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Volumn 10, Issue 4, 2012, Pages 186-196

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition

Author keywords

GC content; Horizontal gene transfer; Purine asymmetry; Strand biased gene distribution; Strand biased nucleotide composition

Indexed keywords

ISOPROTEIN; NUCLEOTIDE; PROTEIN DNAE; PURINE; UNCLASSIFIED DRUG;

EID: 84867710959     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2012.08.001     Document Type: Article
Times cited : (12)

References (47)
  • 1
    • 84867720119 scopus 로고    scopus 로고
    • Genes IX. 9th ed. Sudbury, Mass, USA: Jones and Bartlett Publishers
    • Lewin B. Genes IX. 9th ed. Sudbury, Mass, USA: Jones and Bartlett Publishers; 2008.
    • (2008)
    • Lewin, B.1
  • 2
    • 34447108347 scopus 로고    scopus 로고
    • Replication-associated purine asymmetry may contribute to strand-biased gene distribution
    • Hu J., Zhao X., Yu J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics 2007, 90:186-194.
    • (2007) Genomics , vol.90 , pp. 186-194
    • Hu, J.1    Zhao, X.2    Yu, J.3
  • 3
    • 78649947901 scopus 로고    scopus 로고
    • Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes
    • 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, 161:838-846.
    • (2010) Res Microbiol , vol.161 , pp. 838-846
    • Qu, H.1    Wu, H.2    Zhang, T.3    Zhang, Z.4    Hu, S.5    Yu, J.6
  • 4
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • Rocha E.P. The organization of the bacterial genome. Annu Rev Genet 2008, 42:211-233.
    • (2008) Annu Rev Genet , vol.42 , pp. 211-233
    • Rocha, E.P.1
  • 5
    • 0026419949 scopus 로고
    • Secondary structure mutagenesis in the lagging strand of replication in E. coli
    • Trinh T.Q., Sinden R.R. Secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 1991, 352:544-547.
    • (1991) Nature , vol.352 , pp. 544-547
    • Trinh, T.Q.1    Sinden, R.R.2
  • 6
    • 0027218812 scopus 로고
    • Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand
    • Veaute X., Fuchs R.P. Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand. Science 1993, 261:598-600.
    • (1993) Science , vol.261 , pp. 598-600
    • Veaute, X.1    Fuchs, R.P.2
  • 7
    • 84856439179 scopus 로고    scopus 로고
    • A Blueprint for a Mutationist Theory of Replicative Strand Asymmetries Formation
    • V. Khrustalev V, V. Barkovsky E. A Blueprint for a Mutationist Theory of Replicative Strand Asymmetries Formation. Current Genomics 2012; 13: 55-64.
    • (2012) Current Genomics , vol.13 , pp. 55-64
    • Khrustalev, V.1    Barkovsky, E.2
  • 8
    • 0023925456 scopus 로고
    • DNA polymerase III holoenzyme of Escherichia coli
    • McHenry C.S. DNA polymerase III holoenzyme of Escherichia coli. Annu Rev Biochem 1988, 57:519-550.
    • (1988) Annu Rev Biochem , vol.57 , pp. 519-550
    • McHenry, C.S.1
  • 9
    • 0029913902 scopus 로고    scopus 로고
    • Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes
    • Koonin E.V., Bork P. Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes. Trends Biochem Sci 1996, 21:128-129.
    • (1996) Trends Biochem Sci , vol.21 , pp. 128-129
    • Koonin, E.V.1    Bork, P.2
  • 10
    • 0035941008 scopus 로고    scopus 로고
    • Two essential DNA polymerases at the bacterial replication fork
    • Dervyn E., Suski C., Daniel R., Bruand C., Chapuis J., Errington J., et al. Two essential DNA polymerases at the bacterial replication fork. Science 2001, 294:1716-1719.
    • (2001) Science , vol.294 , pp. 1716-1719
    • Dervyn, E.1    Suski, C.2    Daniel, R.3    Bruand, C.4    Chapuis, J.5    Errington, J.6
  • 11
    • 33947177875 scopus 로고    scopus 로고
    • Comparative analysis of eubacterial DNA polymerase III alpha subunits
    • Zhao X., Hu J., Yu J. Comparative analysis of eubacterial DNA polymerase III alpha subunits. Genomics Proteomics Bioinformatics 2006, 4:203-211.
    • (2006) Genomics Proteomics Bioinformatics , vol.4 , pp. 203-211
    • Zhao, X.1    Hu, J.2    Yu, J.3
  • 12
    • 84855498305 scopus 로고    scopus 로고
    • On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes
    • Wu H., Zhang Z., Hu S., Yu J. On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes. Biology Direct 2012, 7:2.
    • (2012) Biology Direct , vol.7 , pp. 2
    • Wu, H.1    Zhang, Z.2    Hu, S.3    Yu, J.4
  • 13
    • 34249341112 scopus 로고    scopus 로고
