Genetic and biophysical studies of diphtheria toxin repressor (DtxR) and the hyperactive mutant DtxR(E175K) support a multistep model of activation

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.

Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539

The accumulation of manganese ions is crucial for scavenging reactive oxygen species and protecting the proteome of Deinococcus radiodurans (Dr). However, metal homeostasis still needs to be tightly regulated to avoid toxicity. DR2539, a dimeric transcription regulator, plays a key role in Dr manganese homeostasis. Despite comprising three well-conserved domains - a DNA-binding domain, a dimerisation domain, and an ancillary domain - the mechanisms underlying both, metal ion activation and DNA recognition remain elusive. In this study, we present biophysical analyses and the structure of the dimerisation and DNA-binding domains of DR2539 in its holo-form and in complex with the 21 base pair pseudo-palindromic repeat of the dr1709 promoter region, shedding light on these activation and recognition mechanisms. The dimer presents eight manganese binding sites that induce structural conformations essential for DNA binding. The analysis of the protein-DNA interfaces elucidates the significance of Tyr59 and helix α3 sequence in the interaction with the DNA. Finally, the structure in solution as determined by small-angle X-ray scattering experiments and supported by AlphaFold modeling provides a model illustrating the conformational changes induced upon metal binding.

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii

Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.

The molecular mechanisms of the bacterial iron sensor IdeR

Life 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.

Corynebacterium diphtheriae: Diphtheria Toxin, the tox Operon, and Its Regulation by Fe2+ Activation of apo-DtxR

Diphtheria is one of the most well studied of all the bacterial infectious diseases. These milestone studies of toxigenic Corynebacterium diphtheriae along with its primary virulence determinant, diphtheria toxin, have established the paradigm for the study of other related bacterial protein toxins. This review highlights those studies that have contributed to our current understanding of the structure-function relationships of diphtheria toxin, the molecular mechanism of its entry into the eukaryotic cell cytosol, the regulation of diphtheria tox expression by holo-DtxR, and the molecular basis of transition metal ion activation of apo-DtxR itself. These seminal studies have laid the foundation for the protein engineering of diphtheria toxin and the development of highly potent eukaryotic cell-surface receptor-targeted fusion protein toxins for the treatment of human diseases that range from T cell malignancies to steroid-resistant graft-versus-host disease to metastatic melanoma. This deeper scientific understanding of diphtheria toxin and the regulation of its expression have metamorphosed the third-most-potent bacterial toxin known into a life-saving targeted protein therapeutic, thereby at least partially fulfilling Paul Erlich's concept of a magic bullet-"a chemical that binds to and specifically kills microbes or tumor cells."

Efficient preparation and metal specificity of the regulatory protein TroR from the human pathogen Treponema pallidum

TroR is a putative metal-dependent regulatory protein that has been linked to the virulence of the human pathogen Treponema pallidum. It shares high homology with the well-known iron-dependent regulatory protein DtxR from Corynebacterium diphtheriae, as well as the manganese-dependent MntR from Bacillus subtilis. However, it has been uncertain whether manganese or zinc is the natural cofactor of TroR to date. Herein, we established an efficient method named "double-fusion tagging" to obtain soluble TroR for the first time. A series of studies, including ICP, CD, fluorescence, ITC, and electrophoresis mobility shift assay (EMSA), were performed to resolve the discrepancies in its metal-binding specificity. In addition, bioinformatic analysis as well as mutation studies were carried out to find the genetic relationships of TroR with its homology proteins. In conclusion, our findings indicate that TroR is a manganese-dependent rather than a zinc-dependent regulatory protein.

A quantitative measure of electrostatic perturbation in holo and apo enzymes induced by structural changes

