The haloarchaeal chromosome replication machinery

Biochemical Society Transactions

Volumn 37, Issue 1, 2009, Pages 108-113

  MacNeill, Stuart A ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Chromosome replication; DNA replication; Genetic analysis; Haloarchaeon; Replication machinery; Replisome

Indexed keywords

CELL CYCLE PROTEIN 6; CYCLINE; DNA POLYMERASE; DNA PRIMASE; DOUBLE STRANDED DNA; INTEIN; MINICHROMOSOME MAINTENANCE PROTEIN; REPLICATION FACTOR A; REPLICATION LICENSING FACTOR CDT1; REPLISOME; ARCHAEAL PROTEIN; DNA; NUCLEAR PROTEIN; OKAZAKI FRAGMENTS;

AMINO ACID SEQUENCE; CELL VIABILITY; CHROMOSOME REPLICATION; DNA REPLICATION; DNA SYNTHESIS; ENZYME ACTIVITY; EUKARYOTIC CELL; GENE SEQUENCE; GENETIC ANALYSIS; GENOMIC FRAGMENT; HALOBACTERIUM; HALOBACTERIUM SALINARUM; HALOFERAX VOLCANII; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; CHROMOSOME; DNA REPLICATION ORIGIN; METABOLISM;

BACTERIA (MICROORGANISMS); EUKARYOTA; HALOBACTERIA; HALOBACTERIUM SP. NRC-1; HALOFERAX VOLCANII;

ARCHAEAL PROTEINS; CHROMOSOMES, ARCHAEAL; DNA; DNA REPLICATION; NUCLEAR PROTEINS; REPLICATION ORIGIN;

EID: 59749096849     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370108     Document Type: Review

References (53)

