1
|
Sokołowski M, Kwasna D, Ravichandran KE, Eggers C, Krutyhołowa R, Kaczmarczyk M, Skupien-Rabian B, Jaciuk M, Walczak M, Dahate P, Pabis M, Jemioła-Rzemińska M, Jankowska U, Leidel SA, Glatt S. Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4. Nucleic Acids Res 2024; 52:13980-13995. [PMID: 39673271 DOI: 10.1093/nar/gkae1111] [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: 03/28/2024] [Revised: 10/22/2024] [Accepted: 11/18/2024] [Indexed: 12/16/2024] Open
Abstract
Ubiquitin-related modifier 1 (Urm1) is a highly conserved member of the ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic transfer RNA (tRNA) thiolation cascade, responsible for introducing sulfur at wobble uridine (U34) in several eukaryotic tRNAs. Urm1 must be thiocarboxylated (Urm1-SH) by its E1 activating enzyme UBL protein activator 4 (Uba4). Uba4 first adenylates and then thiocarboxylates the C-terminus of Urm1 using its adenyl-transferase (AD) and rhodanese (RHD) domains. However, the detailed mechanisms of Uba4, the interplay between the two domains, and the release of Urm1 remain elusive. Here, we report a cryo-EM-based structural model of the Uba4/Urm1 complex that reveals the position of its RHD domains after Urm1 binding, and by analyzing the in vitro and in vivo consequence of mutations at the interface, we show its importance for the thiocarboxylation of Urm1. Our results confirm that the formation of the Uba4-Urm1 thioester and thiocarboxylation of Urm1's C-terminus depend on conserved cysteine residues of Uba4 and that the complex avoids unwanted side-reactions of the adenylate by forming a thioester intermediate. We show how the Urm1-SH product can be released and how Urm1 interacts with upstream (Tum1) and downstream (Ncs6) components of the pathway. Our work provides a detailed mechanistic description of the reaction steps that are needed to produce Urm1-SH, which is required to thiolate tRNAs and persulfidate proteins.
Collapse
Affiliation(s)
- Mikołaj Sokołowski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, Zwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Dominika Kwasna
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Keerthiraju E Ravichandran
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, Zwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Cristian Eggers
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Magdalena Kaczmarczyk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Bozena Skupien-Rabian
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, prof. S. Łojasiewicza 11, 30-348 Krakow, Poland
| | - Priyanka Dahate
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, prof. S. Łojasiewicza 11, 30-348 Krakow, Poland
| | - Marta Pabis
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Małgorzata Jemioła-Rzemińska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa7a, 30-387 Krakow, Poland
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| |
Collapse
|
2
|
Hasebe F, Adachi K, Maruyama C, Hamano Y. Discovery of a novel methionine biosynthetic route via O-phospho-l-homoserine. Appl Environ Microbiol 2024; 90:e0124724. [PMID: 39311576 PMCID: PMC11497804 DOI: 10.1128/aem.01247-24] [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: 06/25/2024] [Accepted: 09/01/2024] [Indexed: 10/25/2024] Open
Abstract
Methionine (Met), a sulfur-containing amino acid, is essential for the underlying biological processes in living organisms. In addition to its importance as a starting building block for peptide chain elongation in protein biosynthesis, Met is a direct precursor of S-adenosyl-l-methionine, an indispensable methyl donor molecule in primary and secondary metabolism. Streptomyces bacteria are well known to produce diverse secondary metabolites, but many strains lack canonical Met pathway genes for l-homocysteine, a direct precursor of Met in bacteria, plants, and archaea. Here, we report the identification of a novel gene (metM) responsible for the Met biosynthesis in Streptomyces strains and demonstrate the catalytic function of the gene product, MetM. We further identified the metO gene, a downstream gene of metM, and showed that it encodes a sulfur-carrier protein (SCP). In in vitro analysis, MetO was found to play an important role in a sulfur donor by forming a thiocarboxylated SCP. Together with MetO (thiocarboxylate), MetM directly converted O-phospho-l-homoserine to l-homocysteine. O-Phospho-l-homoserine is also known as an intermediate for threonine biosynthesis in bacteria and plants, and MetM shares sequence homology with threonine synthase. Our findings thus revealed that MetM seizes O-phospho-l-homoserine from the threonine biosynthetic pathway and uses it as an intermediate of the Met biosynthesis to generate the sulfur-containing amino acid. Importantly, this MetM/MetO pathway is highly conserved in Streptomyces bacteria and distributed in other bacteria and archaea.IMPORTANCEMethionine (Met) is a sulfur-containing proteinogenic amino acid. Moreover, Met is a direct precursor of S-adenosyl-l-methionine, an indispensable molecule for expanding the structural diversity of natural products. Because Met and its derivatives benefit humans, the knowledge of Met biosynthesis is important as a basis for improving their fermentation. Streptomyces bacteria are well known to produce diverse and valuable natural products, but many strains lack canonical Met pathway genes. Here, we identified a novel l-homocysteine synthase (MetM) in Streptomyces and demonstrated that it converts O-phospho-L-homoserine to l-homocysteine using a thiocarboxylated sulfur-carrier protein as a sulfur donor. Since the metM is distributed in other bacteria and archaea, our pioneering study contributes to understanding Met biosynthesis in these organisms.
