From Genes to Metalloproteins: A Bioinformatic Approach

Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants

Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.

Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling

Iron is an essential element for all living organisms, playing a major role in plant biochemistry as a redox catalyst based on iron redox properties. Iron is the fourth most abundant element of the Earth's crust, but its uptake by plants is complex because it is often in insoluble forms that are not easily accessible for plants to use. The physical and chemical speciation of iron, as well as rhizosphere activity, are key factors controlling the bioavailability of Fe. Iron can be under reduced (Fe²⁺) or oxidized (Fe³⁺) ionic forms, adsorbed onto mineral surfaces, forming complexes with organic molecules, precipitated to form poorly crystalline hydroxides to highly crystalline iron oxides, or included in crystalline Fe-rich mineral phases. Plants must thus adapt to a complex and changing iron environment, and their response is finely regulated by multiple signaling pathways initiated by a diversity of stimulus perceptions. Higher plants possess two separate strategies to uptake iron from rhizosphere soil: the chelation strategy and the reduction strategy in grass and non-grass plants, respectively. Molecular actors involved in iron uptake and mobilization through the plant have been characterized for both strategies. All these processes that contribute to iron homeostasis in plants are highly regulated in response to iron availability by downstream signaling responses, some of which are characteristic signaling signatures of iron dynamics, while others are shared with other environmental stimuli. Recent research has thus revealed key transcription factors, cis-acting elements, post-translational regulators, and other molecular mechanisms controlling these genes or their encoded proteins in response to iron availability. In addition, the most recent research is increasingly highlighting the crosstalk between iron homeostasis and nutrient response regulation. These regulatory processes help to avoid plant iron concentrations building up to potential cell functioning disruptions that could adversely affect plant fitness. Indeed, when iron is in excess in the plant, it can lead to the production and accumulation of dangerous reactive oxygen species and free radicals (H₂O₂, HO^•, O₂^•-, HO^•₂) that can cause considerable damages to most cellular components. To cope with iron oxidative stress, plants have developed defense systems involving the complementary action of antioxidant enzymes and molecular antioxidants, safe iron-storage mechanisms, and appropriate morphological adaptations.

Simultaneous Quantification and Speciation of Trace Metals in Paired Serum and CSF Samples by Size Exclusion Chromatography-Inductively Coupled Plasma-Dynamic Reaction Cell-Mass Spectrometry (SEC-DRC-ICP-MS)

BACKGROUND

Transition metals play a crucial role in brain metabolism: since they exist in different oxidation states they are involved in ROS generation, but they are also co-factors of enzymes in cellular energy metabolism or oxidative defense.

METHODS

Paired serum and cerebrospinal fluid (CSF) samples were analyzed for iron, zinc, copper and manganese as well as for speciation using SEC-ICP-DRC-MS. Brain extracts from Mn-exposed rats were additionally analyzed with SEC-ICP-DRC-MS.

RESULTS

The concentration patterns of transition metal size fractions were correlated between serum and CSF: Total element concentrations were significantly lower in CSF. Fe-ferritin was decreased in CSF whereas a LMW Fe fraction was relatively increased. The 400-600 kDa Zn fraction and the Cu-ceruloplasmin fraction were decreased in CSF, by contrast the 40-80 kDa fraction, containing Cu- and Zn-albumin, relatively increased. For manganese, the α-2-macroglobulin fraction showed significantly lower concentration in CSF, whereas the citrate Mn fraction was enriched. Results from the rat brain extracts supported the findings from human paired serum and CSF samples.

CONCLUSIONS

Transition metals are strictly controlled at neural barriers (NB) of neurologic healthy patients. High molecular weight species are down-concentrated along NB, however, the Mn-citrate fraction seems to be less controlled, which may be problematic under environmental load.

Biogenic metallic elements in the human brain?

