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Gervason S, Sen S, Fontecave M, Golinelli-Pimpaneau B. [4Fe-4S]-dependent enzymes in non-redox tRNA thiolation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119807. [PMID: 39106920 DOI: 10.1016/j.bbamcr.2024.119807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/09/2024]
Abstract
Post-transcriptional modification of nucleosides in transfer RNAs (tRNAs) is an important process for accurate and efficient translation of the genetic information during protein synthesis in all domains of life. In particular, specific enzymes catalyze the biosynthesis of sulfur-containing nucleosides, such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A), within tRNAs. Whereas the mechanism that has prevailed for decades involved persulfide chemistry, more and more tRNA thiolation enzymes have now been shown to contain a [4Fe-4S] cluster. This review summarizes the information over the last ten years concerning the biochemical, spectroscopic and structural characterization of [4Fe-4S]-dependent non-redox tRNA thiolation enzymes.
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Affiliation(s)
- Sylvain Gervason
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Sambuddha Sen
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France.
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2
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Jamontas R, Laurynėnas A, Povilaitytė D, Meškys R, Aučynaitė A. RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification. Nucleic Acids Res 2024; 52:10543-10562. [PMID: 39166491 PMCID: PMC11417400 DOI: 10.1093/nar/gkae716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
In this study, we present an extensive analysis of a widespread group of bacterial tRNA de-modifying enzymes, dubbed RudS, which consist of a TudS desulfidase fused to a Domain of Unknown Function 1722 (DUF1722). RudS enzymes exhibit specific de-modification activity towards the 4-thiouridine modification (s4U) in tRNA molecules, as indicated by our experimental findings. The heterologous overexpression of RudS genes in Escherichia coli significantly reduces the tRNA 4-thiouridine content and diminishes UVA-induced growth delay, indicating the enzyme's role in regulating photosensitive tRNA s4U modification. Through a combination of protein modeling, docking studies, and molecular dynamics simulations, we have identified amino acid residues involved in catalysis and tRNA binding. Experimental validation through targeted mutagenesis confirms the TudS domain as the catalytic core of RudS, with the DUF1722 domain facilitating tRNA binding in the anticodon region. Our results suggest that RudS tRNA modification eraser proteins may play a role in regulating tRNA during prokaryotic stress responses.
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Affiliation(s)
- Rapolas Jamontas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Deimantė Povilaitytė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
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3
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Zecchin P, Pecqueur L, Oltmanns J, Velours C, Schünemann V, Fontecave M, Golinelli‐Pimpaneau B. Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE. Protein Sci 2024; 33:e4874. [PMID: 38100250 PMCID: PMC10806937 DOI: 10.1002/pro.4874] [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] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine as a sacrificial sulfur donor, and the other one that uses a [4Fe-4S] cluster as a cofactor. Only the crystal structure of LarE from Lactobacillus plantarum (LpLarE) from the first class has been solved. We report here the crystal structure of LarE from Methanococcus maripaludis (MmLarE), belonging to the second class, in the cluster-free (apo-) and cluster-bound (holo-) forms. The structure of holo-MmLarE shows that the [4Fe-4S] cluster is chelated by three cysteines only, leaving an open coordination site on one Fe atom. Moreover, the fourth nonprotein-bonded iron atom was able to bind an anionic ligand such as a phosphate group or a chloride ion. Together with the spectroscopic analysis of holo-MmLarE and the previously reported biochemical investigations of holo-LarE from Thermotoga maritima, these crystal structures support the hypothesis of a reaction mechanism, in which the [4Fe-4S] cluster binds a hydrogenosulfide ligand in place of the chloride anion, thus generating a [4Fe-5S] intermediate, and transfers it to the substrate, as in the case of [4Fe-4S]-dependent tRNA thiolation enzymes.
