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Wang D, Rensing C, Zheng S. Microbial reduction and resistance to selenium: Mechanisms, applications and prospects. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126684. [PMID: 34339989 DOI: 10.1016/j.jhazmat.2021.126684] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Selenium is an essential trace element for humans, animals and microorganisms. Microbial transformations, in particular, selenium dissimilatory reduction and bioremediation applications have received increasing attention in recent years. This review focuses on multiple Se-reducing pathways under anaerobic and aerobic conditions, and the phylogenetic clustering of selenium reducing enzymes that are involved in these processes. It is emphasized that a selenium reductase may have more than one metabolic function, meanwhile, there are several Se(VI) and/or Se(IV) reduction pathways in a bacterial strain. It is noted that Se(IV)-reducing efficiency is inconsistent with Se(IV) resistance in bacteria. Moreover, we discussed the links of selenium transformations to biogeochemical cycling of other elements, roles of Se-reducing bacteria in soil, plant and digestion system, and the possibility of using functional genes involved in Se transformation as biomarker in different environments. In addition, we point out the gaps and perspectives both on Se transformation mechanisms and applications in terms of bioremediation, Se fortification or dietary supplementation.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou, Fujian 350002, PR China.
| | - Shixue Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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Tobe R, Mihara H. Delivery of selenium to selenophosphate synthetase for selenoprotein biosynthesis. Biochim Biophys Acta Gen Subj 2018; 1862:2433-2440. [PMID: 29859962 DOI: 10.1016/j.bbagen.2018.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Selenophosphate, the key selenium donor for the synthesis of selenoprotein and selenium-modified tRNA, is produced by selenophosphate synthetase (SPS) from ATP, selenide, and H2O. Although free selenide can be used as the in vitro selenium substrate for selenophosphate synthesis, the precise physiological system that donates in vivo selenium substrate to SPS has not yet been characterized completely. SCOPE OF REVIEW In this review, we discuss selenium metabolism with respect to the delivery of selenium to SPS in selenoprotein biosynthesis. MAJOR CONCLUSIONS Glutathione, selenocysteine lyase, cysteine desulfurase, and selenium-binding proteins are the candidates of selenium delivery system to SPS. The thioredoxin system is also implicated in the selenium delivery to SPS in Escherichia coli. GENERAL SIGNIFICANCE Selenium delivered via a protein-bound selenopersulfide intermediate emerges as a central element not only in achieving specific selenoprotein biosynthesis but also in preventing the occurrence of toxic free selenide in the cell. This article is part of a Special Issue entitled "Selenium research in biochemistry and biophysics - 200 year anniversary".
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Affiliation(s)
- Ryuta Tobe
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hisaaki Mihara
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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Yim SH, Tobe R, Turanov AA, Carlson BA. Radioactive 75Se Labeling and Detection of Selenoproteins. Methods Mol Biol 2018; 1661:177-192. [PMID: 28917045 DOI: 10.1007/978-1-4939-7258-6_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The trace element selenium (Se) is incorporated into proteins as the amino acid selenocysteine (Sec), which is cotranslationally inserted into specific proteins in response to a UGA codon. Proteins containing Sec at these specific positions are called selenoproteins. Most selenoproteins function as oxidoreductases, while some serve other important functions. There are 25 known selenoprotein genes in humans and 24 in mice. The use of Sec allows selenoproteins to be detected by a convenient method involving metabolic labeling with 75Se. Labeling of cells and whole animals are used for the examination of selenoprotein expression profiles and the investigation of selenoprotein functions. In mammals, nonspecific 75Se insertion is very low, and sensitivity and specificity of selenoprotein detection approaches that of Western blotting. This method allows for the examination of selenoprotein expression and Se metabolism in model and non-model organisms. Herein, we describe experimental protocols for analyzing selenoproteins by metabolic labeling with 75Se both in vitro and in vivo. As an example, the procedure for metabolic labeling of HEK293T human embryonic kidney cells is described in detail. This approach remains a method of choice for the detection of selenoproteins in diverse settings.
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Affiliation(s)
- Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ryuta Tobe
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Anton A Turanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Abstract
About 50 years ago, research on the biological function of the element selenium was initiated by the report of J. Pinsent that generation of formate dehydrogenase activity by Escherichia coli requires the presence of both selenite and molybdate in the growth medium. In nature, selenium is predominantly associated with sulfur minerals, the Se/S ratios of which vary widely depending on the geological formation. Because of the chemical similarity between the two elements, selenium can intrude into the sulfur pathway at high Se/S ratios and can be statistically incorporated into polypeptides. The central macromolecule for the synthesis and incorporation of selenocysteine is a specialized tRNA, designated tRNASec. It is the product of the selC (previously fdhC) gene. tRNASec fulfils a multitude of functions, which are based on its unique structural properties, compared to canonical elongator RNAs. tRNASec possesses the discriminator base G73 and the identity elements of serine-specific tRNA isoacceptors. The conversion of seryl-tRNASec into selenocysteyl-tRNASec is catalyzed by selenocysteine synthase, the product of the selA gene (previously the fdhA locus, which was later shown to harbor two genes, selA and selB). The crucial element for the regulation is a putative secondary structure at the 5' end of the untranslated region of the selAB mRNA. The generation and analysis of transcriptional and translational reporter gene fusions of selA and selB yield an expression pattern identical to that obtained by measuring the actual amounts of SelA and SelB proteins.
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Volker AR, Gogerty DS, Bartholomay C, Hennen-Bierwagen T, Zhu H, Bobik TA. Fermentative production of short-chain fatty acids in Escherichia coli. Microbiology (Reading) 2014; 160:1513-1522. [DOI: 10.1099/mic.0.078329-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Escherichia coli was engineered for the production of even- and odd-chain fatty acids (FAs) by fermentation. Co-production of thiolase, hydroxybutyryl-CoA dehydrogenase, crotonase and trans-enoyl-CoA reductase from a synthetic operon allowed the production of butyrate, hexanoate and octanoate. Elimination of native fermentation pathways by genetic deletion (ΔldhA, ΔadhE, ΔackA, Δpta, ΔfrdC) helped eliminate undesired by-products and increase product yields. Initial butyrate production rates were high (0.7 g l−1 h−1) but quickly levelled off and further study suggested this was due to product toxicity and/or acidification of the growth medium. Results also showed that endogenous thioesterases significantly influenced product formation. In particular, deletion of the yciA thioesterase gene substantially increased hexanoate production while decreasing the production of butyrate. E. coli was also engineered to co-produce enzymes for even-chain FA production (described above) together with a coenzyme B12-dependent pathway for the production of propionyl-CoA, which allowed the production of odd-chain FAs (pentanoate and heptanoate). The B12-dependent pathway used here has the potential to allow the production of odd-chain FAs from a single growth substrate (glucose) in a more energy-efficient manner than the prior methods.
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Affiliation(s)
- Alexandra R. Volker
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - David S. Gogerty
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Christian Bartholomay
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Tracie Hennen-Bierwagen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Huilin Zhu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
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Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase. J Bacteriol 2011; 194:499-508. [PMID: 22081394 DOI: 10.1128/jb.06012-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selenophosphate synthetase (SPS) catalyzes the synthesis of selenophosphate, the selenium donor for the biosynthesis of selenocysteine and 2-selenouridine residues in seleno-tRNA. Selenocysteine, known as the 21st amino acid, is then incorporated into proteins during translation to form selenoproteins which serve a variety of cellular processes. SPS activity is dependent on both Mg(2+) and K(+) and uses ATP, selenide, and water to catalyze the formation of AMP, orthophosphate, and selenophosphate. In this reaction, the gamma phosphate of ATP is transferred to the selenide to form selenophosphate, while ADP is hydrolyzed to form orthophosphate and AMP. Most of what is known about the function of SPS has derived from studies investigating Escherichia coli SPS (EcSPS) as a model system. Here we report the crystal structure of the C17S mutant of SPS from E. coli (EcSPS(C17S)) in apo form (without ATP bound). EcSPS(C17S) crystallizes as a homodimer, which was further characterized by analytical ultracentrifugation experiments. The glycine-rich N-terminal region (residues 1 through 47) was found in the open conformation and was mostly ordered in both structures, with a magnesium cofactor bound at the active site of each monomer involving conserved aspartate residues. Mutating these conserved residues (D51, D68, D91, and D227) along with N87, also found at the active site, to alanine completely abolished AMP production in our activity assays, highlighting their essential role for catalysis in EcSPS. Based on the structural and biochemical analysis of EcSPS reported here and using information obtained from similar studies done with SPS orthologs from Aquifex aeolicus and humans, we propose a catalytic mechanism for EcSPS-mediated selenophosphate synthesis.
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Hartmanis MG, Gatenbeck S. Intermediary Metabolism in Clostridium acetobutylicum: Levels of Enzymes Involved in the Formation of Acetate and Butyrate. Appl Environ Microbiol 2010; 47:1277-83. [PMID: 16346566 PMCID: PMC240219 DOI: 10.1128/aem.47.6.1277-1283.1984] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The levels of seven intermediary enzymes involved in acetate and butyrate formation from acetyl coenzyme A in the saccharolytic anaerobe Clostridium acetobutylicum were investigated as a function of time in solvent-producing batch fermentations. Phosphate acetyltransferase and acetate kinase, which are known to form acetate from acetyl coenzyme A, both showed a decrease in specific activity when the organism reached the solvent formation stage. The three consecutive enzymes thiolase, beta-hydroxybutyrylcoenzyme A dehydrogenase, and crotonase exhibited a coordinate expression and a maximal activity after growth had ceased. Only low levels of butyryl coenzyme A dehydrogenase activity were found. Phosphate butyryltransferase activity rapidly decreased after 20 h from 5 to 11 U/mg of protein to below the detection limit (1 mU/mg). Butyrate no longer can be formed, and the metabolic flux may be diverted to butanol. Butyrate kinase showed a 2.5- to 10-fold increase in specific activity after phosphate butyryltransferase activity no longer could be detected. These results suggest that the uptake of acetate and butyrate during solvent formation can not proceed via a complete reversal of the phosphate transferase and kinase reactions. The activities of all enzymes investigated as a function of time in vitro are much higher than the metabolic fluxes through them in vivo. This indicates that none of the maximal activities of the enzymes assayed is rate limiting in C. acetobutylicum.
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Affiliation(s)
- M G Hartmanis
- Department of Biochemistry and Biotechnology, Royal Institute of Technology, S-100 44 Stockholm, Sweden
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Wiesenborn DP, Rudolph FB, Papoutsakis ET. Thiolase from Clostridium acetobutylicum ATCC 824 and Its Role in the Synthesis of Acids and Solvents. Appl Environ Microbiol 2010; 54:2717-22. [PMID: 16347774 PMCID: PMC204361 DOI: 10.1128/aem.54.11.2717-2722.1988] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiolase (acetyl-coenzyme A [CoA] acetyltransferase, E.C. 2.3.1.19) from Clostridium acetobutylicum ATCC 824 has been purified 70-fold to homogeneity. Unlike the thiolase in Clostridium pasteurianum, this thiolase has high relative activity throughout the physiological range of internal pH of 5.5 to 7.0, indicating that change in internal pH during acid production is not an important factor in the regulation of this thiolase. In the condensation direction, the thiolase is inhibited by micromolar levels of CoA, and this may be an important factor in modulating the net condensation of acetyl-CoA to acetoacetyl-CoA. Other cofactors and metabolites that were tested and shown to be inhibitors are ATP and butyryl-CoA. The native enzyme consists of four 44,000-molecular-weight subunits. The kinetic binding mechanism is ping-pong. The K(m) value for acetyl-CoA is 0.27 mM at 30 degrees C and pH 7.4. The K(m) values for sulfhydryl-CoA and acetoacetyl-CoA are, respectively, 0.0048 and 0.032 mM at 30 degrees C and pH 8.0. The active site apparently contains a sulfhydryl group, but unlike other thiolases, this thiolase is relatively stable in the presence of 5,5'-dithiobis(2-nitrobenzoic acid). Studies of thiolase specific activity under various types of continuous fermentations show that regulation of this enzyme at both the genetic and enzyme levels is important.
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Affiliation(s)
- D P Wiesenborn
- Department of Chemical Engineering and Department of Biochemistry, Rice University, Houston, Texas 77251
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9
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Stock T, Rother M. Selenoproteins in Archaea and Gram-positive bacteria. Biochim Biophys Acta Gen Subj 2009; 1790:1520-32. [PMID: 19344749 DOI: 10.1016/j.bbagen.2009.03.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 03/23/2009] [Accepted: 03/23/2009] [Indexed: 01/23/2023]
Abstract
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.
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Affiliation(s)
- Tilmann Stock
- Molekulare Mikrobiologie und Bioenergetik, Institut für Molekulare Biowissenschaften, Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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10
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The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci U S A 2008; 105:2128-33. [PMID: 18218779 DOI: 10.1073/pnas.0711093105] [Citation(s) in RCA: 296] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clostridium kluyveri is unique among the clostridia; it grows anaerobically on ethanol and acetate as sole energy sources. Fermentation products are butyrate, caproate, and H2. We report here the genome sequence of C. kluyveri, which revealed new insights into the metabolic capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB) coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for microcompartment proteins, suggesting that the two enzymes, which are isolated together in a macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe, C. kluyveri harbors three sets of genes predicted to encode for polyketide/nonribosomal peptide synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth conditions.
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11
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Stadtman TC. Specific Occurence of Selenium in Certain Enzymes and Amino Acid Transfer Ribonucleic Acids. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/03086648508073402] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Ching WM, Wittwer AJ, Tsai L, Stadtman TC. Distribution of two selenonucleosides among the selenium-containing tRNAs from Methanococcus vannielii. Proc Natl Acad Sci U S A 2005; 81:57-60. [PMID: 16082779 PMCID: PMC344609 DOI: 10.1073/pnas.81.1.57] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Naturally occurring seleno-tRNAs from Methanococcus vannielii account for 13-20% of the total tRNA population. Two different selenium-modified nucleosides were detected in these seleno-tRNAs. Of the total selenium incorporated, about 60% is present in 5-methylaminomethyl-2-selenouridine, and the other 40% occurs in a second selenonucleoside with spectral characteristics typical of a derivative of 2-selenouridine. The 5-methylaminomethyl-2-selenouridine was found in the seleno-tRNA species present in the early fractions of a linear salt gradient elution profile from a reversed-phase chromatographic system 5 (RPC-5) column, whereas the second selenonucleoside occurred in the tRNA species eluted late in the profile.
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Affiliation(s)
- W M Ching
- Laboratory of Biochemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20205
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Affiliation(s)
- Takashi Tamura
- Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Tsushima, Okayama 700-8530, Japan
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Esaki N, Tanaka H, Miles EW, Soda K. Enzymatic synthesis of Se-substituted L-selenocysteine with tryptophan synthase. FEBS Lett 2001. [DOI: 10.1016/0014-5793(83)81008-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Liu Q, Lauridsen E, Clausen J. The major selenium-containing protein in human peripheral granulocytes. Biol Trace Elem Res 1999; 68:193-207. [PMID: 10328336 DOI: 10.1007/bf02783903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Previously, a selenium-containing protein with subunit molecular weight of 15 kDa was found in peripheral human granulocytes. In continuation of this work, the present communication accounts for purification, identification, and characterization of this major selenium-containing protein. The protein was purified on a heparin-Sepharose column followed by Sephacryl S-200 column chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis visualized two bands with subunit molecular weights around 15 kDa. o-Phthaldialdehyde precolumn derivatization and reverse-phase high-performance liquid chromatography showed that the protein contains selenocysteine or selenocystine residues. High-performance gel filtration and isoelectric focusing revealed that the protein had an apparent molecular weight of 32 kDa and a pI value of 7.9. The addition of the protein synthesis inhibitor puromycin to the cell culture medium decreased the 15-kDa protein synthesis. These data suggest that the major selenium-containing protein in peripheral human granulocytes might be a protein with two subunits around 15 kDa. Enzyme studies showed that the protein had peroxidase activity assayed with H2O2 as a substrate and O-dianisidine as a hydrogen donor. This enzymatic activity competed with glutathione peroxidase on the consumption of H2O2, leading to an "inhibiton" of glutathione peroxidase (GSH-Px) activity. Sodium azide could eliminate the inhibition of the protein to GSH-Px. All of the above results implicated that the protein might be a H2O2-dependent selenium containing peroxidase different from GSH-Px. Therefore, the biological function of the protein could be related to eliminating H2O2 generated in the respiratory burst reaction of granulocytes, thus protecting these cells from oxidative damage during phagocytosis.
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Affiliation(s)
- Q Liu
- Department of Life Sciences and Chemistry, Roskilde University, Denmark
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Bennett GN, Rudolph FB. The central metabolic pathway from acetyl-CoA to butyryl-CoA inClostridium acetobutylicum. FEMS Microbiol Rev 1995. [DOI: 10.1111/j.1574-6976.1995.tb00208.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Low SC, Harney JW, Berry MJ. Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis. J Biol Chem 1995; 270:21659-64. [PMID: 7665581 DOI: 10.1074/jbc.270.37.21659] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Selenocysteine is co-translationally incorporated into prokaryotic and eukaryotic selenoproteins at in-frame UGA codons. However, the only component of the eukaryotic selenocysteine incorporation machinery identified to date is the selenocysteine-specific tRNA(Sec). In prokaryotes, selenocysteine is synthesized from seryl-tRNA(Sec) and the active selenium donor, selenophosphate. Selenophosphate is synthesized from selenide and ATP by the selD gene product, selenophosphate synthetase, and is required for selenocysteine synthesis and incorporation into bacterial selenoproteins. We have now cloned human selD and shown that transfection of the human selD cDNA into mammalian cells results in increased selenium labeling of a mammalian selenoprotein, type 1 iodothyronine deiodinase. Despite significant differences between the mechanisms of selenoprotein synthesis in prokaryotes and eukaryotes, human selD weakly complements a bacterial selD mutation, partially restoring selenium incorporation into bacterial selenoproteins. Human selenophosphate synthetase has only 32% homology with the bacterial protein, although a highly homologous region that has similarity to a consensus ATP/GTP binding domain has been identified. Point mutations within this region result in decreased incorporation of selenium into type 1 iodothyronine deiodinase in all but one case. Further analysis revealed that reduced selenium labeling was due to altered ATP binding properties of the mutant selenophosphate synthetases.
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Affiliation(s)
- S C Low
- Thyroid Division, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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Determination of selenocyst(e)amine, selenocyst(e)ine and selenomethionine by gas chromatography with flame photometric detection. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)85091-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- J Heider
- Lehrstuhl für Mikrobiologie, Universität München, Germany
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Abstract
The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.
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Affiliation(s)
- S Osawa
- Department of Biology, Nagoya University, Japan
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Petersen DJ, Bennett GN. Cloning of the Clostridium acetobutylicum ATCC 824 acetyl coenzyme A acetyltransferase (thiolase; EC 2.3.1.9) gene. Appl Environ Microbiol 1991; 57:2735-41. [PMID: 1685080 PMCID: PMC183649 DOI: 10.1128/aem.57.9.2735-2741.1991] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Thiolase (acetyl coenzyme A acetyltransferase; EC 2.3.1.9) from Clostridium acetobutylicum is a key enzyme in the production of acids and solvents in this organism. The purification and properties of the enzyme have already been described (D. P. Wiesenborn, F. B. Rudolph, and E.T. Papoutsakis, Appl. Environ. Microbiol. 54:2717-2722, 1988). The thl gene encoding the thiolase has been cloned by using primary antibodies raised to the purified enzyme. A bacteriophage lambda EMBL3 library of C. acetobutylicum DNA was prepared and screened by immunoblots with the antithiolase antibodies. Phage DNA was purified from positive plaques, and restriction enzyme digests identified an approximately 4.8-kb AccI fragment common to all positive plaques. A corresponding fragment was also found in AccI digests of C. acetobutylicum chromosomal DNA. The fragment was purified and EcoRI linkers were attached before being subcloned into pUC19. Maxicell analysis showed the production of an approximately 42-kDa protein, whose size corresponded to the molecular size of the purified thiolase, from the clostridial insert. Enzyme activity assays and Western blot (immunoblot) analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated whole-cell extracts of Escherichia coli harboring the cloned thl confirmed the presence of the thiolase encoded within the cloned DNA.
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Affiliation(s)
- D J Petersen
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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Abstract
The genetic code is evolving as shown by 9 departures from the universal code: 6 of them are in mitochondria and 3 are in nuclear codes. We propose that these changes are preceded by disappearance of a codon from coding sequences in mRNA of an organism or organelle. The function of the codon that disappears is taken by other, synonymous codons, so that there is no change in amino acid sequences of proteins. The deleted codon then reappears with a new function. Wobble pairing between anticodons and codons has evolved, starting with a single UNN anticodon pairing with 4 codons. Directional mutation pressure affects codon usage and may produce codon reassignments, especially of stop codons. Selenocysteine is coded by UGA, which is also a stop codon, and this anomaly is discussed. The outlook for discovery of more changes in the code is favorable, and open reading frames should be compared with actual sequential analyses of protein molecules in this search.
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Affiliation(s)
- T H Jukes
- Space Sciences Laboratory, University of California/Berkeley, Oakland 94608
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Biosynthetic thiolase from Zoogloea ramigera. III. Isolation and characterization of the structural gene. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75893-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Purification and characterization of selenocysteine beta-lyase from Citrobacter freundii. J Bacteriol 1985; 163:669-76. [PMID: 2991201 PMCID: PMC219174 DOI: 10.1128/jb.163.2.669-676.1985] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The purification and characterization of bacterial selenocysteine beta-lyase, an enzyme which specifically catalyzes the cleavage of L-selenocysteine to L-alanine and Se0, are presented. The enzyme, purified to near homogeneity from Citrobacter freundii, is monomeric with a molecular weight of ca. 64,000 and contains 1 mol of pyridoxal 5'-phosphate as a cofactor per mol of enzyme. L-Selenocysteine is the sole substrate (Km, 0.95 mM). L-Cysteine is a competitive inhibitor of the enzyme (Ki, 0.65 mM). The enzyme also catalyzes the alpha, beta elimination of beta-chloro-L-alanine to form NH3, pyruvate, and Cl- and is irreversibly inactivated during the reaction. The physicochemical properties, e.g., amino acid composition and subunit structure, of the bacterial enzyme are fairly different from those of the pig liver enzyme (Esaki et al., J. Biol. Chem. 257:4386-4391, 1982). However, the catalytic properties of both enzymes, e.g., substrate specificity and inactivation by the substrate or a mechanism-based inactivator, beta-chloro-L-alanine, are very similar.
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Sliwkowski MX, Stadtman TC. Incorporation and distribution of selenium into thiolase from Clostridium kluyveri. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89484-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Adamiak RW, Górnicki P. Hypermodified nucleosides of tRNA: synthesis, chemistry, and structural features of biological interest. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1985; 32:27-74. [PMID: 3911278 DOI: 10.1016/s0079-6603(08)60345-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hartmanis MG, Sliwkowski MX. Selenomethionine-containing thiolase and 3-hydroxybutyryl-CoA dehydrogenase from Clostridium kluyveri. CURRENT TOPICS IN CELLULAR REGULATION 1985; 27:479-86. [PMID: 4092496 DOI: 10.1016/b978-0-12-152827-0.50048-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Tanaka H, Esaki N, Soda K. Selenocysteine metabolism in mammals. CURRENT TOPICS IN CELLULAR REGULATION 1985; 27:487-95. [PMID: 2936577 DOI: 10.1016/b978-0-12-152827-0.50049-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Renosto F, Seubert PA, Segel IH. Adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. Purification and kinetic characterization. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43324-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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