Open Journal of Plant Science
Review Article       Open Access      Peer-Reviewed

Metals from cell to environment: Connecting Metallomics with other omics

Vijeta Singh1* and Kusum Verma2

1Amity Institute of Biotechnology, Amity University, Gautam Budha Nagar, India
2Department of Microbiology, KNIPSS, Sultanpur-228001, U.P., India
*Corresponding author: Vijeta Singh, Amity Institute of Biotechnology, Amity University, Gautam Budha Nagar, India, Tel No: +91-9990250103; E-mail:;
Received: 03 February, 2018 | Accepted: 10 March, 2018 | Published: 12 March, 2018
Keywords: Environment; Metals; Metallomics; Metalloproteins; Metalloenzymes; Metallochaperones

Cite this as

Singh V, Verma K (2018) Metals from cell to environment: Connecting Metallomics with other omics. Open J Plant Sci 3(1): 001-014. DOI: 10.17352/ojps.000008

Research activities and data collection of metals present in living organisms are called as “metallomics”. In metallomics, biomolecules incorporating metal ions viz. metalloenzymes and metalloproteins, are known as “metallomes”. Metallomics aims to identify metallomes of living organisms and to annotate the physiological significance as well as the biological functions. However, in order to ascertain metallomics to be the part of biometal science, recent analytical technologies like chemical speciation are required to analyze the metallomes. Environmental applications like bioleaching, phytoremediation of soil by using microbes, and to deal with the uptake, transport, storage of trace metals necessary for protein functions and biomarkers identification under ecotoxicological studies really require metallomics involvement. As an interdisciplinary research area, metallomics cover plant and animal physiology, nutrition and become a potential candidate in pharmacology, biogeochemistry and clinical chemistry. Metallomics uses analytical and spectroscopic methods to find the quantitative and qualitative information about metal ions that are present as ligands a well multifaceted biological matrix in trace amounts or occur as non-covalent complexes in order to perform different biological processes. Latest spectroscopic methods along with in-silico approaches including bioinformatics are the important tools needed for research activities in metallomics. The present review highlights the basics of metallomics in biological sciences and its emergence as a novel omics era in relation to other fields. Besides the above aspects, applications and future prospects of metallomics have been highlighted.

Introduction from Metals to Omics

Biological systems utilize metal ions for their fundamental processes like signaling, catalysis and gene expression. Few metals due to their metallic properties cause various diseases like Pt, Cr, as are carcinogenic whereas Pt, Co, Cr, Ni, Au cause immunological diseases. Mercury is teratogenic and causes diseases related to embryos. Nephrological disorders are caused by Cd and U whereas Al, Hg, and Mn are neurotoxic [1]. The essential transition metals e.g. Zn, Fe, Se, Cu are generally used by cells as cofactors of enzymes, can also potentially catalyze cytotoxic reactions [2]. Further, metals ions govern important properties like the folding of proteins, their conformation, assembly, stability, and catalysis. Many metals mostly transition metals (Mo, Fe, Zn, Cu, Mn) are required as a cofactor of various enzymes for their specific activities [3]. Metal ions also up-and down-regulate protein expression in the cells. Metallothionein proteins play a crucial role in cellular homeostasis and detoxification responses [4]. Therefore, metal ion concentration in the cell, their integration in metalloproteins and their allocation to different cell organelles has been considered to be under tight regulation [5]. The DNA, RNA, and biosynthesis of protein require various metalloenzymes and related metal ions [6]. In this line, nowadays with the help of the high-throughput approaches the complete genetic blueprint of various organisms has been studied which resulted in various ‘’omics’’; the disciplines aiming at the annotation of a particular class of components of a living organism in its ensemble [7]. Therefore, metallomics is a very needful area to be focused scientifically among researchers along with other omics such as genomics and proteomics.

Other than “metallome” and “metallomics” many related definitions have emerged, for instance, ionomics [8], hetero-atom tagged proteomics [9], or elementomics. It is very important to define the terms and render their use systematically [10]. Among various omics, metallomics is defined to apprehend the metal-dependent life processes [11], or the assemblage of metals related research in the living organisms. However, the word “metallome” was first given by Williams who referred to it as an element distribution, metal ion concentration, or as free elements present in the cellular organelles, cell or organism [12]. Under metallomics, ‘’metallomes’’ is a general annotation for metalloenzymes, metalloproteins, and many other biomolecules containing metal ions which are similar to genomes for genomics (the study of nucleic acids) and proteomes for proteomics (the study of proteins and amino acids). The main research objectives of metallomics involve the study of physiological and biological functions of living systems and identification of metallomes, however, chemical speciation, the important technology required for the establishment of metallomics is an integral branch of biometal science [13]. Now metallomics has become the hot topic of various reviews [14-17], and special issues of many reputed journals [18,19].

Recently, the advanced technologies make platforms for acquiring the “omics” data generated through numerous experimental sources to come-up with the system level broad perspective of organisms. The genomics and proteomics data helped a lot in knowing cell molecules and their interrelations at the molecular level, so one can determine the biological activity of those components [20]. In this direction, the initial approach is to construct the dataset for metalloproteins that can be used with other proteomics data for the modulation of multifaceted cellular processes integrating metals for which “omics” data could be extremely useful. In the present review, we discuss the recent scientific achievements on metallomics and related fields advocating the uptake, role, upkeep, and movement of metal ions crucial for living beings. Compared to other omics such as genomics and proteomics, metallomics is a relatively new field; however, they have constructed a tremendous data that can be used to study metallomics. Metallomics must be the core focus of scientific investigation because functional genomics and proteomics cannot be completed without the role of metalloenzymes and metal ions [21].

In order to understand the science of ‘’metallomics’’, it is essential to use a novel way to look at the relevance of metals in organisms and as the fraction of ecosystem thus bringing together the environment and cellular life (Singh et al. 2011). The molecular basis for many metal-dependent biochemical processes even now remains ambiguous [3]. Mechanism of metal sensing, metal uptake and storing or incorporation of metals as a cofactor in the cell is few of the thrust areas to work or to meet the coming challenges in metallomics.

Hence, it is crucial to interpret the significance of metals in governing various biological processes and stress responses by systematic evaluation of metal ions, speciation, and localization in various tissues or under particular conditions. In this report, ‘’metallomics’’ is suggested as a novel scientific area emphasizing the importance of research in biometals.

Metals in an environment and their biological significance

Metals in the environment are generally beneficial but can become a source of toxicity if they exceed a certain limit [22]. With increasing pollution, metal toxicity in the water and soil is constantly growing. The environmental pollutants can be the inorganic, organic or heterogeneous combination of both. Inorganic pollutants from anthropogenic activities include carcinogenic heavy metals for instance arsenic (As), mercury (Hg), nickel (Ni) and many others [23]. The sources of environmental pollution include extermination and improvisation activities, mineral processing and mining, agriculture-related activities, wind-blown dust, sea spray, transportation activities and automobiles and other anthropogenic operations [24]. The environmental contamination by inhabitance of deleterious metals pose threat to living beings and ecological community through direct consumption or contact with polluted soil, the food web, imbibition of infected groundwater, attrition in food quality, decrement in land adoption for agriculture thus eliciting food insecurity, and land occupancy disagreements [25]. Although metals are deleterious when present in excess amount but are also essential in order to perform important processes of life [22]. Since the harmful consequences of metals are widely known, the present review emphasizes the significant and crucial aspects of metals in the living system.

Evolution of metal biology from prokaryotes to eukaryotes

Millions of years ago, environmental conditions were reductive and therefore drastically different from today [26]. The primitive cells being anaerobic could not utilize all the elements accessible due to the presence of a substantial volume of hydrogen sulphide (H2S) in the environment [27]. The archean ocean which was reductive and anoxic was rich in iron (Fe), manganese (Mn), and cobalt (Co), thus far low in copper (Cu), zinc (Zn) and molybdenum (Mo) [28]. Therefore, the earliest organisms utilized metals that were abundant in the earliest ocean, Mn, Fe, and Co. The composition of the primitive ocean determined the metal-binding architectures evolution and the organisms’ choice of elements [29]. However, as organisms evolved the presence of metals determined the metals inside the cell which further became available to perform the biological functions. Anaerobes utilize part of Co(B12) and Ni as reducing catalysts and Fe as the electron transferring agent while Mg ions are used in catalysis of weak acids. Initially, aerobic bacteria developed utilizing Mo and Cu due to sulfides oxidation. The cell utilized copper ions in the periplasmic space where they operated on novel substrates like Nitric Oxide produced by oxygen [30]. The prokaryotic cells largely utilized Fe and Mg ions in various metabolic pathways and assisted transcription factors as messengers. However, there was no involvement of metal ions such as Ca, Zn and Cu [31]. Reductive environment supported the evolution of prokaryotic organisms when certain transition metals became available. During the advancement of evolution, this condition, additionally with the redox chemical activity of transition metals culminated in the small free cytosolic compartments in prokaryotes [32]. In order to maintain the moderate metal ion accumulation in the cytosol and to defend the cell against cytotoxic augmentation effects of these intracellular metal ions, modern prokaryotic cells evolved new metal binding proteins [33]. This state of proportionately low metal ions in the cytosol is observed in the present day eukaryotes. However, increased abundance and availability of metal ions due to increased oxygen availability was conducive for eukaryotic organism’s evolution [34]. For messenger systems, catalysts, structure etc. both metals and non-metals are crucial but their introduction into cellular activity at the comparable amount at the same period of evolution is an uncommon phenomenon. The changing environment leads to this evolution [32].

