei M, Tye BK. A lesion in the DNA replication initiation factor Mcm10 induces pausing of elongation forks through chromosomal replication origins in Saccharomyces cerevisiae. of special interest Mol Cell Biol. 17:1997;3261-3271 The cloning and characterization of a new minichromosome maintenance factor, Mcm10p, involved in the initiation of DNA replication is described. Although Mcm10p is not structurally related to members of the Mcm2-7 family, mcm10-1 mutants also show an ARS-specific MCM phenotype and are defective for initiation. Interestingly, the forks pause at origins when the Mcm10p function is disrupted, suggesting a role for this factor in the dissociation of the pre-RC.
42. Chong JP, Mahbubani HM, Khoo CY, Blow JJ. Purification of an MCM-containing complex as a component of the DNA replication licensing system. Nature. 375:1995;418-421.
43. Madine MA, Khoo CY, Mills AD, Laskey RA. MCM3 complex required for cell cycle regulation of DNA replication in vertebrate cells. Nature. 375:1995;421-424.
44. Carpenter PB, Mueller PR, Dunphy WG. Role for a Xenopus Orc2-related protein in controlling DNA replication. Nature. 379:1996;357-360.
45. Walter J, Sun L, Newport J. Regulated chromosomal DNA replication in the absence of a nucleus. of outstanding interest Molecular Cell. 1:1998;519-529 This paper describes a new Xenopus replication assay providing the first direct evidence that the 'two-step' mechanism governing initiation in yeast also applies to Xenopus egg extract. A single round of DNA replication is obtained by incubating demembranated sperm chromatin, or plasmid DNA, sequentially in a cytoplasmic and a highly concentrated nucleoplasmic extract in the absence of nuclear envelope formation. This suggests that the nuclear membrane concentrates SPF in the nucleus to activate the origins and to inhibit their licensing before the end of mitosis.
46. Hua XH, Yan H, Newport J. A role for Cdk2 kinase in negatively regulating DNA replication during S phase of the cell cycle. J Cell Biol. 137:1997;183-192. of special interest.
47. Mahbubani HM, Chong JP, Chevalier S, Thommes P, Blow JJ. Cell cycle regulation of the replication licensing system: involvement of a Cdk-dependent inhibitor. of special interest J Cell Biol. 136:1997;125-135 This paper, together with Hua 1997 [46], shows that in Xenopus like in yeast, a high cyclin-dependent activity prevents the binding of MCMs to chromatin and the licensing of the replication origins.
48. Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 10:1996;1796-1811.
49. Raghuraman MK, Brewer BJ, Fangman WL. Cell cycle-dependent establishment of a late replication program. of special interest Science. 276:1997;806-809 In yeast, the proximity of telomeres can delay origin activation until the end of S phase. The telomeric position effect on replication is established between mitosis and START. Interestingly, once established, this temporal program is maintained through S phase, even if site-specific recombination is used to separate the origin from the telomere.
50. Cardoso MC, Joseph C, Rahn HP, Reusch R, Nadal-Ginard B, Leonhardt H. Mapping and use of a sequence that targets DNA ligase I to sites of DNA replication in vivo. of special interest J Cell Biol. 139:1997;579-587 Identification of a targeting sequence that directs DNA ligase I to subnuclear replication foci. This sequence works as an independent module. It is used here to target a green fluorescent protein (GFP) fusion protein to the replication foci, which can be then visualized in vivo.
51. Ferreira J, Paolella G, Ramos C, Lamond AI. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. of special interest J Cell Biol. 139:1997;1597-1610 This paper shows that inactive chromatin domains that correlate with G bands in metaphase chromosomes are compartmentalized within the nucleus and replicate late in S phase.
52. Lawlis SJ, Keezer SM, Wu JR, Gilbert DM. Chromosome architecture can dictate site-specific initiation of DNA replication in Xenopus egg extracts. J Cell Biol. 135:1996;1207-1218.
53. 1 step required to specify the Chinese hamster DHFR replication origin. Science. 271:1996;1270-1272.
54. 1 phase, the ODP, which defines the use of specific replication origins. These replication origins that can be recognized by Xenopus extracts providing that the template nuclei are maintained intact. This paper shows that the protein kinase inhibitor 2-aminopurine inhibits the ODP, and that this transition is a mitogen-independent event occurring after licensing, but before the R-point control.
55. 1. Transformation with SV40, however, abrogates this arrest point and cells proceed through S phase, although origin choice has been disrupted.
56. Spann TP, Moir RD, Goldman AE, Stick R, Goldman RD. Disruption of nuclear lamin organization alters the distribution of replication factors and inhibits DNA synthesis. of special interest J Cell Biol. 136:1997;1201-1212 Disruption of lamin organization by microinjection of a truncated human Lamin A in mammalian cells affects the subnuclear localization of proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) and inhibit genomic DNA replication. Interestingly, this dominant negative mutant does not interfere with the distribution of several proteins involved in initiation (Orc2p, Mcm3p, pol alpha), suggesting that nuclear lamins may be required for elongation.
57. Pak DT, Pflumm M, Chesnokov I, Huang DW, Kellum R, Marr J, Romanowski P, Botchan MR. Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes. of special interest Cell. 91:1997;311-323 Orc2p colocalizes and interacts biochemically with HP1p, a heterochromatin protein involved in position effect variegation (PEV) in Drosophila. Moreover, heterozygous orc2 recessive lethal mutations result in a suppression of PEV, suggesting that ORC plays a role in higher-order chromatin organization.
58. Madine MA, Khoo CY, Mills AD, Mushal C, Laskey RA. The nuclear envelope prevents reinitiation of replication by regulating the binding of MCM3 to chromatin in Xenopus egg extracts. Curr Biol. 5:1995;1270-1279.
59. 1.
60. Dowell SJ, Romanowski P, Diffley JF. Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science. 265:1994;1243-1246.