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Volumn 5, Issue , 2011, Pages

Global transcription regulation of RK2 plasmids: A case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 79960886799     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-119     Document Type: Article
Times cited : (9)

References (40)
  • 1
    • 0003965498 scopus 로고    scopus 로고
    • The horizontal Gene Pool: bacterial plasmids and gene spread
    • Amsterdam: Harwood Academic Publishers
    • Thomas CM. The horizontal Gene Pool: bacterial plasmids and gene spread. 2000, Amsterdam: Harwood Academic Publishers.
    • (2000)
    • Thomas, C.M.1
  • 2
    • 34249872978 scopus 로고    scopus 로고
    • The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated form a solid environment is phylogenetically divergent from members of the previously established α, β, δ sub-groups
    • 10.1016/j.plasmid.2006.11.007, 17306874
    • Bahl MI, Hansen LH, Goesmann A, Sorensen SJ. The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated form a solid environment is phylogenetically divergent from members of the previously established α, β, δ sub-groups. Plasmid 2007, 58(1):31-43. 10.1016/j.plasmid.2006.11.007, 17306874.
    • (2007) Plasmid , vol.58 , Issue.1 , pp. 31-43
    • Bahl, M.I.1    Hansen, L.H.2    Goesmann, A.3    Sorensen, S.J.4
  • 3
    • 0016707715 scopus 로고
    • Molecular Vehicle Properties of the Broad Host Range Plasmid RK2
    • 10.1126/science.1060178, 1060178
    • Meyer R, Figurski D, Helinski DR. Molecular Vehicle Properties of the Broad Host Range Plasmid RK2. Science 1975, 190:1226-1228. 10.1126/science.1060178, 1060178.
    • (1975) Science , vol.190 , pp. 1226-1228
    • Meyer, R.1    Figurski, D.2    Helinski, D.R.3
  • 4
    • 0004136246 scopus 로고    scopus 로고
    • Molecular cloning: a laboratory manual
    • New York: Cold Spring Harbor Laboratory Press, 3
    • Sambrook J, Russell DW. Molecular cloning: a laboratory manual. 2001, New York: Cold Spring Harbor Laboratory Press, 3.
    • (2001)
    • Sambrook, J.1    Russell, D.W.2
  • 5
    • 80052273397 scopus 로고
    • Plasmid Technology Methods
    • New York: Academic Press
    • Bennett PM, Grinsted J. Plasmid Technology Methods. Microbiology 1984, 17. New York: Academic Press.
    • (1984) Microbiology , vol.17
    • Bennett, P.M.1    Grinsted, J.2
  • 6
    • 29144461520 scopus 로고    scopus 로고
    • Plasmid R1 - replication and its control
    • 10.1016/j.plasmid.2005.07.002, 16199086
    • Nordstrom K. Plasmid R1 - replication and its control. Plasmid 2006, 55(1):1-26. 10.1016/j.plasmid.2005.07.002, 16199086.
    • (2006) Plasmid , vol.55 , Issue.1 , pp. 1-26
    • Nordstrom, K.1
  • 7
    • 70350195337 scopus 로고    scopus 로고
    • Gene Amplification and Adaptive Evolution in Bacteria
    • Anderson DI, Hughes D. Gene Amplification and Adaptive Evolution in Bacteria. Ann Rev of Genetics 2009, 43:167-195.
    • (2009) Ann Rev of Genetics , vol.43 , pp. 167-195
    • Anderson, D.I.1    Hughes, D.2
  • 8
    • 0023506940 scopus 로고
    • Incompatibility group P plasmids: Genetics, Evolution, and use in Genetic manipulation
    • Thomas CM, Smith CA. Incompatibility group P plasmids: Genetics, Evolution, and use in Genetic manipulation. Ann Rev Microbiol 1987, 41:77-101.
    • (1987) Ann Rev Microbiol , vol.41 , pp. 77-101
    • Thomas, C.M.1    Smith, C.A.2
  • 9
    • 77956884381 scopus 로고    scopus 로고
    • Replication and partitioning of the broad-host-range plasmid RK2
    • Kolatka K, Kubik S, Rajewska M, Konieczny I. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 2010, 64(2):119-134.
