Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry

On the genesis and unique functions of zinc neuromodulation

In addition to the essential structural and catalytic functions of zinc, evolution has adopted synaptic zinc as a neuromodulator. In the brain, synaptic zinc is released primarily from glutamatergic neurons, notably in the neocortex, hippocampus, amygdala, and auditory brainstem. In these brain areas, synaptic zinc is essential for neuronal and sensory processing fine-tuning. But what niche does zinc fill in neural signaling that other neuromodulators do not? Here, we discuss the evolutionary history of zinc as a signaling agent and its eventual adoption as an essential neuromodulator in the mammalian brain. We then attempt to describe the unique roles that zinc has carved out of the vast and diverse landscape of neuromodulators.

Activation of zinc uptake regulator by zinc binding to three regulatory sites

Zur is a Fur-family metalloregulator that is widely used to control zinc homeostasis in bacteria. In Streptomyces coelicolor, Zur (ScZur) acts as both a repressor for zinc uptake (znuA) gene and an activator for zinc exporter (zitB) gene. Previous structural studies revealed three zinc ions specifically bound per ScZur monomer; a structural one to allow dimeric architecture and two regulatory ones for DNA-binding activity. In this study, we present evidence that Zur contains a fourth specific zinc-binding site with a key histidine residue (H36), widely conserved among actinobacteria, for regulatory function. Biochemical, genetic, and calorimetric data revealed that H36 is critical for hexameric binding of Zur to the zitB zurbox and further binding to its upstream region required for full activation. A comprehensive thermodynamic model demonstrated that the DNA-binding affinity of Zur to both znuA and zitB zurboxes is remarkably enhanced upon saturation of all three regulatory zinc sites. The model also predicts that the strong coupling between zinc binding and DNA binding equilibria of Zur drives a biphasic activation of the zitB gene in response to a wide concentration change of zinc. Similar mechanisms may be pertinent to other metalloproteins, expanding their response spectrum through binding multiple regulatory metals.

An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome

Bacteria have developed fine-tuned responses to cope with potential zinc limitation. The Zur protein is a key player in coordinating this response in most species. Comparative proteomics conducted on the cyanobacterium Anabaena highlighted the more abundant proteins in a zur mutant compared to the wild type. Experimental evidence showed that the exoprotein ZepA mediates zinc uptake. Genomic context of the zepA gene and protein structure prediction provided additional insights on the regulation and putative function of ZepA homologs. Phylogenetic analysis suggests that ZepA represents a primordial system for zinc acquisition that has been conserved for billions of years in a handful of species from distant bacterial lineages. Furthermore, these results show that Zur may have been one of the first regulators of the FUR family to evolve, consistent with the scarcity of zinc in the ecosystems of the Archean eon.

Effect of Divalent Metal Ions on the Ribonuclease Activity of the Toxin Molecule HP0894 from Helicobacter pylori

Bacteria and archaea respond and adapt to environmental stress conditions by modulating the toxin-antitoxin (TA) system for survival. Within the bacterium Helicobacter pylori, the protein HP0894 is a key player in the HP0894-HP0895 TA system, in which HP0894 serves as a toxin and HP0895 as an antitoxin. HP0894 has intrinsic ribonuclease (RNase) activity that regulates gene expression and translation, significantly influencing bacterial physiology and survival. This activity is influenced by the presence of metal ions such as Mg2+. In this study, we explore the metal-dependent RNase activity of HP0894. Surprisingly, all tested metal ions lead to a reduction in RNase activity, with zinc ions (Zn2+) causing the most significant decrease. The secondary structure of HP0894 remained largely unaffected by Zn2+ binding, whereas structural rigidity was notably increased, as revealed using CD analysis. NMR characterized the Zn2+ binding, implicating numerous His, Asp, and Glu residues in HP0894. In summary, these results suggest that metal ions play a regulatory role in the RNase activity of HP0894, contributing to maintaining the toxin molecule in an inactive state under normal conditions.

Oxidoreductases and metal cofactors in the functioning of the earth

Life sustains itself using energy generated by thermodynamic disequilibria, commonly existing as redox disequilibria. Metals are significant players in controlling redox reactions, as they are essential components of the engine that life uses to tap into the thermodynamic disequilibria necessary for metabolism. The number of proteins that evolved to catalyze redox reactions is extraordinary, as is the diversification level of metal cofactors and catalytic domain structures involved. Notwithstanding the importance of the topic, the relationship between metals and the redox reactions they are involved in has been poorly explored. This work reviews the structure and function of different prokaryotic organometallic-protein complexes, highlighting their pivotal role in controlling biogeochemistry. We focus on a specific subset of metal-containing oxidoreductases (EC1 or EC7.1), which are directly involved in biogeochemical cycles, i.e., at least one substrate or product is a small inorganic molecule that is or can be exchanged with the environment. Based on these inclusion criteria, we select and report 59 metalloenzymes, describing the organometallic structure of their active sites, the redox reactions in which they are involved, and their biogeochemical roles.

