DNA asymmetry and the replicational mutational pressure

Journal of Applied Genetics

Volumn 42, Issue 4, 2001, Pages 553-577

  Kowalczuk, Maria ^a   Mackiewicz, Paweł ^a   Mackiewicz, Dorota ^a   Nowicka, Aleksandra ^a   Dudkiewicz, Małgorzata ^a   Dudek, Mirosław R ^b   Cebrat, Stanisław ^a  

^a UNIVERSITY OF WROC AW   (Poland)

^b PEDAGOGICAL UNIVERSITY   (Poland)

Author keywords

AT skew; DNA asymmetry; DNA walk; GC skew; Mutational pressure; Rate of evolution; Selection pressure

Indexed keywords

EID: 0012534043     PISSN: 12341983     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (113)

1. ADACHI J., HASEGAWA M. (1996). Tempo and mode of synonymous substitutions in mitochondrial DNA of primates. Mol. Biol. Evol. 13: 200-208.
2. ANDERSSON S.G., ZOMORODIPOUR A., ANDERSSON J.O., SICHERITZ-PONTEN T., ALSMARK U.C., PODOWSKI R.M., NASLUND A.K., ERIKSSON A.S., WINKLER H.H., KURLAND C.G. (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396: 133-140.
3. BAKER T.A., WICKNER S.H. (1992). Genetics and enzymology of DNA replication in Escherichia coli. Annu. Rev. Genet. 26: 447-477.
4. BASIC-ZANINOVIC T., PALOMBO F., BIGNAMI M., DOGLIOTTI E. (1992). Fidelity of replication of the leading and the lagging DNA strands opposite N-methyl-N-nitrosourea-induced DNA damage in human cells. Nucleic Acids Res. 20: 6543-6548.
5. BELETSKII A., BHAGWAT A.S. (1996). Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc. Natl. Acad. Sci. USA 93: 13919-13924.
6. BENNETZEN J.H., HALL B.D. (1982). Codon selection in yeast. J. Biol. Chem. 257: 3026-3031.
7. BERTHELSEN Ch.L., GLAZIER J.A., SKOLNICK M.H. (1992). Global fractal dimension of human DNA sequences treated as pseudorandom walks. Phys. Rev. A45: 8902-8913.
8. BLATTNER F.R., PLUNKETT G. 3rd, BLOCH C.A., PERNA N.T., BURLAND V., RILEY M., COLLADO-VIDES J., GLASNER J.D., RODE C.K., MAYHEW G.F., et al. (1997). The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
9. BREWER B.J. (1988). When polymerases collide: Replication and the transcriptional organisation of the E. coli chromosome. Cell 53: 679-686.
10. CEBRAT S., DUDEK M.R. (1998). The effect of DNA phase structure on DNA walks. Eur. Phys. J. 3: 271-276.
11. CEBRAT S., DUDEK MR., GIERLIK A., KOWALCZUK M., MACKIEWICZ P. (1999). Effect of replication on the third base of codons. Physica A 265: 78-94.
12. CEBRAT S., DUDEK M.R., MACKIEWICZ P. (1998). Sequence asymmetry as a parameter indicating coding sequences in Saccharomyces cerevisiae genome. Theory Bioscienc. 117: 78-89.
13. CEBRAT S., DUDEK M.R., ROGOWSKA A. (1997a). Asymmetry innucleotide composition of sense and antisense strands as a parameter for discriminating open reading frames as protein coding sequences. J. Appl. Genet. 38: 1-9.
14. CEBRAT S., DUDEK M.R., MACKIEWICZ P., KOWALCZUK M., FITA M. (1997b). Asymmetry of coding versus non-coding strands in coding sequences of different genomes. Microb. & Comp. Genom. 2: 259-268.
15. CHARGAFF E. (1950). Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 6: 201-240.
16. DANIELS D.L., SANGER F. COULSON A.R. (1983). Features of bacteriophage lambda: analysis of the complete nucleotide sequence. Cold Spring Harbor Symp. on Quantum Biology Vol. 47: 1009-1024.
17. DESCHAVANNE P., FILIPSKI J. (1995). Correlation of GC content with replication timing and repair mechanisms in weakly expressed E. coli genes. Nucleic Acids Res. 23:1350-1353.
