Multiple replication origins with diverse control mechanisms in Haloarcula hispanica

Nucleic Acids Research

Volumn 42, Issue 4, 2014, Pages 2282-2294

  Wu, Zhenfang ^a,b   Liu, Jingfang ^a,b   Yang, Haibo ^a   Liu, Hailong ^a   Xiang, Hua ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL PROTEIN; CELL CYCLE PROTEIN 6;

ARCHAEAL GENE; ARCHAEAL GENOME; ARTICLE; BACTERIAL GROWTH; CDC6 GENE; CDC6E GENE; CONTROLLED STUDY; DNA REPLICATION ORIGIN; GENE ACTIVITY; GENE CONTROL; GENE DELETION; GENE FREQUENCY; GENE LOCATION; GENETIC ASSOCIATION; GENETIC CONSERVATION; HALOARCULA HISPANICA; INVERTED REPEAT; MINICHROMOSOME; MOLECULAR RECOGNITION; NONHUMAN; ORC1 GENE; ORC2 GENE; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; REPLICON;

CELL CYCLE PROTEINS; CHROMOSOME MAPPING; GENE DELETION; GENES, CDC; HALOARCULA; INVERTED REPEAT SEQUENCES; PLASMIDS; REGULATORY SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; REPLICON;

EID: 84895791233     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1214     Document Type: Article

References (46)

