메뉴 건너뛰기




Volumn 13, Issue 9, 2011, Pages 2389-2402

The logicome of environmental bacteria: Merging catabolic and regulatory events with Boolean formalisms

Author keywords

[No Author keywords available]

Indexed keywords

3 XYLENE; 3-XYLENE; TRANSCRIPTION FACTOR; XYLENE;

EID: 80052612366     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02455.x     Document Type: Short Survey
Times cited : (35)

References (101)
  • 1
    • 0026049422 scopus 로고
    • Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein
    • Abril, M.A., Buck, M., and Ramos, J.L. (1991) Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein. J Biol Chem 266: 15832-15838.
    • (1991) J Biol Chem , vol.266 , pp. 15832-15838
    • Abril, M.A.1    Buck, M.2    Ramos, J.L.3
  • 3
    • 23744431554 scopus 로고    scopus 로고
    • Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0
    • Aranda-Olmedo, I., Ramos, J.L., and Marques, S. (2005) Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl Environ Microbiol 71: 4191-4198.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 4191-4198
    • Aranda-Olmedo, I.1    Ramos, J.L.2    Marques, S.3
  • 4
    • 58849106769 scopus 로고    scopus 로고
    • Systems biology: parameter estimation for biochemical models
    • Ashyraliyev, M., Fomekong-Nanfack, Y., Kaandorp, J.A., and Blom, J.G. (2009) Systems biology: parameter estimation for biochemical models. FEBS J 276: 886-902.
    • (2009) FEBS J , vol.276 , pp. 886-902
    • Ashyraliyev, M.1    Fomekong-Nanfack, Y.2    Kaandorp, J.A.3    Blom, J.G.4
  • 5
    • 0025005226 scopus 로고
    • The TOL plasmids: determinants of the catabolism of toluene and the xylenes
    • Assinder, S.J., and Williams, P.A. (1990) The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv Microb Physiol 31: 1-69.
    • (1990) Adv Microb Physiol , vol.31 , pp. 1-69
    • Assinder, S.J.1    Williams, P.A.2
  • 6
    • 20344379457 scopus 로고    scopus 로고
    • Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
    • Balazsi, G., Barabasi, A.L., and Oltvai, Z.N. (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 102: 7841-7846.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7841-7846
    • Balazsi, G.1    Barabasi, A.L.2    Oltvai, Z.N.3
  • 7
    • 77955499190 scopus 로고    scopus 로고
    • The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes
    • Baldazzi, V., Ropers, D., Markowicz, Y., Kahn, D., Geiselmann, J., and de Jong, H. (2010) The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. PLoS Comput Biol 6: e1000812.
    • (2010) PLoS Comput Biol , vol.6
    • Baldazzi, V.1    Ropers, D.2    Markowicz, Y.3    Kahn, D.4    Geiselmann, J.5    de Jong, H.6
  • 8
    • 0030901173 scopus 로고    scopus 로고
    • Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWW0, of Pseudomonas putida
    • Bertoni, G., Perez-Martin, J., and de Lorenzo, V. (1997) Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWW0, of Pseudomonas putida. Mol Microbiol 23: 1221-1227.
    • (1997) Mol Microbiol , vol.23 , pp. 1221-1227
    • Bertoni, G.1    Perez-Martin, J.2    de Lorenzo, V.3
  • 9
    • 0032164070 scopus 로고    scopus 로고
    • Active recruitment of sigma 54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and αCTD
    • Bertoni, G., Fujita, N., Ishihama, A., and de Lorenzo, V. (1998) Active recruitment of sigma 54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and αCTD. EMBO J 17: 5120-5128.
    • (1998) EMBO J , vol.17 , pp. 5120-5128
    • Bertoni, G.1    Fujita, N.2    Ishihama, A.3    de Lorenzo, V.4
  • 10
    • 38349079839 scopus 로고    scopus 로고
    • New surveyor tools for charting microbial metabolic maps
    • Breitling, R., Vitkup, D., and Barrett, M.P. (2008) New surveyor tools for charting microbial metabolic maps. Nat Rev Microbiol 6: 156-161.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 156-161
    • Breitling, R.1    Vitkup, D.2    Barrett, M.P.3
  • 11
    • 0037046271 scopus 로고    scopus 로고
    • Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization
    • Bruckner, R., and Titgemeyer, F. (2002) Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett 209: 141-148.