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Affiliation(s)
- Paolo Zecchin
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Jonathan Oltmanns
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris‐SaclayGif‐sur‐Yvette cedexFrance
- Present address:
Fundamental Microbiology and Pathogenicity LaboratoryUMR 5234 CNRS‐University of Bordeaux, SFR TransBioMedBordeauxFrance
| | - Volker Schünemann
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Béatrice Golinelli‐Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
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Alings F, Scharmann K, Eggers C, Böttcher B, Sokołowski M, Shvetsova E, Sharma P, Roth J, Rashiti L, Glatt S, Brunke S, Leidel SA. Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA. Nucleic Acids Res 2023; 51:8133-8149. [PMID: 37462076 PMCID: PMC10450187 DOI: 10.1093/nar/gkad564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 08/26/2023] Open
Abstract
Fungal pathogens threaten ecosystems and human health. Understanding the molecular basis of their virulence is key to develop new treatment strategies. Here, we characterize NCS2*, a point mutation identified in a clinical baker's yeast isolate. Ncs2 is essential for 2-thiolation of tRNA and the NCS2* mutation leads to increased thiolation at body temperature. NCS2* yeast exhibits enhanced fitness when grown at elevated temperatures or when exposed to oxidative stress, inhibition of nutrient signalling, and cell-wall stress. Importantly, Ncs2* alters the interaction and stability of the thiolase complex likely mediated by nucleotide binding. The absence of 2-thiolation abrogates the in vivo virulence of pathogenic baker's yeast in infected mice. Finally, hypomodification triggers changes in colony morphology and hyphae formation in the common commensal pathogen Candida albicans resulting in decreased virulence in a human cell culture model. These findings demonstrate that 2-thiolation of tRNA acts as a key mediator of fungal virulence and reveal new mechanistic insights into the function of the highly conserved tRNA-thiolase complex.
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Affiliation(s)
- Fiona Alings
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Karin Scharmann
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Cristian Eggers
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Böttcher
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Mikołaj Sokołowski
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ekaterina Shvetsova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Joël Roth
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Leon Rashiti
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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Bimai O, Legrand P, Ravanat JL, Touati N, Zhou J, He N, Lénon M, Barras F, Fontecave M, Golinelli-Pimpaneau B. The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis. Sci Rep 2023; 13:5351. [PMID: 37005440 PMCID: PMC10067955 DOI: 10.1038/s41598-023-32423-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/24/2023] [Indexed: 04/04/2023] Open
Abstract
Thiolation of uridine 34 in the anticodon loop of several tRNAs is conserved in the three domains of life and guarantees fidelity of protein translation. U34-tRNA thiolation is catalyzed by a complex of two proteins in the eukaryotic cytosol (named Ctu1/Ctu2 in humans), but by a single NcsA enzyme in archaea. We report here spectroscopic and biochemical experiments showing that NcsA from Methanococcus maripaludis (MmNcsA) is a dimer that binds a [4Fe-4S] cluster, which is required for catalysis. Moreover, the crystal structure of MmNcsA at 2.8 Å resolution shows that the [4Fe-4S] cluster is coordinated by three conserved cysteines only, in each monomer. Extra electron density on the fourth nonprotein-bonded iron most likely locates the binding site for a hydrogenosulfide ligand, in agreement with the [4Fe-4S] cluster being used to bind and activate the sulfur atom of the sulfur donor. Comparison of the crystal structure of MmNcsA with the AlphaFold model of the human Ctu1/Ctu2 complex shows a very close superposition of the catalytic site residues, including the cysteines that coordinate the [4Fe-4S] cluster in MmNcsA. We thus propose that the same mechanism for U34-tRNA thiolation, mediated by a [4Fe-4S]-dependent enzyme, operates in archaea and eukaryotes.
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Affiliation(s)
- Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91198, Gif-sur-Yvette, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, 38000, Grenoble, France
| | - Nadia Touati
- IR CNRS Renard, Chimie-ParisTech, 11 rue Pierre et Marie Curie, 75005, Paris, France
| | - Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Nisha He
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Marine Lénon
- Stress Adaptation and Metabolism in Enterobacteria Unit, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | - Frédéric Barras
- Stress Adaptation and Metabolism in Enterobacteria Unit, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France.