The change was slow as Oxygen was removed at first by the ferrous and sulfide in the sea. The need was for organisms to acclimatize to the new environment and they were able to adapt due to the multi-chambered bigger, gradual reproducing, cell system, and the eukaryotes, simultaneously with fast-reproducing prokaryotes [35]. The main applicability of additional compartments is the isolation of reductive reactions from the oxidative reactions of the cytoplasm and ions storage vesicles of the cytoplasm was not allowed. The bigger cells possessed filaments, had an extensible membrane and integrated aerobic bacteria and other symbiotic chambers. An elementary and beneficial modulation of messenger inter-communication was necessary among the non-flexible compartments to provide homeostasis and from the environment to provide an elevated sensitivity to cellular surroundings [32]. The Ca ions were utilized in essential messengers, Zn ions in transcription agents and Cu ions generally in vesicles [36]. The Zn and Cu became more accessible as their sulphides can be partially oxidized.

Anaerobic cells acquired defensive mechanisms so as to survive in the oxidizing environment. In addition, cell mastered to use oxygen for respiratory metabolism, thereby augmenting the efficacy of ATP synthesis [37]. For instance, the role of superoxide dismutase and catalase is well demonstrated in protecting the cell against the toxic residues of oxygen metabolism. Cells made use of at least some metals that today are called the “essential” metals. Due to the adequacy of essential metals at the time of prokaryotic and subsequently eukaryotic organism’s evolution many metals integrated with biochemical functions as elementary factors [38] (Figure 1).

Emergence of novel omics: Metallomics

The fields like genomics, proteomics, and metabolomics have collectively known as “omics” had been subjected to tremendous improvement in the past. The first to develop was genomics, which produces complete genomic DNA sequences of living creatures. The next “omics” includes proteomics i.e. the interpretation of the structure, stability, localization, and interaction of cellular or organism’s proteins [39]. Further, metabolomics annotates the complete metabolites of an organism [40]. The techniques used in proteomics and metabolomics have usually evaded the metals present in proteins and metabolites. However, the cell chemistry should be characterized not only by its nucleic acids, proteins, and metabolites but also with its metallome [16]. Therefore, metallomics should be recognized as emerging omics that characterize the metallomes and find out the interactions and functional associations of metals with proteins, genes, and metabolites [11]. The high-throughput technologies provided tremendous data about the genome. “Omics” data are accessible for many cell constituents and interactions, in addition to, for instance, genomics, proteomics, transcriptomics and protein-protein interaction maps (interactomics) [41]. The availability of large-scale information has largely helped researchers in interpreting functions of organisms but due to inadequate metallome data, the understanding remains partial. However, to explore any biological function/signaling pathway/cellular mechanism, metallomics should be linked with other omics and so in this review further we explain how other omics require metallomics to retrieve any information.

Integration of metallomics with genomics

The tremendous advancement in omics technology has led to the growth of genomics to such an extent that, it is divided into structural genomics and functional genomics. Structural genomics procreates high-resolution, 3D structural models of DNA whereas functional genomics tries to decipher functions of various genes through RNA analysis [42]. The metallomics and metalloproteomics are comparatively novel areas of study; however, data generated by genomics can be utilized to rapidly enhance our perceptive of metalloids and metalloproteomics [43].

Metals are important for maintaining the structural integrity of DNA and RNA which are polyanionic in nature. Besides being required for replication, metals are also utilized in structure formation, folding and in catalytic mechanisms e.g. in ribozymes. In prokaryotic DNA replication divalent cations assist the 3’OH to commence a nucleophilic encounter on alpha phosphate of deoxyribonucleotide stabilizing the negative charges of triphosphate [44]. The thermodynamic equalization of tertiary structures of RNA is implemented by monovalent (K+), divalent (Mg2+) or trivalent metal cations in various ways. To shield unfavorable electrostatic interactions monovalent ions affiliate periphrastically with the RNA backbone. The distinct components of the tertiary structure of RNA are stabilized by site-bound ions. For example, in primary groove magnesium hexahydrate and guanosine interaction stabilizes definite motifs of the tertiary structure of RNA [45]. Similarly, various cations stabilize the multiple phases of RNA folding. The RNA secondary structure is stabilized when the polyanionic RNA backbone is neutralized by mono or divalent cations and amines. Hence, metal cations stabilize the RNA backbone when the regions of heavy negative charge develop due to the stacking of phosphates. Several motifs in RNA duplexes are identified where metal ions bind. For example, in the group I introns of Tetrahymena thermophila the successive adenosines in the RNA strand form a non-conical pseudo base pair in the ion binding motif [46]. The lack of cations in several of such motifs leads to damaged or more flexible tertiary structure [47]. Additionally, to stabilize the junctions in DNA such as transitional Holliday junction in genetic recombination, the divalent ions mainly magnesium is crucial. The magnesium ions in the junction shield the negatively charged phosphate groups. This helps to position the phosphate groups adjacent to one another conceding stacked conformation [48].

The several metalloenzymes and metal ions assist in the synthesis and the metabolic roles of genes and proteins. The amplest transition metal, Zn, aids in carrying out the activity of over three hundred enzymes, stabilization of DNA and expression of genes [49]. The zinc in the eggs of salmon probably assists in the synthesis of DNA/RNA, processes such as the production of energy adenosine triphosphatase (ATPase) and regulation of cell division. Further, calcium ions associate with the carbonyl terminals in the proteins so as to stabilize the structure. Therefore, the imaging of metallomics will concede co-localization of gene expression as well as localization of protein patterns with metals thus providing gene, protein, and metal function linkage [8]. Unlike the correlation of metallo-proteome and genome, the correlation of metallo-metabolome and genome is not so distinct and may be missing. With the molecular cloning methods the metallo-metabolome interaction can be established by investigating metal resistance genes in organisms [11]. Therefore, the three -omics are correlative, and the aggregation of authenticated metallomic data with the transcriptome and proteome knowledge of a cell is the largest challenges for future investigation in this area. One way forward is that better established -omics (transcriptomics and proteomics) incorporate metallomics in their studies on model organisms whose gene/protein sequences are well annotated in databases.

Metallomics interaction with proteomics

The metalloproteins three-dimensional structure incorporates inorganic ions and comprises nearly 30% of the proteins [50]. Metalloproteins catalyze significant processes of water oxidation and photosynthesis [51]. The subclass of metalloproteins i.e. metalloenzymes performs specific catalytic functions. Metalloenzymes act on the molecule termed as the substrate which undergoes a net chemical transformation. Biological pathways require metalloenzymes to preserve life [52], and consequently use metal ions specifically K, Fe, Ca, Zn, Mn, Mg [26]. Extensive protein networks comprising metal sensing proteins and transporters retain the proper subcellular concentration of elements within the cell. Metalloenzymes are required inside the cell for various metabolic pathways (Table 1). The protein networks shuttle each metal relevant metalloprotein in the cellular compartment as metals compete for protein binding sites [53]. Metalloproteins containing complex metal clusters metabolize small glucose molecules, assemble proteins containing iron-sulfur clusters, and enzymes incorporating metal ions catalyze the halogenation of organic molecules [54]. The metalloenzymes/ metalloproteins evolution explains the reasons for this diversity. Iron-sulfur proteins, containing FeS clusters exist in many metalloproteins, viz. ferredoxins, hydrogenases, succinate-coenzyme Q reductase, nitrogenase, coenzyme Q-cytochrome c reductase, NADH dehydrogenase [55]. Iron-sulfur clusters play a significant role in the oxidation-reduction process in mitochondria and others coordinate gene expression. They also perform other activities, for instance, catalysis by aconitase, donors of sulfur during biotin and lipoic acid biosynthesis etc. [56]. Metalloproteins also carry out some crucial functions of dioxygen transportation in respiration. In three known classes of proteins for transportation of dioxygen i.e. haemoglobin-myoglobin, hemocyanins, and hemerythrins, a sensitive equilibrium exists for oxygen binding to metal center without irreversible oxidation of metal [57] (Table 1).

