Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes

Evolutionary Bioinformatics

Volumn 3, Issue , 2007, Pages 279-286

  Arakawa, Kazuharu ^a   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

DNA replication; GC skew; Genome organization; Replicational selection

Indexed keywords

BACTERIAL CHROMOSOME; BACTERIAL GENOME; CODON USAGE; DNA REPLICATION ORIGIN; DNA STRAND; DNA TRANSCRIPTION; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENOMICS; REST; SPECIES;

EID: 74549129151     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.1177/117693430700300005     Document Type: Article

References (37)

1. Arakawa, K., Mori, K., Ikeda, K. et al. 2003. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics, 19:305-6.
2. Arakawa, K., Saito, R. and Tomita, M. 2007a. Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. FEBS Lett, 581:253-8.
3. Arakawa, K. and Tomita, M. 2006. G-language System as a platform for large-scale analysis of high-throughput omics data. Journal of Pesticide Science, 31:282-8.
4. Arakawa, K., Uno, R., Nakayama, Y. et al. 2007b. Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene, in press.
5. Arakawa, K. and Tomita, M. 2007. The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection. Evolutionary Bioinformatics, 3:145-154.
6. Brewer, B.J. 1988. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell, 53:679-86.
7. Couturier, E. and Rocha, E.P. 2006. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol. Microbiol., 59:1506-18.
8. Daubin, V. and Perriere, G. 2003. G + C3 structuring along the genome: a common feature in prokaryotes. Mol. Biol. Evol., 20:471-83.
9. Frank, A.C. and Lobry, J.R. 1999. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 238:65-77.
10. Frank, A.C. and Lobry, J.R. 2000. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics, 16:560-1.
11. Freeman, J.M., Plasterer, T.N., Smith, T.F. et al. 1998. Patterns of Genome Organization in Bacteria. Science, 279:1827a.
12. Grigoriev, A. 1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res., 26:2286-90.
13. Hashimoto, M., Ichimura, T., Mizoguchi, H. et al. 2005. Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol., 55:137-49.
14. Hendrickson, H. and Lawrence, J.G. 2006. Selection for chromosome architecture in bacteria. J. Mol. Evol., 62:615-29.
15. Hooper, S.D. and Berg, O.G. 2003. Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol., 4:R48.
16. Kowalczuk, M., Mackiewicz, P., Mackiewicz, D. et al. 2001. DNA asymmetry and the replicational mutational pressure. J. Appl. Genet., 42:553-77.
17. Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K. et al. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev., 58:401-65.
18. Levy, O., Ptacin, J.L., Pease, P.J. et al. 2005. Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc. Natl. Acad. Sci. U.S.A., 102:17618-23.
19. Liu, B. and Alberts, B.M. 1995. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science, 267:1131-7.
20. Lobry, J.R. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol., 13:660-5.
21. Lobry, J.R. and Louarn, J.M. 2003. Polarisation of prokaryotic chromosomes. Curr. Opin. Microbiol., 6:101-8.
22. Lobry, J.R. and Sueoka, N. 2002. Asymmetric directional mutation pressures in bacteria. Genome Biol., 3:RESEARCH0058.
23. McLean, M.J., Wolfe, K.H. and Devine, K.M. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol., 47:691-6.
24. Omont, N. and Kepes, F. 2004. Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication. Bioinformatics, 20:2719-25.
25. Pease, P.J., Levy, O., Cost, G.J. et al. 2005. Sequence-directed DNA translocation by purified FtsK. Science, 307:586-90.
26. Perals, K., Capiaux, H., Vincourt, J.B. et al. 2001. Interplay between recombination, cell division and chromosome structure during chromosome dimer resolution in Escherichia coli. Mol. Microbiol., 39:904-13.
27. Perals, K., Cornet, F., Merlet, Y. et al. 2000. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol., 36:33-43.
28. Price, M.N., Alm, E.J. and Arkin, A.P. 2005. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res., 33:3224-34.
29. Rocha, E.P. 2004a. Order and disorder in bacterial genomes. Curr. Opin. Microbiol., 7:519-27.
30. Rocha, E.P. 2004b. The replication-related organization of bacterial genomes. Microbiology., 150:1609-27.
31. Rocha, E.P. and Danchin, A. 2003. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat. Genet., 34:377-8.
32. Salzberg, S.L., Salzberg, A.J., Kerlavage, A.R. et al. 1998. Skewed oligomers and origins of replication. Gene, 217:57-67.
33. Sharp, P.M., Cowe, E., Higgins, D.G. et al. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res., 16:8207-11.
34. Sharp, P.M. and Li, W.H. 1987. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15:1281-95.
35. Uno, R., Nakayama, Y., Arakawa, K. et al. 2000. The orientation bias of Chi sequences is a general tendency of G-rich oligomers. Gene, 259:207-15.
36. Uno, R., Nakayama, Y. and Tomita, M. 2006. Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12. Gene, 380:30-37.
37. Worning, P., Jensen, L.J., Hallin, P.F. et al. 2006. Origin of replication in circular prokaryotic chromosomes. Environ. Microbiol., 8:353-61.