In vitro activities of an N-terminal truncated form of XylR, a σ54-dependent transcriptional activator of Pseudomonas putida

Journal of Molecular Biology

Volumn 258, Issue 4, 1996, Pages 575-587

  Pérez Martín, José ^a,b   De Lorenzo, Víctor ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ATPase; Enhancers; Pseudomonas; Sigma 54; XylR

Indexed keywords

PSEUDOMONAS; PSEUDOMONAS PUTIDA;

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEIN; DNA BINDING PROTEIN; INTEGRATION HOST FACTOR; MUTANT PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PSEUDOMONAS PUTIDA; TRANSCRIPTION INITIATION;

EID: 0029919623     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0270     Document Type: Article

References (54)

1. Abril, M. A., Buck, M. & Ramos, J. L. (1991). Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for the integration host factor protein. J. Biol. Chem. 266, 5832-5838.
2. Austin, S. & Dixon, R. (1992). The prokaryotic enhancer binding protein NtrC has an ATPase activity which is phosphorylation and DNA dependent. EMBO J. 11, 2219-2228.
3. 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, 18141-18148.
4. 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, 103-107.
5. Berger, D. K., Narberhaus, F., Lee, H. S. & Kustu, S. (1995). In vitro studies of the domains of the nitrogen fixation regulatory protein NifA. J. Bacteriol. 177, 191-199.
6. 54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter. Mol. Microbiol. 19, 7-17.
7. Claverie-Martin, F. & Magasanik, B. (1991). Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli. Proc. Natl Acad. Sci. USA, 88, 1631-1635.
8. 54-dependent Pu promoter of TOL plasmid. EMBO J. 10, 1159-1167.
9. de Lorenzo, V., Cases, I., Herrero, M. & Timmis, K. N. (1993). Early and late response of TOL promoters to pathway inducers: identification of postexponential promoters in Pseudomonas putida with lacZ-tet bicistronic reporters. J. Bacteriol. 175, 6902-6907.
10. 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, 8059-8062.
11. Drummond, M., Whitty P. & Wooten, J. (1986). Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. EMBO J. 5, 441-447.
12. Elliott, T. & Geiduschek, E. P. (1984). Defining a bacteriophage T4 late promoter: absence of a ″-35″ region. Cell, 36, 211-219.
13. 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, 205-213.
14. Flashner, Y., Weiss, D. S., Keener, J. & Kustu, S. (1995). Constitutive forms of the enhancer-binding protein NtrC: evidence that essential oligomerization determinants lie in the central activation domain. J. Mol. Biol. 249, 700-713.
15. Gober, J. W. & Shapiro, L. (1990). Integration host factor is required for the activation of developmentally regulated genes in Caulobacter. Genes Dev. 4, 1494-1504.
16. 54-dependent transcriptional activator, may be negatively controlled by a subdomain in the C-terminal end of its two-component receiver module. Mol. Microbiol. 13, 51-66.
17. Harayama, S. & Timmis, K. N. (1989). Catabolism of aromatic hydrocarbons by Pseudomonas. In Genetics of Bacterial Diversity (Hoopwod, D. A. & Chater, K. I., eds), pp. 154-174, Academic Press, London.
18. 54-dependent transcriptional activator FhlA from Escherichia coli. J. Bacteriol. 177, 2798-2803.
19. Hooper, S., Babst, M., Schlensog, V., Fischer, H. M., Hennecke, H. & Bock, A. (1994). Regulated expression in vitro of genes coding for formate hydrogenolyase components of Escherichia coli. J. Biol. Chem. 269, 19597-19604.
20. Hoover, T. R., Santero, E., Porter, S. & Kustu, S. (1990). Integration host factor stimulates interaction of RNA polymerase with NifA, the transcriptional activator for nitrogen fixation operons. Cell, 63, 11-22.
21. Huala, E. & Ausubel, F. M. (1989). The central domain of Rhizobium meliloti NifA is sufficient to activate transcription from the R. meliloti nifH promoter. J. Bacteriol. 171, 3354-3365.
22. Huala, E., Stigter, J. & Ausubel, F. M. (1992). The central domain of Rhizobium leguminosarum DctD functions independently to activate transcription. J. Bacteriol. 174, 1428-1431.
23. 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, 5182-5186.
24. Inouye, S., Nakazawa, A. & Nakazawa, T. (1988). Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene, 66, 301-306.