18. ECHOLS H., GOODMAN M.F. (1991). Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60: 477-511.
19. EISEN J.A., HEIDELBERG J.F., WHITE O., SALZBERG S.L. (2000). Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1: 0011.1-0011.9.
20. FIJALKOWSKA I.J., JONCZYK P., MALISZEWSKA-TKACZYK M., BIALOSKORSKA M., SCHAAPER R.M. (1998). Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. USA 95: 10020-10025.
21. FIJALKOWSKA I.J., SCHAAPER R.M. (1996). Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc. Natl. Acad. Sci. USA 93: 2856-2861.
22. FILIPSKI J. (1990). Evolution of DNA sequences. Contributions of mutational bias and selection to the origin of chromosomal compartments. In: Advances in mutagenesis research 2 (G. Obe ed.). Springer Verlag, Berlin.
23. FRANCINO M.P., CHAO L., RILEY M.A., OCHMAN H. (1996). Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science 272: 107-109.
24. FRANCINO M.P., OCHMAN H. (1997). Strand asymmetries in DNA evolution. Trends Genet. 13: 240-245.
25. FRANK A.C., LOBRY J.R. (1999). Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238: 65-77.
26. FRASER C.M., CASJENS S., HUANG W.M., SUTTON G.G., CLAYTON R., LATHIGRA R., WHITE O., KETCHUM K.A., DODSON R., HICKEY E.K. et al. (1997). Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580-586
27. FRASER C.M., GOCAYNE J.D., WHITE O., ADAMS M.D., CLAYTON R.A., FLEISCHMANN R.D., BULT C.J., KERLAVAGE A.R., SUTTON G.G., KELLEY J.M. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
28. FRASER C.M., NORRIS S.J., WEINSTOCK G.M., WHITE O., SUTTON G.G., DODSON R., GWINN M., HICKEY E.K., CLAYTON R., KETCHUM K.A. et al. (1998). Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281: 375-388.
29. FREDERICO L.A., KUNKEL T.A., SHAW B.R. (1990). A sensitive genetic assay for the detection of cytosine deamination: determination of rare constants and the activation energy. Biochemistry 29: 2532-2537.
30. FREEMAN J.M., PLASTERER T.N., SMITH T.F., MOHR S.C. (1998). Patterns of genome organisation in bacteria. Science 279: 1827.
31. GATES M.A. (1986). A simple way to look at DNA. J. Theor. Biol. 119: 281-300.
32. GIERLIK A., KOWALCZUK M., MACKIEWICZ P., DUDEK M.R., CEBRAT S. (2000). Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J. Theor. Biol. 202: 305-314.
33. GOJOBORI T., LI W.-H., GRAUR D. (1982). Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18: 360-369.
34. GOUY M., GAUTIER C. (1982). Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10: 7055-7074.
35. GRIGORIEV A. (1998). Analysing genomes with cumulative skew diagrams. Nucleic Acids Res. 26: 2286-2290.
36. GRIGORIEV A. (1999). Strand-specific compositional asymmetries in double-stranded DNA viruses. Virol. Res. 60:1-19.
37. GUTIERREZ G., MARQUEZ L., MARTIN A. (1996). Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translation efficiency. Nucleic Acids Res. 24: 2525-2528.
38. HANAWALT P.C. (1991). Heterogenity of DNA repair at the gene level. Mutat. Res. 247: 203-211.
39. HIMMELREICH R., HILBERT H., PLAGENS H., PIRKL E., LI B.C., HERRMANN R. (1996). Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24: 4420-4449.
40. HUTCHINSON F. (1996). Mutagenesis. In: Escherichia coli and Salmonella. Cellular and molecular biology (F.C. Neidhardt ed.). Asm. Press, Washington D.C.: 749-763.
41. IKEMURA T. (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein sequence: a proposal for a synonymous codon choice that is optimal for the E. coli translation system. J. Mol. Biol. 151: 389-409.
