Interaction of Cd2+ with Zn finger 3 of transcription factor IIIA: structures and binding to cognate DNA

Comparative transcriptome analysis reveals key genes and coordinated mechanisms in two rice cultivars differing in cadmium accumulation

Although Cd accumulation varies among rice varieties is recognized, the underlying mechanisms are not well clarified. In this study, comparative transcriptome analysis were performed by hydroponic culture system with two rice varieties, Y1540 (high Cd accumulator) and Y15 (low Cd accumulator) under 20 μM Cd stress. Results revealed 17,320 differentially expressed genes (DEGs) in roots of Y15 (7,655 upregulated and 9,665 downregulated) and 17,386 DEGs in roots of Y1540 (8,823 upregulated and 8,563 downregulated) expose to 20 μM Cd stress. Gene ontology (GO) analysis enriched 24 and 26 terms in Y15 and Y1540 respectively, including 23 common terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed 27 and 28 significant pathways in Y15 and Y1540 respectively, with 19 common pathways. Different responses to Cd stress between cultivars were not only reflected in differently enriched GO terms and KEGG pathways but also in different DEGs of 23 common GO terms and significant sequences represented by p-values of 19 common KEGG pathways. Both cultivars resist Cd through common processes with different weights; hence glutathione metabolism, mineral absorption, biosynthesis of secondary metabolites, and degradation of aromatic compounds could be playing a more important role in Y1540, whereas ribosome biogenesis in eukaryotes, mismatch repair, aminoacyl-tRNA biosynthesis, and the cell cycle maybe playing a more important role in Y15. Weighted gene co-expression network analysis (WGCNA) showed that five and three modules were clustered in Y15 and Y1540, respectively, with yellow and brown modules in Y15 and brown modules in Y1540 being significantly related to Cd stress. Further analysis showed that most of hub genes in Y15 were related to signal transduction or transcription factors, while most of hub genes in Y1540 were related to binding, metabolic, and secondary metabolic processes, which demonstrated their different response patterns at transcriptomic level to Cd stress.

Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding

Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.

Zinc finger structure determination by NMR: Why zinc fingers can be a handful

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.

Calcium in Signaling: Its Specificity and Vulnerabilities toward Biogenic and Abiogenic Metal Ions

Divalent calcium ion (Ca²⁺) plays an indispensable role as a second messenger in a myriad of signal transduction processes. Of utmost importance for the faultless functioning of calcium-modulated signaling proteins is their binding selectivity of the native metal cation over rival biogenic/abiogenic metal ion contenders in the intra/extracellular fluids. In this Perspective, we summarize recent findings on the competition between the cognate Ca²⁺ and other biogenic or abiogenic divalent cations for binding to Ca²⁺-signaling proteins or organic cofactors. We describe the competition between the two most abundant intracellular biogenic metal ions (Mg²⁺ and Ca²⁺) for Ca²⁺-binding sites in signaling proteins, followed by the rivalry between native Ca²⁺ and "therapeutic" Li⁺ as well as "toxic" Pb²⁺. We delineate the key factors governing the rivalry between the native and non-native cations in proteins and highlight key implications for the biological performance of the respective proteins/organic cofactors.

Proteomic High Affinity Zn2+ Trafficking: Where Does Metallothionein Fit in?

The cellular constitution of Zn-proteins and Zn-dependent signaling depend on the capacity of Zn²⁺ to find specific binding sites in the face of a plethora of other high affinity ligands. The most prominent of these is metallothionein (MT). It serves as a storage site for Zn²⁺ under various conditions, and has chemical properties that support a dynamic role for MT in zinc trafficking. Consistent with these characteristics, changing the availability of zinc for cells and tissues causes rapid alteration of zinc bound to MT. Nevertheless, zinc trafficking occurs in metallothionein-null animals and cells, hypothetically making use of proteomic binding sites to mediate the intracellular movements of zinc. Like metallothionein, the proteome contains a large concentration of proteins that strongly coordinate zinc. In this environment, free Zn²⁺ may be of little significance. Instead, this review sets forth the basis for the hypothesis that components of the proteome and MT jointly provide the platform for zinc trafficking.