The chemistry of copper and iron plays a critical role in normal brain function. A variety of enzymes and proteins containing positively charged Cu+, Cu2+, Fe2+, and Fe3+ control key processes, catalyzing oxidative metabolism and neurotransmitter and neuropeptide production. Here, we report the discovery of elemental (zero-oxidation state) metallic Cu0 accompanying ferromagnetic elemental Fe0 in the human brain. These nanoscale biometal deposits were identified within amyloid plaque cores isolated from Alzheimer's disease subjects, using synchrotron x-ray spectromicroscopy. The surfaces of nanodeposits of metallic copper and iron are highly reactive, with distinctly different chemical and magnetic properties from their predominant oxide counterparts. The discovery of metals in their elemental form in the brain raises new questions regarding their generation and their role in neurochemistry, neurobiology, and the etiology of neurodegenerative disease.

Leveraging computational genomics to understand the molecular basis of metal homeostasis

Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.

Fertigation of Ajwain (Trachyspermum ammi L.) with Fe-Glutamate Confers Better Plant Performance and Drought Tolerance in Comparison with FeSO4

Shortage of fresh water limits crop yield. Different ways including the use of chemicals are being employed for the improvement in yield through induction of plant performance. In the present study, ajwain plants grown under water stress and normal irrigation conditions were fertigated with Fe-chelated glutamate (Fe-Glu), as a foliar spray for the induction of plant performance in comparison with FeSO4. Water shortage adversely affected the plant growth and seed yield, associated with decreased uptake of water and nutrients, along with perturbations in different physio-biochemical attributes. On the other hand, Fe-Glu and FeSO4 fertigation improved plant performance under water stress and normal irrigation conditions. Fe-Glu and FeSO4 fertigation ameliorated the adverse effects of water stress on biomass and seed production, improved water and nutrients uptake, increased the accumulation of essential amino acids, leaf chlorophyll and carotenoids, and reduced the lipid peroxidation due to the induction of antioxidative mechanisms. Fertigation of Fe-Glu and FeSO4 also improved Fe uptake and conferred better mobility and availability of Fe for plants when applied in chelated form. Overall, a significant improvement in ajwain performance under water stress and normal irrigation conditions was recorded due to the fertigation of Fe-Glu as compared with FeSO4.

Foliar Spray of Fe-Asp Confers Better Drought Tolerance in Sunflower as Compared with FeSO4: Yield Traits, Osmotic Adjustment, and Antioxidative Defense Mechanisms

Different techniques are being employed to reduce the adverse effects of water stress on seed yield and quality of crop plants. The current study aimed to improve the water stress tolerance of field-grown sunflower by foliar-supplied ecofriendly iron-chelated aspartate (Fe-Asp) in comparison with FeSO4. Water stress decreased the plant growth and yield, accompanied with disturbed water relations, nutrient acquisition, accumulation of amino acids, and antioxidative defense mechanisms. However, lipid peroxidation, total anthocyanin, and photosynthetic pigments were increased. Fertigation of FeSO4 and Fe-Asp as foliar sprays proved effective to reduce the negativities of limited irrigation on biomass production and seed yield, accompanied with a reduction in lipid peroxidation and improvements in water relations, antioxidative defense mechanisms, and leaf photosynthetic pigments. In comparison with FeSO4, foliary applied Fe-Asp better improved the plant water relations with more accumulation of essential amino acids and nutrient acquisition, especially leaf aspartate (Asp) and Fe accumulation which showed better translocation. Overall, foliary applied Fe-Asp proved better for induction of drought tolerance in sunflower plants as compared with FeSO4. The study recommended the use of the ecofriendly Fe-Asp as a foliar spray for better growth and production of sunflower under limited irrigation.

