449 research outputs found
The mycobacterial iron-dependent regulator IdeR induces ferritin (bfrB) by alleviating Lsr2 repression
No full textEmerging evidence indicates that precise regulation of iron (Fe) metabolism and maintenance of Fe homeostasis in Mycobacterium tuberculosis (Mtb) are essential for its survival and proliferation in the host. IdeR is a central transcriptional regulator of Mtb genes involved in Fe metabolism. While it is well understood how IdeR functions as a repressor, how it induces transcription of a subset of its targets is still unclear. We investigated the molecular mechanism of IdeR-mediated positive regulation of bfrB, the gene encoding the major Fe-storage protein of Mtb. We found that bfrB induction by Fe required direct interaction of IdeR with a DNA sequence containing four tandem IdeR-binding boxes located upstream of the bfrB promoter. Results of in vivo and in vitro transcription assays identified a direct repressor of bfrB, the histone-like protein Lsr2. IdeR counteracted Lsr2-mediated repression in vitro, suggesting that IdeR induces bfrB transcription by antagonizing the repressor activity of Lsr2. Together, these results elucidate the main mechanism of bfrB positive regulation by IdeR and identify Lsr2 as a new factor contributing to Fe homeostasis in mycobacteria
The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
No full textThe iron-dependent regulator IdeR is the main transcriptional regulator controlling iron homeostasis genes in Actinobacteria, including species from the Corynebacterium, Mycobacterium and Streptomyces genera, as well as the erythromycin-producing bacterium Saccharopolyspora erythraea. Despite being a well-studied transcription factor since the identification of the Diphtheria toxin repressor DtxR three decades ago, the details of how IdeR proteins recognize their highly conserved 19-bp DNA target remain to be elucidated. IdeR makes few direct contacts with DNA bases in its target sequence, and we show here that these contacts are not required for target recognition. The results of our structural and mutational studies support a model wherein IdeR mainly uses an indirect readout mechanism, identifying its targets via the sequence-dependent DNA backbone structure rather than through specific contacts with the DNA bases. Furthermore, we show that IdeR efficiently recognizes a shorter palindromic sequence corresponding to a half binding site as compared to the full 19-bp target previously reported, expanding the number of potential target genes controlled by IdeR proteins.Francisco Javier Marcos-Torres and Dirk Maurer contributed equally to this work.List of authors in preprint: Francisco Javier Marcos-Torres, Dirk Maurer, Julia J. Griese</p
ider(20q) in Myeloid Malignancies
No full textReview on ider(20q) in Myeloid Malignancies, with data on clinics, and the genes involved
The molecular mechanisms of the bacterial iron sensor IdeR
No full textLife came to depend on iron as a cofactor for many essential enzymatic reactions. However, once the atmosphere was oxygenated, iron became both scarce and toxic. Therefore, complex mechanisms have evolved to scavenge iron from an environment in which it is poorly bioavailable, and to tightly regulate intracellular iron contents. In bacteria, this is typically accomplished with the help of one key regulator, an iron-sensing transcription factor. While Gram-negative bacteria and Gram-positive species with low guanine-cytosine (GC) content generally use Fur (ferric uptake regulator) proteins to regulate iron homeostasis, Gram-positive species with high GC content use the functional homolog IdeR (iron-dependent regulator). IdeR controls the expression of iron acquisition and storage genes, repressing the former, and activating the latter in an iron-dependent manner. In bacterial pathogens such as Corynebacterium diphtheriae and Mycobacterium tuberculosis, IdeR is also involved in virulence, whereas in non-pathogenic species such as Streptomyces, it regulates secondary metabolism as well. Although in recent years the focus of research on IdeR has shifted towards drug development, there is much left to learn about the molecular mechanisms of IdeR. Here, we summarize our current understanding of how this important bacterial transcriptional regulator represses and activates transcription, how it is allosterically activated by iron binding, and how it recognizes its DNA target sites, highlighting the open questions that remain to be addressed
Crystal Structures, Metal Activation, and DNA-Binding Properties of Two-Domain IdeR from Mycobacterium tuberculosis