    • (2002) FEMS Microbiol Lett , vol.209 , pp. 141-148
    • Bruckner, R.1    Titgemeyer, F.2
  • 12
    • 0037965981 scopus 로고    scopus 로고
    • On schemes of combinatorial transcription logic
    • Buchler, N.E., Gerland, U., and Hwa, T. (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100: 5136-5141.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 5136-5141
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 14
    • 10344229939 scopus 로고    scopus 로고
    • Structure and function of the Pseudomonas putida integration host factor
    • Calb, R., Davidovitch, A., Koby, S., Giladi, H., Goldenberg, D., Margalit, H., etal. (1996) Structure and function of the Pseudomonas putida integration host factor. J Bacteriol 178: 6319-6326.
    • (1996) J Bacteriol , vol.178 , pp. 6319-6326
    • Calb, R.1    Davidovitch, A.2    Koby, S.3    Giladi, H.4    Goldenberg, D.5    Margalit, H.6
  • 15
    • 0033871148 scopus 로고    scopus 로고
    • In vivo and in vitro effects of (p)ppGpp on the sigma 54 promoter Pu of the TOL plasmid of Pseudomonas putida
    • Carmona, M., Rodriguez, M.J., Martinez-Costa, O., and de Lorenzo, V. (2000) In vivo and in vitro effects of (p)ppGpp on the sigma 54 promoter Pu of the TOL plasmid of Pseudomonas putida. J Bacteriol 182: 4711-4718.
    • (2000) J Bacteriol , vol.182 , pp. 4711-4718
    • Carmona, M.1    Rodriguez, M.J.2    Martinez-Costa, O.3    de Lorenzo, V.4
  • 17
    • 24944583078 scopus 로고    scopus 로고
    • Genetically modified organisms for the environment: stories of success and failure and what we have learned from them
    • Cases, I., and de Lorenzo, V. (2005) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8: 213-222.
    • (2005) Int Microbiol , vol.8 , pp. 213-222
    • Cases, I.1    de Lorenzo, V.2
  • 18
    • 0032589264 scopus 로고    scopus 로고
    • The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid
    • Cases, I., Perez-Martin, J., and de Lorenzo, V. (1999) The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid. J Biol Chem 274: 15562-15568.
    • (1999) J Biol Chem , vol.274 , pp. 15562-15568
    • Cases, I.1    Perez-Martin, J.2    de Lorenzo, V.3
  • 19
    • 0037665941 scopus 로고    scopus 로고
    • Transcription regulation and environmental adaptation in bacteria
    • Cases, I., de Lorenzo, V., and Ouzounis, C.A. (2003) Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 11: 248-253.
    • (2003) Trends Microbiol , vol.11 , pp. 248-253
    • Cases, I.1    de Lorenzo, V.2    Ouzounis, C.A.3
  • 20
    • 34548548565 scopus 로고    scopus 로고
    • Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways
    • del Castillo, T., and Ramos, J.L. (2007) Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 189: 6602-6610.
    • (2007) J Bacteriol , vol.189 , pp. 6602-6610
    • del Castillo, T.1    Ramos, J.L.2
  • 22
    • 29244480001 scopus 로고    scopus 로고
    • RNA polymerase holoenzymes can share a single transcription start site for the Pm promoter. Critical nucleotides in the -7 to -18 region are needed to select between RNA polymerase with sigma 38 or sigma 32
    • Dominguez-Cuevas, P., Marin, P., Ramos, J.L., and Marques, S. (2005) RNA polymerase holoenzymes can share a single transcription start site for the Pm promoter. Critical nucleotides in the -7 to -18 region are needed to select between RNA polymerase with sigma 38 or sigma 32. J Biol Chem 280: 41315-41323.
    • (2005) J Biol Chem , vol.280 , pp. 41315-41323
    • Dominguez-Cuevas, P.1    Marin, P.2    Ramos, J.L.3    Marques, S.4
  • 23
    • 33744951971 scopus 로고    scopus 로고
    • Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene
    • Dominguez-Cuevas, P., Gonzalez-Pastor, J.E., Marques, S., Ramos, J.L., and de Lorenzo, V. (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 281: 11981-11991.
