Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Yerba mate (YM, Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex, in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions.

Microalgae: A good carrier for biological selenium enrichment

Selenium is a crucial micronutrient for human well-being, with significant contributions to antioxidant, anti-ageing, and antiviral activities. However, over one billion people globally struggle with selenium deficiency, leading to a pressing need for selenium supplementation. Conventional selenium-enrich food from plants and animals provides challenges in achieving precise selenium supplementation. Thus, it is crucial to discover selenium carriers that can be cultured in a controlled environment. Multiple studies have shown that microalgae are excellent carriers for selenium enrichment due to their rapid growth, suitability for plant consumption, ease of industrialization, high efficiency in converting organic selenium, and many others. This review focuses on single-celled microalgae, comprehensively reviewing their metabolic pathway, biological transformation, and valuable forms of selenium. Additionally, it forecasts the current application status and prospects of selenium-enriched microalgae in agriculture and global human health. This review provides a reference for the industrial supply of precise selenium-rich raw materials.

Industrial Production of Functional Foods for Human Health and Sustainability

Functional foods significantly affect social stability, human health, and food security. Plants and microorganisms are high-quality chassis for the bioactive ingredients in functional foods. Characterised by precise nutrition and the provision of both nutritive and medicinal value, functional foods serve a as key extension of functional agriculture and offer assurance of food availability for future space exploration efforts. This review summarises the main bioactive ingredients in functional foods and their functions, describes the strategies used for the nutritional fortification and industrial production of functional foods, and provides insights into the challenges and future developments in the applications of plants and microorganisms in functional foods. Our review aims to provide a theoretical basis for the development of functional foods, ensure the successful production of new products, and support the U.N. Sustainable Development Goals, including no poverty, zero hunger, and good health and well-being.

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.

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.

Life-cycle selenium accumulation and its correlations with the rhizobacteria and endophytes in the hyperaccumulating plant Cardamine hupingshanensis

Cardamine hupingshanensis (C. hupingshanensis) is known for its ability to hyperaccumulate selenium (Se). However, the roles of the rhizobacteria or endophytes in Se hyperaccumulation have not been explored in C. hupingshanensis. Here, in-situ-like pot experiments were conducted to investigate the characteristics of Se accumulation throughout C. hupingshanensis growth stages and its correlations with rhizobacteria and endophytes under varying soil Se levels. Results showed that Se levels in roots, stems and leaves increased from the seedling to bolting stage, but remained relatively stable during the flowering and maturity. Leaves exhibited the highest Se levels (736.48 ± 6.51 mg/kg DW), followed by stems (575.39 ± 27.05 mg/kg DW), and lowest in roots (306.62 ± 65.45 mg/kg DW) under high-Se stress. The Se translocation factors from soils to C. hupingshanensis roots was significantly higher (p < 0.05) in low-Se soils compared to medium- and high-Se soils. Rhizobacterial diversity showed significant positive correlations (p < 0.05) with both total and bioavailable soil Se contents. The levels of soil Se and growth stages of C. hupingshanensis were found to have significant effects (p < 0.03) on the compositions of rhizosphere bacteria and C. hupingshanensis endophytes. Low-abundance bacteria (< 5%), including Gemmatimonadetes, Latescibacteria and Nitrospirae, were identified to potentially increase the bioavailable Se levels in the rhizosphere. The Se accumulation significantly decreased (p < 0.05) in C. hupingshanensis grown in sterilized low- (32.4%), medium- (17%) and high-Se (42%) soils. Endophytes in C. hupingshanensis, such as Firmicutes and Proteobacteria, were likely recruited from the rhizobacteria, as evidenced by the isolated bacterial strains, and played an important role in Se hyperaccumulation, particularly during the flowering stage. This study provides new insights into potential mechanism underlying Se hyperaccumulation in C. hupingshanensis.

