SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.

Common modifications of selenocysteine in selenoproteins

Selenocysteine (Sec), the sulfur-to-selenium substituted variant of cysteine (Cys), is the defining entity of selenoproteins. These are naturally expressed in many diverse organisms and constitute a unique class of proteins. As a result of the physicochemical characteristics of selenium when compared with sulfur, Sec is typically more reactive than Cys while participating in similar reactions, and there are also some qualitative differences in the reactivities between the two amino acids. This minireview discusses the types of modifications of Sec in selenoproteins that have thus far been experimentally validated. These modifications include direct covalent binding through the Se atom of Sec to other chalcogen atoms (S, O and Se) as present in redox active molecular motifs, derivatization of Sec via the direct covalent binding to non-chalcogen elements (Ni, Mb, N, Au and C), and the loss of Se from Sec resulting in formation of dehydroalanine. To understand the nature of these Sec modifications is crucial for an understanding of selenoprotein reactivities in biological, physiological and pathophysiological contexts.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology

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

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.

Role of Key Micronutrients from Nutrigenetic and Nutrigenomic Perspectives in Cancer Prevention

Regarding cancer as a genetic multi-factorial disease, a number of aspects need to be investigated and analyzed in terms of cancer's predisposition, development and prognosis. One of these multi-dimensional factors, which has gained increased attention in the oncological field due to its unelucidated role in risk assessment for cancer, is diet. Moreover, as studies advance, a clearer connection between diet and the molecular alteration of patients is becoming identifiable and quantifiable, thereby replacing the old general view associating specific phenotypical changes with the differential intake of nutrients. Respectively, there are two major fields concentrated on the interrelation between genome and diet: nutrigenetics and nutrigenomics. Nutrigenetics studies the effects of nutrition at the gene level, whereas nutrigenomics studies the effect of nutrients on genome and transcriptome patterns. By precisely evaluating the interaction between the genomic profile of patients and their nutrient intake, it is possible to envision a concept of personalized medicine encompassing nutrition and health care. The list of nutrients that could have an inhibitory effect on cancer development is quite extensive, with evidence in the scientific literature. The administration of these nutrients showed significant results in vitro and in vivo regarding cancer inhibition, although more studies regarding administration in effective doses in actual patients need to be done.

Marine versus Continental Sources of Iodine and Selenium in Rainfall at Two European High-Altitude Locations

The essential elements selenium (Se) and iodine (I) are often present in low levels in terrestrial diets, leading to potential deficiencies. Marine I and Se emissions and subsequent atmospheric wet deposition has been suggested to be an important source of I and Se to soils and terrestrial food chains. However, the contribution of recycled moisture of continental origin to I and Se to precipitation has never been analyzed. Here we report concentrations and speciation of I and Se, as well as of bromine (Br), sulfur (S), and DOC-δ¹³C signatures for weekly collected precipitation samples (in the period of April 2015 to September 2016) at two high altitude sites, i.e., Jungfraujoch (JFJ; Switzerland) and Pic du Midi (PDM; France). Analysis of precipitation chemistry and moisture sources indicate combined marine and continental sources of precipitation and Se, I, Br, and S at both sites. At JFJ, concentrations of I and Se were highest when continental moisture sources were dominant, indicating important terrestrial sources for these elements. Furthermore, correlations between investigated elements and DOC-δ¹³C, particularly when continental moisture source contributions were high, indicate a link between these elements and the source of dissolved organic matter, especially for I (JFJ and PDM) and Se (JFJ).

Overexpression of Recombinant Selenoproteins in E. coli

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

Selenoprotein T is required for pathogenic bacteria avoidance in Caenorhabditis elegans