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6
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Quick and Spontaneous Transformation between [3Fe-4S] and [4Fe-4S] Iron-Sulfur Clusters in the tRNA-Thiolation Enzyme TtuA. Int J Mol Sci 2023; 24:ijms24010833. [PMID: 36614280 PMCID: PMC9821441 DOI: 10.3390/ijms24010833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential cofactors for enzyme activity. These Fe-S clusters are present in structurally diverse forms, including [4Fe-4S] and [3Fe-4S]. Type-identification of the Fe-S cluster is indispensable in understanding the catalytic mechanism of enzymes. However, identifying [4Fe-4S] and [3Fe-4S] clusters in particular is challenging because of their rapid transformation in response to oxidation-reduction events. In this study, we focused on the relationship between the Fe-S cluster type and the catalytic activity of a tRNA-thiolation enzyme (TtuA). We reconstituted [4Fe-4S]-TtuA, prepared [3Fe-4S]-TtuA by oxidizing [4Fe-4S]-TtuA under strictly anaerobic conditions, and then observed changes in the Fe-S clusters in the samples and the enzymatic activity in the time-course experiments. Electron paramagnetic resonance analysis revealed that [3Fe-4S]-TtuA spontaneously transforms into [4Fe-4S]-TtuA in minutes to one hour without an additional free Fe source in the solution. Although the TtuA immediately after oxidation of [4Fe-4S]-TtuA was inactive [3Fe-4S]-TtuA, its activity recovered to a significant level compared to [4Fe-4S]-TtuA after one hour, corresponding to an increase of [4Fe-4S]-TtuA in the solution. Our findings reveal that [3Fe-4S]-TtuA is highly inactive and unstable. Moreover, time-course analysis of structural changes and activity under strictly anaerobic conditions further unraveled the Fe-S cluster type used by the tRNA-thiolation enzyme.
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7
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He N, Zhou J, Bimai O, Oltmanns J, Ravanat JL, Velours C, Schünemann V, Fontecave M, Golinelli-Pimpaneau B. A subclass of archaeal U8-tRNA sulfurases requires a [4Fe-4S] cluster for catalysis. Nucleic Acids Res 2022; 50:12969-12978. [PMID: 36533440 PMCID: PMC9825150 DOI: 10.1093/nar/gkac1156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/22/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
Sulfuration of uridine 8, in bacterial and archaeal tRNAs, is catalyzed by enzymes formerly known as ThiI, but renamed here TtuI. Two different classes of TtuI proteins, which possess a PP-loop-containing pyrophosphatase domain that includes a conserved cysteine important for catalysis, have been identified. The first class, as exemplified by the prototypic Escherichia coli enzyme, possesses an additional C-terminal rhodanese domain harboring a second cysteine, which serves to form a catalytic persulfide. Among the second class of TtuI proteins that do not possess the rhodanese domain, some archaeal proteins display a conserved CXXC + C motif. We report here spectroscopic and enzymatic studies showing that TtuI from Methanococcus maripaludis and Pyrococcus furiosus can assemble a [4Fe-4S] cluster that is essential for tRNA sulfuration activity. Moreover, structural modeling studies, together with previously reported mutagenesis experiments of M. maripaludis TtuI, indicate that the [4Fe-4S] cluster is coordinated by the three cysteines of the CXXC + C motif. Altogether, our results raise a novel mechanism for U8-tRNA sulfuration, in which the cluster is proposed to catalyze the transfer of sulfur atoms to the activated tRNA substrate.