    • (2006) J Biol Chem , vol.281 , pp. 11981-11991
    • Dominguez-Cuevas, P.1    Gonzalez-Pastor, J.E.2    Marques, S.3    Ramos, J.L.4    de Lorenzo, V.5
  • 24
    • 10044292705 scopus 로고    scopus 로고
    • Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440
    • Dos Santos, V.A., Heim, S., Moore, E.R., Stratz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286.
    • (2004) Environ Microbiol , vol.6 , pp. 1264-1286
    • Dos Santos, V.A.1    Heim, S.2    Moore, E.R.3    Stratz, M.4    Timmis, K.N.5
  • 26
    • 72949096331 scopus 로고    scopus 로고
    • Logical modelling of cell cycle control in eukaryotes: a comparative study
    • Faure, A., and Thieffry, D. (2009) Logical modelling of cell cycle control in eukaryotes: a comparative study. Mol Biosyst 5: 1569-1581.
    • (2009) Mol Biosyst , vol.5 , pp. 1569-1581
    • Faure, A.1    Thieffry, D.2
  • 28
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman, N., Linial, M., Nachman, I., and Pe'er, D. (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7: 601-620.
    • (2000) J Comput Biol , vol.7 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 29
    • 0029920970 scopus 로고    scopus 로고
    • Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and alpha 54-dependent tandem promoters according to the compound used for growth
    • Gallegos, M.T., Marques, S., and Ramos, J.L. (1996) Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and alpha 54-dependent tandem promoters according to the compound used for growth. J Bacteriol 178: 2356-2361.
    • (1996) J Bacteriol , vol.178 , pp. 2356-2361
    • Gallegos, M.T.1    Marques, S.2    Ramos, J.L.3
  • 30
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T. (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 31
    • 42449123222 scopus 로고    scopus 로고
    • Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
    • Goelzer, A., Bekkal Brikci, F., Martin-Verstraete, I., Noirot, P., Bessieres, P., Aymerich, S., and Fromion, V. (2008) Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Syst Biol 2: 20.
    • (2008) BMC Syst Biol , vol.2 , pp. 20
    • Goelzer, A.1    Bekkal Brikci, F.2    Martin-Verstraete, I.3    Noirot, P.4    Bessieres, P.5    Aymerich, S.6    Fromion, V.7
  • 32
    • 0036933239 scopus 로고    scopus 로고
    • Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida
    • Greated, A., Lambertsen, L., Williams, P.A., and Thomas, C.M. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4: 856-871.
    • (2002) Environ Microbiol , vol.4 , pp. 856-871
    • Greated, A.1    Lambertsen, L.2    Williams, P.A.3    Thomas, C.M.4
  • 33
    • 40049097594 scopus 로고    scopus 로고
    • Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs
    • Hale, V., Keasling, J.D., Renninger, N., and Diagana, T.T. (2007) Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs. Am J Trop Med Hyg 77: 198-202.
    • (2007) Am J Trop Med Hyg , vol.77 , pp. 198-202
    • Hale, V.1    Keasling, J.D.2    Renninger, N.3    Diagana, T.T.4
  • 34
    • 0037079012 scopus 로고    scopus 로고
    • Engineered gene circuits
    • Hasty, J., McMillen, D., and Collins, J.J. (2002) Engineered gene circuits. Nature 420: 224-230.
    • (2002) Nature , vol.420 , pp. 224-230
    • Hasty, J.1    McMillen, D.2    Collins, J.J.3
  • 35
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • Herrgard, M.J., Covert, M.W., and Palsson, B.O. (2004) Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 15: 70-77.
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 70-77
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 36
    • 33746660425 scopus 로고    scopus 로고
    • Identification of genome-scale metabolic network models using experimentally measured flux profiles
    • Herrgard, M.J., Fong, S.S., and Palsson, B.O. (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2: e72.
    • (2006) PLoS Comput Biol , vol.2
    • Herrgard, M.J.1    Fong, S.S.2    Palsson, B.O.3
  • 37
    • 0037044575 scopus 로고    scopus 로고
    • The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation
    • Hoffmann, A., Levchenko, A., Scott, M.L., and Baltimore, D. (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298: 1241-1245.
