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Volumn 11, Issue 1, 2010, Pages

Relationship between operon preference and functional properties of persistent genes in bacterial genomes

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME PROTEIN;

EID: 77649282211     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-71     Document Type: Article
Times cited : (24)

References (85)
  • 1
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • 10.1146/annurev.genet.42.110807.091653, 18605898
    • Rocha EP. The organization of the bacterial genome. Annu Rev Genet 2008, 42:211-233. 10.1146/annurev.genet.42.110807.091653, 18605898.
    • (2008) Annu Rev Genet , vol.42 , pp. 211-233
    • Rocha, E.P.1
  • 2
    • 33745712583 scopus 로고    scopus 로고
    • The life-cycle of operons
    • 10.1371/journal.pgen.0020096, 1480536,1480536, 16789824
    • Price MN, Arkin AP, Alm EJ. The life-cycle of operons. PLoS Genet 2006, 2(6):e96. 10.1371/journal.pgen.0020096, 1480536,1480536, 16789824.
    • (2006) PLoS Genet , vol.2 , Issue.6
    • Price, M.N.1    Arkin, A.P.2    Alm, E.J.3
  • 3
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • 10.1016/S0022-2836(61)80072-7, 13718526
    • Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961, 3:318-356. 10.1016/S0022-2836(61)80072-7, 13718526.
    • (1961) J Mol Biol , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 4
    • 0242440314 scopus 로고    scopus 로고
    • Gene organization: selection, selfishness, and serendipity
    • 10.1146/annurev.micro.57.030502.090816, 14527286
    • Lawrence JG. Gene organization: selection, selfishness, and serendipity. Annu Rev Microbiol 2003, 57:419-440. 10.1146/annurev.micro.57.030502.090816, 14527286.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 419-440
    • Lawrence, J.G.1
  • 5
    • 0029847554 scopus 로고    scopus 로고
    • Selfish operons: horizontal transfer may drive the evolution of gene clusters
    • 1207444, 8844169
    • Lawrence JG, Roth JR. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143(4):1843-1860. 1207444, 8844169.
    • (1996) Genetics , vol.143 , Issue.4 , pp. 1843-1860
    • Lawrence, J.G.1    Roth, J.R.2
  • 6
    • 22444441190 scopus 로고    scopus 로고
    • Operon formation is driven by co-regulation and not by horizontal gene transfer
    • 10.1101/gr.3368805, 1142471, 15930492
    • Price MN, Huang KH, Arkin AP, Alm EJ. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 2005, 15(6):809-819. 10.1101/gr.3368805, 1142471, 15930492.
    • (2005) Genome Res , vol.15 , Issue.6 , pp. 809-819
    • Price, M.N.1    Huang, K.H.2    Arkin, A.P.3    Alm, E.J.4
  • 7
    • 8544264562 scopus 로고    scopus 로고
    • Efficient attenuation of stochasticity in gene expression through post-transcriptional control
    • 10.1016/j.jmb.2004.09.073, 15544806
    • Swain PS. Efficient attenuation of stochasticity in gene expression through post-transcriptional control. J Mol Biol 2004, 344(4):965-976. 10.1016/j.jmb.2004.09.073, 15544806.
    • (2004) J Mol Biol , vol.344 , Issue.4 , pp. 965-976
    • Swain, P.S.1
  • 8
    • 17144459133 scopus 로고    scopus 로고
    • Evidence against the selfish operon theory
    • 10.1016/j.tig.2004.04.001, 15145575
    • Pal C, Hurst LD. Evidence against the selfish operon theory. Trends Genet 2004, 20(6):232-234. 10.1016/j.tig.2004.04.001, 15145575.
    • (2004) Trends Genet , vol.20 , Issue.6 , pp. 232-234
    • Pal, C.1    Hurst, L.D.2
  • 9
    • 50049106504 scopus 로고    scopus 로고
    • The relative value of operon predictions
    • 10.1093/bib/bbn019, 18420711
    • Brouwer RW, Kuipers OP, van Hijum SA. The relative value of operon predictions. Brief Bioinform 2008, 9(5):367-375. 10.1093/bib/bbn019, 18420711.