1. Barry, E.R. and Bell, S.D. (2006) DNA replication in the archaea. Microbiol. Mol. Biol. Rev. 70, 876-887
2. Grabowski, B. and Kelman, Z. (2003) Archeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57, 487-516
3. MacNeill, S.A. (2001) Understanding the enzymology of archaeal DNA replication: progress in form and function. Mol. Mircobiol. 40, 520-529
4. Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R. et al. (2004) Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14, 2221-2234
5. Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F. and Oesterhelt, D. (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7, 169
6. Falb, M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J. and Oesterhelt, D. (2005) Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res. 15, 1336-1343
7. Ng, W.V., Kennedy, S.P., Mahairas, G.G., Berquist, B., Pan, M., Shukla, H.D., Lasky, S.R., Baliga, N.S., Thorsson, V., Sbrogna, J. et al. (2000) Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. U.S.A. 97, 12176-12181
8. Pfeiffer, F., Schuster, S.C., Broicher, A., Falb, M., Palm, P., Rodewald, K., Ruepp, A., Soppa, J., Tittor, J. and Oesterhelt, D. (2008) Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics 91, 335-346
9. Ng, W.V., Berquist, B.R., Coker, J.A., Capes, M., Wu, T.H., Dassarma, P. and Dassarma, S. (2008) Genome sequences of Halobacterium species. Genomics 91, 548-552
10. Pfeiffer, F., Shuster, S.C., Broicher, A., Falb, M., Palm, P., Rodewald, K., Tittor, J. and Oesterhelt, D. (2008) Genome sequences of Halobacterium salinarum: a reply. Genomics 91, 553-554
11. Schneider, K.L., Pollard, K.S., Baertsch, R., Pohl, A. and Lowe, T.M. (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Res. 34, D407-D410
12. Pfeiffer, F., Broicher, A., Gillich, T., Klee, K., Mejia, J., Rampp, M. and Oesterhelt, D. (2008) Genome information management and integrated data analysis with HaloLex. Arch. Microbiol. 190, 281-299
13. Bell, S.P. and Dutta, A. (2002) DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71, 333-374
14. Robinson, N.P., Dionne, I., Lundgren, M., Marsh, V.L., Bernander, R. and Bell, S.D. (2004) Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116, 25-38
15. Norais, C., Hawkins, M., Hartman, A.L., Eisen, J.A., Myllykallio, H. and Allers, T. (2007) Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet. 3, e77
16. Lundgren, M., Andersson, A., Chen, L., Nilsson, P. and Bernander, R. (2004) Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc. Natl. Acad. Sci. U.S.A. 101, 7046-7051
17. Berquist, B.R. and DasSarma, S. (2003) An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J. Bact. 185, 5959-5966
18. Zhang, R. and Zhang, C.T. (2003) Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem. Biophys. Res. Commun. 302, 728-734
19. Zhang, R. and Zhang, C.T. (2005) Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 1, 335-346
20. Berquist, B.R., DasSarma, P. and DasSarma, S. (2007) Essential and non-essential DNA replication genes in the model halophilic archaeon, Halobacterium sp. NRC-1. BMC Genet. 8, 31
21. Costa, A. and Onesti, S. (2008) The MCM complex: (just) a replicative helicase? Biochem. Soc. Trans. 36, 136-140
22. Perler, F.B. (2002) InBase: the Intein Database. Nucleic Acids Res. 30, 383-384
23. Pacek, M., Tutter, A.V., Kubota, Y., Takisawa, H. and Walter, J.C. (2006) Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication. Mol. Cell 21, 581-587
24. Moyer, S.E., Lewis, P.W. and Botchan, M.R. (2006) Isolation of the Cdc45/ Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc. Natl. Acad. Sci. U.S.A. 103, 10236-10241
25. Aparicio, T., Ibarra, A. and Mendez, J. (2006) Cdc45-MCM-GINS, a new power player for DNA replication. Cell Div. 1, 18
26. Marinsek, N., Barry, E.R., Makarova, K.S., Dionne, I., Koonin, E.V. and Bell, S.D. (2006) GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep. 7, 539-545
27. Yoshimochi, T., Fujikane, R., Kawanami, M., Matsunaga, F. and Ishino, Y. (2008) The GINS complex from Pyrococcus furiosus stimulates the MCM helicase activity. J. Biol. Chem. 283, 1601-1609
28. Kamada, K., Kubota, Y., Arata, T., Shindo, Y. and Hanaoka, F. (2007) Structure of the human GINS complex and its assembly and functional interface in replication initiation. Nat. Struct. Mol. Biol. 14, 388-396
29. Choi, J.M., Lim, H.S., Kim, J.J., Song, O.K. and Cho, Y. (2007) Crystal structure of the human GINS complex. Genes Dev. 21, 1316-1321
30. Chang, Y.P., Wang, G., Bermudez, V., Hurwitz, J. and Chen, X.S. (2007) Crystal structure of the GINS complex and functional insights into its role in DNA replication. Proc. Natl. Acad. Sci. U.S.A. 104, 12685-12690
31. Le Breton, M., Henneke, G., Norais, C., Flament, D., Myllykallio, H., Querellou, J. and Raffin, J.P. (2007) The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? J. Mol. Biol. 374, 1172-1185
32. Wold, M.S. (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66, 61-92
33. Robbins, J.B., McKinney, M.C., Guzman, C.E., Sriratana, B., Fitz-Gibbon, S., Ha, T. and Cann, I.K. (2005) The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins. J. Biol. Chem. 280, 15325-15339
34. Lin, Y., Robbins, J.B., Nyannor, E.K., Chen, Y.H. and Cann, I.K. (2005) A CCCH zinc finger conserved in a replication protein a homolog found in diverse Euryarchaeotes. J. Bacteriol. 187, 7881-7889
35. DeVeaux, L.C., Muller, J.A., Smith, J., Petrisko, J., Wells, D.P. and DasSarma, S. (2007) Extremely radiation-resistant mutants of a halophilic archaeon with increased single-stranded DNA-binding protein (RPA) gene expression. Radiat. Res. 168, 507-514
36. Chapados, B.R., Hosfield, D.J., Han, S., Qiu, J., Yelent, B., Shen, B. and Tainer, J.A. (2004) Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116, 39-50
37. Matsumiya, S., Ishino, S., Ishino, Y. and Morikawa, K. (2002) Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus. Genes Cells 7, 911-922
38. Warbrick, E. (1998) PCNA binding through a conserved motif. BioEssays 20, 195-199
39. Rogozin, I.B., Makarova, K.S., Pavlov, Y.I. and Koonin, E.V. (2008) A highly conserved family of inactivated archaeal B family DNA polymerases. Biol. Direct 3, 32
40. Ishino, Y., Komori, K., Cann, I.K.O. and Koga, Y. (1998) A novel DNA polymerase family found in archaea. J. Bacteriol. 180, 2232-2236
41. Cann, I.K. O., Komori, K., Toh, H., Kanai, S. and Ishino, Y. (1998) A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 95, 14250-14255
42. Moldovan, G.L., Pfander, B. and Jentsch, S. (2007) PCNA, the maestro of the replication fork. Cell 129, 665-679
43. Klein, R., Baranyi, U., Rossler, N., Greineder, B., Scholz, H. and Witte, A. (2002) Natrialba magadii virus ΦCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol. Microbiol. 45, 851-863
44. Gropp, F., Grampp, B., Stolt, P., Palm, P. and Zillig, W. (1992) The immunity-conferring plasmid pΦHL from the Halobacterium salinarium phage ΦH: nucleotide sequence and transcription. Virology 190, 45-54
45. Duderstadt, K.E. and Berger, J.M. (2008) AAA+ ATPases in the initiation of DNA replication. Crit. Rev. Biochem. Mol. Biol. 43, 163-187
46. Chen, Y.H., Kocherginskaya, S.A., Lin, Y., Sriratana, B., Lagunas, A.M., Robbins, J.B., Mackie, R.I. and Cann, I.K. (2005) Biochemical and mutational analyses of a unique clamp loader complex in the archaeon Methanosarcina acetivorans. J. Biol. Chem. 280, 41852-41863
47. Meslet-Cladiere, L., Norais, C., Kuhn, J., Briffotaux, J., Sloostra, J.W., Ferrari, E., Hubscher, U., Flament, D. and Myllykallio, H. (2007) A novel proteomic approach identifies new interaction partners for proliferating cell nuclear antigen. J. Mol. Biol. 372, 1137-1148
48. +-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii. Mol. Mircobiol. 59, 743-752
49. +-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations. BMC Mol. Biol. 7, 44
50. Allers, T. and Mevarech, M. (2005) Archaeal genetics: the third way. Nat. Rev. Genet. 6, 58-73
51. Soppa, J., Baumann, A., Brenneis, M., Dambeck, M., Hering, O. and Lange, C. (2008) Genomics and functional genomics with haloarchaea. Arch. Microbiol. 190, 197-215
52. Perriere, G. and Gouy, M. (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364-369
53. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948