    • (2002) Science , vol.298 , pp. 1241-1245
    • Hoffmann, A.1    Levchenko, A.2    Scott, M.L.3    Baltimore, D.4
  • 38
    • 0025185118 scopus 로고
    • Promoter-upstream activator sequences are required for expression of the xylS gene and upper-pathway operon on the Pseudomonas TOL plasmid
    • Holtel, A., Abril, M.A., Marques, S., Timmis, K.N., and Ramos, J.L. (1990) Promoter-upstream activator sequences are required for expression of the xylS gene and upper-pathway operon on the Pseudomonas TOL plasmid. Mol Microbiol 4: 1551-1556.
    • (1990) Mol Microbiol , vol.4 , pp. 1551-1556
    • Holtel, A.1    Abril, M.A.2    Marques, S.3    Timmis, K.N.4    Ramos, J.L.5
  • 39
    • 0028204795 scopus 로고
    • Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid
    • Holtel, A., Marques, S., Mohler, I., Jakubzik, U., and Timmis, K.N. (1994) Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid. J Bacteriol 176: 1773-1776.
    • (1994) J Bacteriol , vol.176 , pp. 1773-1776
    • Holtel, A.1    Marques, S.2    Mohler, I.3    Jakubzik, U.4    Timmis, K.N.5
  • 41
    • 0019456994 scopus 로고
    • Molecular cloning of TOL genes xylB and xylE in Escherichia coli
    • Inouye, S., Nakazawa, A., and Nakazawa, T. (1981) Molecular cloning of TOL genes xylB and xylE in Escherichia coli. J Bacteriol 145: 1137-1143.
    • (1981) J Bacteriol , vol.145 , pp. 1137-1143
    • Inouye, S.1    Nakazawa, A.2    Nakazawa, T.3
  • 42
    • 0021994728 scopus 로고
    • Determination of the transcription initiation site and identification of the protein product of the regulatory gene xylR for xyl operons on the TOL plasmid
    • Inouye, S., Nakazawa, A., and Nakazawa, T. (1985) Determination of the transcription initiation site and identification of the protein product of the regulatory gene xylR for xyl operons on the TOL plasmid. J Bacteriol 163: 863-869.
    • (1985) J Bacteriol , vol.163 , pp. 863-869
    • Inouye, S.1    Nakazawa, A.2    Nakazawa, T.3
  • 43
    • 17044396348 scopus 로고    scopus 로고
    • Logic functions of the genomic cis-regulatory code
    • Istrail, S., and Davidson, E.H. (2005) Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci USA 102: 4954-4959.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4954-4959
    • Istrail, S.1    Davidson, E.H.2
  • 44
    • 34748881464 scopus 로고    scopus 로고
    • The regulatory genome and the computer
    • Istrail, S., De Leon, S.B., and Davidson, E.H. (2007) The regulatory genome and the computer. Dev Biol 310: 187-195.
    • (2007) Dev Biol , vol.310 , pp. 187-195
    • Istrail, S.1    De Leon, S.B.2    Davidson, E.H.3
  • 45
    • 33750374139 scopus 로고    scopus 로고
    • Linking data to models: data regression
    • Jaqaman, K., and Danuser, G. (2006) Linking data to models: data regression. Nat Rev Mol Cell Biol 7: 813-819.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 813-819
    • Jaqaman, K.1    Danuser, G.2
  • 46
    • 4143089549 scopus 로고    scopus 로고
    • Simulating complex intracellular processes using object-oriented computational modelling
    • Johnson, C.G., Goldman, J.P., and Gullick, W.J. (2004) Simulating complex intracellular processes using object-oriented computational modelling. Prog Biophys Mol Biol 86: 379-406.
    • (2004) Prog Biophys Mol Biol , vol.86 , pp. 379-406
    • Johnson, C.G.1    Goldman, J.P.2    Gullick, W.J.3
  • 47
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • de Jong, H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103.
