Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition
Tài liệu tham khảo
Lewin B. Genes IX. 9th ed. Sudbury, Mass, USA: Jones and Bartlett Publishers; 2008.
Hu, 2007, Replication-associated purine asymmetry may contribute to strand-biased gene distribution, Genomics, 90, 186, 10.1016/j.ygeno.2007.04.002
Qu, 2010, Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes, Res Microbiol, 161, 838, 10.1016/j.resmic.2010.09.015
Rocha, 2008, The organization of the bacterial genome, Annu Rev Genet, 42, 211, 10.1146/annurev.genet.42.110807.091653
Trinh, 1991, Secondary structure mutagenesis in the lagging strand of replication in E. coli, Nature, 352, 544, 10.1038/352544a0
Veaute, 1993, Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand, Science, 261, 598, 10.1126/science.8342022
V. Khrustalev V, V. Barkovsky E. A Blueprint for a Mutationist Theory of Replicative Strand Asymmetries Formation. Current Genomics 2012; 13: 55–64.
McHenry, 1988, DNA polymerase III holoenzyme of Escherichia coli, Annu Rev Biochem, 57, 519, 10.1146/annurev.bi.57.070188.002511
Koonin, 1996, Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes, Trends Biochem Sci, 21, 128, 10.1016/S0968-0004(96)80165-4
Dervyn, 2001, Two essential DNA polymerases at the bacterial replication fork, Science, 294, 1716, 10.1126/science.1066351
Zhao, 2006, Comparative analysis of eubacterial DNA polymerase III alpha subunits, Genomics Proteomics Bioinformatics, 4, 203, 10.1016/S1672-0229(07)60001-1
Wu, 2012, On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes, Biology Direct, 7, 2, 10.1186/1745-6150-7-2
Hu, 2007, Compositional dynamics of guanine and cytosine content in prokaryotic genomes, Res Microbiol, 158, 363, 10.1016/j.resmic.2007.02.007
Zhao, 2007, GC content variability of eubacteria is governed by the pol III alpha subunit, Biochem Biophys Res Commun, 356, 20, 10.1016/j.bbrc.2007.02.109
Omont, 2004, Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication, Bioinformatics, 20, 2719, 10.1093/bioinformatics/bth317
Mirkin, 2005, Mechanisms of transcription-replication collisions in bacteria, Mol Cell Biol, 25, 888, 10.1128/MCB.25.3.888-895.2005
Wang, 2007, Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis, Proc Natl Acad Sci U S A, 104, 5608, 10.1073/pnas.0608999104
Brewer, 1988, When polymerases collide: replication and the transcriptional organization of the E. coli chromosome, Cell, 53, 679, 10.1016/0092-8674(88)90086-4
McLean, 1998, Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes, J Mol Evol, 47, 691, 10.1007/PL00006428
Price, 2005, Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication, Nucleic Acids Res, 33, 3224, 10.1093/nar/gki638
Rocha, 2003, Essentiality, not expressiveness, drives gene-strand bias in bacteria, Nat Genet, 34, 377, 10.1038/ng1209
Rocha, 2003, Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res, 31, 6570, 10.1093/nar/gkg859
Rocha, 2002, Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?, Trends Microbiol, 10, 393, 10.1016/S0966-842X(02)02420-4
Zhang, 2004, DEG: a database of essential genes, Nucleic Acids Res, 32, D271, 10.1093/nar/gkh024
Vinuelas, 2007, Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola, BMC Genomics, 8, 143, 10.1186/1471-2164-8-143
Moran, 2002, Microbial minimalism: genome reduction in bacterial pathogens, Cell, 108, 583, 10.1016/S0092-8674(02)00665-7
Ochman, 2000, Lateral gene transfer and the nature of bacterial innovation, Nature, 405, 299, 10.1038/35012500
Koonin, 2008, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Res, 36, 6688, 10.1093/nar/gkn668
Kunin, 2003, The balance of driving forces during genome evolution in prokaryotes, Genome Res, 13, 1589, 10.1101/gr.1092603
Jordan, 2002, Essential genes are more evolutionarily conserved than are nonessential genes in bacteria, Genome Res, 12, 962, 10.1101/gr.87702. Article published online before print in May 2002
Tillier, 2000, Genome rearrangement by replication-directed translocation, Nat Genet, 26, 195, 10.1038/79918
Tamas, 2002, 50 million years of genomic stasis in endosymbiotic bacteria, Science, 296, 2376, 10.1126/science.1071278
Moran, 1993, A Molecular Clock in Endosymbiotic Bacteria is Calibrated Using the Insect Hosts, Proceedings of the Royal Society of London Series B: Biological Sciences, 253, 167, 10.1098/rspb.1993.0098
van Ham, 2003, Reductive genome evolution in Buchnera aphidicola, Proc Natl Acad Sci U S A, 100, 581, 10.1073/pnas.0235981100
Lin, 2010, Functionality of essential genes drives gene strand-bias in bacterial genomes, Biochem Biophys Res Commun, 396, 472, 10.1016/j.bbrc.2010.04.119
Smith, 1995, Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome, Science, 269, 538, 10.1126/science.7542802
de Vries, 2002, Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination, Proc Natl Acad Sci U S A, 99, 2094, 10.1073/pnas.042263399
Davidsen, 2004, Biased distribution of DNA uptake sequences towards genome maintenance genes, Nucleic Acids Res, 32, 1050, 10.1093/nar/gkh255
Garcia-Vallve, 2003, HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes, Nucleic Acids Res, 31, 187, 10.1093/nar/gkg004
Hao, 2009, Does gene translocation accelerate the evolution of laterally transferred genes?, Genetics, 182, 1365, 10.1534/genetics.109.104216
Wang, 2006, Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans, Microbiology, 152, 3319, 10.1099/mic.0.29018-0
Treangen, 2008, The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biol, 9, R60, 10.1186/gb-2008-9-3-r60
Lobry, 1996, Asymmetric substitution patterns in the two DNA strands of bacteria, Mol Biol Evol, 13, 660, 10.1093/oxfordjournals.molbev.a025626
Gao, 2007, DoriC: a database of oriC regions in bacterial genomes, Bioinformatics, 23, 1866, 10.1093/bioinformatics/btm255
Guo, 2003, ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes, Nucleic Acids Res, 31, 1780, 10.1093/nar/gkg254
Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, 25, 3389, 10.1093/nar/25.17.3389
Ogata, 1999, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res, 27, 29, 10.1093/nar/27.1.29