1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Jamontas R, Laurynėnas A, Povilaitytė D, Meškys R, Aučynaitė A. RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification. Nucleic Acids Res 2024:gkae716. [PMID: 39166491 DOI: 10.1093/nar/gkae716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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
| |
Collapse
|
3
|
Medvedev KE, Zhang J, Schaeffer RD, Kinch LN, Cong Q, Grishin NV. Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands. Sci Rep 2024; 14:12260. [PMID: 38806511 PMCID: PMC11133325 DOI: 10.1038/s41598-024-60991-x] [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: 02/20/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lisa N Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Lachowicz JC, Lennox-Hvenekilde D, Myling-Petersen N, Salomonsen B, Verkleij G, Acevedo-Rocha CG, Caddell B, Gronenberg LS, Almo SC, Sommer MOA, Genee HJ, Grove TL. Discovery of a Biotin Synthase That Utilizes an Auxiliary 4Fe-5S Cluster for Sulfur Insertion. J Am Chem Soc 2024; 146:1860-1873. [PMID: 38215281 PMCID: PMC10813225 DOI: 10.1021/jacs.3c05481] [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: 06/03/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Biotin synthase (BioB) is a member of the Radical SAM superfamily of enzymes that catalyzes the terminal step of biotin (vitamin B7) biosynthesis, in which it inserts a sulfur atom in desthiobiotin to form a thiolane ring. How BioB accomplishes this difficult reaction has been the subject of much controversy, mainly around the source of the sulfur atom. However, it is now widely accepted that the sulfur atom inserted to form biotin stems from the sacrifice of the auxiliary 2Fe-2S cluster of BioB. Here, we bioinformatically explore the diversity of BioBs available in sequence databases and find an unexpected variation in the coordination of the auxiliary iron-sulfur cluster. After in vitro characterization, including the determination of biotin formation and representative crystal structures, we report a new type of BioB utilized by virtually all obligate anaerobic organisms. Instead of a 2Fe-2S cluster, this novel type of BioB utilizes an auxiliary 4Fe-5S cluster. Interestingly, this auxiliary 4Fe-5S cluster contains a ligated sulfide that we propose is used for biotin formation. We have termed this novel type of BioB, Type II BioB, with the E. coli 2Fe-2S cluster sacrificial BioB representing Type I. This surprisingly ubiquitous Type II BioB has implications for our understanding of the function and evolution of Fe-S clusters in enzyme catalysis, highlighting the difference in strategies between the anaerobic and aerobic world.
Collapse
Affiliation(s)
- Jake C. Lachowicz
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - David Lennox-Hvenekilde
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Biosyntia
ApS, Copenhagen, 2100, Denmark
| | | | | | | | - Carlos G. Acevedo-Rocha
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Biosyntia
ApS, Copenhagen, 2100, Denmark
| | | | | | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Morten O. A. Sommer
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
6
|
Fuchs J, Jamontas R, Hoock MH, Oltmanns J, Golinelli-Pimpaneau B, Schünemann V, Pierik AJ, Meškys R, Aučynaitė A, Boll M. TudS desulfidases recycle 4-thiouridine-5'-monophosphate at a catalytic [4Fe-4S] cluster. Commun Biol 2023; 6:1092. [PMID: 37891428 PMCID: PMC10611767 DOI: 10.1038/s42003-023-05450-5] [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: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
In all domains of life, transfer RNAs (tRNAs) contain post-transcriptionally sulfur-modified nucleosides such as 2- and 4-thiouridine. We have previously reported that a recombinant [4Fe-4S] cluster-containing bacterial desulfidase (TudS) from an uncultured bacterium catalyzes the desulfuration of 2- and 4-thiouracil via a [4Fe-5S] cluster intermediate. However, the in vivo function of TudS enzymes has remained unclear and direct evidence for substrate binding to the [4Fe-4S] cluster during catalysis was lacking. Here, we provide kinetic evidence that 4-thiouridine-5'-monophosphate rather than sulfurated tRNA, thiouracil, thiouridine or 4-thiouridine-5'-triphosphate is the preferred substrate of TudS. The occurrence of sulfur- and substrate-bound catalytic intermediates was uncovered from the observed switch of the S = 3/2 spin state of the catalytic [4Fe-4S] cluster to a S = 1/2 spin state upon substrate addition. We show that a putative gene product from Pseudomonas putida KT2440 acts as a TudS desulfidase in vivo and conclude that TudS-like enzymes are widespread desulfidases involved in recycling and detoxifying tRNA-derived 4-thiouridine monophosphate nucleosides for RNA synthesis.
Collapse
Affiliation(s)
- Jonathan Fuchs
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Rapolas Jamontas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257, Vilnius, Lithuania
| | - Maren Hellen Hoock
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Jonathan Oltmanns
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris, CEDEX 05, France
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Antonio J Pierik
- Department of Chemistry, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - 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
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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
| | | |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Sulfur Availability Impacts Accumulation of the 2-Thiouridine tRNA Modification in Bacillus subtilis. J Bacteriol 2022; 204:e0000922. [PMID: 35467390 DOI: 10.1128/jb.00009-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Posttranscriptional modifications to tRNA are critical elements for the folding and functionality of these adaptor molecules. Sulfur modifications in tRNA are installed by specialized enzymes that act on cognate tRNA substrates at specific locations. Most studied organisms contain a general cysteine desulfurase to mobilize sulfur for the synthesis of S-tRNA and other thio-cofactors. Bacillus subtilis and other Gram-positive bacteria encode multiple cysteine desulfurases that partner with specific sulfur acceptors in the biosynthesis of thio-cofactors. This metabolic layout suggests an alternate mode of regulation in these biosynthetic pathways. In this study, tRNA modifications were exploited as a readout for the functionality of pathways involving cysteine desulfurases. These analyses showed that the relative abundance of 2-thiouridine-modified tRNA (s2U) responds to sulfur availability in the growth medium in a dose-dependent manner. This study found that low sulfur concentrations lead to decreased levels of the s2U cysteine desulfurase YrvO and thiouridylase MnmA, without altering the levels of other cysteine desulfurases, SufS, NifS, and NifZ. Analysis of pathway metabolites that depend on the activity of cysteine desulfurases indicates that sulfur nutrient availability specifically impacts s2U accumulation while having no effect on the levels of other S-modified tRNA or activity levels of Fe-S enzymes. Collectively, these results support a model in which s2U tRNA serves as a marker for sulfur availability in B. subtilis. IMPORTANCE The 2-thiouridine (s2U) tRNA modification is found ubiquitously across all domains of life. YrvO and MnmA, the enzymes involved in this modification, are essential in B. subtilis, confirming the well-established role of s2U in maintaining translational efficiency and, consequently, cellular viability. Herein, we show that in the model Gram-positive organism Bacillus subtilis, the levels of s2U are responsive to sulfur availability. Downregulation of the s2U biosynthetic components leads to lower s2U levels, which may serve as a signal for the slowing of the translational apparatus during cellular nutrient insufficiency. Our findings provide the basis for the identification of a potential bacterial mode of regulation during S-metabolite depletion that may use s2U as a marker of suboptimal metabolic status.
Collapse
|
11
|
Lénon M, Arias-Cartín R, Barras F. The Fe-S proteome of Escherichia coli: prediction, function and fate. Metallomics 2022; 14:6555457. [PMID: 35349713 DOI: 10.1093/mtomcs/mfac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic ubiquitous and ancient cofactors. Fe-S bound proteins contribute to most cellular processes, including DNA replication and integrity, genetic expression and regulation, metabolism, biosynthesis and most bioenergetics systems. Also, Fe-S proteins hold a great biotechnological potential in metabolite and chemical production, including antibiotics. From classic biophysics and spectroscopy methodologies to recent development in bioinformatics, including structural modeling and chemoproteomics, our capacity to predict and identify Fe-S proteins has spectacularly increased over the recent years. Here, these developments are presented and collectively used to update the composition of Escherichia coli Fe-S proteome, for which we predict 181 occurrences, i.e. 40 more candidates than in our last catalog (Py and Barras, 2010), and equivalent to 4% of its total proteome. Besides, Fe-S clusters can be targeted by redox active compounds or reactive oxygen and nitrosative species, and even be destabilized by contaminant metals. Accordingly, we discuss how cells handle damaged Fe-S proteins, i.e. degradation, recycling or repair.
Collapse
Affiliation(s)
- Marine Lénon
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
| | - Rodrigo Arias-Cartín
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
| | - Frédéric Barras
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
| |
Collapse
|
12
|
Velours C, Zhou J, Zecchin P, He N, Salameh M, Golinelli-Cohen MP, Golinelli-Pimpaneau B. Determination of the Absolute Molar Mass of [Fe-S]-Containing Proteins Using Size Exclusion Chromatography-Multi-Angle Light Scattering (SEC-MALS). Biomolecules 2022; 12:biom12020270. [PMID: 35204772 PMCID: PMC8961635 DOI: 10.3390/biom12020270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Size Exclusion Chromatography coupled with Multi-Angle Light Scattering (SEC-MALS) is a technique that determines the absolute molar mass (molecular weight) of macromolecules in solution, such as proteins or polymers, by detecting their light scattering intensity. Because SEC-MALS does not rely on the assumption of the globular state of the analyte and the calibration of standards, the molar mass can be obtained for proteins of any shape, as well as for intrinsically disordered proteins and aggregates. Yet, corrections need to be made for samples that absorb light at the wavelength of the MALS laser, such as iron–sulfur [Fe-S] cluster-containing proteins. We analyze several examples of [2Fe-2S] and [4Fe-4S] cluster-containing proteins, for which various corrections were applied to determine the absolute molar mass of both the apo- and holo-forms. Importantly, the determination of the absolute molar mass of the [2Fe-2S]-containing holo-NEET proteins allowed us to ascertain a change in the oligomerization state upon cluster binding and, thus, to highlight one essential function of the cluster.
Collapse
Affiliation(s)
- Christophe Velours
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 33076 Bordeaux, France
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Correspondence: (C.V.); (B.G.-P.)
| | - Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Paolo Zecchin
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Nisha He
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Myriam Salameh
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR2301, 91198 Gif-sur-Yvette, France; (M.S.); (M.-P.G.-C.)
| | - Marie-Pierre Golinelli-Cohen
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR2301, 91198 Gif-sur-Yvette, France; (M.S.); (M.-P.G.-C.)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
- Correspondence: (C.V.); (B.G.-P.)
| |
Collapse
|
13
|
Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
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.
Collapse
|
15
|
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.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|