    • (2002) J Comput Biol , vol.9 , pp. 67-103
    • de Jong, H.1
  • 48
    • 0345269975 scopus 로고    scopus 로고
    • Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
    • de Jong, H., Geiselmann, J., Hernandez, C., and Page, M. (2003) Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19: 336-344.
    • (2003) Bioinformatics , vol.19 , pp. 336-344
    • de Jong, H.1    Geiselmann, J.2    Hernandez, C.3    Page, M.4
  • 50
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Karlebach, G., and Shamir, R. (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9: 770-780.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 51
    • 77951588007 scopus 로고    scopus 로고
    • Enzyme-based logic systems for information processing
    • Katz, E., and Privman, V. (2010) Enzyme-based logic systems for information processing. Chem Soc Rev 39: 1835-1857.
    • (2010) Chem Soc Rev , vol.39 , pp. 1835-1857
    • Katz, E.1    Privman, V.2
  • 52
    • 1542327668 scopus 로고    scopus 로고
    • Trends between gene content and genome size in prokaryotic species with larger genomes
    • Konstantinidis, K.T., and Tiedje, J.M. (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA 101: 3160-3165.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3160-3165
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 53
    • 77949385752 scopus 로고    scopus 로고
    • Bacterial adaptation through distributed sensing of metabolic fluxes
    • Kotte, O., Zaugg, J.B., and Heinemann, M. (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6: 355.
    • (2010) Mol Syst Biol , vol.6 , pp. 355
    • Kotte, O.1    Zaugg, J.B.2    Heinemann, M.3
  • 55
    • 77957967615 scopus 로고    scopus 로고
    • The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid
    • Koutinas, M., Lam, M.C., Kiparissides, A., Silva-Rocha, R., Godinho, M., Livingston, A.G., etal. (2010) The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol 12: 1705-1718.
    • (2010) Environ Microbiol , vol.12 , pp. 1705-1718
    • Koutinas, M.1    Lam, M.C.2    Kiparissides, A.3    Silva-Rocha, R.4    Godinho, M.5    Livingston, A.G.6
  • 57
    • 57049091573 scopus 로고    scopus 로고
    • Systems biology approaches to bioremediation
    • de Lorenzo, V. (2008) Systems biology approaches to bioremediation. Curr Opin Biotechnol 19: 579-589.
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 579-589
    • de Lorenzo, V.1
  • 58
    • 0025797356 scopus 로고
    • An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid
    • de Lorenzo, V., Herrero, M., Metzke, M., and Timmis, K.N. (1991) An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid. EMBO J 10: 1159-1167.
    • (1991) EMBO J , vol.10 , pp. 1159-1167
    • de Lorenzo, V.1    Herrero, M.2    Metzke, M.3    Timmis, K.N.4
  • 59
    • 0033083733 scopus 로고    scopus 로고
    • It's a noisy business! Genetic regulation at the nanomolar scale
    • McAdams, H.H., and Arkin, A. (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15: 65-69.
    • (1999) Trends Genet , vol.15 , pp. 65-69
    • McAdams, H.H.1    Arkin, A.2
  • 60
    • 1542380403 scopus 로고    scopus 로고
    • The evolution of genetic regulatory systems in bacteria
    • McAdams, H.H., Srinivasan, B., and Arkin, A.P. (2004) The evolution of genetic regulatory systems in bacteria. Nat Rev Genet 5: 169-178.
    • (2004) Nat Rev Genet , vol.5 , pp. 169-178
    • McAdams, H.H.1    Srinivasan, B.2    Arkin, A.P.3
  • 61
    • 0142027814 scopus 로고    scopus 로고
    • Structure and function of the feed-forward loop network motif
    • Mangan, S., and Alon, U. (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100: 11980-11985.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 11980-11985
    • Mangan, S.1    Alon, U.2
  • 62
    • 0242364231 scopus 로고    scopus 로고
    • The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
    • Mangan, S., Zaslaver, A., and Alon, U. (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334: 197-204.
    • (2003) J Mol Biol , vol.334 , pp. 197-204
    • Mangan, S.1    Zaslaver, A.2    Alon, U.3
  • 63
    • 70349782009 scopus 로고    scopus 로고
    • Computational design tools for synthetic biology
    • Marchisio, M.A., and Stelling, J. (2009) Computational design tools for synthetic biology. Curr Opin Biotechnol 20: 479-485.
