• 1
    Abril, M.A., Michan, C., Timmis, K.N., Ramos, J.L. (1989) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J Bacteriol 171: 67826790.
  • 2
    Amann, E., Ochs, B., Abel, K.J. (1988) Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene 69: 301315.
  • 3
    Austin, S. & Dixon, R. (1992) The prokaryotic enhancer binding protein NtrC has an ATPase activity which is phosphorylation and DNA dependent. EMBO J 11: 22192228.
  • 4
    Austin, S. & Lambert, J. (1994) Purification and in vitro activity of a truncated form of AnfA, transcriptional activator protein of alternative nitrogenase from Azotobacter vinelandii. J Biol Chem 269: 1814118148.
  • 5
    Berger, D.K., Narberhaus, F., Kustu, S. (1994) The isolated catalytic domain of NifA, a bacterial enhancer-binding protein, activates transcription in vitro: activation is inhibited by NifL. Proc Natl Acad Sci USA 91: 103107.
  • 6
    Bertoni, G., Pérez-Martín, J., 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: 12211227.
  • 7
    Collado-Vives, J., Magasanik, B., Gralla, J.D. (1991) Control site location and transcriptional regulation in Escherichia coli. Microbiol Rev 55: 371394.
  • 8
    Delgado, A. & Ramos, J.L. (1994) Genetic evidence for activation of the positive transcriptional regulator XylR, a member of the NtrC family of regulators, by effector binding. J Biol Chem 269: 80598062.
  • 9
    De Lorenzo, V., Herrero, M., Metzke, M., Timmis, K.N. (1991) An upstream XylR-and IHF-induced nucleoprotein complex regulates the σ54-dependent Pu promoter of TOL plasmid. EMBO J 10: 11591167.
  • 10
    Deretic, V., Gill, J.F., Chakrabarty, A.M. (1987) Alginate biosynthesis: a model for gene regulation and function in Pseudomonas. Bio/Technology 7: 12491254.
  • 11
    Fernández, S., De Lorenzo, V., Pérez-Martín, J. (1995) Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains. Mol Microbiol 16: 205213.
  • 12
    Gomada, M., Inouye, S., Imaishi, H., Nakazawa, A., Nakazawa, T. (1992) Analysis of an upstream regulatory sequence required for activation of the regulatory gene xylS in xylene metabolism directed by the TOL plasmid of Pseudomonas putida. Mol Gen Genet 233: 419426.
  • 13
    Goosen, N. & Van De Putten, P. (1995) The regulation of transcription initiation by integration host factor. Mol Microbiol 16: 17.
  • 14
    Gu, B., Lee, J.H., Hoover, T.R., Scholl, D., Nixon, B.T. (1994) Rhizobium meliloti DctD, a σ54-dependent transcriptional activator, may be negatively controlled by a subdomain in the C-terminal end of its two-component receiver module. Mol Microbiol 13: 5166.
  • 15
    Holtel, A., Timmis, K.N., Ramos, J.L. (1992) Upstream binding sequences of the XylR activator protein and integration host factor in the xylS gene promoter region of Pseudomonas TOL plasmid. Nucleic Acids Res 20: 17551762.
  • 16
    Hooper, S. & Böck, A. (1995) Effector-mediated stimulation of ATPase activity by the σ54-dependent transcriptional activator FhlA from Escherichia coli. J Bacteriol 177: 27982803.
  • 17
    Hooper, S., Babst, M., Schlensog, V., Fischer, H.M., Hennecke, H., Böck, A. (1994) Regulated expression in vitro of genes coding for formate hydrogenolyase components of Escherichia coli. J Biol Chem 269: 1959719604.
  • 18
    Huala, E., Stigter, J., Ausubel, F.M. (1992) The central domain of Rhizobium leguminosarum DctD functions independently to activate transcription. J Bacteriol 174: 14281431.
  • 19
    Inouye, S., Nakazawa, A., Nakazawa, T. (1987) Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product. Proc Natl Acad Sci USA 84: 51825186.
  • 20
    Inouye, S., Nakazawa, A., Nakazawa, T. (1988) Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene 66: 301306.
  • 21
    Keener, J. & Kustu, S. (1988) Protein kinase and phosphoprotein phosphatase activities of nitrogen regulatory proteins NTRB and NTRC of enteric bacteria: roles of the conserved amino-terminal domain of NTRC. Proc Natl Acad Sci USA 85: 49764980.
  • 22
    Keiler, K.C., Waller, P.R., Sauer, R.T. (1996) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger mRNA. Science 271: 990993.
  • 23
    Kolb, A., Busby, S., Buc, H., Garges, S., Adhya, S. (1993) Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62: 749795.
  • 24
    Klose, K.E., Weiss, D.S., Kustu, S. (1993) Glutamate at the site of phosphorylation of nitrogen-regulatory protein NTRC mimics aspartyl-phosphate and activates the protein. J Mol Biol 232: 6778.
  • 25
    Kwok, T., Yang, J., Pittard, A.J., Wilson, T.J., Davidson, B.E. (1995) Analysis of an Escherichia coli mutant TyrR protein with impaired capacity for tyrosine-mediated repression, but still able to activate at sigma 70 promoters. Mol Microbiol 17: 471481.
