1887

Abstract

Expression from the W operon promoter () is under a strict catabolic repression control mediated by the cAMP-catabolite repression protein (CRP) complex in a glucose-containing medium. The promoter is also activated by the integration host factor (IHF) and repressed by the specific transcriptional regulator HpaR when 4-hydroxyphenylacetate (4HPA) is not present in the medium. Expression from the promoter is also repressed in undefined rich medium such as LB, but the molecular basis of this mechanism is not understood. We present and studies to demonstrate the involvement of FIS protein in this catabolic repression. DNase I footprinting experiments show that FIS binds to multiple sites within the promoter. FIS-site I overlaps the CRP-binding site. By using an electromobility shift assay, we demonstrated that FIS efficiently competes with CRP for binding to the promoter, suggesting an antagonist/competitive mechanism. RT-PCR showed that the repression effect is relieved in a FIS deleted strain. The repression role of FIS at was further demonstrated by transcription assays. These results suggest that FIS contributes to silencing the promoter in the exponential phase of growth in an undefined rich medium when FIS is predominantly expressed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/015578-0
2008-07-01
2024-12-07
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/7/2151.html?itemId=/content/journal/micro/10.1099/mic.0.2007/015578-0&mimeType=html&fmt=ahah

References

  1. Azam A. Z., Ishihama A. 1999; Twelve species of DNA-binding protein from Escherichia coli : sequence recognition specificity and DNA binding affinity. J Biol Chem 274:33105–33113
    [Google Scholar]
  2. Ball C. A., Osuna R., Ferguson K. C., Johnson R. C. 1992; Dramatic changes in FIS levels upon nutrient upshift in Escherichia coli . J Bacteriol 174:8043–8056
    [Google Scholar]
  3. Bell A., Gaston K., Williams R., Chapman K., Kolb A., Buc H., Minchin S., Williams J., Busby S. 1990; Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucleic Acids Res 18:7243–7250
    [Google Scholar]
  4. Bosch L., Nilsson L., Vijgenboom E., Verbeek H. 1990; FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli . Biochim Biophys Acta 1050:293–301
    [Google Scholar]
  5. Bradley M. D., Beach M., de Koning J., Pratt T., Osuna R. 2007; Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology 153:2922–2940
    [Google Scholar]
  6. Browning D. F., Beatty C. M., Sanstad E. A., Gunn K. E., Busby S. J. W., Wolfe A. J. 2004a; Modulation of CRP dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol 51:241–254
    [Google Scholar]
  7. Browning D. F., Cole J., Busby S. 2004b; Transcription activation by remodeling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol Microbiol 53:203–215
    [Google Scholar]
  8. Browning D. F., Graninger D., Beatty C., Wolfe A., Cole J., Busby S. 2005; Integration of three signals at the Escherichia coli nrf promoter: a role for FIS protein in catabolic repression. Mol Microbiol 57:496–510
    [Google Scholar]
  9. Busby S., Ebright R. 1999; Transcription activation by catabolite activator protein (CAP). J Mol Biol 293:199–213
    [Google Scholar]
  10. Caramel A., Schnetz K. 2000; Antagonistic control of the Escherichia coli bgl promoter by FIS and CAP in vitro . Mol Microbiol 36:85–92
    [Google Scholar]
  11. Cases I., de Lorenzo V. 1998; Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol 1:303–310
    [Google Scholar]
  12. Cases I., de Lorenzo V. 2000; Genetic evidence of distinct physiological regulation mechanisms in the σ 54 Pu promoter of Pseudomonas putida . J Bacteriol 182:956–960
    [Google Scholar]
  13. Cases I., de Lorenzo V., Pérez-Martin J. 1996; Involvement of σ 54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter. Mol Microbiol 19:7–17
    [Google Scholar]