Occurrence and conversion of progestogens and androgens are conserved in land plants

Progestogens and androgens have been found in many plants, but little is known about their biosynthesis and the evolution of steroidogenesis in these organisms. Here, we show that the occurrence and biosynthesis of progestogens and androgens are conserved across the viridiplantae lineage. An UHPLC-ESI-MS/MS method allowed high-throughput analysis of the occurrence and chemical conversion of progestogens and androgens in 41 species across the green plant lineage. Dehydroepiandrosterone, testosterone, and 5α-dihydrotestosterone are plants' most abundant mammalian-like steroids. Progestogens are converted into 17α-hydroxyprogesterone and 5α-pregnane-3,20-dione. Androgens are converted into testosterone and 5α-dihydrotestosterone. 17,20-Lyases, essential for converting progestogens to androgens, seem to be most effective in monocot species. Our data suggest that the occurrence of progestogens and androgens is highly conserved in plants, and their biosynthesis might favor a route using the Δ4 pathway.

Systematic Analysis of Genes Related to Selenium Bioaccumulation in Microalgae: A Review

Se is one of the essential nutrients for human health and animal growth; it participates in various physiological functions, such as antioxidant and immune response and metabolism. Se deficiency is related in the animal industry to poor production performance and the appearance of health problems in humans. Therefore, interest has arisen in producing fortified foods, nutritional supplements, and animal feed products enriched with Se. A sustainable strategy for bio-based products enriched with Se is microalgae. These are characterized by the ability to bioaccumulate inorganic Se and metabolize it into organic Se for product formulations of industrial interest. Although there are some reports on Se bioaccumulation, further exploration is needed to understand the effects of Se bioaccumulation in microalgae. Therefore, this article presents a systematic review of the genes or groups of genes that trigger biological responses associated with the metabolization of Se in microalgae. A total of 54,541 genes related to Se metabolization distributed in 160 different classes were found. Similarly, trends were identified through bibliometric networks on strains of greatest interest, bioproducts, and scientific production.

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

Proteomics Provide Insight into the Interaction between Selenite and the Microalgae Dunaliella salina

Dunaliella salina is currently one of the most commercially valuable microalgae species in the world. In reponse to selenite, D. salina is a microalgae with a high selenium content, thereby increasing its value, which is crucial for increasing its economic value as a nutrional supplement. However, the effects of selenite on D. salina are still unclear, and its molecular mechanism of the response to selenite stress is also elusive. Here, in order to study the effects of selenite on D. salina and the corresponding regulatory mechanism, we characterized the physiological phenotypes of D. salina under different selenite concentrations and carried out a quantitative proteomic study. The results showed that the effective concentration for 50% growth inhibition (EC50) of the algae was 192.7 mg/L after 11 days of cultivation. When selenite concentration was lower than 100 mg/L, selenite did not hinder the growth of D. salina in the early stage, but shortened the cell growth cycle, although cell growth was significantly inhibited when the concentration of selenium was higher than 250 mg/L. Bioaccumulation experiments showed that the content of intracellular selenium in D. salina cells reached the highest level under the treatment with 50 mg/L selenite, and the contents of total selenium and organic selenium in D. salina cells were 499.77 μg/g and 303.01 μg/g (dry weight), respectively. Proteomic analysis revealed that a series of proteins related to stress responses, amino acid metabolism and energy production pathways were profoundly altered by the selenite treatment. Glutathione peroxidase (GPX7), a selenium-containing protein, was identified in the group given the selenium treatment. Moreover, proteins involved in photoreactions and oxidative phosphorylation were significantly upregulated, indicating that D. salina effectively balanced the energy demand and energy production under selenite stress. This study provides novel insights into the responses to selenite of D. salina, a microalgae candidate as a biological carrier of selenium and would be helpful for the development of industrial strains rich in selenium.

Decoding the Virtual 2D Map of the Chloroplast Proteomes

BACKGROUND

The chloroplast is a semi-autonomous organelle having its own genome and corresponding proteome. Although chloroplast genomes have been reported, no reports exist on their corresponding proteomes. Therefore, a proteome-wide analysis of the chloroplast proteomes of 2893 species was conducted, and a virtual 2D map was constructed.

