Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method

Biochemical and Biophysical Research Communications

Volumn 297, Issue 2, 2002, Pages 396-400

  Zhang, Ren ^a   Zhang, Chun Ting ^b  

^a KEY LABORATORY OF CANCER PREVENTION AND THERAPY   (China)

^b TIANJIN UNIVERSITY   (China)

Author keywords

Archaea; cdc6 Gene; Methanosarcina mazei; Replication origin; Z curve

Indexed keywords

BACTERIAL PROTEIN; CELL CYCLE PROTEIN 6; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BACTERIAL GENOME; DNA SEQUENCE; GENE LOCATION; GENE REPLICATION; GENE SEQUENCE; METHANOSARCINA; PRIORITY JOURNAL;

BASE SEQUENCE; GENES, ARCHAEAL; METHANOSARCINA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; REPLICATION ORIGIN;

ARCHAEA; METHANOSARCINA; METHANOSARCINA MAZEI;

EID: 0036401109     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(02)02214-3     Document Type: Article

References (27)

1. T.J. Kelly, G.W. Brown, Regulation of chromosome replication, Annu. Rev. Biochem. 69 (2000) 829-880.
2. R. Bernander, Chromosome replication, nucleoid segregation and cell division in archaea, Trends Microbiol. 8 (2000) 278-283.
3. Z. Kelman, The replication origin of archaea is finally revealed, Trends Biochem. Sci. 25 (2000) 521-523.
4. B.K. Tye, Insights into DNA replication from the third domain of life, Proc. Natl. Acad. Sci. USA 97 (2000) 2399-2401.
5. C.R. Woese, G.E. Fox, Phylogenetic structure of the prokaryotic domain the primary kingdoms, Proc. Natl. Acad. Sci. USA 74 (1977) 5088-5090.
6. D.R. Edgell, W.F. Doolittle, Archaea and the origins of DNA replication proteins, Cell 89 (1997) 995-998.
7. I.K. Cann, Y. Ishino, Archaeal DNA replication identifying the pieces to solve a puzzle, Genetics 152 (1999) 1249-1267.
8. K. Bohlke, F.M. Pisani, M. Rossi, G. Antranikian, Archaeal DNA replication spotlight on a rapidly moving field, Extremophiles 6 (2002) 1-14.
9. U. Deppenmeier et al., The genome of methanosarcina mazei evidence for lateral gene transfer between bacteria and archaea, J. Mol. Microbiol. Biotechnol. 4 (2002) 453-461.
10. J.R. Lobry, A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria, Biochimie 78 (1996) 323-326.
11. J.R. Lobry, Asymmetric substitution patterns in the two DNA strands of bacteria, Mol. Biol. Evol. 3 (1996) 660-665.
12. A. Grigoriev, Analyzing genomes with cumulative skew diagrams, Nucleic Acids Res. 26 (1998) 2286-2290.
13. J. Mrazek, S. Karlin, Strand compositional asymmetry in bacterial and large viral genomes, Proc. Natl. Acad. Sci. USA 95 (1998) 3720-3725.
14. M.J. McLean, K.H. Wolfe, K.M. Devine, Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes, J. Mol. Evol. 47 (1998) 691-696.
15. E.P. Rocha, A. Danchin, A. Viari, Universal replication biases in bacteria, Mol. Microbiol. 32 (1999) 11-16.
16. M.P. Francino, H. Ochman, Strand asymmetries in DNA evolution, Trends Genet. 13 (1997) 240-245.
17. A.C. Frank, J.R. Lobry, Asymmetric substitution patterns a review of possible underlying mutational or selective mechanisms, Gene 238 (1999) 65-77.
18. S.L. Salzberg, A.J. Salzberg, A.R. Kerlavage, J.F. Tomb, Skewed oligomers and origins of replication, Gene 217 (1998) 57-67.
19. P. Lopez, H. Philippe, H. Myllykallio, P. Forterre, Identification of putative chromosomal origins of replication in archaea, Mol. Microbiol. 32 (1999) 883-886.
20. H. Myllykallio, P. Lopez, P. Lopez-Garcia, R. Heilig, W. Saurin, Y. Zivanovic, H. Philippe, P. Forterre, Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon, Science 288 (2000) 2212-2215.
21. C.T. Zhang, R. Zhang, Analysis of distribution of bases in the coding sequences by a diagrammatic technique, Nucleic Acids Res. 19 (1991) 6313-6317.
22. R. Zhang, C.T. Zhang, Z curves, an intuitive tool for visualizing and analyzing DNA sequences, J. Biomol. Struct. Dyn. 11 (1994) 767-782.
23. Cornish-Bowden, Nomenclature for incompletely specified bases in nucleic acid sequences Recommendation 1984, Nucleic Acids Res. 13 (1985) 3021-3030.
24. Kornberg, T.A. Baker, DNA Replication, Freeman, San Francisco, 1992.
25. S.P. Bell, B. Stillman, ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex, Nature 357 (1992) 128-134.
26. R. Bernander, Archaea and the cell cycle, Mol. Microbiol. 29 (1998) 955-961.
27. R. Rudner, J.D. Karkas, E. Chargaff, Separation of B. subtilis DNA into complementary strands. III. Direct analysis, Proc. Natl. Acad. Sci. USA 60 (1968) 921-922.