Bioinformatics of Selenoproteins

Defining the methanogenic SECIS element in vivo by targeted mutagenesis

In all domains of life, Archaea, Eukarya and Bacteria, the unusual amino acid selenocysteine (Sec) is co-translationally incorporated into proteins by recoding a UGA stop codon to a sense codon. A secondary structure on the mRNA, the selenocysteine insertion sequence (SECIS), is required, but its position, secondary structure and binding partner(s) are not conserved across the tree of life. Thus far, the nature of archaeal SECIS elements has been derived mainly from sequence analyses. A recently developed in vivo reporter system was used to study the structure-function relationships of SECIS elements in Methanococcus maripaludis. Through targeted mutagenesis, we defined the minimal functional SECIS element, the parts of the SECIS where structure and not the identity of the bases are relevant for function, and identified two conserved -and invariant- adenines that are most likely to interact with the other factor(s) of the Sec recoding machinery. Finally, we demonstrated the functionality of SECIS elements in the 5`-untranslated region of the mRNA and identified a potential mechanism of SECIS repositioning in the vicinity of the UGA for efficient selenocysteine insertion.

Dietary supplementation of male mice with inorganic, organic or nanoparticle selenium preparations: evidence supporting a putative gut-thyroid-male fertility axis

Selenium (Se) is linked to physiological homeostasis. Male mice (n = 8/group) were fed control (AIN93G) or diets enriched in sodium selenite (NaSe, 5.6 ppm), methylselenocysteine (Met, 4.7 ppm), diphenyl diselenide (DPDS, 14.2 ppm), or nanoselenium (NanoSe, 2.7 ppm); dietary Se ascertained by inductively-coupled plasma mass spectrometry. At 4 weeks testes, sperm, thyroids, blood and stool were collected to assess histoarchitecture, circulating hormones (thyroxine, T4; triiodothyronine, T3; thyroid stimulating hormone, TSH) and gut microbiome (16S rRNAV3-V4 amplicon sequencing). Supplemented NaSe, Met, and NanoSe increased plasma testosterone and testis glutathione peroxidases (GPx-1/4) while testicular superoxide dismutase and catalase increased slightly in the NanoSe group indicating a selective antioxidant response. Overall, NanoSe and NaSe enhanced male reproductive factors. All thyroids isolated from Se-supplemented mice contained marginal vacuoles and a lower follicle area vs control. Nano-Se enhanced thyroidiodothyronine deiodinase-1 (DIO1) expression however, thyroid GPx-1/4 remained unchanged. Supplemented NaSe and DPDSl increased plasma T3/T4 ratio, while plasma TSH was unchanged. Microbiome analyses showed that NanoSe was most efficacious in altering composition (judged by α-diversity, Shannon index and taxon richness) while the NaSe diet showed the greatest overall change in α-diversity. Dietary Se supplementation, particularly encapsulated NanoSe, may improve male fertility factors by enhancing the gut-thyroid-fertility axis.

Insights from selenoprotein I mouse models for understanding biological roles of this enzyme

Selenoprotein I (selenoi) is a metabolic enzyme expressed in a wide variety of tissues that catalyzes the transfer of the ethanolamine phosphate group from CDP-ethanolamine to lipid acceptors to generate ethanolamine phospholipids. It is a member of the selenoprotein family, a class of proteins that mostly play fundamental roles in redox homeostasis and are defined by the co-translational incorporation of selenium in the form of selenocysteine. Loss-of-function mutations in the human SELENOI gene have been found in rare cases leading to a complex form of hereditary spastic paraplegia. Understanding the roles of this selenoprotein and its phospholipid products in different cell types has benefited from the development of mouse models. In particular, global and conditional knockout (KO) of the Selenoi gene in mice has enabled a more complete picture to emerge of how this important selenoprotein is integrated into metabolic pathways. These data have revealed how Selenoi loss-of-function affects embryogenesis, neurodevelopment, the immune system and liver physiology. This review summarizes the insights gained through mouse model experiments and the current understanding the different physiological roles played by this selenoprotein.

deep-Sep: a deep learning-based method for fast and accurate prediction of selenoprotein genes in bacteria

Selenoproteins are a special group of proteins with major roles in cellular antioxidant defense. They contain the 21st amino acid selenocysteine (Sec) in the active sites, which is encoded by an in-frame UGA codon. Compared to eukaryotes, identification of selenoprotein genes in bacteria remains challenging due to the absence of an effective strategy for distinguishing the Sec-encoding UGA codon from a normal stop signal. In this study, we have developed a deep learning-based algorithm, deep-Sep, for quickly and precisely identifying selenoprotein genes in bacterial genomic sequences. This algorithm uses a Transformer-based neural network architecture to construct an optimal model for detecting Sec-encoding UGA codons and a homology search-based strategy to remove additional false positives. During the training and testing stages, deep-Sep has demonstrated commendable performance, including an F1 score of 0.939 and an area under the receiver operating characteristic curve of 0.987. Furthermore, when applied to 20 bacterial genomes as independent test data sets, deep-Sep exhibited remarkable capability in identifying both known and new selenoprotein genes, which significantly outperforms the existing state-of-the-art method. Our algorithm has proved to be a powerful tool for comprehensively characterizing selenoprotein genes in bacterial genomes, which should not only assist in accurate annotation of selenoprotein genes in genome sequencing projects but also provide new insights for a deeper understanding of the roles of selenium in bacteria.IMPORTANCESelenium is an essential micronutrient present in selenoproteins in the form of Sec, which is a rare amino acid encoded by the opal stop codon UGA. Identification of all selenoproteins is of vital importance for investigating the functions of selenium in nature. Previous strategies for predicting selenoprotein genes mainly relied on the identification of a special cis-acting Sec insertion sequence (SECIS) element within mRNAs. However, due to the complexity and variability of SECIS elements, recognition of all selenoprotein genes in bacteria is still a major challenge in the annotation of bacterial genomes. We have developed a deep learning-based algorithm to predict selenoprotein genes in bacterial genomic sequences, which demonstrates superior performance compared to currently available methods. This algorithm can be utilized in either web-based or local (standalone) modes, serving as a promising tool for identifying the complete set of selenoprotein genes in bacteria.