Nickel and zinc micronutrient availability in Phanerozoic oceans

Nickel and zinc are both bio-essential micronutrients with a nutrient-like distribution in the modern ocean, but show key differences in their biological functions and geochemical behavior. Eukaryotic phytoplankton, and especially diatoms, have high Zn quotas, whereas cyanobacteria generally require relatively more Ni. Secular changes in the relative availability of these micronutrients may, therefore, have affected the evolution and diversification of phytoplankton. In this study, we use a large compilation of Ni and Zn concentration data for Phanerozoic sediments to evaluate long-term changes in Ni and Zn availability and possible links to phytoplankton evolution. Modern data suggest that organic-rich sediments capture the dissolved deep ocean Ni/Zn ratio, regardless of local depositional conditions. We use this observation to constrain Ni/Zn ratios for past oceans, based on data from the sedimentary record. This record highlights long-term changes in the relative availability of these micronutrients that can be linked to the (bio)geochemical conditions on the Earth's surface. Early Palaeozoic oceans were likely relatively Ni rich, with sedimentary Ni/Zn ratios for this interval mostly being around ~1 or higher. A comparison with Phanerozoic strontium-, carbon-, and sulfur-isotopic records suggests that the late Palaeozoic decrease in sulfidic conditions and increase in hydrothermal inputs and organic-carbon burial rates caused a shift towards more Zn-rich conditions. Mesozoic and Cenozoic sediments show relatively Zn-rich oceans for these time intervals, with sedimentary Ni/Zn ratios mostly being around ~1 or lower. These observations imply that the diversification of the dominant groups of modern eukaryotic phytoplankton occurred in relatively Zn-rich oceans and that these organisms still carry this signature in their stoichiometries. However, the Phanerozoic transition to a more Zn-rich ocean pre-dates the origin and diversification of modern eukaryotes and, therefore, this transition was likely not the main direct cause for eukaryotic diversification in the Mesozoic and Cenozoic Eras.

The Metal-binding Protein Atlas (MbPA): an integrated database for curating metalloproteins in all aspects

Metal-binding proteins are essential for the vital activities and engage in their roles by acting in concert with metal cations. MbPA (The Metal-binding Protein Atlas) is the most comprehensive resource up to now dedicated to curating metal-binding proteins. Currently, it contains 106373 entries and 440187 sites related to 54 metals and 8169 species. Users can view all metal-binding proteins and species-specific proteins in MbPA. There are also metal-proteomics data that quantitatively describes protein expression in different tissues and organs. By analyzing the data of the amino acid residues at the metal-binding site, it is found that about 80% of the metal ions tend to bind to cysteine, aspartic acid, glutamic acid, and histidine. Moreover, we use Diversity Measure to confirm that the diversity of metal-binding is specific in different area of periodic table, and further elucidate the binding modes of 19 transition metals on 20 amino acids. In addition, MbPA also embraces 6855 potential pathogenic mutations related to metalloprotein. The resource is freely available at http://bioinfor.imu.edu.cn/mbpa.

Grazing on Marine Viruses and Its Biogeochemical Implications

Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

A Tribute to Phil Bourne-Scientist and Human

This Special Issue of Biomolecules[...].

The Co-Evolution Aspects of the Biogeochemical Role of Phytoplankton in Aquatic Ecosystems: A Review

In freshwater and marine ecosystems, the phytoplankton community is based on microalgae and cyanobacteria, which include phylogenetically very diverse groups of oxygenic photoautotrophs. In the process of evolution, they developed a wide range of bio(geo)chemical adaptations that allow them to effectively use solar radiation, CO2, and nutrients, as well as major and trace elements, to form O2 and organic compounds with a high chemical bond energy. The inclusion of chemical elements in the key processes of energy and plastic metabolism in the cell is determined by redox conditions and the abundance and metabolic availability of elements in the paleoenvironment. Geochemical evolution, which proceeded simultaneously with the evolution of biosystems, contributed to an increase in the number of metals and trace elements acting as cofactors of enzymes involved in metabolism and maintaining homeostasis in the first photoautotrophs. The diversity of metal-containing enzymes and the adaptive ability to replace one element with another without losing the functional properties of enzymes ensured the high ecological plasticity of species and allowed microalgae and cyanobacteria to successfully colonize a wide variety of habitats. In this review, we consider the main aspects of the modern concepts of the biogeochemical evolution of aquatic ecosystems and the role of some metals in the main bioenergetic processes in photosynthetic prokaryotes and eukaryotes. We present generalized data on the efficiency of the assimilation of key nutrients by phytoplankton and their importance in the cycle of carbon, silicon, nitrogen, phosphorus, sulfur, and iron. This article presents modern views on the evolutionary prerequisites for the formation of elemental signatures in different systematic groups of microalgae, as well as the possibility of using the stoichiometric ratio in the study of biological and geochemical processes in aquatic ecosystems.