25. Inouye, S., Gomada, M., Sangodkar, U. M. X., Nakazawa, A. & Nakazawa, T. (1990). Upstream regulatory sequences for transcriptional activator XylR in the first operon of xylene metabolism of the TOL plasmid. J. Mol. Biol. 216, 251-260.
26. Kustu, S., Santero, E., Keener, J., Popham, D. & Weiss, D. (1989). Expression of sigma-54 (ntrA)-dependent genes is probably united by a common mechanism. Microbiol. Rev. 53, 367-376.
27. Kustu, S., North, A. K. & Weiss, D. (1991). Prokaryotic transcriptional enhancers and enhancer-binding proteins. Trends Biochem. Sci. 16, 397-402.
28. 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, 2266-2270.
29. 54-dependent transcriptional activator. J. Biol. Chem. 269, 20401-20409.
30. Marqués, S. & Ramos, J. L. (1993). Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways. Mol. Microbiol. 9, 923-929.
31. Maxam, A. M. & Gilbert, W. (1980). Sequencing end-labelled DNA with base-specific chemical cleavages. Methods Enzymol. 65, 499-560.
32. Mettke, I., Fiedler, U. & Weiss, V. (1995). Mechanism of activation of a response regulator: interaction of NtrC-P dimers induces ATPase activity J. Bacteriol. 177, 5056-5061.
33. Miller, J. H. (1972). Experiments in Molecular Genetics, pp. 352-355, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. 54-bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 178, 6067-6074.
35. Myers, R. M., Maniatis, T. & Lerman, L. S. (1985). Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 155, 501-527.
36. Nakazawa, T., Inouye, S. & Nakazawa, A. (1990). Regulatory systems for expression of xyl genes on the TOL plasmid. In Pseudomonas: Biotransformations, Pathogenesis & evolving Biotechnology (Silver, S., Chakrabarty A., Glewski, I. & Kaplan, S., eds), pp. 133-140, American Society of Microbiology Washington DC.
37. North, A. K., Klose, K. E., Stedman, K. M. & Kustu, S. (1993). Prokaryotic enhancer-binding proteins reflect eukaryote-like modularity: the puzzle of nitrogen regulatory protein C. J. Bacteriol. 175, 4267-4273.
38. 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.
39. Pérez-Martín, J. & de Lorenzo, V. (1995b). The N-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor. Proc. Natl Acad. Sci. USA, 92, 9392-9396.
40. 54-promoters of the TOL plasmid of Pseudomonas putida. J. Mol. Biol. 258, 562-574.
41. Pérez-Martín, J. & de Lorenzo, V. (1996b). Identification of the repressor subdomain within the signal reception module of the prokaryotic enhancer-binding protein XylR of Pseudomonas putida. J. Biol. Chem. In the press.
42. 54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences. J. Biol. Chem. 269, 22657-22662.
43. Popham, D. L., Szeto, D., Keener, J. & Kustu, S. (1989). Function of a bacterial activator protein that binds to transcriptional enhancers. Science, 243, 629-635.
44. Porter, S. C., North, A. K., Wedel, A. B. & Kustu, S. (1993). Oligomerization of NtrC at the glnA enhancer is required for transcriptional activation. Genes Dev. 7, 2258-2273.
45. Porter, S. C., North, A. K. & Kustu, S. (1995). Mechanism of transcriptional activation by NtrC (Nitrogen Regulatory Protein C): requirement for oligomerization and phosphorylation. In Two-component Signal Transduction (Silhavy, T. & Hoch, J., eds), pp. 147-158, American Society of Microbiology Washington DC.
46. Reitzer, L. & Magasanik, B. (1986). Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell, 45, 785-792.
47. 54-dependent nifH promoter. J. Mol. Biol. 227, 602-620.
48. 54. Cell, 62, 945-954.
49. Shingler, V. & Moore, T. (1994). Sensing aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J. Bacteriol. 176, 1555-1560.
50. Shingler, V. & Pavel, H. (1995). Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds. Mol. Microbiol. 17, 505-513.
51. Su, W., Porter, S. C., Kustu, S. & Echols, H. (1990). DNA-looping and enhancer activity: association between DNA-bound NtrC activator & RNA polymerase at the bacterial glnA promoter. Proc. Natl Acad. Sci. USA, 87, 5504-5508.
52. 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, 2042-2052.
53. 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, 155-167.
54. Wooton, J. C. & Drummond, M. H. (1989). The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins. Protein Eng. 2, 535-543.