These are mostly two-electron redox mechanisms and involve atom or group transfers. The oxygen atom is added to the substrate in many important and common reactions. Examples include iron porphyrin centers in cytochrome P-450 enzymes catalyzing the oxidation process of formation of alcohols from hydrocarbons [58], tyrosinase which contains a dinuclear-Cu active site catalyzes the ortho-hydroxylation of phenolic substrates [59], and sulfite to sulfate oxidation by sulfite oxidase which contains a molybdenum atom [60]. These enzymes differ in the source of oxygen added to substrate and metal ions identity present. Dehydrogenations constitute another class redox processes involving two electrons. The removal of electrons and protons is equivalent to the loss of dihydrogen from a substrate. For example, the liver alcohol dehydrogenase active sites contain a Zn (II) ion and catalyze the synthesis of acetaldehyde from ethanol. One of the molecules of hydrogen out of the two hydrogens released is added to the organic cofactor NAD+ to form NADH [61].

However, metalloenzymes which catalyze redox reactions with several electron pairs involve redox reactions with more than two electrons in one reaction and are crucial in living organisms. The reversible conversion of two H2O molecules to one O2 molecule with an exchange of four electrons is a significant reaction of this type. The production of H2O from O2 reduction is significant for the phosphorylation of ADP to ATP and requires cytochrome c oxidase that contains two Cu and two Fe-heme centers [62]. The reverse reaction, involving four Mn ions is water splitting to oxygen which has an important function in photosynthesis [63].

Metalloenzymes in rearrangement reactions that occur without a change in oxidation involve the enzymes like chorismate mutase (EC5.4.99.5) that catalyzes the production of proprehenate ion from chorismate ion via Claisen rearrangement [64]. Vitamin B12, an alkyl-cobalt (III) complex of a substituted corrin, is a cofactor of enzymes catalyzing 1, 2-carbon rearrangement [65]. Many hydrolytic enzymes contain Zn2+ ion. Besides Zn2+; Mn2+, Ni2+, Ca2+, and Mg2+ are the metal ions encountered in hydrolytic enzymes. Hydrolytic enzymes catalyze the disruption of proteins, carbohydrates, and fats to their monomer units. The covalent bond attaching monomers is cleaved due to hydrolysis as a water molecule adds to the polymer. Examples include carbonic anhydrase (Zn prosthetic group) that promotes hydrolysis of carbon dioxide, peptidases (a majority of the metallopeptidases contain zinc atom), esterases that catalytically hydrolyze carbonyl compounds, and phosphatases (Mg2+ or Mn2+), catalyzing the splitting of phosphate esters. Another hydrolytic metalloenzyme, thiocyanate hydrolase, purified from the bacteria Thiobacillus thioparus TH115 contain cobalt and hydrolyzes thiocyanate to ammonia and carbonyl sulfide [66].

Metallochaperones guide the ions and defend it from the over-chelation potentiality of the cell [67]. Metallochaperones sort specific metal co-factor to the precise metalloenzymes and transport them to diverse location. Many metal ions present in the enzymes acting as co-factors remain located intracellularly or transported extracellularly [68]. For instance, copper is toxic element yet crucial for the living systems. Cells acquire many mechanisms so as to sustain copper homeostasis such as; the protein-mediated intracellular delivery of copper to target proteins. This is consummated by a group of proteins, the copper chaperons, which conserved proteins present in prokaryotes and eukaryotes. Three different classes of Cu-metallochaperones namely cytochrome oxidase (COX17), antioxidant (ATX1/ HAH1) and copper chaperones of SOD1 (CCS) are known [69]. The copper ion incorporation into SOD1 requires a Cu metallochaperone [67]. Metallochaperones incorporating metals other than copper involve similar cofactor trafficking pathways. However, the chaperones integrating metals besides copper are not present in eukaryotes. The ArsD, arsenic chaperone present in Escherichia coli has been established to transfer trivalent arsenic to ArsA. ArsA is the subunit embodied in As(III)/Sb(III) pump for efflux and performs catalytic function. The affinity for arsenite increases as ArsA and ArsD interact. This enhances arsenite extrusion even at lower arsenite concentrations as the activity of ATPase increases. Thus, to prevent intracellular toxicity of arsenite, cells exploit arsenic chaperones [70]. Additionally, proteins which bind nickel is described which may promote metal insertion to the enzymes requiring nickel such as urease, Co-dehydrogenase, Ni-superoxide dismutase, glyoxidenalase etc.

Prokaryotes do not need metal carriers such as COX17 as intracellular compartmentalization is not present is prokaryotes as in eukaryotes. However, in the periplasm of prokaryotes and in gram-negative bacteria cupro-proteins are present. In the gram-negative bacteria, the porins are located in the peripheral membrane through which metals diffuse from the external medium [71]. The proteins like soluble periplasm protein CucA acquire the appropriate metals and export them in unfurled form through the secretory pathway. The most copious Cu2+ and Mn2+ proteins, CucA and MncA, were diagnosed in the cyanobacterium Synechocystis PCC 6803 [68]. Further, Zn SOD and Cu SOD are expressed in bacteria, but no CCS homolog has been established in prokaryotes. However, for enterobacteria, ATX1 (CopZ) homolog has been defined. The isolated CopZ has potential to contribute copper to CopY for a transcription factor. A model proposes that this transfer of copper displaces the Zn ion required for CopY binding to DNA [72]. Several biological processes require metal-ion binding proteins. Metallothionein is rich in cysteine, low molecular weight protein family in animals, angiosperms, eukaryotes and few prokaryotes. Metallothioneins contain metal ions viz. Cd (II), Zn(II) and Cu(I) in metal clusters [73]. Through the thiols present in cysteine residues, MTs bind the physiological (Cu, Zn Se) and xenobiotic (Ag, As, Cd, Hg) heavy metals [74]. The metal clusters Me(II)3(Cys)9 and Me(II)4(Cys)11 are present in mammalian MTs. These clusters bind heptad of metal ions (Me) through thiolate coordination [75]. Biosynthesis of MTs is induced by several agents and is coordinated at the level of transcription. MTs sequester mainly metals which are non-essential [76].

Metallomics role in metabolomics

Metabolomics, a rapidly developing technology deals with metabolome which is described as the metabolites compilation of the cell [77]. Metabolic fingerprinting, targeted analysis and metabolite profiling are the major approaches presently adopted in metabolomics related research [78]. The three components are significant in metabolomics in order to carry out such processes: (1) antioxidants (2) stress by-products due to disruption of homeostasis; and (3) molecule involved in signal transduction responsible for adaptation response. The molecules involved in signal transduction are either recurrently synthesized or compounds liberated from conjugated forms such as salicylic acid [79]. The metals and ligands interaction is a significant area of metallomics research. The defensive mechanisms of numerous organisms against toxic metals comprise of many organic acids such as succinate, malate, oxalate etc. [16], metallophores [80], and peptides binding metals [81]. Hyper accumulating plants developing metal homeostasis are of particular interest. They can live and reproduce in metal-rich environments [82]. In such plant cells, the complexity of metals leads to many relatively poorly characterized metal complexes.

The study of detoxification controlling mechanisms can benefit from the establishment of the species formed. The metabolite and gene networks can be deciphered through assimilation of the data of metabolomics and transcriptomics [83]. For example, the proteomics and the metabolomics were integrated to establish the response of Arabidopsis to cesium stress [84]. However, in view of the problem of data integration, the collective study of the data from metabolomics and other omics is actually challenging [85]. Though other targets for approaches related to genomics are attainable, to identify metabolites produced in streptomycetes grown in growth media with 0.2 mM Ni or Cd indicates huge probability for revealing strains from cultures. This would help to decipher cluster of genes during metal stress [86]. Metals could be used as inducers of new metabolites such as antibiotics i.e. another area of metallo-metabolomics used in biotechnology [14].

