Transition metals in control of gene expression

Nano-biogenic heavy metals adsorptive remediation for enhanced soil health and sustainable agricultural production

Hazardous heavy metal (HM) pollution constitutes a pervasive global challenge, posing substantial risks to ecosystems and human health. The exigency for expeditious detection, meticulous monitoring, and efficacious remediation of HM within ecosystems is indisputable. Soil contamination, stemming from a myriad of anthropogenic activities, emerges as a principal conduit for HM ingress into the food chain. Traditional soil remediation modalities for HM elimination, while effective are labor-intensive, susceptible to secondary contamination, and exhibit limited efficacy in regions characterized by low metal toxicity. In response to these exigencies, the eco-friendly paradigm of bioremediation has garnered prominence as a financially judicious and sustainable remedial strategy. This approach entails the utilization of hyperaccumulators, Genetically Modified Microorganisms (GMM), and advantageous microbes. The current review offers a comprehensive elucidation of cutting-edge phyto/microbe-based bioremediation techniques, with a specific emphasis on their amalgamation with nanotechnology. Accentuating their pivotal role in advancing sustainable agricultural practices, the review meticulously dissects the synergistic interplay between plants and microbes, underscoring their adeptness in HM remediation sans secondary contamination. Moreover, the review scrutinizes the challenges intrinsic to implementing bioremediation-nanotechnology interface techniques and propounds innovative resolutions. These discernments proffer auspicious trajectories for the future of agriculture. Through the environmentally conscientious marvels of phyto/microbe bioremediation, an optimistic outlook emerges for environmental preservation and the cultivation of a sustainable, salubrious planet via the conduit of cleaner agricultural production.

Novel pyrazoline and pyrazole "turn on" fluorescent sensors selective for Zn2+/Cd2+ at λem 480 nm and Fe3+/Fe2+ at λem 465 nm in MeCN

A small series of simple pyrazoline and pyrazole based sensors, all derived from the same chalcone precursors, were synthesised, characterised and screened for their fluorescence "turn on" properties in the presence of multiple metals. Pyrazole 8 displayed an excellent fluorescence profile with approx. 20× fold increase in λem 480 nm with Zn2+ compared to a 2.5× fold increase with Cd2+. Pyrazole 9 displayed a 30× fold increase at λem 465 nm for Fe3+ compared to Fe2+ with a Fe3+ limit of detection of 0.025 μM. The corresponding pyrazolines displayed contrasting properties with important implications for future pyrazoline and pyrazole sensor design.

The Copper Efflux Regulator (CueR)

The copper efflux regulator (CueR) is a classical member of the MerR family of metalloregulators and is common in gram-negative bacteria. Through its C-terminal effector-binding domain, CueR senses cytoplasmic copper ions to regulate the transcription of genes contributing to copper homeostasis, an essential process for survival of all cells. In this chapter, we review the regulatory roles of CueR in the model organism Escherichia coli and the mechanisms for CueR in copper binding, DNA recognition, and interplay with RNA polymerase in regulating transcription. In light of biochemical and structural analyses, we provide molecular details for how CueR represses transcription in the absence of copper ions, how copper ions mediate CueR conformational change to form holo CueR, and how CueR bends and twists promoter DNA to activate transcription. We also characterize the functional domains and key residues involved in these processes. Since CueR is a representative member of the MerR family, elucidating its regulatory mechanisms could help to understand the CueR-like regulators in other organisms and facilitate the understanding of other metalloregulators in the same family.

Transition Metal Sensing with Nitrogenated Holey Graphene: A First-Principles Investigation

The toxicity of transition metals, including copper(II), manganese(II), iron(II), zinc(II), hexavalent chromium, and cobalt(II), at elevated concentrations presents a significant threat to living organisms. Thus, the development of efficient sensors capable of detecting these metals is of utmost importance. This study explores the utilization of two-dimensional nitrogenated holey graphene (C₂N) nanosheet as a sensor for toxic transition metals. The C₂N nanosheet's periodic shape and standard pore size render it well suited for adsorbing transition metals. The interaction energies between transition metals and C₂N nanosheets were calculated in both gas and solvent phases and were found to primarily result from physisorption, except for manganese and iron which exhibited chemisorption. To assess the interactions, we employed NCI, SAPT0, and QTAIM analyses, as well as FMO and NBO analysis, to examine the electronic properties of the TM@C₂N system. Our results indicated that the adsorption of copper and chromium significantly reduced the HOMO-LUMO energy gap of C₂N and significantly increased its electrical conductivity, confirming the high sensitivity of C₂N towards copper and chromium. The sensitivity test further confirmed the superior sensitivity and selectivity of C₂N towards copper. These findings offer valuable insight into the design and development of sensors for the detection of toxic transition metals.