    • (2008) Brief Bioinform , vol.9 , Issue.5 , pp. 367-375
    • Brouwer, R.W.1    Kuipers, O.P.2    van Hijum, S.A.3
  • 10
    • 9144230986 scopus 로고    scopus 로고
    • Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
    • 10.1093/bib/5.2.131, 15260894
    • Rogozin IB, Makarova KS, Wolf YI, Koonin EV. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform 2004, 5(2):131-149. 10.1093/bib/5.2.131, 15260894.
    • (2004) Brief Bioinform , vol.5 , Issue.2 , pp. 131-149
    • Rogozin, I.B.1    Makarova, K.S.2    Wolf, Y.I.3    Koonin, E.V.4
  • 11
    • 33748569118 scopus 로고    scopus 로고
    • The distinctive signatures of promoter regions and operon junctions across prokaryotes
    • 10.1093/nar/gkl563, 1557821, 16914446
    • Janga SC, Lamboy WF, Huerta AM, Moreno-Hagelsieb G. The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucleic Acids Res 2006, 34(14):3980-3987. 10.1093/nar/gkl563, 1557821, 16914446.
    • (2006) Nucleic Acids Res , vol.34 , Issue.14 , pp. 3980-3987
    • Janga, S.C.1    Lamboy, W.F.2    Huerta, A.M.3    Moreno-Hagelsieb, G.4
  • 12
    • 10944248427 scopus 로고    scopus 로고
    • Computing prokaryotic gene ubiquity: rescuing the core from extinction
    • 10.1101/gr.3024704, 534671, 15574825
    • Charlebois RL, Doolittle WF. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 2004, 14(12):2469-2477. 10.1101/gr.3024704, 534671, 15574825.
    • (2004) Genome Res , vol.14 , Issue.12 , pp. 2469-2477
    • Charlebois, R.L.1    Doolittle, W.F.2
  • 13
    • 4544371669 scopus 로고    scopus 로고
    • Determination of the core of a minimal bacterial gene set
    • 10.1128/MMBR.68.3.518-537.2004, 515251, 15353568
    • Gil R, Silva FJ, Pereto J, Moya A. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 2004, 68(3):518-537. 10.1128/MMBR.68.3.518-537.2004, 515251, 15353568.
    • (2004) Microbiol Mol Biol Rev , vol.68 , Issue.3 , pp. 518-537
    • Gil, R.1    Silva, F.J.2    Pereto, J.3    Moya, A.4
  • 15
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics, minimal gene-sets and the last universal common ancestor
    • 10.1038/nrmicro751, 15035042
    • Koonin EV. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 2003, 1(2):127-136. 10.1038/nrmicro751, 15035042.
    • (2003) Nat Rev Microbiol , vol.1 , Issue.2 , pp. 127-136
    • Koonin, E.V.1
  • 16
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • 10.1146/annurev.genet.39.073003.114725, 16285863
    • Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725, 16285863.
    • (2005) Annu Rev Genet , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 17
    • 8744268628 scopus 로고    scopus 로고
    • Duplicated genes evolve slower than singletons despite the initial rate increase
    • 10.1186/1471-2148-4-22, 481058, 15238160
    • Jordan IK, Wolf YI, Koonin EV. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004, 4:22. 10.1186/1471-2148-4-22, 481058, 15238160.
    • (2004) BMC Evol Biol , vol.4 , pp. 22
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 18
    • 19344363466 scopus 로고    scopus 로고
    • Preferential duplication of conserved proteins in eukaryotic genomes
    • 10.1371/journal.pbio.0020055, 368158, 15024414
    • Davis JC, Petrov DA. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol 2004, 2(3):E55. 10.1371/journal.pbio.0020055, 368158, 15024414.
    • (2004) PLoS Biol , vol.2 , Issue.3
    • Davis, J.C.1    Petrov, D.A.2
  • 20
    • 0029789824 scopus 로고    scopus 로고
    • A minimal gene set for cellular life derived by comparison of complete bacterial genomes
    • 10.1073/pnas.93.19.10268, 38373, 8816789
    • Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 1996, 93(19):10268-10273. 10.1073/pnas.93.19.10268, 38373, 8816789.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.19 , pp. 10268-10273
    • Mushegian, A.R.1    Koonin, E.V.2
  • 21
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 10.1126/science.278.5338.631, 9381173
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278(5338):631-637. 10.1126/science.278.5338.631, 9381173.
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 22
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • 10.1093/nar/30.7.1575, 101833, 11917018
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30(7):1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
    • (2002) Nucleic Acids Res , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 23
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197, 11743721
    • Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197, 11743721.
