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

The genomic sequence of the archaeon Methanosarcina mazei has been analyzed by the Z curve method. The Z curve is a three-dimensional curve that uniquely represents the given DNA sequence. The three-dimensional Z curve and its x and y components for the genome of M. mazei show a sharp peak and relatively broad peak, respectively. The cdc6 gene is located exactly at the position of the sharp peak. Based on the known behavior of the Z curves for the archaea whose replication origins have been identified, we hypothesize that the replication origin and termination sites correspond to the positions of the sharp peak and broad peak, respectively. We have located an intergenic region that is between the cdc6 gene (MM1314) and the gene for an adjacent protein (MM1315), which shows strong characteristics of the known replication origins. This region is highly rich in AT and contains multiple copies of consecutive repeats. Our results strongly suggest that the single replication origin of M. mazei is situated at the intergenic region between the cdc6 gene and the gene for the adjacent protein, from 1,564,657 to 1,566,241 bp of the genome.

[1]  A. Danchin,et al.  Universal replication biases in bacteria , 1999, Molecular microbiology.

[2]  W. Doolittle,et al.  Archaea and the Origin(s) of DNA Replication Proteins , 1997, Cell.

[3]  S. Salzberg,et al.  Skewed oligomers and origins of replication. , 1998, Gene.

[4]  R. Overbeek,et al.  The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. , 2002, Journal of molecular microbiology and biotechnology.

[5]  J. Lobry.  Asymmetric substitution patterns in the two DNA strands of bacteria. , 1996, Molecular biology and evolution.

[6]  E. Chargaff,et al.  Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. , 1968, Proceedings of the National Academy of Sciences of the United States of America.

[7]  B. Tye.  Insights into DNA replication from the third domain of life. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R Zhang,et al.  Analysis of distribution of bases in the coding sequences by a diagrammatic technique. , 1991, Nucleic acids research.

[9]  H Philippe,et al.  Identification of putative chromosomal origins of replication in Archaea , 1999, Molecular microbiology.

[10]  Y. Ishino,et al.  Archaeal DNA replication: identifying the pieces to solve a puzzle. , 1999, Genetics.

[11]  J. Lobry,et al.  Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. , 1999, Gene.

[12]  C. Woese,et al.  Phylogenetic structure of the prokaryotic domain: The primary kingdoms , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Z. Kelman.  The replication origin of archaea is finally revealed. , 2000, Trends in biochemical sciences.

[14]  A Grigoriev,et al.  Analyzing genomes with cumulative skew diagrams. , 1998, Nucleic acids research.

[15]  A. Cornish-Bowden.  Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. , 1985, Nucleic acids research.

[16]  R Zhang,et al.  Z curves, an intutive tool for visualizing and analyzing the DNA sequences. , 1994, Journal of biomolecular structure & dynamics.

[17]  H Philippe,et al.  Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. , 2000, Science.

[18]  R. Bernander.  Chromosome replication, nucleoid segregation and cell division in archaea. , 2000, Trends in microbiology.

[19]  R. Bernander.  Archaea and the cell cycle , 1998, Molecular microbiology.

[20]  H. Ochman,et al.  Strand asymmetries in DNA evolution. , 1997, Trends in genetics : TIG.

[21]  K. H. Wolfe,et al.  Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes , 1998, Journal of Molecular Evolution.

[22]  T. Kelly,et al.  Regulation of chromosome replication. , 2000, Annual review of biochemistry.

[23]  Bruce Stillman,et al.  ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex , 1992, Nature.

[24]  S. Karlin,et al.  Strand compositional asymmetry in bacterial and large viral genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Rossi,et al.  Archaeal DNA replication: spotlight on a rapidly moving field , 2002, Extremophiles.

[26]  J. Lobry,et al.  A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. , 1996, Biochimie.