    • (2009) Curr Opin Biotechnol , vol.20 , pp. 479-485
    • Marchisio, M.A.1    Stelling, J.2
  • 64
    • 0032586644 scopus 로고    scopus 로고
    • The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase
    • Marques, S., Manzanera, M., Gonzalez-Perez, M.M., Gallegos, M.T., and Ramos, J.L. (1999) The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase. Mol Microbiol 31: 1105-1113.
    • (1999) Mol Microbiol , vol.31 , pp. 1105-1113
    • Marques, S.1    Manzanera, M.2    Gonzalez-Perez, M.M.3    Gallegos, M.T.4    Ramos, J.L.5
  • 65
    • 33646167129 scopus 로고    scopus 로고
    • Plasticity of the cis-regulatory input function of a gene
    • Mayo, A.E., Setty, Y., Shavit, S., Zaslaver, A., and Alon, U. (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4: e45.
    • (2006) PLoS Biol , vol.4
    • Mayo, A.E.1    Setty, Y.2    Shavit, S.3    Zaslaver, A.4    Alon, U.5
  • 66
    • 0027370376 scopus 로고
    • GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes, P. (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci 9: 563-571.
    • (1993) Comput Appl Biosci , vol.9 , pp. 563-571
    • Mendes, P.1
  • 67
    • 0023190414 scopus 로고
    • The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon
    • Mermod, N., Ramos, J.L., Bairoch, A., and Timmis, K.N. (1987) The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon. Mol Gen Genet 207: 349-354.
    • (1987) Mol Gen Genet , vol.207 , pp. 349-354
    • Mermod, N.1    Ramos, J.L.2    Bairoch, A.3    Timmis, K.N.4
  • 68
    • 79551504187 scopus 로고    scopus 로고
    • Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida
    • Milanesio, P., Arce-Rodríguez, A., Muñoz, A., Calles, B., and de Lorenzo, V. (2011) Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ Microbiol 13: 324-329.
    • (2011) Environ Microbiol , vol.13 , pp. 324-329
    • Milanesio, P.1    Arce-Rodríguez, A.2    Muñoz, A.3    Calles, B.4    de Lorenzo, V.5
  • 70
    • 33751229022 scopus 로고    scopus 로고
    • Concatenated logic gates using four coupled biocatalysts operating in series
    • Niazov, T., Baron, R., Katz, E., Lioubashevski, O., and Willner, I. (2006) Concatenated logic gates using four coupled biocatalysts operating in series. Proc Natl Acad Sci USA 103: 17160-17163.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17160-17163
    • Niazov, T.1    Baron, R.2    Katz, E.3    Lioubashevski, O.4    Willner, I.5
  • 71
    • 54449092307 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
    • Nogales, J., Palsson, B.O., and Thiele, I. (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79.
    • (2008) BMC Syst Biol , vol.2 , pp. 79
    • Nogales, J.1    Palsson, B.O.2    Thiele, I.3
  • 73
    • 0029086738 scopus 로고
    • Integration host factor suppresses promiscuous activation of the sigma 54-dependent promoter Pu of Pseudomonas putida
    • Perez-Martin, J., and de Lorenzo, V. (1995a) Integration host factor suppresses promiscuous activation of the sigma 54-dependent promoter Pu of Pseudomonas putida. Proc Natl Acad Sci USA 92: 7277-7281.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 7277-7281
    • Perez-Martin, J.1    de Lorenzo, V.2
  • 74
    • 0028980296 scopus 로고
    • The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR
    • Perez-Martin, J., and de Lorenzo, V. (1995b) The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR. J Bacteriol 177: 3758-3763.
    • (1995) J Bacteriol , vol.177 , pp. 3758-3763
    • Perez-Martin, J.1    de Lorenzo, V.2
  • 75
    • 0030612037 scopus 로고    scopus 로고
    • Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein
    • Perez-Martin, J., and de Lorenzo, V. (1997) Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein. J Bacteriol 179: 2757-2760.