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Affiliation(s)
| | | | - Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Jonathan Oltmanns
- Technische Universität Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES UMR 5819, F-38000 Grenoble, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France,Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Volker Schünemann
- Technische Universität Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
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Chatterjee S, Hausinger RP. Sulfur incorporation into biomolecules: recent advances. Crit Rev Biochem Mol Biol 2022; 57:461-476. [PMID: 36403141 PMCID: PMC10192010 DOI: 10.1080/10409238.2022.2141678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022]
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
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9
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Chatterjee S, Parson KF, Ruotolo BT, McCracken J, Hu J, Hausinger RP. Characterization of a [4Fe-4S]-dependent LarE sulfur insertase that facilitates nickel-pincer nucleotide cofactor biosynthesis in Thermotoga maritima. J Biol Chem 2022; 298:102131. [PMID: 35700827 PMCID: PMC9283937 DOI: 10.1016/j.jbc.2022.102131] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Sulfur-insertion reactions are essential for the biosynthesis of several cellular metabolites, including enzyme cofactors. In Lactobacillus plantarum, a sulfur-containing nickel-pincer nucleotide (NPN) cofactor is used as a coenzyme of lactic acid racemase, LarA. During NPN biosynthesis in L. plantarum, sulfur is transferred to a nicotinic acid-derived substrate by LarE, which sacrifices the sulfur atom of its single cysteinyl side chain, forming a dehydroalanine residue. Most LarE homologs contain three conserved cysteine residues that are predicted to cluster at the active site; however, the function of this cysteine cluster is unclear. In this study, we characterized LarE from Thermotoga maritima (LarETm) and show that it uses these three conserved cysteine residues to bind a [4Fe-4S] cluster that is required for sulfur transfer. Notably, we found LarETm retains all side chain sulfur atoms, in contrast to LarELp. We also demonstrate that when provided with L-cysteine and cysteine desulfurase from Escherichia coli (IscSEc), LarETm functions catalytically with IscSEc transferring sulfane sulfur atoms to LarETm. Native mass spectrometry results are consistent with a model wherein the enzyme coordinates sulfide at the nonligated iron atom of the [4Fe-4S] cluster, forming a [4Fe-5S] species, and transferring the noncore sulfide to the activated substrate. This proposed mechanism is like that of TtuA that catalyzes sulfur transfer during 2-thiouridine synthesis. In conclusion, we found that LarE sulfur insertases associated with NPN biosynthesis function either by sacrificial sulfur transfer from the protein or by transfer of a noncore sulfide bound to a [4Fe-4S] cluster.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Jian Hu
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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10
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Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold. INORGANICS 2021. [DOI: 10.3390/inorganics10010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis.
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11
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Biosynthesis and Degradation of Sulfur Modifications in tRNAs. Int J Mol Sci 2021; 22:ijms222111937. [PMID: 34769366 PMCID: PMC8584467 DOI: 10.3390/ijms222111937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Various sulfur-containing biomolecules include iron–sulfur clusters that act as cofactors for enzymes, sulfur-containing vitamins such as thiamin, and sulfur-modified nucleosides in RNA, in addition to methionine and cysteine in proteins. Sulfur-containing nucleosides are post-transcriptionally introduced into tRNA molecules, where they ensure precise codon recognition or stabilization of tRNA structure, thereby maintaining cellular proteome integrity. Modulating sulfur modification controls the translation efficiency of specific groups of genes, allowing organisms to adapt to specific environments. The biosynthesis of tRNA sulfur nucleosides involves elaborate ‘sulfur trafficking systems’ within cellular sulfur metabolism and ‘modification enzymes’ that incorporate sulfur atoms into tRNA. This review provides an up-to-date overview of advances in our knowledge of the mechanisms involved. It covers the functions, biosynthesis, and biodegradation of sulfur-containing nucleosides as well as the reaction mechanisms of biosynthetic enzymes catalyzed by the iron–sulfur clusters, and identification of enzymes involved in the de-modification of sulfur atoms of RNA. The mechanistic similarity of these opposite reactions is discussed. Mutations in genes related to these pathways can cause human diseases (e.g., cancer, diabetes, and mitochondrial diseases), emphasizing the importance of these pathways.
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Zhou J, Lénon M, Ravanat JL, Touati N, Velours C, Podskoczyj K, Leszczynska G, Fontecave M, Barras F, Golinelli-Pimpaneau B. Iron-sulfur biology invades tRNA modification: the case of U34 sulfuration. Nucleic Acids Res 2021; 49:3997-4007. [PMID: 33744947 PMCID: PMC8053098 DOI: 10.1093/nar/gkab138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Sulfuration of uridine 34 in the anticodon of tRNAs is conserved in the three domains of life, guaranteeing fidelity of protein translation. In eubacteria, it is catalyzed by MnmA-type enzymes, which were previously concluded not to depend on an iron-sulfur [Fe-S] cluster. However, we report here spectroscopic and iron/sulfur analysis, as well as in vitro catalytic assays and site-directed mutagenesis studies unambiguously showing that MnmA from Escherichia coli can bind a [4Fe-4S] cluster, which is essential for sulfuration of U34-tRNA. We propose that the cluster serves to bind and activate hydrosulfide for nucleophilic attack on the adenylated nucleoside. Intriguingly, we found that E. coli cells retain s2U34 biosynthesis in the ΔiscUA ΔsufABCDSE strain, lacking functional ISC and SUF [Fe-S] cluster assembly machineries, thus suggesting an original and yet undescribed way of maturation of MnmA. Moreover, we report genetic analysis showing the importance of MnmA for sustaining oxidative stress.