Zinc and Central Nervous System Disorders

Zinc (Zn²⁺) is the second most abundant necessary trace element in the human body, exerting a critical role in many physiological processes such as cellular proliferation, transcription, apoptosis, growth, immunity, and wound healing. It is an essential catalyst ion for many enzymes and transcription factors. The maintenance of Zn²⁺ homeostasis is essential for the central nervous system, in which Zn²⁺ is abundantly distributed and accumulates in presynaptic vesicles. Synaptic Zn²⁺ is necessary for neural transmission, playing a pivotal role in neurogenesis, cognition, memory, and learning. Emerging data suggest that disruption of Zn²⁺ homeostasis is associated with several central nervous system disorders including Alzheimer's disease, depression, Parkinson's disease, multiple sclerosis, schizophrenia, epilepsy, and traumatic brain injury. Here, we reviewed the correlation between Zn²⁺ and these central nervous system disorders. The potential mechanisms were also included. We hope that this review can provide new clues for the prevention and treatment of nervous system disorders.

Conformations and Local Dynamics of the CopY Metal Sensor Revealed by EPR Spectroscopy

Metal transcription factors regulate metal concentrations in eukaryotic and prokaryotic cells. Copper is a metal ion that is being tightly regulated, owing to its dual nature. Whereas copper is an essential nutrient for bacteria, it is also toxic at high concentrations. CopY is a metal-sensitive transcription factor belonging to the copper-responsive repressor family found in Gram-positive bacteria. CopY represses transcription in the presence of Zn(II) ions and initiates transcription in the presence of Cu(I) ions. The complete crystal structure of CopY has not been reported yet, therefore most of the structural information on this protein is based on its similarity to the well-studied MecI protein. In this study, electron paramagnetic resonance (EPR) spectroscopy was used to characterize structural and local dynamical changes in Streptococcus pneumoniae CopY as a function of Zn(II), Cu(I), and DNA binding. We detected different conformations and changes in local dynamics when CopY bound Zn(II), as opposed to Cu(I) ions. Furthermore, we explored the effects of metal ions and DNA on CopY conformation. Our results revealed the sensitivity and selectivity of CopY towards metal ions and provide new insight into the structural mechanism of the CopY transcription factor.

Evaluation of Haloferax mediterranei Strain R4 Capabilities for Cadmium Removal from Brines

Haloferax mediterranei has revealed a high bioremediation potential for several inorganic anions (e.g., nitrates and nitrites) and metals from hypersaline waters and brines. However, it is unclear, to date, whether this microorganism allows Cd (II) bioremediation. Consequently, the main objective of this work was to assess the Cd (II) bioremediation potential of Hfx. mediterranei R4. To this end, Hfx. mediterranei cell growth rate and metal bioaccumulation were investigated using different culture media (complex, CM, and defined medium, DM) containing Cd (II) up to 1 mM. In addition, the elemental profile of the biomass (i.e., Al, Ba, Ca, Co, Cu, Fe, K, Mg, Mn, Na, Ni, Sr and Zn) has also been monitored to gain insight into the metabolic processes that may be taking place at the intracellular level for Cd (II) removal. Because of the formation of CdS precipitate, CM is not a suitable culture media for evaluating Cd bioremediation since metal concentration could not be appropriately controlled. When operating in DM, it was observed that the cell doubling time increases three times in the presence of Cd (II). Hfx. mediterranei can bioaccumulate Cd, showing the highest significant accumulation at concentrations of 0.4 mM (108 ± 12 mg Cd/g dry tissue). Finally, the presence of Cd (II) affects the content of K, Mg, Mn and Zn in the biomass, by increasing K levels up to 27 ± 18% and Mn up to 310 ± 140% and reducing Mg levels up to 55 ± 36% and Zn up to 30 ± 4%. These results suggest that different mechanisms are involved in Cd (II) tolerance by Hfx. mediterranei, resulting in increasing the cell concentration of stress-tolerant elements in the biomass (K and Mn), while lowering the concentration of elements which Cd (II) competes with (Mg and Zn), and that all affects the physiological response of the organism by decreasing its growth rate.

Metal trafficking in the cell: Combining atomic resolution with cellular dimension

Metals are widely present in biological systems as simple ions or complex cofactors, and are involved in a variety of processes essential for life. Their transport inside cells and insertion into the binding sites of the proteins that need metals to function occur through complex and selective pathways involving dedicated multiprotein machineries specifically and transiently interacting with each other, often sharing the coordination of metal ions and/or cofactors. The understanding of these machineries requires integrated approaches, ranging from bioinformatics to experimental investigations, possibly in the cellular context. In this review, we report two case studies where the use of integrated in vitro and in cellulo approaches is necessary to clarify at atomic resolution essential aspects of metal trafficking in cells.

Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor

In Helicobacter pylori, the nickel-responsive NikR transcription factor plays a key role in regulating intracellular nickel concentrations, which is an essential process for survival of this pathogen in the acidic human stomach. Nickel binding to H. pylori NikR (HpNikR) allosterically activates DNA binding to target promoters encoding genes involved in nickel homeostasis and acid adaptation, to either activate or repress their transcription. We previously showed that HpNikR adopts an equilibrium between an open conformation and DNA-binding competent cis and trans states. Nickel binding slows down conformational exchange between these states and shifts the equilibrium toward the binding-competent states. The protein then becomes stabilized in a cis conformation upon binding the ureA promoter. Here, we investigate how nickel binding creates this response and how it is transmitted to the DNA-binding domains. Through mutagenesis, DNA-binding studies, and computational methods, the allosteric response to nickel was found to be propagated from the nickel-binding sites to the DNA-binding domains via the β-sheets of the metal-binding domain and a network of residues at the inter-domain interface. Our computational results suggest that nickel binding increases protein rigidity to slow down the conformational exchange. A thymine base in the ureA promoter sequence, known to be critical for high affinity DNA binding by HpNikR, was also found to be important for the allosteric response, while a modified version of this promoter further highlighted the importance of the DNA sequence in modulating the response. Collectively, our results provide insights into regulation of a key protein for H. pylori survival.

ROI-Finder: machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli (E. Coli), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

ESIPT-Active 8-Hydroxyquinoline-Based Fluorescence Sensor for Zn(II) Detection and Aggregation-Induced Emission of the Zn(II) Complex

A D-π-A type quinoline derivative, 2-(((4-(1, 2, 2-triphenylvinyl)phenyl)imino)methyl)quinolin-8-ol (HL), was synthesized and structurally characterized. The five-membered ring formed by the O-H···N hydrogen bond in HL contributed to the excited-state intramolecular proton transfer (ESIPT) behavior of HL, which was further verified by theoretical computations. Upon coordination with Zn²⁺, the hydroxyl proton in HL was removed, resulting in the inhibition of ESIPT. In the meanwhile, the formed Zn ₂ L ₄ complex displayed aggregation-induced emission (AIE) character in THF/H₂O mixtures, which is conducive to the fluorescence enhancement in aqueous media. Structure analysis suggested that the origin of the AIE characteristic was attributed to restriction of intramolecular rotations along with the formation of J-aggregates. Based on ESIPT coupled with AIE, HL could recognize Zn(II) in aqueous media via an orange fluorescence turn-on mode. Benefitting from the AIE property, chemosensor HL was successfully applied to fabricate test strips for rapid sensing of Zn(II) ions.

Comparison of metal burden in different muscle tissues of Great cormorant (Phalacrocorax carbo)

Concentrations of 12 metals (As, Ba, Cd, Co, Cr, Cu, Hg, Mn, Mo, Ni, Pb and Zn) were examined in the pectoral and thigh muscle of great cormorants (Phalacrocorax carbo). The samples were collected from Central Tisza-Jászság Nature Conservation Area in Hungary. The tissue samples were analysed by inductively coupled plasma optical emission spectroscopy (ICP-OES). The aim of the study was to examine the impacts of heavy metal pollution on the water birds, determine the concentrations of the abovementioned metals in the different muscle tissues of these wetland birds, and provide the basic materials for monitoring the environmental pollution. Among the investigated elements/metals, the detected concentrations of As, Ba, Cd, Co, Cr, Mo and Ni were below the detection limit. Higher concentration of Cu, Hg, Mn and Pb was measured in the pectoral muscle compared to the thigh muscle, but only in the case of Cu and Mn were found significant differences between the tissues. In the case of the Zn concentration, the higher value was detected in the thigh muscle. There were no statistical differences between males and females in either metal concentrations.

Benzimidazole–acid hydrazide Schiff–Mannich combo ligands enable nano–molar detection of Zn2+ via fluorescence turn–on mode from semi–aqueous medium, HuH–7 cells, and plants

Herein, we have synthesized two unsymmetrical and dipodal Schiff–Mannich combo ligands, benzoic acid (3–benzoimidazol–1–ylmethyl–2–hydroxy–5–methyl–benzylidene)–hydrazide (H2BBH) and the hydroxyl analogue, 2–hydroxy–benzoic acid (3–benzoimidazol–1–ylmethyl–2–hydroxy–5–methyl–benzylidene)–hydrazide (H3BSH) for selective detection of Zn2+ in semi–aqueous...

Understanding the Logistics for the Distribution of Heme in Cells

Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.