Determination of ultra-trace metal-protein interactions in co-formulated monoclonal antibody drug product by SEC-ICP-MS

Transition metals can be introduced in therapeutic protein drugs at various steps of the manufacturing process (e.g. manufacturing raw materials, formulation, storage), and can cause a variety of modifications on the protein. These modifications can potentially influence the efficacy, safety, and stability of the therapeutic protein, especially if critical quality attributes (CQAs) are affected. Therefore, it is meaningful to understand the interactions between proteins and metals that can occur during the manufacturing process, formulation, and storage of biotherapeutics. Here, we describe a novel strategy to differentiate between ultra-trace levels of transition metals (cobalt, chromium, copper, iron, and nickel) interacting with therapeutic proteins and free metal in solution in the drug formulation using size exclusion chromatography coupled to inductively coupled plasma mass spectrometry (SEC-ICP-MS). Two monoclonal antibodies (mAbs) were coformulated and stored up to nine days in a scaled down model to mimic metal exposure from manufacturing tanks. The samples containing the mAbs were first analyzed by ICP-MS for bulk metal analysis, then studied using SEC-ICP-MS to measure the extent of metal-protein interactions. The SEC separation was used to differentiate metal associated with the mAbs from free metal in solution. Relative quantitation of metal-protein interaction was then calculated using the relative peak areas of protein-associated metal to free metal in solution and weighting it to the total metal concentration in the mixture as measured by bulk metal analysis by ICP-MS. The SEC-ICP-MS method offers an informative means of measuring metal-protein interactions during drug development.

Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures

Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.

Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function

Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M²⁺ _R ), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M²⁺ _A ) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M²⁺ _A affords the overall lowest energy complex, which drives the transition from M²⁺ _R to M²⁺ _A . While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures.

On the trail of iron uptake in ancestral Cyanobacteria on early Earth

Cyanobacteria oxygenated Earth's atmosphere ~2.4 billion years ago, during the Great Oxygenation Event (GOE), through oxygenic photosynthesis. Their high iron requirement was presumably met by high levels of Fe(II) in the anoxic Archean environment. We found that many deeply branching Cyanobacteria, including two Gloeobacter and four Pseudanabaena spp., cannot synthesize the Fe(II) specific transporter, FeoB. Phylogenetic and relaxed molecular clock analyses find evidence that FeoB and the Fe(III) transporters, cFTR1 and FutB, were present in Proterozoic, but not earlier Archaean lineages of Cyanobacteria. Furthermore Pseudanabaena sp. PCC7367, an early diverging marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). Our genetic profiling suggests that, prior to the GOE, ancestral Cyanobacteria may have utilized alternative metal iron transporters such as ZIP, NRAMP, or FicI, and possibly also scavenged exogenous siderophore bound Fe(III), as they only acquired the necessary Fe(II) and Fe(III) transporters during the Proterozoic. Given that Cyanobacteria arose 3.3-3.6 billion years ago, it is possible that limitations in iron uptake may have contributed to the delay in their expansion during the Archean, and hence the oxygenation of the early Earth.

Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin

Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the "ancestors" are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.

The quintessence of metallomics: a harbinger of a different life science based on the periodic table of the bioelements

This year marks the 20th anniversary of the field of metallomics. As a landmark in time, it is an occasion to reflect on the past, present, and future of this integrated field of biometal sciences. A fundamental bias is one reason for having metallomics as a scientific discipline. The focus of biochemistry on the six non-metal chemical elements, collectively known with the acronym SPONCH (sulphur, phosphorus, oxygen, nitrogen, carbon, hydrogen), glosses over the fact that the lower quantities of many other elements have qualities that made them instrumental in the evolution of life and pivotal in numerous life processes. The metallome, alongside the genome, proteome, lipidome, and glycome, should be regarded as a fifth pillar of elemental-vis-à-vis molecular-building blocks in biochemistry. Metallomics as 'global approaches to metals in the biosciences' considers the biological significance of most chemical elements in the periodic table, not only the ones essential for life, but also the non-essential ones that are present in living matter-some at higher concentrations than the essential ones. The non-essential elements are bioactive with either positive or negative effects. Integrating the significance of many more chemical elements into the life sciences requires a transformation in learning and teaching with a focus on elemental biology in addition to molecular biology. It should include the dynamic interactions between the biosphere and the geosphere and how the human footprint is changing the ecology globally and exposing us to many additional chemical elements that become new bioelements.

