Iron-regulatory proteins DmdR1 and DmdR2 of Streptomyces coelicolor form two different DNA-protein complexes with iron boxes

Biochemical Journal

Volumn 380, Issue 2, 2004, Pages 497-503

  Flores, Francisco J ^a   Martín, Juan F ^a,b  

^a UNIVERSITY OF LEÓN   (Spain)

^b Institute of Biotechnology INBIOTEC Parque Científico de León   (Spain)

Author keywords

Divalent metal dependent regulatory proteins (DmdR1 and DmdR2); Genome; Iron boxes; Iron metabolism; Siderophores; Streptomyces

Indexed keywords

ALDEHYDES; ANTIBODIES; BACTERIA; BIOSYNTHESIS; CHELATION; COMPLEXATION; DNA; ESCHERICHIA COLI; GENES; IRON; METABOLISM;

BIVALENT IONS; GRAM-POSITIVE BACTERIA; HOMOGENEITY; STREPTOMYCES COELICOLOR;

PROTEINS;

2,2' BIPYRIDINE; BACTERIAL PROTEIN; DIMER; DIVALENT METAL DEPENDENT REGULATORY PROTEIN 1; DIVALENT METAL DEPENDENT REGULATORY PROTEIN 2; DNA FRAGMENT; GLUTARALDEHYDE; IRON; IRON REGULATORY FACTOR; METAL CHELATE; SIDEROPHORE; TETRAMER; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CROSS LINKING; DIMERIZATION; DNA PROTEIN COMPLEX; ESCHERICHIA COLI; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PURIFICATION; STREPTOMYCES COELICOLOR;

BACTERIAL PROTEINS; CARBOXY-LYASES; CROSS-LINKING REAGENTS; DIPHTHERIA TOXIN; DNA, BACTERIAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GLUTARAL; IRON-REGULATORY PROTEINS; MACROMOLECULAR SUBSTANCES; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; STREPTOMYCES;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; POSIBACTERIA; STREPTOMYCES; STREPTOMYCES COELICOLOR; SYNTHETIC CONSTRUCT; UNCULTURED ACTINOMYCETE;

EID: 2942707687     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20031945     Document Type: Article

References (39)

1. Boyd, J. and Murphy, J. R. (1988) Analysis of the diphtheria tox promoter by site-directed mutagenesis. J. Bacteriol. 170, 5949-5952
2. Boyd, J., Oza, M. N. and Murphy, J. R. (1990) Molecular cloning and DNA sequence analysis of a diphtheria tox iron-dependent regulatory element (dtxR) from Corynebacterium diphtheriae. Proc. Natl. Acad. Sci. U.S.A. 87, 5968-5972
3. 2+- dependent DNA-binding repressor, DtoxR, in Corynebacterium diphtheriae. Infect. Immun. 57, 3221-3225
4. Rincón, J. (2000) Analysis of the genome region encoding the principal sigma factors RofA and RofB of Rhodococcus fascians D188. Ph.D. thesis, University of León, Spain
5. Tao, X. and Murphy, J. R. (1992) Binding of the metalloregulatory protein DtxR to the diphtheria tox operator requires a divalent heavy metal ion and protects the palindromic sequence from DNase I digestion. J. Biol. Chem. 267, 21761-21764
6. Schmidt, M. P., Twiddy, E. M. and Holmes, R. K. (1992) Purification and characterization of the diphtheria toxin repressor. Proc. Natl. Acad. Sci. U.S.A. 89, 7576-7580
7. Tao, X. and Murphy, J. R. (1993) Cysteine 102 is positioned in the metal binding activation site of the Corynebacterium diphtheriae regulatory element DtxR. Proc. Natl. Acad. Sci. U.S.A. 90, 8524-8528
8. Tao, X., Zeng, H.-Y. and Murphy, J. F. (1995) Transition metal ion activation of DNA binding by the diphtheria tox repressor (DtxR) requires the formation of stable homodimers. Proc. Natl. Acad. Sci. U.S.A. 92, 6803-6807
9. Schmidt, M. P. and Holmes, R. K. (1993) Analysis of diphtheria toxin repressor-operator interaction and characterization of a mutant repressor with decreased binding activity for divalent metals. Mol. Microbiol. 9, 173-181
10. Amador, E., Castro, J. M., Correia, A. and Martín, J. F. (1999) Structure and organization of the rrnD operon of Brevibacterium lactofermentum: analysis of the 16 S rRNA gene. Microbiology 145, 915-924
11. Oguiza, J. A., Marcos, A. T., Malumbres, M. and Martín, J. F. (1996) Multiple sigma factor genes in Brevibacterium lactofermentum: characterization of sigA and sigB. Gene 177, 103-107
12. Oguiza, J. A., Tao, X., Marcos, A. T., Martín, J. F. and Murphy, J. R. (1995) Molecular cloning, DNA sequence analysis, and characterization of the Corynebacterium diphtheriae dtxR homolog from Brevibacterium lactofermentum. J. Bacteriol. 177, 465-467
13. Doukhan, L., Predich, M., Nair, G., Dussurget, O., Mandic-Mulec, I., Cole, S. T., Smith, D. R. and Smith, I. (1995) Genomic organization of the mycobacterial sigma gene cluster. Gene 165, 67-70
14. Schmitt, M. P., Predich, M., Doukhan, L., Smith, I. and Holmes, R. K. (1995) Characterization of an iron-dependent regulatory protein (IdeR) of Mycobacterium tuberculosis as a functional homolog of the diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae. Infect. Immun. 63, 4284-4289
15. Günter-Seeboth, K. and Schupp, T. (1995) Cloning and sequence analysis of the Corynebacterium diphtheriae dtxR homologue from Streptomyces lividans and Streptomyces pilosus encoding a putative iron repressor protein. Gene 166, 117-119
16. Flores, F. J., Rincón, J. and Martín, J. F. (2003) Characterization of the iron-regulated desA promoter of Streptomyces pilosus as a system for controlled gene expression in actinomycetes. Microb. Cell Factories 2, 5
17. Günter-Seeboth, K., Toupet, C. and Schupp, T. (1993) Characterization of an iron-regulated promoter involved in desferrioxamine B synthesis in Streptomyces pilosus: repressor-binding site and homology to the diphtheria toxin gene promoter. J. Bacteriol. 175, 3295-3302
18. Schupp, T., Toupet, C. and Divers, M. (1988) Cloning and expression of two genes of Streptomyces pilosus involved in the biosynthesis of the siderophore desferroxamine B. Gene 64, 179-188
19. Imbert, M., Béchet, M. and Blondeau, R. (1995) Comparison of the main siderophores produced by some species of Streptomyces. Curr. Microbiol. 31, 123-129
20. Kieser, T., Bibb, M. J., Buttner, M. J., Chater, K. F. and Hopwood, D. A. (2000) Practical Streptomyces Genetics. The John Innes Foundation, Norwich, U.K.
21. Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn., Cold Spring Harbor Laboratory Press, Plainview, NY
22. Dunbar, B. S. and Schwoebel, E. D. (1990) Preparation of polyclonal antibodies. Methods Enzymol. 182, 663-670
23. Harlow, E. and Lane, D. (1988) Antibodies. A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, NY
24. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of head of bacteriophage T4. Nature (London) 227, 680-685
25. Feese, M. D., Ingason, B. P., Goranson-Siekierke, J., Holmes, R. K. and Hol, W. G. (2001) Crystal structure of the iron-dependent regulator from Mycobacterium tuberculosis at 2.0-Å resolution reveals the Src homology domain 3-like fold and metal binding function of the third domain. J. Biol. Chem. 276, 5959-5966
26. Pohl, E., Holmes, R. K. and Hol, W. G. J. (1999) Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied. J. Mol. Biol. 285, 1145-1156
27. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714-2723
28. Peitsch, M. C. (1995) Protein modelling by e-mail. Biotechniques 13, 658-660
29. Peitsch, M. C. (1996) ProMod and Swiss-Model: internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24, 274-279
30. Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M., Challis, G. L., Thompson, N. R., James, K. D., Harris, D. E., Quail, M. A., Kieser, H., Harper, D. et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature (London) 417, 141-147
31. Challis, G. L. and Ravel, J. (2000) Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS Microbiol. Lett. 187, 111-114
32. Boland, C. A. and Meijer, W. G. (2000) The iron dependent regulatory protein IdeR (DtxR) of Rhodococcus equi. FEMS Microbiol. Lett. 191, 1-5
33. Lieser, S. A., Davis, T. C., Helmann, J. D. and Cohen, S. M. (2003) DNA-binding and oligomerization studies of the manganese (II) metalloregulatory protein MntR from Bacillus subtilis. Biochemistry 42, 12634-12642
34. Hill, P. J., Cockayne, A., Landers, P., Morrisey, J. A., Sims, C. M. and Williams, P. (1998) SirR, a novel iron-dependent repressor in Staphylococcus epidermidis. Infect. Immun. 66, 4123-4129
35. 2+) permease in Streptococcus gordonii is regulated by a diphtheria toxin metallorepressor-like protein ScaR. Mol. Microbiol. 38, 140-153
36. Kitten, T., Munro, C. L., Michalek, S. M. and Macrima, F. (2000) Genetic characterization of a Streptococcus mutatis Lral family operon and role in virulence. Infect. Immun. 68, 4441-4451
37. 2+-dependent mechanism. J. Bacteriol. 184, 6882-6892
38. Chen, C. S., White, A., Love, J., Murphy, J. R. and Ringe, D. (2000) Methyl groups of thymine bases are important for nucleic acid recognition by DtxR. Biochemistry 39, 10397-10407
39. White, A., Ding, X., van der Spek, J. C., Murphy, J. R. and Ringe, D. (1998) Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature (London) 394, 502-506