Selenoprotein T (SELENOT) is an endoplasmatic reticulum (ER)-associated redoxin that contains the amino acid selenocysteine (Sec, U) within a CXXU motif within a thioredoxin-like fold. Its precise function in multicellular organisms is not completely understood although it has been shown in mammals to be involved in Ca²⁺ homeostasis, antioxidant and neuroendocrine functions. Here, we use the model organism C. elegans to address SELENOT function in a whole organism throughout its life cycle. C. elegans possess two genes encoding SELENOT protein orthologues (SELT-1.1 and SELT-1.2), which lack Sec and contain the CXXC redox motif instead. Our results show that a Sec→Cys replacement and a gene duplication were two major evolutionary events that occurred in the nematode lineage. We find that worm SELT-1.1 localizes to the ER and is expressed in different cell types, including the nervous system. In contrast, SELT-1.2 exclusively localizes in the cytoplasm of the AWB neurons. We find that selt-1.1 and selt-1.2 single mutants as well as the double mutant are viable, but the selt-1.1 mutant is compromised under rotenone-induced oxidative stress. We demonstrate that selt-1.1, but not selt-1.2, is required for avoidance to the bacterial pathogens Serratia marcescens and Pseudomonas aeruginosa. Aversion to the noxious signal 2-nonanone is also significantly impaired in selt-1.1, but not in selt-1.2 mutant animals. Our results suggest that selt-1.1 would be a redox transducer required for nociception and optimal organismal fitness. The results highlight C. elegans as a valuable model organism to study SELENOT-dependent processes.

Selenocysteine Insertion at a Predefined UAG Codon in a Release Factor 1 (RF1)-depleted Escherichia coli Host Strain Bypasses Species Barriers in Recombinant Selenoprotein Translation

Selenoproteins contain the amino acid selenocysteine (Sec), co-translationally inserted at a predefined UGA opal codon by means of Sec-specific translation machineries. In Escherichia coli, this process is dependent upon binding of the Sec-dedicated elongation factor SelB to a Sec insertion sequence (SECIS) element in the selenoprotein-encoding mRNA and competes with UGA-directed translational termination. Here, we found that Sec can also be efficiently incorporated at a predefined UAG amber codon, thereby competing with RF1 rather than RF2. Subsequently, utilizing the RF1-depleted E. coli strain C321.ΔA, we could produce mammalian selenoprotein thioredoxin reductases with unsurpassed purity and yield. We also found that a SECIS element was no longer absolutely required in such a system. Human glutathione peroxidase 1 could thereby also be produced, and we could confirm a previously proposed catalytic tetrad in this selenoprotein. We believe that the versatility of this new UAG-directed production methodology should enable many further studies of diverse selenoproteins.

Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression

Untranslated regions (UTRs) and, to a lesser extent, coding sequences of mRNAs are involved in defining the fate of the mature transcripts through the modulation of three primary control processes, mRNA localization, degradation and translation; the action of trans-factors such as RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) combined with the presence of defined sequence and structural cis-elements ultimately determines translation levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these regions is thus of paramount importance to understand the spectrum of regulatory possibilities for any given mRNA. This tasks can now be approached computationally, to reduce the space of testable hypotheses and to drive experimental validation.This chapter focuses on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including motif search (sequence and secondary structure), prediction of regulatory networks (e.g., RBP and ncRNA binding sites), profiling of the mRNAs translational state, and other aspects of this level of gene expression regulation. Two analysis pipelines are also presented as practical examples of how the described tools could be integrated and effectively employed.

Update on selenoprotein biosynthesis

SIGNIFICANCE

Selenium is an essential trace element that is incorporated in the small but vital family of proteins, namely the selenoproteins, as the selenocysteine amino acid residue. In humans, 25 selenoprotein genes have been characterized. The most remarkable trait of selenoprotein biosynthesis is the cotranslational insertion of selenocysteine by the recoding of a UGA codon, normally decoded as a stop signal.

RECENT ADVANCES

In eukaryotes, a set of dedicated cis- and trans-acting factors have been identified as well as a variety of regulatory mechanisms, factors, or elements that control the selenoprotein expression at the level of the UGA-selenocysteine recoding process, offering a fascinating playground in the field of translational control. It appeared that the central players are two RNA molecules: the selenocysteine insertion sequence (SECIS) element within selenoprotein mRNA and the selenocysteine-tRNA([Ser]Sec); and their interacting partners.

CRITICAL ISSUES

After a couple of decades, despite many advances in the field and the discovery of many essential and regulatory components, the precise mechanism of UGA-selenocysteine recoding remains elusive and more complex than anticipated, with many layers of control. This review offers an update of selenoproteome biosynthesis and regulation in eukaryotes.