    • (1997) J Bacteriol , vol.179 , pp. 2757-2760
    • Perez-Martin, J.1    de Lorenzo, V.2
  • 77
    • 59449098785 scopus 로고    scopus 로고
    • Enzyme-based logic systems and their applications for novel multi-signal-responsive materials
    • Pita, M., Minko, S., and Katz, E. (2009) Enzyme-based logic systems and their applications for novel multi-signal-responsive materials. J Mater Sci Mater Med 20: 457-462.
    • (2009) J Mater Sci Mater Med , vol.20 , pp. 457-462
    • Pita, M.1    Minko, S.2    Katz, E.3
  • 78
    • 70350569876 scopus 로고    scopus 로고
    • Comparing different ODE modelling approaches for gene regulatory networks
    • Polynikis, A., Hogan, S.J., and Bernardo, M. (2009) Comparing different ODE modelling approaches for gene regulatory networks. J Theor Biol 261: 511-530.
    • (2009) J Theor Biol , vol.261 , pp. 511-530
    • Polynikis, A.1    Hogan, S.J.2    Bernardo, M.3
  • 79
    • 34848865681 scopus 로고    scopus 로고
    • Orthologous transcription factors in bacteria have different functions and regulate different genes
    • Price, M.N., Dehal, P.S., and Arkin, A.P. (2007) Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol 3: 1739-1750.
    • (2007) PLoS Comput Biol , vol.3 , pp. 1739-1750
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 80
    • 55449096123 scopus 로고    scopus 로고
    • Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
    • Puchalka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., etal. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4: e1000210.
    • (2008) PLoS Comput Biol , vol.4
    • Puchalka, J.1    Oberhardt, M.A.2    Godinho, M.3    Bielecka, A.4    Regenhardt, D.5    Timmis, K.N.6
  • 81
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: stochastic gene expression and its consequences
    • Raj, A., and van Oudenaarden, A. (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226.
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    van Oudenaarden, A.2
  • 82
    • 0030860391 scopus 로고    scopus 로고
    • Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators
    • Ramos, J.L., Marques, S., and Timmis, K.N. (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 51: 341-373.
    • (1997) Annu Rev Microbiol , vol.51 , pp. 341-373
    • Ramos, J.L.1    Marques, S.2    Timmis, K.N.3
  • 84
    • 1542319979 scopus 로고    scopus 로고
    • Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures
    • Rescalli, E., Saini, S., Bartocci, C., Rychlewski, L., de Lorenzo, V., and Bertoni, G. (2004) Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. J Biol Chem 279: 7777-7784.
    • (2004) J Biol Chem , vol.279 , pp. 7777-7784
    • Rescalli, E.1    Saini, S.2    Bartocci, C.3    Rychlewski, L.4    de Lorenzo, V.5    Bertoni, G.6
  • 85
    • 46249108209 scopus 로고    scopus 로고
    • Computational design of digital and memory biological devices
    • Rodrigo, G., and Jaramillo, A. (2007) Computational design of digital and memory biological devices. Syst Synth Biol 1: 183-195.
    • (2007) Syst Synth Biol , vol.1 , pp. 183-195
    • Rodrigo, G.1    Jaramillo, A.2
  • 86
    • 54949140438 scopus 로고    scopus 로고
    • DESHARKY: automatic design of metabolic pathways for optimal cell growth
    • Rodrigo, G., Carrera, J., Prather, K.J., and Jaramillo, A. (2008) DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24: 2554-2556.
    • (2008) Bioinformatics , vol.24 , pp. 2554-2556
    • Rodrigo, G.1    Carrera, J.2    Prather, K.J.3    Jaramillo, A.4
  • 87
    • 77955132055 scopus 로고    scopus 로고
    • Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment
    • Rojo, F. (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34: 658-684.
    • (2010) FEMS Microbiol Rev , vol.34 , pp. 658-684
    • Rojo, F.1
  • 88
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen, M., Rosenberg, R., Shraiman, B.I., and Alon, U. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 99: 10555-10560.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Alon, U.4
  • 89
    • 11144261097 scopus 로고    scopus 로고
    • Transcriptional regulation of the toluene catabolic pathways
    • Ramos, J.L. (ed.). New York, NY, USA: Kluwer Academic/Plenum Publishers
    • Ruiz, R., Aranda-Olmedo, M.I., Dominguez-Cuevas, P., Ramos-Gonzalez, M.I., and Marques, S. (2004) Transcriptional regulation of the toluene catabolic pathways. In Pseudomonas. Ramos, J.L. (ed.). New York, NY, USA: Kluwer Academic/Plenum Publishers, pp. 509-537.