Cruz PC, Borromeo TH, Lalusin A, Hernandez JE, Acuin C, Reinke R, Swamy BPM. Zinc and Iron Nutrition Status in the Philippines Population and Local Soils

The Philippines is one of the major rice-producing and rice-consuming countries of Asia. A large portion of its population depends on rice for their daily caloric intake and nutritional needs. The lack of dietary diversity among poor communities has led to nutritional consequences, particularly micronutrient deficiencies. Iron-deficiency anemia (IDA) and zinc deficiency (ZnD) are two serious nutritional problems that affect the health and economic sector of the country. Since rice dominates the Filipino diet by default, biofortification of rice will help improve the micronutrient status. The Philippine government has proactively initiated various programs and policies to address micronutrient deficiencies, particularly through fortification of basic food commodities. Biofortification, the fortification of rice with micronutrients through breeding, is considered the most sustainable and cost-effective strategy that can benefit large vulnerable populations. However, developing promising genotypes with micronutrient-enriched grains should be coupled with improving micronutrient bioavailability in the soil in order to optimize biofortification. This review documents the prevailing soil Zn-deficiency problems in the major rice production areas in the Philippines that may influence the Zn nutritional status of the population. The article also reports on the biofortification efforts that have resulted in the development of two biofortified varieties approved for commercial release in the Philippines. As nutritional security is increasingly recognized as a priority area, greater efforts are required to develop biofortified rice varieties that suit both farmers' and consumers' preferences, and that can address these critical needs for human health in a sustainable and cost-effective manner.

Investigation of an optimal cell lysis method for the study of the zinc metalloproteome of Histoplasma capsulatum

This work sought to assess optimal extraction conditions in the study of the metalloproteome of the dimorphic fungus Histoplasma capsulatum. One of the body's responses to H. capsulatum infection is sequestration of zinc within host macrophage (MØ), as reported by Vignesh et al. (Immunity 39:697-710, 2013) and Vignesh et al. (PLOS Pathog 9:E1003815, 2013). Thus, metalloproteins containing zinc were of greatest interest as it plays a critical role in survival of the fungus. One challenge in metalloproteomics is the preservation of the native structure of proteins to retain non-covalently bound metals. Many of the conventional cell lysis, separation, and identification techniques in proteomics are carried out under conditions that could lead to protein denaturation. Various cell lysis techniques were investigated in an effort to both maintain the metalloproteins during lysis and subsequent analysis while, at the same time, serving to be strong enough to break the cell wall, allowing access to cytosolic metalloproteins. The addition of 1% Triton x-100, a non-ionic detergent, to the lysis buffer was also studied. Seven lysis methods were considered and these included: Glass Homogenizer (H), Bead Beater (BB), Sonication Probe (SP), Vortex with 1% Triton x-100 (V, T), Vortex with no Triton x-100 (V, NT), Sonication Bath, Vortex, and 1% Triton x-100 (SB, V, T) and Sonication Bath, Vortex, and no Triton x-100 (SB, V, NT). A Qubit® Assay was used to compare total protein concentration and inductively coupled plasma-mass spectrometry (ICP-MS) was utilized for total metal analysis of cell lysates. Size exclusion chromatography coupled to ICP-MS (SEC-HPLC-ICP-MS) was used for separation of the metalloproteins in the cell lysate and the concentration of Zn over a wide molecular weight range was examined. Additional factors such as potential contamination sources were also considered. A cell lysis method involving vortexing H. capsulatum yeast cells with 500 μm glass beads in a 1% Triton x-100 lysis buffer (V, T) was found to be most advantageous to extract intact zinc metalloproteins as demonstrated by the highest Zn to protein ratio, 1.030 ng Zn/μg protein, and Zn distribution among high, mid, and low molecular weights suggesting the least amount of protein denaturation. Graphical abstract In this work, several cell lysis techniques and two lysis buffers were investigated to evaluate the preservation of the zinc metalloproteome of H. capsulatum while maintaining compatibility with the analytical techniques employed.