The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart

Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.

Zinc to cadmium replacement in the prokaryotic zinc-finger domain

Given the similar chemical properties of zinc and cadmium, zinc finger domains have been often proposed as mediators of the toxic and carcinogenic effects exerted by this xenobiotic metal. The effects of zinc replacement by cadmium in different eukaryotic zinc fingers have been reported. In the present work, to evaluate the effects of such substitution in the prokaryotic zinc finger, we report a detailed study of its functional and structural consequences on the Ros DNA binding domain (Ros87). We show that this protein, which bears important structural differences with respect to the eukaryotic domains, appears to structurally tolerate the zinc to cadmium substitution and the presence of cadmium does not affect the DNA binding activity of the protein. Moreover, we show for the first time how zinc to cadmium replacement can also take place in a cellular context. Our findings both complement and extend previous results obtained for different eukaryotic zinc fingers, suggesting that metal substitution in zinc fingers may be of relevance to the toxicity and/or carcinogenicity mechanisms of this metal.

Use of (113)Cd NMR to probe the native metal binding sites in metalloproteins: an overview

Our laboratories have actively published in this area for several years and the objective of this chapter is to present as comprehensive an overview as possible. Following a brief review of the basic principles associated with (113)Cd NMR methods, we will present the results from a thorough literature search for (113)Cd chemical shifts from metalloproteins. The updated (113)Cd chemical shift figure in this chapter will further illustrate the excellent correlation of the (113)Cd chemical shift with the nature of the coordinating ligands (N, O, S) and coordination number/geometry, reaffirming how this method can be used not only to identify the nature of the protein ligands in uncharacterized cases but also the dynamics at the metal binding site. Specific examples will be drawn from studies on alkaline phosphatase, Ca(2+) binding proteins, and metallothioneins.In the case of Escherichia coli alkaline phosphatase, a dimeric zinc metalloenzyme where a total of six metal ions (three per monomer) are involved directly or indirectly in providing the enzyme with maximal catalytic activity and structural stability, (113)Cd NMR, in conjunction with (13)C and (31)P NMR methods, were instrumental in separating out the function of each class of metal binding sites. Perhaps most importantly, these studies revealed the chemical basis for negative cooperativity that had been reported for this enzyme under metal deficient conditions. Also noteworthy was the fact that these NMR studies preceded the availability of the X-ray crystal structure.In the case of the calcium binding proteins, we will focus on two proteins: calbindin D(9k) and calmodulin. For calbindin D(9k) and its mutants, (113)Cd NMR has been useful both to follow actual changes in the metal binding sites and the cooperativity in the metal binding. Ligand binding to calmodulin has been studied extensively with (113)Cd NMR showing that the metal binding sites are not directly involved in the ligand binding. The (113)Cd chemical shifts are, however, exquisitely sensitive to minute changes in the metal ion environment.In the case of metallothionein, we will reflect upon how (113)Cd substitution and the establishment of specific Cd to Cys residue connectivity by proton-detected heteronuclear (1)H-(113)Cd multiple-quantum coherence methods (HMQC) was essential for the initial establishment of the 3D structure of metallothioneins, a protein family deficient in the regular secondary structural elements of α-helix and β-sheet and the first native protein identified with bound Cd. The (113)Cd NMR studies also enabled the characterization of the affinity of the individual sites for (113)Cd and, in competition experiments, for other divalent metal ions: Zn, Cu, and Hg.

Mammalian metallothionein in toxicology, cancer, and cancer chemotherapy

The present paper centers on mammalian metallothionein 1 and 2 in relationship to cell and tissue injury beginning with its reaction with Cd²⁺ and then considering its role in the toxicology and chemotherapy of both metals and non-metal electrophiles and oxidants. Intertwined is a consideration of MTs role in tumor cell Zn²⁺ metabolism. The paper updates and expands on our recent review by Petering et al. (Met Ions Life Sci 5:353-398, 2009).