    • (2004) Pseudomonas , pp. 509-537
    • Ruiz, R.1    Aranda-Olmedo, M.I.2    Dominguez-Cuevas, P.3    Ramos-Gonzalez, M.I.4    Marques, S.5
  • 90
    • 45149101194 scopus 로고    scopus 로고
    • Current approaches to gene regulatory network modelling
    • Schlitt, T., and Brazma, A. (2007) Current approaches to gene regulatory network modelling. BMC Bioinformatics 8 (Suppl. 6): S9.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 6
    • Schlitt, T.1    Brazma, A.2
  • 91
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 92
    • 0344475305 scopus 로고    scopus 로고
    • Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour
    • Shingler, V. (2003) Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ Microbiol 5: 1226-1241.
    • (2003) Environ Microbiol , vol.5 , pp. 1226-1241
    • Shingler, V.1
  • 93
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • Shlomi, T., Eisenberg, Y., Sharan, R., and Ruppin, E. (2007) A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 3: 101.
    • (2007) Mol Syst Biol , vol.3 , pp. 101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 94
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich, I., Dougherty, E.R., Kim, S., and Zhang, W. (2002) Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-274.
    • (2002) Bioinformatics , vol.18 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 95
    • 41149090591 scopus 로고    scopus 로고
    • Mining logic gates in prokaryotic transcriptional regulation networks
    • Silva-Rocha, R., and de Lorenzo, V. (2008) Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett 582: 1237-1244.
    • (2008) FEBS Lett , vol.582 , pp. 1237-1244
    • Silva-Rocha, R.1    de Lorenzo, V.2
  • 96
    • 77955155615 scopus 로고    scopus 로고
    • Noise and robustness in prokaryotic regulatory networks
    • Silva-Rocha, R., and de Lorenzo, V. (2010) Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol 64: 257-275.
    • (2010) Annu Rev Microbiol , vol.64 , pp. 257-275
    • Silva-Rocha, R.1    de Lorenzo, V.2
  • 97
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele, I., and Palsson, B.O. (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 98
    • 4544275675 scopus 로고    scopus 로고
    • Bacterial transcriptional regulators for degradation pathways of aromatic compounds
    • Tropel, D., and Van Der Meer, J.R. (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68: 474-500.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 474-500
    • Tropel, D.1    Van Der Meer, J.R.2
  • 99
    • 25144446779 scopus 로고    scopus 로고
    • Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2
    • Velazquez, F., Parro, V., and de Lorenzo, V. (2005) Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2. Mol Microbiol 57: 1557-1569.
    • (2005) Mol Microbiol , vol.57 , pp. 1557-1569
    • Velazquez, F.1    Parro, V.2    de Lorenzo, V.3
  • 100
    • 47049120518 scopus 로고    scopus 로고
    • Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma 54-promoter Pu to the response regulator PprA
    • Vitale, E., Milani, A., Renzi, F., Galli, E., Rescalli, E., de Lorenzo, V., and Bertoni, G. (2008) Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma 54-promoter Pu to the response regulator PprA. Mol Microbiol 69: 698-713.
    • (2008) Mol Microbiol , vol.69 , pp. 698-713
    • Vitale, E.1    Milani, A.2    Renzi, F.3    Galli, E.4    Rescalli, E.5    de Lorenzo, V.6    Bertoni, G.7
  • 101
    • 77958162913 scopus 로고    scopus 로고
    • Develop reusable and combinable designs for transcriptional logic gates
    • Zhan, J., Ding, B., Ma, R., Ma, X., Su, X., Zhao, Y., etal. (2010) Develop reusable and combinable designs for transcriptional logic gates. Mol Syst Biol 6: 388.
    • (2010) Mol Syst Biol , vol.6 , pp. 388
    • Zhan, J.1    Ding, B.2    Ma, R.3    Ma, X.4    Su, X.5    Zhao, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.