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 24
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • 10.1101/gr.1224503, 403725, 12952885
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13(9):2178-2189. 10.1101/gr.1224503, 403725, 12952885.
    • (2003) Genome Res , vol.13 , Issue.9 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 25
    • 77949914761 scopus 로고    scopus 로고
    • The database of Cluster of Orthologous Groups of proteins
    • The database of Cluster of Orthologous Groups of proteins. , http://www.ncbi.nlm.nih.gov/COG/
  • 26
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • 10.1371/journal.pone.0000383, 1849888, 17440619
    • Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2007, 2(4):e383. 10.1371/journal.pone.0000383, 1849888, 17440619.
    • (2007) PLoS ONE , vol.2 , Issue.4
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 27
    • 0003880161 scopus 로고    scopus 로고
    • Molecular Biology of the Cell
    • New York and London: Garland Science, Fourth
    • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 2002, New York and London: Garland Science, Fourth.
    • (2002)
    • Alberts, B.1    Johnson, A.2    Lewis, J.3    Raff, M.4    Roberts, K.5    Walter, P.6
  • 28
    • 33750488443 scopus 로고    scopus 로고
    • Towards the identification of essential genes using targeted genome sequencing and comparative analysis
    • 10.1186/1471-2164-7-265, 1624830, 17052348
    • Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 2006, 7:265. 10.1186/1471-2164-7-265, 1624830, 17052348.
    • (2006) BMC Genomics , vol.7 , pp. 265
    • Gustafson, A.M.1    Snitkin, E.S.2    Parker, S.C.3    DeLisi, C.4    Kasif, S.5
  • 29
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • 1461684, 11430355
    • Pal C, Papp B, Hurst LD. Highly expressed genes in yeast evolve slowly. Genetics 2001, 158(2):927-931. 1461684, 11430355.
    • (2001) Genetics , vol.158 , Issue.2 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 30
    • 77949915459 scopus 로고    scopus 로고
    • TIGR
    • TIGR. , http://www.tigr.org/
  • 31
    • 77949918812 scopus 로고    scopus 로고
    • NCBI
    • NCBI. , http://www.ncbi.nlm.nih.gov/
  • 32
    • 4644315656 scopus 로고    scopus 로고
    • Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism
    • 10.1093/nar/gkh830, 519118, 15383646
    • Ueda K, Yamashita A, Ishikawa J, Shimada M, Watsuji TO, Morimura K, Ikeda H, Hattori M, Beppu T. Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res 2004, 32(16):4937-4944. 10.1093/nar/gkh830, 519118, 15383646.
    • (2004) Nucleic Acids Res , vol.32 , Issue.16 , pp. 4937-4944
    • Ueda, K.1    Yamashita, A.2    Ishikawa, J.3    Shimada, M.4    Watsuji, T.O.5    Morimura, K.6    Ikeda, H.7    Hattori, M.8    Beppu, T.9
  • 33
    • 77949915037 scopus 로고    scopus 로고
    • COGnitor
    • COGnitor. , http://www.ncbi.nlm.nih.gov/COG/old/xognitor.html
  • 34
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • 10.1038/nprot.2008.211, 19131956
    • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57. 10.1038/nprot.2008.211, 19131956.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 35
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for Annotation, Visualization, and Integrated Discovery
    • 10.1186/gb-2003-4-5-p3, 12734009
    • Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
    • (2003) Genome Biol , vol.4 , Issue.5
    • Dennis, G.1    Sherman, B.T.2    Hosack, D.A.3    Yang, J.4    Gao, W.5    Lane, H.C.6    Lempicki, R.A.7
  • 36
    • 14644438364 scopus 로고    scopus 로고
    • Circular genome visualization and exploration using CGView
    • 10.1093/bioinformatics/bti054, 15479716
    • Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21(4):537-539. 10.1093/bioinformatics/bti054, 15479716.
    • (2005) Bioinformatics , vol.21 , Issue.4 , pp. 537-539
    • Stothard, P.1    Wishart, D.S.2
  • 37
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 38
    • 0037115872 scopus 로고    scopus 로고
    • Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale
    • 10.1093/nar/gkf693, 140077, 12490706
    • Lecompte O, Ripp R, Thierry JC, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 2002, 30(24):5382-5390. 10.1093/nar/gkf693, 140077, 12490706.