    • (2010) Plasmid , vol.64 , Issue.2 , pp. 119-134
    • Kolatka, K.1    Kubik, S.2    Rajewska, M.3    Konieczny, I.4
  • 10
    • 0023624434 scopus 로고
    • Plasmid transfer by conjugation from Escherichia-coli to gram-positive bacteria
    • Trieu-Cuot P, Carlier C, Martin P, Courvalin P. Plasmid transfer by conjugation from Escherichia-coli to gram-positive bacteria. FEMS Microbiol Lett 1987, 48:289-294.
    • (1987) FEMS Microbiol Lett , vol.48 , pp. 289-294
    • Trieu-Cuot, P.1    Carlier, C.2    Martin, P.3    Courvalin, P.4
  • 11
    • 0035735294 scopus 로고    scopus 로고
    • Conjugation between bacterial and mammalian cells
    • 10.1038/ng779, 11726922
    • Waters VL. Conjugation between bacterial and mammalian cells. Nat Genet 2001, 29:375-376. 10.1038/ng779, 11726922.
    • (2001) Nat Genet , vol.29 , pp. 375-376
    • Waters, V.L.1
  • 12
    • 0024323555 scopus 로고
    • Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast
    • 10.1038/340205a0, 2666856
    • Heinemann JA, Sprague GF. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 1989, 340:205-209. 10.1038/340205a0, 2666856.
    • (1989) Nature , vol.340 , pp. 205-209
    • Heinemann, J.A.1    Sprague, G.F.2
  • 14
    • 34249907825 scopus 로고    scopus 로고
    • Sequence of plasmid pBS228 and reconstruction of the IncP-1α phylogeny
    • 10.1016/j.plasmid.2007.01.001, 17320955
    • Haines AS, Jones K, Batt SM, Kosheleva IA, Thomas CM. Sequence of plasmid pBS228 and reconstruction of the IncP-1α phylogeny. Plasmid 2007, 58(1):76-83. 10.1016/j.plasmid.2007.01.001, 17320955.
    • (2007) Plasmid , vol.58 , Issue.1 , pp. 76-83
    • Haines, A.S.1    Jones, K.2    Batt, S.M.3    Kosheleva, I.A.4    Thomas, C.M.5
  • 17
    • 0024295790 scopus 로고
    • Gene-regulation on broad host range plasmid RK2 - identification of three novel operons whose transcription is repressed by both KorA and KorC
    • 10.1093/nar/16.12.5345, 336771, 2838814
    • Thomas CM, Ibbotson JP, Wang NY, Smith CA, Tipping R, Loader NM. Gene-regulation on broad host range plasmid RK2 - identification of three novel operons whose transcription is repressed by both KorA and KorC. Nucleic Acids Res 1988, 16:5345-5359. 10.1093/nar/16.12.5345, 336771, 2838814.
    • (1988) Nucleic Acids Res , vol.16 , pp. 5345-5359
    • Thomas, C.M.1    Ibbotson, J.P.2    Wang, N.Y.3    Smith, C.A.4    Tipping, R.5    Loader, N.M.6
  • 18
    • 0028844048 scopus 로고
    • Purification of KorA protein from broad host range plasmid RK2: definition of a hierarchy of KorA operators
    • 10.1006/jmbi.1995.0534, 7473715
    • Jagura-Burdzy G, Thomas CM. Purification of KorA protein from broad host range plasmid RK2: definition of a hierarchy of KorA operators. J Mol Biol 1995, 253:39-50. 10.1006/jmbi.1995.0534, 7473715.
    • (1995) J Mol Biol , vol.253 , pp. 39-50
    • Jagura-Burdzy, G.1    Thomas, C.M.2
  • 19
    • 0022536778 scopus 로고
    • Gene control in broad host range plasmid RK2: Expression, polypeptide product, and multiple regulatory functions of korB
    • Bechhofer DH, Kornacki JA, Firshein W, Figurski DH. Gene control in broad host range plasmid RK2: Expression, polypeptide product, and multiple regulatory functions of korB. Genetics 1986, 83:394-398.
    • (1986) Genetics , vol.83 , pp. 394-398
    • Bechhofer, D.H.1    Kornacki, J.A.2    Firshein, W.3    Figurski, D.H.4
  • 20
    • 0023664967 scopus 로고
    • Nucleotide-sequence of the transcriptional repressor gene korB which plays a key role in regulation of the copy number of broad host range plasmid RK2
    • 10.1093/nar/15.18.7443, 306259, 3309894
    • Theophilus BDM, Thomas CM. Nucleotide-sequence of the transcriptional repressor gene korB which plays a key role in regulation of the copy number of broad host range plasmid RK2. Nucleic Acids Res 1987, 15:7443-7450. 10.1093/nar/15.18.7443, 306259, 3309894.