Effects of 4-Br-A23187 on Bacillus subtilis cells and unilamellar vesicles reveal it to be a potent copper ionophore

Ionophores are small molecules or peptides that transport metal ions across biological membranes. Their transport capabilities are typically characterized in vitro using vesicles and single ion species. It is difficult to infer from these data which effects ionophores have on living cells in a complex environment (e.g. culture medium), since net ion movement is influenced by many factors including ion composition of the medium, concentration gradients, pH gradient, and protein-mediated transport processes across the membrane. To gain insights into the antibacterial mechanism of action of the semisynthetic polyether ionophore 4-Br-A23187, known to efficiently transport zinc and manganese in vitro, we investigated its effects on the gram-positive model organism Bacillus subtilis. In addition to monitoring cellular ion concentrations, the physiological impact of treatment was assessed on the proteome level. 4-Br-A23187 treatment resulted in an increase in intracellular copper levels, the extent of which depended on the copper concentration of the medium. Effects of copper accumulation mirrored by the proteomic response included oxidative stress, disturbance of proteostasis, metal and sulfur homeostasis. The antibiotic effect of 4-Br-A23187 is further aggravated by a decrease in intracellular manganese and magnesium. A liposome model confirmed that 4-Br-A23187 acts as copper ionophore in vitro. This article is protected by copyright. All rights reserved.

Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy

Metalloproteins are involved in key cell processes such as photosynthesis, respiration, and oxygen transport. However, the presence of transition metals (notably iron as a component of [Fe-S] clusters) often makes these proteins sensitive to oxygen-induced degradation. Consequently, their study usually requires strict anaerobic conditions. Although X-ray crystallography has been the method of choice for solving macromolecular structures for many years, recently electron microscopy has also become an increasingly powerful structure-solving technique. We have used our previous experience with cryo-crystallography to develop a method to prepare cryo-EM grids in an anaerobic chamber and have applied it to solve the structures of apoferritin and the 3 [Fe₄S₄]-containing pyruvate ferredoxin oxidoreductase (PFOR) at 2.40 Å and 2.90 Å resolution, respectively. The maps are of similar quality to the ones obtained under air, thereby validating our method as an improvement in the structural investigation of oxygen-sensitive metalloproteins by cryo-EM.

High spatial resolution imaging of subcellular macro and trace element distribution during phagocytosis

The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface was investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry (ICP-MS). In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe / Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was about 90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to subcellular level. At a comparable resolution, several low abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of nuclear envelope was observed indicating an interesting but still unknown distribution of this trace element in murine macrophages.

Structural characterization of the urease accessory protein UreF from Klebsiella pneumoniae

Klebsiella pneumoniae is an opportunistic pathogen that mostly affects those with weakened immune systems. Urease is a vital enzyme that can hydrolyze urea to ammonia and carbon dioxide as a source of nitrogen for growth. Urease is also a K. pneumoniae virulence factor that enables survival of the bacterium under nutrient-limiting conditions. UreF, an important nickel-binding urease accessory protein, is involved in the insertion of Ni²⁺ into the active site of urease. Here, the crystal structure of UreF from K. pneumoniae (KpUreF) is reported. Functional data show that KpUreF forms a stable dimer in solution. These results may provide a starting point for the design of urease inhibitors.

A review on bacterial redox dependent iron transporters and their evolutionary relationship

Iron is an essential yet toxic micronutrient and its transport across biological membranes is tightly regulated in all living organisms. One such iron transporter, the Ftr-type permeases, is found in both eukaryotic and prokaryotic cells. These Ftr-type transporters are required for iron transport, predicted to form α-helical transmembrane structures, and conserve two ArgGluxxGlu (x = any amino acid) motifs. In the yeast Ftr transporter (Ftr1p), a ferroxidase (Fet3p) is required for iron transport in an oxidation coupled transport step. None of the bacterial Ftr-type transporters (EfeU and FetM from E. coli; cFtr from Campylobacter jejuni; FtrC from Brucella, Bordetella, and Burkholderia spp.) contain a ferroxidase protein. Bioinformatics report predicted periplasmic EfeO and FtrB (from the EfeUOB and FtrABCD systems) as novel cupredoxins. The Cu²⁺ binding and the ferrous oxidation properties of these proteins are uncharacterized and the other two bacterial Ftr-systems are expressed without any ferroxidase/cupredoxin, leading to controversy about the mode of function of these transporters. Here, we review published data on Ftr-type transporters to gain insight into their functional diversity. Based on original bioinformatics data presented here evolutionary relations between these systems are presented.