    • (2002) Nucleic Acids Res , vol.30 , Issue.24 , pp. 5382-5390
    • Lecompte, O.1    Ripp, R.2    Thierry, J.C.3    Moras, D.4    Poch, O.5
  • 39
    • 0035229986 scopus 로고    scopus 로고
    • New approaches for reconstructing phylogenies from gene order data
    • Moret BM, Wang LS, Warnow T, Wyman SK. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 2001, 17(Suppl 1):S165-173.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Moret, B.M.1    Wang, L.S.2    Warnow, T.3    Wyman, S.K.4
  • 40
    • 25444461672 scopus 로고    scopus 로고
    • Scoredist: a simple and robust protein sequence distance estimator
    • 10.1186/1471-2105-6-108, 1131889, 15857510
    • Sonnhammer EL, Hollich V. Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics 2005, 6:108. 10.1186/1471-2105-6-108, 1131889, 15857510.
    • (2005) BMC Bioinformatics , vol.6 , pp. 108
    • Sonnhammer, E.L.1    Hollich, V.2
  • 41
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • 10.1126/science.1068696, 11976460
    • Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002, 296(5568):750-752. 10.1126/science.1068696, 11976460.
    • (2002) Science , vol.296 , Issue.5568 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 42
    • 2942624159 scopus 로고    scopus 로고
    • Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets
    • 10.1186/1471-2148-3-21, 270031, 14525624
    • Bloom JD, Adami C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol Biol 2003, 3:21. 10.1186/1471-2148-3-21, 270031, 14525624.
    • (2003) BMC Evol Biol , vol.3 , pp. 21
    • Bloom, J.D.1    Adami, C.2
  • 44
    • 0032919364 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • 10.1093/nar/27.1.29, 148090, 9847135
    • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27(1):29-34. 10.1093/nar/27.1.29, 148090, 9847135.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 29-34
    • Ogata, H.1    Goto, S.2    Sato, K.3    Fujibuchi, W.4    Bono, H.5    Kanehisa, M.6
  • 45
    • 3342977757 scopus 로고    scopus 로고
    • Mycoplasma penetrans is capable of activating V gamma 9/V delta 2 T cells while other human pathogenic mycoplasmas fail to do so
    • 10.1128/IAI.72.8.4881-4883.2004, 470652, 15271953
    • Eberl M, Hintz M, Jamba Z, Beck E, Jomaa H, Christiansen G. Mycoplasma penetrans is capable of activating V gamma 9/V delta 2 T cells while other human pathogenic mycoplasmas fail to do so. Infect Immun 2004, 72(8):4881-4883. 10.1128/IAI.72.8.4881-4883.2004, 470652, 15271953.
    • (2004) Infect Immun , vol.72 , Issue.8 , pp. 4881-4883
    • Eberl, M.1    Hintz, M.2    Jamba, Z.3    Beck, E.4    Jomaa, H.5    Christiansen, G.6
  • 46
    • 0030249023 scopus 로고    scopus 로고
    • Non-orthologous gene displacement
    • 10.1016/0168-9525(96)20010-1, 8855656
    • Koonin EV, Mushegian AR, Bork P. Non-orthologous gene displacement. Trends Genet 1996, 12(9):334-336. 10.1016/0168-9525(96)20010-1, 8855656.
    • (1996) Trends Genet , vol.12 , Issue.9 , pp. 334-336
    • Koonin, E.V.1    Mushegian, A.R.2    Bork, P.3
  • 47
    • 13144259695 scopus 로고    scopus 로고
    • Relative rates of gene fusion and fission in multi-domain proteins
    • 10.1016/j.tig.2004.11.007, 15680510
    • Kummerfeld SK, Teichmann SA. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet 2005, 21(1):25-30. 10.1016/j.tig.2004.11.007, 15680510.
    • (2005) Trends Genet , vol.21 , Issue.1 , pp. 25-30
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 48
    • 11144283225 scopus 로고    scopus 로고
    • Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes
    • 10.1016/j.femsle.2004.10.050, 15621428
    • Coenye T, Vandamme P. Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes. FEMS Microbiol Lett 2005, 242(1):117-126. 10.1016/j.femsle.2004.10.050, 15621428.
    • (2005) FEMS Microbiol Lett , vol.242 , Issue.1 , pp. 117-126
    • Coenye, T.1    Vandamme, P.2
  • 49
    • 0035225012 scopus 로고    scopus 로고
    • Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    • 10.1186/gb-2001-2-9-research0033, 11574053
    • Makarova KS, Ponomarev VA, Koonin EV. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol 2001, 2(9):RESEARCH 0033. 10.1186/gb-2001-2-9-research0033, 11574053.
    • (2001) Genome Biol , vol.2 , Issue.9
    • Makarova, K.S.1    Ponomarev, V.A.2    Koonin, E.V.3
  • 50
    • 0024468299 scopus 로고
    • A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA
    • 10.1021/bi00446a002, 2690930
    • Lin JJ, Sancar A. A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA. Biochemistry 1989, 28(20):7979-7984. 10.1021/bi00446a002, 2690930.
    • (1989) Biochemistry , vol.28 , Issue.20 , pp. 7979-7984
    • Lin, J.J.1    Sancar, A.2
  • 51
    • 33746602313 scopus 로고    scopus 로고
    • UvrD helicase suppresses recombination and DNA damage-induced deletions
    • 10.1128/JB.00275-06, 1540021, 16855234
    • Kang J, Blaser MJ. UvrD helicase suppresses recombination and DNA damage-induced deletions. J Bacteriol 2006, 188(15):5450-5459. 10.1128/JB.00275-06, 1540021, 16855234.
    • (2006) J Bacteriol , vol.188 , Issue.15 , pp. 5450-5459
    • Kang, J.1    Blaser, M.J.2
  • 52
    • 0442307793 scopus 로고    scopus 로고
    • Low temperature or GroEL/ES overproduction permits growth of Escherichia coli cells lacking trigger factor and DnaK
    • 10.1016/S0014-5793(04)00052-3, 14960329
    • Vorderwulbecke S, Kramer G, Merz F, Kurz TA, Rauch T, Zachmann-Brand B, Bukau B, Deuerling E. Low temperature or GroEL/ES overproduction permits growth of Escherichia coli cells lacking trigger factor and DnaK. FEBS Lett 2004, 559(1-3):181-187. 10.1016/S0014-5793(04)00052-3, 14960329.
    • (2004) FEBS Lett , vol.559 , Issue.1-3 , pp. 181-187
    • Vorderwulbecke, S.1    Kramer, G.2    Merz, F.3    Kurz, T.A.4    Rauch, T.5    Zachmann-Brand, B.6    Bukau, B.7    Deuerling, E.8
  • 53
    • 0020024650 scopus 로고
    • Damage to DNA induces expression of the ruv gene of Escherichia coli
    • 10.1007/BF00330811, 7045590
    • Shurvinton CE, Lloyd RG. Damage to DNA induces expression of the ruv gene of Escherichia coli. Mol Gen Genet 1982, 185(2):352-355. 10.1007/BF00330811, 7045590.
    • (1982) Mol Gen Genet , vol.185 , Issue.2 , pp. 352-355
    • Shurvinton, C.E.1    Lloyd, R.G.2
  • 54
    • 34147099429 scopus 로고    scopus 로고
    • Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli
    • 10.1128/JB.01713-06, 1855809, 17277072
    • Bubunenko M, Baker T, Court DL. Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 2007, 189(7):2844-2853. 10.1128/JB.01713-06, 1855809, 17277072.
    • (2007) J Bacteriol , vol.189 , Issue.7 , pp. 2844-2853
    • Bubunenko, M.1    Baker, T.2    Court, D.L.3
  • 56
    • 0034720815 scopus 로고    scopus 로고
    • Organization and transcription of the division cell wall (dcw) cluster in Neisseria gonorrhoeae
    • 10.1016/S0378-1119(00)00200-6, 10876091
    • Francis F, Ramirez-Arcos S, Salimnia H, Victor C, Dillon JR. Organization and transcription of the division cell wall (dcw) cluster in Neisseria gonorrhoeae. Gene 2000, 251(2):141-151. 10.1016/S0378-1119(00)00200-6, 10876091.
