Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life

Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis

Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.

The selenium-independent phospholipid hydroperoxide glutathione peroxidase from Theobroma cacao (TcPHGPX) protects plant cells against damages and cell death

Proteins from the glutathione peroxidase (GPX) family, such as GPX4 or PHGPX in animals, are extensively studied for their antioxidant functions and apoptosis inhibition. GPXs can be selenium-independent or selenium-dependent, with selenium acting as a potential cofactor for GPX activity. However, the relationship of plant GPXs to these functions remains unclear. Recent research indicated an upregulation of Theobroma cacao phospholipid hydroperoxide glutathione peroxidase gene (TcPHGPX) expression during early witches' broom disease stages, suggesting the use of antioxidant mechanisms as a plant defense strategy to reduce disease progression. Witches' broom disease, caused by the hemibiotrophic fungus Moniliophthora perniciosa, induces cell death through elicitors like MpNEP2 in advanced infection stages. In this context, in silico and in vitro analyses of TcPHGPX's physicochemical and functional characteristics may elucidate its antioxidant potential and effects against cell death, enhancing understanding of plant GPXs and informing strategies to control witches' broom disease. Results indicated TcPHGPX interaction with selenium compounds, mainly sodium selenite, but without improving the protein function. Protein-protein interaction network suggested cacao GPXs association with glutathione and thioredoxin metabolism, engaging in pathways like signaling, peroxide detection for ABA pathway components, and anthocyanin transport. Tests on tobacco cells revealed that TcPHGPX reduced cell death, associated with decreased membrane damage and H2O2 production induced by MpNEP2. This study is the first functional analysis of TcPHGPX, contributing to knowledge about plant GPXs and supporting studies for witches' broom disease control.

Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery

Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.

Biosynthesis, Engineering, and Delivery of Selenoproteins

Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.

Reactive Oxygen Species: A Crosslink between Plant and Human Eukaryotic Cell Systems

Reactive oxygen species (ROS) are important regulating factors that play a dual role in plant and human cells. As the first messenger response in organisms, ROS coordinate signals in growth, development, and metabolic activity pathways. They also can act as an alarm mechanism, triggering cellular responses to harmful stimuli. However, excess ROS cause oxidative stress-related damage and oxidize organic substances, leading to cellular malfunctions. This review summarizes the current research status and mechanisms of ROS in plant and human eukaryotic cells, highlighting the differences and similarities between the two and elucidating their interactions with other reactive substances and ROS. Based on the similar regulatory and metabolic ROS pathways in the two kingdoms, this review proposes future developments that can provide opportunities to develop novel strategies for treating human diseases or creating greater agricultural value.

Selenium alleviates cadmium and copper toxicity in Gracilaria lemaneiformis (rhodophyta) with contrasting detoxification strategies

Selenium (Se) is a beneficial element for plants, and can be used to mitigate the toxicity of heavy metals. However, the detoxification of Se in macroalgae, a crucial part of aquatic ecosystem productivity, has rarely been reported. In the present study, a red macroalga Gracilaria lemaneiformis was exposed to non-essential metal cadmium (Cd) or essential metal copper (Cu) with addition of different levels of Se. We then examined the changes in growth rate, metal accumulation, metal uptake rate, subcellular distribution, as well as thiol compound induction in this alga. Se addition alleviated Cd/Cu-induced stress in G. lemaneiformis by regulating cellular metal accumulation and intracellular detoxification. Specifically, supplementation of low-level Se displayed a significant decrease in Cd accumulation, and thus alleviated the growth inhibition induced by Cd. This may be caused by the inhibitory effect of endogenous Se instead of exogenous Se on Cd uptake. Although Se addition increased bioaccumulation of Cu in G. lemaneiformis, the important intracellular metal chelators, phytochelatins (PCs), were massively induced to alleviate Cu-induced growth inhibition. High-dose Se addition did not deteriorate but failed to normalize the growth of algae under metal stress conditions. Reduction in Cd accumulation or induction of PCs by Cu could not suppress the toxicity of Se above safe levels. Se addition also altered metal subcellular distribution in G. lemaneiformis, which might affect the subsequent metal trophic transfer. Our results demonstrated that the detoxification strategies of Se between Cd and Cu were different in macroalgae. Elucidating the protective mechanisms of Se against metal stress may help us better apply Se to regulate metal accumulation, toxicity, and transfer in aquatic environment.

A Novel Glucose-6-Phosphate Isomerase Exists in Chicken Breast Meat: A Selenium-Containing Enzyme that Should Be Re-recognized Through New Eyes

Glucose-6-phosphate isomerase (GPI) is a highly conserved glycolytic enzyme in nature, and less information was available for GPI from hens. In this study a newly discovered selenocysteine (Sec)-containing GPI in common chicken breast meat was first isolated, purified and identified. Data about LC-MS/MS, FTIR and Se species analyses show that the molecular weight of the enzyme is 62,091 Da and only one Sec is inserted at the 403rd position in the highly conserved primary domain SIS_PGI with sugar conversion function. The enzyme shows excellent activity against hydroxyl radicals as vitamin C (Vc) in vitro. It is deduced that the Sec-containing GPI in the chicken meat may depend on Sec in its molecular structure to resist reactive oxygen species (ROS) stress produced by the accompanying biochemical reactions in cells, to protect its stability and maintain its efficient function that catalyzes the conversion of glucose-6-phosphate to fructose-6-phosphate in the critical glycolytic pathway.

Voyage of selenium from environment to life: Beneficial or toxic?

Selenium (Se), a naturally occurring metalloid, is an essential micronutrient for life as it is incorporated as selenocysteine in proteins. Although beneficial at low doses, Se is hazardous at high concentrations and poses a serious threat to various ecosystems. Due to this contrasting 'dual' nature, Se has garnered the attention of researchers wishing to unravel its puzzling properties. In this review, we describe the impact of selenium's journey from environment to diverse biological systems, with an emphasis on its chemical advantage. We describe the uneven distribution of Se and how this affects the bioavailability of this element, which, in turn, profoundly affects the habitat of a region. Once taken up, the subsequent incorporation of Se into proteins as selenocysteine and its antioxidant functions are detailed here. The causes of improved protein function due to the incorporation of redox-active Se atom (instead of S) are examined. Subsequently, the reasons for the deleterious effects of Se, which depend on its chemical form (organo-selenium or the inorganic forms) in different organisms are elaborated. Although Se is vital for the function of many antioxidant enzymes, how the pro-oxidant nature of Se can be potentially exploited in different therapies is highlighted. Furthermore, we succinctly explain how the presence of Se in biological systems offsets the toxic effects of heavy metal mercury. Finally, the different avenues of research that are fundamental to expand our understanding of selenium biology are suggested.

Safety of selenium exposure and limitations of selenoprotein maximization: Molecular and epidemiologic perspectives

Recent evidence from laboratory and epidemiologic studies has shed a different light on selenium health effects and its recommended range of environmental exposure, compared with earlier research. Specifically, epidemiologic studies in Western populations have shown adverse effects of selenium exposure at low levels, sometimes below or slightly above selenium intakes needed to maximize selenoprotein expression and activity. In addition, three recent lines of evidence in molecular and biochemical studies suggest some potential drawbacks associated with selenoprotein maximization: 1) the possibility that selenoprotein upregulation is a compensatory response to oxidative challenge, induced by selenium itself or other oxidants; 2) the capacity of selenoproteins to trigger tumor growth in some circumstances; and 3) the deleterious metabolic effects of selenoproteins and particularly of selenoprotein P. The last observation provides a toxicological basis to explain why in humans selenium intake levels as low as 60 μg/day, still in the range of selenium exposure upregulating selenoprotein expression, might start to increase risk of type 2 diabetes. Overall, these new pieces of evidence from the literature call into question the purported benefit of selenoprotein maximization, and indicate the need to reassess selenium dietary reference values and upper intake level. This reassessment should clarify which range of selenoprotein upregulation follows restoration of adequate selenium availability and which range is driven by a compensatory response to selenium toxicity and oxidative stress.

Hyperaccumulator Stanleya pinnata: In Situ Fitness in Relation to Tissue Selenium Concentration

Earlier studies have shown that Stanleya pinnata benefits from selenium hyperaccumulation through ecological benefits and enhanced growth. However, no investigation has assayed the effects of Se hyperaccumulation on plant fitness in the field. This research aimed to analyze how variation in Se accumulation affects S. pinnata fitness, judged from physiological and biochemical performance parameters and herbivory while growing naturally on two seleniferous sites. Natural variation in Se concentration in vegetative and reproductive tissues was determined, and correlations were explored between Se levels with fitness parameters, herbivory damage, and plant defense compounds. Leaf Se concentration varied between 13- and 55-fold in the two populations, averaging 868 and 2482 mg kg−1 dry weight (DW). Furthermore, 83% and 31% of plants from the two populations showed Se hyperaccumulator levels in leaves (>1000 mg kg−1 DW). In seeds, the Se levels varied 3−4-fold and averaged 3372 and 2267 mg kg−1 DW, well above the hyperaccumulator threshold. Plant size and reproductive parameters were not correlated with Se concentration. There was significant herbivory pressure even on the highest-Se plants, likely from Se-resistant herbivores. We conclude that the variation in Se hyperaccumulation did not appear to enhance or compromise S. pinnata fitness in seleniferous habitats within the observed Se range.

Interplay between Selenium, Selenoproteins and HIV-1 Replication in Human CD4 T-Lymphocytes

The infection of CD4 T-lymphocytes with human immunodeficiency virus (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), disrupts cellular homeostasis, increases oxidative stress and interferes with micronutrient metabolism. Viral replication simultaneously increases the demand for micronutrients and causes their loss, as for selenium (Se). In HIV-infected patients, selenium deficiency was associated with a lower CD4 T-cell count and a shorter life expectancy. Selenium has an important role in antioxidant defense, redox signaling and redox homeostasis, and most of these biological activities are mediated by its incorporation in an essential family of redox enzymes, namely the selenoproteins. Here, we have investigated how selenium and selenoproteins interplay with HIV infection in different cellular models of human CD4 T lymphocytes derived from established cell lines (Jurkat and SupT1) and isolated primary CD4 T cells. First, we characterized the expression of the selenoproteome in various human T-cell models and found it tightly regulated by the selenium level of the culture media, which was in agreement with reports from non-immune cells. Then, we showed that selenium had no significant effect on HIV-1 protein production nor on infectivity, but slightly reduced the percentage of infected cells in a Jurkat cell line and isolated primary CD4 T cells. Finally, in response to HIV-1 infection, the selenoproteome was slightly altered.

Kingdom-Wide Analysis of Fungal Transcriptomes and tRNAs Reveals Conserved Patterns of Adaptive Evolution

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

Historical Roles of Selenium and Selenoproteins in Health and Development: The Good, the Bad and the Ugly

Selenium is a fascinating element that has a long history, most of which documents it as a deleterious element to health. In more recent years, selenium has been found to be an essential element in the diet of humans, all other mammals, and many other life forms. It has many health benefits that include, for example, roles in preventing heart disease and certain forms of cancer, slowing AIDS progression in HIV patients, supporting male reproduction, inhibiting viral expression, and boosting the immune system, and it also plays essential roles in mammalian development. Elucidating the molecular biology of selenium over the past 40 years generated an entirely new field of science which encompassed the many novel features of selenium. These features were (1) how this element makes its way into protein as the 21st amino acid in the genetic code, selenocysteine (Sec); (2) the vast amount of machinery dedicated to synthesizing Sec uniquely on its tRNA; (3) the incorporation of Sec into protein; and (4) the roles of the resulting Sec-containing proteins (selenoproteins) in health and development. One of the research areas receiving the most attention regarding selenium in health has been its role in cancer prevention, but further research has also exposed the role of this element as a facilitator of various maladies, including cancer.

Edible Aquatic Insects: Diversities, Nutrition, and Safety

Edible insects have great potential to be human food; among them, aquatic insects have unique characteristics and deserve special attention. Before consuming these insects, the nutrition and food safety should always be considered. In this review, we summarized the species diversity, nutrition composition, and food safety of edible aquatic insects, and also compared their distinguished characteristics with those of terrestrial insects. Generally, in contrast with the role of plant feeders that most terrestrial edible insect species play, most aquatic edible insects are carnivorous animals. Besides the differences in physiology and metabolism, there are differences in fat, fatty acid, limiting/flavor amino acid, and mineral element contents between terrestrial and aquatic insects. Furthermore, heavy metal, pesticide residue, and uric acid composition, concerning food safety, are also discussed. Combined with the nutritional characteristics of aquatic insects, it is not recommended to eat the wild resources on a large scale. For the aquatic insects with large consumption, it is better to realize the standardized cultivation before they can be safely eaten.

Unravelling the attributes of novel cyanobacteria Jacksonvillea sp. ISTCYN1 by draft genome sequencing

Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE’s ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the program's ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits.

Comparative proteomics analysis of the responses to selenium in selenium-enriched alfalfa (Medicago sativa L.) leaves

The mass of leaves and the chlorophyll and selenium content of alfalfa can be increased by the foliar spraying of selenite. To better understand the relationship between changes in the expression of specific proteins and the various metabolic and regulatory pathways affected by selenium treatment, labeling with Tandem Mass Tags (TMT) was used as a proteomics technique to compare control leaves with those enriched with Se. A total of 8,411 proteins were identified, the expression levels of 195 of which were significantly modified, 67 significantly up-regulated and 128 significantly down-regulated. Using gene functional classification and metabolic pathway annotation, selenium treatment was found to have a significant impact on metabolic processes. The energy and substances produced by the metabolic processes of a variety of carbohydrates, lipids, and amino acids, and the metabolism of carbon may be responsible for increasing the yield of alfalfa leaves. Administration of selenium substantially influenced Se-responsive proteins, including ABC transporter G family member 36, Probable glutathione S-transferase and cysteine tRNA ligase. Selenium treatment may also enhance photosynthesis and the defense response of cells. Furthermore, protein ubiquitination also played an important role in the selenium response of alfalfa leaves. In summary, a basic analysis of the selenium response pathway in alfalfa leaves at the proteomics level was conducted, which may assist in a more detailed elucidation of selenium enrichment in alfalfa in the future.

The physiology and evolution of microbial selenium metabolism

Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

Selenium(Ⅳ) alleviates chromium(Ⅵ)-induced toxicity in the green alga Chlamydomonas reinhardtii

The wide range of industrial applications of chromium (Cr) has led to an increasing risk of water contamination by Cr(Ⅵ). However, efficient methods to remove or decrease the toxicity of Cr(Ⅵ) in situ are lacking. The main aim of this study was to investigate the mechanisms by which selenite alleviates chromium(Ⅵ)-induced toxicity in Chlamydomonas reinhardtii. Our results showed that K₂Cr₂O₇ had toxic effects on both the structure and physiology of C. reinhardtii in a dose-dependent manner. Adding selenite significantly alleviated chromium accumulation and toxicity in cells. RNA-seq data showed that the expression level of selenoproteins such as SELENOH was significantly increased. Both SELENOH-amiRNA knockdown mutants and selenoh insertional mutant produced more reactive oxygen species (ROS) and grew slower than the wild type, suggesting that SELENOH can reduce chromium toxicity by decreasing the levels of ROS produced by Cr(Ⅵ). We also demonstrated that selenite can reduce the absorption of Cr(Ⅵ) by cells but does not affect the process of Cr(Ⅵ) adsorption and efflux. This information on the molecular mechanism by which selenite alleviates Cr(Ⅵ) toxicity can be used to increase the bioremediation capacity of algae and reduce the human health risks associated with Cr(Ⅵ) toxicity.

Supplementation of nano-selenium in fish diet: Impact on selenium assimilation and immune-regulated selenoproteome expression in monosex Nile tilapia (Oreochromis niloticus)

Selenium (Se), a fundamental element of nutrigenomic science in fish nutrition, was used to investigate its impact on selenoproteome expression and Se regulation in tilapia. Different concentrations (T₁ - 0, T₂ - 0.5, T₃ - 1.0 and T₄ - 2.0 mg/kg of feed) of dietary nano-Se were incorporated in the diets of monosex Nile tilapia. A total of 180 tilapia fingerlings with initial weight (15.73 ± 0.05 g) were stocked in 150 L capacity FRP tanks categorized into four diet groups with triplicate each for a feeding trial of 90 days. At the end of first, second and third months of the feeding trial, gill, liver, kidney and muscle tissues were harvested to evaluate the effect on the kinetics of Se bioaccumulation and assimilation as well as immune-regulated selenoprotein transcripts (GPx2, SelJ, SelL, SelK, SelS, SelW and Sepp1a) and their synthesis factors (SPS1 and Scly). The findings depicted that significantly (p < 0.05) higher weight gain was found in the diet supplemented with 1.0 mg/kg of nano-Se. The theory of second-order polynomial regression supported the same. The liver showed significantly (p < 0.05) higher Se accumulation and concentration factor among the harvested tissues in a different timeline. All the selected immune-regulated selenoproteins and synthesis factors in different fish tissues showed significantly (p < 0.05) up-regulation in the diet supplemented with 1.0 mg/kg of nano-Se for the second month. Therefore, the present findings suggested that the supplementation of nano-Se could be more effective for improved growth, better selenium regulation and expression of immune-regulated selenoproteins in the fish model.

SECISBP2 is a novel prognostic predictor that regulates selenoproteins in diffuse large B-cell lymphoma

The overexpression of glutathione peroxidase 4 (GPX4; an enzyme that suppresses peroxidation of membrane phospholipids) is considered a poor prognostic predictor of diffuse large B-cell lymphoma (DLBCL). However, the mechanisms employed in GPX4 overexpression remain unknown. GPX4 is translated as a complete protein upon the binding of SECISBP2 to the selenocysteine insertion sequence (SECIS) on the 3'UTR of GPX4 mRNA. In this study, we investigated the expression of SECISBP2 and its subsequent regulation of GPX4 and TXNRD1 in DLBCL patients. Moreover, we determined the significance of the expression of these selenoproteins in vitro using MD901 and Raji cells. SECISBP2 was positive in 45.5% (75/165 cases) of DLBCL samples. The SECISBP2-positive group was associated with low overall survival (OS) as compared to the SECISBP2-negative group (P = 0.006). Similarly, the SECISBP2 and GPX4 or TXNRD1 double-positive groups (P < 0.001), as well as the SECISBP2, GPX4, and TXNRD1 triple-positive group correlated with poor OS (P = 0.001), suggesting that SECISBP2 may serve as an independent prognostic predictor for DLBCL (hazard ratio (HR): 2.693, P = 0.008). In addition, western blotting showed a decrease in GPX4 and TXNRD1 levels in SECISBP2-knockout (KO) MD901 and Raji cells. Oxidative stress increased the accumulation of reactive oxygen species in SECISBP2-KO cells (MD901; P < 0.001, Raji; P = 0.020), and reduced cell proliferation (MD901; P = 0.001, Raji; P = 0.030), suggesting that SECISBP2-KO suppressed resistance to oxidative stress. Doxorubicin treatment increased the rate of cell death in SECISBP2-KO cells (MD901; P < 0.001, Raji; P = 0.048). Removal of oxidative stress inhibited the altered cell death rate. Taken together, our results suggest that SECISBP2 may be a novel therapeutic target in DLBCL.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology

Selenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.

The algal selenoproteomes

Background

Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited.

Results

In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families.

Conclusions

This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.

Bioinformatics of Selenoproteins

Significance: Bioinformatics has brought important insights into the field of selenium research. The progress made in the development of computational tools in the last two decades, coordinated with growing genome resources, provided new opportunities to study selenoproteins. The present review discusses existing tools for selenoprotein gene finding and other bioinformatic approaches to study the biology of selenium. Recent Advances: The availability of complete selenoproteomes allowed assessing a global distribution of the use of selenocysteine (Sec) across the tree of life, as well as studying the evolution of selenoproteins and their biosynthetic pathway. Beyond gene identification and characterization, human genetic variants in selenoprotein genes were used to examine adaptations to selenium levels in diverse human populations and to estimate selective constraints against gene loss. Critical Issues: The synthesis of selenoproteins is essential for development in mice. In humans, several mutations in selenoprotein genes have been linked to rare congenital disorders. And yet, the mechanism of Sec insertion and the regulation of selenoprotein synthesis in mammalian cells are not completely understood. Future Directions: Omics technologies offer new possibilities to study selenoproteins and mechanisms of Sec incorporation in cells, tissues, and organisms.

Bioinformatics of Metalloproteins and Metalloproteomes

Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.

Tetrahymena Glutathione Peroxidase Family: A Comparative Analysis of These Antioxidant Enzymes and Differential Gene Expression to Metals and Oxidizing Agents

In the present work, an extensive analysis of the putative glutathione peroxidases (GPx) of the eukaryotic microorganism model Tetrahymena thermophila is carried out. A comparative analysis with GPx present in other Tetrahymena species and other very taxonomically diverse ciliates is also performed. A majority of ciliate GPx have replaced the selenocysteine (Sec) by Cys in its catalytic center, so they can be considered as phospholipid hydroperoxide glutathione peroxidases (PHGPx). Selenocysteine insertion sequence (SECIS) elements have been detected in several ciliate GPx that do not incorporate Sec in their amino acid sequences, and conversely, in other ciliate GPx with Sec, no SECIS elements are detected. These anomalies are analyzed and discussed. From the phylogenetic analysis using the ciliate GPx amino acid sequences, the existence of extensive intra- and interspecific gene duplications that produced multiple GPx isoforms in each species is inferred. The ancestral character of the selenoproteins is also corroborated. The analysis by qRT-PCR of six selected T. thermophila GPx genes has shown a quantitative differential expression between them, depending on the stressor (oxidizing agents, apoptotic inducer or metals) and the time of exposure.

Selenium Interactions with Algae: Chemical Processes at Biological Uptake Sites, Bioaccumulation, and Intracellular Metabolism

Selenium (Se) uptake by primary producers is the most variable and important step in determining Se concentrations at higher trophic levels in aquatic food webs. We gathered data available about the Se bioaccumulation at the base of aquatic food webs and analyzed its relationship with Se concentrations in water. This important dataset was separated into lotic and lentic systems to provide a reliable model to estimate Se in primary producers from aqueous exposure. We observed that lentic systems had higher organic selenium and selenite concentrations than in lotic systems and selenate concentrations were higher in lotic environments. Selenium uptake by algae is mostly driven by Se concentrations, speciation and competition with other anions, and is as well influenced by pH. Based on Se species uptake by algae in the laboratory, we proposed an accurate mechanistic model of competition between sulfate and inorganic Se species at algal uptake sites. Intracellular Se transformations and incorporation into selenoproteins as well as the mechanisms through which Se can induce toxicity in algae has also been reviewed. We provided a new tool for risk assessment strategies to better predict accumulation in primary consumers and consequently to higher trophic levels, and we identified some research needs that could fill knowledge gaps.

Selenium nanovirus and its cytotoxicity in selenite-exposed higher living organisms

Selenium (Se) is an essential micronutrient in living organisms, having a narrow margin between essential and potentially toxic intake/exposure. Thus, the biochemistry of Se in living organisms must be studied in-depth to determine the underlying mechanism of Se cytotoxicity. In this study, we report the emergence of selenium nanovirus (SeNVs) in selenite-exposed fish (freshwater and saltwater) and plants (dryland) and its toxicity in them. SeNVs were found in both the abdomen and tail of Oryzias melastigma and saltwater Rhodeus ocellatus, which led to their death. The occurrence of the intracellular assembly of SeNVs was observed in the roots and leaves of corn Zea mays, but not in those of Limnobium laevigatum. SeNVs led to the death of Z. mays but caused chronic toxicity in L. laevigatum. SeNVs should be a system or structure that dissipates the intracellular redox gradients of the host cells, with simple information consisting Se-O, Se-N, or Se-S bond, that would ensure elemental Se ligand binding with nearly specific biomolecules in host cells, thereby maintaining their composition and stabilizing their structure. The multiple toxic effects of Se, therefore, could be the consequence of increase of entropy in the host cells caused by the intracellular assembly of SeNVs. This study may provide an insight into the underlying mechanism of Se in environmental toxicology and its applications in human health.

Comparative genomic analysis of selenium utilization traits in different marine environments

Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.

Systems Biology of Selenium and Complex Disease

Selenium is an essential trace element for maintenance of overall health, whose deficiency and dyshomeostasis have been linked to a variety of diseases and disorders. The majority of previous researches focused on characterization of genes encoding selenoproteins or proteins involved in selenium metabolism as well as their functions. Many studies in humans also investigated the relationship between selenium and complex diseases, but their results have been inconsistent. In recent years, systems biology and "-omics" approaches have been widely used to study complex and global variations of selenium metabolism and function in physiological and different pathological conditions. The present paper reviews recent progress in large-scale and systematic analyses of the relationship between selenium status or selenoproteins and several complex diseases, mainly including population-based cohort studies and meta-analyses, genetic association studies, and some other omics-based studies. Advances in ionomics and its application in studying the interaction between selenium and other trace elements in human health and diseases are also discussed.

Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs

Selenoproteins typically contain a single selenocysteine, the 21st amino acid, encoded by a context-redefined UGA. However, human selenoprotein P (SelenoP) has a redox-functioning selenocysteine in its N-terminal domain and nine selenium transporter-functioning selenocysteines in its C-terminal domain. Here we show that diverse SelenoP genes are present across metazoa with highly variable numbers of Sec-UGAs, ranging from a single UGA in certain insects, to 9 in common spider, and up to 132 in bivalve molluscs. SelenoP genes were shaped by a dynamic evolutionary process linked to selenium usage. Gene evolution featured modular expansions of an ancestral multi-Sec domain, which led to particularly Sec-rich SelenoP proteins in many aquatic organisms. We focused on molluscs, and chose Pacific oyster Magallana gigas as experimental model. We show that oyster SelenoP mRNA with 46 UGAs is translated full-length in vivo. Ribosome profiling indicates that selenocysteine specification occurs with ∼5% efficiency at UGA1 and approaches 100% efficiency at distal 3' UGAs. We report genetic elements relevant to its expression, including a leader open reading frame and an RNA structure overlapping the initiation codon that modulates ribosome progression in a selenium-dependent manner. Unlike their mammalian counterparts, the two SECIS elements in oyster SelenoP (3'UTR recoding elements) do not show functional differentiation in vitro. Oysters can increase their tissue selenium level up to 50-fold upon supplementation, which also results in extensive changes in selenoprotein expression.

Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida

Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.

Distinct Patterns of Selection in Selenium-Dependent Genes between Land and Aquatic Vertebrates

Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their constituent residues. Selenocysteine is analogous to the amino acid cysteine (Cys), which uses the abounding element sulfur instead. Despite the irregular distribution of Se worldwide, its distinct biochemical properties have made the substitution of Sec for Cys rare in vertebrate proteins. Still, vertebrates inhabited environments with different amounts of Se and may have distinctly adapted to it. To address this question, we compared the evolutionary forces acting on the coding sequences of selenoprotein genes and genes that regulate Se between vertebrate clades and between the Se-dependent genes and their paralogs with Cys. We find that the strength of natural selection in genes that use or regulate Se is distinct between land vertebrates and teleost fishes and more variable than in the Cys paralogs, particularly in genes involved in the preferential supply of Se to some organs and the tissue-specific expression of selenoproteins. This is compatible with vertebrates adapting to Se scarcity in land and its abundance in waters. In agreement, teleost fishes duplicated and subfunctionalized or neofunctionalized selenoprotein genes and maintained their capacity for Se transport in the body, which declined (under neutrality) for millions of years in terrestrial vertebrates. Dietary Se has thus distinctly shaped vertebrate evolution.

Maize Sep15-like functions in endoplasmic reticulum and reactive oxygen species homeostasis to promote salt and osmotic stress resistance

In animals, the Sep15 protein participates in disease resistance, growth, and development, but the function of its plant homologues remains unclear. Here, the function of maize Sep15 was analysed by characterization of two independent Sep15-like loss-of-function mutants. In the absence of ZmSep15-like, seedling tolerance to both water and salinity stress was compromised. The mutants experienced a heightened level of endoplasmic reticulum stress, and over-accumulated reactive oxygen species, resulting in leaf necrosis. Characterization of Arabidopsis thaliana atsep15 mutant as well as like with ectopic expression of ZmSep15-like indicated that ZmSep15-like contributed to tolerance of both osmotic and salinity stress. ZmSep15-like interacted physically with UDP-glucose: glycoprotein glucosyltransferase1 (UGGT1). When the interaction was disrupted, the response to both osmotic and salinity stresses was impaired in maize or Arabidopsis. Co-expressing ZmUGGT1 and ZmUGGT2 enhanced the tolerance of A. thaliana to both stressors, indicating a functional interaction between them. Together, the data indicated that plants Sep15-like proteins promote osmotic and salinity stress resistance by influencing endoplasmic reticulum stress response and reactive oxygen species level.

Utilization of selenocysteine in early-branching fungal phyla

Selenoproteins are a diverse group of proteins containing selenocysteine (Sec)-the twenty-first amino acid-incorporated during translation via a unique recoding mechanism^1,2. Selenoproteins fulfil essential roles in many organisms¹, yet are not ubiquitous across the tree of life^3-7. In particular, fungi were deemed devoid of selenoproteins^4,5,8. However, we show here that Sec is utilized by nine species belonging to diverse early-branching fungal phyla, as evidenced by the genomic presence of both Sec machinery and selenoproteins. Most fungal selenoproteins lack consensus Sec recoding signals (SECIS elements⁹) but exhibit other RNA structures, suggesting altered mechanisms of Sec insertion in fungi. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages. Notably, Sec was lost at the base of Dikarya, resulting in the absence of selenoproteins in Saccharomyces cerevisiae and other well-studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life.

Comparative genomics and metagenomics of the metallomes

Recent achievements and advances in comparative genomic and metagenomic analyses of trace metals were reviewed and discussed.

Selenium and GPX4, a vital symbiosis

Selenium has transitioned from an environmental poison and carcinogen to an essential micronutrient associated with a broad array of health promoting effects. These beneficial effects are now accepted to be linked to its incorporation into selenoproteins, a family of rare proteins utilizing a specialized translation machinery to integrate selenium in the form of selenocysteine. Despite this recognized role, much less is known regarding the actual role of selenium in these proteins. Here, we will provide the reader with an overview of the essential role of specific selenoproteins and their link to pathology based on mouse studies and relevant mutations discovered in humans. Additionally, we will cover recent insights linking a non-interchangeable role for selenium in glutathione peroxidase 4 and its function in suppressing ferroptosis. This critical dependency ultimately generates a strong reliance on metabolic pathways that regulate selenium metabolism and its incorporation into proteins, such as the mevalonate pathway.

Evolution, regulation, and function of porcine selenogenome

Much less research on regulation and function of selenoproteins has been conducted in domestic pigs than in rodents or humans, although pigs are an excellent model of human nutrition and medicine and pork is a widely consumed meat in the world. Phylogenetically, the 25 identified porcine selenoproteins fell into two primitive groups, and might be further divided into three parallel branches. Despite a high similarity to that of humans and rodents, the porcine selenoproteome exhibited the closest evolutionary relationship with that of sheep and cattle among eight domestic species. Expression (mRNA, protein, and/or enzyme activity) of 2/3 of the 25 porcine selenoproteins in various tissues of pigs was affected by dietary Se intakes, and 14 of them showed responses to a high fat diet. When dietary Se deficiency mainly down-regulated the expression of selected selenoproteins, dietary Se excess exerted rather diverse effects on their expression. Overdosing pigs with dietary Se induced hyperinsulinemia, along with lipid accumulation and protein increase, in the liver and muscle by affecting key genes and(or) proteins involved in the metabolisms of glucose, lipid, and protein. In conclusion, expression of porcine selenoproteins was highly responsive to dietary Se and fat intakes, and was involved in body glucose, lipid, and protein metabolism as those of rodents and humans.

A Quantitative Chemoproteomic Platform to Monitor Selenocysteine Reactivity within a Complex Proteome

Mammalian selenocysteine (Sec)-containing proteins, selenoproteins, are important to (patho)physiological processes, including redox homeostasis. Sec residues have been recalcitrant to mass spectrometry-based chemoproteomic methods that enrich for reactive cysteine (Cys) residues with electrophilic chemical probes, despite confirmed reactivity of Sec with these electrophiles. Highly abundant Cys peptides likely suppress low-abundant Sec peptides. By exploiting the decreased pK_a of Sec relative to Cys, we have developed a chemoproteomic platform that relies on low pH (pH 5.75) electrophile labeling, reducing Cys reactivity and enhancing identification of Sec-containing peptides across mouse tissues and cell lines. The utility of this Sec-profiling platform is underscored by evaluation of the selectivity of auranofin, an inhibitor of the selenoprotein, thioredoxin reductase, against both reactive Cys- and Sec-containing proteins. Platform limitations pertain to the non-physiological low-pH conditions that could perturb protein structure and function. Future work necessitates the discovery of Sec-selective electrophiles that function at physiological pH.

SELENOPROTEIN O is a chloroplast protein involved in ROS scavenging and its absence increases dehydration tolerance in Arabidopsis thaliana

The evolutionary conserved family of Selenoproteins performs redox-regulatory functions in bacteria, archaea and eukaryotes. Among them, members of the SELENOPROTEIN O (SELO) subfamily are located in mammalian and yeast mitochondria, but their functions are thus far enigmatic. Screening of T-DNA knockout mutants for resistance to the proline analogue thioproline (T4C), identified mutant alleles of the plant SELO homologue in Arabidopsis thaliana. Absence of SELO resulted in a stress-induced transcriptional activation instead of silencing of mitochondrial proline dehydrogenase, and also high elevation of Δ(1)-pyrroline-5-carboxylate dehydrogenase involved in degradation of proline, thereby alleviating T4C inhibition and lessening drought-induced proline accumulation. Unlike its animal homologues, SELO was localized to chloroplasts of plants ectopically expressing SELO-GFP. The protein was co-fractionated with thylakoid membrane complexes, and co-immunoprecipitated with FNR, PGRL1 and STN7, all involved in regulating PSI and downstream electron flow. The selo mutants displayed extended survival under dehydration, accompanied by longer photosynthetic activity, compared with wild-type plants. Enhanced expression of genes encoding ROS scavenging enzymes in the unstressed selo mutant correlated with higher oxidant scavenging capacity and reduced methyl viologen damage. The study elucidates SELO as a PSI-related component involved in regulating ROS levels and stress responses.

Mechanisms of selenium hyperaccumulation in plants: A survey of molecular, biochemical and ecological cues

BACKGROUND

Selenium (Se) is a micronutrient required for many life forms, but toxic at higher concentration. Plants do not have a Se requirement, but can benefit from Se via enhanced antioxidant activity. Some plant species can accumulate Se to concentrations above 0.1% of dry weight and seem to possess mechanisms that distinguish Se from its analog sulfur (S). Research on these so-called Se hyperaccumulators aims to identify key genes for this remarkable trait and to understand ecological implications.

SCOPE OF REVIEW

This review gives a broad overview of the current knowledge about Se uptake and metabolism in plants, with a special emphasis on hypothesized mechanisms of Se hyperaccumulation. The role of Se in plant defense responses and the associated ecological implications are discussed.

MAJOR CONCLUSIONS

Hyperaccumulators have enhanced expression of S transport and assimilation genes, and may possess transporters with higher specificity for selenate over sulfate. Genes involved in antioxidant reactions and biotic stress resistance are also upregulated. Key regulators in these processes appear to be the growth regulators jasmonic acid, salicylic acid and ethylene. Hyperaccumulation may have evolved owing to associated ecological benefits, particularly protection against pathogens and herbivores, and as a form of elemental allelopathy.

GENERAL SIGNIFICANCE

Understanding plant Se uptake and metabolism in hyperaccumulators has broad relevance for the environment, agriculture and human and animal nutrition and may help generate crops with selenate-specific uptake and high capacity to convert selenate to less toxic, anticarcinogenic, organic Se compounds.

Characterization of Selenoprotein P cDNA of the Antarctic toothfish Dissostichus mawsoni and its role under cold pressure

Our previous study using comparative genome analysis revealed a significant gene copy number gain of Dissostichus mawsoni selenoprotein P (Dm-SEPP) during the evolutionary radiation of Antarctic notothenioids, suggesting that Dm-SEPP contribute to this process, but the detailed structure and function of this gene product remain unclear. In the present study, the Dm-SEPP cDNA was cloned and characterized. The Dm-SEPP cDNA contains 17 selenocysteines (Sec) encoded by TGA codons and 2 typical SECIS elements located in the 3'-UTR. Evolutionary analysis of the Dm-SEPP gene revealed that it's closely related to the SEPP gene of zebrafish (Danio rerio), showing 51% amino acid similarity. Over-expression of Dm-SEPP could protect mammalian cells under cold pressure, probably via eliminating ROS. Further study showed an increase of endogenous SEPP in zebrafish ZF4 cells under cold pressure, and knockdown of SEPP decreased cell viability, accompanied with increased ROS. Our results suggested a protective role of Dm-SEPP in cold adaptation in Antarctic notothenioids.

Trace Elements and Healthcare: A Bioinformatics Perspective

Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals. The relationship between individual elements and several diseases based on recent large-scale systematic studies such as genome-wide association studies and case-control studies is discussed. Lastly, developments of ionomics and its recent application in human health are also introduced.

Overexpression of Recombinant Selenoproteins in E. coli

Expression of selenoproteins necessitates a process of decoding of a UGA codon from termination of translation to insertion of selenocysteine. The mechanisms of this process pose major challenges with regards to recombinant selenoprotein production in E. coli, which however can be overcome especially if the Sec residue is located close to the C-terminal end, as is the case for several naturally found selenoproteins. This chapter summarizes a method to achieve such a production.

Radioactive 75Se Labeling and Detection of Selenoproteins

The trace element selenium (Se) is incorporated into proteins as the amino acid selenocysteine (Sec), which is cotranslationally inserted into specific proteins in response to a UGA codon. Proteins containing Sec at these specific positions are called selenoproteins. Most selenoproteins function as oxidoreductases, while some serve other important functions. There are 25 known selenoprotein genes in humans and 24 in mice. The use of Sec allows selenoproteins to be detected by a convenient method involving metabolic labeling with ⁷⁵Se. Labeling of cells and whole animals are used for the examination of selenoprotein expression profiles and the investigation of selenoprotein functions. In mammals, nonspecific ⁷⁵Se insertion is very low, and sensitivity and specificity of selenoprotein detection approaches that of Western blotting. This method allows for the examination of selenoprotein expression and Se metabolism in model and non-model organisms. Herein, we describe experimental protocols for analyzing selenoproteins by metabolic labeling with ⁷⁵Se both in vitro and in vivo. As an example, the procedure for metabolic labeling of HEK293T human embryonic kidney cells is described in detail. This approach remains a method of choice for the detection of selenoproteins in diverse settings.

Organoselenium compounds as mimics of selenoproteins and thiol modifier agents

Selenium is an essential trace element for animals and its role in the chemistry of life relies on a unique functional group: the selenol (-SeH) group. The selenol group participates in critical redox reactions. The antioxidant enzymes glutathione peroxidase (GPx) and thioredoxin reductase (TrxR) exemplify important selenoproteins. The selenol group shares several chemical properties with the thiol group (-SH), but it is much more reactive than the sulfur analogue. The substitution of S by Se has been exploited in organic synthesis for a long time, but in the last 4 decades the re-discovery of ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) and the demonstration that it has antioxidant and therapeutic properties has renovated interest in the field. The ability of ebselen to mimic the reaction catalyzed by GPx has been viewed as the most important molecular mechanism of action of this class of compound. The term GPx-like or thiol peroxidase-like reaction was previously coined in the field and it is now accepted as the most important chemical attribute of organoselenium compounds. Here, we will critically review the literature on the capacity of organoselenium compounds to mimic selenoproteins (particularly GPx) and discuss some of the bottlenecks in the field. Although the GPx-like activity of organoselenium compounds contributes to their pharmacological effects, the superestimation of the GPx-like activity has to be questioned. The ability of these compounds to oxidize the thiol groups of proteins (the thiol modifier effects of organoselenium compounds) and to spare selenoproteins from inactivation by soft-electrophiles (MeHg⁺, Hg²⁺, Cd²⁺, etc.) might be more relevant for the explanation of their pharmacological effects than their GPx-like activity. In our view, the exploitation of the thiol modifier properties of organoselenium compounds can be harnessed more rationally than the use of low mass molecular structures to mimic the activity of high mass macromolecules that have been shaped by millions to billions of years of evolution.