1. Robinson, N.P. and Bell, S.D. (2005) Origins of DNA replication in the three domains of life. FEBS J., 272, 3757-3766.
2. Kelman, Z. and White, M. (2005) Archaeal DNA replication and repair. Curr. Opin. Microbiol., 8, 669-676.
3. Myllykallio, H., Lopez, P., Lopez-Garcia, P., Heilig, R., Saurin, W., Zivanovic, Y., Philippe, H. and Forterre, P. (2000) Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science, 288, 2212-2215.
4. Berquist, B.R. and DasSarma, S. (2003) An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J. Bacteriol., 185, 5959-5966.
5. 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.
6. 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. USA, 101, 7046-7051.
7. Robinson, N.P. and Bell, S.D. (2007) Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc. Natl Acad. Sci. USA, 104, 5806-5811.
8. Grainge, I., Gaudier, M., Schuwirth, B.S., Westcott, S.L., Sandall, J., Atanassova, N. and Wigley, D.B. (2006) Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix. J. Mol. Biol., 363, 355-369.
9. Coker, J.A., DasSarma, P., Capes, M., Wallace, T., McGarrity, K., Gessler, R., Liu, J., Xiang, H., Tatusov, R., Berquist, B.R. et al. (2009) Multiple replication origins of Halobacterium sp. strain NRC-1: properties of the conserved orc7-dependent oriC1. J. Bacteriol., 191, 5253-5261.
10. 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.
11. Maisnier-Patin, S., Malandrin, L., Birkeland, N.K. and Bernander, R. (2002) Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii. Mol. Microbiol., 45, 1443-1450.
12. Majernik, A.I. and Chong, J.P. (2008) A conserved mechanism for replication origin recognition and binding in archaea. Biochem. J., 409, 511-518.
13. Matsunaga, F., Forterre, P., Ishino, Y. and Myllykallio, H. (2001) In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc. Natl Acad. Sci. USA, 98, 11152-11157.
14. Matsunaga, F., Norais, C., Forterre, P. and Myllykallio, H. (2003) Identification of short 'eukaryotic' Okazaki fragments synthesized from a prokaryotic replication origin. EMBO Rep., 4, 154-158.
15. Wu, Z., Liu, H., Liu, J., Liu, X. and Xiang, H. (2012) Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea. BMC Genomics, 13, 478.
16. Duggin, I.G., McCallum, S.A. and Bell, S.D. (2008) Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius. Proc. Natl Acad. Sci. USA, 105, 16737-16742.
17. Samson, R.Y., Xu, Y., Gadelha, C., Stone, T.A., Faqiri, J.N., Li, D., Qin, N., Pu, F., Liang, Y.X., She, Q. et al. (2013) Specificity and function of archaeal DNA replication initiator proteins. Cell Rep., 3, 485-496.
18. Dueber, E.C., Costa, A., Corn, J.E., Bell, S.D. and Berger, J.M. (2011) Molecular determinants of origin discrimination by Orc1 initiators in archaea. Nucleic Acids Res., 39, 3621-3631.
19. Mott, M.L. and Berger, J.M. (2007) DNA replication initiation: mechanisms and regulation in bacteria. Nat. Rev. Microbiol., 5, 343-354.
20. Kitagawa, R., Ozaki, T., Moriya, S. and Ogawa, T. (1998) Negative control of replication initiation by a novel chromosomal locus exhibiting exceptional affinity for Escherichia coli DnaA protein. Genes Dev., 12, 3032-3043.
21. Braun, R.E., O'Day, K. and Wright, A. (1985) Autoregulation of the DNA replication gene dnaA in E. coli K-12. Cell, 40, 159-169.
22. Rajewska, M., Wegrzyn, K. and Konieczny, I. (2012) AT-rich region and repeated sequences-the essential elements of replication origins of bacterial replicons. FEMS Microbiol. Rev., 36, 408-434.
23. Nordman, J. and Orr-Weaver, T.L. (2012) Regulation of DNA replication during development. Development, 139, 455-464.
24. Mechali, M. (2010) Eukaryotic DNA replication origins: many choices for appropriate answers. Nat. Rev. Mol. Cell. Biol., 11, 728-738.
25. Aparicio, O.M. (2013) Location, location, location: it's all in the timing for replication origins. Genes Dev., 27, 117-128.
26. Lundgren, M. and Bernander, R. (2007) Genome-wide transcription map of an archaeal cell cycle. Proc. Natl Acad. Sci. USA, 104, 2939-2944.
27. Han, J., Lu, Q., Zhou, L., Liu, H. and Xiang, H. (2009) Identification of the polyhydroxyalkanoate (PHA)-specific acetoacetyl coenzyme A reductase among multiple FabG paralogs in Haloarcula hispanica and reconstruction of the PHA Biosynthetic pathway in Haloferax volcanii. Appl. Environ. Microbiol., 75, 6168-6175.
28. Liu, H., Han, J., Liu, X., Zhou, J. and Xiang, H. (2011) Development of pyrF-based gene knockout systems for genome-wide manipulation of the archaea Haloferax mediterranei and Haloarcula hispanica. J. Genet. Genomics, 38, 261-269.
29. Sun, C., Zhou, M., Li, Y. and Xiang, H. (2006) Molecular characterization of the minimal replicon and the unidirectional theta replication of pSCM201 in extremely halophilic archaea. J. Bacteriol., 188, 8136-8144.
30. Zhou, L., Zhou, M., Sun, C., Xiang, H. and Tan, H. (2007) Genetic analysis of a novel plasmid pZMX101 from Halorubrum saccharovorum: determination of the minimal replicon and comparison with the related haloarchaeal plasmid pSCM201. FEMS Microbiol. Lett., 270, 104-108.
31. Liu, H., Wu, Z., Li, M., Zhang, F., Zheng, H., Han, J., Liu, J., Zhou, J., Wang, S. and Xiang, H. (2011) Complete genome sequence of Haloarcula hispanica, a model haloarchaeon for studying genetics, metabolism, and virus-host interaction. J. Bacteriol., 193, 6086-6087.
32. Cao, F.L., Liu, H.H., Wang, Y.H., Liu, Y., Zhang, X.Y., Zhao, J.Q., Sun, Y.M., Zhou, J. and Zhang, L. (2010) An optimized RNA amplification method for prokaryotic expression profiling analysis. Appl. Microbiol. Biotechnol., 87, 343-352.
33. Breuert, S., Allers, T., Spohn, G. and Soppa, J. (2006) Regulated polyploidy in halophilic archaea. PLoS One, 1, e92.
34. Cline, S.W., Lam, W.L., Charlebois, R.L., Schalkwyk, L.C. and Doolittle, W.F. (1989) Transformation methods for halophilic archaebacteria. Can. J. Microbiol., 35, 148-152.
35. Kim, S. and Huberman, J.A. (1999) Influence of a replication enhancer on the hierarchy of origin efficiencies within a cluster of DNA replication origins. J. Mol. Biol., 288, 867-882.
36. Forterre, P. (1999) Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol., 33, 457-465.
37. Capes, M.D., Coker, J.A., Gessler, R., Grinblat-Huse, V., DasSarma, S.L., Jacob, C.G., Kim, J.M., DasSarma, P. and DasSarma, S. (2011) The information transfer system of halophilic archaea. Plasmid, 65, 77-101.
38. 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.
39. Liu, X., Miao, D., Zhang, F., Wu, Z., Liu, J. and Xiang, H. (2013) Characterization of the minimal replicon of pHM300 and independent copy number control of major and minor chromosomes of Haloferax mediterranei. FEMS Microbiol. Lett., 339, 66-74.
40. Cervantes-Rivera, R., Pedraza-Lopez, F., Perez-Segura, G. and Cevallos, M.A. (2011) The replication origin of a repABC plasmid. BMC Microbiol., 11, 158.
41. Pinto, U.M., Flores-Mireles, A.L., Costa, E.D. and Winans, S.C. (2011) RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis. Mol. Microbiol., 81, 1593-1606.
42. Dueber, E.L., Corn, J.E., Bell, S.D. and Berger, J.M. (2007) Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science, 317, 1210-1213.
43. Gaudier, M., Schuwirth, B.S., Westcott, S.L. and Wigley, D.B. (2007) Structural basis of DNA replication origin recognition by an ORC protein. Science, 317, 1213-1216.
44. Egan, E.S. and Waldor, M.K. (2003) Distinct replication requirements for the two Vibrio cholerae chromosomes. Cell, 114, 521-530.
45. Duigou, S., Knudsen, K.G., Skovgaard, O., Egan, E.S. and Løbner-Olesen, A. (2006) Independent control of replication initiation of the two Vibrio cholerae chromosomes by DnaA and RctB. J. Bacteriol., 188, 6419-6424.
46. Scholefield, G., Veening, J.W. and Murray, H. (2011) DnaA and ORC: more than DNA replication initiators. Trends Cell Biol., 21, 188-194.