Interplay between central carbon metabolism and metal homeostasis in mycobacteria and other human pathogens

Bacterial nutrition is a fundamental aspect of pathogenesis. While the host environment is in principle nutrient-rich, hosts have evolved strategies to interfere with nutrient acquisition by pathogens. In turn, pathogens have developed mechanisms to circumvent these restrictions. Changing the availability of bioavailable metal ions is a common strategy used by hosts to limit bacterial replication. Macrophages and neutrophils withhold iron, manganese, and zinc ions to starve bacteria. Alternatively, they can release manganese, zinc, and copper ions to intoxicate microorganisms. Metals are essential micronutrients and participate in catalysis, macromolecular structure, and signalling. This review summarises our current understanding of how central carbon metabolism in pathogens adapts to local fluctuations in free metal ion concentrations. We focus on the transcriptomics and proteomics data produced in studies of the iron-sparing response in Mycobacterium tuberculosis, the etiological agent of tuberculosis, and consequently generate a hypothetical model linking trehalose accumulation, succinate secretion and substrate-level phosphorylation in iron-starved M. tuberculosis. This review also aims to highlight a large gap in our knowledge of pathogen physiology: the interplay between metal homeostasis and central carbon metabolism, two cellular processes which are usually studied separately. Integrating metabolism and metal biology would allow the discovery of new weaknesses in bacterial physiology, leading to the development of novel and improved antibacterial therapies.

Unravelling the mechanisms controlling heme supply and demand

In addition to heme's role as the prosthetic group buried inside many different proteins that are ubiquitous in biology, there is new evidence that heme has substantive roles in cellular signaling and regulation. This means that heme must be available in locations distant from its place of synthesis (mitochondria) in response to transient cellular demands. A longstanding question has been to establish the mechanisms that control the supply and demand for cellular heme. By fusing a monomeric heme-binding peroxidase (ascorbate peroxidase, mAPX) to a monomeric form of green-fluorescent protein (mEGFP), we have developed a heme sensor (mAPXmEGFP) that can respond to heme availability. By means of fluorescence lifetime imaging, this heme sensor can be used to quantify heme concentrations; values of the mean fluorescence lifetime (τ_Mean) for mAPX-mEGFP are shown to be responsive to changes in free (unbound) heme concentration in cells. The results demonstrate that concentrations are typically limited to one molecule or less within cellular compartments. These miniscule amounts of free heme are consistent with a system that sequesters the heme and is able to buffer changes in heme availability while retaining the capability to mobilize heme when and where it is needed. We propose that this exchangeable supply of heme can operate using mechanisms for heme transfer that are analogous to classical ligand-exchange mechanisms. This exquisite control, in which heme is made available for transfer one molecule at a time, protects the cell against the toxic effect of excess heme and offers a simple mechanism for heme-dependent regulation in single-molecule steps.

Lead and zinc interactions - An influence of zinc over lead related toxic manifestations

BACKGROUND

Interaction between metals is known from earlier studies, in which one metal influences the absorption and functional role of other. Lead is known to cause debilitating effects in living organisms and also prevents several essential trace metals from functioning normally.

METHODS

The relevant literature using the key words lead toxicity, lead zinc interaction, zinc nutrition and the ability of zinc to act against lead has been reviewed.

RESULTS

Role of several nutrients in reducing the manifestations of toxic metals have been elucidated recently. Lead damages bio-membranes, causes cognitive disabilities and disturbs the normal process of DNA replication and transcription. Zinc on the other hand helps in proper maintenance of the cellular membranes and plays an important role as a metal cofactor in most of the proteins vital for membrane integrity. Zinc has essential role in cognitive functioning, zinc finger proteins and significantly neutralizes most toxic effects of lead.

CONCLUSION

Increased lead exposure and limited resources for tackling lead poisoning may cause an increased possibility of future environmental emergencies. Interactions between essential nutrient metals and non-essential toxic metals may act as important factor which can be used to target the metal toxicities. An assumption is made that the lead toxicity can be reduced by maintaining the status of essential trace metals like zinc.

CueR activates transcription through a DNA distortion mechanism

The MerR-family transcription factors (TFs) are a large group of bacterial proteins responding to cellular metal ions and multiple antibiotics by binding within central RNA polymerase-binding regions of a promoter. While most TFs alter transcription through protein-protein interactions, MerR TFs are capable of reshaping promoter DNA. To address the question of which mechanism prevails, we determined two cryo-EM structures of transcription activation complexes (TAC) comprising Escherichia coli CueR (a prototype MerR TF), RNAP holoenzyme and promoter DNA. The structures reveal that this TF promotes productive promoter-polymerase association without canonical protein-protein contacts seen between other activator proteins and RNAP. Instead, CueR realigns the key promoter elements in the transcription activation complex by clamp-like protein-DNA interactions: these induce four distinct kinks that ultimately position the -10 element for formation of the transcription bubble. These structural and biochemical results provide strong support for the DNA distortion paradigm of allosteric transcriptional control by MerR TFs.

