IdeR in Mycobacteria: From Target Recognition to Physiological Function

REFERENCES

• Agranoff D., Krishna S. Metal ion homeostasis and intracellular parasitism. Mol Microbio 1998; 28: 403–412, [CSA]
   PubMedGoogle Scholar
• Agranoff D., Monahan I. M., Mangan J. A., Butcher P. D., Krishna S. Mycobacterium tuberculosis expresses a novel pH-dependent divalent cation transporter belonging to the Nramp family. J. Exp. Med. 1999; 5: 717–724, [CSA], [CROSSREF]
   Google Scholar
• Berish S. A., Subbarao S., Chen C. Y., Trees D. L., Morse S. A. Identification and cloning of a fur homolog from Neisseria gonorrhoeae. Infect. Immun. 1993; 61: 4599–4606, [CSA]
   Google Scholar
• Bijlsma J. J., Waidner B., Vliet A. H., Hughes N. J., Hag S., Bereswill S., Kelly D. J., Vandenbroucke-Grauls C. M., Kist M., Kusters J. G. The Helicobacter pylori homologue of the ferric uptake regulator is involved in acid resistance. Infect. Immun. 2002; 70: 606–611, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Boland C. A., Meijer W. G. The iron dependent regulatory protein IdeR DtxR of Rhodococcus equi. FEMS Microbiol. Lett. 2000; 191: 1–5, [CSA]
   Google Scholar
• Butterton J. R., Calderwood S. B. Identification, cloning, and sequencing of a gene required for ferric vibriobactin utilization by Vibrio cholerae. J. Bacteriol. 1994; 176: 5631–5638, [CSA]
   Google Scholar
• Chen C. S., White A., Love J., Murphy J. R., Ringe D. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR. Biochemistry 2000; 39: 10397–10407, [CSA], [CROSSREF]
   PubMedGoogle Scholar
• Chou C. J., Wisedchaisri G., Monfeli R. R., Oram D. M., Holmes R. K., Hol W. G., Beeson C. Functional Studies of the Mycobacterium tuberculosis Iron-dependent Regulator. J. Biol. Chem. 2004; 279: 53554–53561, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Clemens D. L., Lee B. Y., Horwitz M. A. Purification, characterization, and genetic analysis of Mycobacterium tuberculosis urease, a potentially critical determinant of host-pathogen interaction. J. Bacteriol. 1995; 177: 5644–5652, [CSA]
   PubMedGoogle Scholar
• Cronje L., Edmondson N., Eisenach K. D., Bornman L. Iron and iron chelating agents modulate Mycobacterium tuberculosis growth and monocyte-macrophage viability and effector functions. FEMS Immunol. Med. Microbiol. 2005; 45: 103–112, [CSA], [CROSSREF]
   Google Scholar
• Dhople A. M., Ibanez M. A., Poirier T. C. Role of iron in the pathogenesis of Mycobacterium avium infection in mice. Microbios. 1996; 87: 77–87, [CSA]
   Google Scholar
• Domenech P., Reed M. B., Barry C. E. 3rd Contribution of the Mycobacterium tuberculosis MmpL protein family to virulence and drug resistance. Infect. Immun. 2005; 73: 3492–3501, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Doukhan L., Predich M., Nair G., Dussurget O., Mandic-Mulec I., Cole S. T., Smith D. R., Smith I. Genomic organization of the mycobacterial sigma gene cluster. Gene. 1995; 165: 67–70, [CSA], [CROSSREF]
   PubMedGoogle Scholar
• Dussurget O., Rodriguez M., Smith I. An ideR mutant of Mycobacterium smegmatis has a derepressed siderophore production and an altered oxidative-stress response. Mol. Microbiol. 1996; 22: 535–544, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Dussurget O., Rodriguez M., Smith I. Protective role of the mycobacterial IdeR against reactive oxygen species and isoniazid toxicity. Tuber. Lung. Dis. 1998; 79: 99–106, [CSA], [CROSSREF]
   Google Scholar
• Dussurget O., Timm J., Gomez M., Gold B., Yu S., Sabol S. Z., Holmes R. K., Jacobs W. R., Jr., Smith I. Transcriptional control of the iron responsive fxbA gene by the mycobacterial regulator IdeR. J. Bacteriol. 1999; 181: 3402–3408, [CSA]
   Google Scholar
• Feese M. D., Ingason B. P., Goranson-Siekierke J., Holmes R. K., Hol W. G. 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. 2001; 276: 5959–5966, [CSA], [CROSSREF]
   Google Scholar
• Fiss E. H., Yu S., Jacobs W. R., Jr. Identification of genes involved in the sequestration of iron in mycobacteria, the ferric exochelin biosynthetic and uptake pathways. Mol. Microbiol. 1994; 14: 557–569, [CSA]
   PubMed Web of Science ®Google Scholar