A good approach to metallo-metabolomics should help in element identification in the species or identifies at least some and account clearly for the non-identified ones (quantitative speciation blueprint). In contrast to metallo-proteomics, the de novo recognition of metabolites is performed by using leading spectrometric techniques. Mass spectrometry (MS) technology and a purification method are a comprehensive approach to metallo-metabolomics [11]. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) ideally monitors the separation of metallo-metabolites. The sensitivity of ICP-MS is autonomous of the metalloid surroundings of the molecule, concomitant compounds, and buffer used for chromatography and the matrix. In addition, ICP-MS monitors the quantifiable restoration of an analyte. This is an important attribute which is not possible to measure through electrospray ionization mass spectrometry (ESI-MS). Note that ICP-MS cannot monitor the nature of separation per se but it is considered that analytic purity increases with each separation step when clean volatile buffers are used [16]. The metallo-metabolites are highly polar and less hydrophobic which make hydrophilic interaction chromatography (HILIC) [87], an optimal approach for sample addition by ESI-MS in metallo-metabolomics. The HILIC is a significant technique to investigate seleno-metabolome of yeast [88], and few organic molecules metal complexes (Weber et al. 2008) and some organic acids (Ni malate, citrate, histidine, EDTA, and nicotianamine) [89].

The absence of well-depicted metabolome of plants is a great challenge in metabolomics of plants. Approximately 90000-200000 distinct metabolites are produced in plants [90], but the exact statistic of metabolites in any individual plant type is still unknown. The microbes have better-understood metabolism, even then the total metabolites present in microbes is not deciphered. The metabolome characterization of the plants is essential in order to uncover the gene function.

Metallomics in environment-related studies

Metals generally exist in the atmosphere but their level is increasing due to industrial revolution via technological advancements. The increase in a number of metals in ecosystem occurs in metropolitan areas, metalliferous mines, major road systems, vehicle emissions, areas characterized by automobile activities etc. [91]. The increased level of metals in the biosphere is the cause of slow environmental poisoning. Thus, it necessitates studies on environmental pollution and biogeochemistry. Further, the knowledge of how living creatures sense, adapt and use metals in dynamic ecosystem or biome is fundamental for the precise view of the metabolism of transition metals [92].

Metallomics comprise various types of information from identification of metals (qualitative metallomics) to finding out their level (quantitative metallomics) [14]. Metallomics may be important in studies relevant to plant metal tolerance and homeostasis [93], biogeochemical metal cycles [94], plant proteome annotation engaged in toxicity of metals [95]. Metallomics may be supportive to the improvement of applications for optimized strategies in metal contaminated soils, including microbial-assisted phytoremediation of polluted land, reclamation of soil and biomarker recognition for eco-toxicological studies [94].

For phytoremediation studies, phytochelatins build-up in the plants is significant phenomenon due to their role in detoxification of heavy metals [96]. The study of plant and soil amount of heavy metals in Opuntia ficus predicated a complex interplay of heavy metals in the environment and phytochelatin production [97]. Many advanced approaches such as HPLC-ICP-MS is utilized in phytoremediation studies for the establishment of seleno-compounds in the plant extracts from Brassica juncea, Allium sativum, [98], and Bertholletia excelsa [99]. In Brassica juncea and Sesuvium portulacastrum, complexes with bio-ligands have been investigated after exposure to different amounts of Pb(NO3)2. Studies have revealed that due to the presence of the isoform phytochelatin3 both the plants are crucial in phytoremediation [96]. Moreover, the metalloproteins have a role as environmental stress biomarkers. The metal and metalloids play a significant function in organisms as large biomolecules (nucleic acids, polysaccharides, and proteins) and organic molecules (oxalate, citrate, tartrate, amino acids, oligopeptides) can be bound to metals, to generate different chemical species [3]. The biomolecules binding metals constitute a considerable quantity of molecules engaged in the metabolism of the cell and assist in identification of metal cofactor present in the protein. This helps to find out the function of the protein in cellular pathways [100]. Many metalloproteins act as organism’s markers, exposure to metals and indicators of their status. For example, metallothioneins are metal binding proteins rich in Cys and are utilized as biomarkers for some organisms exposed to metals in the environment. Metallothioneins in the organisms bind metals and thus act as a detoxifying mechanism [101]. Metallothioneins are utilized to find out the effect of heavy metals in marine organisms [102]. The method of determination of hepatic metallothioneins is confirmed biomarker for determination of biological implication of metal contamination. Other metalloproteins have been established as markers such as metal superoxide dismutase in biological creatures in contact with xenobiotics. Metal superoxide dismutase (SOD) is studied upon drought stress [103], in rice and ozone [104], action. The probability of deciphering more metalloproteins that can act as biomarkers for pollution is potentially high in fish. The metalloproteins which are being studied as environmental biomarkers in fish are matrix metalloproteinases, iron-binding metalloproteins, selenoproteins, Hg-, Se- and As- containing proteins and superoxide dismutases. The research of the biomolecules using metallomic approach simplifies the significance of complex biological matrices. The interpretation of the structure, elucidation of the pathways, and characterization of the metalloproteins are the areas which require further investigation.

Metallomics in communication biology

Metals not only perform an important function in various crucial processes of life but they are also used as magnetic compasses in living organisms. The various animals such as bees, birds, sea turtles etc. possess compasses inside them. With their compasses, some species navigate entire oceans [105]. Magnetoreception or magnetoception allows the animals which show biomagnetism (magnetic field production by organisms) to investigate magnetic field so as to perceive directions. Magnetoception illustrates the navigational skills of many animal species [106]. The phenomenon of magnetoception is noticed in bacteria, birds, fungi, insects and many other animals. Such cellular communication roles by metals are a very exciting frontier in biology. Magnetotactic bacteria incorporate magnetosomes (magnetite or greigite nanocrystals) which help bacteria navigate geomagnetic field to avoid the higher oxygen concentrations of surface waters, which are toxic to them [107]. They orient on the earth’s magnetic pole, and, when transported to the opposite hemisphere, disorient and swim upward.

The Clumbia livia commonly known as homing pigeon provides the best example of magnetoreception. Pigeons have magnetic minerals in the beak that remain in contact with the nerve and react to alteration in a magnetic field [105]. Likewise, based on behavioral evidence of Apis mellifera or honeybee characteristic of magnetoreception has been provided. Free flying honeybees can perceive static intensity fluctuations as weak as 26nT against the magnetic field [108]. Biomagnitites (Fe3O4) are present as magnetoreceptor and play an important role to transduce information of magnetic field. Honeybees go through iron biomineralization which causes magnetoreception [109].

Some ions, especially Na+, K+, and Ca2+, trigger cellular response. For example, calcium-binding proteins control functions of the cell and the sodium ions influx into cell membrane causes the neurons to respond. Calcium controls many significant cell activities starting with new life creation at fertilization to ending with apoptosis [110]. Likewise, Zinc fingers are metal ion classes in biology that regulate transcription. These pieces of evidence suggest the importance of metal ions in communication biology.

Metallomics in pharmacy / medicine

Metal complexes are important to carry out biological and biomedical processes. Metal complexes consist of meal atoms surrounded by ligands. Organic compounds in medicine have different modes of action; some are biotransformed by metalloenzymes (Holm and Solomon 1996) others have an effect on the metabolism of metals. Metal complexes are used as drugs for curing various human diseases like lymphomas, carcinomas, infection control, anti-inflammatory, diabetes, and olfactory disorder. The transition metals upon interaction with molecules having negative charges display different oxidation states. This phenomenon of transition metals is significant for the advancement of drugs based on metals having therapeutic values and pharmacological applications [111]. The metal complexes significance in pharmacy and the recent developments are indexed in table 2.

Novel therapeutics with metal complexes offers real possibilities to pharmaceutical industries. The smooth encounter of the metal complexes in ligand substitution and redox reactions presumably indicate active species to be the biotransformation products of the administered complex [112].

Therefore, metal compounds could be used more effectively as drugs following the active species identification. The metal complexes identification and their biotransformation still require investigation. Further, the toxicity and metal compounds are correlated therefore targeting metal-based drugs to specific locations (cells, tissues or receptors) where they are needed, could lower the toxicity to a significant extent [113]. Thus, to understand bio-coordination chemistries of drugs having metal ions, thermodynamics and kinetics of metal complex reactions, mainly under biologically relevant conditions is significant [114]. Hence, the study of elemental medicine would help to decipher diagnostic and therapeutic approaches and contribute to our insight of natural biological processes.

Contribution of bioinformatics in exploration of metallomics

The huge repository of genome sequence data is responsible for the boom in bioinformatics. Although the information of metalloproteome is required for the comprehensive understanding of life processes, the presently available experimental methods or techniques are not capable of achieving such a demanding task. At this point, bioinformatics provides a considerable contribution to subjugate the limitation of empirical methods by using predictive tools and information technology [115]. The metal binding domains can be deciphered with the help of protein sequence data available in Pfam and other libraries [116]. Bertini and Cavallaro [117], have reviewed the bioinformatics approaches dedicated to bimetals. Many metalloprotein databases using primary sequence information have been generated utilizing various bioinformatics methods [118].