FUTURE DIRECTIONS

The regulation of selenoproteins in response to a variety of pathophysiological conditions and cellular stressors, including selenium levels, oxidative stress, replicative senescence, or cancer, awaits further detailed investigation. Clearly, the efficiency of UGA-selenocysteine recoding is the limiting stage of selenoprotein synthesis. The sequence of events leading Sec-tRNA([Ser]Sec) delivery to ribosomal A site awaits further analysis, notably at the level of a three-dimensional structure.

Evolution of the Selenoproteome in Helicobacter pylori and Epsilonproteobacteria

By competing for the acquisition of essential nutrients, Helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. Although the H. pylori genome apparently encodes selenocysteine synthase (SelA, HP1513), a key pyridoxal phosphate (PLP)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. We analyzed the evolution of the complete machinery for incorporation of selenium into proteins and the selenoproteome of several H. pylori strains and related Epsilonproteobacteria. Our searches identified the presence of selenoproteins-including the previously unknown DUF466 family-in various Epsilonproteobacteria, but not in H. pylori. We found that a complete system for selenocysteine incorporation was present in the Helicobacteriaceae ancestor and has been recently lost before the split of Helicobacter acinonychis and H. pylori. Our results indicate that H. pylori, at variance with other gastric and enterohepatic Helicobacter, does not use selenocysteine in protein synthesis and does not use selenium for tRNA wobble base modification. However, selA has survived as a functional gene, having lost the domain for the binding of selenocysteine tRNA, but maintaining the ability to bind the PLP cofactor. The evolutionary modifications described for the SelA protein of H. pylori find parallels in other bacterial and archaeal species, suggesting that an alternative enzymatic function is hidden in many proteins annotated as selenocysteinyl-tRNA synthase.

Bioaccessibility of selenium, selenomethionine and selenocysteine from foods and influence of heat processing on the same

Selenium (Se) is an essential nutrient with diverse physiological functions. The selenium content of commonly consumed cereals, pulses and green leafy vegetables (GLV) was determined. Bioaccessibility of Se, and its organic forms selenomethionine (SeMet), and selenocysteine (SeCys2) was also examined, and the effect of heat processing on the same was studied. The bioaccessibility of Se in cereals ranged from 10% to 24%, that of pulses was between 12% and 29%, and of GLV, 10-31%. The concentration of SeMet in the dialysates of the cereals, pulses and GLV ranged from 5.15 to 28.7, 2.7 to 36.2, and 0.03 to 5ngg(-1), respectively. The concentration of SeCys2 in the dialysates of the foods examined was negligible. Heat processing significantly decreased the bioaccessibility of Se, SeMet and SeCys2. This is the first report on the bioaccessibility of Se and its major organic forms from commonly consumed staples, and the effect of heat processing on the same.

Selenium cycling across soil-plant-atmosphere interfaces: a critical review

Selenium (Se) is an essential element for humans and animals, which occurs ubiquitously in the environment. It is present in trace amounts in both organic and inorganic forms in marine and freshwater systems, soils, biomass and in the atmosphere. Low Se levels in certain terrestrial environments have resulted in Se deficiency in humans, while elevated Se levels in waters and soils can be toxic and result in the death of aquatic wildlife and other animals. Human dietary Se intake is largely governed by Se concentrations in plants, which are controlled by root uptake of Se as a function of soil Se concentrations, speciation and bioavailability. In addition, plants and microorganisms can biomethylate Se, which can result in a loss of Se to the atmosphere. The mobilization of Se across soil-plant-atmosphere interfaces is thus of crucial importance for human Se status. This review gives an overview of current knowledge on Se cycling with a specific focus on soil-plant-atmosphere interfaces. Sources, speciation and mobility of Se in soils and plants will be discussed as well as Se hyperaccumulation by plants, biofortification and biomethylation. Future research on Se cycling in the environment is essential to minimize the adverse health effects associated with unsafe environmental Se levels.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.

SLC30A3 and SEP15 gene polymorphisms influence the serum concentrations of zinc and selenium in mature adults

Because of their numerous roles in several biological processes, zinc and selenium are the most commonly studied micronutrients in the elderly. Therefore, we hypothesized that the polymorphisms in the genes that are responsible for the transport of zinc and selenium may have a genotype-dependent effect on the serum concentration of these micronutrients. The objective of this study was to determine the effects of solute carrier family 30 member 3 (SLC30A3) and 15-kd selenoprotein (SEP15) polymorphisms on zinc and selenium concentrations, respectively, in the serum. This cross-sectional study included 110 individuals who were aged 50 years or older. Serum micronutrient concentrations were determined by flame atomic absorption spectrophotometry (for zinc) and by atomic absorption spectrophotometry with a graphite furnace (for selenium). The single-nucleotide polymorphisms, rs73924411 and rs11126936 of the SLC30A3 gene and rs5859, rs5854, and rs561104 of the SEP15 gene, were examined by real-time polymerase chain reaction. Regarding rs11126936, the serum zinc concentration was lower in CC homozygotes (0.75 ± 0.31 mg/L) than in A carriers (0.89 ± 0.28 mg/L, P = .016). Concerning rs561104, the serum selenium concentration was higher in CC homozygotes (5.65 ± 1.11 μg/dL) compared with T carriers (4.88 ± 1.25 μg/dL, P = .044). Our results demonstrate the influence of SLC30A3 and SEP15 gene polymorphisms on the serum concentrations of zinc and selenium, respectively. The effects of these associations should be further investigated to help elucidate the modes of action of trace elements and to identify biomarkers, which could ultimately define the optimal intake of these micronutrients at the molecular level. More research must be performed before the roles of these polymorphisms in the serum concentrations of zinc and selenium can be fully understood.

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. DOI: http://dx.doi.org/10.7554/eLife.01179.001.

SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans

SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. In addition, we annotate the homologous genes containing cysteine (Cys) instead of Sec. Finally, we have surveyed genetic variation in the annotated genes in humans. We use exon capture and resequencing approaches to identify single-nucleotide polymorphisms in more than 50 human populations around the world. We thus present a detailed view of the genetic divergence of Sec- and Cys-containing genes in animals and their diversity in humans. The addition of these datasets into the second release of the database provides a valuable resource for addressing medical and evolutionary questions in selenium biology.

A novel insight into the mechanism of mammalian selenoprotein synthesis

The amino acid selenocysteine is encoded by UGA, usually a stop codon, thus requiring a specialized machinery to enable its incorporation into selenoproteins. The machinery comprises the tRNA(Sec), a 3'-UTR mRNA stem-loop termed SElenoCysteine Insertion Sequence (SECIS), which is mandatory for recoding UGA as a Sec codon, the SECIS Binding Protein 2 (SBP2), and other proteins. Little is known about the molecular mechanism and, in particular, when, where, and how the SECIS and SBP2 contact the ribosome. Previous work by others used the isolated SECIS RNA to address this question. Here, we developed a novel approach using instead engineered minimal selenoprotein mRNAs containing SECIS elements derivatized with photoreactive groups. By cross-linking experiments in rabbit reticulocyte lysate, new information could be gained about the SBP2 and SECIS contacts with components of the translation machinery at various translation steps. In particular, we found that SBP2 was bound only to the SECIS in 48S pre-initiation and 80S pretranslocation complexes. In the complex where the Sec-tRNA(Sec) was accommodated to the A site but transpeptidation was blocked, SBP2 bound the ribosome and possibly the SECIS element as well, and the SECIS had flexible contacts with the 60S ribosomal subunit involving several ribosomal proteins. Altogether, our findings led to broadening our understanding about the unique mechanism of selenocysteine incorporation in mammals.

Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes

Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.

Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression

In the last years post-transcriptional regulation (PTR) of gene expression has been increasingly recognized to be a powerful and general determinant of the quantitative changes in proteomes, and therefore a driving force for cell phenotypes. By means of networks of trans-factors on one hand, and cis-elements found primarily in untranslated regions (UTRs) of mRNA on the other hand, mRNA availability to translation and translation rates are tightly controlled and can be rapidly tuned according to the changing state of the cell. A number of dedicated resources and tools, including databases and predictive algorithms, have been proposed as bioinformatics aids for the study of this fundamental layer of gene expression regulation. Their use, however, is rendered difficult by heterogeneity and fragmentation.   This review aims to locate these resources in their proper space, classifying them according to their goals, limitations and integration capabilities and, in the end, to provide the user with an initial toolbox for the bioinformatic analysis of post-transcriptional regulation of gene expression. The accompanying website, available at www.ptrguide.org, lists all resources, provides summary and features for each one and will be regularly updated in the future.

Encapsulated nanoepigallocatechin-3-gallate and elemental selenium nanoparticles as paradigms for nanochemoprevention

Chemoprevention that impedes one or more steps in carcinogenesis, via long-term administration of naturally occurring or synthetic compounds, is widely considered to be a crucial strategy for cancer control. Selenium (Se) has chemopreventive effects, but its application is limited due to a low therapeutic index as shown in numerous animal experiments. In contrast to Se, which was known for its toxicity prior to the discovery of its beneficial effects, the natural compound epigallocatechin-3-gallate (EGCG) was originally considered to be nontoxic. Due to its preventive effects on many types of cancer in various animal models, EGCG has been regarded as a prime example of a promising chemopreventive agent without major toxicity concerns. However, very recently, evidence has accumulated showing that efficacious doses of EGCG used in health promotion may not be far from its toxic dose level. Therefore, both Se and EGCG need to be modified by novel pharmaceutical technologies to attain enhanced efficacy and/or reduced toxicity. Nanotechnology may be one of these technologies. In support of this hypothesis, the characteristics of polylactic acid and polyethylene glycol-encapsulated nano-EGCG and elemental Se nanoparticles dispersed by bovine serum albumin are reviewed in this article. Encapsulation of EGCG to form nano-EGCG leads to its enhanced stability in plasma and remarkably superior chemopreventive effects, with more than tenfold dose advantages in inducing apoptosis and inhibition of both angiogenesis and tumor growth. Se at nanoparticle size (“Nano-Se”), compared with Se compounds commonly used in dietary supplements, has significantly lower toxicity, without compromising its ability to upregulate selenoenzymes at nutritional levels and induce phase II enzymes at supranutritional levels.

Gene prediction

Evolutionary genomics is a field that relies heavily upon comparing genomes, that is, the full complement of genes of one species with another. However, given a genome sequence and little else, as is now often the case, genes must first be found and annotated before downstream analyses can be done. Computational gene prediction techniques are brought to bear on the problem of constructing a genome annotation as manual annotation is extremely time-consuming and costly. This chapter reviews the methods by which the individual components of a typical gene structure are detected in genomic sequence and then discusses several popular statistical frameworks for integrated gene prediction on eukaryotic genome sequences.

Nutrigenetics, nutrigenomics, and selenium

Selenium (Se) is an important micronutrient that, as a component of selenoproteins, influences oxidative and inflammatory processes. Its’ levels vary considerably, with different ethnic and geographic population groups showing varied conditions, ranging from frank Se deficiencies to toxic effects. An optimum Se level is essential for the maintenance of homeostasis, and this optimum may vary according to life stage, general state of health, and genotype. Nutrigenetic studies of different Se levels, in the presence of genetic variants in selenoproteins, suggest that an effective dietary Se intake for one individual may be very different from that for others. However, we are just starting to learn the significance of various genes in selenoprotein pathways, functional variants in these, and how to combine such data from genes into pathways, alongside dietary intake or serum levels of Se. Advances in systems biology, genetics, and genomics technologies, including genetic/genomic, epigenetic/epigenomic, transcriptomic, proteomic, and metabolomic information, start to make it feasible to assess a comprehensive spectrum of the biological activity of Se. Such nutrigenomic approaches may prove very sensitive biomarkers of optimal Se status at the individual or population level. The premature cessation of a major human Se intervention trial has led to considerable controversy as to the value of Se supplementation at the population level. New websites provide convenient links to current information on methodologies available for nutrigenetics and nutrigenomics. These new technologies will increasingly become an essential tool in optimizing the level of Se and other micronutrients for optimal health, in individuals and in population groups. However, definitive proof of such effects will require very large collaborative studies, international agreement on study design, and innovative approaches to data analysis.

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes. Optimum micronutrient supply is important for the maintenance of homeostasis in metabolism and, ultimately, for maintaining good health. With advances in systems biology and genomics technologies, it is becoming feasible to assess the activity of single and multiple micronutrients in their complete biological context. Existing research collects fragments of information, which are not stored systematically and are thus not optimally disseminated. The Micronutrient Genomics Project (MGP) was established as a community-driven project to facilitate the development of systematic capture, storage, management, analyses, and dissemination of data and knowledge generated by biological studies focused on micronutrient–genome interactions. Specifically, the MGP creates a public portal and open-source bioinformatics toolbox for all “omics” information and evaluation of micronutrient and health studies. The core of the project focuses on access to, and visualization of, genetic/genomic, transcriptomic, proteomic and metabolomic information related to micronutrients. For each micronutrient, an expert group is or will be established combining the various relevant areas (including genetics, nutrition, biochemistry, and epidemiology). Each expert group will (1) collect all available knowledge, (2) collaborate with bioinformatics teams towards constructing the pathways and biological networks, and (3) publish their findings on a regular basis. The project is coordinated in a transparent manner, regular meetings are organized and dissemination is arranged through tools, a toolbox web portal, a communications website and dedicated publications.

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes

Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases.

Results: We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queries to scan genomic sequences. Results of the scan are processed through a number of steps, to produce highly accurate predictions of selenoprotein genes with little or no human intervention. Selenoprofiles is a valuable tool for bioinformatic characterization of eukaryotic selenoproteomes, and can complement genome annotation pipelines.

Availability and Implementation: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. The program is available at http://big.crg.cat/services/selenoprofiles. The predictions presented in this article are available through DAS at http://genome.crg.cat:9000/das/Selenoprofiles_ensembl.

Contact:marco.mariotti@crg.es

Supplementary information:Supplementary data are available at Bioinformatics online.

Selenium bioavailability: current knowledge and future research requirements

Information on selenium bioavailability is required to derive dietary recommendations and to evaluate and improve the quality of food products. The need for robust data is particularly important in light of recent suggestions of potential health benefits associated with different intakes of selenium. The issue is not straightforward, however, because of large variations in the selenium content of foods (determined by a combination of geologic/environmental factors and selenium supplementation of fertilizers and animal feedstuffs) and the chemical forms of the element, which are absorbed and metabolized differently. Although most dietary selenium is absorbed efficiently, the retention of organic forms is higher than that of inorganic forms. There are also complications in the assessment and quantification of selenium species within foodstuffs. Often, extraction is only partial, and the process can alter the form or forms present in the food. Efforts to improve, standardize, and make more widely available techniques for species quantification are required. Similarly, reliable and sensitive functional biomarkers of selenium status are required, together with improvements in current biomarker methods. This requirement is particularly important for the assessment of bioavailability, because some functional biomarkers respond differently to the various selenium species. The effect of genotype adds a potential further dimension to the process of deriving bioavailability estimates and underlines the need for further research to facilitate the process of deriving dietary recommendations in the future.

dbTEU: a protein database of trace element utilization

Biological trace elements are required for numerous biological processes and by all organisms. We describe a database, dbTEU (DataBase of Trace Element Utilization), that features known transporters and user proteins for five trace elements (copper, molybdenum, nickel, cobalt and selenium) and represents sequenced organisms from the three domains of life. The manually curated dbTEU currently includes approximately 16,500 proteins from >700 organisms, and offers interactive trace element, protein, organism and sequence search and browse tools.