Development of affinity bead-based in vitro metal-ligand binding assay reveals dominant cadmium affinity of thiol-rich small peptides phytochelatins beyond glutathione

For a better understanding of metal-ligand interaction and its function in cells, we developed an easy, sensitive, and high-throughput method to quantify ligand-metal(loid) binding affinity under physiological conditions by combining ligand-attached affinity beads and inductively coupled plasma-optical emission spectrometry (ICP-OES). Glutathione (GSH) and two phytochelatins (PC2 and PC3, small peptides with different numbers of free thiols) were employed as model ligands and attached to hydrophilic beads. The principle of the assay resembles that of affinity purification of proteins in biochemistry: metals binding to the ligand on the beads and the rest in the buffer are separated by a spin column and quantified by ICP-OES. The binding assay using the GSH-attached beads and various metal(loid)s suggested the different affinity of the metal-GSH interactions, in accordance with the order of the Irving-Williams series and the reported stability constants. The binding assay using PC2 or PC3-attached beads suggested positive binding between PCs and Ni(II), Cu(II), Zn(II), Cd(II), and As(III) in accordance with the number of thiols in PC2 and PC3. We then conducted the competition assay using Cd(II), Mn(II), Fe(II), Cu(II), and Zn(II), and the results suggested a better binding affinity of PC2 with Cd(II) than with the essential metals. Another competition assay using PC2 and GSH suggested a robust binding affinity between PCs and Cd(II) compared to GSH and Cd(II). These results suggested the dominance of PC-Cd complex formation in vitro, supporting the physiological importance of PCs for the detoxification of cadmium in vivo. We also discuss the potential application of the assay.

Temporal variation of planetary iron as a driver of evolution

Iron is an irreplaceable component of proteins and enzyme systems required for life. This need for iron is a well-characterized evolutionary mechanism for genetic selection. However, there is limited consideration of how iron bioavailability, initially determined by planetary accretion but fluctuating considerably at global scale over geological time frames, has shaped the biosphere. We describe influences of iron on planetary habitability from formation events >4 Gya and initiation of biochemistry from geochemistry through oxygenation of the atmosphere to current host–pathogen dynamics. By determining the iron and transition element distribution within the terrestrial planets, planetary core formation is a constraint on both the crustal composition and the longevity of surface water, hence a planet’s habitability. As such, stellar compositions, combined with metallic core-mass fraction, may be an observable characteristic of exoplanets that relates to their ability to support life. On Earth, the stepwise rise of atmospheric oxygen effectively removed gigatons of soluble ferrous iron from habitats, generating evolutionary pressures. Phagocytic, infectious, and symbiotic behaviors, dating from around the Great Oxygenation Event, refocused iron acquisition onto biotic sources, while eukaryotic multicellularity allows iron recycling within an organism. These developments allow life to more efficiently utilize a scarce but vital nutrient. Initiation of terrestrial life benefitted from the biochemical properties of abundant mantle/crustal iron, but the subsequent loss of iron bioavailability may have been an equally important driver of compensatory diversity. This latter concept may have relevance for the predicted future increase in iron deficiency across the food chain caused by elevated atmospheric CO₂.

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.

The Invisible Hand of the Periodic Table: How Micronutrients Shape Ecology

Beyond the better-studied carbohydrates and the macronutrients nitrogen and phosphorus, a remaining 20 or so elements are essential for life and have distinct geographical distributions, making them of keen interest to ecologists. Here, I provide a framework for understanding how shortfalls in micronutrients like iodine, copper, and zinc can regulate individual fitness, abundance, and ecosystem function. With a special focus on sodium, I show how simple experiments manipulating biogeochemistry can reveal why many of the variables that ecologists study vary so dramatically from place to place. I conclude with a discussion of how the Anthropocene's changing temperature, precipitation, and atmospheric CO2 levels are contributing to nutrient dilution (decreases in the nutrient quality at the base of food webs).

Environment and coordination of FeMo-co in the nitrogenase metallochaperone NafY

In nitrogenase biosynthesis, the iron-molybdenum cofactor (FeMo–co) is externally assembled at scaffold proteins and delivered to the NifDK nitrogenase component by the NafY metallochaperone. Here we have used nuclear magnetic resonance, molecular dynamics, and functional analysis to elucidate the environment and coordination of FeMo–co in NafY. H¹²¹ stands as the key FeMo–co ligand. Regions near FeMo–co diverge from H¹²¹ and include the η1, α1, α2 helical lobe and a narrow path between H¹²¹ and C¹⁹⁶.

Broadening of NMR resonance spins used to map binding of paramagnetic FeMo–co to the nitrogenase metallocluster escort protein NafY.

Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean

Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Using novel Southern Ocean meta-omics resources including 133 metagenome-assembled genomes (MAGs), we show a mosaic of taxonomy-specific ecological strategies in naturally iron-fertilized and high nutrient low chlorophyll (HNLC) waters. Taxonomic profiling revealed apparent community shifts across contrasting nutrient regimes. Community-level and genome-resolved metatranscriptomics evidenced a moderate association between taxonomic affiliations and iron and carbon-related functional roles. Diverse ecological strategies emerged when considering the central metabolic pathways of individual MAGs. Closely related lineages appear to adapt to distinct ecological niches, based on their distribution and gene regulation patterns. Our in-depth observations emphasize the complex interplay between the genetic repertoire of individual taxa and their environment and how this shapes prokaryotic responses to iron and organic carbon availability in the Southern Ocean.