A DCM-based NIR sensor for selective and sensitive detection of Zn2+ in living cells

Zinc ion is the 2nd abundant transition metal element in human's body. It is responsible for many physiological and biological functioning in the body, such as growth of people, immunity, endocrine, etc. The deficiency of zinc could result in an increasing risk for growth retardation, neurological disorder and infectious disease. Thus, developing a nondestructive method for detecting Zn²⁺ in living systems is important. Here we reported a 2-(2-methyl-4H-ylidene)- malononitrile (DCM)-based NIR probe DF-Zn for selective and sensitive detection of Zn²⁺. The probe DF-Zn is cell-permeable and stable at broad pH range. DF-Zn showed a fast response to Zn²⁺, big stock's shift, and "nude-eye" recognition for Zn²⁺. Moreover, the selective binding of probe DF-Zn to Zn²⁺ was reversible. With the addition of EDTA in buffer solution, reversible response of probe to Zn²⁺ could be observed in MCF-7 cells imaging.

Identification of novel activators of the metal responsive transcription factor (MTF-1) using a gene expression biomarker in a microarray compendium

Environmental exposure to metals is known to cause a number of human toxicities including cancer. Metal-responsive transcription factor 1 (MTF-1) is an important component of metal regulation systems in mammalian cells. Here, we describe a novel method to identify chemicals that activate MTF-1 based on microarray profiling data. MTF-1 biomarker genes were identified that exhibited consistent, robust expression across 10 microarray comparisons examining the effects of metals (zinc, nickel, lead, arsenic, mercury, and silver) on gene expression in human cells. A subset of the resulting 81 biomarker genes was shown to be altered by knockdown of the MTF1 gene including metallothionein family members and a zinc transporter. The ability to correctly identify treatment conditions that activate MTF-1 was determined by comparing the biomarker to microarray comparisons from cells exposed to reference metal activators of MTF-1 using the rank-based Running Fisher algorithm. The balanced accuracy for prediction was 93%. The biomarker was then used to identify organic chemicals that activate MTF-1 from a compendium of 11 725 human gene expression comparisons representing 2582 chemicals. There were 700 chemicals identified that included those known to interact with cellular metals, such as clioquinol and disulfiram, as well as a set of novel chemicals. All nine of the novel chemicals selected for validation were confirmed to activate MTF-1 biomarker genes in MCF-7 cells and to lesser extents in MTF1-null cells by qPCR and targeted RNA-Seq. Overall, our work demonstrates that the biomarker for MTF-1 coupled with the Running Fisher test is a reliable strategy to identify novel chemical modulators of metal homeostasis using gene expression profiling.

A FRET-based fluorescent Zn2+ sensor: 3D ratiometric imaging, flow cytometric tracking and cisplatin-induced Zn2+ fluctuation monitoring

Monitoring labile Zn²⁺ homeostasis is of great importance for the study of physiological functions of Zn²⁺ in biological systems. Here we report a novel ratiometric fluorescent Zn²⁺ sensor, CPBT, which was constructed based on chelation-induced alteration of FRET efficiency. CPBT was readily cell membrane permeable and showed a slight preferential localization in the endoplasmic reticulum. With this sensor, 3D ratiometric Zn²⁺ imaging was first realized in the head of zebra fish larvae via Z-stack mode. CPBT could track labile Zn²⁺ in a large number of cells through ratiometric flow cytometric assay. More interestingly, both ratiometric fluorescence imaging and flow cytometric assay demonstrated that the labile Zn²⁺ level in MCF-7 cells (cisplatin-sensitive) decreased while that in SKOV3 cells (cisplatin-insensitive) increased after cisplatin treatment, indicating that Zn²⁺ may play an important role in cisplatin induced signaling pathways in these cancer cells.

A Zn²⁺ sensor exhibiting 3D ratiometric imaging and flow cytometric ability was constructed based on the FRET mechanism, and cisplatin-induced endogenous labile Zn²⁺ fluctuations were monitored in real time.

A rationally designed peptoid for the selective chelation of Zn2+ over Cu2

The selective removal of Zn²⁺ from proteins by using a synthetic chelator is a promising therapeutic approach for the treatment of various diseases including cancer. Although the chelation of Zn²⁺ is well known, its removal from a protein in the presence of potential competing biologically relevant ions such as Cu²⁺ is hardly explored. Herein we present a peptoid - N-substituted glycine trimer - incorporating a picolyl group at the N-terminus, a non-coordinating but structurally directing benzyl group at the C-terminus and a 2,2':6',2''-terpyridine group in the second position, that selectively binds Zn²⁺ ions in the presence of excess Cu²⁺ ions in water. We further demonstrate that this chelator can selectively bind Zn²⁺ from a pool of excess biologically relevant and competitive ions (Cu²⁺, Fe³⁺, Ca²⁺, Mg²⁺, Na⁺, and K⁺) in a simulated body fluid (SBF), and also its ability to remove Zn²⁺ from a natural zinc protein domain (PYKCPECGKSFSQKSDLVKHQRTHTG) in a SBF.

Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study

Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.

Harnessing chemical exchange: 19F magnetic resonance OFF/ON zinc sensing with a Tm(iii) complex

A fluorinated, thulium(iii) complex (Tm-PFZ-1) serves as an off-on ¹⁹F magnetic resonance probe for Zn(ii). Rapid exchange among different conformations combined with paramagnetic relaxation and chemical shift effects of Tm(iii) effectively eliminate the ¹⁹F NMR/MRI signal in Tm-PFZ-1. Chelation of Zn(ii) induces increased structural rigidity and reduces exchange rate, affording a robust ¹⁹F NMR/MRI signal. Tm-PFZ-1 represents a first-in-class paramagnetic ¹⁹F MR agent that exploits a novel sensing mechanism for Zn(ii) and is the first ¹⁹F MR-based scaffold to provide an "off-on" response to Zn(ii) in aqueous solution.

When is a transcription factor a NAP?

Proteins that regulate transcription often also play an architectural role in the genome. Thus, it has been difficult to define with precision the distinctions between transcription factors and nucleoid-associated proteins (NAPs). Anachronistic descriptions of NAPs as 'histone-like' implied an organizational function in a bacterial chromatin-like complex. Definitions based on protein abundance, regulatory mechanisms, target gene number, or the features of their DNA-binding sites are insufficient as marks of distinction, and trying to distinguish transcription factors and NAPs based on their ranking within regulatory hierarchies or positions in gene-control networks is also unsatisfactory. The terms 'transcription factor' and 'NAP' are ad hoc operational definitions with each protein lying along a spectrum of structural and functional features extending from highly specific actors with few gene targets to those with a pervasive influence on the transcriptome. The Streptomyces BldC protein is used to illustrate these issues.

Allosteric control of metal-responsive transcriptional regulators in bacteria

Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.

Prenatal zinc supplementation attenuates lipopolysaccharide-induced behavioral impairments in maternal immune activation model

Maternal infection during pregnancy is considered a key risk factor for developing schizophrenia in offspring. There is evidence that maternal exposure to infectious agents is associated with fetal zinc deficiency. Due to the essential role of zinc in brain function and development, in the present study, we activated maternal immune system using lipopolysaccharide (LPS) as a model of schizophrenia to examine whether zinc supplementation throughout pregnancy can reverse LPS-induced deleterious effects. To test the hypothesis, pregnant rats were treated with intraperitoneal injection of either saline or LPS (0.5 mg/kg) at gestational day 15 and 16, and zinc supplementation (30 mg/kg) was administered throughout pregnancy by gavage. At postnatal day 60, Y-maze was used to evaluate working memory of offspring. Moreover, the expression levels of catechol O-methyltransferase (COMT) and glutamate decarboxylase 67 (GAD67) were measured in the frontal cortex of the brain samples. Only male offspring prenatally exposed to LPS showed a significant impairment in working memory. In addition, prenatal LPS exposure causes a moderate decrease in GAD67 expression level in the male pups, while COMT expression was found unchanged. Interestingly, zinc supplementation restored the alterations in working memory as well as GAD67 mRNA level in the male rats. No alteration was detected for neither working memory nor COMT/GAD67 genes expression in female offspring. This study demonstrates that zinc supplementation during pregnancy can attenuate LPS-induced impairments in male pups. These results support the idea to consume zinc supplementation during pregnancy to limit neurodevelopmental deficits induced by infections in offspring.

Full-color emission of a Eu3+-based mesoporous hybrid material modulated by Zn2+ ions: emission color changes for Zn2+ sensing via an ion exchange approach

We reported on the fabrication of a multicolor fluorescent sensor for Zn2+ ions based on the Eu complex functionalized mesoporous hybrid material Eu(TTA-MSN)2L (TTA: 2-thenoyltrifluoroacetone, HL: 4'-(4-carboxy-methyleneoxyphenyl)-2,2':6',2''-terpyridinel). The material was characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, and N2 adsorption measurements. The results revealed that the material preserves mesoscopically ordered structures and exhibited highly uniform pore size distributions. Spectroscopic analyses showed that the mesoporous hybrid material Eu(TTA-MSN)2L exhibited the characteristic emission of Eu3+ ions, reasonably long lifetimes (0.62 ms), and high quantum yields (18.4%). Moreover, the material displayed a highly selective and sensitive function toward Zn2+ ions in aqueous solutions. This sensing function could be attributed to the cation exchange of Eu3+ in the parent material Eu(TTA-MSN)2L with Zn2+. More importantly, by only modulating the concentration of Zn2+ ions in the water solution of Eu(TTA-MSN)2L, a tunable full-color emission (including white-light emission) can be generated under single-wavelength excitation. To our knowledge, this effort is the first example of a multicolor emissive sensor for Zn2+ ions in water solutions based on lanthanide mesoporous hybrid material.