RESULTS

The resulting virtual 2D map of the chloroplast proteome exhibited a bimodal distribution. The molecular mass of the chloroplast proteome ranged from 0.448 to 616.334 kDa, and the isoelectric point (pI) ranged from 2.854 to 12.954. Chloroplast proteomes were dominated by basic pI proteins with an average pI of 7.852. The molecular weight and isoelectric point of chloroplast proteome were found to show bimodal distribution. Leu was the most abundant and Cys the least abundant amino acid in the chloroplast proteome. Notably, Trp amino acid was absent in the chloroplast protein sequences of Pilostyles aethiopica. In addition, Selenocysteine (Sec) and Pyrrolysine (Pyl) amino acids were also found to be lacking in the chloroplast proteomes.

CONCLUSION

The virtual 2D map and amino acid composition of chloroplast proteome will enable the researchers to understand the biochemistry of chloroplast protein in detail. Further, the amino acid composition of the chloroplast proteome will also allow us to understand the codon usage bias. The codon usage bias and amino acid usage bias of chloroplast will be crucial to understanding their relationship.

Characterization of a new selenoprotein methionine sulfoxide reductase from Haematococcus pluvialis and its antioxidant activity in response to high light intensity, hydrogen peroxide, glyphosate, and cadmium exposure

Selenium incorporates into selenocysteine (Sec) which is a key component of selenoproteins implicated in antioxidant defense and redox homeostasis. Methionine sulfoxide reductases (Msr) play crucial roles in cellular defense against environmental stress. Whereas mammals have the MsrB selenoprotein form, unicellular organisms have MsrA. The Sec residue at the conserved catalytic sites of selenoprotein MsrA confers a metabolic advantage over the non-selenoprotein type MsrA. In the present study, the novel selenoprotein HpMsrA from Haematococcus pluvialis was cloned by the rapid amplification of cDNA ends and transformed into the model green alga Chlamydomonas reinhardtii. Alignment of homologs revealed the presence of the conserved catalytic domain GUFW and showed that the HpMsrA protein comprises Sec (U) at the N-terminus but no recycled Cys at the C-terminus. We studied the response of HpMsrA expression to selenite, high light intensity, hydrogen peroxide, cadmium nitrate, and glyphosate exposure via real-time quantitative PCR and enzyme activity analysis. The results demonstrated that HpMsrA protects cellular proteins against oxidative and environmental stressors. Compared with wild type C. reinhardtii, the transformant exhibited a superior antioxidant ability. The discoveries made herein shed light on the antioxidant physiology and environmental stress resistance mechanisms of the selenoproteins in microalgae. This information may aid in conducting environmental risk assessments of aquatic ecosystems involving microalgae known to respond rapidly and quantitatively to abiotic stress factors promoting excessive reactive oxygen species generation.

Selenoprotein: Potential Player in Redox Regulation in Chlamydomonas reinhardtii

Selenium (Se) is an essential micro-element for many organisms, including Chlamydomonas reinhardtii, and is required in trace amounts. It is obtained from the 21st amino acid selenocysteine (Sec, U), genetically encoded by the UGA codon. Proteins containing Sec are known as selenoproteins. In eukaryotes, selenoproteins are present in animals and algae, whereas fungi and higher plants lack them. The human genome contains 25 selenoproteins, most of which are involved in antioxidant defense activity, redox regulation, and redox signaling. In algae, 42 selenoprotein families were identified using various bioinformatics approaches, out of which C. reinhardtii is known to have 10 selenoprotein genes. However, the role of selenoproteins in Chlamydomonas is yet to be reported. Chlamydomonas selenoproteins contain conserved domains such as CVNVGC and GCUG, in the case of thioredoxin reductase, and CXXU in other selenoproteins. Interestingly, Sec amino acid residue is present in a catalytically active domain in Chlamydomonas selenoproteins, similar to human selenoproteins. Based on catalytical active sites and conserved domains present in Chlamydomonas selenoproteins, we suggest that Chlamydomonas selenoproteins could have a role in redox regulation and defense by acting as antioxidants in various physiological conditions.

Discriminative Long-Distance Transport of Selenate and Selenite Triggers Glutathione Oxidation in Specific Subcellular Compartments of Root and Shoot Cells in Arabidopsis

Selenium is an essential trace element required for seleno-protein synthesis in many eukaryotic cells excluding higher plants. However, a substantial fraction of organically bound selenide in human nutrition is directly or indirectly derived from plants, which assimilate inorganic selenium into organic seleno-compounds. In humans, selenium deficiency is associated with several health disorders Despite its importance for human health, selenium assimilation and metabolism is barely understood in plants. Here, we analyzed the impact of the two dominant forms of soil-available selenium, selenite and selenate, on plant development and selenium partitioning in plants. We found that the reference plant Arabidopsis thaliana discriminated between selenate and selenite application. In contrast to selenite, selenate was predominantly deposited in leaves. This explicit deposition of selenate caused chlorosis and impaired plant morphology, which was not observed upon selenite application. However, only selenate triggered the accumulation of the macronutrient sulfur, the sister element of selenium in the oxygen group. To understand the oxidation state-specific toxicity mechanisms for selenium in plants, we quantified the impact of selenate and selenite on the redox environment in the plastids and the cytosol in a time-resolved manner. Surprisingly, we found that selenite first caused the oxidation of the plastid-localized glutathione pool and had a marginal impact on the redox state of the cytosolic glutathione pool, specifically in roots. In contrast, selenate application caused more vigorous oxidation of the cytosolic glutathione pool but also impaired the plastidic redox environment. In agreement with the predominant deposition in leaves, the selenate-induced oxidation of both glutathione pools was more pronounced in leaves than in roots. Our results demonstrate that Se-species dependent differences in Se partitioning substantially contribute to whole plant Se toxicity and that these Se species have subcellular compartment-specific impacts on the glutathione redox buffer that correlate with toxicity symptoms.

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.

The mammalian-type thioredoxin reductase 1 confers a high-light tolerance to the green alga Chlamydomonas reinhardtii

Reactive oxygen species (ROS) can both act as a poison causing cell death and important signaling molecules among various organisms. Photosynthetic organisms inevitably produce ROS, making the appropriate elimination of ROS an essential strategy for survival. Interestingly, the unicellular green alga Chlamydomonas reinhardtii expresses a mammalian form of thioredoxin reductase, TR1, which functions as a ROS scavenger in animal cells. To investigate the properties of TR1 in C. reinhardtii, we generated TR1 knockout strains using CRISPR/Cas9-based genome editing. We found a reduced tolerance to high-light and ROS stresses in the TR1 knockout strains compared to the parental strain. In addition, the regulation of phototactic orientation, known to be regulated by ROS, was affected in the knockout strains. These results suggest that TR1 contributes to a ROS-scavenging pathway in C. reinhardtii.

Selenium uptake, volatilization, and transformation by the cyanobacterium Microcystis aeruginosa and post-treatment of Se-laden biomass

With a narrow margin between beneficial and toxic effects, selenium (Se) is of great concern due to its increasing level in aquatic environments. The accumulation and transformation of Se by the cyanobacterium Microcystis aeruginosa and effects of nutrients, particularly sulfate, were investigated. The nutrient-deprived cyanobacterium removed water-borne selenate (82.2 ± 0.93%) faster than selenite (58.9 ± 1.77%), with 86.0 ± 1.41% and 77.2 ± 1.00%, respectively, of the Se accumulated in the biomass and the rest volatilized. When supplied with excess nutrients, the Se accumulation and volatilization rates were significantly inhibited, with the removal efficiency dropping to 50.2 ± 2.59% and 7.37 ± 0.93% for selenite and selenate, respectively. When M. aeruginosa was tested with inadequate, appropriate, and adequate levels of sulfate, Se uptake decreased with increasing sulfate concentrations, particularly for selenate (from 34.1 to 4.81%). Using X-ray absorption near-edge structure to speciate biomass Se, selenite and selenate were transformed to organo-Se (87.3-100%), with or without nutrients present, suggesting M. aeruginosa could efficiently reduce Se oxyanions to more bioavailable forms. With increasing sulfate levels (5.0 and 10.0 mg S/L), percentages of SeMet converted from selenite decreased by 28.2-33.0%, with 19.1-33.2% as elemental Se, while organo-Se remained dominant (93.6-95.1%) in selenate-treated M. aeruginosa. Transmission electron microscopy shows structural damage in the cell wall at exposure to selenite (1600 μg Se/L), with the intracellular structure intact. To prevent Se biomagnification along aquatic food chains, the Se-laden biomass was combusted as a post-treatment, leading to a significant reduction in Se content (∼99.2%) and Se bioavailability, with inorganic Se (45.0-70.5%) predominant in the residue.

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.

MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome

Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs.

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.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Structural and biophysical characterization of the selenoprotein SelW1 from Chlamydomonas reinhardtii

Selenoprotein W is widespread among pro- and eukaryotic organisms. It possesses antioxidant activity and plays pivotal roles in mammalian embryonic development and cellular functions. A very simple, prototypical selenoprotein W is SelW1 from Chlamydomonas. The U14C mutant of SelW1 was isolated and biophysically characterized. It contains an intramolecular disulfide bond and is thermally stable up to 70 °C. NMR resonance assignment of reduced and oxidized SelW1 showed that SelW1 adopts a thioredoxin fold. Interestingly, both forms show two additional sets of resonance for amino acid residues near the termini and have basically identical dynamic behavior. Since SelW1 from Chlamydomonas resembles the ancestor of mammalian selenoproteins in certain aspects, this study lays the basis for future characterization of SelW1 function and possible interaction partners.

Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation

Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.

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.

Same but different - Molecular comparison of human KTI12 and PSTK

Kti12 and PSTK are closely related and highly similar proteins implicated in different aspects of tRNA metabolism. Kti12 has been identified as an essential regulatory factor of the Elongator complex, involved in the modification of uridine bases in eukaryotic tRNAs. PSTK phosphorylates the tRNA^Sec-bound amino acid serine, which is required to synthesize selenocysteine. Kti12 and PSTK have previously been studied independently in various organisms, but only appear simultaneously in some animalia, including humans. As Kti12- and PSTK-related pathways are clinically relevant, it is of prime importance to understand their biological functions and mutual relationship in humans. Here, we use different tRNA substrates to directly compare the enzymatic activities of purified human KTI12 and human PSTK proteins. Our complementary Co-IP and BioID2 approaches in human cells confirm that Elongator is the main interaction partner of KTI12 but additionally indicate potential links to proteins involved in vesicular transport, RNA metabolism and deubiquitination. Moreover, we identify and validate a yet uncharacterized interaction between PSTK and γ-taxilin. Foremost, we demonstrate that human KTI12 and PSTK do not share interactors or influence their respective biological functions. Our data provide a comprehensive analysis of the regulatory networks controlling the activity of the human Elongator complex and selenocysteine biosynthesis.