AVAILABILITY AND IMPLEMENTATION

dbTEU is freely available at http://gladyshevlab.bwh.harvard.edu/trace_element/

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine

The selenocysteine insertion sequence (SECIS) element directs the translational recoding of UGA as selenocysteine. In eukaryotes, the SECIS is located downstream of the UGA codon in the 3'-UTR of the selenoprotein mRNA. Despite poor sequence conservation, all SECIS elements form a similar stem-loop structure containing a putative kink-turn motif. We functionally characterized the 26 SECIS elements encoded in the human genome. Surprisingly, the SECIS elements displayed a wide range of UGA recoding activities, spanning several 1000-fold in vivo and several 100-fold in vitro. The difference in activity between a representative strong and weak SECIS element was not explained by differential binding affinity of SECIS binding Protein 2, a limiting factor for selenocysteine incorporation. Using chimeric SECIS molecules, we identified the internal loop and helix 2, which flank the kink-turn motif, as critical determinants of UGA recoding activity. The simultaneous presence of a GC base pair in helix 2 and a U in the 5'-side of the internal loop was a statistically significant predictor of weak recoding activity. Thus, the SECIS contains intrinsic information that modulates selenocysteine incorporation efficiency.

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees

Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive N. ceranae proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in E. cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee–Nosema interactions.

Honey bee colonies are in decline in many parts of the world, in part due to pressures from a diverse assemblage of parasites and pathogens. The range and prevalence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we describe the N. ceranae genome, presenting genome traits, gene models and regulatory motifs. N. ceranae has an extremely reduced and AT-biased genome, yet one with substantial numbers of repetitive elements. We identify novel genes that appear to be conserved among microsporidia but undetected outside this phylum, which are of special interest as potential virulence factors for these obligate pathogens. A previously unrecognized motif is found upstream of many start codons and likely plays a role in gene regulation across the microsporidia. These and other comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and provide the first genetic tools for understanding how this pathogen interacts with honey bee hosts.

Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins

Selenocysteine (Sec), the 21st amino acid, is incorporated into proteins through the recoding of a termination codon, an inefficient translational process mediated by a complex molecular machinery. Sec is a rare amino acid in extant proteins, chemically similar to cysteine (Cys), found in homologous position to Cys of nonselenoprotein families. Selenoproteins account for the dependence of vertebrates on environmental selenium (Se) and have an important role in several Se-deficiency diseases. Selenoproteins are poorly characterized enzymes and reports on the functional exchangeability of Sec with Cys are limited and controversial. Whether the unique role of Sec in some selenoenzymes illustrates the broader contribution of Se to protein function is unknown (Gromer S, Johansson L, Bauer H, Arscott LD, Rauch S, Ballou DP, Williams CH Jr, Schirmer RH, Arnér ES. 2003. Active sites of thioredoxin reductases: why selenoproteins? Proc Natl Acad Sci USA. 100:12618-12623). Here, we address this question from an evolutionary perspective by the simultaneous identification of the patterns of divergence in almost half a billion years of vertebrate evolution and diversity within the human lineage for the full complement of enzymatic Sec residues in these proteomes. We complete this analysis with data for the homologous Cys residues in the same genomes. Our results indicate concerted purifying selection across Sec and Cys sites in all selenoproteomes, consistent with a unique role of Sec in protein function, low exchangeability, and an unknown degree of functional divergence with Cys homologs. The distinct biochemical properties of Sec, rather than the geographical distribution of Se, global O(2) levels or Sec metabolic cost, appear to play a major role in driving adaptive changes in vertebrate selenoproteomes. A better understanding of the selenoproteomes and neutral evolutionary patterns in other taxa will be necessary to fully assess the generality of this conclusion.

The selenium to selenoprotein pathway in eukaryotes: more molecular partners than anticipated

The amino acid selenocysteine (Sec) is the major biological form of the trace element selenium. Sec is co-translationally incorporated in selenoproteins. There are 25 selenoprotein genes in humans, and Sec was found in the active site of those that have been attributed a function. This review will discuss how selenocysteine is synthesized and incorporated into selenoproteins in eukaryotes. Sec biosynthesis from serine on the tRNA(Sec) requires four enzymes. Incorporation of Sec in response to an in-frame UGA codon, otherwise signaling termination of translation, is achieved by a complex recoding machinery to inform the ribosomes not to stop at this position on the mRNA. A number of the molecular partners acting in this machinery have been identified but their detailed mechanism of action has not been deciphered yet. Here we provide an overview of the literature in the field. Particularly striking is the higher than originally envisaged number of factors necessary to synthesize Sec and selenoproteins. Clearly, selenoprotein synthesis is an exciting and very active field of research.