• Gold B., Rodriguez G. M., Marras S. A., Pentecost M., Smith I. The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages. Mol. Microbiol. 2001; 42: 851–865, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Heimer S. R., Welch R. A., Perna N. T., Posfai G., Evans P. S., Kaper J. B., Blattner F. R., Mobley H. L. Urease of enterohemorrhagic Escherichia coli, evidence for regulation by fur and a trans-acting factor. Infect. Immun. 2002; 70: 1027–1031, [CSA], [CROSSREF]
   Google Scholar
• Ho W. L., Yu R. C., Chou C. C. Effect of iron limitation on the growth and cytotoxin production of Salmonella choleraesuis SC-5. Int. J. Food. Microbiol. 2004; 3: 295–302, [CSA], [CROSSREF]
   Google Scholar
• Hobson R. J., McBride A. J., Kempsell K. E., Dale J. W. Use of an arrayed promoter-probe library for the identification of macrophage-regulated genes in Mycobacterium tuberculosis. Microbiology 2002; 148: 1571–1579, [CSA]
   PubMed Web of Science ®Google Scholar
• Macham L. P., Ratledge C. A new group of water-soluble iron-binding compounds from Mycobacteria, the exochelins. J. Gen. Microbiol. 1975; 89: 379–382, [CSA]
   Google Scholar
• Manabe Y. C., Saviola B. J., Sun L., Murphy J. R., Bishai W. R. Attenuation of virulence in Mycobacterium tuberculosis expressing a constitutively active iron repressor. Proc. Natl. Acad. Sci. USA 1999; 96: 12844–12848, [CSA], [CROSSREF]
   Google Scholar
• Manabe Y. C., Hatem C. L., Kesavan A. K., Durack J., Murphy J. R. Both Corynebacterium diphtheriae DtxRE175K) and Mycobacterium tuberculosis IdeRD177K) are dominant positive repressors of IdeR-regulated genes in M. tuberculosis. Infect. Immun. 2005; 73: 5988–5994, [CSA], [CROSSREF]
   Google Scholar
• Martinez A., Kolter R. Protection of DNA during oxidative stress by the non specific DNA-binding protein Dps. J. Bacteriol. 1997; 179: 5188–5194, [CSA]
   PubMed Web of Science ®Google Scholar
• Neilands J. B. Evolution of biological iron binding centers. Struct. Bond. 1972; 11: 145–170, [CSA]
   Google Scholar
• Neilands J. B. Microbial iron compounds. Annu. Rev. Biochem. 1981; 50: 715–731, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Neilands J. B. Microbial envelope proteins related to iron. Annu. Rev. Microbiol. 1982; 36: 285–309, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Payne S. M. Iron and virulence in Shigella. Mol. Microbiol. 1989; 3: 1301–1306, [CSA]
   PubMed Web of Science ®Google Scholar
• Pohl E., Qui X., Must L. M., Holmes R. K., Hol W. G. Comparison of high-resolution structures of the diphtheria toxin repressor in complex with cobalt and zinc at the cation-anion binding site. Protein Sci. 1997; 6: 1114–1118, [CSA]
   Google Scholar
• Pohl E., Holmes R. K., Hol W. G. Crystal structure of the iron-dependent regulator IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied. J. Mol. Biol. 1999; 285: 1145–1156, [CSA], [CROSSREF]
   Google Scholar
• Prakash P., Yellaboina S., Ranjan A., Hasnain S. E. Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis ORFs. Bioinformatics 2005; 21: 2161–2166, [CSA], [CROSSREF]
   Google Scholar
• Pressler U., Staudenmaier H., Zimmermann L., Braun V. Genetics of the iron dicitrate transport system of Escherichia coli. J. Bacteriol. 1988; 170: 2716–2724, [CSA]
   PubMed Web of Science ®Google Scholar
• Qiu X., Verlinde C. L., Zhang S., Schmitt M. P., Holmes R. K., Hol W. G. Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors. Structure 1995; 3: 87–100, [CSA], [CROSSREF]
   Google Scholar
• Qiu X., Pohl E., Holmes R. K., Hol W. G. High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor. Biochemistry 1996; 35: 12292–12302, [CSA], [CROSSREF]
   Google Scholar
• Quadri L. E., Sello J., Keating T. A., Weinreb P. H., Walsh C. T. Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. Chem. Biol. 1998; 5: 631–645, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Ratledge C. Iron, mycobacteria and tuberculosis. Tuberculosis 2004; 84: 110–130, [CSA], [CROSSREF]
   PubMedGoogle Scholar
• Ren J., Prescott J. F. Analysis of virulence plasmid gene expression of intra-macrophage and in vitro grown Rhodococcus equi ATCC 33701. Vet. Microbiol. 2003; 94: 167–182, [CSA], [CROSSREF]
   Google Scholar
• Rodriguez G. M., Gold B., Gomez M., Dussurget O., Smith I. Identification and characterization of two divergently transcribed iron regulated genes in Mycobacterium tuberculosis. Tuber Lung Dis. 1999; 79: 287–298, [CSA], [CROSSREF]
   Google Scholar