Strategies for Zinc Uptake in Pseudomonas aeruginosa at the Host-Pathogen Interface

As a structural, catalytic, and signaling component, zinc is necessary for the growth and development of plants, animals, and microorganisms. Zinc is also essential for the growth of pathogenic microorganisms and is involved in their metabolism as well as the regulation of various virulence factors. Additionally, zinc is necessary for infection and colonization of pathogenic microorganisms in the host. Upon infection in healthy organisms, the host sequesters zinc both intracellularly and extracellularly to enhance the immune response and prevent the proliferation and infection of the pathogen. Intracellularly, the host manipulates zinc levels through Zrt/Irt-like protein (ZIP)/ZnT family proteins and various zinc storage proteins. Extracellularly, members of the S100 protein family, such as calgranulin C, sequester zinc to inhibit microbial growth. In the face of these nutritional limitations, bacteria rely on an efficient zinc transport system to maintain zinc supplementation for proliferation and disruption of the host defense system to establish infection. Here, we summarize the strategies for zinc uptake in conditional pathogenic Pseudomonas aeruginosa, including known zinc uptake systems (ZnuABC, HmtA, and ZrmABCD) and the zinc uptake regulator (Zur). In addition, other potential zinc uptake pathways were analyzed. This review systematically summarizes the process of zinc uptake by P. aeruginosa to provide guidance for the development of new drug targets.

Timing the evolution of antioxidant enzymes in cyanobacteria

The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.

Oxygenation, Life, and the Planetary System during Earth's Middle History: An Overview

The long history of life on Earth has unfolded as a cause-and-effect relationship with the evolving amount of oxygen (O₂) in the oceans and atmosphere. Oxygen deficiency characterized our planet's first 2 billion years, yet evidence for biological O₂ production and local enrichments in the surface ocean appear long before the first accumulations of O₂ in the atmosphere roughly 2.4 to 2.3 billion years ago. Much has been written about this fundamental transition and the related balance between biological O₂ production and sinks coupled to deep Earth processes that could buffer against the accumulation of biogenic O₂. However, the relationship between complex life (eukaryotes, including animals) and later oxygenation is less clear. Some data suggest O₂ was higher but still mostly low for another billion and a half years before increasing again around 800 million years ago, potentially setting a challenging course for complex life during its initial development and ecological expansion. The apparent rise in O₂ around 800 million years ago is coincident with major developments in complex life. Multiple geochemical and paleontological records point to a major biogeochemical transition at that time, but whether rising and still dynamic biospheric oxygen triggered or merely followed from innovations in eukaryotic ecology, including the emergence of animals, is still debated. This paper focuses on the geochemical records of Earth's middle history, roughly 1.8 to 0.5 billion years ago, as a backdrop for exploring possible cause-and-effect relationships with biological evolution and the primary controls that may have set its pace, including solid Earth/tectonic processes, nutrient limitation, and their possible linkages. A richer mechanistic understanding of the interplay between coevolving life and Earth surface environments can provide a template for understanding and remotely searching for sustained habitability and even life on distant exoplanets.

Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches

Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.

Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins

Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors.

Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus

Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.

Roles for intracellular cation transporters in respiratory growth of yeast

Potassium is involved in copper and iron metabolism in eukaryotic Golgi apparatus, but it is not clear yet whether potassium distributions in other vesicles also affect copper and iron metabolism. Here we show that respiratory growth and iron acquisition by the yeast Saccharomyces cerevisiae relies on potassium (K+) compartmentalization to the mitochondria, as well as the vacuole and late endosome via K+/H+ exchangers Mdm38p, Vnx1p and Nhx1p, respectively. The data indicate that NHX1 and VNX1 knock-out cells grow better than wild type cells on non-fermentable YPEG media, while MDM38 knock-out cells display a growth defect on YPEG media. The over expression of the KHA1 gene located on the Golgi apparatus partially compensates for the growth defect of the MDM38 knock-out strain. The results suggest that the vacuole and late endosome are important potassium storage vesicles and Mdm38p affects the mitochondrial function by regulating copper and iron metabolism. Our study reveals potassium compartmentalization to the subcellular vesicles is relevant for respiratory growth by improving copper utilization and promoting iron absorption.