    • (2000) Gene , vol.251 , Issue.2 , pp. 141-151
    • Francis, F.1    Ramirez-Arcos, S.2    Salimnia, H.3    Victor, C.4    Dillon, J.R.5
  • 57
    • 48549106162 scopus 로고    scopus 로고
    • The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation
    • 10.1099/ijs.0.65641-0, 18523188
    • Teixeira DC, Eveillard S, Sirand-Pugnet P, Wulff A, Saillard C, Ayres AJ, Bove JM. The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation. Int J Syst Evol Microbiol 2008, 58(Pt 6):1414-1421. 10.1099/ijs.0.65641-0, 18523188.
    • (2008) Int J Syst Evol Microbiol , vol.58 , Issue.PART 6 , pp. 1414-1421
    • Teixeira, D.C.1    Eveillard, S.2    Sirand-Pugnet, P.3    Wulff, A.4    Saillard, C.5    Ayres, A.J.6    Bove, J.M.7
  • 58
    • 0029619250 scopus 로고
    • Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics
    • 177364, 7559342
    • Persson BC, Bylund GO, Berg DE, Wikstrom PM. Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics. J Bacteriol 1995, 177(19):5554-5560. 177364, 7559342.
    • (1995) J Bacteriol , vol.177 , Issue.19 , pp. 5554-5560
    • Persson, B.C.1    Bylund, G.O.2    Berg, D.E.3    Wikstrom, P.M.4
  • 59
    • 6044261571 scopus 로고    scopus 로고
    • Conservation of adjacency as evidence of paralogous operons
    • 10.1093/nar/gkh882, 524292, 15477389
    • Janga SC, Moreno-Hagelsieb G. Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res 2004, 32(18):5392-5397. 10.1093/nar/gkh882, 524292, 15477389.
    • (2004) Nucleic Acids Res , vol.32 , Issue.18 , pp. 5392-5397
    • Janga, S.C.1    Moreno-Hagelsieb, G.2
  • 60
    • 0025355395 scopus 로고
    • Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli
    • 208867, 1692017
    • Granston AE, Thompson DL, Friedman DI. Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli. J Bacteriol 1990, 172(5):2336-2342. 208867, 1692017.
    • (1990) J Bacteriol , vol.172 , Issue.5 , pp. 2336-2342
    • Granston, A.E.1    Thompson, D.L.2    Friedman, D.I.3
  • 61
    • 0034811078 scopus 로고    scopus 로고
    • Characterization of mutations in the metY-nusA-infB operon that suppress the slow growth of a DeltarimM mutant
    • 10.1128/JB.183.20.6095-6106.2001, 99689, 11567010
    • Bylund GO, Lovgren JM, Wikstrom PM. Characterization of mutations in the metY-nusA-infB operon that suppress the slow growth of a DeltarimM mutant. J Bacteriol 2001, 183(20):6095-6106. 10.1128/JB.183.20.6095-6106.2001, 99689, 11567010.
    • (2001) J Bacteriol , vol.183 , Issue.20 , pp. 6095-6106
    • Bylund, G.O.1    Lovgren, J.M.2    Wikstrom, P.M.3
  • 62
    • 0031801906 scopus 로고    scopus 로고
    • Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster
    • 107281, 9642179
    • Zhang Y, Cronan JE. Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster. J Bacteriol 1998, 180(13):3295-3303. 107281, 9642179.
    • (1998) J Bacteriol , vol.180 , Issue.13 , pp. 3295-3303
    • Zhang, Y.1    Cronan, J.E.2
  • 63
    • 0036306989 scopus 로고    scopus 로고
    • Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis
    • 10.1007/s00239-002-2317-1, 12107597
    • de Daruvar A, Collado-Vides J, Valencia A. Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J Mol Evol 2002, 55(2):211-221. 10.1007/s00239-002-2317-1, 12107597.
    • (2002) J Mol Evol , vol.55 , Issue.2 , pp. 211-221
    • de Daruvar, A.1    Collado-Vides, J.2    Valencia, A.3
  • 64
    • 39549098697 scopus 로고    scopus 로고
    • Persistence drives gene clustering in bacterial genomes
    • 10.1186/1471-2164-9-4, 2234087, 18179692
    • Fang G, Rocha EP, Danchin A. Persistence drives gene clustering in bacterial genomes. BMC Genomics 2008, 9:4. 10.1186/1471-2164-9-4, 2234087, 18179692.