  14. Cases I., Pérez-Martín J., de Lorenzo V. 1999; The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma54-dependent Pu promoter of the TOL plasmid. J Biol Chem 274:15562–15568
    [Google Scholar]
  15. Claret L., Rouviere-Yaniv J. 1996; Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli . J Mol Biol 263:126–139
    [Google Scholar]
  16. de Lorenzo V., Timmis K. 1994; Analysis and construction of stable phenotypes in gram-negative bacteria with Tn 5 - and Tn 10 -derived minitransposons. Methods Enzymol 235:386–405
    [Google Scholar]
  17. Díaz E., Prieto M. A. 2000; Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11:467–475
    [Google Scholar]
  18. Dinamarca M. A., Ruiz-Manzano A., Rojo F. 2002; Inactivation of cytochrome o ubiquinol oxidase relieves catabolic repression of the Pseudomonas putida GPo1 alkane degradation pathway. J Bacteriol 184:3785–3793
    [Google Scholar]
  19. Ferrández A., García J. L., Díaz E. 2000; Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli . J Biol Chem 275:12214–12222
    [Google Scholar]
  20. Finkel S. E., Johnson R. C. 1992; The FIS protein: it's not for DNA inversion anymore. Mol Microbiol 6:3257
    [Google Scholar]
  21. Galán B., Díaz E., Prieto M. A., García J. L. 2000; Functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of Escherichia coli W: a prototype of a new flavin : NAD(P)H reductase subfamily. J Bacteriol 182:627–636
    [Google Scholar]
  22. Galán B., Kolb A., García J. L., Prieto M. A. 2001; Superimposed levels of regulation of the 4-hydroxyphenylacetate catabolic pathway in Escherichia coli . J Biol Chem 276:37060–37068
    [Google Scholar]
  23. Galán B., Kolb A., Sanz J. M., García J. L., Prieto M. A. 2003; Molecular determinants of the hpa regulatory system: the HpaR repressor. Nucleic Acids Res 31:6598–6609
    [Google Scholar]
  24. Galán B., García J. L., Prieto M. A. 2004; The PaaX repressor, a link between penicillin G acylase and the phenylacetyl-coenzymeA catabolon of Escherichia coli W. J Bacteriol 186:2215–2220
    [Google Scholar]
  25. González-Gil G., Bringmann P., Kahmann R. 1996; FIS is a regulator of metabolism of Escherichia coli . Mol Microbiol 22:21–29
    [Google Scholar]
  26. González-Gil G., Kahmann R., Muskhelishvili G. 1998; Regulation of crp transcription by oscillation between distinct nucleoprotein complexes. EMBO J 17:2877–2885
    [Google Scholar]
  27. Gralla J. D. 2005; Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol 55:973–977
    [Google Scholar]
  28. Hengen P. N., Batram S., Stewart L., Scheneider T. 1997; Information analysis of Fis binding sites. Nucleic Acids Res 25:4994–5002
    [Google Scholar]
  29. Herrero M., de Lorenzo V., Timmis K. N. 1990; Transposon vector containing non-antibiotic selection markers for cloning and stable chromosomal insertion of foreign DNA in gram-negative bacteria. J Bacteriol 172:6557–6567
    [Google Scholar]
  30. Holtel A., Marqués S., Möhler L., Jakubzik U., Timmis K. N. 1994; Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid. J Bacteriol 176:1773–1776
    [Google Scholar]
  31. Kaniga K., Delor I., Cornelis G. R. 1991; A wide-host-range suicide vector for improving reverse genetics in Gram-negative bacteria: inactivation of the blaA gene of Yersinia enterocolitica . Gene 109:137–141
    [Google Scholar]
  32. Kelly A., Goldberg M., Carroll R., Danino V., Hinton J., Dorman C. 2004; A global role for FIS in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 150:2037–2053
    [Google Scholar]
  33. Kolb A., Busby S., Buc H., Garges S., Adhya S. 1993; Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62:749–795
    [Google Scholar]
  34. Marschall C., Labrousse V., Kreimer M., Weichart D., Kolb A., Hengge-Aronis R. 1998; Molecular analysis of the regulation of csiD , a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on σ S and requires activation by cAMP-CRP. J Mol Biol 276:339–353