    • (1987) Nucleic Acids Res , vol.15 , pp. 7443-7450
    • Theophilus, B.D.M.1    Thomas, C.M.2
  • 21
    • 0026552342 scopus 로고
    • KorB protein of promiscuous plasmid RP4 recognizes inverted sequence repetitions in regions essential for conjugative plasmid transfer
    • 10.1093/nar/20.8.1851, 312297, 1579485
    • Balzer D, Ziegelin G, Pansegrau W, Kruft V, Lanka E. KorB protein of promiscuous plasmid RP4 recognizes inverted sequence repetitions in regions essential for conjugative plasmid transfer. Nucleic Acids Res 1992, 20:1851-1858. 10.1093/nar/20.8.1851, 312297, 1579485.
    • (1992) Nucleic Acids Res , vol.20 , pp. 1851-1858
    • Balzer, D.1    Ziegelin, G.2    Pansegrau, W.3    Kruft, V.4    Lanka, E.5
  • 22
    • 0034695418 scopus 로고    scopus 로고
    • The hierarchy of KorB binding at its 12 binding sites on the broad-host-range plasmid RK2 and modulation of this binding by IncC1 protein
    • 10.1006/jmbi.1999.3359, 10623535
    • Kostelidou K, Thomas CM. The hierarchy of KorB binding at its 12 binding sites on the broad-host-range plasmid RK2 and modulation of this binding by IncC1 protein. J Mol Biol 2000, 295:411-422. 10.1006/jmbi.1999.3359, 10623535.
    • (2000) J Mol Biol , vol.295 , pp. 411-422
    • Kostelidou, K.1    Thomas, C.M.2
  • 23
    • 0035155185 scopus 로고    scopus 로고
    • Cooperativity between KorB and TrbA Repressors of Broad-Host-Range Plasmid RK2
    • 10.1128/JB.183.3.1022-1031.2001, 94970, 11208801
    • Zatyka M, Bingle LE, Jones AC, Thomas CM. Cooperativity between KorB and TrbA Repressors of Broad-Host-Range Plasmid RK2. J Bacteriol 2001, 183:1022-1031. 10.1128/JB.183.3.1022-1031.2001, 94970, 11208801.
    • (2001) J Bacteriol , vol.183 , pp. 1022-1031
    • Zatyka, M.1    Bingle, L.E.2    Jones, A.C.3    Thomas, C.M.4
  • 25
    • 0033522906 scopus 로고    scopus 로고
    • Conserved C-terminal Region of Global Repressor KorA of Boad-host-range Plasmid RK2 is Required for Co-operativity between KorA and a Second RK2 Global Regulator, KorB
    • 10.1006/jmbi.1999.2761, 10366500
    • Kostelidou K, Jones AC, Thomas CM. Conserved C-terminal Region of Global Repressor KorA of Boad-host-range Plasmid RK2 is Required for Co-operativity between KorA and a Second RK2 Global Regulator, KorB. J Mol Biol 1999, 289:211-221. 10.1006/jmbi.1999.2761, 10366500.
    • (1999) J Mol Biol , vol.289 , pp. 211-221
    • Kostelidou, K.1    Jones, A.C.2    Thomas, C.M.3
  • 26
    • 0027229646 scopus 로고
    • Multifunctional repressor KorB can block transcription by preventing isomerization of RNA polymerase-promoter complexes
    • 10.1093/nar/21.5.1141, 309274, 8464698
    • Williams DR, Motallebi-Veshareh M, Thomas CM. Multifunctional repressor KorB can block transcription by preventing isomerization of RNA polymerase-promoter complexes. Nucleic Acids Res 1993, 21:1141-1148. 10.1093/nar/21.5.1141, 309274, 8464698.
    • (1993) Nucleic Acids Res , vol.21 , pp. 1141-1148
    • Williams, D.R.1    Motallebi-Veshareh, M.2    Thomas, C.M.3
  • 27
    • 56749092077 scopus 로고    scopus 로고
    • A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB
    • 10.1111/j.1365-2958.2008.06498.x, 2680271, 19019158
    • Bingle LE, Rajasekar KV, Muntaha S, Nadella V, Hyde EI, Thomas CM. A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB. Mol Microbiol 2008, 70:1502-1514. 10.1111/j.1365-2958.2008.06498.x, 2680271, 19019158.