The glutathione peroxidase family of Theobroma cacao: Involvement in the oxidative stress during witches' broom disease

The glutathione peroxidases (GPXs) are enzymes which are part of the cell antioxidant system inhibiting the ROS-induced damages of membranes and proteins. In cacao (Theobroma cacao L.) genome, five GPX genes were identified. Cysteine insertion codons (UGU) were found in TcPHGPX, TcGPX2, TcGPX4, TcGPX6 and tryptophan insertion codon (UGG) in TcGPX8. Multiple alignments revealed conserved domains between TcGPXs and other plants and human GPXs. Homology modeling was performed using the Populus trichocarpa GPX5 structure as template, and the molecular modeling showed that TcGPXs have affinity with selenometionine in their active site. In silico analysis of the TcGPXs promoter region revealed the presence of conserved cis-elements related to biotic stresses and hormone responsiveness. The expression analysis of TcGPXs in cacao plantlet meristems infected by M. perniciosa showed that TcGPXs are most expressed in susceptible variety than in resistant one, mainly in disease stages in which oxidative stress and programmed cell death occurred. This data, associated with phylogenetic and location analysis suggested that TcGPXs may play a role in protecting cells from oxidative stress as a try of disease progression reduction. To our knowledge, this is the first study of the overall GPX family from T. cacao.

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.

Structural elucidation of selenocysteine insertion machinery of microalgal selenoprotein T and its transcriptional analysis

Essential trace element selenium in association with selenoproteins, which is found in almost all organisms except higher plants and fungi, is involved in various biological functions. Advancement in the field of whole genome sequencing and data analyzing bioinformatic tools led to the accumulation of genome information of organisms. However, selenoproteins are unique and it needs specialized genomics tool for its identification as well as characterization. In this study, the presence of selenoprotein T (SelT) from Scenedesmus quadricauda was shown for the first time with experimental evidence and compared with SelT of marine microalgae Nannochloropsis oceanica. Along with SelT, all the associated machineries required to synthesize the selenoproteins were also identified. Also, the present study tried to explicate the evolutionary relatedness of SelT of these two organisms with other known bacteria and eukaryotes. Transcript level analysis in S. quadricauda under endoplasmic reticulum stress showed a 1.2 ± 0.28-fold increase in SelT expression. Thus, it provided the first experimental evidence on SelT expression from microalgae.

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.

The molecular mass and isoelectric point of plant proteomes

Background

Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. Therefore, it was important to understand the detail regarding the molecular weight and pI of the plant proteins.

Results

A proteome-wide analysis of plant proteomes from 145 species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The spectrum of molecular mass of the plant proteins varied from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom. However, Type-I polyketide synthase was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteins showed a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain selenocysteine (Sec), amino acid that was found only in lower eukaryotic aquatic plant lineage. Amino acid composition analysis showed Leu was high and Trp was low abundant amino acids in the plant proteome. Additionally, the plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well.

Conclusion

The diverse molecular weight and isoelectric point range of plant proteome will be helpful to understand their biochemical and functional aspects. The presence of selenocysteine proteins in lower eukaryotic organism is of interest and their expression in higher plant system can help us to understand their functional role.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5983-8) contains supplementary material, which is available to authorized users.

Selenium as a Protective Agent Against Pests: A Review

The aim of the present review is to summarize selenium's connection to pests. Phytopharmaceuticals for pest control, which increase the pollution in the environment, are still widely used nowadays regardless of their negative characteristics. The use of trace elements, including selenium, can be an alternative method of pest control. Selenium can repel pests, reduce their growth, or cause toxic effects while having a positive effect on the growth of plants. In conclusion, accumulated selenium protects plants against aphids, weevils, cabbage loopers, cabbage root flies, beetles, caterpillars, and crickets due to both deterrence and toxicity.

Iron-sulphur cluster biogenesis via the SUF pathway

Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.

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.

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.