    [Google Scholar]
  35. Maxam A. M., Gilbert W. 1977; A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564
    [Google Scholar]
  36. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  37. Moreno R., Ruiz-Manzano A., Yuste L., Rojo F. 2007; The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. Mol Microbiol 64:665–675
    [Google Scholar]
  38. Nash H. A., Robertson C. A., Flamm E., Weisberg R. A., Miller H. I. 1987; Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J Bacteriol 169:4124–4127
    [Google Scholar]
  39. Nilsson L., Emilson V. 1994; Factor for inversion stimulation-dependent growth rate regulation of individual tRNA species in Escherichia coli . J Biol Chem 269:9460–9465
    [Google Scholar]
  40. Petruschka L., Burchhardt G., Muller C., Weihe C., Herrmann H. 2001; The cyo operon of Pseudomonas putida is involved in carbon catabolite repression of phenol degradation. Mol Genet Genomics 266:199–206
    [Google Scholar]
  41. Prieto M. A., García J. L. 1994; Molecular characterization of 4-hydroxyphenylacetate 3-hydroxylase of Escherichia coli . J Biol Chem 269:22823–22829
    [Google Scholar]
  42. Prieto M. A., García J. L. 1997; Identification of a novel positive regulator of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli . Biochem Biophys Res Commun 232:759–765
    [Google Scholar]
  43. Prieto M. A., Pérez-Aranda A., García J. L. 1993; Characterization of an Escherichia coli aromatic hydroxylase with a broad substrate range. J Bacteriol 175:2162–2167
    [Google Scholar]
  44. Prieto M. A., Díaz E., García J. L. 1996; Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J Bacteriol 178:111–120
    [Google Scholar]
  45. Prieto M. A., Galán B., Torres B., Fernández A., Miñambres B., García J. L., Díaz E. 2004; Aromatic metabolism versus carbon availability: the regulatory network that controls catabolism of less preferred carbon sources in Escherichia coli . FEMS Microbiol Rev 28:503–518
    [Google Scholar]
  46. Roper D. I., Fawcett T., Cooper R. A. 1993; The Escherichia coli C homoprotocatechuate degradative operon: hpc gene order, direction of transcription and control of expression. Mol Gen Genet 237:241–250
    [Google Scholar]
  47. Ross W., Thompson J. F., Newlands J. T., Gourse R. L. 1990; E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo . EMBO J 9:3733–3742
    [Google Scholar]
  48. Saier M. H. Jr, Chauvaux S., Deutscher J., Reizer J., Ye J. J. 1995; Protein phosphorylation and regulation of carbon metabolism in gram-negative versus gram-positive bacteria. Trends Biochem Sci 20:267–271
    [Google Scholar]
  49. Saier M. H. Jr, Chauvaux S., Cook G. M., Deutscher J., Paulsen I. T., Reizer J., Ye J. J. 1996; Catabolite repression and inducer control in Gram-positive bacteria. Microbiology 142:217–230
    [Google Scholar]
  50. Sambrook J., Russell D. W. 2001 Molecular Cloning. A Laboratory Manual Cold Spring Harbor, NY: CSHL Press;
  51. Sze C. C., Shingler V. 1999; The alarmone (p)ppGpp mediates physiological-responsive control at the sigma 54-dependent Po promoter. Mol Microbiol 31:1217–1228
    [Google Scholar]
  52. Sze C. C., Moore T., Shingler V. 1996; Growth phase dependent transcription of the σ 54-dependent Po promoter controlling the Pseudomonas derived (methyl) phenol dmp operon of pVI150. J Bacteriol 178:3727–3735
    [Google Scholar]
  53. Xu J., Johnson R. 1995; aldB , an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by FIS and activated by CRP. J Bacteriol 177:3166–3175
    [Google Scholar]
  54. Yuste L., Rojo F. 2001; Role of the crc gene in the catabolite repression of the Pseudomonas putida GPo1 alkane degradation pathway. J Bacteriol 183:6197–6206
    [Google Scholar]
/content/journal/micro/10.1099/mic.0.2007/015578-0
Loading
/content/journal/micro/10.1099/mic.0.2007/015578-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error