Bioinformatics survey of the metal usage by psychrophilic yeast Glaciozyma antarctica PI12

Metal ions are one of the essential elements which are extensively involved in many cellular activities. With rapid advancements in genome sequencing techniques, bioinformatics approaches have provided a promising way to extract functional information of a protein directly from its primary structure. Recent findings have suggested that the metal content of an organism can be predicted from its complete genome sequences. Characterizing the biological metal usage of cold-adapted organisms may help to outline a comprehensive understanding of the metal-partnerships between the psychrophile and its adjacent environment. The focus of this study is targeted towards the analysis of the metal composition of a psychrophilic yeast Glaciozyma antarctica PI12 isolated from sea ice of Antarctica. Since the cellular metal content of an organism is usually reflected in the expressed metal-binding proteins, the putative metal-binding sequences from G. antarctica PI12 were identified with respect to their sequence homologies, domain compositions, protein families and cellular distribution. Most of the analyses revealed that the proteome was enriched with zinc, and the content of metal decreased in the order of Zn > Fe > Mg > Mn, Ca > Cu. Upon comparison, it was found that the metal compositions among yeasts were almost identical. These observations suggested that G. antarctica PI12 could have inherited a conserved trend of metal usage similar to modern eukaryotes, despite its geographically isolated habitat.

Probing the viral metallome: searching for metalloproteins in bacteriophage λ-- the hunt begins

Although the proteome and genome of bacteriophages are well developed, there is little knowledge about metals and their interactions with the phages, even though metals have been observed in stabilizing phage particles. With expanding studies of phage display and its promising applications, metalloprotein investigations in the bacteriophage areas are necessary to understand whether or not metalloproteins are included in the viral coat proteome. Since these virus studies are still in their infancy, lambda phage was chosen due to its high metal-binding potential as suggested by the cysteine/methionine rich proteins in the viral coat. After large-scale preparation and further purification of lambda phage according to standard protocols, state-of-the-art metallomics techniques via combinations of chromatographies and mass spectrometries were utilized for screening metal-associated species in lambda phage. The lambda phage sample was first separated using non-denaturing size exclusion chromatography with selective metal detection by ICPMS for screening associated metals and generating size distribution fractions for the various metal species, some of which include metalloproteins. Various molecular size distribution patterns were exhibited for the metals detected, Mn, Fe, Co, Ni, Cu and Zn, at different molecular weight ranges. On the other hand numerous other metals were not associated with the coat proteins, as they were not detected in the different molecular weight fractions. Further identification for putative metallopeptides and metalloproteins was accomplished by collecting various metal species' fractions offline and subsequently analyzing tryptically-digested fractions via nanoLC-Chip-ESI-MS. By searching appropriate MS databases with both Spectrum Mill and MASCOT search engines, the main capsid protein, gpE, a capsid decoration protein, gpD, and main tail component protein, gpV, were found and are known for associations with the detected transition metals. These findings will likely provide valuable information for lambda phage engineered applications.

Metallomics: Guidelines for terminology and critical evaluation of analytical chemistry approaches (IUPAC Technical Report)

Definitions for the terms "metallome" and "metallomics" are proposed. The state of the art of analytical techniques and methods for systematic studies of metal content, speciation, localization, and use in biological systems is briefly summarized and critically evaluated.

Bioinformatics in bioinorganic chemistry

Bioinformatics is a central discipline in modern life sciences aimed at describing the complex properties of living organisms starting from large-scale data sets of cellular constituents such as genes and proteins. In order for this wealth of information to provide useful biological knowledge, databases and software tools for data collection, analysis and interpretation need to be developed. In this paper, we review recent advances in the design and implementation of bioinformatics resources devoted to the study of metals in biological systems, a research field traditionally at the heart of bioinorganic chemistry. We show how metalloproteomes can be extracted from genome sequences, how structural properties can be related to function, how databases can be implemented, and how hints on interactions can be obtained from bioinformatics.