Biological pathways are subject to subtle manipulations that achieve a wide range of functional variation in differing physiological niches. In many instances, changes in the structure of an enzyme on ligand binding germinate electrostatic perturbations that form the basis of its changed catalytic or transcriptional efficiency. Computational methods that seek to gain insights into the electrostatic changes in enzymes require expertise to setup and computing prowess. In the current work, we present a fast, easy and reliable methodology to compute electrostatic perturbations induced by ligand binding (MEPP). The theoretical foundation of MEPP is the conserved electrostatic potential difference (EPD) in cognate pairs of active site residues in proteins with the same functionality. Previously, this invariance has been used to unravel promiscuous serine protease and metallo-β-lactamase scaffolds in alkaline phosphatases. Given that a similarity in EPD is significant, we expect differences in the EPD to be significant too. MEPP identifies residues or domains that undergo significant electrostatic perturbations, and also enumerates residue pairs that undergo significant polarity change. The gain in a certain polarity of a residue with respect to neighboring residues, or the reversal of polarity between two residues might indicate a change in the preferred ligand. The methodology of MEPP has been demonstrated on several enzymes that employ varying mechanisms to perform their roles. For example, we have attributed the change in polarity in residue pairs to be responsible for the loss of metal ion binding in fructose 1,6-bisphosphatases, and corroborated the pre-organized state of the active site of the enzyme with respect to functionally relevant changes in electric fields in ketosteroid isomerases.

Zn(II) stimulation of Fe(II)-activated repression in the iron-dependent repressor from Mycobacterium tuberculosis

Thermodynamic measurements of Fe(II) binding and activation of repressor function in the iron-dependent repressor from Mycobacterium tuberculosis (IdeR) are reported. IdeR, a member of the diphtheria toxin repressor family of proteins, regulates iron homeostasis and contributes to the virulence response in M. tuberculosis. Although iron is the physiological ligand, this is the first detailed analysis of iron binding and activation in this protein. The results showed that IdeR binds 2 equiv of Fe(II) with dissociation constants that differ by a factor of 25. The high- and low-affinity iron binding sites were assigned to physical binding sites I and II, respectively, using metal binding site mutants. IdeR was also found to contain a high-affinity Zn(II) binding site that was assigned to physical metal binding site II through the use of binding site mutants and metal competition assays. Fe(II) binding was modestly weaker in the presence of Zn(II), but the coupled metal binding-DNA binding affinity was significantly stronger, requiring 30-fold less Fe(II) to activate DNA binding compared to Fe(II) alone. Together, these results suggest that IdeR is a mixed-metal repressor, where Zn(II) acts as a structural metal and Fe(II) acts to trigger the physiologically relevant promoter binding. This new model for IdeR activation provides a better understanding of IdeR and the biology of iron homeostasis in M. tuberculosis.

Metalloregulatory proteins: metal selectivity and allosteric switching

Prokaryotic organisms have evolved the capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins controls the expression of genes encoding membrane transporters and metal trafficking proteins that collectively manage metal homeostasis and resistance. These "metal sensors" are specialized allosteric proteins, in which the direct binding of a specific or small number of "cognate" metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structure thereby converting a poor promoter to a strong one. In this review, we discuss our current understanding of the features that control metal specificity of the allosteric response in these systems, and the role that structure, thermodynamics and conformational dynamics play in mediating allosteric activation or inhibition of DNA binding.

Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K)

The metal-ion-activated diphtheria toxin repressor (DtxR) is responsible for the regulation of virulence and other genes in Corynebacterium diphtheriae. A single point mutation in DtxR, DtxR(E175K), causes this mutant repressor to have a hyperactive phenotype. Mice infected with Mycobacterium tuberculosis transformed with plasmids carrying this mutant gene show reduced signs of the tuberculosis infection. Corynebacterial DtxR is able to complement mycobacterial IdeR and vice versa. To date, an explanation for the hyperactivity of DtxR(E175K) has remained elusive. In an attempt to address this issue, we have solved the first crystal structure of DtxR(E175K) and characterized this mutant using circular dichroism, isothermal titration calorimetry, and other biochemical techniques. The results show that although DtxR(E175K) and the wild type have similar secondary structures, DtxR(E175K) gains additional thermostability upon activation with metal ions, which may lead to this mutant requiring a lower concentration of metal ions to reach the same levels of thermostability as the wild-type protein. The E175K mutation causes binding site 1 to retain metal ion bound at all times, which can only be removed by incubation with an ion chelator. The crystal structure of DtxR(E175K) shows an empty binding site 2 without evidence of oxidation of Cys102. The association constant for this low-affinity binding site of DtxR(E175K) obtained from calorimetric titration with Ni(II) is K(a)=7.6+/-0.5x10(4), which is very similar to the reported value for the wild-type repressor, K(a)=6.3x10(4). Both the wild type and DtxR(E175K) require the same amount of metal ion to produce a shift in the electrophoretic mobility shift assay, but unlike the wild type, DtxR(E175K) binding to its cognate DNA [tox promoter-operator (toxPO)] does not require metal-ion supplementation in the running buffer. In the timescale of these experiments, the Mn(II)-DtxR(E175K)-toxPO complex is insensitive to changes in the environmental cation concentrations. In addition to Mn(II), Ni(II), Co(II), Cd(II), and Zn(II) are able to sustain the hyperactive phenotype. These results demonstrate a prominent role of binding site 1 in the activation of DtxR and support the hypothesis that DtxR(E175K) attenuates the expression of virulence due to the decreased ability of the Me(II)-DtxR(E175K)-toxPO complex to dissociate at low concentrations of metal ions.