42. IWAKI T., KAWAMURA A., ISHINO Y., KOHNO K., KANO Y., GOSHIMA N., YARA M., FURUSAWA M., DOI H., IMAMOTO F. (1996). Preferential replication-dependent mutagenesis in the lagging DNA strand in Escherichia coli. Mol. Gen. Genet. 251: 657-664.
43. KARLIN S. (1999). Bacterial DNA strand compositional asymmetry. Trends Microbiol. 8: 305-308.
44. KARLIN S., BURGE C. (1995). Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11: 283-290.
45. KARLIN S., MRAZEK J. (1996). What drives codon choices in human genome? J. Mol. Biol. 262: 459-472.
46. KARLIN S., BLAISDELL B.E., BUCHER P. (1992). Quantile distributions of amino acid usage in protein classes. Protein Eng. 5: 729-738.
47. KIMURA M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
48. KOWALCZUK M., GIERLIK A., MACKIEWICZ P., CEBRAT S., DUDEK M.R. (1999b). Optimization of gene sequences under constant mutational pressure and selection. Phys. A 273: 116-131.
49. KOWALCZUK M., MACKIEWICZ P., GIERLIK A., DUDEK M.R., CEBRAT S. (1999a). Total number of coding open reading frames in the yeast genome. Yeast 15: 1031-1034.
50. KOWALCZUK M., MACKIEWICZ P., SZCZEPANIK D., NOWICKA A., DUDKIEWICZ M., DUDEK M.R., CEBRAT S. (2001a). Precise genome evolution law of turnover of nucleotides under mutational pressure. Submitted to BMC Evolutionary Biology.
51. KOWALCZUK M., MACKIEWICZ P., SZCZEPANIK D., NOWICKA A., DUDKIEWICZ M., DUDEK M.R., CEBRAT S. (2001b). Multiple base substitution corrections in DNA sequence evolution. Int. J. Modern Phys. C 12(7), in press.
52. KREUTZER D.A., ESSIGMANN J.M. (1998). Oxidized, deaminated cytosines are a source of C→T transitions in vivo. Proc. Natl. Acad. Sci. USA 95: 3578-3582.
53. KUNST F., OGASAWARA N., MOSZER I., ALBERTINI A.M., ALLONI G., AZEVEDO V., BERTERO M.G., BESSIERES P., BOLOTIN A., BORCHERT S., et al. (1997). The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
54. LAFAY B., LLOYD A.T., MCLEAN M.J., DEVINE K.M., SHARP P.M., WOLFE K.H. (1999). Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27: 1642-1649.
55. LAGUNEZ-OTERO J., TRIFONOV E.N. (1992). mRNA periodocal infrastructure complementary to the proof-reading site in the ribosome. J. Biomol. Struct. Dyn. 10: 455-464.
56. LI W.-H., WU C.I., LUO C.-C. (1984). Nonrandomness of point mutation as reflected in nucleotide substitution in pseudogenes and its evolutionary implications. J. Mol. Evol. 12: 58-71.
57. LINDAHL T. (1993). Instability and decay of the primary structure of DNA. Nature 362: 709-715.
58. LIU S.L., SANDERSON K.E. (1995). Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92: 1018-1022.
59. LIU S.L., SANDERSON K.E. (1996). Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93: 10303-10308.
60. LOBRY J.R. (1995). Properties of a general model of DNA evolution under no-strand bias conditions. J. Mol. Evol. 40: 326-330. Erratum 41:680.
61. LOBRY J.R. (1996a). Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
62. LOBRY J.R. (1996b). A simple vectorial representation of DNA sequence for the detection of replication origins in bacteria. Biochimie 78: 323-326.
63. LOPEZ P., FORTERRE P., le GUYADER H., PHILIPPE H. (2000). Origin of replication of Thermotoga maritima. Trends Genet. 16: 59-60.
64. LOPEZ P., PHILIPPE H., MYLLYKALLIO H., FORTERRE P. (1999). Identification of putative chromosomal origins of replication in Archaea. Mol. Microbiol. 32: 881-891.