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Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Marine Lénon
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, F-38000 Grenoble, France
| | - Nadia Touati
- IR CNRS Renard, Chimie-ParisTech, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Frédéric Barras
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
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13
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Liu A, Si Y, Dong SH, Mahanta N, Penkala HN, Nair SK, Mitchell DA. Functional elucidation of TfuA in peptide backbone thioamidation. Nat Chem Biol 2021; 17:585-592. [PMID: 33707784 PMCID: PMC8084935 DOI: 10.1038/s41589-021-00771-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023]
Abstract
YcaO enzymes catalyze several post-translational modifications on peptide substrates, including thioamidation, which substitutes an amide oxygen with sulfur. Most predicted thioamide-forming YcaO enzymes are encoded adjacent to TfuA, which when present, is required for thioamidation. While activation of the peptide amide backbone is well established for YcaO enzymes, the function of TfuA has remained enigmatic. Here we characterize the TfuA protein involved in methyl-coenzyme M reductase thioamidation and demonstrate that TfuA catalyzes the hydrolysis of thiocarboxylated ThiS (ThiS-COSH), a proteinaceous sulfur donor, and enhances the affinity of YcaO toward the thioamidation substrate. We also report a crystal structure of a TfuA, which displays a new protein fold. Our structural and mutational analyses of TfuA have uncovered conserved binding interfaces with YcaO and ThiS in addition to revealing a hydrolase-like active site featuring a Ser-Lys catalytic pair.
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Affiliation(s)
- Andi Liu
- Department of Microbiology, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Yuanyuan Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Nilkamal Mahanta
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Chemistry, University of Illinois, Urbana, IL, USA
- Department of Chemistry, Indian Institute of Technology Dharwad, Karnataka, India
| | - Haley N Penkala
- Department of Microbiology, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Satish K Nair
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Chemistry, University of Illinois, Urbana, IL, USA
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
| | - Douglas A Mitchell
- Department of Microbiology, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
- Department of Chemistry, University of Illinois, Urbana, IL, USA.
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14
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Dai Y, Qi CB, Feng Y, Cheng QY, Liu FL, Cheng MY, Yuan BF, Feng YQ. Sensitive and Simultaneous Determination of Uridine Thiolation and Hydroxylation Modifications in Eukaryotic RNA by Derivatization Coupled with Mass Spectrometry Analysis. Anal Chem 2021; 93:6938-6946. [PMID: 33908769 DOI: 10.1021/acs.analchem.0c04630] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The discovery of dynamic and reversible modifications in RNA expands their functional repertoires. Now, RNA modifications have been viewed as new regulators involved in a variety of biological processes. Among these modifications, thiolation is one kind of special modification in RNA. Several thiouridines have been identified to be present in RNA, and they are essential in the natural growth and metabolism of cells. However, detection of these thiouridines generally is challenging, and few studies could offer the quantitative levels of uridine modifications in RNA, which limits the in-depth elucidation of their functions. Herein, we developed a chemical derivatization in combination with mass spectrometry analysis for the sensitive and simultaneous determination of uridine thiolation and hydroxylation modifications in eukaryotic RNA. The chemical derivatization strategy enables the addition of easily ionizable groups to the uridine thiolation and hydroxylation modifications, leading up to a 339-fold increase in detection sensitivities of these modifications by mass spectrometry analysis. The limits of detection of these uridine modifications can be down to 17 amol. With the established method, we discovered and confirmed that a new modification of 5-hydroxyuridine (ho5U) was widely present in small RNAs of mammalian cells, expanding the diversity of RNA modifications. The developed method shows superior capability in determining low-abundance RNA modifications and may promote identifying new modifications in RNA, which should be valuable in uncovering the unknown functions of RNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Chu-Bo Qi
- Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430079, China