With the advancement in high throughput techniques the characterization of metallome would be easy and thus the huge amount of data will be obtained. Therefore, bioinformatics approaches would be required to retrieve the data from the tremendous data set. The computational program utilizes sequence information by taking into count position-specific evolutionary profiles and aspects such as protein length and amino acid composition. This method provides information on transition metal binding site components and is highly complementary to the high-throughput techniques based on X-ray absorption spectroscopy (HT-XAS), which identifies the metal binding to protein [119]. Further, comparative structure modeling is a very powerful tool in driving protein function. MODBASE is structural models data [120], established on template-target alignments accessible at the website ( In general, the accuracy of constructed models is based on sequence similarity of model sequence and the templates. Many applications such as functional analysis and screening of small-molecule databases for potential drug discovery utilizes models based on 30% sequence identity. Databases devoted to metal binding comprise of metalloprotein database (MDB, [121], which consists of quantitative data of all the metal consisting sites accessible from PDB, and PROMISE, which provides information about metalloproteins and is now discontinued [122]. Other related databases include BIND (, which is the compilation of complete information of interactions with ligands, including metals. It is built up from peer-reviewed literature and only published results are accepted. In addition, databases from the large genomics centers usually include a biophysical depiction of targets and may contain metal binding information. These servers and databases are very beneficial in providing the broad scientific communities easy connection to the existing data on the characterization of metalloproteins.

The availability of genomic data of a large number of organisms spurs enthusiasm for the advancement of bioinformatics methods allowing the prediction (in silico identification) of trace-element containing proteins [123]. A pioneering study reported the progress of bioinformatics tools to identify almost all the genes in many organisms which encode proteins containing selenocysteine, including humans. The introductory algorithms utilized the recognized SECIS (selenocysteine insertion sequence) element (AUGA_AA_GA) as an endorsement for mammalian selenoproteins [124], and subsequently searched for SECIS-containing genes within the frame of UGA codon [125]. SECIS element is harbored by mRNAs encoding selenoproteins in their 30 untranslated regions and triggers the UGA codon (normally stop codon) recoding into selenocysteine. Note that whereas the SECIS elements of the eukaryotes concurrence are well characterized and can be determined in data bases, conservation of bacterial SECIS element was inadequate for the computational description [126]. The characterization of the seleno proteomes and metalloproteomes via experimental approaches is very tedious, this leads to the search for in silico methods in order decipher the role of metalloproteins. Recently, a series of bioinformatics studies reported the disposal of iron-, copper- and Zn-binding proteins in several organisms such as eukaryotes, bacteria, and archaea [123-158].

Conclusion and Future Prospective

Metallomics is projected as the interdisciplinary research field for the promotion of biometal science. Metal ions conserve the physiological functions in living organisms, thus keep us healthy under stable conditions. Paradoxically, some metals are needed in trace amounts and cause toxicity at elevated levels whereas living cells tolerate other metals at extremely high levels. The biometallics has not received significant attention as a systemic scientific field as the researches on biometals are performed independently or distinctly in various scientific fields. The advancement in metal technologies would expedite the course of identification, characterization of novel metalloproteins, metal folds and establish the usage of metal ions in living organisms. Hence, in near future, metallomics and metalloproteomics could be utilized to understand complex biological systems. The various biochemical processes such as respiration, biological nitrogen fixation, sulfur and carbon cycle are dependent on metalloproteins. Thus, the knowledge of metalloproteins is essential to many research areas from climate change, carbon capture, and bioenergy to plant biology and medicine. The applications of metal-technologies would elaborate the understanding of metal function in the physiology of microbes, ecology, and human disease, and would impact various aspects of biological science in the coming years. The metal ions significance in bioactive macro-molecules present in various organisms makes necessary the advancement of novel analytical tools which, under a multi-dimensional approach, contribute the comprehensive characterization of metal-macromolecules. The breakthrough in spectrometry especially tandem (MS), makes the study of metallomics feasible. This would lead to the estimation of biomarkers, quality of food, diagnosis of diseases and designing of metallodrugs and their action. Metallomics combines separation, detection of metal ions and elucidation of the structure and thus has a multidisciplinary basis. For the rapid process in metallomics the interface among analytical chemists, biologists and biochemists is required. Further, metallomics data of the cell should be analyzed with the genomic and proteomic data. This would aid in perceiving the role of metalloproteins. The metallomics shows integration with different omics and addresses the important role of metal ions in various disciplines of science (Figure 2).

The study of metallomics in line with other -omics spots the emerging pieces of the zigzag puzzle of systems biology; contributes to different fields such as molecular biology, pharmacology, toxicology, medicinal chemistry, nutrition, environmental chemistry, and animal and plant physiology. The progressive technological advancement in analytical instrumentation and interdisciplinary collaborations will link pure and applied parts for a correlative approach and accelerate the pace of studies in metallomics which will positively reflect on different areas of life.

Metallomics should be established as a methodological field of study to demonstrate the functions and chemical evolution of organisms. Thus, though metallomics is a post-genomic and post-proteomic field but needs to be developed in cooperation with genomics, proteomics, and metabolomics with the assistance of advanced techniques for quantization and quality analysis.

Metallomics should be established as a methodological field of study to demonstrate the functions and chemical evolution of organisms. Thus, though metallomics is a post-genomic and post-proteomic field but needs to be developed in cooperation with genomics, proteomics, and metabolomics with the assistance of advanced techniques for quantization and quality analysis.

VS thanks Founder President, Dr. Ashok K Chauhan at Amity University for providing a conducive environment and for being a constant source of inspiration.