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle of harmful metal(loids), including that of arsenic, which doubtlessly imposed substantial barriers to the physiology and diversification of life. Evaluating the adaptive biological responses to these environmental challenges is inherently difficult because of the paucity of fossil records. Here we applied molecular clock analyses to 13 gene families participating in principal pathways of arsenic resistance and cycling, to explore the nature of early arsenic biogeocycles and decipher feedbacks associated with planetary oxygenation. Our results reveal the advent of nascent arsenic resistance systems under the anoxic environment predating the Great Oxidation Event (GOE), with the primary function of detoxifying reduced arsenic compounds that were abundant in Archean environments. To cope with the increased toxicity of oxidized arsenic species that occurred as oxygen built up in Earth's atmosphere, we found that parts of preexisting detoxification systems for trivalent arsenicals were merged with newly emerged pathways that originated via convergent evolution. Further expansion of arsenic resistance systems was made feasible by incorporation of oxygen-dependent enzymatic pathways into the detoxification network. These genetic innovations, together with adaptive responses to other redox-sensitive metals, provided organisms with novel mechanisms for adaption to changes in global biogeocycles that emerged as a consequence of the GOE.

Metallomics in deep time and the influence of ocean chemistry on the metabolic landscapes of Earth's earliest ecosystems

Modern biological dependency on trace elements is proposed to be a consequence of their enrichment in the habitats of early life together with Earth’s evolving physicochemical conditions; the resulting metallic biological complement is termed the metallome. Herein, we detail a protocol for describing metallomes in deep time, with applications to the earliest fossil record. Our approach extends the metallome record by more than 3 Ga and provides a novel, non-destructive method of estimating biogenicity in the absence of cellular preservation. Using microbeam particle-induced X-ray emission (µPIXE), we spatially quantify transition metals and metalloids within organic material from 3.33 billion-year-old cherts of the Barberton greenstone belt, and demonstrate that elements key to anaerobic prokaryotic molecular nanomachines, including Fe, V, Ni, As and Co, are enriched within carbonaceous material. Moreover, Mo and Zn, likely incorporated into enzymes only after the Great Oxygenation Event, are either absent or present at concentrations below the limit of detection of µPIXE, suggesting minor biological utilisation in this environmental setting. Scanning and transmission electron microscopy demonstrates that metal enrichments do not arise from accumulation in nanomineral phases and thus unambiguously reflect the primary composition of the carbonaceous material. This carbonaceous material also has δ¹³C between −41.3‰ and 0.03‰, dominantly −21.0‰ to −11.5‰, consistent with biological fractionation and mostly within a restricted range inconsistent with abiotic processes. Considering spatially quantified trace metal enrichments and negative δ¹³C fractionations together, we propose that, although lacking cellular preservation, this organic material has biological origins and, moreover, that its precursor metabolism may be estimated from the fossilised “palaeo-metallome”. Enriched Fe, V, Ni and Co, together with petrographic context, suggests that this kerogen reflects the remnants of a lithotrophic or organotrophic consortium cycling methane or nitrogen. Palaeo-metallome compositions could be used to deduce the metabolic networks of Earth’s earliest ecosystems and, potentially, as a biosignature for evaluating the origin of preserved organic materials found on Mars.

The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time

The fixation of inorganic carbon species like CO₂ to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O₂ in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O₂ into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.

A novel functional role of nickel in sperm motility and eukaryotic cell growth

BACKGROUND

Metal ions are essential for numerous life processes. This study aims to investigate the relationship between seminal quality and ion levels in seminal plasma.

BASIC PROCEDURES

A total of 205 semen samples were collected and seminal plasma ion levels were examined with inductively-coupled plasma-mass spectrometry. The nickel function was demonstrated by in vitro assay and cell growth.

MAIN FINDINGS

The low sperm motility group showed distinctively reduced nickel concentration in seminal plasma compared with the normal sperm motility group. However, arsenic, sulfur, selenium, magnesium and zinc were negatively associated with sperm quality. No significant relationship between other examined cations and semen quality was observed. In vitro assay suggested low concentration of nickel significantly increased sperm total motility and progressive motility. Cell growth assay further confirmed nickel promoted eukaryotic yeast cell growth. Nickel level in seminal plasma may play important functions to determine sperm quality.

PRINCIPAL CONCLUSIONS

Our study reveals a strong correlation between S, Mg, Se, Zn, As, Ni and seminal quality as well as discovers a novel functional role of nickel in sperm motility and eukaryotic cell growth. These findings may provide a potential avenue for assessment of sperm quality and treatment of reproduction disorders.

Specificity in the Susceptibilities of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus Clinical Isolates to Six Metal Antimicrobials

In response to the occurrence of antibiotic resistance, there has been rapid developments in the field of metal-based antimicrobials. Although it is largely assumed that metals provide broad-spectrum microbial efficacy, studies have shown that this is not always the case. Therefore, in this study, we compared the susceptibilities of 93 clinical isolates belonging to the species Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus against six metals, namely aluminum, copper, gallium, nickel, silver and zinc. To provide qualitative comparative information, the resulting zones of growth inhibition were compared to the minimal inhibitory concentrations of three indicator strains E. coli ATCC 25922, P. aeruginosa ATCC 27853 and S. aureus ATCC 25923. Here, we demonstrate that the metal efficacies were species- and isolate-specific. Only several isolates were either resistant or sensitive to all of the six metals, with great variability found between isolates. However, the greatest degree of similarity was found with the E. coli isolates. In contrast, the susceptibilities of the remaining two collections, S. aureus and P. aeruginosa, were more highly dispersed. Using this information, we have shown that metals are not equal in their efficacies. Hence, their use should be tailored against a particular microorganism and care should be taken to ensure the use of the correct concentration.