65. MACKIEWICZ P., GIERLIK A., KOWALCZUK M., DUDEK M.R., CEBRAT S. (1999a). Asymmetry of nucleotide composition of prokaryotic chromosomes. J. Appl. Genet. 40: 1-14.
66. MACKIEWICZ P., GIERLIK A., KOWALCZUK M., DUDEK M.R, CEBRAT S. (1999b). How does replication-associated mutational pressure influence amino acid composition of proteins? Gen. Res. 9: 409-416.
67. MACKIEWICZ P., GIERLIK A., KOWALCZUK M., SZCZEPANIK D., DUDEK M.R., CEBRAT S. (1999c). Mechanisms generating long-range correlation in nucleotide composition of the Borrelia burgdorferi genome. Phys. A 273: 103-115.
68. MACKIEWICZ P., SZCZEPANIK D., GIERLIK A., KOWALCZUK M., NOWICKA A., DUDKIEWICZ M., DUDEK M.R., CEBRAT S. (2001a). The differential killing of genes by inversions in prokaryotic genomes. J. Mol. Evol. 53, in press.
69. MACKIEWICZ P., SZCZEPANIK D., KOWALCZUK M., CEBRAT S. (2001b). Flip-flop around the origin and terminus of replication in prokaryotic genomes. Submitted to Genome Biology.
70. MARIANS K.J. (1992). Prokaryotic DNA replication. Annu. Rev. Biochem. 61: 673-719.
71. MCINERNEY J.O. (1998). Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 95: 10698-10703.
72. MCLEAN M.J., WOLFE K.H., DEVINE K.M. (1998). Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47: 691-696.
73. MELLON I., HANAWALT P.C. (1989). Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature 342: 95-98.
74. MIZRAJI E., NINIO J. (1985). Graphical coding of nucleic acids sequences. Biochimie 67: 445-448.
75. MRAZEK J., KARLIN S. (1998). Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95: 3720-3725.
76. OKAZAKI R., OKAZAKI T., SAKABE K., SUGIMOTO K., SUGINO A. (1968). Mechanism of DNA chain growth. I. Possible discontinuity and unusual secondary structure of newly synthesised chains. Proc. Natl. Acad. Sci. USA 59(2): 598-605.
77. PERRIERE G., LOBRY J.R., THIOULOUSE J. (1996). Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acids sequences. Comput. Appl. Biosci. 12: 519-524.
78. PICARDEAU M., LOBRY J.R., HINNEBUSCH B.J. (1999). Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol. Microbiol. 32: 437-445.
79. PICARDEAU M., LOBRY J.R., HINNEBUSCH B.J. (2000). Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Gen. Res. 10: 1594-1604.
80. QIN M.H., MADIRAJU M.V., RAJAGOPALAN M. (1999). Characterization of the functional replication origin of Mycobacterium tuberculosis. Gene 233: 121-130.
81. RADMAN M. (1998). DNA replication: one strand may be more equal. Proc. Natl. Acad. Sci. USA 95: 9718-9719.
82. READ T.D., BRUNHAM R.C., SHEN C., GILL S.R., HEIDELBERG J.F., WHITE O., HICKEY E.K., PETERSON J., UTTERBACK T., BERRY K. et al. (2000). Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28: 1397-1406.
83. REYES A., GISSI C., PESOLE G., SACCONE C. (1998). Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 15: 957-966.
84. ROBERTS J.D., IZUTA S., THOMAS D.C., KUNKEL T.A. (1994). Mispair-, site-, and strand-specific error rates during simian virus 40 origin-dependent replication in vitro with excess deoxythymidine triphosphate. J. Biol. Chem. 269: 1711-1717.
85. ROCHA E.P.C., DANCHIN A., VIARI A. (1999a). Universal replication biases in bacteria. Mol. Microbiol. 32: 11-16.
86. ROCHA E.P.C., DANCHIN A., VIARI A. (1999b). Bacterial DNA strand compositional asymmetry: Response. Trends Microbiol. 7: 308.
87. ROCHA E.P.C., VIARI A., DANCHIN A. (1998). Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res. 26: 2971-2980.
88. ROMERO H., ZAVALA A., MUSTO H. (2000). Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucl. Acids Res. 28: 2084-2090.
89. SALZBERG S.L., SALZBERG A.J., KERLAVAGE A.R. TOMB J-F. (1998). Skewed oligomers and origins of replication. Gene 217: 57-67.
90. SHARP P.M., COWE E. (1991). Synonymous codon usage in Saccharomyces cerevisiae. Yeast 7: 657-678.
91. SHARP P.M., LI W.-H. (1987). The codon adaptation index: a measure of directional synonymous codon usage bias and its potential applications. Nucleic Acids Res. 15: 1281-1295.
92. SHEPHERD J.C. (1981). Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl. Acad. Sci. USA 78: 1596-1600.
93. g fetal globin gene region. Cell 26: 345-353.
94. SUYAMA M., BORK P. (2001). Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17, 10-13.
95. SZCZEPANIK D., MACKIEWICZ P., KOWALCZUK M., GIERLIK A., NOWICKA A., DUDEK MR., CEBRAT S. (2001). Evolution rates of genes on leading and lagging DNA strands. J. Mol. Evol. 52, 426-433.
96. TAMURA K. (1992). The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol. Biol. Evol. 9: 814-825.
97. TANAKA M., OZAWA T. (1994). Strand asymmetry in human mitochondrial DNA mutations. Genomics 22: 327-335.
98. THOMAS D.C., SVOBODA D.L., VOS J.M., KUNKEL T.A. (1996). Strand specificity of mutagenic bypass replication of DNA containing psoralen monoadducts in a human cell extract. Mol. Cell. Biol. 16: 2537-2544.
99. TILLIER E.R.M., COLLINS R.A. (2000a). The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J. Mol. Evol. 50: 249-257.
100. TILLIER E.R.M., COLLINS R.A. (2000b). Genome rearrangement by replication-directed translocation. Nat. Genet. 26: 195-197.
101. TILLIER E.R.M., COLLINS R.A. (2000c). Replication orientation affects the rate and direction of bacterial gene evolution. J. Mol. Evol. 51: 459-463.
102. TRIFONOV E.N. (1987). Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J. Mol. Biol. 194: 643-652.
103. TRIFONOV E.N. (1992). Recognition of correct reading frame by the ribosome. Biochimie 74: 357-362.
104. TRINH T.Q., SINDEN R.R. (1991). Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352: 544-547.
105. VEAUTE X., FUCHS R.P.P. (1993). Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand. Science 261: 598-600.
106. WANG J. (1998). The base contents of A, C, G, or U for three codon positions and the total coding sequences show positive correlation. J. Biomol. Struct. Dyn. 16: 51-57.
107. WATSON J.D., CRICK F.C.H. (1953). A structure for deoxyribose nucleic acid. Nature 171: 737-738.
108. WONG J.T., CEDERGREN R. (1986). Natural selection versus primitive gene structure as determinant of codon usage. Eur. J. Biochem. 159: 175-180.
109. YANG Z. (1994). Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39: 105-111.
110. YUZHAKOV A., TURNER J., O'DONNEL M. (1996). Replisome assembly reveals the basis for asymmetric function in leading and lagging strand replication. Cell 86: 877-886.
111. ZAWILAK A., CEBRAT S., MACKIEWICZ P., KRÓL-HULEWICZ A., JAKIMOWICZ D., MESSER W., GOSCINAK G., ZAKRZEWSKA-CZERWINSKA J. (2001). Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA. Nucleic Acids Res. 29: 2251-2259.
112. ZHANG J. (1999). Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16: 868-875.
113. ZHANG C.T., ZHANG R. (1991). Analysis of distribution of bases in codon in the coding sequences by a diagrammatic technique. Nucleic Acids Res. 19: 6313-6317.