Cys-92, Cys-95, and the C-terminal 12 residues of the Vibrio harveyi ferric uptake regulator (Fur) are functionally inessential

Ferric uptake regulator (Fur) is a global regulator involved in multiple aspects of bacterial life. The gene encoding the Vibrio harveyi Fur (FurVh) was cloned from a pathogenic V. harveyi strain isolated from diseased fish. FurVh shares 77% overall sequence identity with the Escherichia coli Fur (FurEc) and could complement a mutant of FurEc. Like FurEc, FurVh, possesses two cysteine residues at positions 92 and 95, yet unlike FurEc, in which these cysteine residues constitute part of the metal ion coordination site and hence are vital to the repressor activity, C92 and C95 of FurVh proved to be functionally inessential. Further study identified a Vibrio Fur signature sequence, which is preserved in all the ten Vibrio Fur proteins that have been discovered to date but in none of the non-vibrio Fur proteins. Site-directed and random mutation analyses of the signature residues, the cysteine residues, and seven highly charged amino acid residues indicated that D9, H32, C137, and K138 of FurVh are functionally important but D9, C137, and K138 can be replaced by more than one functional substitutes. Systematic deletion analysis demonstrated that the C-terminal 12 residues of FurVh are functionally inessential. These results (i) indicated that the activation mechanism, or certain aspects of which, of FurVh is possibly different from that of FurEc; and (ii) suggested that it is not very likely that the C-terminal 12 residues play any significant role in the activation or stability of FurVh; and (iii) provided insights into the potential function of the local structure involving C137 and K138.

The SH3-like domain switches its interaction partners to modulate the repression activity of mycobacterial iron-dependent transcription regulator in response to metal ion fluctuations

Iron-dependent regulator (IdeR), a metal ion-activated pleiotropic transcription factor, plays a critical role in maintaining the intracellular iron homeostasis in Mycobacteria, which is important for the normal growth of the cells. This study was initially performed in an attempt to elucidate all potential interactions between the various domains of IdeR that occur in living mycobacterial cells. This led to a hitherto unidentified self-association for the SH3-like domain of IdeR. Further studies demonstrate that the SH3-like domain interacts with different partners in the dimeric forms of IdeR depending on the levels of metal ions in the environment: it undergoes inter-subunit self-association in the metal-free DNA-non-binding form, but interacts with the N-terminal domain in the metal-bound DNA-binding form in an intra-subunit manner to finely modulate the transcription repression activity of IdeR. Our more detailed mapping studies reveal that the SH3-like domain uses an overlapping surface to participate in these two interactions, which therefore occur in a mutually exclusive fashion. This novel mechanism would allow an effective and cooperative interconversion between the two functional forms of IdeR. Our data also demonstrate that a disturbance of the interactions involving the SH3-like domain impairs the transcription repression activity of IdeR and delays the growth of mycobacterial cells.

Transcription of the contiguous sigB, dtxR, and galE genes in Corynebacterium diphtheriae: evidence for multiple transcripts and regulation by environmental factors

The iron-dependent transcriptional regulator DtxR from Corynebacterium diphtheriae is the prototype for a family of metal-dependent regulators found in diverse bacterial species. The structure of DtxR and its action as a repressor have been extensively characterized, but little is known about expression of dtxR. In the current study, we investigated transcription of dtxR as well as the sigB and galE genes located immediately upstream and downstream from dtxR, respectively. We identified two promoters that determine transcription of dtxR. The first, located upstream of sigB, appears to be controlled by an extracytoplasmic function sigma factor. The second, located in the intergenic region between sigB and dtxR, is similar to promoters used by the primary vegetative sigma factors in other actinomycete species. Using quantitative real-time assays, we demonstrated that the number of transcripts initiated upstream from sigB is affected by several environmental factors. In contrast, the presence of sodium dodecyl sulfate was the only factor tested that conclusively affects the number of transcripts initiated in the sigB-dtxR intergenic region. Additionally, we provided evidence for the existence of transcripts that contain sigB, dtxR, and galE. Our studies provide the first quantitative transcriptional analysis of a gene encoding a DtxR family regulator and give new insights into transcriptional regulation in C. diphtheriae.