    • Compositional dynamics of guanine and cytosine content in prokaryotic genomes
    • Hu J., Zhao X., Zhang Z., Yu J. Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Res Microbiol 2007, 158:363-370.
    • (2007) Res Microbiol , vol.158 , pp. 363-370
    • Hu, J.1    Zhao, X.2    Zhang, Z.3    Yu, J.4
  • 14
    • 33947138128 scopus 로고    scopus 로고
    • GC content variability of eubacteria is governed by the pol III alpha subunit
    • Zhao X., Zhang Z., Yan J., Yu J. GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem Biophys Res Commun 2007, 356:20-25.
    • (2007) Biochem Biophys Res Commun , vol.356 , pp. 20-25
    • Zhao, X.1    Zhang, Z.2    Yan, J.3    Yu, J.4
  • 15
    • 8844263096 scopus 로고    scopus 로고
    • Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
    • Omont N., Kepes F. Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication. Bioinformatics 2004, 20:2719-2725.
    • (2004) Bioinformatics , vol.20 , pp. 2719-2725
    • Omont, N.1    Kepes, F.2
  • 16
    • 12844265439 scopus 로고    scopus 로고
    • Mechanisms of transcription-replication collisions in bacteria
    • Mirkin E.V., Mirkin S.M. Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol 2005, 25:888-895.
    • (2005) Mol Cell Biol , vol.25 , pp. 888-895
    • Mirkin, E.V.1    Mirkin, S.M.2
  • 17
    • 34248394295 scopus 로고    scopus 로고
    • Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis
    • Wang J.D., Berkmen M.B., Grossman A.D. Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis. Proc Natl Acad Sci U S A 2007, 104:5608-5613.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 5608-5613
    • Wang, J.D.1    Berkmen, M.B.2    Grossman, A.D.3
  • 18
    • 0024276903 scopus 로고
    • When polymerases collide: replication and the transcriptional organization of the E. coli chromosome
    • Brewer B.J. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 1988, 53:679-686.
    • (1988) Cell , vol.53 , pp. 679-686
    • Brewer, B.J.1
  • 19
    • 0032417093 scopus 로고    scopus 로고
    • Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
    • McLean M.J., Wolfe K.H., Devine K.M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 1998, 47:691-696.
    • (1998) J Mol Evol , vol.47 , pp. 691-696
    • McLean, M.J.1    Wolfe, K.H.2    Devine, K.M.3
  • 20
    • 20444485193 scopus 로고    scopus 로고
    • Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication
    • Price M.N., Alm E.J., Arkin A.P. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res 2005, 33:3224-3234.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3224-3234
    • Price, M.N.1    Alm, E.J.2    Arkin, A.P.3
  • 21
    • 0042667165 scopus 로고    scopus 로고
    • Essentiality, not expressiveness, drives gene-strand bias in bacteria
    • Rocha E.P., Danchin A. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 2003, 34:377-378.
    • (2003) Nat Genet , vol.34 , pp. 377-378
    • Rocha, E.P.1    Danchin, A.2
  • 22
    • 0344668838 scopus 로고    scopus 로고
    • Gene essentiality determines chromosome organisation in bacteria
    • Rocha E.P., Danchin A. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res 2003, 31:6570-6577.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6570-6577
    • Rocha, E.P.1    Danchin, A.2
  • 23
    • 0036709941 scopus 로고    scopus 로고
    • Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?
    • Rocha E. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?. Trends Microbiol 2002, 10:393-395.
    • (2002) Trends Microbiol , vol.10 , pp. 393-395
    • Rocha, E.1
  • 25
    • 34347244597 scopus 로고    scopus 로고
    • Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola
    • Vinuelas J., Calevro F., Remond D., Bernillon J., Rahbe Y., Febvay G., et al. Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola. BMC Genomics 2007, 8:143.
    • (2007) BMC Genomics , vol.8 , pp. 143
    • Vinuelas, J.1    Calevro, F.2    Remond, D.3    Bernillon, J.4    Rahbe, Y.5    Febvay, G.6
  • 26
    • 0037040394 scopus 로고    scopus 로고
    • Microbial minimalism: genome reduction in bacterial pathogens
    • Moran N.A. Microbial minimalism: genome reduction in bacterial pathogens. Cell 2002, 108:583-586.
    • (2002) Cell , vol.108 , pp. 583-586
    • Moran, N.A.1
  • 27
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 28
    • 57149085868 scopus 로고    scopus 로고
    • Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