NADPH-dependent and -independent disulfide reductase systems

Over the past seven decades, research on autotrophic and heterotrophic model organisms has defined how the flow of electrons ("reducing power") from high-energy inorganic sources, through biological systems, to low-energy inorganic products like water, powers all of Life's processes. Universally, an initial major biological recipient of these electrons is nicotinamide adenine dinucleotide-phosphate, which thereby transits from an oxidized state (NADP+) to a reduced state (NADPH). A portion of this reducing power is then distributed via the cellular NADPH-dependent disulfide reductase systems as sequential reductions of disulfide bonds. Along the disulfide reduction pathways, some enzymes have active sites that use the selenium-containing amino acid, selenocysteine, in place of the common but less reactive sulfur-containing cysteine. In particular, the mammalian/metazoan thioredoxin systems are usually selenium-dependent as, across metazoan phyla, most thioredoxin reductases are selenoproteins. Among the roles of the NADPH-dependent disulfide reductase systems, the most universal is that they provide the reducing power for the production of DNA precursors by ribonucleotide reductase (RNR). Some studies, however, have uncovered examples of NADPH-independent disulfide reductase systems that can also support RNR. These systems are summarized here and their implications are discussed.

SelGenAmic: An Algorithm for Selenoprotein Gene Assembly

Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active center of selenoprotein is traditionally a terminal signal of protein translation. A gene assembly algorithm SelGenAmic has been constructed and presented in this chapter for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes from these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. The method based on the SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes.

Effect of selenium on Penaeus monodon and Perna viridis: Enzyme activities and histopathological responses

The study was carried out to evaluate enzyme activities and histopathological changes due to the effect of acute and chronic definitive toxicity of selenium (Se) on the post larvae (PL) of giant tiger shrimp (Penaeus monodon), and green mussel (Perna viridis). The 96-h Median Lethal concentration (LC₅₀) for the PL of shrimp was 3.36 mg L^-1 and the chronic value for the long-term survival endpoint in a 21-d exposure was 0.10 mg L^-1. The green mussel 96-h LC₅₀ was 28.41 mg L^-1 and the chronic value for the long-term survival endpoint in a 30-d exposure was 3.06 mg L^-1. Native polyacrylamide gel electrophoresis revealed altered diverse isoforms of esterase, superoxide dismutase and malate dehydrogenase activities in the PL of shrimp and green mussel exposed to sublethal concentration of Se. Cellular anomalies such as deformation and fusion of corneal cells, detachment of corneal cells from cornea facet and increased space between ommatidia were observed in the compound eye of PL of shrimp exposed to Se for 21-d. Shrinkage and clumping of mucous gland, degenerative changes in phenol gland, and ciliated epithelium were observed in the foot of green mussel exposed to Se for 30-d. This study shows that cellular anomalies in the compound eye of PL of P. monodon and foot tissues of P. viridis described would affect the vision of shrimp and byssus thread formation in green mussel.

Promoter analysis and functional implications of the selenium binding protein (SBP) gene family in Arabidopsis thaliana

Selenium Βinding Protein (SBP, originally termed SBP56) was identified in mouse liver as a cytosolic protein that could bind radioactive selenium. SBPs are highly conserved proteins present in a wide array of species across all kingdoms and are likely to be involved in selenium metabolism. In Arabidopsis, the selenium binding protein (SBP) gene family comprises three genes (AtSBP1, AtSBP2 and AtSBP3). AtSBP1 and AtSBP2 are clustered in a head-to-tail arrangement on chromosome IV, while AtSBP3 is located on chromosome III. In this work, we studied the promoter activity of the Arabidopsis SBP genes, determined their tissue specificity and showed that they are differentially regulated by sodium selenite and sodium selenate. All three SBP genes are upregulated in response to externally applied selenium compounds and the antioxidant NAC selectively downregulates SBP2. Although the effect on SBP2 levels was the most prominent, in all cases, the concurrent exposure of plants to selenite and the antioxidant supressed the expression of the SBP genes. We provide evidence that (at least) SBP1 expression is tightly linked to detoxification processes related to oxidative stress, since it is downregulated in the presence of NAC in selenium-treated plants. Furthermore, our results suggest that SBP genes may participate in the mechanisms that sense redox imbalance.

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.

SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins

The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step. This chapter constitutes a practical guide to use SECISearch3 and Seblastian, which can be run via webservers at http://seblastian.crg.eu / or http://gladyshevlab.org/SelenoproteinPredictionServer/ .

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.