• Rodriguez G. M., Voskuil M. I., Gold B., Schoolnik G. K., Smith I. IdeR, an Essential Gene in Mycobacterium tuberculosis, Role of IdeR in Iron-Dependent Gene Expression, Iron Metabolism, and Oxidative Stress Response. Infect. Immun. 2002; 70: 3371–3381, [CSA], [CROSSREF]
   PubMed Web of Science ®Google Scholar
• Rodriguez G. M., Smith I. Mechanisms of iron regulation in mycobacteria, role in physiology and virulence. Mol. Microbiol. 2003; 47: 1485–1494, [CSA], [CROSSREF]
   Google Scholar
• Schiering N., Tao X., Zeng H., Murphy J. R., Petsko G. A., Ringe D. Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae. Proc. Natl. Acad. Sci. USA 1995; 92: 9843–9850, [CSA]
   Google Scholar
• Schmitt M. P., Holmes R. K. Iron dependent regulation of diphtheria toxin and siderophore expression by the cloned Corynebacterium diphtheriae repressor gene dtxR in C. diphtheriae C7 strains. Infect. Immun. 1991; 59: 1899–1904, [CSA]
   PubMed Web of Science ®Google Scholar
• Schmitt M. P., Twiddy E. M., Holmes R. K. Purification and Characterization of the Diphtheria Toxin Repressor. Proc. Natl. Acad. Sci. USA 1992; 89: 7576–7580, [CSA]
   Google Scholar
• Schmitt M. P., Holmes R. K. Analysis of diphtheria toxin repressor-operator interactions and characterization of a mutant repressor with decreased binding activity for divalent metals. Mol. Microbiol. 1993; 9: 173–181, [CSA]
   Google Scholar
• Schmitt M. P., Holmes R. K. Cloning, sequence, and footprint analysis of two promoter/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor and iron. J. Bacteriol. 1994; 176: 1141–1149, [CSA]
   Google Scholar
• Schmitt M. P., Predich M., Doukhan L., Smith I., Holmes R. K. 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. 1995; 63: 4284–4289, [CSA]
   Google Scholar
• Skamene E., Schurr E., Gros P. Infection genomics, Nramp1 as a major determinant of natural resistance to intracellular infections. Annu. Rev. Med. 1998; 49: 275–287, [CSA], [CROSSREF]
   Google Scholar
• Sritharan M. Iron as a candidate in virulence and pathogenesis in mycobacteria and other microorganisms. World J. Microbio. Biotech. 2000; 16: 769–780, [CSA], [CROSSREF]
   Google Scholar
• Supek F., Supekova L., Nelson H., Nelson N. Function of metal-ion homeostasis on the cell division cycle, mitochondrial protein processing, sensitivity to mycobacterial infection and brain function. J. Exp. Biol. 1997; 200: 321–330, [CSA]
   Google Scholar
• Tao X., Murphy J. R. 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. 1992; 267: 21761–21764, [CSA]
   Google Scholar
• Tao X., Boyd J., Murphy J. R. Specific Binding of the Diphtheria tox Regulatory Element DtxR to the tox Operator Requires Divalent Heavy Metal Ions and a 9-Base-Pair Interrupted Palindromic Sequence. Proc. Natl. Acad. Sci. USA. 1992; 89: 5897–5901, [CSA]
   PubMedGoogle Scholar
• Tolmasky M. E., Wertheimer A. M., Actis L. A., Crosa J. H. Characterization of the Vibrio anguillarum fur gene, role in regulation of expression of the FatA outer membrane protein and catechols. J. Bacteriol. 1994; 176: 213–220, [CSA]
   Google Scholar
• Venturi V., Ottevanger C., Bracke M., Weisbeek P. Iron regulation of siderophore biosynthesis and transport in Pseudomonas putida WCS358, involvement of a transcriptional activator and the Fur protein. Mol. Microbiol. 1995; 15: 1081–1093, [CSA]
   Google Scholar
• White A., Ding X., vanderSpek J. C., Murphy J. R., Ringe D. Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature 1998; 394: 502–506, [CSA], [CROSSREF]
   Google Scholar
• Wisedchaisri G., Holmes R. K., Hol W. G. Crystal structure of an IdeR-DNA complex reveals a conformational change in activated IdeR for base-specific interactions. J. Mol. Biol. 2004; 342: 1155–1169, [CSA], [CROSSREF]
   Google Scholar
• Yellaboina S., Seshadri J., Kumar M. S., Ranjan A. PredictRegulon, a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic. Acids Res. 2004a; 32: W318–W320, [CSA]
   Google Scholar
• Yellaboina S., Ranjan S., Chakhaiyar P., Hasnain S. E., Ranjan A. Prediction of DtxR regulon, Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiology 2004b; 4: 38, [CSA], [CROSSREF]
   Google Scholar
• Zimmermann L., Hantke K., Braun V. Exogenous induction of the iron dicitrate transport system of Escherichia coli K-12. J. Bacteriol. 1984; 159: 271–277, [CSA]
   Google Scholar