Selenocysteine: the 21st amino acid

Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation

The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.

Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges

The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.

Bacterial selenocysteine synthase structure revealed by single-particle cryoEM

The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNASec). In bacteria, Sec is synthesized from Ser-tRNA[Ser]Sec by Selenocysteine Synthase (SelA), which is a pivotal enzyme in the biosynthesis of Sec. The structural characterization of bacterial SelA is of paramount importance to decipher its catalytic mechanism and its role in the regulation of the Sec-synthesis pathway. Here, we present a comprehensive single-particle cryo-electron microscopy (SPA cryoEM) structure of the bacterial SelA with an overall resolution of 2.69 Å. Using recombinant Escherichia coli SelA, we purified and prepared samples for single-particle cryoEM. The structural insights from SelA, combined with previous in vivo and in vitro knowledge, underscore the indispensable role of decamerization in SelA's function. Moreover, our structural analysis corroborates previous results that show that SelA adopts a pentamer of dimers configuration, and the active site architecture, substrate binding pocket, and key K295 catalytic residue are identified and described in detail. The differences in protein architecture and substrate coordination between the bacterial enzyme and its counterparts offer compelling structural evidence supporting the independent molecular evolution of the bacterial and archaea/eukarya Ser-Sec biosynthesis present in the natural world.

Enhanced Induction of Apoptosis and Cell Cycle Arrest in MCF-7 Breast Cancer and HT-29 Colon Cancer Cell Lines via Low-Dose Biosynthesis of Selenium Nanoparticles Utilizing Lactobacillus casei

As a leading global cause of mortality, cancer continues to pose a significant challenge. The shortcomings of prevalent cancer treatments, such as surgery, radiation therapy, and chemotherapy, necessitate the exploration of alternative therapeutic strategies. Selenium nanoparticles (SeNPs) have emerged as a promising solution, with their synthesis being widely researched due to their potential applications. Among the diverse synthesis methods for SeNPs, the green chemistry approach holds a distinctive position within nanotechnology. This research delves into the anti-proliferative and anticancer properties of green-synthesized SeNPs via the cell-free supernatant (CFS) of Lactobacillus casei (LC-SeNPs), with a specific focus on MCF-7 and HT-29 cancer cell lines. SeNPs were synthesized employing the supernatant of L. casei. The characterization of these green-synthesized SeNPs was performed using TEM, FE-SEM, XRD, FT-IR, UV-vis, energy-dispersive X-ray spectroscopy, and DLS. The biological impact of LC-SNPs on MCF-7 and HT-29 cancer cells was examined via MTT, flow cytometry, scratch tests, and qRT-PCR. Both FE-SEM and TEM images substantiated the spherical shape of the synthesized nanoparticles. The biosynthesized LC-SNPs reduced the survival of MCF-7 (by 20%) and HT-29 (by 30%) cells at a concentration of 100 μg/mL. Flow cytometry revealed that LC-SNPs were capable of inducing 28% and 23% apoptosis in MCF-7 and HT-29 cells, respectively. In addition, it was found that LC-SNPs treated MCF-7 and HT-29 cells were arrested in the sub-G1 phase. Gene expression analysis indicated that the expression levels of the CASP3, CASP9, and BAX genes were elevated after treating MCF-7 and HT-29 cells with LC-SNPs. Further, SeNPs were observed to inhibit migration and invasion of MCF-7 and HT-29 cancer cells. The SeNPs, produced via L. casei, demonstrated strong anticancer effects on MCF-7 and HT-29 cells, suggesting their potential as biological agents in cancer treatment following additional in vivo experiments.

iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation

The incorporation of non-canonical amino acids (ncAAs) into proteins is a powerful technique used in various research fields. Genetic code expansion (GCE) is the most common way to achieve this: a specific codon is selected to be decoded by a dedicated tRNA orthogonal to the endogenous ones. In the past 30 years, great progress has been made to obtain novel tRNA synthetases (aaRSs) accepting a variety of ncAAs with distinct physicochemical properties, to develop robust in vitro assays or approaches for codon reassignment. This sparked the use of the technique, leading to the accumulation of publications, from which gathering all relevant information can appear daunting. Here we present iNClusive (https://non-canonical-aas.biologie.uni-freiburg.de/), a manually curated, extensive repository using standardized nomenclature that provides organized information on ncAAs successfully incorporated into target proteins as verified by mass spectrometry. Since we focused on tRNA synthetase-based tRNA loading, we provide the sequence of the tRNA and aaRS used for the incorporation. Derived from more than 687 peer-reviewed publications, it currently contains 2432 entries about 466 ncAAs, 569 protein targets, 500 aaRSs and 144 tRNAs. We foresee iNClusive will encourage more researchers to experiment with ncAA incorporation thus contributing to the further development of this exciting technique.

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis

Analyses of microbial genomes have revealed unexpectedly wide distributions of enzymes from specialized metabolism, including methanogenesis, providing exciting opportunities for discovery. Here, we identify a family of gene clusters (the type 1 mlp gene clusters (MGCs)) that encodes homologs of the soluble coenzyme M methyltransferases (SCMTs) involved in methylotrophic methanogenesis and is widespread in bacteria and archaea. Type 1 MGCs are expressed and regulated in medically, environmentally, and industrially important organisms, making them likely to be physiologically relevant. Enzyme annotation, analysis of genomic context, and biochemical experiments suggests these gene clusters play a role in methyl-sulfur and/or methyl-selenide metabolism in numerous anoxic environments, including the human gut microbiome, potentially impacting sulfur and selenium cycling in diverse, anoxic environments.

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.

Selenium vitaminology: The connection between selenium, vitamin C, vitamin E, and ergothioneine

Selenium is connected to three small molecule antioxidant compounds, ascorbate, α-tocopherol, and ergothioneine. Ascorbate and α-tocopherol are true vitamins, while ergothioneine is a "vitamin-like" compound. Here we review how selenium is connected to all three. Selenium and vitamin E work together as a team to prevent lipid peroxidation. Vitamin E quenches lipid hydroperoxyl radicals and the resulting lipid hydroperoxide is then converted to the lipid alcohol by selenocysteine-containing glutathione peroxidase. Ascorbate reduces the resulting α-tocopheroxyl radical in this reaction back to α-tocopherol with concomitant production of the ascorbyl radical. The ascorbyl radical can be reduced back to ascorbate by selenocysteine-containing thioredoxin reductase. Ergothioneine and ascorbate are both water soluble, small molecule reductants that can reduce free radicals and redox-active metals. Thioredoxin reductase can reduce oxidized forms of ergothioneine. While the biological significance of this is not yet realized, this discovery underscores the centrality of selenium to all three antioxidants.

Biological and Catalytic Properties of Selenoproteins

Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium-carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions.

Peptide Selenocysteine Substitutions Reveal Direct Substrate-Enzyme Interactions at Auxiliary Clusters in Radical S-Adenosyl-l-methionine Maturases

Radical S-adenosyl-l-methionine (SAM) enzymes leverage the properties of one or more iron- and sulfide-containing metallocenters to catalyze complex and radical-mediated transformations. By far the most populous superfamily of radical SAM enzymes are those that, in addition to a 4Fe-4S cluster that binds and activates the SAM cofactor, also bind one or more additional auxiliary clusters (ACs) of largely unknown catalytic significance. In this report we examine the role of ACs in two RS enzymes, PapB and Tte1186, that catalyze formation of thioether cross-links in ribosomally synthesized and post-translationally modified peptides (RiPPs). Both enzymes catalyze a sulfur-to-carbon cross-link in a reaction that entails H atom transfer from an unactivated C-H to initiate catalysis, followed by formation of a C-S bond to yield the thioether. We show that both enzymes tolerate substitution of SeCys instead of Cys at the cross-linking site, allowing the systems to be subjected to Se K-edge X-ray spectroscopy. The EXAFS data show a direct interaction with the Fe of one of the ACs in the Michaelis complex, which is replaced with a Se-C interaction under reducing conditions that lead to the product complex. Site-directed deletion of the clusters in Tte1186 provide evidence for the identity of the AC. The implications of these observations in the context of the mechanism of these thioether cross-linking enzymes are discussed.

Introduction of Methyl Group in Substituted Isoselenazolones: Catalytic and Mechanistic Study

Copper-catalyzed direct selenation of substituted 2-bromo-N-phenylbenzamide substrates with elemental selenium powder provided a series of methoxy-substituted isoselenazolones via the C-Se and Se-N bond formations. Phenolic substituted isoselenazolones have been obtained by O-demethylation of the corresponding methoxy-substituted analogues using boron tribromide. Some isoselenazolones have been structurally characterized by X-ray single-crystal analysis. The glutathione peroxidase (GPx)-like antioxidant activity of isoselenazolones has been evaluated both in thiophenol and coupled-reductase assays. All isoselenazolones showed good GPx-like activities in the coupled-reductase assay. The ferric-reducing antioxidant power of phenolic antioxidants has also been evaluated. The best phenolic antioxidants were found to be good ferric-reducing antioxidant power agents. The single electron transfer, hydrogen atom transfer, and proton-coupled electron transfer mechanisms for the antioxidant properties of all catalysts have been supported by density functional theory calculations. The catalytic cycle was proposed for one of the phenolic isoselenazolones involving diselenide, selenenyl sulfide, selenol, and selenenic acid as intermediates using ⁷⁷Se{¹H} NMR spectroscopy.

Synthesis, Reactions, and Antioxidant Properties of Bis(3-amino-1-hydroxybenzyl)diselenide

Bis(3-amino-1-hydroxybenzyl)diselenide containing two ortho groups was synthesized from 7-nitro-3H-2,1-benzoxaselenole and in situ generated sodium benzene tellurolate (PhTeNa). One-pot synthesis of 1,3-benzoselenazoles was achieved from bis(3-amino-1-hydroxybenzyl)diselenide and aryl aldehydes using acetic acid as a catalyst. The X-ray crystal structure of chloro-substituted benzoselenazole revealed a planar structure with T-shaped geometry around the Se atom. Both natural bond orbital and atoms in molecules calculations confirmed the presence of secondary Se···H interactions in bis(3-amino-1-hydroxybenzyl)diselenide and Se···O interactions in benzoselenazoles, respectively. The glutathione peroxidase (GPx)-like antioxidant activities of all compounds were evaluated using a thiophenol assay. Bis(3-amino-1-hydroxybenzyl)diselenide and benzoselenazoles showed better GPx-like activity compared to that of the diphenyl diselenide and ebselen, used as references, respectively. Based on ⁷⁷Se{¹H} NMR spectroscopy, a catalytic cycle for bis(3-amino-1-hydroxybenzyl)diselenide using thiophenol and hydrogen peroxide was proposed involving selenol, selenosulfide, and selenenic acid as intermediates. The potency of all GPx mimics was confirmed by their in vitro antibacterial properties against the biofilm formation of Bacillus subtilis and Pseudomonas aeruginosa. Additionally, molecular docking studies were used to evaluate the in silico interactions between the active sites of the TsaA and LasR-based proteins found in Bacillus subtilis and Pseudomonas aeruginosa.

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.

Exploring nanoselenium to tackle mutated SARS-CoV-2 for efficient COVID-19 management

Despite ongoing public health measures and increasing vaccination rates, deaths and disease severity caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its new emergent variants continue to threaten the health of people around the world. Therefore, there is an urgent need to develop novel strategies for research, diagnosis, treatment, and government policies to combat the variant strains of SARS-CoV-2. Since the state-of-the-art COVID-19 pandemic, the role of selenium in dealing with COVID-19 disease has been widely discussed due to its importance as an essential micronutrient. This review aims at providing all antiviral activities of nanoselenium (Nano-Se) ever explored using different methods in the literature. We systematically summarize the studied antiviral activities of Nano-Se required to project it as an efficient antiviral system as a function of shape, size, and synthesis method. The outcomes of this article not only introduce Nano-Se to the scientific community but also motivate scholars to adopt Nano-Se to tackle any serious virus such as mutated SARS-CoV-2 to achieve an effective antiviral activity in a desired manner.

Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags

Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

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

Nonsense Mutations in Eukaryotes

Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.

Tellurite and Selenite: how can these two oxyanions be chemically different yet so similar in the way they are transformed to their metal forms by bacteria?

This opinion review explores the microbiology of tellurite, TeO₃²⁻ and selenite, SeO₃²⁻ oxyanions, two similar Group 16 chalcogen elements, but with slightly different physicochemical properties that lead to intriguing biological differences. Selenium, Se, is a required trace element compared to tellurium, Te, which is not. Here, the challenges around understanding the uptake transport mechanisms of these anions, as reflected in the model organisms used by different groups, are described. This leads to a discussion around how these oxyanions are subsequently reduced to nanomaterials, which mechanistically, has controversies between ideas around the molecule chemistry, chemical reactions involving reduced glutathione and reactive oxygen species (ROS) production along with the bioenergetics at the membrane versus the cytoplasm. Of particular interest is the linkage of glutathione and thioredoxin chemistry from the cytoplasm through the membrane electron transport chain (ETC) system/quinones to the periplasm. Throughout the opinion review we identify open and unanswered questions about the microbial physiology under selenite and tellurite exposure. Thus, demonstrating how far we have come, yet the exciting research directions that are still possible. The review is written in a conversational manner from three long-term researchers in the field, through which to play homage to the late Professor Claudio Vásquez.

A paean to the ineffable Marjory Stephenson

It is now 75 years since Marjory Stephenson became the second President of the Society for General Microbiology (SGM). Around the time of her death at the end of 1948 many articles appeared extolling Marjory Stephenson’s contribution to the fields of Biochemistry and Microbiology. Not that much has been written about her since that time, which is unfortunate. Therefore, this brief review is intended as a form of redress and aims to highlight the role of this remarkable scientist in establishing the Society and in promoting Microbiology as a discipline. Notwithstanding the significance of these achievements, however, it is her overall impact on the field of ‘Chemical Microbiology’ and what she achieved through her research that are extraordinary, even by today’s standards. Marjory Stephenson recognized that in order to understand a biological system, the ‘whole’ organism must be considered and this can only be achieved by adopting an interdisciplinary approach: inorganic and organic chemistry, biochemistry, genetics, metabolism and ultimately physiology. Her scientific ethos serves today as a beacon for how scientific research should be conducted, and what we as scientists can learn about how to inspire and mentor the next generation. It is impossible to overstate Marjory Stephenson’s scientific legacy, or her overall contribution to Microbiology.

One-Pot Chemical Protein Synthesis Utilizing Fmoc-Masked Selenazolidine to Address the Redox Functionality of Human Selenoprotein F

Human SELENOF is an endoplasmic reticulum (ER) selenoprotein that contains the redox active motif CXU (C is cysteine and U is selenocysteine), resembling the redox motif of thiol-disulfide oxidoreductases (CXXC). Like other selenoproteins, the challenge in accessing SELENOF has somewhat limited its full biological characterization thus far. Here we present the one-pot chemical synthesis of the thioredoxin-like domain of SELENOF, highlighted by the use of Fmoc-protected selenazolidine, native chemical ligations and deselenization reactions. The redox potential of the CXU motif, together with insulin turbidimetric assay suggested that SELENOF may catalyze the reduction of disulfides in misfolded proteins. Furthermore, we demonstrate that SELENOF is not a protein disulfide isomerase (PDI)-like enzyme, as it did not enhance the folding of the two protein models; bovine pancreatic trypsin inhibitor and hirudin. These studies suggest that SELENOF may be responsible for reducing the non-native disulfide bonds of misfolded glycoproteins as part of the quality control system in the ER.

Commentary on "Comparison of the chemical properties of selenocysteine and selenocystine with their sulfur analogs"

Selenium was initially considered a toxic element found in plants growing in soils rich in this element. However, a few years later, selenocysteine was recognized as the 21st amino acid. Huber and Criddle's article has been crucial in discovering selenium-containing proteins and other related works on selenocysteine.

Diselenide-selenoester ligation in the chemical synthesis of proteins

Peptides and proteins represent an important class of biomolecules responsible for a plethora of structural and functional roles in vivo. Following their translation on the ribosome, the majority of eukaryotic proteins are post-translationally modified, leading to a proteome that is much larger than the number of genes present in a given organism. In order to understand the functional role of a given protein modification, it is necessary to access peptides and proteins bearing homogeneous and site-specific modifications. Accordingly, there has been significant research effort centered on the development of peptide ligation methodologies for the chemical synthesis of modified proteins. In this chapter we outline the discovery and development of a contemporary methodology called the diselenide-selenoester ligation (DSL) that enables the rapid and efficient fusion of peptide fragments to generate synthetic proteins. The practical aspects of using DSL for the preparation of chemically modified peptides and proteins in the laboratory is described. In addition, recent advances in the application of the methodology are outlined, exemplified by the synthesis and biological evaluation of a number of complex protein targets.

An accelerated and optimized algorithm of selenium-encoded isotopic signature targeted profiling for global selenoproteome analysis

Selenoproteins play crucial roles including protection and recovery from oxidative stress in organisms. Direct profiling of selenoproteins in proteomes is challenging due to their extremely low abundance. We have developed a computational algorithm termed selenium-encoded isotopic signature targeted profiling (SESTAR) to increase the sensitivity of detecting selenoproteins in complex proteomic samples. In this chapter, we briefly described the basic algorithm of SESTAR. We then introduced SESTAR++, an updated version of SESTAR, with accelerated computation speed and lowered false positive rate. We also provided a detailed workflow to apply SESTAR++ to proteomic profiling of selenoproteins, including the instruction of running the software and implementing it in a targeted profiling mode.

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

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

Reprogramming the Biosynthesis of Precursor Peptide to Create a Selenazole-Containing Nosiheptide Analogue

Nosiheptide (NOS), a potent bactericidal thiopeptide, belongs to a class of natural products produced by ribosomal synthesis and post-translational modifications, and its biosynthetic pathway has largely been elucidated. However, the central trithiazolylpyridine structure of NOS remains inaccessible to structural changes. Here we report the creation of a NOS analogue containing a unique selenazole ring by the construction of an artificial system in Streptomyces actuosus ATCC25421, where the genes responsible for the biosynthesis of selenoprotein from Escherichia coli and the biosynthetic gene cluster of NOS were rationally integrated to produce a selenazole-containing analogue of NOS. The thiazole at the fifth position in NOS was specifically replaced by a selenazole to afford the first selenazole-containing "unnatural" natural product. The present strategy is useful for structural manipulation of various RiPP natural products.

Functions and Regulation of Translation Elongation Factors

Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA₂-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.

Group 6 transition metal-based molecular complexes for sustainable catalytic CO2 activation

CO2 activation is one of the key steps towards CO2 mitigation. In this context, the group 6 transition metal-based molecular catalysts can lead the way.

Selenium Metabolism and Biosynthesis of Selenoproteins in the Human Body

As an essential trace element, selenium (Se) plays a tremendous role in the functioning of the human organism being used for the biosynthesis of selenoproteins (proteins containing one or several selenocysteine residues). The functions of human selenoproteins in vivo are extremely diverse. Many selenoproteins have an antioxidant activity and, hence, play a key role in cell antioxidant defense and maintenance of redox homeostasis, which accounts for their involvement in diverse biological processes, such as signal transduction, proliferation, cell transformation and aging, ferroptosis, immune system functioning, etc. One of the critical functions of selenoenzymes is participation in the synthesis of thyroid hormones regulating basal metabolism in all body tissues. Over the last decades, optimization of population Se intake for prevention of diseases related to Se deficiency or excess has been recognized as a pressing issue in modern healthcare worldwide.

Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications

Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.

Genetic Code Expansion System for Tight Control of Gene Expression in Bombyx mori Cell Lines

Simple Summary

Bombyx mori is a lepidopteran insect with economic value. Its genetic background is clear, and genome sequence is relatively complete, but the function of many genes has not been determined. The genetic code expansion system has become an important means of gene function research. In this study, a genetic code expansion system suitable for B. mori cells was established. This system included a modified tRNA^Pyl/Pyrrolysyl-tRNA synthetase (PylRS) pair from Methanosarcina mazei, the reporter gene D[TAG]G formed by DsRed and EGFP through amber stop codon TAG connection and the unnatural amino acid H-Lys(Boc)-OH. In silkworm BmE and BmNs cell lines, the reporter gene expression was strictly controlled by H-Lys(Boc)-OH in the presence of both PylRS and tRNA^Pyl. The silkworm genetic code expansion system established here is another useful controllable gene expression system besides tetracycline induced expression system.

Abstract

Inducible gene expression systems are important tools for studying gene function and to control protein synthesis. With the completion of the detailed map of the silkworm (Bombyx mori) genome, the study of Bombyx mori has entered the post-genome era. While the functions of many genes have been described in detail, many coding genes remain unidentified. Except for the available tetracycline induction system, there is currently a dearth of other effective induction systems for B. mori. A genetic code expansion system can be used for protein labeling and to regulate gene expression. Here, we have established a genetic code expansion system for B. mori based on the well-researched tRNA^Pyl/PylRS pair from Methanosarcina mazei. We used H-Lys(Boc)-OH, which is a lysine derivative to efficiently and tightly control the expression of the reporter gene DsRed[TAG]EGFP (D[TAG]G), which encoded a H-Lys(Boc)-OH-bearing protein fused with DsRed and EGFP (here regarded as D[Boc]G) in B. mori cell lines BmE and BmNs. In D[TAG]G, the amber stop codon is recognized as the orthogonal tRNA^Pyl. Successful application of genetic code expansion system in silkworm cell lines will support the research into the function of silkworm genes and paves the way for the identification of new genes and protein markers in silkworm.

Macrophage Selenoproteins Restrict Intracellular Replication of Francisella tularensis and Are Essential for Host Immunity

The essential micronutrient Selenium (Se) is co-translationally incorporated as selenocysteine into proteins. Selenoproteins contain one or more selenocysteines and are vital for optimum immunity. Interestingly, many pathogenic bacteria utilize Se for various biological processes suggesting that Se may play a role in bacterial pathogenesis. A previous study had speculated that Francisella tularensis, a facultative intracellular bacterium and the causative agent of tularemia, sequesters Se by upregulating Se-metabolism genes in type II alveolar epithelial cells. Therefore, we investigated the contribution of host vs. pathogen-associated selenoproteins in bacterial disease using F. tularensis as a model organism. We found that F. tularensis was devoid of any Se utilization traits, neither incorporated elemental Se, nor exhibited Se-dependent growth. However, 100% of Se-deficient mice (0.01 ppm Se), which express low levels of selenoproteins, succumbed to F. tularensis-live vaccine strain pulmonary challenge, whereas 50% of mice on Se-supplemented (0.4 ppm Se) and 25% of mice on Se-adequate (0.1 ppm Se) diet succumbed to infection. Median survival time for Se-deficient mice was 8 days post-infection while Se-supplemented and -adequate mice was 11.5 and >14 days post-infection, respectively. Se-deficient macrophages permitted significantly higher intracellular bacterial replication than Se-supplemented macrophages ex vivo, corroborating in vivo observations. Since Francisella replicates in alveolar macrophages during the acute phase of pneumonic infection, we hypothesized that macrophage-specific host selenoproteins may restrict replication and systemic spread of bacteria. F. tularensis infection led to an increased expression of several macrophage selenoproteins, suggesting their key role in limiting bacterial replication. Upon challenge with F. tularensis, mice lacking selenoproteins in macrophages (TrspM) displayed lower survival and increased bacterial burden in the lung and systemic tissues in comparison to WT littermate controls. Furthermore, macrophages from TrspM mice were unable to restrict bacterial replication ex vivo in comparison to macrophages from littermate controls. We herein describe a novel function of host macrophage-specific selenoproteins in restriction of intracellular bacterial replication. These data suggest that host selenoproteins may be considered as novel targets for modulating immune response to control a bacterial infection.

Initial Step of Selenite Reduction via Thioredoxin for Bacterial Selenoprotein Biosynthesis

Many organisms reductively assimilate selenite to synthesize selenoprotein. Although the thioredoxin system, consisting of thioredoxin 1 (TrxA) and thioredoxin reductase with NADPH, can reduce selenite and is considered to facilitate selenite assimilation, the detailed mechanism remains obscure. Here, we show that selenite was reduced by the thioredoxin system from Pseudomonas stutzeri only in the presence of the TrxA (PsTrxA), and this system was specific to selenite among the oxyanions examined. Mutational analysis revealed that Cys33 and Cys36 residues in PsTrxA are important for selenite reduction. Free thiol-labeling assays suggested that Cys33 is more reactive than Cys36. Mass spectrometry analysis suggested that PsTrxA reduces selenite via PsTrxA-SeO intermediate formation. Furthermore, an in vivo formate dehydrogenase activity assay in Escherichia coli with a gene disruption suggested that TrxA is important for selenoprotein biosynthesis. The introduction of PsTrxA complemented the effects of TrxA disruption in E. coli cells, only when PsTrxA contained Cys33 and Cys36. Based on these results, we proposed the early steps of the link between selenite and selenoprotein biosynthesis via the formation of TrxA–selenium complexes.

Biogenic synthesis and characterization of selenium nanoparticles and their applications with special reference to antibacterial, antioxidant, anticancer and photocatalytic activity

Oxyanions of selenium, selenite (SeO₃)^2- and selenate (SeO₄)^2- are toxic to terrestrial and aquatic biota but few microorganisms including cyanobacteria are resistant to high levels of selenite. Cyanobacteria evade selenite toxicity through bioreduction and synthesis of selenium nanoparticles (SeNPs). In this study, extracellular biosynthesis of SeNPs (Se⁰) using cyanobacterium, Anabaena sp. PCC 7120 on exposure to sodium selenite and characterization was done by using UV-visible spectroscopy, SEM-EDX, TEM and FTIR analyses which confirmed spherical shape with size range of 5-50 nm diameter. These biogenic SeNPs demonstrated significant antibacterial and anti-biofilm activity against bacterial pathogens. Furthermore, these SeNPs showed high antioxidant activity at minimum concentration of 50 µg/mL and significant anti-proliferative activity against HeLa cell line with IC₅₀ value of 5.5 µg/mL. The SeNPs also induced accumulation of cancer cells in the sub-G1 phase which was clearly observed in cellular and nuclear morphology. These biofabricated SeNPs also reduced and decolorized toxic methylene blue dye significantly through photocatalytic degradation. Therefore Anabaena sp. PCC 7120 may be employed as a green bioresource to synthesize SeNPs with potential applications in medicine and environmental bioremediation.

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.

Models of genetic code structure evolution with variable number of coded labels

It is assumed that at the early stage of cell evolution its translation machinery was characterized by high noise, i.e. ambiguous assignment of codons to amino acids in the genetic code, which initially encoded only few amino acids. Next, during its evolution new amino acids were added to this code. Taking into account this facts, we investigated theoretical models of genetic code's structure, which evolved from a set of ambiguous codons assignments into a coding system with a low level of uncertainty. We considered three types of translational inaccuracies assuming a different number of fixed codon positions. We applied a modified version of evolutionary algorithm for finding the genetic codes that the most effectively reduced the initial uncertainty in the assignment of codons to encoded labels, i.e. amino acids and a stop translation signal. We examined codes with the number of labels from four to 22. Our results indicated that the quality of genetic code structure is strongly dependent on the number of encoded labels as well as the type of translational mechanism. The more strict assignments of codon to the labels was preferred by the codes encoding more number of labels. The results showed that a smaller degeneracy of codes evolved from a more tolerant coding with the stepwise addition of coded amino acids to the genetic code. The distribution of codon groups in the standard genetic code corresponds well to the translation model assuming two fixed codon positions, whereas the six-codon groups can be relics form previous stages of evolution when the code characterized by a greater uncertainty.

Capture of carbon dioxide and hydrogen by engineered Escherichia coli: hydrogen-dependent CO2 reduction to formate

In times of global climate change and the fear of dwindling resources, we are facing different considerable challenges such as the replacement of fossil fuel-based energy carriers with the coincident maintenance of the increasing energy supply of our growing world population. Therefore, CO₂ capturing and H₂ storing solutions are urgently needed. In this study, we demonstrate the production of a functional and biotechnological interesting enzyme complex from acetogenic bacteria, the hydrogen-dependent CO₂ reductase (HDCR), in the well-known model organism Escherichia coli. We identified the metabolic bottlenecks of the host organisms for the production of the HDCR enzyme complex. Here we show that the recombinant expression of a heterologous enzyme complex transforms E. coli into a whole-cell biocatalyst for hydrogen-driven CO₂ reduction to formate without the need of any external co-factors or endogenous enzymes in the reaction process. This shifts the industrial platform organism E. coli more and more into the focus as biocatalyst for CO₂-capturing and H₂-storage. KEY POINTS: • A functional HDCR enzyme complex was heterologously produced in E. coli. • The metabolic bottlenecks for HDCR production were identified. • HDCR enabled E. coli cell to capture and store H₂ and CO₂ in the form of formate.

An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria

Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. Marine sediments in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary strategies. Genetic code expansion is a strategy that increases the structural and functional diversity of proteins in cells, by repurposing stop codons to encode non-canonical amino acids: pyrrolysine (Pyl) and selenocysteine (Sec). Here, we report both a study of the microbiome at a deep sea industrial waste dumpsite and an unanticipated discovery of codon reassignment in its most abundant member, with potential ramifications for interpreting microbial interactions with ocean-dumped wastes. The genomes of abundant Deltaproteobacteria from the sediments of a deep-ocean chemical waste dump site have undergone genetic code expansion. Pyl and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, representing an increased metabolic versatility. The inferred metabolism of these sulfate-reducing bacteria places them in competition with methylotrophic methanogens for TMA, a contention further supported by earlier isotope tracer studies and reanalysis of metatranscriptomic studies. A survey of genomic data further reveals a broad geographic distribution of a niche group of similarly specialized Deltaproteobacteria, including at sulfidic sites in the Atlantic Ocean, Gulf of Mexico, Guaymas Basin, and North Sea, as well as in terrestrial and estuarine environments. These findings reveal an important biogeochemical role for specialized Deltaproteobacteria at the interface of the carbon, nitrogen, selenium, and sulfur cycles, with their niche adaptation and ecological success potentially augmented by genetic code expansion.

The Relevance of Plant-Derived Se Compounds to Human Health in the SARS-CoV-2 (COVID-19) Pandemic Era

Dietary selenium (Se)-compounds accumulated in plants are essential for human metabolism and normal physiological processes. Inorganic and organic Se species can be readily absorbed by the human body, but are metabolized differently and thus exhibit distinct mechanisms of action. They can act as antioxidants or serve as a source of Se for the synthesis of selenoproteins. Selenocysteine, in particular, is incorporated at the catalytic center of these proteins through a specific insertion mechanism and, due to its electronic features, enhances their catalytic activity against biological oxidants. Selenite and other Se-organic compounds may also act as direct antioxidants in cells due to their strong nucleophilic properties. In addition, Se-amino acids are more easily subjected to oxidation than the corresponding thiols/thioethers and can bind redox-active metal ions. Adequate Se intake aids in preventing several metabolic disorders and affords protection against viral infections. At present, an epidemic caused by a novel coronavirus (SARS-CoV-2) threatens human health across several countries and impacts the global economy. Therefore, Se-supplementation could be a complementary treatment to vaccines and pharmacological drugs to reduce the viral load, mutation frequency, and enhance the immune system of populations with low Se intake in the diet.

Redox-Neutral Selenium-Catalysed Isomerisation of para-Hydroxamic Acids into para-Aminophenols

A selenium-catalysed para-hydroxylation of N-aryl-hydroxamic acids is reported. Mechanistically, the reaction comprises an N-O bond cleavage and consecutive selenium-induced [2,3]-rearrangement to deliver para-hydroxyaniline derivatives. The mechanism is studied through both 18 O-crossover experiments as well as quantum chemical calculations. This redox-neutral transformation provides an unconventional synthetic approach to para-aminophenols.

Redox-Neutrale Selen-katalysierte Isomerisierung von para-Hydroxamsäuren zu para-Aminophenolen

Über eine Selen‐katalysierte para‐Hydroxylierung von N‐Arylhydroxamsäuren wird berichtet. Mechanistisch verläuft diese über N‐O‐Bindungsbruch und nachfolgende Selen‐induzierte [2,3]‐Umlagerungen um para‐Hydroxylanilinderivate zu erzeugen. Der Mechanismus wurde sowohl mittels 18O‐Überkreuzungsexperimenten als auch quantenchemischen Berechnungen untersucht. Diese redox‐neutrale Transformation ermöglicht einen ungewöhnlichen synthetischen Zugang zu para‐Aminophenolen.

Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry

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

Autonomous Non Antioxidant Roles for Fasciola hepatica Secreted Thioredoxin-1 and Peroxiredoxin-1

Trematode parasites of the genus Fasciola are the cause of liver fluke disease (fasciolosis) in humans and their livestock. Infection of the host involves invasion through the intestinal wall followed by migration in the liver that results in extensive damage, before the parasite settles as a mature egg-laying adult in the bile ducts. Genomic and transcriptomic studies revealed that increased metabolic stress during the rapid growth and development of F. hepatica is balanced with the up-regulation of the thiol-independent antioxidant system. In this cascade system thioredoxin/glutathione reductase (TGR) reduces thioredoxin (Trx), which then reduces and activates peroxiredoxin (Prx), whose major function is to protect cells against the damaging hydrogen peroxide free radicals. F. hepatica expresses a single TGR, three Trx and three Prx genes; however, the transcriptional expression of Trx1 and Prx1 far out-weighs (>50-fold) other members of their family, and both are major components of the parasite secretome. While Prx1 possesses a leader signal peptide that directs its secretion through the classical pathway and explains why this enzyme is found freely soluble in the secretome, Trx1 lacks a leader peptide and is secreted via an alternative pathway that packages the majority of this enzyme into extracellular vesicles (EVs). Here we propose that F. hepatica Prx1 and Trx1 do not function as part of the parasite’s stress-inducible thiol-dependant cascade, but play autonomous roles in defence against the general anti-pathogen oxidative burst by innate immune cells, in the modulation of host immune responses and regulation of inflammation.

The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy

Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. An upcoming field of protein labeling is incorporating unnatural amino acids (UAAs) with an attached fluorescent dye for precise localization and visualization of individual molecules. For this technique, fluorescent probes are conjugated to UAAs and are introduced into the protein of interest (POI) as a label. Here we contrast this labeling method with other commonly used protein-based labeling methods such as fluorescent proteins (FPs) or self-labeling tags such as Halotag, SNAP-tags, and CLIP-tags, and highlight the benefits and shortcomings of the site-specific incorporation of UAAs coupled with fluorescent dyes in SMLM.

Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.

Diselenides and Selenocyanates as Versatile Precursors for the Synthesis of Pharmaceutically Relevant Compounds

Organoselenium chemistry has undergone extensive development during the past decades, mostly due to the unique chemical properties of organoselenium compounds that have been widely explored in a number of synthetic transformations, as well as due to the interesting biological properties of these compounds. Diselenides and selenocyanates constitute the promising classes of organoselenium compounds that possess interesting biological effects and that can be used in the preparation of other selenium compounds. The combination of diselenide and selenocyanate moieties with other biologically relevant molecules (such as heterocycles, steroids, etc.) is a way for the development of compounds with promising pharmaceutical potential. Therefore, the aim of this review is to highlight the recent achievements in the use of diselenides or selenocyanates as precursors for the synthesis of pharmaceutically relevant compounds, preferentially compounds with antitumor and antimicrobial activities.

Chemical modifications of proteins and their applications in metalloenzyme studies

Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.