Metal uptake by manganese superoxide dismutase

Manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. Many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. In contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the protein and one that is absolutely required for its biological function. Recent work is beginning to provide insight into the mechanisms of metal delivery to manganese superoxide dismutase in vivo and in vitro.

Protein engineering of redox-active enzymes

Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.

Enrichment of fertilizers with zinc: An excellent investment for humanity and crop production in India

Micronutrient malnutrition is a growing concern in the developing world, resulting in diverse health and social problems, such as mental retardations, impairments of the immune system and overall poor health. In recent years, the zinc (Zn) deficiency problem has received increasing attention and appears to be the most serious micronutrient deficiency together with vitamin A deficiency. Zinc deficiency is particularly widespread among children and represents a major cause of child death in the world. In countries where Zn deficiency is well documented as an important public health problem, cereal-based foods are the predominant source of daily calorie and protein intake. Because the concentration of Zn in cereal crops is inherently very low, growing cereals on potentially Zn-deficient soils further decreases grain Zn concentrations. It is, therefore, not surprising that high Zn deficiency incidence in humans occurs predominantly on areas where soils are deficient in plant-available Zn, as shown in many Southeast Asian countries. India has some of the most Zn-deficient soils in the world. Nearly 50% of cultivated soils in India are low in plant-available Zn; these soils are under intensive cultivation of wheat and rice with no or little application of Zn fertilizers. Consequently, cereal crops grown on such Zn-deficient soils contribute only marginally to daily Zn intake. In the rural areas of India, rice and wheat contributes nearly 75% of the daily calorie intake. These facts clearly point to an urgent need for improved Zn concentration of cereal grains in India. Recent calculations indicate that biofortification (enrichment) of rice and wheat grain with Zn, for example by breeding, may save lives of up to 48,000 children in India annually. Breeding new cereal genotypes for high grain Zn concentration is the most realistic and cost-effective strategy to address the problem. However, this strategy is a long-term one, and the size of plant-available Zn pools in soils may greatly affect the capacity of Zn-efficient (biofortified) cultivars to take up Zn and accumulate it in grains. Therefore, application of Zn-containing fertilizers represents a quick and effective approach to biofortifying cereal grains with Zn, thus being an excellent complementary tool to the breeding strategy for successful biofortification of cereals with Zn. Increasing evidence is available from field trials showing that soil and/or foliar application of Zn fertilizers improves grain Zn concentration up to 2- or 3-fold. In the countries where Zn deficiency is both a public health issue and an important soil constraint to crop production, like in India, enrichment of widely applied fertilizers with Zn would be an excellent investment for improving grain Zn while contributing to increased crop production. Recent work by the scientists of the Indian Agricultural Research Institute indicates that the use of Zn-enriched urea in rice and wheat significantly improves both grain Zn concentration and grain yield. It is obvious that enrichment of widely applied fertilizers with Zn and/or foliar application of Zn fertilizers appear to be a high priority with the strongest potential to alleviate Zn deficiency-related problems in India. A Government action and policy plan for enrichment of selected major fertilizers with Zn is required urgently.

Challenges to metallomics and analytical chemistry solutions

Metal ions play a fundamental role in the chemistry of life. The understanding of the molecular bases of the living process requires the knowledge of the correlations existing between metal ions and the genome and the derived -omes: transcriptome, proteome, and metabolome. An indispensable step on this way is the characterization of the coordination environment of metal ions present and the identification and quantification of metal-containing chemical species. The ensemble of research activities related to metal ions in biological systems has been recently referred to as "metallomics" [1]. The progress in this field is largely dependent on the high-throughput acquisition of multielement and -species analytical data in biological samples. The paper gives a brief overview of the state of the art of analytical techniques and methods for the multielement quantitative analysis of biological microsamples, and for the detection, identification, and quantitation of metal-containing proteins and low-molecular-weight metabolites. The potential contribution of molecular biology techniques in terms of linking information on metals and metal-species to the genome of an organism is highlighted.