| | - Yang Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Qing-Yun Cheng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Fei-Long Liu
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Ming-Yu Cheng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
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15
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Zhou J, Pecqueur L, Aučynaitė A, Fuchs J, Rutkienė R, Vaitekūnas J, Meškys R, Boll M, Fontecave M, Urbonavičius J, Golinelli‐Pimpaneau B. Structural Evidence for a [4Fe‐5S] Intermediate in the Non‐Redox Desulfuration of Thiouracil. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Jonathan Fuchs
- Faculty of Biology—Microbiology University of Freiburg 79104 Freiburg Germany
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Matthias Boll
- Faculty of Biology—Microbiology University of Freiburg 79104 Freiburg Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
- Department of Chemistry and Bioengineering Vilnius Gediminas Technical University Vilnius Lithuania
| | - Béatrice Golinelli‐Pimpaneau
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
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16
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Zhou J, Pecqueur L, Aučynaitė A, Fuchs J, Rutkienė R, Vaitekūnas J, Meškys R, Boll M, Fontecave M, Urbonavičius J, Golinelli-Pimpaneau B. Structural Evidence for a [4Fe-5S] Intermediate in the Non-Redox Desulfuration of Thiouracil. Angew Chem Int Ed Engl 2020; 60:424-431. [PMID: 32929873 DOI: 10.1002/anie.202011211] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Indexed: 11/10/2022]
Abstract
We recently discovered a [Fe-S]-containing protein with in vivo thiouracil desulfidase activity, dubbed TudS. The crystal structure of TudS refined at 1.5 Å resolution is reported; it harbors a [4Fe-4S] cluster bound by three cysteines only. Incubation of TudS crystals with 4-thiouracil trapped the cluster with a hydrosulfide ligand bound to the fourth non-protein-bonded iron, as established by the sulfur anomalous signal. This indicates that a [4Fe-5S] state of the cluster is a catalytic intermediate in the desulfuration reaction. Structural data and site-directed mutagenesis indicate that a water molecule is located next to the hydrosulfide ligand and to two catalytically important residues, Ser101 and Glu45. This information, together with modeling studies allow us to propose a mechanism for the unprecedented non-redox enzymatic desulfuration of thiouracil, in which a [4Fe-4S] cluster binds and activates the sulfur atom of the substrate.
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Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jonathan Fuchs
- Faculty of Biology-Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Matthias Boll
- Faculty of Biology-Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
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17
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Yu J, Shinoda A, Kato K, Tanaka I, Yao M. A solution-free crystal-mounting platform for native SAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:938-945. [PMID: 33021495 DOI: 10.1107/s2059798320011584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/25/2020] [Indexed: 11/11/2022]
Abstract
The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.
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Affiliation(s)
- Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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18
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Bimai O, Arragain S, Golinelli-Pimpaneau B. Structure-based mechanistic insights into catalysis by tRNA thiolation enzymes. Curr Opin Struct Biol 2020; 65:69-78. [PMID: 32652441 DOI: 10.1016/j.sbi.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
In all domains of life, ribonucleic acid (RNA) maturation includes post-transcriptional chemical modifications of nucleosides. Many sulfur-containing nucleosides have been identified in transfer RNAs (tRNAs), such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), 2-methylthioadenosine (ms2A). These modifications are essential for accurate and efficient translation of the genetic code from messenger RNA (mRNA) for protein synthesis. This review summarizes the recent discoveries concerning the mechanistic and structural characterization of tRNA thiolation enzymes that catalyze the non-redox substitution of oxygen for sulfur in nucleosides. Two mechanisms have been described. One involves persulfide formation on catalytic cysteines, while the other uses a [4Fe-4S] cluster, chelated by three conserved cysteines only, as a sulfur carrier.
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Affiliation(s)
- Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Simon Arragain
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France.
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