  • 26
    Lee, H.S., Berger, D.K., Kustu, S. (1993) Activity of purified NifA, a transcriptional activator of nitrogen fixation genes. Proc Natl Acad Sci USA 90: 22662270.
  • 27
    Lee, J.H., Scholl, D., Nixon, B.T., Hoover, T.R. (1994) Constitutive ATP hydrolysis and transcription activation by a stable truncated form of Rhizobium meliloti DctD, a σ54-dependent transcriptional activator. J Biol Chem 269: 2040120409.
  • 28
    Marqués, S., Holtel, A., Timmis, K.N., Ramos, J.L. (1994) Transcriptional induction kinetics from the promoters of the catabolic pathways of the TOL plasmid pWW0 of Pseudomonas putida for metabolism of aromatic. J Bacteriol 176: 25172524.
  • 29
    Miller, J.H. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  • 30
    Morett, E. & Segovia, L. (1993) The σ54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J Bacteriol 178: 60676074.
  • 31
    Ninfa, A.J. & Magasanik, B. (1986) Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci USA 83: 59095913.
  • 32
    North, A.K., Klose, K.E., Stedman, M., Kustu, S. (1993) Prokaryotic enhancer-binding proteins reflect eukaryotic-like modularity: the puzzle of nitrogen regulatory protein C. J Bacteriol 175: 42674273.
  • 33
    Pérez-Martin, J. & De Lorenzo, V. (1996a) ATP binding to the σ54-dependent activator XylR triggers a protein multimerization cycle catalyzed by UAS DNA. Cell 86: 331339.
  • 34
    Pérez-Martin, J. & De Lorenzo, V. (1996b) In vitro activities of an N-terminal truncated form of XylR, a σ54-dependent transcriptional activator of Pseudomonas putida. J Mol Biol 258: 575587.
  • 35
    Pérez-Martin, J. & De Lorenzo, V. (1996c) Physical and functional analysis of the prokaryotic enhancer of the σ54-promoters of the TOL plasmid of Pseudomonas putida. J Mol Biol 258: 562574.
  • 36
    Pérez-Martin, J., Rojo, F., De Lorenzo, V. (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58: 268290.
  • 37
    Pérez-Martin, J. & De Lorenzo, V. (1997) Clues and consequences of DNA bending in transcription. Annu Rev Microbiol 51: 593628.
  • 38
    Pittard, A.J. (1996) In Escherichia coli and Salmonella. Neidhardt, F.C. (ed.). Washington, DC: American Society for Microbiology Press, pp. 458484.
  • 39
    Pittard, A.J. & Davidson, B.E. (1991) TyrR protein of Escherichia coli., and its role as repressor and activator. Mol Microbiol 5: 15851592.
  • 40
    Popham, D.L., Szeto, D., Keener, J., Kustu, S. (1989) Function of a bacterial activator protein that binds to transcriptional enhancers. Science 243: 629635.
  • 41
    Ramos, J.L., Marqués, S., 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: 341373.
  • 42
    Rojo, F., Nuez, B., Mencía, M., Salas, M. (1993) The main early and late promoters of Bacillus subtilis phage Φ29 form unstable open complexes with σA-RNA polymerase that are stabilized by DNA supercoiling. Nucleic Acids Res 21: 935940.
  • 43
    Sambrook, J., Fritsch, E.F., Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  • 44
    Sasse-Dwight, S. & Gralla, J.D. (1988) Role of eukaryotic type functional domains found in the prokaryotic enhancer receptor factor σ54. Cell 62: 945954.
  • 45
    Shingler, V. & Pavel, H. (1995) Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds. Mol Microbiol 17: 505513.
  • 46
    Soldati, L., Jeenes, D.J., Haas, D. (1987) Effective gene expression in Pseudomonas aeruginosa under the control of the Escherichia coli consensus promoter. FEMS Microbiol Lett 42: 163167.
  • 47
    Song, S. & Jensen, R.A. (1996) PhhR, a divergently transcribed activator of the phenylalanine hydroxylase gene cluster of Pseudomonas aeruginosa. Mol Microbiol 22: 497507.
  • 48
    Valentin-Hansen, P., Søgaard-Andersen, L., Pedersen, H. (1996) A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcription control. Mol Microbiol 20: 461466.
  • 49
    Walker, J.E., Saraste, M., Runswick, M.J., Gay, N.J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1: 945951.
  • 50
    Wedel, A. & Kustu, S. (1995) The bacterial enhancer-binding protein NtrC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. Genes Dev 9: 20422052.
  • 51
    Weiss, D., Batut, J., Klose, K., Kustu, S. (1991) The phosphorylated form of the enhancer-binding protein NtrC has an ATPase activity that is essential for activation of transcription. Cell 67: 155167.
  • 52
    Wilson, T.J., Maroudas, P., Howlett, G.J., Davidson, B.E. (1994) Ligand-induced self-association of the Escherichia coli regulatory protein TyrR. J Mol Biol 238: 309318.
  • 53
    Wooton, J.C. & Drummond, M.H. (1989) The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins. Protein Eng 2: 535543.
  • 54
    Wyman, C., Rombel, I., North, A.K., Bustamante, C., Kustu, S. (1997) Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science 275: 16581661.