A fluorescent and colorimetric Schiff base chemosensor for the detection of Zn2+ and Cu2+: Application in live cell imaging and colorimetric test kit

A novel Schiff base chemosensor HMID, ((E)‑1‑((2‑hydroxy‑3‑methoxybenzylidene)amino)imidazolidine‑2,4‑dione), have been designed and synthesized. Sensor HMID showed a selectivity to Zn²⁺ through fluorescence enhancement in aqueous solution. Its detection limit was analyzed as 11.9 μM. Importantly, compound HMID could be applied to image Zn²⁺ in live cells. Detection mechanism of Zn²⁺ by HMID was suggested to be an effect of chelation-enhanced fluorescence (CHEF) by DFT calculations. Moreover, HMID could detect Cu²⁺ with a change of color from colorless to pink. The selective detection mechanism of Cu²⁺ by HMID was demonstrated to be the promotion of intramolecular charge transfer band by DFT calculations. Additionally, HMID could be employed as a naked-eye colorimetric kit for Cu²⁺. Therefore, HMID has the ability as a 'single sensor for dual targets'.

Transcriptional Regulation of Gene Expression by Metalloproteins

FNR and SoxR are transcriptional regulators containing an iron–sulfur cluster. The iron–sulfur cluster in FNR acts as an oxygen sensor by reacting with oxygen. The structural change of the iron–sulfur cluster takes place when FNR senses oxygen, which regulates the transcriptional regulator activity of FNR through the change of the quaternary structure. SoxR contains the [2Fe–2S] cluster that regulates the transcriptional activator activity of SoxR. Only the oxidized SoxR containing the [2Fe–2S]2+ cluster is active as the transcriptional activator. CooA is a transcriptional activator containing a protoheme that acts as a CO sensor. CO is a physiological effector of CooA and regulates the transcriptional activator activity of CooA. In this review, the biochemical and biophysical properties of FNR, SoxR, and CooA are described.

Small addition of Zn2+ in Ca2+@DNA results in elevated gene transfection by aminated PGMA-modified silicon nanowire arrays

Gene therapy, a promising and effective treatment, has ignited new hope in overcoming difficult-to-cure diseases. The key question in gene therapy is how to efficiently and safely deliver exogenous nucleic acids into the nuclei of target cells. To achieve stable, efficient and safe gene transfer and to ensure efficiency of gene transfer into cell nuclei, a zinc ion-assisted gene delivery nanosystem was proposed in the present study by loading a low concentration of Zn²⁺ in Ca²⁺@DNA nanoparticles on ethanolamine-functionalized poly(glycidyl methacrylate) (PGEA)-modified SiNWAs (Zn²⁺/Ca²⁺@DNA + SN-PGEA). The results showed that with the help of Zn ions, this composite nanosystem could promote more DNA in the cell nuclei and thus dramatically increased the transfection efficiency by as much as 7-fold. The nanosystem with 0.2 mM Zn²⁺, 100 mM Ca²⁺ and PGEA modification on SiNWAs displayed the highest transfection efficiency and good biocompatibility. This new composite nanosystem will have great potential in gene transfection for biomedical research.

MiRNA-target interactions in osteogenic signaling pathways involving zinc via the metal regulatory element

Adequate zinc nutriture is necessary for normal bone growth and development, though the precise mechanisms for zinc-mediated bone growth remain poorly defined. A key transcription factor activated by zinc is metal response element-binding transcription factor 1 (MTF-1), which binds to the metal regulatory element (MRE). We hypothesize that MREs will be found upstream of miRNA genes as well as miRNA target genes in the following bone growth and development signaling pathways: TGF-β, MAPK, and Wnt. A Bioconductor-based workflow in R was designed to identify interactions between MREs, miRNAs, and target genes. MRE sequences were found upstream from 64 mature miRNAs that interact with 213 genes which have MRE sequences in their own promoter regions. MAPK1 exhibited the most miRNA-target interactions (MTIs) in the TGF-β and MAPK signaling pathways; CCND2 exhibited the most interactions in the Wnt signaling pathway. Hsa-miR-124-3p exhibited the most MTIs in the TGF-β and MAPK signaling pathways; hsa-miR-20b-5p exhibited the most MTIs in the Wnt signaling pathway. MYC and hsa-miR-34a-5p were shared between all three signaling pathways, also forming an MTI unit. JUN exhibited the most protein-protein interactions, followed by MAPK8. These in silico data support the hypothesis that intracellular zinc status plays a role in osteogenesis through the transcriptional regulation of miRNA genes via the zinc/MTF-1/MRE complex.