Selenocysteine tRNA[Ser]Sec, the Central Component of Selenoprotein Biosynthesis: Isolation, Identification, Modification, and Sequencing

The selenocysteine (Sec) tRNA^[Ser]Sec population consists of two isoforms that differ from each other by a single 2'-O-methylribosyl moiety at position 34 (Um34). These two isoforms, which are encoded in a single gene, Trsp, and modified posttranscriptionally, are involved individually in the synthesis of two subclasses of selenoproteins, designated housekeeping and stress-related selenoproteins. Techniques used in obtaining these isoforms for their characterization include extraction of RNA from mammalian cells and tissues, purifying the tRNA^[Ser]Sec population by one or more procedures, and finally resolving the two isoforms from each other. Since some of the older techniques for isolating tRNA^[Ser]Sec and resolving the isoforms are used in only a few laboratories, these procedures will be discussed briefly and references provided for more detailed information, while the more recently developed procedures are discussed in detail. In addition, a novel technique that was developed in sequencing tRNA^[Ser]Sec for identifying their occurrence in other organisms is also presented.

Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues

Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

The synergistic effect of Selenium (selenite, -SeO32-) dose and irradiance intensity in Chlorella cultures

Microalgae are able to metabolize inorganic selenium (Se) to organic forms (e.g. Se-proteins); nevertheless at certain Se concentration culture growth is inhibited. The aim of this work was to confirm the hypothesis that the limit of Se tolerance in Chlorella cultures is related to photosynthetic performance, i.e. depends on light intensity. We studied the relation between the dose and irradiance to find the range of Se tolerance in laboratory and outdoor cultures. At low irradiance (250 µmol photons m⁻² s⁻¹), the daily dose of Se below 8.5 mg per g of biomass (<20 µM) partially stimulated the photosynthetic activity (relative electron transport rate) and growth of Chlorella cultures (biomass density of ~1.5 g DW L⁻¹) compared to the control (no Se added). It was accompanied by substantial Se incorporation to microalgae biomass (~0.5 mg Se g⁻¹ DW). When the Se daily dose and level of irradiance were doubled (16 mg Se g⁻¹ DW; 500 µmol photons m⁻² s⁻¹), the photosynthetic activity and growth were stimulated for several days and ample incorporation of Se to biomass (7.1 mg g⁻¹ DW) was observed. Yet, the same Se daily dose under increased irradiance (750 µmol photons m⁻² s⁻¹) caused the synergistic effect manifested by significant inhibition of photosynthesis, growth and lowered Se incorporation to biomass. In the present experiments Chl fluorescence techniques were used to monitor photosynthetic activity for determination of optimal Se doses in order to achieve efficient incorporation without substantial inhibition of microalgae growth when producing Se-enriched biomass.

Assessment of toxicity of selenium and cadmium selenium quantum dots: A review

This paper reviews the current understanding of the toxicity of selenium (Se) to terrestrial mammalian and aquatic organisms. Adverse biological effects occur in the case of Se deficiencies, associated with this element having essential biological functions and a narrow window between essentiality and toxicity. Several inorganic species of Se (-2, 0, +4, and +6) and organic species (monomethylated and dimethylated) have been reported in aquatic systems. The toxicity of Se in any given sample depends not only on its speciation and concentration, but also on the concomitant presence of other compounds that may have synergistic or antagonistic effects, affecting the target organism as well, usually spanning 2 or 3 orders of magnitude for inorganic Se species. In aquatic ecosystems, indirect toxic effects, linked to the trophic transfer of excess Se, are usually of much more concern than direct Se toxicity. Studies on the toxicity of selenium nanoparticles indicate the greater toxicity of chemically generated selenium nanoparticles relative to selenium oxyanions for fish and fish embryos while oxyanions of selenium have been found to be more highly toxic to rats as compared to nano-Se. Studies on polymer coated Cd/Se quantum dots suggest significant differences in toxicity of weathered vs. non-weathered QD's as well as a significant role for cadmium with respect to toxicity.