    • Koonin E.V., Wolf Y.I. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008, 36:6688-6719.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6688-6719
    • Koonin, E.V.1    Wolf, Y.I.2
  • 29
    • 0038486918 scopus 로고    scopus 로고
    • The balance of driving forces during genome evolution in prokaryotes
    • Kunin V., Ouzounis C.A. The balance of driving forces during genome evolution in prokaryotes. Genome Res 2003, 13:1589-1594.
    • (2003) Genome Res , vol.13 , pp. 1589-1594
    • Kunin, V.1    Ouzounis, C.A.2
  • 30
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • Jordan I.K., Rogozin I.B., Wolf Y.I., Koonin E.V. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12:962-968.
    • (2002) Genome Res , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 31
    • 0033776631 scopus 로고    scopus 로고
    • Genome rearrangement by replication-directed translocation
    • Tillier E.R., Collins R.A. Genome rearrangement by replication-directed translocation. Nat Genet 2000, 26:195-197.
    • (2000) Nat Genet , vol.26 , pp. 195-197
    • Tillier, E.R.1    Collins, R.A.2
  • 35
    • 77952744822 scopus 로고    scopus 로고
    • Functionality of essential genes drives gene strand-bias in bacterial genomes
    • Lin Y., Gao F., Zhang C.T. Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem Biophys Res Commun 2010, 396:472-476.
    • (2010) Biochem Biophys Res Commun , vol.396 , pp. 472-476
    • Lin, Y.1    Gao, F.2    Zhang, C.T.3
  • 36
    • 0029038068 scopus 로고
    • Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome
    • Smith H.O., Tomb J.F., Dougherty B.A., Fleischmann R.D., Venter J.C. Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 1995, 269:538-540.
    • (1995) Science , vol.269 , pp. 538-540
    • Smith, H.O.1    Tomb, J.F.2    Dougherty, B.A.3    Fleischmann, R.D.4    Venter, J.C.5
  • 37
    • 0037133327 scopus 로고    scopus 로고
    • Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination
    • de Vries J., Wackernagel W. Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc Natl Acad Sci U S A 2002, 99:2094-2099.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 2094-2099
    • de Vries, J.1    Wackernagel, W.2
  • 39
    • 0037250391 scopus 로고    scopus 로고
    • HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
    • Garcia-Vallve S., Guzman E., Montero M.A., Romeu A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 2003, 31:187-189.
    • (2003) Nucleic Acids Res , vol.31 , pp. 187-189
    • Garcia-Vallve, S.1    Guzman, E.2    Montero, M.A.3    Romeu, A.4
  • 40
    • 70350147283 scopus 로고    scopus 로고
    • Does gene translocation accelerate the evolution of laterally transferred genes?
    • Hao W., Golding G.B. Does gene translocation accelerate the evolution of laterally transferred genes?. Genetics 2009, 182:1365-1375.
    • (2009) Genetics , vol.182 , pp. 1365-1375
    • Hao, W.1    Golding, G.B.2
  • 41
    • 33750950259 scopus 로고    scopus 로고
    • Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans
    • Wang Y., Orvis J., Dyer D., Chen C. Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans. Microbiology 2006, 152:3319-3325.
    • (2006) Microbiology , vol.152 , pp. 3319-3325
    • Wang, Y.1    Orvis, J.2    Dyer, D.3    Chen, C.4
  • 42
    • 45549105909 scopus 로고    scopus 로고
    • The impact of the neisserial DNA uptake sequences on genome evolution and stability
    • Treangen T.J., Ambur O.H., Tonjum T., Rocha E.P. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 2008, 9:R60.
    • (2008) Genome Biol , vol.9
    • Treangen, T.J.1    Ambur, O.H.2    Tonjum, T.3    Rocha, E.P.4
  • 43
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13:660-665.
    • (1996) Mol Biol Evol , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 44
    • 34547912489 scopus 로고    scopus 로고
    • DoriC: a database of oriC regions in bacterial genomes
    • Gao F., Zhang C.T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 2007, 23:1866-1867.
    • (2007) Bioinformatics , vol.23 , pp. 1866-1867
    • Gao, F.1    Zhang, C.T.2
  • 45
    • 0037444091 scopus 로고    scopus 로고
    • ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes
    • Guo F.B., Ou H.Y., Zhang C.T. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res 2003, 31:1780-1789.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1780-1789
    • Guo, F.B.1    Ou, H.Y.2    Zhang, C.T.3


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