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Utilization of selenocysteine in early-branching fungal phyla

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Abstract and Figures

Selenoproteins are a diverse group of proteins containing selenocysteine (Sec)—the twenty-first amino acid—incorporated during translation via a unique recoding mechanism 1,2 . Selenoproteins fulfil essential roles in many organisms ¹ , yet are not ubiquitous across the tree of life 3–7 . In particular, fungi were deemed devoid of selenoproteins 4,5,8 . However, we show here that Sec is utilized by nine species belonging to diverse early-branching fungal phyla, as evidenced by the genomic presence of both Sec machinery and selenoproteins. Most fungal selenoproteins lack consensus Sec recoding signals (SECIS elements ⁹ ) but exhibit other RNA structures, suggesting altered mechanisms of Sec insertion in fungi. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages. Notably, Sec was lost at the base of Dikarya, resulting in the absence of selenoproteins in Saccharomyces cerevisiae and other well-studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.
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1Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA. 2Departamento
de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay. 3Worm Biology Laboratory, Institut Pasteur de Montevideo,
Montevideo, Uruguay. 4Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology,
Barcelona, Spain. 5Universitat Pompeu Fabra, Barcelona, Spain. 6Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
Selenoproteins are a diverse group of proteins containing
selenocysteine (Sec)—the twenty-first amino acid—incorpo-
rated during translation via a unique recoding mechanism1,2.
Selenoproteins fulfil essential roles in many organisms1, yet
are not ubiquitous across the tree of life37. In particular, fungi
were deemed devoid of selenoproteins4,5,8. However, we show
here that Sec is utilized by nine species belonging to diverse
early-branching fungal phyla, as evidenced by the genomic
presence of both Sec machinery and selenoproteins. Most
fungal selenoproteins lack consensus Sec recoding signals
(SECIS elements9) but exhibit other RNA structures, suggest-
ing altered mechanisms of Sec insertion in fungi. Phylogenetic
analyses support a scenario of vertical inheritance of the Sec
trait within eukaryotes and fungi. Sec was then lost in numer-
ous independent events in various fungal lineages. Notably,
Sec was lost at the base of Dikarya, resulting in the absence
of selenoproteins in Saccharomyces cerevisiae and other well-
studied fungi. Our results indicate that, despite scattered
occurrence, selenoproteins are found in all kingdoms of life.
Selenocysteine (Sec)—the twenty-first amino acid—is co-trans-
lationally inserted via an unusual recoding mechanism, wherein
UGA (normally a stop codon) is translated as Sec1. Sec insertion
occurs specifically in selenoprotein genes, due to cis-acting RNA
structures known as SECIS elements9. Sec machinery genes (Sec
transfer RNA (tRNASec), Sec-specific eukaryotic elongation factor
(EFsec), phosphoseryl-tRNA kinase (PSTK), SECIS binding pro-
tein 2 (SBP2), Sec synthase (SecS), and selenophosphate synthe-
tase (SPS)) are trans-factors necessary and sufficient for eukaryotic
Sec synthesis and insertion1,2,10. Sec is believed to confer catalytic
advantage over cysteine (Cys, its sulphur-containing analogue) for
specific oxidoreductase functions11,12. Nevertheless, selenoproteins
are not found in all organisms. Sec usage is scattered across bac-
teria3,4,13 and archaea14. Within eukaryotes, selenoproteins are pres-
ent in most metazoans (including all vertebrates15), some protists
and certain algae4,5,16. They are absent in many insects6, few nema-
todes7, plants5 and various protists4. Notably, fungi were considered
the only kingdom of life entirely devoid of Sec4,5,8. However, here
we provide conclusive genomic evidence for Sec utilization by nine
fungal species belonging to three early-branching phyla.
We downloaded all available fungal genomes from the National
Center for Biotechnology Information (NCBI) (1,201 species;
Supplementary Table 1) and searched them for the presence of
eukaryotic Sec machinery genes (Methods) using Selenoprofiles17
and Secmarker18. These automatically generated predictions
(Supplementary Fig. 1) were analysed for two potential confounders:
the occurrence of protein families with similarity to those of inter-
est, and contaminant sequences in fungal genome assemblies.
For this, we reconstructed gene trees of candidate proteins together
with their most similar annotated sequences (Methods) and
inspected them to distinguish protein families (Supplementary Figs.
2–5). This procedure led to the dismissal of several candidates. After
filtering, Sec machinery proteins (Supplementary Data 1) localized
only in a handful of genomes, and co-occurred with tRNASec (Fig. 1).
After extensive analysis, we filtered out three species with Sec
machinery that we presumed resulted from genome contamination
from Sec-utilizing bacteria (Supplementary Note 1). In contrast, we
concluded that Bifiguratus adelaidae (Mucoromycota), Gonapodya
prolifera (Chytridiomycota), Capniomyces stellatus, Zancudomyces
culisetae, Smittium culicis, Smittium simulii, Smittium megazy-
gosporum, Smittium angustum and Furculomyces boomerangus
(Zoopagomycota) were Sec-utilizing fungi (Fig. 2). These species
formed distinct clades in three early-branching fungal phyla. The
order of Harpellales was particularly well represented: seven of the
eight species analysed had Sec.
We identified selenoproteins in all Sec-utilizing fungi
(Supplementary Data 1), which belonged to seven known seleno-
protein families (gene trees provided in Supplementary Figs. 6–10).
Two of them were found in all Sec-utilizing fungi: SelenoH (a
nuclear oxidoreductase possibly involved in redox homeostasis19)
and SPS (Fig. 3; an essential Sec machinery component4). Other
fungal selenoproteins included SelenoU (an uncharacterized oxi-
doreductase20), AhpC (alkyl hydroperoxide reductase C; found as
selenoprotein in certain bacteria, protists and porifera21), MsrA
(methionine sulfoxide reductase A; identified as selenoprotein
in algae, protists and various non-vertebrate metazoa22), DI-like
(homologous to vertebrate iodothyronine deiodinases23 and present
as selenoprotein in various invertebrates, protists and bacteria16) and
TXNRD (thioredoxin reductase; a selenoprotein present in most
Sec-utilizing eukaryotes24). Notably, this constitutes the first case of
animal-like TXNRD described in fungi, since this kingdom uses a
shorter and Sec-independent form of TXNRD24. G. prolifera was the
species with most selenoproteins, covering all selenoprotein fami-
lies discussed above. Analysis of a publicly available transcriptome
for this species confirmed the expression of all selenoprotein and
Sec machinery genes except tRNASec (Methods). Selenoprotein tran-
scripts appear to occur at high levels in G. prolifera (Supplementary
Fig. 11). SPS was particularly highly expressed, ranking in the top
1–6% transcripts (depending on the background distribution used).
We searched fungal selenoprotein genes for the occurrence of
eukaryotic SECIS elements. Surprisingly, we found canonical SECIS
Utilization of selenocysteine in early-branching
fungal phyla
MarcoMariotti 1*, GustavoSalinas2,3, ToniGabaldón4,5,6 and VadimN.Gladyshev1*
NATURE MICROBIOLOGY | VOL 4 | MAY 2019 | 759–765 | 759
Content courtesy of Springer Nature, terms of use apply. Rights reserved
... Selenoprotein biosynthetic pathways have widely been lost in evolution of the fungal kingdom, except for nine species recently discovered that have selenoprotein genes along with the biochemical pathway components required for Sec-tRNA Sec biosynthesis (Mariotti et al. 2019). Despite Saccharomyces cerevisiae lacking Sec utilizing traits, including a tRNA Sec , selenium can accumulate intracellularly at high concentrations, largely in the form of selenomethionine (SeMet) (Ponce de Leon et al. 2002). ...
... The Sec-decoding trait is found among organisms representing all three domains of life (Romero et al. 2005;Su et al. 2009), yet selenoprotein biosynthesis is notably absent in higher plants and most Fungi except for a few species among the early branching fungal phyla, including the Zoopagomycota and the Chytridiomycetes (Mariotti et al. 2019). Phylogenetic analysis suggested that the Sec trait was lost early in the evolution of the Dikarya, a fungal subkingdom that includes S. cerevisiae. ...
... Several independent components of selenoprotein biosynthesis were required to expand the genetic code of yeast with Sec. Transplanting a eukaryotic or fungal Sec biosynthetic system, such as the complete Sec system found in Bifiguratus adelaidae (Mariotti et al. 2019), would represent a fascinating experiment. Such an approach, however, would produce a yeast strain that encodes Sec at UGA codons in the appropriate sequence context of a required SECIS element. ...
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Unique chemical and physical properties are introduced by inserting selenocysteine (Sec) at specific sites within proteins. Recombinant and facile production of eukaryotic selenoproteins would benefit from a yeast expression system, however, the selenoprotein biosynthetic pathway was lost in the evolution of the kingdom Fungi as it diverged from its eukaryotic relatives. Based on our previous development of efficient selenoprotein production in bacteria, we designed a novel selenocysteine biosynthesis pathway in Saccharomyces cerevisiae using Aeromonas salmonicida translation components. S. cerevisiae tRNASer was mutated to resemble A. salmonicida tRNASec to allow recognition by S. cerevisiae seryl-tRNA synthetase as well as A. salmonicida selenocysteine synthase (SelA) and selenophosphate synthetase (SelD). Expression of these selenocysteine pathway components was then combined with metabolic engineering of yeast to enable the production of active methionine sulfate reductase enzyme containing genetically encoded selenocysteine. Our report is the first demonstration that yeast is capable of selenoprotein production by site-specific incorporation of selenocysteine.
... However, the insect pathogens (Hypocreales and Entomophthoromycotina members) tend to have genomes enriched in genes that are useful for pathogenic processes such as the platelet-activating factor acetyl-hydrolase coding genes, whereas the gut commensals have genomes enriched in cell adhesion genes for a successful gut-dwelling lifestyle [128]. In addition, Harpellales genomes also facilitated a kingdom-wide study to confirm the production of selenoproteins in early-diverging fungal lineages [138]. As a major group of early-diverging fungi, representing seven of the nine fungal species that utilize selenoproteins, Harpellales may take the advantages of selenocysteine over cysteine for specific oxidoreductase functions. ...
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The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades—primarily plant—associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
... Genes encoding selenocysteine-containing MSRA have been identified in all major kingdoms except archaea (Table 1), but they are usually restricted to a very few organisms in each kingdom [19,53,54]. On the contrary, selenocysteine-containing MSRBs are strictly restricted to the animal lineage (Table 1) but are present throughout the lineage with few exceptions like insects and nematodes [55]. ...
Methionine (Met) can be oxidized to methionine sulfoxide (MetO), which exist as R- and S-diastereomers. Present in all three domains of life, methionine sulfoxide reductases (MSR) are the enzymes that reduce MetO back to Met. Most characterized among them are MSRA and MSRB, which are strictly stereospecific for the S- and R-diastereomers of MetO, respectively. While the majority of MSRs use a catalytic Cys to reduce their substrates, some employ selenocysteine. This is the case of mammalian MSRB1, which was initially discovered as selenoprotein SELR or SELX and later was found to exhibit an MSRB activity. Genomic analyses demonstrated its occurrence in most animal lineages, and biochemical and structural analyses uncovered its catalytic mechanism. The use of transgenic mice and mammalian cell culture revealed its physiological importance in the protection against oxidative stress, maintenance of neuronal cells, cognition, cancer cell proliferation, and the immune response. Coincident with the discovery of Met oxidizing MICAL enzymes, recent findings of MSRB1 regulating the innate immunity response through reversible stereospecific Met-R-oxidation of cytoskeletal actin opened up new avenues for biological importance of MSRB1 and its role in disease. In this review, we discuss the current state of research on MSRB1, compare it with other animal Msrs, and offer a perspective on further understanding of biological functions of this selenoprotein.
... Discovery of widespread diploidy in zoosporic fungi parallels recent studies that show interpretation of fungal traits based only on analysis of Dikarya may be misleading (4,5,7,8,39). Many of these misinterpreted traits were those inherited from the Opisthokont MRCA, i.e., are plesiomorphic. ...
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Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane– and cell-wall–associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.
... Se is another interesting non-canonical trace element in biology that, although found in all three domains of life, is not universally used, occurring only in trace quantities. Given that seleno-biology has been discussed in depth in recent publications [97][98][99], will only briefly mention the most important aspects here. Se is incorporated into the traditional sulfur-amino acids cysteine and methionine instead of sulfur atoms. ...
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The relatively narrow spectrum of chemical elements within the microbial 'biochemical palate' limits the reach of biotechnology, because several added-value compounds can only be produced with traditional organic chemistry. Synthetic biology offers enabling tools to tackle this issue by facilitating 'biologization' of non-canonical chemical atoms. The interplay between xenobiology and synthetic metabolism multiplies routes for incorporating nonbiological atoms into engineered microbes. In this review, we survey natural assimilation routes for elements beyond the essential biology atoms [i.e., carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)], discussing how these mechanisms could be repurposed for biotechnology. Furthermore, we propose a computational framework to identify chemical elements amenable to biologization, ranking reactions suitable to build synthetic metabolism. When combined and deployed in robust microbial hosts, these approaches will offer sustainable alternatives for smart chemical production.
... Selenium (Se) is an essential micronutrient that mainly exists as selenocysteine (Sec) in human selenoproteins [8]. For instance, Sec is the critical catalytic residue of two selenoproteins named thioredoxin reductase (TrxR; TXNRD) and glutathione peroxidase (GPx; GPX) which protect cells from ROS-induced damage [9][10][11]. Earlier studies have shown that Se antagonizes Cd-induced liver, lung, and kidney injury in animal models and in cell cultures [12,13]. ...
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Cadmium (Cd) as a ubiquitous toxic heavy metal in the environment, causes severe hazards to human health, such as cellular stress and organ injury. Selenium (Se) was reported to reduce Cd toxicity and the mechanisms have been intensively studied so far. However, it is not yet crystal clear whether the protective effect of Se against Cd-induced cytotoxicity is related to selenoproteins in nerve cells or not. In this study, we found that Cd inhibited selenoprotein thioredoxin reductase 1 (TrxR1; TXNRD1) and decreased the expression level of TrxR1, resulting in cellular oxidative stress, and Se supplements ameliorated Cd-induced cytotoxicity in SH-SY5Y cells. Mechanistically, the detoxification of Se against Cd is attributed to the increase of the cellular TrxR activity and upregulated TrxR1 protein level, culminating in strengthened antioxidant capacity. Results showed that Se supplements attenuated the ROS production and apoptosis in SH-SY5Y cells, and significantly mitigated Cd-induced SH-SY5Y cell death. This study may be a valuable reference for shedding light on the mechanism of Cd-induced cytotoxicity and the role of TrxR1 in Se-mitigated cytotoxicity of Cd in neuroblast cells, which may be helpful for understanding the therapeutic potential of Cd and Se in treating or preventing neurodegenerative diseases, like Alzheimer’s disease (AD) and Parkinson’s disease (PD). Graphical abstract
Selenium (Se) is both a micronutrient required for most life and an element of environmental concern due to its toxicity at high concentrations, and both bioavailability and toxicity are largely influenced by the Se oxidation state. Environmentally relevant fungi have been shown to aerobically reduce Se(IV) and Se(VI), the generally more toxic and bioavailable Se forms. The goal of this study was to shed light on fungal Se(IV) reduction pathways and biotransformation products over time and fungal growth stages. Two Ascomycete fungi were grown with moderate (0.1 mM) and high (0.5 mM) Se(IV) concentrations in batch culture over 1 month. Fungal growth was measured throughout the experiments, and aqueous and biomass-associated Se was quantified and speciated using analytical geochemistry, transmission electron microscopy (TEM), and synchrotron-based X-ray absorption spectroscopy (XAS) approaches. The results show that Se transformation products were largely Se(0) nanoparticles, with a smaller proportion of volatile, methylated Se compounds and Se-containing amino acids. Interestingly, the relative proportions of these products were consistent throughout all fungal growth stages, and the products appeared stable over time even as growth and Se(IV) concentration declined. This time-series experiment showing different biotransformation products throughout the different growth phases suggests that multiple mechanisms are responsible for Se detoxification, but some of these mechanisms might be independent of Se presence and serve other cellular functions. Knowing and predicting fungal Se transformation products has important implications for environmental and biological health as well as for biotechnology applications such as bioremediation, nanobiosensors, and chemotherapeutic agents.
The selenium element is essential of some life forms and its biological-chemistry function is mainly performed by the selenol/selenolate moiety (-SeH/-Se-) in a few selenoproteins. Many synthetic organoselenium compounds (OSeCs)...
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects.
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Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment datasets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and datasets are now also available for nematodes, protists, and plants. Here we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics datasets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.
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The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include iCn3D, MutaBind, and the Antimicrobial Resistance Gene Reference Database; and resources that were updated in the past year include My Bibliography, SciENcv, the Pathogen Detection Project, Assembly, Genome, the Genome Data Viewer, BLAST and PubChem. All of these resources can be accessed through the NCBI home page at
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Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at
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Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phyloge-netic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopago-mycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopa-gomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucor-omycota comprises Glomeromycotina, Mortierellomy-cotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank ® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at © Published by Oxford University Press on behalf of Nucleic Acids Research 2017.
Progress in high-throughput sequencing and development of computational tools for identification of SECIS elements, selenoprotein genes and selenocysteine machinery allows recognition of organisms that are dependent, or not dependent, on selenium (Se) and identification of selenoproteins responsible for this trait. Full sets of selenoproteins in organisms, designated selenoproteomes, have been characterized for humans, which have 25 selenoprotein genes, as well as for most other organisms with sequenced genomes. This chapter offers an overview of eukaryotic selenoproteins at the level of individual proteins, protein families and entire selenoproteomes. Comparative genomic and ionomic analyses offer exciting avenues for studying selenoprotein function and evolution, provide insights into the biological functions of the trace element, Se, and allow addressing other important biological questions.
The essential micronutrient selenium is known to be used in a variety of biological processes in both prokaryotes and eukaryotes. The major biological form of selenium is selenocysteine, which is co-translationally inserted into selenoproteins. In the past decade, bioinformatics tools have been successfully developed to identify all, or almost all, selenoprotein genes in sequenced genomes. This chapter provides general information about currently known prokaryotic selenoprotein families and their major functions. In addition, recent comparative analyses of selenocysteine utilization and selenoproteomes across large groups of species offer important insights into evolutionary trends of different selenoprotein families and key factors that may influence selenoprotein evolution in prokaryotes.