Both Corynebacterium diphtheriae DtxR(E175K) and Mycobacterium tuberculosis IdeR(D177K) are dominant positive repressors of IdeR-regulated genes in M. tuberculosis

The diphtheria toxin repressor (DtxR) is an important iron-dependent transcriptional regulator of known virulence genes in Corynebacterium diphtheriae. The mycobacterial iron-dependent repressor (IdeR) is phylogenetically closely related to DtxR, with high amino acid similarity in the DNA binding and metal ion binding site domains. We have previously shown that an iron-insensitive, dominant-positive dtxR(E175K) mutant allele from Corynebacterium diphtheriae can be expressed in Mycobacterium tuberculosis and results in an attenuated phenotype in mice. In this paper, we report the M. tuberculosis IdeR(D177K) strain that has the cognate point mutation. We tested four known and predicted IdeR-regulated gene promoters (mbtI, Rv2123, Rv3402c, and Rv1519) using a promoterless green fluorescent protein (GFP) construct. GFP expression from these promoters was abrogated under low-iron conditions in the presence of both IdeR(D177K) and DtxR(E175K), a result confirmed by reverse transcription-PCR. The IdeR regulon can be constitutively repressed in the presence of an integrated copy of ideR containing this point mutation. These data also suggest that mutant IdeR(D177K) has a mechanism similar to that of DtxR(E175K); iron insensitivity occurs as a result of SH3-like domain binding interactions that stabilize the intermediate form of the repressor after ancillary metal ion binding. This construct can be used to elucidate further the IdeR regulon and its virulence genes and to differentiate these from genes regulated by SirR, which does not have this domain.

Analysis of truncated variants of the iron dependent transcriptional regulators fromCorynebacterium diphtheriaeandMycobacterium tuberculosis

Iron dependent regulatory proteins of the diphtheria toxin repressor family regulate transcription in a variety of bacterial species. These regulators have three domains. Domains 1 and 2 are required for DNA- and metal-binding while the role of the third domain is only partially defined. We compared full-length and carboxyl-terminally truncated variants of Corynebacterium diphtheriae DtxR and Mycobacterium tuberculosis IdeR for recognition by antibodies, DNA binding, and repressor activity. The third domain of DtxR contains immunodominant epitopes and is required for full repressor activity in an Escherichia coli reporter system, but it is not required for binding to DNA in vitro. In contrast, the third domain of IdeR is required both for full DNA binding activity in vitro and for repressor activity in vivo. DtxR and IdeR differ significantly in their requirements for domain 3 for DNA-binding and repressor activity.

Functional studies of the Mycobacterium tuberculosis iron-dependent regulator

The iron-dependent regulator (IdeR) protein in Mycobacterium tuberculosis, and its better characterized homologue, the diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae, are iron-dependent regulatory proteins that control gene expression in response to iron availability in bacteria. IdeR regulates several genes required for iron uptake and storage including those involved in the synthesis of transition metal chelators called siderophores that are linked to the M. tuberculosis virulence. In this study, the metal ion and binding affinities for IdeR binding to an fxbA operator duplex DNA were estimated using fluorescence assays. The Fe(2+), Co(2+), and Ni(2+) affinities of the two metal ion binding sites in IdeR that are involved in the activation of the regulator DNA binding process in vitro were independently estimated. Binding to the two metal ion binding sites is apparently cooperative and the two affinities differ significantly. Occupation of the first metal ion binding site causes dimerization of IdeR, and the metal ion affinity is about 4 microM for Ni(2+) and much less for Fe(2+) and Co(2+). Binding of the second metal ion fully activates IdeR for binding to the fxbA operator. The equilibrium metal ion dissociation constants for IdeR-fxbA operator binding are approximately 9 microM for Fe(2+), 13 microM for Ni(2+), and 23 microM for Co(2+). Interestingly, the natural IdeR cofactor, Fe(2+), shows high affinities toward both binding sites. These results provide insight into the possible roles for each metal binding site in IdeR activation.