    • (2008) Mol Microbiol , vol.70 , pp. 1502-1514
    • Bingle, L.E.1    Rajasekar, K.V.2    Muntaha, S.3    Nadella, V.4    Hyde, E.I.5    Thomas, C.M.6
  • 28
    • 41549112784 scopus 로고    scopus 로고
    • Distribution of the partitioning protein KorB on the IncP-1 plasmid genome
    • 10.1016/j.plasmid.2008.02.001, 18374415
    • Chiu CM, Manzoor SE, Batt SM, Muntaha ST, Bingle LE, Thomas CM. Distribution of the partitioning protein KorB on the IncP-1 plasmid genome. Plasmid 2008, 59:163-175. 10.1016/j.plasmid.2008.02.001, 18374415.
    • (2008) Plasmid , vol.59 , pp. 163-175
    • Chiu, C.M.1    Manzoor, S.E.2    Batt, S.M.3    Muntaha, S.T.4    Bingle, L.E.5    Thomas, C.M.6
  • 30
    • 34250658998 scopus 로고    scopus 로고
    • Bayesian methods in bioinformatics and computational systems biology
    • Wilkinson DJ. Bayesian methods in bioinformatics and computational systems biology. Briefings in Bioinformatics 2007, 8(1):109-116.
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.1 , pp. 109-116
    • Wilkinson, D.J.1
  • 31
    • 54349110857 scopus 로고    scopus 로고
    • Bayesian inference for differential equations
    • Girolami M. Bayesian inference for differential equations. Theoretical Computer Science 2008, 408:4-16.
    • (2008) Theoretical Computer Science , vol.408 , pp. 4-16
    • Girolami, M.1
  • 32
    • 71749100925 scopus 로고    scopus 로고
    • Bayesian inference of biochemical kinetic parameters using the linear noise approximation
    • Komorowski M, Finkenstadt B, Harper CV, Rand DA. Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics 2009, 10(343).
    • (2009) BMC Bioinformatics , vol.10 , Issue.343
    • Komorowski, M.1    Finkenstadt, B.2    Harper, C.V.3    Rand, D.A.4
  • 33
    • 42649096925 scopus 로고    scopus 로고
    • Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo
    • 10.1093/bioinformatics/btn103, 18356193
    • Jayawardhana B, Kell DB, Rattray M. Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo. Bioinformatics 2008, 24(9):1191-1197. 10.1093/bioinformatics/btn103, 18356193.
    • (2008) Bioinformatics , vol.24 , Issue.9 , pp. 1191-1197
    • Jayawardhana, B.1    Kell, D.B.2    Rattray, M.3
  • 34
    • 75649151459 scopus 로고    scopus 로고
    • Reconstructing nonlinear dynamics models of gene regulation using stochastic sampling
    • Mazur J, Ritter D, Reinelt G, Kaderali L. Reconstructing nonlinear dynamics models of gene regulation using stochastic sampling. BMC Bioinformatics 2009, 10(448).
    • (2009) BMC Bioinformatics , vol.10 , Issue.448
    • Mazur, J.1    Ritter, D.2    Reinelt, G.3    Kaderali, L.4
  • 35
    • 77956890234 scopus 로고
    • Monte Carlo Sampling Methods Using Markov Chains and Their Applications
    • Hastings WK. Monte Carlo Sampling Methods Using Markov Chains and Their Applications. Biometrica 1970, 57(1):97-109.
    • (1970) Biometrica , vol.57 , Issue.1 , pp. 97-109
    • Hastings, W.K.1
  • 38
    • 0031285157 scopus 로고    scopus 로고
    • Weak convergence and optimal scaling of random walk metropolis algorithm
    • Roberts GO, Gelman A, Gilks WR. Weak convergence and optimal scaling of random walk metropolis algorithm. Ann Appl Probab 1997, 7(1):110-120.
    • (1997) Ann Appl Probab , vol.7 , Issue.1 , pp. 110-120
    • Roberts, G.O.1    Gelman, A.2    Gilks, W.R.3
  • 40
    • 0030105583 scopus 로고    scopus 로고
    • CVODE, A Stiff/Nonstiff ODE Solver in C
    • Cohen SD, Hindmarsh AC. CVODE, A Stiff/Nonstiff ODE Solver in C. Computers in Physics 1996, 10(2):138-143.
    • (1996) Computers in Physics , vol.10 , Issue.2 , pp. 138-143
    • Cohen, S.D.1    Hindmarsh, A.C.2


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