Selenium-containing compounds, selenium nanoparticles and selenoproteins in the prevention and treatment of lung cancer

THE OBJECTIVE

Is to review the latest data on the role of key organic and inorganic compounds of the essential trace element selenium, selenium-containing nanocomposites and nanoparticles, and selenoproteins in lung cancer therapy.

OBJECT OF RESEARCH

Sodium selenite, methylselenic acid, selenomethionine, selenium nanoparticles, mammalian selenoproteins KEY OBJECTIVES:: To describe the molecular mechanisms of the cytotoxic effect of sodium selenite, methylselenic acid and selenomethionine on lung cancer cells, to discuss the latest advances in lung cancer nanomedicine using selenium-based nanoparticles and nanocomposites and to assess the prospects for creating antitumor drugs based on them, to assess the role of selenoproteins in the progression or inhibition of lung cancer and to study the molecular mechanisms of such regulation CONCLUSIONS:: This review provides a complete picture of the role of selenium and selenium-containing agents of various natures in the regulation of carcinogenesis and therapy of lung cancer, which significantly complements the fundamental data on the functions of these compounds, on the molecular mechanisms of regulation of processes associated with lung cancer. This knowledge provides insight into the latest developments and future prospects in the treatment and prevention of lung cancer with the active participation of the trace element selenium.

Genomic Insights into Selenate Reduction by Anaerobacillus Species

Selenium (Se), a potentially toxic trace element, undergoes complex biogeochemical cycling in the environment, largely driven by microbial activity. The reduction in selenate or selenite to elemental selenium is an environmentally beneficial process, as it decreases both Se toxicity and mobility. This reduction is catalyzed by enzymes encoded by various related genes. The link between Se reduction gene clusters and specific taxonomic groups is significant for elucidating the ecological roles and processes of Se reduction in diverse environments. In this study, a new species of Se-reducing microorganism belonging to the genus Anaerobacillus was isolated from a mining site. A comparative analysis of the growth characteristics reveals that Anaerobacillus species exhibit notable metabolic versatility, particularly in their fermentation abilities and utilization of diverse electron donors and acceptors. Genome analysis identified a diverse array of gene clusters associated with selenate uptake (sul, pst), selenate reduction (ser), and selenite reduction (hig, frd, trx, and bsh). Since selenate reduction is the first crucial step in Se reduction, genes linked to selenate reductase are the focus. The serA gene clusters analysis suggests that the serA gene is highly conserved across Anaerobacillus species. The surrounding genes of serA show significant variability in both presence and gene size. This evolutionary difference in coenzyme utilization and serA regulation suggests distinct survival strategies among Anaerobacillus species. This study offers insights into Se bio-transformations and the adaptive strategies of Se-reducing microorganisms.

Glutathione peroxidase gene regulates substrate development and prevents strain aging in Volvariella volvacea

Degradation of Volvariella volvacea is associated with the accumulation of reactive oxygen species (ROS), and glutathione peroxidase (GPX) is one of the key antioxidant enzyme. The purpose of this research is to uncover the importance of the gpx gene in the degradation and revitalization of V. volvacea. In this study, a gpx-silenced strain of the primordial strain T0 and an overexpression strain of the degraded strain T19 of V. volvacea were constructed, and their antioxidant properties, matrix degradation ability, and production traits were determined. The results showed that the expression level of gpx altered the homeostasis of the V. volvacea redox system and affected the substrate degradation ability of V. volvacea, which altered the physiological traits of the V. volvacea mycelium. Most importantly, the primordial strain T0 was unable to produce fruiting bodies due to the silence of the gpx gene. On the other hand, the gpx gene overexpression promoted the regrowth of fruiting bodies in degenerated strains of V. volvacea T19. This study provides a new biotechnological strategy to control the degeneration of V. volvacea and other edible fungi.

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.

Structure of POU2AF1 recombinant protein and it affects the progression and treatment of liver cancer based on WGCNA and molecular docking analysis

Hepatocellular carcinoma, also referred to as HCC, is the most frequent form of primary liver cancer. It is anticipated that the discovery of the molecular pathways related with HCC would open up new possibilities for the treatment of HCC.WGCNA (Weighted gene co-expression network analysis) and molecular docking analysis were used to study the structural characteristics of POU2AF1 recombinant protein and its interaction with related proteins. Normal samples were placed in one group, and tumor samples were placed in another group inside the GEO database. We continued our investigation of the DEGs by performing an enrichment analysis using GO and KEGG. The GSCA platform is utilized in the process of doing an analysis of the connection between gene expression and medication sensitivity. In the end, the core target and the active molecule were both given the green light for a molecular docking investigation. POU2AF1 is being considered as a possible therapeutic target for HCC, and the results of our work have presented novel concepts for the treatment of HCC.

Selenium elicited an enhanced anti-inflammatory effect in primary bovine endometrial stromal cells with high cortisol background

BACKGROUND

An elevated endogenous cortisol level due to the peripartum stress is one of the risk factors of postpartum bovine uterine infections. Selenium is a trace element that elicits anti-inflammation and antioxidation properties. This study aimed to reveal the modulatory effect of selenium on the inflammatory response of primary bovine endometrial stromal cells in the presence of high-level cortisol. The cells were subjected to lipopolysaccharide to establish cellular inflammation. The mRNA expression of toll-like receptor 4 (TLR4), proinflammatory factors, and selenoproteins was measured with qPCR. The activation of NF-κB and MAPK signalling pathways was detected with Western blot and immunofluorescence.

RESULTS

The pretreatment with sodium selenite (2 and 4 µΜ) resulted in a down-regulation of TLR4 and genes encoding proinflammatory factors, including interleukin (IL)-1β, IL-6, IL-8, tumour necrosis factor α, cyclooxygenase 2, and inducible nitric oxide synthase. Selenium inhibited the activation of NF-κB and the phosphorylation of mitogen-activated protein kinase kinase, extracellular signal-regulated kinase, p38MAPK and c-Jun N-terminal kinase/stress-activated protein kinase. The suppression of those genes and pathways by selenium was more significant in the presence of high cortisol level (30 ng/mL). Meanwhile the gene expression of glutathione peroxidase 1 and 4 was promoted by selenium, and was even higher in the presence of cortisol and selenium.

CONCLUSIONS

The anti-inflammatory action of selenium is probably mediated through NF-κB and MAPK, and is augmented by cortisol in primary bovine endometrial stromal cells.

Prevotella copri Improves Selenium Deposition and Meat Quality in the longissimus dorsi Muscle of Fattening Pigs

Selenium is among the important trace elements that influence the quality of meat. Although it has been established that the gut microbiota is closely associated with selenium metabolism, it has yet to be determined whether these microbes influence the accumulation of selenium in muscles. To identify gut microbiota that potentially influence the deposition of selenium in muscles, we compared the colonic microbial composition of pigs characterized by high and low contents of selenium in the longissimus dorsi muscle and accordingly detected a higher abundance of the bacterium Prevotella copri (P. copri) in pigs with a higher muscle selenium content. To verify the effect of P. copri, 16 pigs weighing approximately 61 kg were fed either a basal diet or a basal diet supplemented with P. copri (1.0 × 1010 CFU/kg feed) for 45 days. The results revealed significant increases in the contents of selenium and selenoprotein in the serum and longissimus dorsi muscle of fattening pigs fed the P. copri-supplemented diet. Moreover, supplementing the feed of pigs with P. copri was observed to promote significant improvement in the antioxidant capacity and quality of meat, including drip loss, pH, and meat color. In conclusion, our findings in this study indicate that P. copri has potential utility as a dietary supplement for improving the selenium status and meat quality in fattening pigs.

Tobacco as bioenergy and medical plant for biofuels and bioproduction

Tobacco, a widely cultivated crop, has been extensively utilized by humans for an extended period. However, the tobacco industry generates a significant amount of organic waste, and the effective utilization of this tobacco waste has been limited. Currently, most tobacco waste is either recycled as reconstituted tobacco sheets or disposed of in landfills. However, tobacco possesses far more potential value than just these applications. This article provides an overview of the diverse uses of tobacco waste in agriculture, medicine, chemical engineering, and energy sectors. In the realm of agriculture, tobacco waste finds primary application as fertilizers and pesticides. In medical applications, the bioactive compounds present in tobacco are fully harnessed, resulting in the production of phenols, solanesol, polysaccharides, proteins, and even alkaloids. These bioactive compounds exhibit beneficial effects on human health. Additionally, the applications of tobacco waste in chemical engineering and energy sectors are centered around the utilization of lignocellulosic compounds and certain fuels. Chemical platform compounds derived from tobacco waste, as well as selected fuel sources, play a significant role in these areas. The rational utilization of tobacco waste represents a promising prospect, particularly in the present era when sustainable development is widely advocated. Moreover, this approach holds significant importance for enhancing energy utilization.

Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis

Methanococcus maripaludis utilizes selenocysteine- (Sec-) containing proteins (selenoproteins), mostly active in the organism's primary energy metabolism, methanogenesis. During selenium depletion, M. maripaludis employs a set of enzymes containing cysteine (Cys) instead of Sec. The genes coding for these Sec-/Cys-containing isoforms were the only genes known of which expression is influenced by the selenium status of the cell. Using proteomics and transcriptomics, approx. 7% and 12%, respectively, of all genes/proteins were found differentially expressed/synthesized in response to the selenium supply. Some of the genes identified involve methanogenesis, nitrogenase functions, and putative transporters. An increase of transcript abundance for putative transporters under selenium depletion indicated the organism's effort to tap into alternative sources of selenium. M. maripaludis is known to utilize selenite and dimethylselenide as selenium sources. To expand this list, a selenium-responsive reporter strain was assessed with nine other, environmentally relevant selenium species. While the effect of some was very similar to that of selenite, others were effectively utilized at lower concentrations. Conversely, selenate and seleno-amino acids were only utilized at unphysiologically high concentrations and two compounds were not utilized at all. To address the role of the selenium-regulated putative transporters, M. maripaludis mutant strains lacking one or two of the putative transporters were tested for the capability to utilize the different selenium species. Of the five putative transporters analyzed by loss-of-function mutagenesis, none appeared to be absolutely required for utilizing any of the selenium species tested, indicating they have redundant and/or overlapping specificities or are not dedicated selenium transporters.

IMPORTANCE

While selenium metabolism in microorganisms has been studied intensively in the past, global gene expression approaches have not been employed so far. Furthermore, the use of different selenium sources, widely environmentally interconvertible via biotic and abiotic processes, was also not extensively studied before. Methanococcus maripaludis JJ is ideally suited for such analyses, thanks to its known selenium usage and available genetic tools. Thus, an overall view on the selenium regulon of M. maripaludis was obtained via transcriptomic and proteomic analyses, which inspired further experimentation. This led to demonstrating the use of selenium sources M. maripaludis was previously not known to employ. Also, an attempt-although so far unsuccessful-was made to pinpoint potential selenium transporter genes, in order to deepen our understanding of trace element utilization in this important model organism.

Validation of ferroptosis in canine cancer cells to enable comparative oncology and translational medicine

Ferroptosis is a cell death mechanism that has attracted significant attention as a potential basis for the development of new cancer therapies. Validation of ferroptosis biology in species commonly used in translation and pre-clinical development is a necessary foundation for enabling the advancement of such ferroptosis modulating drugs. Here, we demonstrate that canine cancer cells exhibit sensitivity to a wide range of ferroptosis-inducing perturbations in a manner indistinguishable from human cancer cells, and recapitulate characteristic patterns of ferroptotic response across tumor types seen in the human setting. The foundation provided herein establishes the dog as a relevant efficacy and toxicology model for ferroptosis and creates new opportunities to leverage the canine comparative oncology paradigm to accelerate the development of ferroptosis-inducing drugs for human cancer patients.

De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features

Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.

Low concentrations of selenium nanoparticles enhance the performance of a generalist parasitoid and its host, with no net effect on host suppression

BACKGROUND

The environmental and economic costs of conventional insecticides have stirred an interest in alternative management tactics, including the use of nanotechnologies. Selenium nanoparticles (SeNPs) have many applications in agriculture but may not be compatible with biological control; however, low concentrations of SeNPs may benefit natural enemies via hormesis. This study investigates the concentration-dependent effects of SeNPs (0-1000 mg L-1 ) on Anisopteromalus calandrae (Howard) (Hymenoptera: Pteromalidae), a generalist parasitoid of stored product pests.

RESULTS

The LC50 of SeNPs was 1540 mg L-1 for female parasitoids and 1164 mg L-1 for males. SeNPs had a significant hormetic effect; average lifespan increased by 10% at a concentration of 4.03 mg L-1 for females and by 35% at 13.83 mg L-1 for males. In a bioassay including hosts [the azuki bean beetle, Callosobruchus chinensis (L.) (Coleoptera: Chrysomelidae: Bruchinae)], a low concentration of SeNPs (25 mg L-1 ) enhanced the performance of female parasitoids; lifespan increased by 23% and the number of offspring increased by 88%. However, the number of emerging hosts did not significantly decrease; in the absence of parasitism, SeNPs actually improved host emergence by 17%.

CONCLUSION

Because higher concentrations of SeNPs reduced parasitoid lifespan, whereas low concentrations enhanced not only parasitoid performance but also host emergence, practitioners should exercise caution when considering SeNPs for use in integrated pest management. © 2023 Society of Chemical Industry.

Selenium Ameliorated Oxidized Fish Oil-Induced Lipotoxicity via the Inhibition of Mitochondrial Oxidative Stress, Remodeling of Usp4-Mediated Deubiquitination, and Stabilization of Pparα

Aims: Studies demonstrated that oxidized fish oil (OFO) promoted oxidative stress and induced mitochondrial dysfunction and lipotoxicity, which attenuated beneficial effects of fish oil supplements in the treatment of nonalcoholic fatty liver disease (NAFLD). The current study was performed on yellow catfish, a good model to study NAFLD, and its hepatocytes to explore whether selenium (Se) could alleviate OFO-induced lipotoxicity via the inhibition of oxidative stress and determine its potential mechanism. Results: The analysis of triglycerides content, oxidative stress parameters, and histological and transmission electronic microscopy observation showed that high dietary Se supplementation alleviated OFO-induced lipotoxicity, oxidative stress, and mitochondrial injury and dysfunction. RNA-sequencing and immunoblotting analysis indicated that high dietary Se reduced OFO-induced decline of peroxisome-proliferator-activated receptor alpha (Pparα) and ubiquitin-specific protease 4 (Usp4) protein expression. High Se supplementation also alleviated OFO-induced reduction of thioredoxin reductase 2 (txnrd2) messenger RNA (mRNA) expression level and activity. The txnrd2 knockdown experiments revealed that txnrd2 mediated Se- and oxidized eicosapentaenoic acid (oxEPA)-induced changes of mitochondrial reactive oxygen species (mtROS) and further altered Usp4 mediated-deubiquitination and stabilization of Pparα, which, in turn, modulated mitochondrial fatty acid β-oxidation and metabolism. Mechanistically, Usp4 deubiquitinated Pparα and ubiquitin-proteasome-mediated Pparα degradation contributed to oxidative stress-induced mitochondrial dysfunction. Innovation: These findings uncovered a previously unknown mechanism by which Se and OFO interacted to affect lipid metabolism via the Txnrd2-mtROS-Usp4-Pparα pathway, which provides the new target for NAFLD prevention and treatment. Conclusion: Se ameliorated OFO-induced lipotoxicity via the inhibition of mitochondrial oxidative stress, remodeling of Usp4-mediated deubiquitination, and stabilization of Pparα. Antioxid. Redox Signal. 40, 433-452.

Maternal seafood consumption is associated with improved selenium status: Implications for child health

Selenium (Se) is required for synthesis of selenocysteine (Sec), an amino acid expressed in the active sites of Se-dependent enzymes (selenoenzymes), including forms with essential functions in fetal development, brain activities, thyroid hormone metabolism, calcium regulation, and to prevent or reverse oxidative damage. Homeostatic mechanisms normally ensure the brain is preferentially supplied with Se to maintain selenoenzymes, but high methylmercury (CH3Hg) exposures irreversibly inhibit their activities and impair Sec synthesis. Due to Hg's high affinity for sulfur, CH3Hg initially binds with the cysteine (Cys) moieties of thiomolecules which are selenoenzyme substrates. These CH3Hg-Cys adducts enter selenoenzyme active sites and transfer CH3Hg to Sec, thus irreversibly inhibiting their activities. High CH3Hg exposures are uniquely able to induce a conditioned Se-deficiency that impairs synthesis of brain selenoenzymes. Since the fetal brain lacks Se reserves, it is far more vulnerable to CH3Hg exposures than adult brains. This prompted concerns that maternal exposures to CH3Hg present in seafood might impair child neurodevelopment. However, typical varieties of ocean fish contain far more Se than CH3Hg. Therefore, eating them should augment Se-status and thus prevent Hg-dependent loss of fetal selenoenzyme activities. To assess this hypothesis, umbilical cord blood and placental tissue samples were collected following delivery of a cohort of 100 babies born on Oahu, Hawaii. Dietary food frequency surveys of the mother's last month of pregnancy identified groups with no (0 g/wk), low (0-12 g/wk), or high (12 + g/wk) levels of ocean fish consumption. Maternal seafood consumption increased Hg contents in fetal tissues and resulted in ∼34% of cord blood samples exceeding the EPA Hg reference level of 5.8 ppb (0.029 µM). However, Se concentrations in these tissues were orders of magnitude higher and ocean fish consumption caused cord blood Se to increase ∼9.4 times faster than Hg. Therefore, this study supports the hypothesis that maternal consumption of typical varieties of ocean fish provides substantial amounts of Se that protect against Hg-dependent losses in Se bioavailability. Recognizing the pivotal nature of the Hg:Se relationship provides a consilient perspective of seafood benefits vs. risks and clarifies the reasons for the contrasting findings of certain early studies.

Diphthamide - a conserved modification of eEF2 with clinical relevance

Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.

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.

Selenoprotein P expression in glioblastoma as a regulator of ferroptosis sensitivity: preservation of GPX4 via the cycling-selenium storage

Glioblastoma (GBM) is one of the most aggressive and deadly brain tumors; however, its current therapeutic strategies are limited. Selenoprotein P (SeP; SELENOP, encoded by the SELENOP gene) is a unique selenium-containing protein that exhibits high expression levels in astroglia. SeP is thought to be associated with ferroptosis sensitivity through the induction of glutathione peroxidase 4 (GPX4) via selenium supplementation. In this study, to elucidate the role of SeP in GBM, we analyzed its expression in GBM patients and found that SeP expression levels were significantly higher when compared to healthy subjects. Knock down of SeP in cultured GBM cells resulted in a decrease in GPX1 and GPX4 protein levels. Under the same conditions, cell death caused by RSL3, a ferroptosis inducer, was enhanced, however this enhancement was canceled by supplementation of selenite. These results indicate that SeP expression contributes to preserving GPX and selenium levels in an autocrine/paracrine manner, i.e., SeP regulates a dynamic cycling-selenium storage system in GBM. We also confirmed the role of SeP expression in ferroptosis sensitivity using patient-derived primary GBM cells. These findings indicate that expression of SeP in GBM can be a significant therapeutic target to overcome anticancer drug resistance.

Spatially varying relationships of soil Se concentration and rice Se concentration in Guangxi, China: A geographically weighted regression approach

In recent years, the biogeochemical behavior and environmental impact of Selenium (Se) on soil-plant systems have received widespread attention, and traditional statistical methods reveal generally positive correlations between rice Se and soil Se. However, that initial positive relationship may have been obscured by local external factors. Using local scale data from the geochemical evaluation of land quality project, this work employed geographically weighted regression (GWR) to examine the spatial variation of rice Se (as the dependent variable) and soil Se (as the independent variable) in Guangxi. Strong and weak correlation coefficients occur between rice Se and soil Se, thereby indicating that their relationships are spatially varying. Guangxi is characterized by significantly positive correlations in most areas, with weak correlations mostly found in the south-western and central-eastern regions. Areas with weak correlation can be divided into two patterns: high soil Se with low rice Se and high rice Se with low soil Se. The unique patterns are correlated with distinct natural factors, particularly the abundance of Fe-rich soils in the carbonate area; by contrast, sandstone areas in central Guangxi may have been affected by anthropogenic activities. To reveal the spatially varying relationships at the local scale, we employed GWR, an effective tool that allowed us to identify the association between environmental variables and influencing factors and explore spatially varying relationships between them. This study breaks through the existing understanding that soil Se is completely positively correlated with rice Se for the first time, and concludes that their correlation is spatially variable, providing an effective approach for the study of complex relationships.

Biology and Roles in Diseases of Selenoprotein I Characterized by Ethanolamine Phosphotransferase Activity and Antioxidant Potential

Selenoprotein I (SELENOI) has been demonstrated to be an ethanolamine phosphotransferase (EPT) characterized by a nonselenoenzymatic domain and to be involved in the main synthetic branch of phosphatidylethanolamine (PE) in the endoplasmic reticulum. Therefore, defects of SELENOI may affect the health status through the multiple functions of PE. On the other hand, selenium (Se) is covalently incorporated into SELENOI as selenocysteine (Sec) in its peptide, which forms a Sec-centered domain as in the other members of the selenoprotein family. Unlike other selenoproteins, Sec-containing SELENOI was formed at a later stage of animal evolution, and the high conservation of the structural domain for PE synthesis across a wide range of species suggests the importance of EPT activity in supporting the survival and evolution of organisms. A variety of factors, such as species characteristics (age and sex), diet and nutrition (dietary Se and fat intakes), SELENOI-specific properties (tissue distribution and rank in the selenoproteome), etc., synergistically regulate the expression of SELENOI in a tentatively unclear interaction. The N- and C-terminal domains confer 2 distinct biochemical functions to SELENOI, namely PE regulation and antioxidant potential, which may allow it to be involved in numerous physiological processes, including neurological diseases (especially hereditary spastic paraplegia), T cell activation, tumorigenesis, and adipocyte differentiation. In this review, we summarize advances in the biology and roles of SELENOI, shedding light on the precise regulation of SELENOI expression and PE homeostasis by dietary Se intake and pharmaceutical or transgenic approaches to modulate the corresponding pathological status.

CCNB2 as a potential biomarker of bladder cancer via the high throughput technology

Bladder cancer and oral squamous cell carcinoma (OSCC) seriously affect people's health. However, the relationship between bladder cancer and OSCC remains unclear. Got GSE138206, GSE146483, GSE184616, and bladder cancer datasets GSE65635, GSE100926 from Gene Expression Omnibus database. Weighted gene co-expression network analysis was used to identify the significant module. Functional enrichment analysis was performed via the Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes. Furthermore, the Gene Set Enrichment Analysis was also used to complete the enrichment analysis. Comparative Toxicogenomics Database found most relevant diseases to core genes. TargetScan is used to forecast analysis of microRNA and target genes. In Gene Ontology analysis, differentially expressed genes were mostly concentrated in cell differentiation, extrallular region, structural molecule activity, and actin binding. In Kyoto Encyclopedia of Genes and Genomes analysis, the differentially expressed genes were mainly enriched in PI3K-Akt signaling pathway, pathway in cancer, and extracellular matrix-receptor interaction. Seven hub genes (cyclin B2 [CCNB2], TK1, CDC20, PCNA, CKS1B, CDCA5, MCM4) were obtained. Hub genes (CCNB2, CDC20) are highly expressed in OSCC and bladder cancer samples. CCNB2 was one common oncogene of bladder cancer and OSCC.

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

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

Gpx4, Selenov, and Txnrd3 Are Three Most Testis-Abundant Selenogenes Resistant to Dietary Selenium Concentrations and Actively Expressed During Reproductive Ages in Rats

Almost all selenogenes are expressed in the testis, and those have the highest and constant expressions will be the primary candidates for functional analysis of selenium (Se) in male reproduction. This study aimed to profile the mRNA expressions of the testis-abundant selenogenes of rat models in responses to growth and dietary Se concentrations. Forty-eight weaning SD male rats were fed Se deficient basal diet (BD) for 5 weeks and then randomly grouped (n = 12/group) for being fed BD or BD plus 0.25, 3, or 5 mg Se/kg for 4 more weeks before sacrifice. Abundances of selenogenomic mRNAs in the liver and testis were determined with relative qPCR and those of the testis-abundant selenogenes in 13 kinds of tissues were assayed with a molecular beacon-based qPCR. Spatiotemporal expressions of rat selenogenome were also analyzed with the RNA-Seq transcriptomic data published by NCBI. mRNA abundances of glutathione peroxidase 4 (Gpx4), nuclear Gpx4 (nGpx4), selenoprotein V (Selenov), and thioredoxin reductase 3 (Txnrd3) in the testis were significantly higher than that in any other tissues (P < 0.05). Moreover, testicular mRNA abundances of Gpx4, Selenov, and Txnrd3 were not affected by levels of dietary Se supplementation (P > 0.05), and much higher at 6-21 weeks old than at 2 and 104 weeks old (P < 0.05). The result showed that Gpx4, Selenov, and Txnrd3 were most highly expressed in the testis of rats especially at reproductive ages and resistant to the impact of dietary Se levels, which suggested their specific importance in male reproduction.

In vivo probing of SECIS-dependent selenocysteine translation in Archaea

Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.

Effects of Dietary Selenium and Oxidized Fish Oils on Intestinal Lipid Metabolism and Antioxidant Responses of Yellow Catfish Pelteobagrus fulvidraco

Currently, the effect of selenium and oxidized fish oil interactions on the intestinal lipid metabolism and antioxidant responses of fish remains unknown. Herein, yellow catfish Pelteobagrus fulvidraco (weight: 3.99 ± 0.01 g) were used as experimental animals and were fed four diets: an adequate amount of selenium (0.25 mg kg⁻¹) with fresh fish oil (A-Se+FFO), an adequate amount of selenium with oxidized fish oil (A-Se+OFO), a high amount of selenium (0.50 mg kg⁻¹) with fresh fish oil (H-Se+FFO), and a high amount of selenium with oxidized fish oil (H-Se+OFO). The feeding experiment was conducted for 10 weeks. The results showed that selenium supplementation alleviated the intestinal tissue damage and reduced the lipid accumulation that was induced by oxidized fish oils. Meanwhile, we also found that 0.50 mg kg⁻¹ selenium reduced the oxidative stress that is caused by oxidized fish oils through increasing the GSH and the activity and mRNA expression of antioxidant enzymes. Dietary selenium and oxidized fish oils also affected the mRNA expression of intestinal selenoproteins including selenow2a, selenop2, and selenot2. Mechanistically, Se and oxidized eicosapentaenoic acid (oxEPA) influenced the GSH content by affecting the DNA binding ability of activating transcription factor (ATF) 3 to the slc7a11 promoter. For the first time, our results suggested that selenium alleviated the oxidized fish oil-induced intestinal lipid deposition and the oxidative stress of the fish. We also elucidated the novel mechanism of selenium increasing the GSH content by affecting the interaction of ATF3 and the slc7a11 promoter.

Deep Learning-Based Medical Data Association Rules to Explore the Connectivity and Regulation Mechanism of miRNA-mRNA Network in Myocarditis

Acute, chronic myocarditis as myocardial localized or diffuse inflammation lesions is usually involving cardiac function in patients with severe adverse outcomes such as heart failure, sudden death, and no unified, but its pathogenesis clinical is mainly composed of a number of factors including infection and autoimmune defects, such as physical and chemical factors; therefore, it is of great significance to explore the regulation mechanism of myocarditis-related miRNA network connectivity and temperament for in-depth understanding of the pathogenesis of myocarditis and the direction of targeted therapy. Based on this, this study explored the miRNA network related to the pathogenesis of myocarditis through deep learning medical data association rules and analyzed its specific mechanism. The results showed that 39 upregulated miRNAs, 88 downregulated miRNAs, 109 upregulated differentially expressed miRNAs, and 589 downregulated mRNAs were obtained by data association through GSE126677 and GSE4172 databases. GO enrichment and KRGG enrichment analysis showed that the differentially expressed mRNAs were involved in the regulation of a variety of biological processes, cellular components, and molecular functions. At the same time, the miRNA with differentially expressed miRNAs and their corresponding mRNAs were connected to further clarify the specific molecular mechanism of the pathological changes of myocarditis by constructing miRNA-mRNA network. It provides effective potential molecular targets for subsequent treatment and diagnosis.

eIF3 Interacts with Selenoprotein mRNAs

The synthesis of selenoproteins requires the co-translational recoding of an in-frame UGASec codon. Interactions between the Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2) in the 3'untranslated region (3'UTR) of selenoprotein mRNAs enable the recruitment of the selenocysteine insertion machinery. Several selenoprotein mRNAs undergo unusual cap hypermethylation and are not recognized by the translation initiation factor 4E (eIF4E) but nevertheless translated. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), can selectively recruit several cellular mRNAs and plays roles in specialized translation initiation. Here, we analyzed the ability of eIF3 to interact with selenoprotein mRNAs. By combining ribonucleoprotein immunoprecipitation (RNP IP) in vivo and in vitro with cross-linking experiments, we found interactions between eIF3 and a subgroup of selenoprotein mRNAs. We showed that eIF3 preferentially interacts with hypermethylated capped selenoprotein mRNAs rather than m⁷G-capped mRNAs. We identified direct contacts between GPx1 mRNA and eIF3 c, d, and e subunits and showed the existence of common interaction patterns for all hypermethylated capped selenoprotein mRNAs. Differential interactions of eIF3 with selenoprotein mRNAs may trigger specific translation pathways independent of eIF4E. eIF3 could represent a new player in the translation regulation and hierarchy of selenoprotein expression.

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.

The Role and Mechanism of Essential Selenoproteins for Homeostasis

Selenium (Se) is one of the essential trace elements that plays a biological role in the body, mainly in the form of selenoproteins. Selenoproteins can be involved in the regulation of oxidative stress, endoplasmic reticulum (ER) stress, antioxidant defense, immune and inflammatory responses and other biological processes, including antioxidant, anti-inflammation, anti-apoptosis, the regulation of immune response and other functions. Over-loading or lack of Se causes certain damage to the body. Se deficiency can reduce the expression and activity of selenoproteins, disrupt the normal physiological function of cells and affect the body in antioxidant, immunity, toxin antagonism, signaling pathways and other aspects, thus causing different degrees of damage to the body. Se intake is mainly in the form of dietary supplements. Due to the important role of Se, people pay increasingly more attention to Se-enriched foods, which also lays a foundation for better research on the mechanism of selenoproteins in the future. In this paper, the synthesis and mechanism of selenoproteins, as well as the role and mechanism of selenoproteins in the regulation of diseases, are reviewed. Meanwhile, the future development of Se-enriched products is prospected, which is of great significance to further understand the role of Se.

Selenium and protozoan parasitic infections: selenocompounds and selenoproteins potential

The current drug treatments against protozoan parasitic diseases including Chagas, malaria, leishmaniasis, and toxoplasmosis represent good examples of drug resistance mechanisms and have shown diverse side effects. Therefore, the identification of novel therapeutic strategies and drug compounds against such life-threatening diseases is urgent. According to the successful usage of selenium (Se) compounds-based therapy against some diseases, this therapeutic strategy has been recently further underlined against these parasitic diseases by targeting different parasite´s essential pathways. On the other hand, due to the important functions played by parasite selenoproteins in their biology (such as modulating the host immune response), they can be also considered as a novel therapeutic strategy by designing specific inhibitors against these important proteins. In addition, the immunomodulatory potentiality of these compounds to trigger T helper type 1 (Th1) cells and cytokine-mediated immune response for the substantial induction of proinflammatory cytokines, thus, Se, selenoproteins, and parasite selenoproteins could be further investigated to find possible vaccine antigens. Herein, we collect and present the results of some studies regarding Se-based therapy against protozoan parasitic diseases and highlight relevant information and some viewpoints that might be insightful to advance toward more effective studies in the future.

Trace Element Selenium Effectively Alleviates Intestinal Diseases

Selenium (Se) is an essential trace element in the body. It is mainly used in the body in the form of selenoproteins and has a variety of biological functions. Intestinal diseases caused by chronic inflammation are among the most important threats to human health, and there is no complete cure at present. Due to its excellent antioxidant function, Se has been proven to be effective in alleviating intestinal diseases such as inflammatory bowel diseases (IBDs). Therefore, this paper introduces the role of Se and selenoproteins in the intestinal tract and the mechanism of their involvement in the mediation of intestinal diseases. In addition, it introduces the advantages and disadvantages of nano-Se as a new Se preparation and traditional Se supplement in the prevention and treatment of intestinal diseases, so as to provide a reference for the further exploration of the interaction between selenium and intestinal health.

From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion

Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.

Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry

Selenoprotein P (SELENOP) is an emerging marker of the nutritional status of selenium and of various diseases, however, its chemical characteristics still need to be investigated and methods for its accurate quantitation improved. SELENOP is unique among selenoproteins, as it contains multiple genetically encoded SeCys residues, whereas all the other characterized selenoproteins contain just one. SELENOP occurs in the form of multiple isoforms, truncated species and post-translationally modified variants which are relatively poorly characterized. The accurate quantification of SELENOP is contingent on the availability of specific primary standards and reference methods. Before recombinant SELENOP becomes available to be used as a primary standard, careful investigation of the characteristics of the SELENOP measured by electrospray MS and strict control of the recoveries at the various steps of the analytical procedures are strongly recommended. This review critically discusses the state-of-the-art of analytical approaches to the characterization and quantification of SELENOP. While immunoassays remain the standard for the determination of human and animal health status, because of their speed and simplicity, mass spectrometry techniques offer many attractive and complementary features that are highlighted and critically evaluated.

Site-Specific Selenocysteine Incorporation into Proteins by Genetic Engineering

Selenocysteine (Sec), a rare naturally proteinogenic amino acid, is the major form of essential trace element selenium in living organisms. Selenoproteins, with one or several Sec residues, are found in all three domains of life. Many selenoproteins play a role in critical cellular functions such as maintaining cell redox homeostasis. Sec is usually encoded by an in-frame stop codon UGA in the selenoprotein mRNA, and its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. This mechanistic complexity of selenoprotein synthesis poses a big challenge to produce synthetic selenoproteins. To understand the functions of natural as well as engineered selenoproteins, many strategies have recently been developed to overcome the inherent barrier for recombinant selenoprotein production. In this review, we will describe the progress in selenoprotein production methodology.

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.