The selenoproteome of Clostridium sp. OhILAs: characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A

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

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

Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis

The bioinformatics of a nine-gene locus, designated selenocysteine-assisted organometallic (SAO), was investigated after identifying six new selenoprotein families and constructing hidden Markov models (HMMs) that find and annotate members of those families. Four are selenoproteins in most SAO loci, including Clostridium difficile. They include two ABC transporter subunits, namely, permease SaoP, with selenocysteine (U) at the channel-gating position, and substrate-binding subunit SaoB. Cytosolic selenoproteins include SaoL, homologous to MerB organomercurial lyases from mercury resistance loci, and SaoT, related to thioredoxins. SaoL, SaoB, and surface protein SaoC (an occasional selenoprotein) share an unusual CU dipeptide motif, which is something rare in selenoproteins but found in selenoprotein variants of mercury resistance transporter subunit MerT. A nonselenoprotein, SaoE, shares homology with Cu/Zn efflux and arsenical efflux pumps. The organization of the SAO system suggests substrate interaction with surface-exposed selenoproteins, followed by import, metabolism that may cleave a carbon-to-heavy metal bond, and finally metal efflux. A novel type of mercury resistance is possible, but SAO instead may support fermentative metabolism, with selenocysteine-mediated formation of organometallic intermediates, followed by import, degradation, and metal efflux. Phylogenetic profiling shows SOA loci consistently co-occur with Stickland fermentation markers but even more consistently with 8Fe-9S cofactor-type double-cubane proteins. Hypothesizing that the SAO system forms organometallic intermediates, we investigated the known methylmercury formation protein families HgcA and HgcB. Both families contained overlooked selenoproteins. Most HgcAs have a CU motif N terminal to their previously accepted start sites. Seeking additional rare and overlooked selenoproteins may help reveal more cryptic aspects of microbial biochemistry. IMPORTANCE This work adds 8 novel prokaryotic selenoproteins to the 80 or so families previously known. It describes the SAO (selenocysteine-assisted organometallic) locus, with the most selenoproteins of any known system. The rare CU motif recurs throughout, suggesting the formation and degradation of organometallic compounds. That suggestion triggered a reexamination of HgcA and HcgB, which are methylmercury formation proteins that can adversely impact food safety. Both are selenoproteins, once corrected, with HgcA again showing a CU motif. The SAO system is plausibly a mercury resistance locus for selenium-dependent anaerobes. But instead, it may exploit heavy metals as cofactors in organometallic intermediate-forming pathways that circumvent high activation energies and facilitate the breakdown of otherwise poorly accessible nutrients. SAO could provide an edge that helps Clostridium difficile, an important pathogen, establish disease.

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.

A critical review on sulfur reduction of aqueous selenite: Mechanisms and applications

Selenite, which is extremely toxic at high concentrations, can easily be enriched in natural aquatic environments due to human activities, which causes great harm to ecosystems. Sulfur reduction can effectively reduce soluble selenite in large quantities to nontoxic solid elemental selenium, which plays a significant role in controlling the toxicity and cycle of selenium. In view of the bright prospects of the sulfur reduction reaction of selenite, this review comprehensively summarizes the continuous development in the sulfidation of selenite. First, the geochemical characteristics of aqueous selenium in different sulfur systems involving species distribution and various phase types at Eh-pH conditions were summarized. Second, sulfur reductions of selenite with chemical sulfide in natural water environments, sulfur reductase and extracellular polymer substances containing thiol groups in sulfate-reducing bacteria have been reviewed to further understand the corresponding mechanisms, rates and influencing factors. Furthermore, applications of sulfur reduction of selenium, including removal of selenium, enrichment of selenium, synthesis of selenoproteins and prevention of leakage of selenium, were also summarized. Finally, this review identified future research needs for the sulfidation of selenite for environmental applications.

Methionine Sulfoxide Reductases Contribute to Anaerobic Fermentative Metabolism in Bacillus cereus

Reversible oxidation of methionine to methionine sulfoxide (Met(O)) is a common posttranslational modification occurring on proteins in all organisms under oxic conditions. Protein-bound Met(O) is reduced by methionine sulfoxide reductases, which thus play a significant antioxidant role. The facultative anaerobe Bacillus cereus produces two methionine sulfoxide reductases: MsrA and MsrAB. MsrAB has been shown to play a crucial physiological role under oxic conditions, but little is known about the role of MsrA. Here, we examined the antioxidant role of both MsrAB and MrsA under fermentative anoxic conditions, which are generally reported to elicit little endogenous oxidant stress. We created single- and double-mutant Δmsr strains. Compared to the wild-type and ΔmsrAB mutant, single- (ΔmsrA) and double- (ΔmsrAΔmsrAB) mutants accumulated higher levels of Met(O) proteins, and their cellular and extracellular Met(O) proteomes were altered. The growth capacity and motility of mutant strains was limited, and their energy metabolism was altered. MsrA therefore appears to play a major physiological role compared to MsrAB, placing methionine sulfoxides at the center of the B. cereus antioxidant system under anoxic fermentative conditions.

The physiology and evolution of microbial selenium metabolism

Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

Monothiol and dithiol glutaredoxin-1 from Clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry

Protein dimerization or oligomerization resulting from swapping part of the protein between neighboring polypeptide chains is known to play a key role in the regulation of protein function and in the formation of protein aggregates. Glutaredoxin-1 from Clostridium oremlandii (cGrx1) was used as a model to explore the formation of multiple domain-swapped conformations, which were made possible by modulating several hinge-loop residues that can form a pivot for domain swapping. Specifically, two alternative domain-swapped structures were generated and analyzed using nuclear magnetic resonance (NMR), X-ray crystallography, circular-dichroism spectroscopy and hydrogen/deuterium-exchange (HDX) mass spectrometry. The first domain-swapped structure (β3-swap) was formed by the hexameric cGrx1-cMsrA complex. The second domain-swapped structure (β1-swap) was formed by monothiol cGrx1 (C16S) alone. In summary, the first domain-swapped structure of an oxidoreductase in a hetero-oligomeric complex is presented. In particular, a single point mutation of a key cysteine residue to serine led to the formation of an intramolecular disulfide bond, as opposed to an intermolecular disulfide bond, and resulted in modulation of the underlying free-energy landscape of protein oligomerization.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology

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

Generation of Recombinant Mammalian Selenoproteins through Genetic Code Expansion with Photocaged Selenocysteine

Selenoproteins contain the amino acid selenocysteine (Sec) and are found in all domains of life. The functions of many selenoproteins are poorly understood, partly due to difficulties in producing recombinant selenoproteins for cell-biological evaluation. Endogenous mammalian selenoproteins are produced through a noncanonical translation mechanism requiring suppression of the UGA stop codon and a Sec insertion sequence (SECIS) element in the 3' untranslated region of the mRNA. Here, recombinant selenoproteins are generated in mammalian cells through genetic code expansion, circumventing the requirement for the SECIS element and selenium availability. An engineered orthogonal E. coli leucyl-tRNA synthetase/tRNA pair is used to incorporate a photocaged Sec (DMNB-Sec) at the UAG amber stop codon. DMNB-Sec is successfully incorporated into GFP and uncaged by irradiation of living cells. Furthermore, DMNB-Sec is used to generate the native selenoprotein methionine-R-sulfoxide reductase B1 (MsrB1). Importantly, MsrB1 is shown to be catalytically active after uncaging, constituting the first use of genetic code expansion to generate a functional selenoprotein in mammalian systems. The ability to site-specifically introduce Sec directly in mammalian cells, and temporally modulate selenoprotein activity, will aid in the characterization of mammalian selenoprotein function.

New insights into the molecular physiology of sulfoxide reduction in bacteria

Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.

CosR is an oxidative stress sensing a MarR-type transcriptional repressor in Corynebacterium glutamicum

The MarR family is unique to both bacteria and archaea. The members of this family, one of the most prevalent families of transcriptional regulators in bacteria, enable bacteria to adapt to changing environmental conditions, such as the presence of antibiotics, toxic chemicals, or reactive oxygen species (ROS), mainly by thiol-disulfide switches. Although the genome of Corynebacterium glutamicum encodes a large number of the putative MarR-type transcriptional regulators, their physiological and biochemical functions have so far been limited to only two proteins, regulator of oxidative stress response RosR and quinone oxidoreductase regulator QosR. Here, we report that the ncgl2617 gene (cosR) of C. glutamicum encoding an MarR-type transcriptional regulator plays an important role in oxidative stress resistance. The cosR null mutant is found to be more resistant to various oxidants and antibiotics, accompanied by a decrease in ROS production and protein carbonylation levels under various stresses. Protein biochemical function analysis shows that two Cys residues presenting at 49 and 62 sites in CosR are redox-active. They form intermolecular disulfide bonds in CosR under oxidative stress. This CosR oxidation leads to its dissociation from promoter DNA, depression of the target DNA, and increased oxidative stress resistance of C. glutamicum. Together, the results reveal that CosR is a redox-sensitive regulator that senses peroxide stress to mediate oxidative stress resistance in C. glutamicum.

Functional comparison of methionine sulphoxide reductase A and B in Corynebacterium glutamicum

Methionine sulphoxide reductases (Msr) are able to reduce methionine sulfoxide to methionine and protect bacteria against reactive oxygen species (ROS). Many organisms express both methionine sulphoxide reductase A (MsrA), specific for methionine-S-sulfoxide and methionine sulphoxide reductase B (MsrB), active against methionine-R-sulfoxide. Corynebacterium glutamicum expresses MsrA, the function of which has been well defined; however, the function of MsrB has not been studied. Whether MsrB and MsrA play an equally important role in the antioxidant process is also poorly understood. In this study, we identified MsrB encoded by ncgl1823 in C. glutamicum, investigated its function and made a comparison with MsrA. The msrB gene showed a slight effect on utilizing methionine sulfoxide (MetO) as the sole Met source; however, the survival rates showed no sensitivity to oxidants. MsrB showed catalytic activity using thioredoxin/thioredoxin reductase (Trx/TrxR) reducing system as electron donors, but independent from the mycoredoxin 1/mycothione reductase/mycothiol (Mrx1/Mtr/MSH) system. Therefore, MsrB plays a limited role in resisting oxidative stress and it could reduce MetO to Met by the Trx/TrxR reducing system, which is useful for expanding the understanding of the functions of Msr in this important industrial microbe.

Bioaccumulation and distribution of selenium in Enterococcus durans

Selenium is an essential nutrient for all living organisms. Under appropriate conditions lactic acid bacteria (LAB) are capable for accumulating large amounts of trace elements, such as selenium, and incorporating them into organic compounds. In this study, the capacity of selenium bioaccumulation by Enterococcus durans LAB18s was evaluated. The distribution of organic selenium in selenium-enriched E. durans LAB18s biomass was analyzed, and the highest percentage of organic selenium was found in the fraction of total protein, followed by the fractions of polysaccharides and nucleic acids. When the protein fraction was obtained by different extractions (water, NaCl, ethanol and NaOH) it was demonstrated that alkali-soluble protein showed the higher Selenium content. Analysis of protein fractions by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed that selenium was present in the proteins ranging from 23 to 100kDa. The cells were analyzed by scanning electron microscopy (SEM); scanning electron microscopy/energy dispersive spectrometry (SEM/EDS) and transmission electron microscopy (TEM). SEM, TEM and SEM/EDS showed the morphology, the selenium particles bioaccumulated into and on the cells and the amounts of selenium present into the cells, respectively. Thus, the isolate E. durans LAB18s can be a promising probiotic to be used as selenium-enriched biomass in feed trials.

Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii

Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.

The discovery of methionine sulfoxide reductase enzymes: An historical account and future perspectives

L-Methionine (L-Met) is the only sulphur-containing proteinogenic amino acid together with cysteine. Its importance is highlighted by it being the initiator amino acid for protein synthesis in all known living organisms. L-Met, free or inserted into proteins, is sensitive to oxidation of its sulfide moiety, with formation of L-Met sulfoxide. The sulfoxide could not be inserted into proteins, and the oxidation of L-Met in proteins often leads to the loss of biological activity of the affected molecule. Key discoveries revealed the existence, in rats, of a metabolic pathway for the reduction of free L-Met sulfoxide and, later, in Escherichia coli, of the enzymatic reduction of L-Met sulfoxide inserted in proteins. Upon oxidation, the sulphur atom becomes a new stereogenic center, and two stable diastereoisomers of L-Met sulfoxide exist. A fundamental discovery revealed the existence of two unrelated families of enzymes, MsrA and MsrB, whose members display opposite stereospecificity of reduction for the two sulfoxides. The importance of Msrs is additionally emphasized by the discovery that one of the only 25 selenoproteins expressed in humans is a Msr. The milestones on the road that led to the discovery and characterization of this group of antioxidant enzymes are recounted in this review.

Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii

We previously determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii (CoMsrA). The overall structure of CoMsrA is unusual, consisting of two domains, the N-terminal catalytic domain and the C-terminal distinct helical domain which is absent from other known MsrA structures. Deletion of the helical domain almost completely abolishes the catalytic activity of CoMsrA. In this study, we determined the crystal structure of the helical domain-deleted (ΔH-domain) form of CoMsrA at a resolution of 1.76 Å. The monomer structure is composed of the central rolled mixed β-sheet surrounded by α-helices. However, there are significant conformational changes in the N- and C-termini and loop regions of the ΔH-domain protein relative to the catalytic domain structure of full-length CoMsrA. The active site structure in the ΔH-domain protein completely collapses, thereby causing loss of catalytic activity of the protein. Interestingly, dimer structures are observed in the crystal formed by N-terminus swapping between two molecules. The ΔH-domain protein primarily exists as a dimer in solution, whereas the full-length CoMsrA exists as a monomer. Collectively, this study provides insight into the structural basis of the essential role of the helical domain of CoMsrA in its catalysis.

Corynebacterium glutamicum methionine sulfoxide reductase A uses both mycoredoxin and thioredoxin for regeneration and oxidative stress resistance

Oxidation of methionine leads to the formation of the S and R diastereomers of methionine sulfoxide (MetO), which can be reversed by the actions of two structurally unrelated classes of methionine sulfoxide reductase (Msr), MsrA and MsrB, respectively. Although MsrAs have long been demonstrated in numerous bacteria, their physiological and biochemical functions remain largely unknown in Actinomycetes. Here, we report that a Corynebacterium glutamicum methionine sulfoxide reductase A (CgMsrA) that belongs to the 3-Cys family of MsrAs plays important roles in oxidative stress resistance. Deletion of the msrA gene in C. glutamicum resulted in decrease of cell viability, increase of ROS production, and increase of protein carbonylation levels under various stress conditions. The physiological roles of CgMsrA in resistance to oxidative stresses were corroborated by its induced expression under various stresses, regulated directly by the stress-responsive extracytoplasmic-function (ECF) sigma factor SigH. Activity assays performed with various regeneration pathways showed that CgMsrA can reduce MetO via both the thioredoxin/thioredoxin reductase (Trx/TrxR) and mycoredoxin 1/mycothione reductase/mycothiol (Mrx1/Mtr/MSH) pathways. Site-directed mutagenesis confirmed that Cys56 is the peroxidatic cysteine that is oxidized to sulfenic acid, while Cys204 and Cys213 are the resolving Cys residues that form an intramolecular disulfide bond. Mrx1 reduces the sulfenic acid intermediate via the formation of an S-mycothiolated MsrA intermediate (MsrA-SSM) which is then recycled by mycoredoxin and the second molecule of mycothiol, similarly to the glutathione/glutaredoxin/glutathione reductase (GSH/Grx/GR) system. However, Trx reduces the Cys204-Cys213 disulfide bond in CgMsrA produced during MetO reduction via the formation of a transient intermolecular disulfide bond between Trx and CgMsrA. While both the Trx/TrxR and Mrx1/Mtr/MSH pathways are operative in reducing CgMsrA under stress conditions in vivo, the Trx/TrxR pathway alone is sufficient to reduce CgMsrA under normal conditions. Based on these results, a catalytic model for the reduction of CgMsrA by Mrx1 and Trx is proposed.

Mechanism of 1-Cys type methionine sulfoxide reductase A regeneration by glutaredoxin

Glutaredoxin (Grx), a major redox regulator, can act as a reductant of methionine sulfoxide reductase A (MsrA). However, the biochemical mechanisms involved in MsrA activity regeneration by Grx remain largely unknown. In this study, we investigated the regeneration mechanism of 1-Cys type Clostridium oremlandii MsrA (cMsrA) lacking a resolving Cys residue in a Grx-dependent assay. Kinetic analysis showed that cMsrA could be reduced by both monothiol and dithiol Grxs as efficiently as by in vitro reductant dithiothreitol. Our data revealed that the catalytic Cys sulfenic acid intermediate is not glutathionylated in the presence of the substrate, and that Grx instead directly formed a complex with cMsrA. Mass spectrometry analysis identified a disulfide bond between the N-terminal catalytic Cys of the active site of Grx and the catalytic Cys of cMsrA. This mixed disulfide bond could be resolved by glutathione. Based on these findings, we propose a model for regeneration of 1-Cys type cMsrA by Grx that involves no glutathionylation on the catalytic Cys of cMsrA. This mechanism contrasts with that of the previously known 1-Cys type MsrB.

Selenoproteins: molecular pathways and physiological roles

Selenium is an essential micronutrient with important functions in human health and relevance to several pathophysiological conditions. The biological effects of selenium are largely mediated by selenium-containing proteins (selenoproteins) that are present in all three domains of life. Although selenoproteins represent diverse molecular pathways and biological functions, all these proteins contain at least one selenocysteine (Sec), a selenium-containing amino acid, and most serve oxidoreductase functions. Sec is cotranslationally inserted into nascent polypeptide chains in response to the UGA codon, whose normal function is to terminate translation. To decode UGA as Sec, organisms evolved the Sec insertion machinery that allows incorporation of this amino acid at specific UGA codons in a process requiring a cis-acting Sec insertion sequence (SECIS) element. Although the basic mechanisms of Sec synthesis and insertion into proteins in both prokaryotes and eukaryotes have been studied in great detail, the identity and functions of many selenoproteins remain largely unknown. In the last decade, there has been significant progress in characterizing selenoproteins and selenoproteomes and understanding their physiological functions. We discuss current knowledge about how these unique proteins perform their functions at the molecular level and highlight new insights into the roles that selenoproteins play in human health.

Methionine sulfoxide reductase: chemistry, substrate binding, recycling process and oxidase activity

Three classes of methionine sulfoxide reductases are known: MsrA and MsrB which are implicated stereo-selectively in the repair of protein oxidized on their methionine residues; and fRMsr, discovered more recently, which binds and reduces selectively free L-Met-R-O. It is now well established that the chemical mechanism of the reductase step passes through formation of a sulfenic acid intermediate. The oxidized catalytic cysteine can then be recycled by either Trx when a recycling cysteine is operative or a reductant like glutathione in the absence of recycling cysteine which is the case for 30% of the MsrBs. Recently, it was shown that a subclass of MsrAs with two recycling cysteines displays an oxidase activity. This reverse activity needs the accumulation of the sulfenic acid intermediate. The present review focuses on recent insights into the catalytic mechanism of action of the Msrs based on kinetic studies, theoretical chemistry investigations and new structural data. Major attention is placed on how the sulfenic acid intermediate can be formed and the oxidized catalytic cysteine returns back to its reduced form.

The methionine sulfoxide reduction system: selenium utilization and methionine sulfoxide reductase enzymes and their functions

SIGNIFICANCE

Selenium is utilized in the methionine sulfoxide reduction system that occurs in most organisms. Methionine sulfoxide reductases (Msrs), MsrA and MsrB, are the enzymes responsible for this system. Msrs repair oxidatively damaged proteins, protect against oxidative stress, and regulate protein function, and have also been implicated in the aging process. Selenoprotein forms of Msrs containing selenocysteine (Sec) at the catalytic site are found in bacteria, algae, and animals.

RECENT ADVANCES

A selenoprotein MsrB1 knockout mouse has been developed. Significant progress in the biochemistry of Msrs has been made, which includes findings of a novel reducing system for Msrs and of an interesting reason for the use of Sec in the Msr system. The effects of mammalian MsrBs, including selenoprotein MsrB1 on fruit fly aging, have been investigated. Furthermore, it is evident that Msrs are involved in methionine metabolism and regulation of the trans-sulfuration pathway.

CRITICAL ISSUES

This article presents recent progress in the Msr field while focusing on the physiological roles of mammalian Msrs, functions of selenoprotein forms of Msrs, and their biochemistry.

FUTURE DIRECTIONS

A deeper understanding of the roles of Msrs in redox signaling, the aging process, and metabolism will be achieved. The identity of selenoproteome of Msrs will be sought along with characterization of the identified selenoprotein forms. Exploring new cellular targets and new functions of Msrs is also warranted.

Glutaredoxin serves as a reductant for methionine sulfoxide reductases with or without resolving cysteine

Methionine sulfoxide reductases A and B (MsrA and MsrB) have been known to be thioredoxin (Trx)-dependent enzymes that catalyze the reduction of methionine sulfoxide in a stereospecific manner. This work reports that glutaredoxin, another major thiol-disulfide oxidoreductase, can serve as a reductant for both MsrA and MsrB. Glutaredoxins efficiently reduced 1-Cys MsrA lacking a resolving Cys, which is not reducible by Trx. Glutaredoxins also reduced 3-Cys MsrA containing two resolving Cys. The glutaredoxin-dependent activity of the 3-Cys MsrA was comparable with the Trx-dependent activity. The kinetic data suggest that 1-Cys MsrA is more efficiently reduced by glutaredoxin than 3-Cys form. Also, glutaredoxins could function as a reductant for 1-Cys MsrB lacking a resolving Cys as previously reported. In contrast to the previous report, 2-Cys MsrB containing a resolving Cys was reducible by the glutaredoxins. Collectively, this study demonstrates that glutaredoxins reduce MsrAs and MsrBs with or without resolving Cys.

The biological significance of methionine sulfoxide stereochemistry

Methionine can be oxidized by reactive oxygen species to a mixture of two diastereomers, methionine-S-sulfoxide and methionine-R-sulfoxide. Both free amino acid and protein-based forms of methionine-S-sulfoxide are stereospecifically reduced by MsrA, whereas the reduction of methionine-R-sulfoxide requires two enzymes, MsrB and fRMsr, which act on its protein-based and free amino acid forms, respectively. However, mammals lack fRMsr and are characterized by deficiency in the reduction of free methionine-R-sulfoxide. The biological significance of such biased reduction of methionine sulfoxide has not been fully explored. MsrA and MsrB activities decrease during aging, leading to accumulation of protein-based and free amino acid forms of methionine sulfoxide. Since methionine is an indispensible amino acid in human nutrition and a key metabolite in sulfur, methylation, and transsulfuration pathways, the consequences of accumulation of its oxidized forms require further studies. Finally, in addition to methionine, methylsulfinyl groups are present in various drugs and natural compounds, and their differential reduction by Msrs may have important therapeutic implications.

Tandem use of selenocysteine: adaptation of a selenoprotein glutaredoxin for reduction of selenoprotein methionine sulfoxide reductase

Several engineered selenocysteine (Sec)-containing glutaredoxins (Grxs) and their enzymatic properties have been reported, but natural selenoprotein Grxs have not been previously characterized. We expressed a bacterial selenoprotein Grx from Clostridium sp. (also known as Alkaliphilus oremlandii) OhILAs in Escherichia coli and characterized this selenoenzyme and its natural Cys homologues in Clostridium and E. coli. The selenoprotein Grx had a 200-fold higher activity than its Sec-to-Cys mutant form, suggesting that Sec is essential for catalysis by this thiol-disulfide oxidoreductase. Kinetic analysis also showed that the selenoprotein Grx had a 10-fold lower K(m) than Cys homologues. Interestingly, this selenoenzyme efficiently reduced a Clostridium selenoprotein methionine sulfoxide reductase A (MsrA), suggesting that it is the natural reductant for the protein that is not reducible by thioredoxin, a common reductant for Cys-containing MsrAs. We also found that the selenoprotein Grx could not efficiently reduce a Cys version of Clostridium MsrA, whereas natural Clostridium and E. coli Cys-containing Grxs, which efficiently reduce Cys-containing MsrAs, poorly acted on the selenoprotein MsrA. This specificity for MsrA reduction could explain why Sec is utilized in Clostridium Grx and more generally provides a novel example of the use of Sec in biological systems.

General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se

Trace elements are used by all organisms and provide proteins with unique coordination and catalytic and electron transfer properties. Although many trace element-containing proteins are well characterized, little is known about the general trends in trace element utilization. We carried out comparative genomic analyses of copper, molybdenum, nickel, cobalt (in the form of vitamin B(12)), and selenium (in the form of selenocysteine) in 747 sequenced organisms at the following levels: (i) transporters and transport-related proteins, (ii) cofactor biosynthesis traits, and (iii) trace element-dependent proteins. Few organisms were found to utilize all five trace elements, whereas many symbionts, parasites, and yeasts used only one or none of these elements. Investigation of metalloproteomes and selenoproteomes revealed examples of increased utilization of proteins that use copper in land plants, cobalt in Dehalococcoides and Dictyostelium, and selenium in fish and algae, whereas nematodes were found to have great diversity of copper transporters. These analyses also characterized trace element metabolism in common model organisms and suggested new model organisms for experimental studies of individual trace elements. Mismatches in the occurrence of user proteins and corresponding transport systems revealed deficiencies in our understanding of trace element biology. Biological interactions among some trace elements were observed; however, such links were limited, and trace elements generally had unique utilization patterns. Finally, environmental factors, such as oxygen requirement and habitat, correlated with the utilization of certain trace elements. These data provide insights into the general features of utilization and evolution of trace elements in the three domains of life.

Recode-2: new design, new search tools, and many more genes

‘Recoding’ is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of ‘recoded’ genes lags far behind annotation of ‘standard’ genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression—a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie

Functions and evolution of selenoprotein methionine sulfoxide reductases

Methionine sulfoxide reductases (Msrs) are thiol-dependent enzymes which catalyze conversion of methionine sulfoxide to methionine. Three Msr families, MsrA, MsrB, and fRMsr, are known. MsrA and MsrB are responsible for the reduction of methionine-S-sulfoxide and methionine-R-sulfoxide residues in proteins, respectively, whereas fRMsr reduces free methionine-R-sulfoxide. Besides acting on proteins, MsrA can additionally reduce free methionine-S-sulfoxide. Some MsrAs and MsrBs evolved to utilize catalytic selenocysteine. This includes MsrB1, which is a major MsrB in cytosol and nucleus in mammalian cells. Specialized machinery is used for insertion of selenocysteine into MsrB1 and other selenoproteins at in-frame UGA codons. Selenocysteine offers catalytic advantage to the protein repair function of Msrs, but also makes these proteins dependent on the supply of selenium and requires adjustments in their strategies for regeneration of active enzymes. Msrs have roles in protecting cellular proteins from oxidative stress and through this function they may regulate lifespan in several model organisms.

Selenoproteins in Archaea and Gram-positive bacteria

Selenium is an essential trace element for many organisms by serving important catalytic roles in the form of the 21st co-translationally inserted amino acid selenocysteine. It is mostly found in redox-active proteins in members of all three domains of life and analysis of the ever-increasing number of genome sequences has facilitated identification of the encoded selenoproteins. Available data from biochemical, sequence, and structure analyses indicate that Gram-positive bacteria synthesize and incorporate selenocysteine via the same pathway as enterobacteria. However, recent in vivo studies indicate that selenocysteine-decoding is much less stringent in Gram-positive bacteria than in Escherichia coli. For years, knowledge about the pathway of selenocysteine synthesis in Archaea and Eukarya was only fragmentary, but genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has not only led to the characterization of the pathways but has also shown that they are principally identical. This review summarizes current knowledge about the metabolic pathways of Archaea and Gram-positive bacteria where selenium is involved, about the known selenoproteins, and about the respective pathways employed in selenoprotein synthesis.