TSQ (6-methoxy-8-p-toluenesulfonamido-quinoline), a common fluorescent sensor for cellular zinc, images zinc proteins

Zn(2+) is a necessary cofactor for thousands of mammalian proteins. Research has suggested that transient fluxes of cellular Zn(2+) are also involved in processes such as apoptosis. Observations of Zn(2+) trafficking have been collected using Zn(2+) responsive fluorescent dyes. A commonly used Zn(2+) fluorophore is 6-methoxy-8-p-toluenesulfonamido-quinoline (TSQ). The chemical species responsible for TSQ's observed fluorescence in resting or activated cells have not been characterized. Parallel fluorescence microscopy and spectrofluorometry of LLC-PK(1) cells incubated with TSQ demonstrated punctate staining that concentrated around the nucleus and was characterized by an emission maximum near 470 nm. Addition of cell permeable Zn-pyrithione resulted in greatly increased, diffuse fluorescence that shifted the emission peak to 490 nm, indicative of the formation of Zn(TSQ)(2). TPEN (N,N,N'N'-tetrakis(-)[2-pyridylmethyl]-ethylenediamine), a cell permeant Zn(2+) chelator, largely quenched TSQ fluorescence returning the residual fluorescence to the 470 nm emission maximum. Gel filtration chromatography of cell supernatant from LLC-PK(1) cells treated with TSQ revealed that TSQ fluorescence (470 nm emission) eluted with the proteome fractions. Similarly, addition of TSQ to proteome prior to chromatography resulted in 470 nm fluorescence emission that was not observed in smaller molecular weight fractions. It is hypothesized that Zn-TSQ fluorescence, blue-shifted from the 490 nm emission maximum of Zn(TSQ)(2), results from ternary complex, TSQ-Zn-protein formation. As an example, Zn-carbonic anhydrase formed a ternary adduct with TSQ characterized by a fluorescence emission maximum of 470 nm and a dissociation constant of 1.55 × 10(-7) M. Quantification of TSQ-Zn-proteome fluorescence indicated that approximately 8% of cellular Zn(2+) was imaged by TSQ. These results were generalized to other cell types and model Zn-proteins.

Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences

Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.

The isolated Cys2His2 site in EC metallothionein mediates metal-specific protein folding

The selectivity of proteins involved in metal ion homeostasis is an important part of the puzzle to understand how cells allocate the correct metal ions to the correct proteins. Due to their similar ligand-binding properties, and their frequent co-existence in soils, essential zinc and toxic cadmium are a particularly challenging couple. Thus, minimisation of competition of Cd(2+) for Zn(2+) sites is of crucial importance for organisms that are in direct contact with soil. Amongst these, plants have an especially critical role, due to their importance for nutrition and energy. We have studied an embryo-specific, zinc-binding metallothionein (E(C)) from wheat by nuclear magnetic resonance, electrospray mass spectrometry, site-directed mutagenesis, and molecular modelling. Wheat E(C) exploits differences in affinities of Cys(4) and Cys(2)His(2) sites for Cd(2+) and Zn(2+) to achieve metal-selective protein folding. We propose that this may constitute a novel mechanism to discriminate between essential Zn(2+) and toxic Cd(2+).

Zinc finger transcription factor Zn3-Sp1 reactions with Cd2+

Cadmium is a major environmental pollutant that causes kidney failure including the inability to resorb nutrients such as glucose. In a mouse kidney cell culture model, Cd(2+) inhibits Na(+)-dependent glucose uptake mediated by SGLT transporters. This defect has been traced to the down-regulation of SGLT mRNA synthesis mediated by the zinc-finger transcription factor, Zn(3)-Sp1. Incubation of Cd(2+) with Zn(2+)-Sp1 inhibited its capacity to bind to GC1, its binding site in the SGLT1 promoter. The extent of reaction was reduced as increasing concentrations of Zn(2+) are simultaneously present in the reaction mixture. The results are consistent with a Cd(2+)-Zn(2+) exchange reaction that inactivates the DNA binding function of the protein. The equilibrium constant for this reaction was calculated as 14 +/- 3 and 7 +/- 4 for the reactions measured by the binding to GC1 and an analogous SGLT2 promoter site. Sequential addition of Cd(2+) and Zn(2+) to Zn(3)-Sp1 failed to inhibit the reduction in DNA binding seen with Cd(2+) alone, indicating that substitution of Zn(2+) by Cd(2+) was followed by a second reaction that failed to respond to Zn(2+). Buffers for the DNA binding reaction (electrophoretic mobility shift assay) contain EDTA and Cd-EDTA is active in the same concentration range as Cd(2+). During the standard 15 min incubation, Cd(2+) down-regulates Zn(3)-Sp1 but is inactive against the adduct, Zn(3)-Sp1.GC1. Kinetic studies demonstrated that with 5 muM Cd(2+), Zn(3)-Sp1 was about 75% inactivated in 15 min, whereas, Zn(3)-Sp1.GC1 was slowly dissociated with 50% still remaining after 60 min. In contrast, Zn(3)-Sp1 bound to a cognate consensus site resisted any reaction over 60 min. An adduct of Zn(3)-Sp1.(polydI-dC) was just as reactive with Cd(2+) as Zn(3)-Sp1. Reexamination of the NMR structure of Zn- and Cd-finger peptides related to Sp1 fingers has revealed subtle changes in conformation of the metalbinding site and DNA-binding helix that occur when Cd(2+) is substituted by Zn(2+).

Cadmium down-regulation of kidney Sp1 binding to mouse SGLT1 and SGLT2 gene promoters: possible reaction of cadmium with the zinc finger domain of Sp1

Cadmium (Cd) exposure causes glucosuria (glucose in the urine). Previously, it was shown that Cd exposure of primary cultures of mouse kidney cells (PMKC) decreased mRNA levels of the glucose transporters, SGLT1 and SGLT2 and that Sp1 from Cd-exposed cells displayed reduced binding to the GC boxes of the mouse SGLT1 promoter in vitro. Here, we identified a GC box upstream of mouse SGLT2 gene. ChIP assays on PMKC revealed that exposure to 5 microM Cd abolished Sp1 binding to SGLT1 GC box while it decreased Sp1 binding to SGLT2 GC sequence by 30% in vivo. The in vitro DNA binding assay, EMSA, demonstrated that binding of Sp1 from Cd (7.5 microM)-treated PMKC to the SGLT2 GC probe was 86% lower than in untreated cells. Sp1 is a zinc finger protein. Compared to PMKC exposed to 5 microM Cd alone, inclusion of 5 microM Zn restored SGLT1 and 2 mRNA levels by 15% and 30%, respectively. Cd (10 microM) decreased the binding of recombinant Sp1 (rhSp1) to SGLT1 and SGLT2 GC probes to 12% and 8% of untreated controls. Cd exerted no effect on GC-bound rhSp1. Co-treatment with Cd and Zn showed that added Zn significantly restored rhSp1 binding to the SGLT1 and SGLT2. Addition of Zn post Cd treatment was not stimulatory. We conclude that Cd can replace Zn in Sp1 DNA binding domain to reduce its binding to GC sites in mouse SGLT1 and SGLT2 promoters.

Metallothionein Toxicology: Metal Ion Trafficking and Cellular Protection

The literature is replete with reports about the involvement of metallothionein in host defense against injurious chemical, biological, and physical agents. Yet, metallothionein's functional roles are still being debated. This review addresses the issues that have left the physiological significance of metallothionein in doubt and moves on to assess the MT's importance in cell toxicology. It is evident that the protein is broadly involved in protecting cells from injury due to toxic metal ions, oxidants, and electrophiles. Attention is focused on MT's structural and chemical properties that confer this widespread role in cell protection. Particular emphasis is placed on the implications of finding that metal ion unsaturated metallothionein is commonly present in many cells and tissues and the question, how does selectivity of reaction with metallothionein take place in the cellular environment that includes large numbers of competing metal binding sites and high concentrations of protein and glutathione sulfhydryl groups?

Zinc binding ligands and cellular zinc trafficking: apo-metallothionein, glutathione, TPEN, proteomic zinc, and Zn-Sp1

Many cell types contain metal-ion unsaturated metallothionein (MT). Considering the Zn(2+) binding affinity of metallothionein, the existence of this species in the intracellular environment constitutes a substantial "thermodynamic sink". Indeed, the mM concentration of glutathione may be thought of in the same way. In order to understand how apo-MT and the rest of the Zn-proteome manage to co-exist, experiments examined the in vitro reactivity of Zn-proteome with apo-MT, glutathione (GSH), and a series of common Zn(2+) chelating agents including N,N,N',N'-(2-pyridylethyl)ethylenediammine (TPEN), EDTA, and [(2,2'-oxyproplylene-dinitrilo]tetraacetic acid (EGTA). Less than 10% of Zn-proteome from U87mg cells reacted with apo-MT or GSH. In contrast, each of the synthetic chelators was 2-3 times more reactive. TPEN, a cell permeant reagent, also reacted rapidly with both Zn-proteome and Zn-MT in LLC-PK(1) cells. Taking a specific zinc finger protein for further study, apo-MT, GSH, and TPEN inhibited the binding of Zn(3)-Sp1 with its cognate DNA site (GC-1) in the sodium-glucose co-transporter promoter of mouse kidney. In contrast, preformation of Zn(3)-Sp1-(GC-1) prevented reaction with apo-MT and GSH; TPEN remained active but at a higher concentration. Whereas, Zn(3)-Sp1 is active in cells containing apo-MT and GSH, exposure of LLC-PK(1) cells to TPEN for 24h largely inactivated its DNA binding activity. The results help to rationalize the steady state presence of cellular apo-MT in the midst of the many, diverse members of the Zn-proteome. They also show that TPEN is a robust intracellular chelator of proteomic Zn(2+).

Reaction of bis[bis(tri-tert-butoxysilanethiolato) cadmium(II)] with 3,5-dimethylpyridine - 113Cd NMR solution study

NMR studies on the reaction of bis[bis(tri-tert-butoxysilanethiolato)cadmium(II)] with 3,5-dimethylpyridine in benzene-d(6) and toluene-d(8) solutions provide clear evidence for the equilibrium character of formation of mixed S,N-ligand cadmium complex.

Effects of Metal Ions on the Conformation and Activity of Acutolysin D from Agkistrodon Acutus Venom

Acutolysin D, isolated from the venom of Agkistrodon acutus, possesses marked haemorrhagic and proteolytic activities. The molecular weight and the absorption coefficients (A (1%) (280)) of acutolyisn D have been determined to be 47,850 +/- 8 amu and 9.3 by mass spectrometer and UV spectrum, respectively. The effects of metal ions on the conformation and activity of acutolysin D have been studied by following fluorescence, circular dichroism and biological activity measurements. Acutolysin D contains two Ca(2+)-binding sites and two Zn(2+)-binding sites determined by atomic absorption spectrophotometer. Zn(2+) is essential for the enzyme activities of acutolysin D, however, the presence of 1 mM Zn(2+) significantly decreases its caseinolytic activity and intrinsic fluorescence intensity at pH 9.0 due to Zn(OH)(2) precipitate formation. Ca(2+) is important for the structural integrity of acutolysin D, and the presence of 1 mM Ca(2+) markedly enhances its caseinolytic activity. Interestingly, the caseinolytic activity which is inhibited partly by Cu(2+), Co(2+), Mn(2+) or Tb(3+) and inhibited completely by Cd(2+), is enhanced by Mg(2+). The fluorescence intensity of the protein decreases in the presence of Cu(2+), Co(2+), Cd(2+) or Mn(2+), but neither for Ca(2+), Mg(2+) nor for Tb(3+). Zn(2+), Ca(2+), Mg(2+), Cu(2+), Mn(2+), Co(2+ )and Tb(3+) have slight effects on its secondary structure contents. In addition, Cd(2+) causes a marked increase of antiparallel beta-sheet content from 45.5% to 60.2%.