  1. Jaishankar M, Tseten T, Anbalagan N, Mathew BB, Beeregowda KN (2014) Toxicity, mechanism and health effects of some heavy metals. Interdiscip Toxicol 7: 60-72. Link:
  2. Finney LA, O’Halloran TV (2003) Transition Metal Speciation in the Cell, Insights from the Chemistry of Metal Ion Receptors. Sci 300 : 931-936. Link:
  3. Szpunar J (2004) Metallomics, a new frontier in Analytical Chemistry. Anal Bioanal Chem 378: 54–56. Link:
  4. Isani G, Carpenè E (2014) Metallothioneins, unconventional proteins from unconventional animals: A long journey from nematodes to mammals. Biomolecules 4: 435-457. Link:
  5. Outten CE, O’Halloran TV (2001) Femtomolar Sensitivity of Metalloregulatory Proteins controlling zinc homeostasis. Science 29: 2488-2492. Link:
  6. Porcheron G, Garénaux A, Proulx J, Sabri M, Dozois CM (2013) Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence. Front Cell Infect Microbiol 3: 90. Link:
  7. Bertini I, Cavallaro G (2008) Metals in the “omics” world, copper homeostasis and cytochrome c oxidase assembly in a new light. J Biol Inog Chem 13: 3-14. Link:
  8. Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, et al. (2005) Characterization of the yeast ionome, a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol 6: R77. Link:
  9. Sanz-Medel A (2005) From metalloproteomics to hetroatom-tagged proteomics. Anal Bioanal Chem 381: 1-2. Link:
  10. Lobinski R, Becker JS, Haraguchi H, Sarkar B (2010) Metallomics, Guidelines for terminology and critical evaluation of analytical chemistry approaches (IUPAC Technical Report). Pure Appl Chem 82: 493. Link: 
  11. Mounicou S, Szpunar J, Lobinski R (2009) Metallomics, the concept and methodology. Chem Soc Rev 38: 1119–1138. Link:
  12. Williams RJP (2001) Chemical selection of elements by cells. Coord Chem Rev 216-217: 583-595. Link:
  13. Haraguchi H (2017) Metallomics: Integrated Biometal Science. In: Ogra Y, Hirata T, (eds) Metallomics. Springer, Tokyo. Link:
  14. Lopez-Bareal J, Gomez-Ariza JL (2006) Environmental proteomics and metallomics. Proteomics 6: S51-S62. Link:
  15. Szpunar J (2005) Advances in analytical methodology for bioinorganic speciation analysis, metallomics, metalloproteomics and hetroatom-tagged proteomics and metabolomics. Analyst 130: 442-465. Link:
  16. Mounicou S, Lobinski R (2008) Challenges to metallomics and analytical chemistry solutions. Pure Appl Chem 80: 2565–2575. Link:
  17. Shi W, Chance MR (2008) Metallomics and metalloproteomics. Cell Molecular Life Science 65: 3040. Link:
  18. Koppenaal DW, Hieftje GM (2007) Metallomics – An Interdisciplinary and evolving field. J Anal Spec 22: 855. Link:
  19. Jakubowski N, Lobinski R, Moens L (2004) Metallobiomolecules. The basis of life, the challenge of atomic spectroscopy. J Anal At Spectrom 19: 1-4. Link:
  20. Yates JR (2000) Mass spectrometry—from genomics to proteomics. Trends Genet 16: 5-8. Link:
  21. Shi W, Chance MR (2011) Metalloproteomics: Forward and reverse approaches in metalloprotein structural and functional characterization. Curr Opin Chem Biol 15: 144–148. Link: 
  22. Tchounwou PB, Yedjou CG, Patlolla AK, Sutton DJ (2012) Heavy Metals Toxicity and the Environment. Experimentia Supplementum 101: 133-164. Link:
  23. Suruchi, Khanna P (2011) Assessment of Heavy Metal Contamination in Different Vegetables Grown in and Around Urban Areas. Res J Environ Toxicol 5: 162-179. Link:
  24. Lopez JM, Callen MS, Murillo R, Garcia T, Navarro MV, de laCruz MT, et al. (2005) Levels of selected metals in ambient air PM10 in an urban site of Zaragoza (Spain). Environ Res 99: 58-67. Link:
  25. Wuana RA, Okieimen FE (2011) Heavy metals in contaminated soils, a review of sources, chemistry, risks and best available strategies for remediation. ISRN Ecol 1-20. Link:
  26. Williams RJP, Frausto da Silva JJR (2006) The chemistry of evolution, the development of our ecosystem. Amsterdam: Elsevier.
  27. Schopf JW, Kudryavtsev AB, Czaja AD, Tripathi AB (2007) Evidence of Archean life: Stromatolites and microfossils. Precambrian Research 158:141-155. Link:
  28. Anbar AD (2008) Oceans, Elements and Evolution. Sci 322: 1481-1483.
  29. Dupont CL, Butchen A, Valas RE, Boume PE, Anolles C (2010) History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci 107: 10567-10572. Link:
  30. Russel MJ, William, M (2003) On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci 358: 59-85. Link:
  31. Frausto da Silva JJR, Williams RJP (2001) The Biological Chemistry of the Elements, The Inorganic Chemistry of Life. 2nd Vol, UK, Oxford University Press. Link:
  32. Williams RJP (2007) Systems biology of evolution, the involvement of metal ions. Biometals 20: 107-112. Link:
  33. Colvin RA, Holmes WR, Fontaine CP, Maret W (2010) Cytosolic zinc buffering and muffling: Their role in intracellular zinc homeostasis. Metallomics 2: 297-356. Link:
  34. Embley TM, Martin W (2006) Eukaryotic evolution, changes and challenges. Nature 440: 623-630. Link:
  35. Kleczkowski M, Garncarz M (2012) The role of metal ions in biological oxidation- the past and the present. Polish Journal of Veterinary Sciences 15: 165–173. Link:
  36. Carafoli E, Klee C (1999) Calcium as a cellular regulator. ed. New York: Oxford Univ Press. Link:
  37. Clarkson T (1995) Health effects of metals, A role for evolution? Environ Health Perspect 103: 9-12. Link:
  38. de Baar HJW, La Roche J (2003) Trace metals in the ocean, Evolution, biology and global change. In: Wefer G, Lamy F, Manutoura F, ed. Marine Science Frontiers for Europe, New York, Springer, 79-105. Link:
  39. Blackstock WP, Weir MP (1999) Proteomics, quantitative and physical mapping of cellular proteins. Trends Biotechnol 17: 121–127. Link:
  40. Davis B (2005) Growing pains for metabolomics. The Scientist 19: 25-28.
  41. Manzoni C, Kia DA, Vandrovcova J, Hardy J, Wood NW, et al. (2016) Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences.Briefings in Bioinformaticsbbw114. Link:
  42. Skolnick J, Fetrow JS, Kolinski A (2000) Structural genomics and its importance for gene function analysis. Nat Biotechnol 18: 283-287. Link:
  43. Da Silva MAO, Sussulini A, Arruda MAZ (2010) Metalloproteomics as an interdisciplinary area involving proteins and metals.  Expert Rev Proteomics 7: 387-400. Link:
  44. Patel PH, Suzuki M, Adman E, Shinkai A, Loeb LA (2001) Prokaryotic DNA polymerase I, Evolution, Structure, and “Base Flipping” Mechanism for Nucleotide Selection. J Mol Biol 308: 823-837. Link:
  45. Pyle AM (2002) Metal ions in the structure and function of RNA. J Biol Inorg Chem 7: 679-690. Link:
  46. Burkhardt C, Zacharias M (2001) Modelling ion binding to AA platform motifs in RNA, a continuum solvent study including conformational adaptation. Nucleic Acids Res 29: 3910-3918. Link:
  47. Rudisser S, Tinocol I (2000) Solution structure of Cobalt (III) hexamine complexed to the GAAA tetra loop, and metal-ion binding to G-A mismatched. J Mol Biol 295: 1211-1223. Link:
  48. Panyutin IG, Biswas I, Hsieh P (1995) A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J 14: 1819-1826. Link:
  49. Andreini C, Banci L, Bertini I, Rosato A (2006) Counting the zinc-proteins encoded in the human genome. J Proteome Res 5: 196-201. Link:
  50. Rosenzweig AC (2002) Metrallochaperones, Bind and deliver. Chem Bio 9: 673-677. Link:
  51. Lu Y, Yeung N, Sieracki N, Marshall NM (2009) Design of Functional Metalloproteins. Nature 460: 855-862. Link:
  52. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM (2008) Metal ions in biological catalysis, from enzyme databases to general principles. J Biol Inorg Chem 13: 1205-1218. Link:
  53. Waldron KJ, Firbank SJ, Dainty SJ, Perez-Rama M, Tottey S, et al. (2010) Structure and metal loading of a soluble periplasm cuproprotein. J Biol Chem 285: 32504-32511. Link:
  54. Finkelstein J (2009) Metalloproteins. Nature 460: 813. Link:
  55. Lippard JS, Bery JM (1995) In principles of Bioinorganic Chemistry. Metal Functions in Metalloproteins 3-12.
  56. Bashkin JK (1999) Hydrolysis of phosphates, esters and related substrates by models of biological catalysts. Curr Opin Chem Biol 3: 752-758. Link:
  57. Riggs A (1998) Self-association, cooperativity and supercooperativity of oxygen binding by hemoglobins. J Exp Biol 201: 1073-1084. Link:
  58. Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J (1995) Structure and function of cytochromes P450, a comparative analysis of three crystal structures. Structure 3: 41-62. Link:
  59. Sánchez-Ferrer A, Rodríguez-López JN, García-Cánovas F, García-Carmona F (1995) Tyrosinase, a comprehensive review of its mechanism. Biochim Biophys Acta 1247: 1-11. Link:
  60. Kisker C, Schindelin H, Pacheco A, Wehbi WA, Garrett RM, et al. (1997) Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase. Cell 91: 973-983. Link:
  61. Staab CA, Hellgren M, Höög JO (2008) Medium- and short-chain dehydrogenase/reductase gene and protein families, Dual functions of alcohol dehydrogenase 3, implications with focus on formaldehyde dehydrogenase and S-nitrosoglutathione reductase activities. Cell Mol Life Sci 65: 3950–60. Link:
  62. Capaldi RA (1990) Structure and function of cytochrome c oxidase. Annu Rev Biochem 59: 569-596. Link:
  63. Pushkar Y, Yano J, Sauer K, Boussac A, Yachandra VK (2008) Structural changes in the Mn4Ca cluster and the mechanism of photosynthetic water splitting. Proc Natl Acad Sci U S A 105: 1879-1884. Link:
  64. Ganem B (1996) The mechanism of the Claisen rearrangement, déjà vu all over again. Angew Chem Int Ed Engl 35: 936-945. Link:
  65. Choi G, Choi S-C, Galan A, Wilk B, Dowd P (1990) Vitamin B12-promoted model rearrangement of methylmalonate to succinate is not a free radical reaction. Proc Natl Acad Sci 87: 3174-3176. Link:
  66. Katayama Y, Hashimoto K, Nakayama H, Mino H, Nojiri TO, et al. (2006) Thiocyanate Hydrolase is a cobalt-containing metalloenzyme with a cysteine-sulfinic acid ligand. J Am Chem Soc 128: 728-729. Link:
  67. O’Halloran TV, Culotta VC (2000) Metallochaperones, an intracellular shuttle service for metal ions. J Biol Chem 275: 25057-25060. Link:
  68. Tottey S, Waldron KJ, Firbank SJ, Reale B, Bessant C, et al. (2008) Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature 455: 1138–1142. Link:
  69. McCord JM, Frodovich I (1969) Superoxide dismutase, an enzymic function for erythrocuprein (Hemocuprein). J Bio Chem 244: 6049-6055. Link:
  70. Lin YF, Walmsley AR, Rosen BP (2006) An arsenic metallochaperone for an arsenic detoxification pump. PNAS 103(42): 15617-15622. Link:
  71. Nies DH, Silver S (2007) Molecular Microbiology of Heavy Metals. ed. Germany, Springer-Verlag. Link:
  72. Harrison MD, Jones CE, Solioz M, Dameron CT (2000) Intracellular copper routing, the role of copper chaperones. Trends Biochem Sci 25: 29-32. Link:
  73. Vasak M, Meloni G (2011) Chemistry and biology of mammalian metallothioneins. J Biol Inorg Chem 16: 1067-1078. Link:
  74. Mulware SJ (2013) Comparative trace elemental analysis in cancerous and noncancerous human tissues using PIXE. J Biophys 2013: 1-8. Link:
  75. Kagi JH, Hunziker P (1989) Mammalian metallothionein. Biol Trace Elem Res 21: 111-118. Link:
  76. Kagi JHR (1991) Overview of metallothioneins. Methods Enzymol 205: 613-616. Link:
  77. Dunn WB, Ellis DI (2005) Metabolomics, Current analytical platforms and methodologies. Trends Analyt Chem 24: 285-294. Link:
  78. Shulaev V (2006) Metabolomics technology and bioinformatics. Brief Bioinform 7: 128-139. Link:
  79. Mittler R, Vanderuwera S, Gollery M, Breusegem FV (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9: 490-498. Link:
  80. Wheal MS, Heller LI, Noevell WA, Welch RM (2001) Reverse-phase liquid chromatographic determination of phytometallophores from strategy II Fe-uptake species by 9-fluorenylmethyl chloroformate fluorescence. Chromatogr J 942: 177-183. Link:
  81. Cobbett C, Goldsbrough P (2002) Phytochelatins and metallothioneins, roles in heavy metal detoxification and homeostasis. Annu Rev Plant Biol 53: 159–182. Link:
  82. Salt DE, Kramer U (2000) Mechanisms of metal hyperaccumulation in plants.  In: Raskin I, Ensley B, ed. Phytoremediation of Toxic Metals. New York: John Wiley and Sons Inc 231-246.
  83. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, et al. (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280: 25590-25595. Link:
  84. Le Lay P, Isaure MP, Sarry JE, Kuhn L, Favard B, et al. (2006) Matabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply. Biochimie 88: 1533-1547. Link:
  85. Mehrotra B, Mendes P (2006) Bioinformatics approaches to integrate metablolomics and other systems biology data. In: Saito K, Dixon RA, Willmitzer L, ed. Plant Metabolomics. Berlin and Heidelberg: Germany, Springer-Verlag. Link:
  86. Haferburg G, Groth I, Mollmann U, Kothe E, Sattler I (2009) Arousing sleeping genes, shifts in secondary metabolism of metal tolerant actinobacteria under conditions of heavy metal stress. Biometals 22: 225–234. Link:
  87. Alpert AJ (1990) Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr 499: 177-196. Link:
  88. Dernovics M, Lobinski R (2008) Speciation analysis of selenium metabolites in yeast-based food supplements by ICPMS-assisted hydrophilic interaction HPLC-hybrid linear ion trap/orbitrap MSn. Anal Chem 80: 3975-3984. Link:
  89. Ouerdane L, Mari S, Czernic P, Lebrun M, Lobinski R (2006) Speciation of non-covalent nickel species in plant tissue extracts by electrospray Q-TOFMS/MS after their isolation by 2D size exclusion-hydrophilic interaction LC (SEC-HILIC) monitored by ICP-MS. J Anal At Spectrom 21: 676-683. Link:
  90. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, et al. (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18: 1157–1161. Link:
  91. Arora S, Jain CK, Lokhande RS (2017) Review of Heavy metal contamination in Soil. Int J Environ Sci Nat Res 3: 1-6. Link:
  92. Doker S, Bosgelmez I, Guvendik G (2011) Metallomics as a junction between life sciences. J Biol and Chem 39: 173-188. Link:
  93. Clemens S (2001) Molecular mechanism of plant metal tolerance and homeostasis. Planta 212: 475-486. Link:
  94. Haferburg G, Kothe E (2010) Metallomics, lessons for metalliferous soil remediation. Appl Microbiol Biotechnol 87: 1271-1280. Link:
  95. Ahsan N, Renaut J, Komatsu S (2009) Recent developments in the application of proteomics to the analysis of plant responses to heavy metals. Proteomics 9: 2602-2621. Link:
  96. Zaier HA, Mudarra D, Kutscher MR, Ferndez de la Campa C, Abdelly A, et al. (2010) Induced lead binding phytochelatins in Brassica juncea and Sesuvium portulacastrum investigated by orthogonal chromatography inductively coupled plasma-mass spectrometry and matrix assisted laser desorption ionization-time of flight-mass spectrometry. Anal Chim Acta 671: 48-54. Link:
  97. Figueroa JAL, Afton S, Wrobel K, Wrobel K, Caruso JA (2007) Analysis of phytochelatins in nopal (Opuntia ficus), a metallomics approach in the soil-plant system. J Anal At Spectrom 22: 897–904. Link:
  98. McSheehy S, Yang W, Pannier F, Szpunar J, Lobinski R, et al. (2000) Speciation analysis of selenium in garlic by two-dimensional high-performance liquid chromatography with parallel inductively coupled plasma mass spectrometric and electrospray tandem mass spectrometric detection. Anal Chim Acta 421:147-153. Link:
  99. Vonderheide AP, Wrobel K, Kannamkumarath SS, B'Hymer C, Montes-Bayon M, et al. (2002) Characterization of selenium species in Brazil Nuts by HPLC-ICP-MS and ES-MS. J Agric Food Chem 50: 5722-5728. Link:
  100. Haraguchi H (2004) Metallomics as integrated biometal science. J Anal At Spectrom 19: 5–14. Link:
  101. Nordberg M (2000) Trace elements and metallothionein related to geo-environment. J Trace Elem Exp Med 13: 97-104. Link:
  102. Viarengo A, Ponzano E, Dondero F, Fabbri R (1997) A simple spectrophotometric method for metallothionein evaluation in marine organisms, an application to Mediterranean and Antarctic molluscs. Mar Environ Res 44: 69-84. Link:
  103. Salekdeh GH, Siopongco J, Wade LJ, Ghareyazie B, Bennett J (2002) Proteomic analysis of rice leaves during drought stress and recovery. Proteomics 2: 1131–1145. Link:
  104. Agrawal GK, Rakwal R, Yonekura M, Kubo A, Saji H (2002) Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings. Proteomics2: 947-959. Link:
  105. Johnsen S, Lohmann KJ (2008) Magnetoreception in animals. Phys Today 61: 29-35. Link:
  106. Lindauer M, Martin H (1972) Magnetic effects on dancing bees. In, Galler SR Schmidt-Koenig R, Jacobs GJ, Belleville RE, editors. Animal orientation and navigation. Washington, US Gov't Printing Office p. 281-304. Link:
  107. Dusenbery, David B (2009) Living at Micro Scale, ed. Cambridge, Harvard University Press. Link:
  108. Walker MM, Bitterman ME (1989) Honeybees can be trained to respond to very small changes in geomagnetic field intensity. J Exp Biol 145: 489–494. Link:
  109. Hsu C-Y, Ko F-Y, Li C-W, Fann K, Lue J-T (2007) Magnetoreception System in Honeybees (Apis mellifera). PLoS One 2: e395. Link:
  110. Berridge MJ (1997) Elementary and global aspects of calcium signaling. J Exp Bio 200: 315-319. Link:
  111. Rafique S, Idrees M, Nasim A, Akbar H, Athar A (2010) Transition metal complexes as potential therapeutic agents. Biotech Mol Biol Rev 5: 38-45. Link:
  112. Sadler PJ, Guo Z (1998) Metal complexes in medicine, Design and mechanism of action. Pure Appl Chem 70: 863-871. Link:
  113. Atiken JB, Levina A, Lay PA (2011) Studies on the biotransformations and biodistributions of metal-containing drugs using X-ray absorption spectroscopy. Curr Top Med Chem 11: 553-571. Link:
  114. Nagy L, Csintalan G, Kalman E, Sipos P, Szyetnik A (2003) Applications of metal ions and their complexes in medicine. Acta Pharm Hung 73: 221-236. Link:
  115. Kersey P, Apweiler R (2006) Linking publication, gene and protein data.  Nat Cell Bio8: 1183-1189. Link:
  116. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2009) The Pfam protein families database. Nucleic Acids Res 38: D211. Link:
  117. Bertini I, Cavallaro G (2010) Bioinformatics in bioinorganic chemistry. Metalloids 2: 39. Link:
  118. Andreini  C,  Bertini  I,  Cavallaro  G,  Holliday  GL,  Thornton  JM (2009) Metal-MACiE, a database of metals involved in biological catalysis. Bioinformatics 25: 2088-2089. Link:
  119. Shi W, Zhan C, Ignatov A, Manjasetty BA, Marinkovic N, et al. (2005) Metalloproteomics, High-throughput structural and functional annotation of proteins in structural genomics. Structure 13: 1473-1486. Link:
  120. Pieper DH, Martins dos Santos VA, Golyshin PN (2004) Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr Opin Biotechnol 15: 215-224. Link:
  121. Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, et al. (2002) MDB, the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res 30: 379–382. Link:
  122. Degtyarenko KN, North ACT, Perkins DN, Findlay JBC (1998) PROMISE, a database of information on prosthetic cen-tres and metal ions in protein active sites. Nucleic Acids Res 26: 376-381. Link:
  123. Bertini I, Rosato A (2007) From Genes to Metalloproteins: A Bioinformatic Approach. Eur J Inorg Chem 18: 2546-2555. Link:
  124. Kryukov GV, Kryukov VM, Gladyshev VN (1999) New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J Biol Chem 274: 33888-33897. Link:
  125. Castellano S, Morozova N, Morey M, Berry MJ, Serras F, et al. (2001) In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep 2: 697-702. Link:
  126. Kryukov GV, Gladyshev VN (2004) The prokaryotic selenoproteome. EMBO Rep 5: 538-543. Link:
  127. Badger MR, Price GD (1994) The role of carbonic anhydrase in photosynthesis. Annu Rev Plant Physiol Plant Mol Biol 45: 369-392. Link:
  128. Schaller A (2004) A cut above this rest, the regulatory function of plant proteases. Planta 220: 183-197. Link:
  129. Goffner D, Doorsselaere JV, Samaj J, Pettenati G J, Boudet MA (1998) A novel aromatic alcohol dehydrogenase in higher plants, molecular cloning and expression. Plant Mol Biol 36: 755-765. Link:
  130. Alscher RG, Erturk N, Heah LS (2002) Role of superoxide dismutase (SODs) in controlling oxidative stress in plants. J Exp Bot 53: 1331-1341. Link:
  131. Wu FYH, Wu CW (1987) Zinc in DNA Replication and Transcription. Annu Rev Nutri 7: 251-272. Link:
  132. Scrutton MC, Wu CW, Goldthwait DA (1971) The presence and possible role of Zinc in RNA polymerase obtained from Escherichia coli. Proc Nat Acad Sci 68: 2497-2501. Link:
  133. Attwood PV (1995) The structure and the mechanism of action of pyruvate carboxylase. Int J Biochem Cell Biol 27: 231-249. Link:
  134. Christianson DW (1997) Structural chemistry and biology of manganese metalloenzymes. Prog Biophys Mol Bio 67: 217-252. Link:
  135. Bowler C, Camp WV, Montague MV, Inze D, Asada K (1994) Superoxide dismutases in plants. Crit Rev Plant Sci 13: 199-218. Link:
  136. Herrmann JM, Funes S (2005) Biogenesis of cytochrome oxidase –Sophisticated assembly lines in the mitochondrial inner membrane. Gene 354: 43-52. Link:
  137. Angelini R, Cona A, Federico R, Fincato P, Tavladoraki P, et al.  (2010) Plant amine oxidases “on the move”, An update. Plant Physiol Biochem 48: 560-564. Link:
  138. Hazid M, Khan TA, Khan ZH, Quddusi S, Mohammad F (2011) Occurance, biosynthesis and potentialities of ascorbic acid in plants. Int J Plant Anim Environ Sci 1: 167-184. Link:
  139. Nakumaru OE, Han H, Matsuno-Yaqi A, Keinan E, Sinha SC, et al. (2010) The ND2 subunit is labeled by photoaffinity analogue of asimicin, a potent complex inhibitor. FEBS Lett 584: 883-888. Link:
  140. Fiqueroa P, Leon G, Elorza A, Holuiquet L, Jordana X (2001) Three different genes encode the iron-sulfur subunit of succinate dehydrogenase in Arabidopsis thaliana. Plant Mol Biol 46: 241-250. Link:
  141. Omarov RT, Akaba S, Koshiba T, Lips SH (1999) Aldehyde oxidase in roots, leaves and seeds of barley (Hordeum vulgare L.). Journal of Experimental Botany 50: 63-69. Link:
  142. Brychkora G, Xia Z, Yang G, Yesberquenova Z, Zhang Z, et al. (2007) Sulfite oxidase protects plants against sulfur dioxide toxicity. Plant J 50: 696-709. Link:
  143. Rubio LM, Ludden PW (2008) Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase. Annu Rev Microbiol 62: 93-111. Link:
  144. Purwar N, McGarry JM, Kostera J, Pacheco AA, Schmidt M (2011) Interaction of nitric oxide with catalase, Structural and kinetic analysis. Biochem 50: 4491-4503. Link:
  145. Das D, Dutta T, Nath K, Kotay SM, Das AK, et al. (2006) Role of Fe-hydrogenase in biological hydrogen production. Curr Sci 90: 1627-1637. Link:
  146. Kung Y, Ando N, Doukov TI, Blasiak LC, Bender G, et al. (2012) Visualizing molecular juggling within a B12-dependent methyltransferase complex. Nature 484: 265-269. Link:
  147. Costanzo DL, Moulin M, Haertlein M, Meilleur F, Christianson DW (2007) Expression, purification, assay and crystal structure of perdeuterated human arginase I. Arch Biochem Biophys 465: 82-90. Link:
  148. Menachem BR, Rudzki RN, Pines O (2011) The aconitase C-terminal domain is an independent dual targeting element. J Mol Biol 3: 113-123. Link:
  149. Dixon NE, Gazzola C, Blakeley RL, Zerner B (1975) Letter, Jack bean urease (EC A metalloenzyme. A simple biological role for nickel? J Am Chem Soc 97: 4131-4133. Link:
  150. Maguire RT, Pascucci VL, Maroli AN, Gulfo JV (1993) Immunoscintigraphy in patients with colorectal, ovarian, a prostrate cancer. Results with site-specific immunoconjugates. Cancer 172: 3453-3462. Link:
  151. Sadler PJ (1991) ChemInform Abstract, In organic Chemistry and Drug Design. Chem Inform 22: 257.
  152. Fricker SP (1994) A role for in vitro cytotoxicity testing in the selection and development of metal-based pharmaceutical and materials products. Toxicol in vitro 8: 879-881. Link:
  153. Cantos G, Barbieri CL, Lacomini M, Gorin PA, Travassos LR (1993) Synthesis of antimony complexes of yeast mannan and mannan derivatives and their effect on Leishmania-infected macrophages. Biochem J 289: 155-160. Link:
  154. La Bonte LR, Davis-Gorman G, Stahl GL, McDonagh PF (2008) Complement inhibition reduces injury in the type 2 diabetic heart following ischemia and reperfusion. Am J Physiol Heat Circ Physiol 294: H1282-H1290. Link:
  155. Hachmeister JE, Valluru L, Bao F, Liu D (2006) Mn (III) Tetrakis (4-Benzoic Acid) Porphyrin Administered into the Intrathecal Space Reduces Oxidative Damage and Neuron Death after Spinal Cord Injury, A Comparison with Methylprednisolone. J Neurotrauma 23: 1766-1778. Link:
  156. Guo Z, Sadler PJ (1999) Metals in Medicine. Angew Chem Int Ed 38: 1512 -1531. Link:
  157. Fricker SP, Slade E, Powell NA, Murrer BA, Megson IL, et al. (1995) Ruthenium complexes as nitric oxide scavengers, a new therapeutic approach to nitric oxide mediated disease. In: Moncada S, Stamler J, Gross S, Higgs AE, editors. Biology of Nitric Oxide, London: Portland Press, 330. Link:
  158. Kadota S, Fantus GI, Deragon G, Guyda HJ, Hersh B, et al. (1987) Peroxide(s) of vanadium, A novel and potent insulin-mimetic agent which activates the insulin receptor kinase. Biochem Biophysic Res Commun 147: 259-266. Link:
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