| [1] Kornberg A, Baker TA. DNA Replication. 2nd ed. New York: WH Freeman and Company, 1992.[2] Rocha EPC. The replication-related organization of bacterial genomes. Microbiology, 2004, 150(6): 1609-1627.[3] Rocha EPC. The organization of the bacterial genome. Annu Rev Genet, 2008, 42: 211-233.[4] Arakawa K, Suzuki H, Tomita M. Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC Genomics, 2009, 10: 640.[5] Lind PA, Andersson DI. Whole-genome mutational biases in bacteria. Proc Natl Acad Sci USA, 2008, 105(46): 17878-17883.[6] Frank AC, Lobry JR. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 1999, 238(1): 65-77.[7] Mrázek J, Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA, 1998, 95(7): 3720-3725.[8] Lobry JR. Origin of replication of Mycoplasma genitalium. Science, 1996, 272(5262): 745-746.[9] Watson JD, Crick FCH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 1953, 171(4356): 737-738.[10] Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia, 1950, 6(6): 201-209.[11] Lin HJ, Chargaff E. On the denaturation of deoxyribonu-cleic acid: II. Effects of concentration. Biochim Bio-phys Acta, 1967, 145(2): 398-409.[12] Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK. A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule). DNA Res, 2009, 16(6): 325-343.[13] Wu CI, Maeda N. Inequality in mutation-rates of the two strands of DNA. Nature, 1987, 327(6118): 169-170.[14] Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura KI, Watanabe K. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J Mol Evol, 1991, 32(6): 511-520.[15] Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol, 1996, 13(5): 660-665.[16] Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Danchin A. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 1997, 390(6657): 249-256.[17] Necsulea A, Lobry JR. A new method for assessing the effect of replication on DNA base composition asymmetry. Mol Biol Evol, 2007, 24(10): 2169-2179.[18] Niu DK, Lin K, Zhang DY. Strand compositional asym-metries of nuclear DNA in eukaryotes. J Mol Evol, 2003, 57(3): 325-334.[19] Mugal CF, von Grünberg HH, Peifer M. Transcription-induced mutational strand bias and its effect on sub-stitution rates in human genes. Mol Biol Evol, 2009, 26(1): 131-142.[20] Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol, 2002, 3(10): RESEARCH0058.[21] Wei W, Guo FB. Strong strand composition bias in the genome of Ehrlichia canis revealed by multiple methods. Open Microbiol J, 2010, 4: 98-102.[22] Tillier ERM, Collins RA. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol, 2000, 50(3): 249-257.[23] Francino MP, Ochman H. Strand asymmetries in DNA evolution. Trends Genet, 1997, 13(6): 240-245.[24] Francino MP, Chao L, Riley MA, Ochman H. Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science, 1996, 272(5258): 107-109.[25] Nikolaou C, Almirantis Y. A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species. Nucleic Acids Res, 2005, 33(21): 6816-6822.[26] Beletskii A, Bhagwat AS. Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci USA, 1996, 93(24): 13919-13924.[27] Zhang R, Zhang CT. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun, 2003, 302(4): 728-734.[28] Berquist BR, DasSarma S. An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol, 2003, 185(20): 5959-5966.[29] Gao F, Zhang CT. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics, 2007, 23(14): 1866-867.[30] Hu J, Zhao X, Yu J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics, 2007, 90(2): 186-194.[31] Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J. Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Res Microbiol, 2010, 161(10): 838-846.[32] Wang HF, Hou WR, Niu DK. Strand compositional asymmetries in vertebrate large genes. Mol Biol Rep, 2008, 35(2): 163-169.[33] Hou WR, Wang HF, Niu DK. Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin, and termination. Biochem Biophys Res Commun, 2006, 344(4): 1258-1262.[34] Song JZ, Ware A, Liu SL. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics, 2003, 4(1): 17.[35] Liu SL, Sanderson KE. Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci USA, 1995, 92(4): 1018-1022.[36] Liu SL, Sanderson KE. Highly plastic chromosomal organization in Salmonella typhi. Proc Natl Acad Sci USA, 1996, 93(19): 10303-10308.[37] 郑鑫, 刘树林. 支原体基因组中ori和ter位点的松弛平衡. 中国科学C辑 (生命科学), 2007, 37(6): 677-682.[38] Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol, 1991, 222(4): 851-856.[39] Mcinerney JO. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA, 1998, 95(18): 10698-10703.[40] Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. Proteome composition and codon usage in spi-rochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res, 1999, 27(7): 1642-1649.[41] Romero H, Zavala A, Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res, 2000, 28(10): 2084-2090.[42] Rispe C, Delmotte F, van Ham RCHJ, Moya A. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res, 2004, 14(1): 44-53.[43] Banerjee T, Basak S, Gupta SK, Ghosh, TC. Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus. J Biomol Struct Dyn, 2004, 22(1): 13-23.[44] Das S, Paul S, Chatterjee S, Dutta C. Codon and amino acid usage in two major human pathogens of genus Bartonella-optimization between replicational-transcriptional selection, translational control and cost minimization. DNA Res, 2005, 12(2): 91-102.[45] Das S, Paul S, Dutta C. Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei. J Mol Evol, 2006, 62(5): 645-658.[46] Guo FB, Yu XJ. Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method. BMC Genomics, 2007, 8: 366.[47] Guo FB, Yuan JB. Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis. DNA Res, 2009, 16(2): 91-104.[48] Rocha EPC, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet, 2002, 18(6): 291-294.[49] Moran NA. Microbial minimalism: genome reduction in bacterial pathogens. Cell, 2002, 108(5): 583-586.[50] Wernegreen JJ. Genome evolution in bacterial endosym-bionts of insects. Nat Rev Genet, 2002, 3(11): 850-861.[51] Guo FB, Lin H, Huang J. A plot of G + C content against sequence length of 640 bacterial chromosomes shows the points are widely scattered in the upper triangular area. Chromosome Res, 2009, 17(3): 359-364.[52] Tamas I, Klasson L, Canbäck B, Näslund AK, Eriksson AS, Wernegreen JJ, Sandström JP, Moran NA, Andersson SGE. 50 million years of genomic stasis in endosymbiotic bacteria. Science, 2002, 296(5577): 2376-2379.[53] Klasson L, Andersson SGE. Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. Mol Biol Evol, 2006, 23(5): 1031-1039.[54] Masai H, Arai KI. Operon structure of dnaT and dnaC genes essential for normal and stable DNA replication of Escherichia coli chromosome. J Biol Chem, 1988, 263(29): 15083-15093.[55] Filutowicz M, Ross W, Wild J, Gourse RL. Involvement of Fis protein in replication of the Escherichia coli chromosome. J Bacteriol, 1992, 174(2): 398-407.[56] Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res, 1998, 26(10): 2286-2290. |