No full textThe iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR) whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants for Co^(2+) and Ni^(2+) activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal ion. However, the Ni^(2+) concentrations required to activate 2D-IdeR for DNA binding appear to be smaller than that for full-length IdeR while the concentration of Co^(2+) required for activation remains the same. We have determined the crystal structures of Ni^(2+)-activated 2D-IdeR at 1.96 Å resolution and its double dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 Å and 2.6 Å, the highest resolutions for DNA complexes for any structures of iron-dependent regulator family members so far. The 2D-IdeR−DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal His_6. This C-terminal tail promotes crystal contacts by forming a β-sheet with the corresponding tail of neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other proteins
The Promoter of Rv0560c Is Induced by Salicylate and Structurally-Related Compounds in <i>Mycobacterium tuberculosis</i>
No full textPMCID: PMC3317779This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
No full textBrune I, Werner H, Hüser AT, Kalinowski J, Pühler A, Tauch A. The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum. BMC Genomics. 2006;7(1): 21.Background: The knowledge about complete bacterial genome sequences opens the way to reconstruct the qualitative topology and global connectivity of transcriptional regulatory networks. Since iron is essential for a variety of cellular processes but also poses problems in biological systems due to its high toxicity, bacteria have evolved complex transcriptional regulatory networks to achieve an effective iron homeostasis. Here, we apply a combination of transcriptomics, bioinformatics, in vitro assays, and comparative genomics to decipher the regulatory network of the iron-dependent transcriptional regulator DtxR of Corynebacterium glutamicum. Results: A deletion of the dtxR gene of C. glutamicum ATCC 13032 led to the mutant strain C. glutamicum IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of C. glutamicum were detected in the dtxR mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in C. glutamicum IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated in vitro by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of C. efficiens, C. diphtheriae and C. jeikeium identified evolutionary conserved elements of the DtxR network. Conclusion: This work adds considerably to our currrent understanding of the transcriptional regulatory network of C. glutamicum genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of C. glutamicum genes
Crystal Structures, Metal Activation, and DNA-Binding Properties of Two-Domain IdeR from <i>Mycobacterium</i> <i>tuberculosis</i><sup>†</sup><sup>,</sup><sup>‡</sup>
No full textThe iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in
Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain
of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR)
whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants
for Co2+ and Ni2+ activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities
of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal
ion. However, the Ni2+ concentrations required to activate 2D-IdeR for DNA binding appear to be smaller
than that for full-length IdeR while the concentration of Co2+ required for activation remains the same.
We have determined the crystal structures of Ni2+-activated 2D-IdeR at 1.96 Å resolution and its double
dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 Å and 2.6 Å, the highest
resolutions for DNA complexes for any structures of iron-dependent regulator family members so far.
The 2D-IdeR−DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases
and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures
reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal
His6. This C-terminal tail promotes crystal contacts by forming a β-sheet with the corresponding tail of
neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other
proteins
Crystal Structures, Metal Activation, and DNA-Binding Properties of Two-Domain IdeR from <i>Mycobacterium</i> <i>tuberculosis</i><sup>†</sup><sup>,</sup><sup>‡</sup>
No full textThe iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in
Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain
of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR)
whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants
for Co2+ and Ni2+ activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities
of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal
ion. However, the Ni2+ concentrations required to activate 2D-IdeR for DNA binding appear to be smaller
than that for full-length IdeR while the concentration of Co2+ required for activation remains the same.
We have determined the crystal structures of Ni2+-activated 2D-IdeR at 1.96 Å resolution and its double
dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 Å and 2.6 Å, the highest
resolutions for DNA complexes for any structures of iron-dependent regulator family members so far.
The 2D-IdeR−DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases
and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures
reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal
His6. This C-terminal tail promotes crystal contacts by forming a β-sheet with the corresponding tail of
neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other
proteins
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