Analysis of bilateral inverse symmetry in whole bacterial chromosomes

Biochemical and Biophysical Research Communications

Volumn 299, Issue 1, 2002, Pages 126-134

  Sanchez J ^a,b   Jose M V ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MORELOS   (Mexico)

Author keywords

Bacterial genome evolution; Bacterial replication origins; Chargaff's DNA parity rules; Codons in leading and lagging strands; Complementary triplets; Dot plot analyses; Strand asymmetry

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BORRELIA BURGDORFERI; CHROMOSOME ANALYSIS; CODON; GENE DUPLICATION; GENE REARRANGEMENT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BORRELIA BURGDORFERI; CHROMOSOMES, BACTERIAL; CODON; GENES, BACTERIAL; GENETIC COMPLEMENTATION TEST; MODELS, GENETIC; TRINUCLEOTIDE REPEATS;

BACTERIA (MICROORGANISMS); BORRELIA; BORRELIA BURGDORFERI;

EID: 0036436219     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(02)02583-4     Document Type: Article

References (32)

1. B. Lewin, Genes, vol. VII, Oxford University Press, New York, 2000.
2. C.M. Fraser et al., Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi, Nature 390 (1997) 553-555.
3. M. Picardeau, J.R. Lobry, B.J. Hinnebusch, Physical mapping of an origin of bi-directional replication at the center of the Borrelia burgdorferi linear chromosome, Mol. Microbiol. 32 (1999) 437-445.
4. F.R. Blattner et al., The complete genome sequence of Escherichia coli K-12, Science 277 (1997) 1453-1474.
5. J.R. Lobry, Asymmetric substitution patterns in the two DNA strands of bacteria, Mol. Biol. Evol. 13 (1996) 660-665.
6. M.P. Francino, H. Ochman, Strand asymmetries in DNA evolution, Trends Genet. 6 (1997) 240-245.
7. M. 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.
8. A.C. Frank, J.R. Lobry, Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms, Gene 238 (1999) 65-77.
9. E.R. Tillier, R.A. Collins, The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes, J. Mol. Evol. 50 (2000) 249-257.
10. A. Grigoriev, Analyzing genomes with cumulative skew diagrams, Nucleic Acids Res. 26 (1998) 2286-2290.
11. X. Veaute, R.P. Fuchs, Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand, Science 261 (1993) 598-600.
12. J.O. McInerney, Replicational and transcriptional selection on codon usage in Borrelia burgdorferi, Proc. Natl. Acad. Sci. USA 95 (1998) 10698-10703.
13. J.M. Freeman, T.N. Plasterer, T.F. Smith, S.C. Mohr, Patterns of genome organization in bacteria, Science 279 (1998) 1827a.
14. J. Mrazek, S. Karlin, Strand compositional asymmetry in bacterial and large viral genomes, Proc. Natl. Acad. Sci. USA 95 (1998) 3720-3725.
15. E.P. Rocha, A. Danchin, A. Viari, Universal replication biases in bacteria, Mol. Microbiol. 32 (1999) 11-16.
16. S.L. Salzberg, A.J. Salzberg, A.R. Kerlavage, J.F. Tomb, Skewed oligomers and origins of replication, Gene 217 (1998) 57-67.
17. D.R. Forsdyke, Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species, J. Mol. Evol. 41 (1995) 573-581.
18. M. Gribskov, J. Deveraux, Sequence Analysis Primer, New York Stockton Press, New York, 1991.
19. E. Chargaff, How genetics got a chemical education, Ann. N. Y. Acad. Sci. 325 (1979) 345-350.
20. C. Shioiri, N. Takahata, Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry, J. Mol. Evol. 53 (2001) 364-376.
21. P.F. Baisnee, S. Hampson, P. Baldi, Why are complementary DNA strands symmetric?, Bioinformatics 18 (2002) 1021-1033.
22. D.A. Dixon, S.C. Kowalcykowski, The recombination hotspot Chi is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme, Cell 73 (1993) 87-96.
23. R. Uno, Y. Nakayama, K. Arakawa, M. Tomita, The orientation bias of Chi sequences is a general tendency of G-rich oligomers, Gene 259 (2000) 207-215.
24. Q. Dong, A.J. Cuticchia, Compositional symmetries in complete genomes, Bioinformatics 17 (2001) 557-559.
25. V.V. Prabhu, Symmetry observations in long nucleotide sequences, Nucleic Acids Res. 12 (1993) 2797-2800.
26. E.P. Rocha, A. Danchin, Base composition bias might result from competition for metabolic resources, Trends Genet. 18 (2002) 291-294.
27. H. Nakashima, M. Ota, K. Nishikawa, T. Ooi, Genes from nine genomes are separated into their organisms in the dinucleotide composition space, DNA Res. 30 (1998) 251-259.
28. D. Zipkas, M. Riley, Proposal concerning mechanism of evolution of the genome of Escherichia coli, Proc. Natl. Acad. Sci. USA 72 (1975) 1354-1358.
29. J.A. Eisen, J.F. Heidelberg, O. White, S.L. Salzberg, Evidence for symmetric chromosomal inversions around the replication origin in bacteria, Genome Biol. 1 (2000) 1-9.
30. N. Handa, Y. Nakayama, M. Sadykov, I. Kobayashi, Experimental genome evolution: Large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex, Mol. Microbiol. 40 (2001) 932-940.
31. E. Rayko, Organization, generation and replication of amphimeric genomes: A review, Gene 199 (1997) 1-18.
32. K. Kobryn, G. Chaconas, The circle is broken: Telomere resolution in linear replicons, Curr. Opin. Micro. 4 (2001) 558-564.