Non-specific interference of cobalt with siderophore-dependent iron uptake pathways

Presence of Co²⁺affects the production of the siderophore Pyochelin inPseudomonas aeruginosa. This repression is not Fur-dependent but due to competition of Pyochelin–Co²⁺with Pyochein–Fe³⁺for PchR (transcriptional activator).

Molecular and thyroid hormone binding properties of lamprey transthyretins: The role of an N-terminal histidine-rich segment in hormone binding with high affinity

Transthyretin (TTR) is a plasma thyroid hormone (TH) binder that emerged from an ancient hydroxyisourate hydrolase by gene duplication. To know how an ancient TTR had high affinity for THs, molecular and TH binding properties of lamprey TTRs were investigated. In adult serum, the lipoprotein LAL was a major T3 binder with low affinity. Lamprey TTRs had an N-terminal histidine-rich segment, and had two classes of binding sites for 3,3',5-triiodo-L-thyronine (T3): a high-affinity and a low-affinity site. Mutant TTRΔ_3-11, lacking the N-terminal histidine-rich segment, lost the high-affinity T3 binding site. [¹²⁵I]T3 binding to wild type TTR and mutant TTRΔ_3-11, was differentially modulated by Zn²⁺. Zn²⁺ contents of wild type TTR were 7-10/TTR (mol/mol). Our results demonstrate that lamprey TTR is a Zn²⁺-dependent T3 binder. The N-terminal histidine-rich segment may be essential for neo-functionalization (i.e., high-affinity T3 binding activity) of an ancient TTR after gene duplication.

Tracking the rise of eukaryotes to ecological dominance with zinc isotopes

The biogeochemical cycling of zinc (Zn) is intimately coupled with organic carbon in the ocean. Based on an extensive new sedimentary Zn isotope record across Earth's history, we provide evidence for a fundamental shift in the marine Zn cycle ~800 million years ago. We discuss a wide range of potential drivers for this transition and propose that, within available constraints, a restructuring of marine ecosystems is the most parsimonious explanation for this shift. Using a global isotope mass balance approach, we show that a change in the organic Zn/C ratio is required to account for observed Zn isotope trends through time. Given the higher affinity of eukaryotes for Zn relative to prokaryotes, we suggest that a shift toward a more eukaryote-rich ecosystem could have provided a means of more efficiently sequestering organic-derived Zn. Despite the much earlier appearance of eukaryotes in the microfossil record (~1700 to 1600 million years ago), our data suggest a delayed rise to ecological prominence during the Neoproterozoic, consistent with the currently accepted organic biomarker records.

The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn2+, Fe2+, and Co2+ binding to taurine/α-ketoglutarate dioxygenase (TauD)

Taurine/α-ketoglutarate (αKG) dioxygenase (TauD) is an E. coli nonheme Fe²⁺- and αKG-dependent metalloenzyme that catalyzes the hydroxylation of taurine, leading to the production of sulfite. The metal-dependent active site in TauD is formed by two histidine and one aspartate that coordinating to one face of an octahedral coordination geometry, known as the 2-His-1-carboxylate facial triad. This motif is found in many nonheme Fe²⁺ proteins, but there is limited information on the thermodynamic parameters that govern metal-ion binding to this site. Here, we report data from calorimetry and related biophysical techniques to generate complete thermodynamic profiles of Mn²⁺ and Co²⁺ binding to TauD, and these values are compared to the Fe²⁺ data reported earlier Henderson et al. (Inorg Chem 54: 2278-2283, 2015). The buffer-independent binding constants (K) were measured to be 1.6 × 10⁶, 2.4 × 10⁷, and 1.7 × 10⁹, for Mn²⁺, Fe²⁺, and Co²⁺, respectively. The corresponding ΔG° values were calculated to be - 8.4, - 10.1, and - 12.5 kcal/mol, respectively. The metal-binding enthalpy changes (ΔH) for these binding events are - 11.1 (± 0.1), - 12.2 (± 0.1), and - 16.0 (± 0.6) kcal/mol, respectively. These data are fully consistent with the Irving-Williams series, which show an increasing affinity for transition metal ions across the periodic table. It appears that the periodic increase in affinity, however, is a result of a complicated summation of enthalpy terms (including favorable metal-ion coordination processes and unfavorable ionization events) and related entropy terms.