    • (2008) BMC Genomics , vol.9 , pp. 4
    • Fang, G.1    Rocha, E.P.2    Danchin, A.3
  • 65
    • 0031035094 scopus 로고    scopus 로고
    • Genome plasticity as a paradigm of eubacteria evolution
    • 10.1007/PL00000052, 9395406
    • Watanabe H, Mori H, Itoh T, Gojobori T. Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol 1997, 44(Suppl 1):S57-64. 10.1007/PL00000052, 9395406.
    • (1997) J Mol Evol , vol.44 , Issue.SUPPL. 1
    • Watanabe, H.1    Mori, H.2    Itoh, T.3    Gojobori, T.4
  • 66
    • 0010414313 scopus 로고    scopus 로고
    • Evolution of gene order conservation in prokaryotes
    • 10.1186/gb-2001-2-6-research0020, 33396, 11423009
    • Tamames J. Evolution of gene order conservation in prokaryotes. Genome Biol 2001, 2(6):RESEARCH0020. 10.1186/gb-2001-2-6-research0020, 33396, 11423009.
    • (2001) Genome Biol , vol.2 , Issue.6
    • Tamames, J.1
  • 67
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: a fingerprint of proteins that physically interact
    • 10.1016/S0968-0004(98)01274-2, 9787636
    • Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 1998, 23(9):324-328. 10.1016/S0968-0004(98)01274-2, 9787636.
    • (1998) Trends Biochem Sci , vol.23 , Issue.9 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 68
    • 34247165419 scopus 로고    scopus 로고
    • Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism
    • 10.1093/nar/gkm011, 1865079, 17289755
    • Choonee N, Even S, Zig L, Putzer H. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res 2007, 35(5):1578-1588. 10.1093/nar/gkm011, 1865079, 17289755.
    • (2007) Nucleic Acids Res , vol.35 , Issue.5 , pp. 1578-1588
    • Choonee, N.1    Even, S.2    Zig, L.3    Putzer, H.4
  • 69
    • 34548513288 scopus 로고    scopus 로고
    • G-protein control of the ribosome-associated stress response protein SpoT
    • 10.1128/JB.00315-07, 1951942, 17616600
    • Jiang M, Sullivan SM, Wout PK, Maddock JR. G-protein control of the ribosome-associated stress response protein SpoT. J Bacteriol 2007, 189(17):6140-6147. 10.1128/JB.00315-07, 1951942, 17616600.
    • (2007) J Bacteriol , vol.189 , Issue.17 , pp. 6140-6147
    • Jiang, M.1    Sullivan, S.M.2    Wout, P.K.3    Maddock, J.R.4
  • 70
    • 24044438506 scopus 로고    scopus 로고
    • 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system
    • Van Houten B, Croteau DL, DellaVecchia MJ, Wang H, Kisker C. 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat Res 2005, 577(1-2):92-117.
    • (2005) Mutat Res , vol.577 , Issue.1-2 , pp. 92-117
    • Van Houten, B.1    Croteau, D.L.2    DellaVecchia, M.J.3    Wang, H.4    Kisker, C.5
  • 71
    • 28444484987 scopus 로고    scopus 로고
    • Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii
    • 10.1016/j.jmb.2005.10.001, 16288921
    • Kadziola A, Jepsen CH, Johansson E, McGuire J, Larsen S, Hove-Jensen B. Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii. J Mol Biol 2005, 354(4):815-828. 10.1016/j.jmb.2005.10.001, 16288921.
    • (2005) J Mol Biol , vol.354 , Issue.4 , pp. 815-828
    • Kadziola, A.1    Jepsen, C.H.2    Johansson, E.3    McGuire, J.4    Larsen, S.5    Hove-Jensen, B.6
  • 72
    • 2342547758 scopus 로고    scopus 로고
    • Organization and expression of the polynucleotide phosphorylase gene (pnp) of Streptomyces: Processing of pnp transcripts in Streptomyces antibioticus
    • 10.1128/JB.186.10.3160-3172.2004, 400608, 15126478
    • Bralley P, Jones GH. Organization and expression of the polynucleotide phosphorylase gene (pnp) of Streptomyces: Processing of pnp transcripts in Streptomyces antibioticus. J Bacteriol 2004, 186(10):3160-3172. 10.1128/JB.186.10.3160-3172.2004, 400608, 15126478.
    • (2004) J Bacteriol , vol.186 , Issue.10 , pp. 3160-3172
    • Bralley, P.1    Jones, G.H.2
  • 73
    • 0036843139 scopus 로고    scopus 로고
    • The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication
    • Messer W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 2002, 26(4):355-374.
    • (2002) FEMS Microbiol Rev , vol.26 , Issue.4 , pp. 355-374
    • Messer, W.1
  • 74
    • 0025286302 scopus 로고
    • Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products
    • 10.1016/0378-1119(90)90199-2, 2197183
    • Zalenskaya K, Lee J, Gujuluva CN, Shin YK, Slutsky M, Goldfarb A. Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products. Gene 1990, 89(1):7-12. 10.1016/0378-1119(90)90199-2, 2197183.
    • (1990) Gene , vol.89 , Issue.1 , pp. 7-12
    • Zalenskaya, K.1    Lee, J.2    Gujuluva, C.N.3    Shin, Y.K.4    Slutsky, M.5    Goldfarb, A.6
  • 75
    • 0027280419 scopus 로고
    • TRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure
    • 10.1006/jmbi.1993.1296, 8323579
    • Garcia GA, Koch KA, Chong S. tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure. J Mol Biol 1993, 231(2):489-497. 10.1006/jmbi.1993.1296, 8323579.
    • (1993) J Mol Biol , vol.231 , Issue.2 , pp. 489-497
    • Garcia, G.A.1    Koch, K.A.2    Chong, S.3
  • 76
    • 0021189277 scopus 로고
    • Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase
    • 10.1016/0092-8674(84)90492-6, 6380764
    • Taylor WE, Straus DB, Grossman AD, Burton ZF, Gross CA, Burgess RR. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell 1984, 38(2):371-381. 10.1016/0092-8674(84)90492-6, 6380764.
    • (1984) Cell , vol.38 , Issue.2 , pp. 371-381
    • Taylor, W.E.1    Straus, D.B.2    Grossman, A.D.3    Burton, Z.F.4    Gross, C.A.5    Burgess, R.R.6
  • 77
    • 0024347025 scopus 로고
    • Methionine aminopeptidase gene of Escherichia coli is essential for cell growth
    • 210164, 2544569
    • Chang SY, McGary EC, Chang S. Methionine aminopeptidase gene of Escherichia coli is essential for cell growth. J Bacteriol 1989, 171(7):4071-4072. 210164, 2544569.
    • (1989) J Bacteriol , vol.171 , Issue.7 , pp. 4071-4072
    • Chang, S.Y.1    McGary, E.C.2    Chang, S.3
  • 78
    • 58449126084 scopus 로고    scopus 로고
    • The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
    • 10.1126/science.1167140, 19150844
    • Moran NA, McLaughlin HJ, Sorek R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 2009, 323(5912):379-382. 10.1126/science.1167140, 19150844.
    • (2009) Science , vol.323 , Issue.5912 , pp. 379-382
    • Moran, N.A.1    McLaughlin, H.J.2    Sorek, R.3
  • 79
    • 36949020293 scopus 로고    scopus 로고
    • Comparative analysis of essential genes and nonessential genes in Escherichia coli K12
    • 10.1007/s00438-007-0298-x, 17943314
    • Gong X, Fan S, Bilderbeck A, Li M, Pang H, Tao S. Comparative analysis of essential genes and nonessential genes in Escherichia coli K12. Mol Genet Genomics 2008, 279(1):87-94. 10.1007/s00438-007-0298-x, 17943314.
    • (2008) Mol Genet Genomics , vol.279 , Issue.1 , pp. 87-94
    • Gong, X.1    Fan, S.2    Bilderbeck, A.3    Li, M.4    Pang, H.5    Tao, S.6
  • 80
    • 84873614255 scopus 로고    scopus 로고
    • NCBI ftp-server
    • NCBI ftp-server. , ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
  • 81
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 82
    • 0041386069 scopus 로고    scopus 로고
    • ClustalW-MPI: ClustalW analysis using distributed and parallel computing
    • 10.1093/bioinformatics/btg192, 12912844
    • Li KB. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 2003, 19(12):1585-1586. 10.1093/bioinformatics/btg192, 12912844.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1585-1586
    • Li, K.B.1
  • 83
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of Phylogenetics and Evolution in R language
    • 10.1093/bioinformatics/btg412, 14734327
    • Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 2004, 20(2):289-290. 10.1093/bioinformatics/btg412, 14734327.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 84
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 1995, 57(1):289-300.
    • (1995) J R Statist Soc B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


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