Novel thiophene-based colorimetric and fluorescent turn-on sensor for highly sensitive and selective simultaneous detection of Al3+ and Zn2+ in water and food samples and its application in bioimaging

A novel bifunctional thiophene-based Schiff base TS as a colorimetric and fluorescent turn-on sensor for rapid and simultaneous detection of Al³⁺ and Zn²⁺ ions with high selectivity and sensitivity has been developed. The sensor shows remarkable fluorescence enhancement response for Al³⁺ and Zn²⁺ over a broad pH range with good anti-interference capability, which accompanied with an obvious color change easily detected by naked eyes. Sensor TS can detect as low as 3.7 × 10^-9 M for Al³⁺ and 3.0 × 10^-8 M for Zn²⁺, whereas respective association constants are 1.16 × 10⁴ M^-1 and 2.08 × 10⁴ M^-1. With the help of fluorescence titration and Job's plot, the stoichiometric ratio of TS with Al³⁺/Zn²⁺ was determined to be 1:1. The sensing mechanism of sensor TS with Al³⁺/Zn²⁺ based on the chelation-enhanced fluorescence (CHEF) was analyzed in detail through ¹H NMR titration, FTIR, HRMS and DFT studies. Moreover, sensor TS has been applied to the detection of Al³⁺ and Zn²⁺ in real environmental water and food samples as well as the filter paper-based test strips. Furthermore, sensor TS has good cell-permeability and can be used to selectively sense intracellular Al³⁺ and Zn²⁺ by bioimaging.

The Fate of Iron in The Organism and Its Regulatory Pathways

Iron is an essential element involved in many life-necessary processes. Interestingly, in mammals there is no active excretion mechanism for iron. Therefore iron kinetics has to be meticulously regulated. The most important step for regulation of iron kinetics is absorption. The absorption takes place in small intestine and it is implicated that it requires several proteins. Iron is then released from enterocytes into the circulation and delivered to the cells. Iron movement inside the cell is only partially elucidated and its traffic to mitochondia is not known. Surprisingly, the regulation of various proteins related to iron kinetics and energy metabolism at the molecular level is better described. On contrary, the complex control of iron absorption cannot be fully explicated with present knowledge.

Bioinformatic analysis of the metal response element and zinc-dependent gene regulation via the metal response element-binding transcription factor 1 in Caco-2 cells

The purpose of this study was to determine the correlation between the position or number of metal regulatory elements (MREs) near gene transcriptional or translational start sites, and the strength of metal response element-binding transcription factor 1 (MTF-1) regulation. A secondary analysis was performed in silico on published results measuring the effects of Zn and MTF-1 on transcriptional regulation of genes (n = 120) in the Caco-2 cell line. MRE sequence variations throughout the human genome were sorted using a position weight matrix. Three null hypotheses (H0) were tested: (1) there is no correlation between the number of MREs and MTF-1 transcriptional strength, (2) there is no correlation between the distance of the MRE upstream from the transcriptional start site (TSS) and MTF-1 transcriptional strength, and (3) there is no correlation between the distance of the MRE downstream from the translational start site (TrSS) and MTF-1 transcriptional strength. Spearman correlation was used to test for significance (p < 0.05). From our results we rejected the first H0; we observed a significant correlation between the total number of MRE sequences - 7Kbp upstream from the TSS, within the 5' untranslated region, and + 1Kbp downstream from the TrSS, versus the strength of MTF-1 regulation (r = 0.202; p = 0.027). The second and third H0 were accepted. These results expand our understanding of the role of the MRE in Zn-dependent gene regulation. The data indicate that Zn influences the transcriptional control of gene expression beyond maintaining intracellular Zn homeostasis.

Fluorescent ZnII Chemosensor Mediated by a 1,8-Naphthyridine Derivative and It's Photophysical Properties

One of the greatest challenges in using fluorescent chemosensors for highly selective and sensitive transition-metal ions is finding an efficient and simple method for its synthesis. In this study, a highly efficient fluorescence chemosensor for ZnII was developed from N-Boc-L-proline modified 1,8-naphthyridine. The fluorescence intensity of the chemosensor was increased significantly only in the presence of ZnII ion which provided a perceived color change for rapid visual sensing, while other metal ions showed fluorescence quenching or little changes. It was worth noting that the chemosensor L distinguished ZnII from CdII commonly having similar properties. The solvent effect and possible bonding mode for fluorescence enhancement have been also discussed. Results of this study indicated that the Boc-group in l-proline significantly improved the sensitivity and selectivity for ZnII detection performance, as confirmed by comparison experiments and time dependent-density functional theory (TD-DFT) calculations.

Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators

The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn²⁺. X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn²⁺, but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd²⁺ and Mn²⁺ bind most tightly, and comparison of three new Cd²⁺-bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd²⁺ and Mn²⁺, but otherwise uncommon) in the softer site. Remarkably, the Cd²⁺- and Mn²⁺-selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity.