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Diemer V, Roy E, Agouridas V, Melnyk O. Protein desulfurization and deselenization. Chem Soc Rev 2024; 53:8521-8545. [PMID: 39010733 DOI: 10.1039/d4cs00135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Methods enabling the dechalcogenation of thiols or selenols have been investigated and developed for a long time in fields of research as diverse as the study of prebiotic chemistry, the engineering of fuel processing techniques, the study of biomolecule structures and function or the chemical synthesis of biomolecules. The dechalcogenation of thiol or selenol amino acids is nowadays a particularly flourishing area of research for being a pillar of modern chemical protein synthesis, when used in combination with thiol or selenol-based chemoselective peptide ligation chemistries. This review offers a comprehensive and scholarly overview of the field, emphasizing emerging trends and providing a detailed and critical mechanistic discussion of the dechalcogenation methods developed so far. Taking advantage of recently published reports, it also clarifies some unexpected desulfurization reactions that were observed in the past and for which no explanation was provided at the time. Additionally, the review includes a discussion on principal desulfurization methods within the framework of newly introduced green chemistry metrics and toolkits, providing a well-rounded exploration of the subject.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Eliott Roy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
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2
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Bennett ZD, Brunold TC. Non-standard amino acid incorporation into thiol dioxygenases. Methods Enzymol 2024; 703:121-145. [PMID: 39260993 PMCID: PMC11391102 DOI: 10.1016/bs.mie.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Thiol dioxygenases (TDOs) are non‑heme Fe(II)‑dependent enzymes that catalyze the O2-dependent oxidation of thiol substrates to their corresponding sulfinic acids. Six classes of TDOs have thus far been identified and two, cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), are found in eukaryotes. All TDOs belong to the cupin superfamily of enzymes, which share a common β‑barrel fold and two cupin motifs: G(X)5HXH(X)3-6E(X)6G and G(X)5-7PXG(X)2H(X)3N. Crystal structures of TDOs revealed that these enzymes contain a relatively rare, neutral 3‑His iron‑binding facial triad. Despite this shared metal-binding site, TDOs vary greatly in their secondary coordination spheres. Site‑directed mutagenesis has been used extensively to explore the impact of changes in secondary sphere residues on substrate specificity and enzymatic efficiency. This chapter summarizes site-directed mutagenesis studies of eukaryotic TDOs, focusing on the tools and practicality of non‑standard amino acid incorporation.
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Affiliation(s)
- Zachary D Bennett
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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3
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Zhao Z, Laps S, Gichtin JS, Metanis N. Selenium chemistry for spatio-selective peptide and protein functionalization. Nat Rev Chem 2024; 8:211-229. [PMID: 38388838 DOI: 10.1038/s41570-024-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
The ability to construct a peptide or protein in a spatio-specific manner is of great interest for therapeutic and biochemical research. However, the various functional groups present in peptide sequences and the need to perform chemistry under mild and aqueous conditions make selective protein functionalization one of the greatest synthetic challenges. The fascinating paradox of selenium (Se) - being found in both toxic compounds and also harnessed by nature for essential biochemical processes - has inspired the recent exploration of selenium chemistry for site-selective functionalization of peptides and proteins. In this Review, we discuss such approaches, including metal-free and metal-catalysed transformations, as well as traceless chemical modifications. We report their advantages, limitations and applications, as well as future research avenues.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shay Laps
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jacob S Gichtin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Casali Center for Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Hoffman KS, Chung CZ, Mukai T, Krahn N, Jiang HK, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1400-1410. [PMID: 37279998 PMCID: PMC10573291 DOI: 10.1261/rna.079658.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Unique chemical and physical properties are introduced by inserting selenocysteine (Sec) at specific sites within proteins. Recombinant and facile production of eukaryotic selenoproteins would benefit from a yeast expression system; however, the selenoprotein biosynthetic pathway was lost in the evolution of the kingdom Fungi as it diverged from its eukaryotic relatives. Based on our previous development of efficient selenoprotein production in bacteria, we designed a novel Sec biosynthesis pathway in Saccharomyces cerevisiae using Aeromonas salmonicida translation components. S. cerevisiae tRNASer was mutated to resemble A. salmonicida tRNASec to allow recognition by S. cerevisiae seryl-tRNA synthetase as well as A. salmonicida selenocysteine synthase (SelA) and selenophosphate synthetase (SelD). Expression of these Sec pathway components was then combined with metabolic engineering of yeast to enable the production of active methionine sulfate reductase enzyme containing genetically encoded Sec. Our report is the first demonstration that yeast is capable of selenoprotein production by site-specific incorporation of Sec.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Han-Kai Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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5
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Chaudière J. Biological and Catalytic Properties of Selenoproteins. Int J Mol Sci 2023; 24:10109. [PMID: 37373256 DOI: 10.3390/ijms241210109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
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.
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Affiliation(s)
- Jean Chaudière
- CBMN (CNRS, UMR 5248), University of Bordeaux, 33600 Pessac, France
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6
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Urrutia-Baca V, Hernández-Hernández S, Martínez L, Dávila-Vega J, Chuck-Hernández C. The Role of Probiotics in Dairy Foods and Strategies to Evaluate Their Functional Modifications. FOOD REVIEWS INTERNATIONAL 2023. [DOI: 10.1080/87559129.2023.2172426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Affiliation(s)
- V.H Urrutia-Baca
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, México
| | | | - L.M. Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, NL, México
| | - J.P Dávila-Vega
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, México
| | - C. Chuck-Hernández
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, México
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7
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Marjanović JS, Ćoćić D, Caković AZ, Petrović N, Kosanić M, Kostić MD, Divac VM. Seleno‐L‐cystine and Vanillin Schiff's base: Synthesis, Reaction Mechanism and Biological activity. ChemistrySelect 2023. [DOI: 10.1002/slct.202204603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jovana S Marjanović
- Department of Chemistry Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
| | - Dušan Ćoćić
- Department of Chemistry Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
| | - Angelina Z Caković
- Department of Chemistry Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
| | - Nevena Petrović
- Department of Biology and Ecology Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
| | - Marijana Kosanić
- Department of Biology and Ecology Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
| | - Marina D Kostić
- Institute for Information Technologies Kragujevac University of Kragujevac Jovana Cvijića bb 34 000 Kragujevac Serbia
| | - Vera M Divac
- Department of Chemistry Faculty of Science University of Kragujevac Radoja Domanovica 12 34 000 Kragujevac Serbia
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8
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Shaaban S, El-Lateef HMA, Khalaf MM, Gouda M, Youssef I. One-Pot Multicomponent Polymerization, Metal-, and Non-Metal-Catalyzed Synthesis of Organoselenium Compounds. Polymers (Basel) 2022; 14:polym14112208. [PMID: 35683881 PMCID: PMC9182861 DOI: 10.3390/polym14112208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
The one-pot multicomponent synthetic strategy of organoselenium compounds represents an alternative and robust protocol to the conventional multistep methods. During the last decade, a potential advance has been made in this domain. This review discusses the latest advances in the polymerization, metal, and metal-free one-pot multicomponent synthesis of organoselenium compounds.
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Affiliation(s)
- Saad Shaaban
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia; (H.M.A.E.-L.); (M.M.K.); (M.G.)
- Department of Chemistry, Organic Chemistry Division, College of Science, Mansoura University, Mansoura 11432, Egypt
- Correspondence: or (S.S.); (I.Y.)
| | - Hany M. Abd El-Lateef
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia; (H.M.A.E.-L.); (M.M.K.); (M.G.)
- Chemistry Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Mai M. Khalaf
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia; (H.M.A.E.-L.); (M.M.K.); (M.G.)
- Chemistry Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Mohamed Gouda
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia; (H.M.A.E.-L.); (M.M.K.); (M.G.)
| | - Ibrahim Youssef
- Department of Chemistry, Organic Chemistry Division, College of Science, Mansoura University, Mansoura 11432, Egypt
- Transcranial Focused Ultrasound Laboratory, UTSW Medical Center, Dallas, TX 75390, USA
- Neuroradiology and Neuro-Intervention Section, Department of Radiology, UTSW Medical Center, Dallas, TX 75390, USA
- Correspondence: or (S.S.); (I.Y.)
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9
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Expressing recombinant selenoproteins using redefinition of a single UAG codon in an RF1-depleted E. coli host strain. Methods Enzymol 2022; 662:95-118. [PMID: 35101220 DOI: 10.1016/bs.mie.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selenoproteins containing the rare amino acid selenocysteine (Sec), typically being enzymes utilizing the selenium atom of Sec for promoted catalysis of redox reactions, are challenging to obtain at high amounts in pure form. The technical challenges limiting selenoprotein supply derive from intricacies in their translation, necessitating the recoding of a UGA stop codon to a sense codon for Sec. This, in turn, involves the interactions of a Sec-dedicated elongation factor, either directly or indirectly, with a structure in the selenoprotein-encoding mRNA called a SECIS element (Selenocysteine Insertion Sequence), a dedicated tRNA species for Sec with an anticodon for the UGA, and several accessory enzymes and proteins involved in the selenoprotein synthesis. Here, we describe an alternative method for recombinant selenoprotein production using UAG as the Sec codon in a specific strain of E. coli lacking other UAG codons and lacking the release factor RF1 that normally terminates translation at UAG. We also describe how such recombinant selenoproteins can be purified and further analyzed for final Sec contents. The methodology can be used for production of natural selenoproteins in recombinant form as well as for production of synthetic selenoproteins that may be designed to use the unique biophysical properties of Sec for diverse biotechnological applications.
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10
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Zhao Z, Mousa R, Metanis N. One-Pot Chemical Protein Synthesis Utilizing Fmoc-Masked Selenazolidine to Address the Redox Functionality of Human Selenoprotein F. Chemistry 2022; 28:e202200279. [PMID: 35112407 PMCID: PMC9304195 DOI: 10.1002/chem.202200279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/25/2022]
Abstract
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.
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Affiliation(s)
- Zhenguang Zhao
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Reem Mousa
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Norman Metanis
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
- The Center for Nanoscience and NanotechnologyThe Hebrew University of JerusalemJerusalem9190401Israel
- Casali Center for Applied ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
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11
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Cáceres JC, Bailey CA, Yokoyama K, Greene BL. Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022; 662:119-141. [DOI: 10.1016/bs.mie.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Kalil H, Fouad F, Azeroual S, Bose T, Bayachou M. Bottom‐Up Design of a Grafted Organic Selenide Interface for Sensitive Electrocatalytic Detection of Peroxynitrite. ChemElectroChem 2021. [DOI: 10.1002/celc.202100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haitham Kalil
- Department of Chemistry College of Science Cleveland State University Cleveland Ohio 44115 USA
- Department of Chemistry Faculty of Science Suez Canal University Ismailia Egypt
| | - Farid Fouad
- Department of Chemistry and Biochemistry Kent State University Ohio 44242 USA
| | - Sami Azeroual
- Department of Chemistry and Biochemistry Kent State University Ohio 44242 USA
| | - Tiyash Bose
- Department of Chemistry College of Science Cleveland State University Cleveland Ohio 44115 USA
| | - Mekki Bayachou
- Department of Chemistry College of Science Cleveland State University Cleveland Ohio 44115 USA
- Department of Inflammation and Immunity Lerner Research Institute Cleveland Clinic Cleveland Ohio 44195 USA
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13
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Chung CZ, Krahn N, Crnković A, Söll D. Intein-based Design Expands Diversity of Selenocysteine Reporters. J Mol Biol 2021; 434:167199. [PMID: 34411545 PMCID: PMC8847544 DOI: 10.1016/j.jmb.2021.167199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/27/2022]
Abstract
The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA.
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14
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Chung CZ, Miller C, Söll D, Krahn N. Introducing Selenocysteine into Recombinant Proteins in Escherichia coli. Curr Protoc 2021; 1:e54. [PMID: 33566458 DOI: 10.1002/cpz1.54] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selenoproteins contain the 21st amino acid, selenocysteine. Selenocysteine is the only amino acid that is synthesized on its cognate tRNA, and it is inserted at specific recoded UGA stop codons via a complex translation system. Although highly similar to cysteine, selenocysteine has unique properties, including a stronger nucleophilic ability and lower reduction potential. Efforts to site-specifically incorporate selenocysteine to create recombinant selenoproteins involve a recoded UAG stop codon and expression of the necessary selenocysteine translation machinery. This article presents a protocol for expressing and purifying selenoproteins in Escherichia coli. © 2021 Wiley Periodicals LLC. Basic Protocol: Recombinant selenoprotein production in E. coli using a rewired translation system.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Corwin Miller
- Department of Biosciences, Rice University, Houston, Texas
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Department of Chemistry, Yale University, New Haven, Connecticut
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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15
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Wang Y, Liu P, Chang J, Xu Y, Wang J. Site-Specific Selenocysteine Incorporation into Proteins by Genetic Engineering. Chembiochem 2021; 22:2918-2924. [PMID: 33949764 DOI: 10.1002/cbic.202100124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/03/2021] [Indexed: 01/23/2023]
Abstract
Selenocysteine (Sec), a rare naturally proteinogenic amino acid, is the major form of essential trace element selenium in living organisms. Selenoproteins, with one or several Sec residues, are found in all three domains of life. Many selenoproteins play a role in critical cellular functions such as maintaining cell redox homeostasis. Sec is usually encoded by an in-frame stop codon UGA in the selenoprotein mRNA, and its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. This mechanistic complexity of selenoprotein synthesis poses a big challenge to produce synthetic selenoproteins. To understand the functions of natural as well as engineered selenoproteins, many strategies have recently been developed to overcome the inherent barrier for recombinant selenoprotein production. In this review, we will describe the progress in selenoprotein production methodology.
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Affiliation(s)
- Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
| | - Pengcheng Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Jiao Chang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Yunping Xu
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China
| | - Jiangyun Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
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16
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Oroz P, Navo CD, Avenoza A, Busto JH, Corzana F, Jiménez-Osés G, Peregrina JM. Toward Enantiomerically Pure β-Seleno-α-amino Acids via Stereoselective Se-Michael Additions to Chiral Dehydroalanines. Org Lett 2021; 23:1955-1959. [PMID: 33373248 DOI: 10.1021/acs.orglett.0c03832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first totally chemo- and diastereoselective 1,4-conjugate additions of Se-nucleophiles to a chiral bicyclic dehydroalanine (Dha) are described. The methodology is simple and does not require any catalyst, providing exceptional yields at room temperature, and involves the treatment of the corresponding diselenide compound with NaBH4 in the presence of the Dha. These Se-Michael additions provide an excellent channel for the synthesis of enantiomerically pure selenocysteine (Sec) derivatives, which pose high potential for chemical biology applications.
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Affiliation(s)
- Paula Oroz
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Alberto Avenoza
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Jesús H Busto
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Jesús M Peregrina
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
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17
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Diselenide crosslinks for enhanced and simplified oxidative protein folding. Commun Chem 2021; 4:30. [PMID: 36697775 PMCID: PMC9814483 DOI: 10.1038/s42004-021-00463-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/29/2021] [Indexed: 01/28/2023] Open
Abstract
The in vitro oxidative folding of proteins has been studied for over sixty years, providing critical insight into protein folding mechanisms. Hirudin, the most potent natural inhibitor of thrombin, is a 65-residue protein with three disulfide bonds, and is viewed as a folding model for a wide range of disulfide-rich proteins. Hirudin's folding pathway is notorious for its highly heterogeneous intermediates and scrambled isomers, limiting its folding rate and yield in vitro. Aiming to overcome these limitations, we undertake systematic investigation of diselenide bridges at native and non-native positions and investigate their effect on hirudin's folding, structure and activity. Our studies demonstrate that, regardless of the specific positions of these substitutions, the diselenide crosslinks enhanced the folding rate and yield of the corresponding hirudin analogues, while reducing the complexity and heterogeneity of the process. Moreover, crystal structure analysis confirms that the diselenide substitutions maintained the overall three-dimensional structure of the protein and left its function virtually unchanged. The choice of hirudin as a study model has implications beyond its specific folding mechanism, demonstrating the high potential of diselenide substitutions in the design, preparation and characterization of disulfide-rich proteins.
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18
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Joardar N, Guevara-Flores A, Martínez-González JDJ, Sinha Babu SP. Thiol antioxidant thioredoxin reductase: A prospective biochemical crossroads between anticancer and antiparasitic treatments of the modern era. Int J Biol Macromol 2020; 165:249-267. [DOI: 10.1016/j.ijbiomac.2020.09.096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 02/08/2023]
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19
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Guo S, He S, Lu P, Zhang Y. Effects of selenium atom on the solution properties of N-alkyl-N-methylpyrrolidinium bromide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Dhayalan B, Chen YS, Phillips NB, Swain M, Rege NK, Mirsalehi A, Jarosinski M, Ismail-Beigi F, Metanis N, Weiss MA. Reassessment of an Innovative Insulin Analogue Excludes Protracted Action yet Highlights the Distinction between External and Internal Diselenide Bridges. Chemistry 2020; 26:4695-4700. [PMID: 31958351 DOI: 10.1002/chem.202000309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Indexed: 01/31/2023]
Abstract
Long-acting insulin analogues represent the most prescribed class of therapeutic proteins. An innovative design strategy was recently proposed: diselenide substitution of an external disulfide bridge. This approach exploited the distinctive physicochemical properties of selenocysteine (U). Relative to wild type (WT), Se-insulin[C7UA , C7UB ] was reported to be protected from proteolysis by insulin-degrading enzyme (IDE), predicting prolonged activity. Because of this strategy's novelty and potential clinical importance, we sought to validate these findings and test their therapeutic utility in an animal model of diabetes mellitus. Surprisingly, the analogue did not exhibit enhanced stability, and its susceptibility to cleavage by either IDE or a canonical serine protease (glutamyl endopeptidase Glu-C) was similar to WT. Moreover, the analogue's pharmacodynamic profile in rats was not prolonged relative to a rapid-acting clinical analogue (insulin lispro). Although [C7UA , C7UB ] does not confer protracted action, nonetheless its comparison to internal diselenide bridges promises to provide broad biophysical insight.
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Affiliation(s)
- Balamurugan Dhayalan
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yen-Shan Chen
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nelson B Phillips
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Mamuni Swain
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Nischay K Rege
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Ali Mirsalehi
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Mark Jarosinski
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Faramarz Ismail-Beigi
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Michael A Weiss
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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21
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Roopesh Kumar L, Sagar NR, Divya K, Madhu C, Sureshbabu VV. Synthesis of an amino phosphinodiselenoic acid ester and β-amino diselenides employing P 2Se 5. NEW J CHEM 2020. [DOI: 10.1039/d0nj00012d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protic solvents furnished amino phosphinodiselenoic acid esters, whereas β-amino diselenides were obtained exclusively when reactions performed in polar aprotic solvents.
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Affiliation(s)
- L. Roopesh Kumar
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Bangalore University
- Bangalore-560 056
- India
| | - N. R. Sagar
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Bangalore University
- Bangalore-560 056
- India
| | - K. Divya
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Bangalore University
- Bangalore-560 056
- India
| | - C. Madhu
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Bangalore University
- Bangalore-560 056
- India
| | - Vommina V Sureshbabu
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Bangalore University
- Bangalore-560 056
- India
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22
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Lim D, Gründemann D, Seebeck FP. Total Synthesis and Functional Characterization of Selenoneine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David Lim
- Department for Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Dirk Gründemann
- Department of Pharmacology University of Cologne, Faculty of Medicine and University Hospital Cologne Gleueler Straße 24 50931 Cologne Germany
| | - Florian P. Seebeck
- Department for Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
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23
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Lim D, Gründemann D, Seebeck FP. Total Synthesis and Functional Characterization of Selenoneine. Angew Chem Int Ed Engl 2019; 58:15026-15030. [DOI: 10.1002/anie.201908967] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Indexed: 12/19/2022]
Affiliation(s)
- David Lim
- Department for Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Dirk Gründemann
- Department of Pharmacology University of Cologne, Faculty of Medicine and University Hospital Cologne Gleueler Straße 24 50931 Cologne Germany
| | - Florian P. Seebeck
- Department for Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
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24
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Metanis N, Notis Dardashti R, Mousa R, Weil-Ktorza O. Miklós Bodanszky Award Lecture: Selective chalcogen chemistry to study protein science. J Pept Sci 2019; 25:e3204. [PMID: 31407415 DOI: 10.1002/psc.3204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Abstract
In recent decades, chemical protein synthesis and the development of chemoselective reactions-including ligation reactions-have led to significant breakthroughs in protein science. Among them are a better understanding of protein structure-function relationships, the study of protein posttranslational modifications, exploration of protein design, unnatural amino acid incorporation, and the study of therapeutic proteins and protein folding. Chalcogen chemistry, especially that of sulfur and selenium, is quite rich, and we have witnessed continuous progress in this field in recent years. In this short review, we will instead summarize three stories that we have recently presented on chalcogen chemistry and its impact on protein science, which was presented in the Miklós Bodanszky Award Lecture at the 35th European Peptide Society Meeting in Dublin, Ireland, 26 August 2018.
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Affiliation(s)
- Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Reem Mousa
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Weil-Ktorza
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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25
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Hamsath A, Wang Y, Yang CT, Xu S, Cañedo D, Chen W, Xian M. Acyl Selenyl Sulfides as the Precursors for Reactive Sulfur Species (Hydrogen Sulfide, Polysulfide, and Selenyl Sulfide). Org Lett 2019; 21:5685-5688. [PMID: 31264875 DOI: 10.1021/acs.orglett.9b02021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Persulfides are receiving increased attention due to their links to hydrogen sulfide (H2S) and hydrogen polysulfide (H2Sn). Their close analogues selenyl sulfides (RSeSHs), however, have limited literature precedent, and their reactivity and possible role in biology are largely unknown. Here, we devised an acyl selenyl sulfide template to study RSeSH chemistry. Their stability and reactivity toward amines/thiols were studied. These compounds can produce H2S or H2S2 under different conditions, suggesting that RSeSHs are possible intermediates.
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Affiliation(s)
- Akil Hamsath
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Yingying Wang
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Chun-Tao Yang
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University , Guangzhou 510095 , China
| | - Shi Xu
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Danica Cañedo
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Wei Chen
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Ming Xian
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
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26
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Guo S, He S, Chen Z, Zhang Y. Reactive oxygen species-responsive vesicle formed by selenium-containing cationic surfactant and SDS. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Wu G, Ge C, Liu X, Wang S, Wang L, Yin L, Lu H. Synthesis of water soluble and multi-responsive selenopolypeptides via ring-opening polymerization of N-carboxyanhydrides. Chem Commun (Camb) 2019; 55:7860-7863. [DOI: 10.1039/c9cc03767e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Synthesis of selenopolypeptides via ring opening polymerization of N-carboxyanhydrides.
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Affiliation(s)
- Guangqi Wu
- Beijing National Laboratory for Molecular Sciences
- Center for Soft Matter Science and Engineering
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Chenglong Ge
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Collaborative Innovation Center of Suzhou Nano Science & Technology
- Soochow University
- Suzhou 215123
| | - Xingyi Liu
- Beijing National Laboratory for Molecular Sciences
- Center for Soft Matter Science and Engineering
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Shuo Wang
- Beijing National Laboratory for Molecular Sciences
- Center for Soft Matter Science and Engineering
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Letian Wang
- Beijing National Laboratory for Molecular Sciences
- Center for Soft Matter Science and Engineering
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Lichen Yin
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Collaborative Innovation Center of Suzhou Nano Science & Technology
- Soochow University
- Suzhou 215123
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences
- Center for Soft Matter Science and Engineering
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
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28
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Micellization of selenium-containing cationic surfactants with different headgroups in aqueous solution. Colloid Polym Sci 2018. [DOI: 10.1007/s00396-018-4454-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Cheignon C, Cordeau E, Prache N, Cantel S, Martinez J, Subra G, Arnaudguilhem C, Bouyssiere B, Enjalbal C. Receptor-Ligand Interaction Measured by Inductively Coupled Plasma Mass Spectrometry and Selenium Labeling. J Med Chem 2018; 61:10173-10184. [PMID: 30395477 DOI: 10.1021/acs.jmedchem.8b01320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the search for an alternative strategy to the radioactivity measurement conventionally performed to probe receptor-ligand interactions in pharmacological assays, we demonstrated that selenium labeling of the studied ligand combined with elemental mass spectrometry was as efficient and robust as the reference method but devoid of its environmental and health hazards. The proof-of-concept was illustrated on two GPCR receptors, vasopressin (V1A) and cholecystokinin B (CCK-B), involving peptides as endogenous ligands. We proposed several methodologies to produce selenium-labeled ligands according to peptide sequences along with binding affinity constraints. A selection of selenopeptides that kept high affinities toward the targeted receptor were engaged in saturation and competitive binding experiments with subsequent sensitive RP-LC-ICP-MS measurements. Experimental values of affinity constant ( Ki) were perfectly correlated to literature data, illustrating the general great potency of replacing radioactive iodine by selenium for ligand labeling to further undergo unaffected pharmacology experiments efficiently monitored by elemental mass spectrometry.
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Affiliation(s)
- Clémence Cheignon
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Emmanuelle Cordeau
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Nolween Prache
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Sonia Cantel
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Jean Martinez
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Gilles Subra
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Carine Arnaudguilhem
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Brice Bouyssiere
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Christine Enjalbal
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
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30
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Versatility of Synthetic tRNAs in Genetic Code Expansion. Genes (Basel) 2018; 9:genes9110537. [PMID: 30405060 PMCID: PMC6267555 DOI: 10.3390/genes9110537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022] Open
Abstract
Transfer RNA (tRNA) is a dynamic molecule used by all forms of life as a key component of the translation apparatus. Each tRNA is highly processed, structured, and modified, to accurately deliver amino acids to the ribosome for protein synthesis. The tRNA molecule is a critical component in synthetic biology methods for the synthesis of proteins designed to contain non-canonical amino acids (ncAAs). The multiple interactions and maturation requirements of a tRNA pose engineering challenges, but also offer tunable features. Major advances in the field of genetic code expansion have repeatedly demonstrated the central importance of suppressor tRNAs for efficient incorporation of ncAAs. Here we review the current status of two fundamentally different translation systems (TSs), selenocysteine (Sec)- and pyrrolysine (Pyl)-TSs. Idiosyncratic requirements of each of these TSs mandate how their tRNAs are adapted and dictate the techniques used to select or identify the best synthetic variants.
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31
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Liu J, Zheng F, Cheng R, Li S, Rozovsky S, Wang Q, Wang L. Site-Specific Incorporation of Selenocysteine Using an Expanded Genetic Code and Palladium-Mediated Chemical Deprotection. J Am Chem Soc 2018; 140:8807-8816. [PMID: 29984990 PMCID: PMC6082430 DOI: 10.1021/jacs.8b04603] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Selenoproteins containing the 21st amino acid selenocysteine (Sec) exist in all three kingdoms of life and play essential roles in human health and development. The distinct low p Ka, high reactivity, and redox property of Sec also afford unique routes to protein modification and engineering. However, natural Sec incorporation requires idiosyncratic translational machineries that are dedicated to Sec and species-dependent, which makes it challenging to recombinantly prepare selenoproteins with high Sec specificity. As a consequence, the function of half of human selenoproteins remains unclear, and Sec-based protein manipulation has been greatly hampered. Here we report a new general method enabling the site-specific incorporation of Sec into proteins in E. coli. An orthogonal tRNAPyl-ASecRS was evolved to specifically incorporate Se-allyl selenocysteine (ASec) in response to the amber codon, and the incorporated ASec was converted to Sec in high efficiency through palladium-mediated cleavage under mild conditions compatible with proteins and cells. This approach completely obviates the natural Sec-dedicated factors, thus allowing various selenoproteins, regardless of Sec position and species source, to be prepared with high Sec specificity and enzyme activity, as shown by the preparation of human thioredoxin and glutathione peroxidase 1. Sec-selective labeling in the presence of Cys was also demonstrated on the surface of live E. coli cells. The tRNAPyl-ASecRS pair was further used in mammalian cells to incorporate ASec, which was converted into Sec by palladium catalyst in cellulo. This robust and versatile method should greatly facilitate the study of diverse natural selenoproteins and the engineering of proteins in general via site-specific introduction of Sec.
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Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
| | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, China, 310018
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Shanshan Li
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, China, 310018
| | - Lei Wang
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
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32
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Mühlhausen S, Schmitt HD, Pan KT, Plessmann U, Urlaub H, Hurst LD, Kollmar M. Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica. Curr Biol 2018; 28:2046-2057.e5. [PMID: 29910077 PMCID: PMC6041473 DOI: 10.1016/j.cub.2018.04.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 12/24/2022]
Abstract
Although the “universal” genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes. Related yeasts solve the problem by loss of function of one of the two tRNAs. This dual coding is consistent with the tRNA-loss-driven codon reassignment hypothesis, and provides a unique example of a proteome that cannot be deterministically predicted. Video Abstract
Ascoidea asiatica stochastically encodes CUG as leucine and serine It is the only known example of a proteome with non-deterministic features Stochastic encoding is caused by competing tRNALeu(CAG) and tRNASer(CAG) A. asiatica copes with stochastic encoding by avoiding CUG at key positions
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Affiliation(s)
- Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hans Dieter Schmitt
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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33
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Dadová J, Galan SR, Davis BG. Synthesis of modified proteins via functionalization of dehydroalanine. Curr Opin Chem Biol 2018; 46:71-81. [PMID: 29913421 DOI: 10.1016/j.cbpa.2018.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Dehydroalanine has emerged in recent years as a non-proteinogenic residue with strong chemical utility in proteins for the study of biology. In this review we cover the several methods now available for its flexible and site-selective incorporation via a variety of complementary chemical and biological techniques and examine its reactivity, allowing both creation of modified protein side-chains through a variety of bond-forming methods (C-S, C-N, C-Se, C-C) and as an activity-based probe in its own right. We illustrate its utility with selected examples of biological and technological discovery and application.
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Affiliation(s)
- Jitka Dadová
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sébastien Rg Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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34
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Zoidis E, Seremelis I, Kontopoulos N, Danezis GP. Selenium-Dependent Antioxidant Enzymes: Actions and Properties of Selenoproteins. Antioxidants (Basel) 2018; 7:E66. [PMID: 29758013 PMCID: PMC5981252 DOI: 10.3390/antiox7050066] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/23/2022] Open
Abstract
Unlike other essential trace elements that interact with proteins in the form of cofactors, selenium (Se) becomes co-translationally incorporated into the polypeptide chain as part of 21st naturally occurring amino acid, selenocysteine (Sec), encoded by the UGA codon. Any protein that includes Sec in its polypeptide chain is defined as selenoprotein. Members of the selenoproteins family exert various functions and their synthesis depends on specific cofactors and on dietary Se. The Se intake in productive animals such as chickens affect nutrient utilization, production performances, antioxidative status and responses of the immune system. Although several functions of selenoproteins are unknown, many disorders are related to alterations in selenoprotein expression or activity. Selenium insufficiency and polymorphisms or mutations in selenoproteins' genes and synthesis cofactors are involved in the pathophysiology of many diseases, including cardiovascular disorders, immune dysfunctions, cancer, muscle and bone disorders, endocrine functions and neurological disorders. Finally, heavy metal poisoning decreases mRNA levels of selenoproteins and increases mRNA levels of inflammatory factors, underlying the antagonistic effect of Se. This review is an update on Se dependent antioxidant enzymes, presenting the current state of the art and is focusing on results obtained mainly in chicken.
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Affiliation(s)
- Evangelos Zoidis
- Department of Nutritional Physiology and Feeding, Faculty of Animal Science and Aquaculture, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece.
| | - Isidoros Seremelis
- Chemistry Laboratory, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece.
| | - Nikolaos Kontopoulos
- Chemistry Laboratory, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece.
| | - Georgios P Danezis
- Chemistry Laboratory, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece.
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35
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Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. Eine einfache Methode zur Produktion von Selenoproteinen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
- Department of Chemistry Yale University New Haven CT 06520 USA
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36
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Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. A Facile Method for Producing Selenocysteine-Containing Proteins. Angew Chem Int Ed Engl 2018; 57:7215-7219. [PMID: 29631320 DOI: 10.1002/anie.201713215] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/20/2018] [Indexed: 01/14/2023]
Abstract
Selenocysteine (Sec, U) confers new chemical properties on proteins. Improved tools are thus required that enable Sec insertion into any desired position of a protein. We report a facile method for synthesizing selenoproteins with multiple Sec residues by expanding the genetic code of Escherichia coli. We recently discovered allo-tRNAs, tRNA species with unusual structure, that are as efficient serine acceptors as E. coli tRNASer . Ser-allo-tRNA was converted into Sec-allo-tRNA by Aeromonas salmonicida selenocysteine synthase (SelA). Sec-allo-tRNA variants were able to read through five UAG codons in the fdhF mRNA coding for E. coli formate dehydrogenase H, and produced active FDHH with five Sec residues in E. coli. Engineering of the E. coli selenium metabolism along with mutational changes in allo-tRNA and SelA improved the yield and purity of recombinant human glutathione peroxidase 1 (to over 80 %). Thus, our allo-tRNAUTu system offers a new selenoprotein engineering platform.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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37
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Liu J, Cheng R, Rozovsky S. Synthesis and semisynthesis of selenopeptides and selenoproteins. Curr Opin Chem Biol 2018; 46:41-47. [PMID: 29723718 DOI: 10.1016/j.cbpa.2018.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 11/19/2022]
Abstract
The versatile chemistry of the genetically encoded amino acid selenocysteine (Sec) is employed in Nature to expand the reactivity of enzymes. In addition to, its role in biology, Sec is used in protein engineering to modify folding, stability, and reactivity of proteins, to introduce conjugations and to facilitate reactions. However, due to limitations related to Sec's insertion mechanism in Nature, much of the production of Sec containing peptides and proteins relies on synthesis and semisynthesis. Here, we review recent advances that have enabled the assembly of complicated selenoproteins, including novel uses of protecting groups for solid phase peptide synthesis, rapid selenoester driven chemical ligations and versatile expressed protein ligations.
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Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA 94158, United States.
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States.
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38
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Ferentinos E, Chatziefthimiou S, Boudalis AK, Pissas M, Mathies G, Gast P, Groenen EJJ, Sanakis Y, Kyritsis P. The [Fe{(SePPh2
)2
N}2
] Complex Revisited: X-ray Crystallography, Magnetometry, High-Frequency EPR, and Mössbauer Studies Reveal Its Tetrahedral FeII
Se4
Coordination Sphere. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eleftherios Ferentinos
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
| | - Spyros Chatziefthimiou
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Athanassios K. Boudalis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Michael Pissas
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Guinevere Mathies
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Peter Gast
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Edgar J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Yiannis Sanakis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Panayotis Kyritsis
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
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39
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Kang J, Ferrell AJ, Chen W, Wang D, Xian M. Cyclic Acyl Disulfides and Acyl Selenylsulfides as the Precursors for Persulfides (RSSH), Selenylsulfides (RSeSH), and Hydrogen Sulfide (H 2S). Org Lett 2018; 20:852-855. [PMID: 29345467 PMCID: PMC5797492 DOI: 10.1021/acs.orglett.7b04005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactions of three model compounds (1-3) for cyclic acyl disulfides and cyclic acyl selenylsulfides are studied. These compounds were found to be effective precursors for persulfides (RSSH) and selenylsulfides (RSeSH) upon reacting with nucleophilic species. They could also act as H2S donors when interacting with cellular thiols. The most interesting discovery was the generation of RSeSH from compound 3 under mild conditions. Selenylsulfides (RSeSH) are expected to be important regulating molecules involved in Sec-related redox signaling. The method of producing RSeSH should allow researchers to better understand the chemical biology of RSeSH.
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Affiliation(s)
- Jianming Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Aaron J. Ferrell
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wei Chen
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland 20850, United States
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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40
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Mousa R, Notis Dardashti R, Metanis N. Selen und Selenocystein in der Proteinchemie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
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41
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Mousa R, Notis Dardashti R, Metanis N. Selenium and Selenocysteine in Protein Chemistry. Angew Chem Int Ed Engl 2017; 56:15818-15827. [PMID: 28857389 DOI: 10.1002/anie.201706876] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/22/2023]
Abstract
Selenocysteine, the selenium-containing analogue of cysteine, is the twenty-first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.
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Affiliation(s)
- Reem Mousa
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
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42
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Dardashti RN, Metanis N. Revisiting ligation at selenomethionine: Insights into native chemical ligation at selenocysteine and homoselenocysteine. Bioorg Med Chem 2017; 25:4983-4989. [DOI: 10.1016/j.bmc.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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43
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Agouridas V, El Mahdi O, Cargoët M, Melnyk O. A statistical view of protein chemical synthesis using NCL and extended methodologies. Bioorg Med Chem 2017; 25:4938-4945. [PMID: 28578993 DOI: 10.1016/j.bmc.2017.05.050] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 11/19/2022]
Abstract
Native chemical ligation and extended methodologies are the most popular chemoselective reactions for protein chemical synthesis. Their combination with desulfurization techniques can give access to small or challenging proteins that are exploited in a large variety of research areas. In this report, we have conducted a statistical review of their use for protein chemical synthesis in order to provide a flavor of the recent trends and identify the most popular chemical tools used by protein chemists. To this end, a protein chemical synthesis (PCS) database (http://pcs-db.fr) was created by collecting a set of relevant data from more than 450 publications covering the period 1994-2017. A preliminary account of what this database tells us is presented in this report.
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Affiliation(s)
- Vangelis Agouridas
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France.
| | | | - Marine Cargoët
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France.
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44
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Li Z, Tan J, Shao L, Dong X, Ye RD, Chen D. Selenium-mediated protection in reversing the sensitivity of bacterium to the bactericidal antibiotics. J Trace Elem Med Biol 2017; 41:23-31. [PMID: 28347459 DOI: 10.1016/j.jtemb.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/12/2017] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
Abstract
Inducing production of damaging reactive oxygen species (ROS) is an important criterion to distinguish the bactericidal antibiotics from bacteriostatic antibiotics. Selenoenzymes were generally recognized to be a powerful antioxidant capable of scavenging free radicals, protecting the cells from the harmful effects of ROS. Therefore, the present study was carried out to investigate the selenium (Se)-mediated protection in reversing antibiotic sensitivity and the role of selenoenzymes in alleviating the negative effects of oxidative stress. The cellular antioxidant activity of Se-enriched bacteria was analyzed, as well as intracellular ROS production and elimination when Se-enriched bacteria in the presence of various antibiotics. Compared to complete inhibition of the parental strain by bactericidal antibiotics, it only exhibited slight and reversible inhibition of Se-enriched Escherichia coli ATCC25922 and Staphylococcus aureus ATCC25923 at the same conditions, which indicated that intracellular selenium provided substantial protection against antibiotics. ROS generation caused by bactericidal antibiotics was confirmed by fluorescence spectrophotometry using 2', 7'-dichloro- uorescein diacetate (DCFH-DA) as substrate. The time course experiments of pretreatment with selenium showed significant decrease of ROS level at 2h. In summary, the present study provides experimental evidence supporting selenoenzymes has good scavenging effect to ROS and can protect bacteria from oxidative stress injury induced by bactericidal antibiotics.
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Affiliation(s)
- Zhonglei Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jun Tan
- China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Lei Shao
- China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Xiaojing Dong
- China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Richard D Ye
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China.
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45
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Liu J, Chen Q, Rozovsky S. Utilizing Selenocysteine for Expressed Protein Ligation and Bioconjugations. J Am Chem Soc 2017; 139:3430-3437. [PMID: 28186733 PMCID: PMC5824972 DOI: 10.1021/jacs.6b10991] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Employing selenocysteine-containing protein fragments to form the amide bond between respective protein fragments significantly extends the current capabilities of the widely used protein engineering method, expressed protein ligation. Selenocysteine-mediated ligation is noteworthy for its high yield and efficiency. However, it has so far been restricted to solid-phase synthesized seleno-peptides and thus constrained by where the selenocysteine can be positioned. Here we employ heterologously expressed seleno-fragments to overcome the placement and size restrictions in selenocysteine-mediated chemical ligation. Following ligation, the selenocysteine can be deselenized into an alanine or serine, resulting in nonselenoproteins. This greatly extends the flexibility in selecting the conjugation site in expressed protein ligations with no influence on native cysteines. Furthermore, the selenocysteine can be used to selectively introduce site-specific protein modifications. Therefore, selenocysteine-mediated expressed protein ligation simplifies incorporation of post-translational modifications into the protein scaffold.
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Affiliation(s)
| | | | - Sharon Rozovsky
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716
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46
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Dery L, Reddy PS, Dery S, Mousa R, Ktorza O, Talhami A, Metanis N. Accessing human selenoproteins through chemical protein synthesis. Chem Sci 2017; 8:1922-1926. [PMID: 28451306 PMCID: PMC5364654 DOI: 10.1039/c6sc04123j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/29/2016] [Indexed: 12/28/2022] Open
Abstract
The human body contains 25 selenoproteins, which contain in their sequence the twenty-first encoded amino acid, selenocysteine. About a dozen of these proteins remain functionally uncharacterized or poorly studied. Challenges in accessing these selenoproteins using traditional recombinant expressions have prevented biological characterization thus far. Chemical protein synthesis has the potential to overcome these hurdles. Here we report the first total chemical syntheses of two human selenoproteins, selenoprotein M (SELM) and selenoprotein W (SELW). The synthesis of the more challenging protein SELM was enabled using recent advances in the field of selenocysteine chemistry. This approach allows the preparation of selenoproteins in milligram quantities and in homogenous form, which should open new horizons for future studies to pursue a fuller biological understanding of their role in health and disease.
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Affiliation(s)
- L Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - P Sai Reddy
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - S Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - R Mousa
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - O Ktorza
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - A Talhami
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
| | - N Metanis
- Institute of Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra, Givat Ram , Jerusalem 91904 , Israel .
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47
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Cheng Q, Arnér ESJ. Selenocysteine Insertion at a Predefined UAG Codon in a Release Factor 1 (RF1)-depleted Escherichia coli Host Strain Bypasses Species Barriers in Recombinant Selenoprotein Translation. J Biol Chem 2017; 292:5476-5487. [PMID: 28193838 DOI: 10.1074/jbc.m117.776310] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/02/2017] [Indexed: 11/06/2022] Open
Abstract
Selenoproteins contain the amino acid selenocysteine (Sec), co-translationally inserted at a predefined UGA opal codon by means of Sec-specific translation machineries. In Escherichia coli, this process is dependent upon binding of the Sec-dedicated elongation factor SelB to a Sec insertion sequence (SECIS) element in the selenoprotein-encoding mRNA and competes with UGA-directed translational termination. Here, we found that Sec can also be efficiently incorporated at a predefined UAG amber codon, thereby competing with RF1 rather than RF2. Subsequently, utilizing the RF1-depleted E. coli strain C321.ΔA, we could produce mammalian selenoprotein thioredoxin reductases with unsurpassed purity and yield. We also found that a SECIS element was no longer absolutely required in such a system. Human glutathione peroxidase 1 could thereby also be produced, and we could confirm a previously proposed catalytic tetrad in this selenoprotein. We believe that the versatility of this new UAG-directed production methodology should enable many further studies of diverse selenoproteins.
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Affiliation(s)
- Qing Cheng
- From the Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Elias S J Arnér
- From the Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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48
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Saxena A, Fayad R, Kaur K, Truman S, Greer J, Carson JA, Chanda A. Dietary selenium protects adiponectin knockout mice against chronic inflammation induced colon cancer. Cancer Biol Ther 2017; 18:257-267. [PMID: 28045589 DOI: 10.1080/15384047.2016.1276130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Selenium (Se) is an essential dietary micronutrient that has been examined for protection against different types of cancers including colon cancer. Despite an established inverse association between Se and chronic inflammation induced colon cancer (CICC), the mechanistic understanding of Se's protective effects requires additional in-vivo studies using preclinical animal models of CICC. Adiponectin (APN) is an adipocytokine that is protective against CICC as well. However, its role in the anti-mutagenic effects of the Se-diet remains unknown. To address this knowledge gap, here we examine the ability of dietary Se in reducing CICC in APN knockout mice (KO) and its wild-type C57BL/6. CICC was induced with the colon cancer agent 1,2 dimethyl hydrazine (DMH) along with dextran sodium sulfate (DSS). Se-enhanced diet increased selenoproteins, Gpx-1 and Gpx-2, in the colon tissues, thereby reducing oxidative stress. Se-mediated reduction of CICC was evident from the histopathological studies in both mouse models. In both mice, reduction in inflammation and tumorigenesis associated well with reduced p65 phosphorylation and elevated 53 phosphorylation. Finally, we show that in both models Se-administration promotes goblet cell differentiation with a concomitant increase in the levels of associated proteins, Muc-2 and Math-1. Our findings suggest that Se's protection against CICC involves both colonic epithelial protection and anti-tumor effects that are independent of APN.
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Affiliation(s)
- Arpit Saxena
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA
| | - Raja Fayad
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA.,b Center for Colon Cancer Research, University of South Carolina , Columbia , SC , USA
| | - Kamaljeet Kaur
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA
| | - Samantha Truman
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA
| | - Julian Greer
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA
| | - James A Carson
- a Department of Exercise Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA.,b Center for Colon Cancer Research, University of South Carolina , Columbia , SC , USA
| | - Anindya Chanda
- b Center for Colon Cancer Research, University of South Carolina , Columbia , SC , USA.,c Department of Environmental Health Science , Arnold School of Public Health, University of South Carolina , Columbia , SC , USA
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49
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Li MD, Cheng WP, Shi MX, Ge TD, Zheng XL, Wu DY, Hu XY, Luo JC, Li FL, Li H. Role of tRNA selenocysteine 1 associated protein 1 in the proliferation and apoptosis of cardiomyocyte‑like H9c2 cells. Mol Med Rep 2016; 15:988-994. [PMID: 28101579 DOI: 10.3892/mmr.2016.6099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/22/2016] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA selenocysteine 1 associated protein 1 (Trnau1ap) serves an essential role in the synthesis of selenoproteins, which have critical functions in numerous biological processes. Selenium deficiency results in a variety of diseases, including cardiac disease. However, the mechanisms underlying myocardial injury induced by selenium deficiency remain unclear. The present study examined the effects of Trnau1ap under‑ and overexpression in cardiomyocyte‑like H9c2 cells, by transfection with small interfering RNA and an overexpression plasmid, respectively. Expression levels of glutathione peroxidase, thioredoxin reductase and selenoprotein K were decreased in Trnau1ap‑underexpressing cells, and increased in Trnau1ap‑overexpressing cells. Using MTT, proliferating cell nuclear antigen, annexin V and caspase‑3 activity assays, it was demonstrated that reducing Trnau1ap expression levels inhibited the proliferation of H9c2 cells and induced apoptosis. Conversely, increasing Trnau1ap expression levels promoted cell growth. Western blot analysis revealed that the phosphoinositide 3‑kinase/protein kinase B signaling pathway was activated in Trnau1ap‑underexpressing cells. Furthermore, the apoptotic pathway was activated in these cells, evidenced by relatively greater expression levels of B‑cell lymphoma (Bcl‑2)‑associated X protein and reduced expression levels of Bcl‑2. Taken together, these findings suggest that Trnau1ap serves a key role in the proliferation and apoptosis of H9c2 cells. The present study provides insight into the underlying mechanisms of myocardial injury induced by selenium deficiency.
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Affiliation(s)
- Meng-Di Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Wan-Peng Cheng
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Min-Xia Shi
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Tang-Dong Ge
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiao-Lin Zheng
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Dong-Yuan Wu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiao-Yan Hu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jin-Cheng Luo
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Feng-Lan Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Hui Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 2016; 540:80-85. [PMID: 27842381 DOI: 10.1038/nature20560] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/24/2016] [Indexed: 01/29/2023]
Abstract
In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNASec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNASec recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNASec binding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB-Sec-tRNASec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASec covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNASec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.
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Affiliation(s)
- Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Zhe Wang
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alena Paleskava
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrey L Konevega
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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