Collapse
Affiliation(s)
- Fumihito Hasebe
- Department of Bioscience, Fukui Prefectural University, Fukui, Japan
- Fukui Bio Incubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, Japan
| | - Kazuya Adachi
- Department of Bioscience, Fukui Prefectural University, Fukui, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Fukui, Japan
- Fukui Bio Incubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Fukui, Japan
- Fukui Bio Incubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, Japan
| |
Collapse
|
3
|
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
|
4
|
Hidese R, Ohira T, Sakakibara S, Suzuki T, Shigi N, Fujiwara S. Functional redundancy of ubiquitin-like sulfur-carrier proteins facilitates flexible, efficient sulfur utilization in the primordial archaeon Thermococcus kodakarensis. mBio 2024; 15:e0053424. [PMID: 38975783 PMCID: PMC11323500 DOI: 10.1128/mbio.00534-24] [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: 03/14/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Ubiquitin-like proteins (Ubls) in eukaryotes and bacteria mediate sulfur transfer for the biosynthesis of sulfur-containing biomolecules and form conjugates with specific protein targets to regulate their functions. Here, we investigated the functions and physiological importance of Ubls in a hyperthermophilic archaeon by constructing a series of deletion mutants. We found that the Ubls (TK1065, TK1093, and TK2118) in Thermococcus kodakarensis are conjugated to their specific target proteins, and all three are involved in varying degrees in the biosynthesis of sulfur-containing biomolecules such as tungsten cofactor (Wco) and tRNA thiouridines. TK2118 (named UblB) is involved in the biosynthesis of Wco in a glyceraldehyde 3-phosphate:ferredoxin oxidoreductase, which is required for glycolytic growth, whereas TK1093 (named UblA) plays a key role in the efficient thiolation of tRNAs, which contributes to cellular thermotolerance. Intriguingly, in the presence of elemental sulfur (S0) in the culture medium, defective synthesis of these sulfur-containing molecules in Ubl mutants was restored, indicating that T. kodakarensis can use S0 as an alternative sulfur source without Ubls. Our analysis indicates that the Ubl-mediated sulfur-transfer system in T. kodakarensis is important for efficient sulfur assimilation, especially under low S0 conditions, which may allow this organism to survive in a low sulfur environment.IMPORTANCESulfur is a crucial element in living organisms, occurring in various sulfur-containing biomolecules including iron-sulfur clusters, vitamins, and RNA thionucleosides, as well as the amino acids cysteine and methionine. In archaea, the biosynthesis routes and sulfur donors of sulfur-containing biomolecules are largely unknown. Here, we explored the functions of Ubls in the deep-blanched hyperthermophilic archaeon, Thermococcus kodakarensis. We demonstrated functional redundancy of these proteins in the biosynthesis of tungsten cofactor and tRNA thiouridines and the significance of these sulfur-carrier functions, especially in low sulfur environments. We propose that acquisition of a Ubl sulfur-transfer system, in addition to an ancient inorganic sulfur assimilation pathway, enabled the primordial archaeon to advance into lower-sulfur environments and expand their habitable zone.
Collapse
Affiliation(s)
- Ryota Hidese
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Satsuki Sakakibara
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Naoki Shigi
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan
| |
Collapse
|
5
|
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
|
6
|
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
|
7
|
Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. RSC Chem Biol 2021; 2:990-1003. [PMID: 34458821 PMCID: PMC8341892 DOI: 10.1039/d1cb00038a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification location and cellular function, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobases with an emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating sulfur modifications is to aid the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapies. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs.
Collapse
Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Ying Wu
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- Department of Biological Science, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| |
Collapse
|
8
|
Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021; 12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.
Collapse
|
9
|
McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the "fifth" ribonucleotide in 1951. Since then, the ever-increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal-Hreidarsson syndrome, Bowen-Conradi syndrome, or Williams-Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under: RNA Processing > RNA Editing and Modification.
Collapse
Affiliation(s)
- Phillip J. McCown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Agnieszka Ruszkowska
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
- Present address:
Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
| | - Charlotte N. Kunkler
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Kurtis Breger
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jacob P. Hulewicz
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew C. Wang
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Noah A. Springer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jessica A. Brown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| |
Collapse
|
10
|
The [4Fe-4S] cluster of sulfurtransferase TtuA desulfurizes TtuB during tRNA modification in Thermus thermophilus. Commun Biol 2020; 3:168. [PMID: 32265486 PMCID: PMC7138817 DOI: 10.1038/s42003-020-0895-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/06/2020] [Indexed: 11/23/2022] Open
Abstract
TtuA and TtuB are the sulfurtransferase and sulfur donor proteins, respectively, for biosynthesis of 2-thioribothymidine (s2T) at position 54 of transfer RNA (tRNA), which is responsible for adaptation to high temperature environments in Thermus thermophilus. The enzymatic activity of TtuA requires an iron-sulfur (Fe-S) cluster, by which a sulfur atom supplied by TtuB is transferred to the tRNA substrate. Here, we demonstrate that the Fe-S cluster directly receives sulfur from TtuB through its inherent coordination ability. TtuB forms a [4Fe-4S]-TtuB intermediate, but that sulfur is not immediately released from TtuB. Further desulfurization assays and mutation studies demonstrated that the release of sulfur from the thiocarboxylated C-terminus of TtuB is dependent on adenylation of the substrate tRNA, and the essential residue for TtuB desulfurization was identified. Based on these findings, the molecular mechanism of sulfur transfer from TtuB to Fe-S cluster is proposed. Chen et al. demonstrate how the Fe-S cluster receives sulfur from TtuB, a ubiquitin-like sulfur donor during tRNA modification. They find that the release of sulfur from the thiocarboxylated C-terminus of TtuB depends on the adenylation of the substrate tRNA. This study provides molecular insights into the sulfur modification of tRNA.
Collapse
|
11
|
Shigi N, Horitani M, Miyauchi K, Suzuki T, Kuroki M. An ancient type of MnmA protein is an iron-sulfur cluster-dependent sulfurtransferase for tRNA anticodons. RNA (NEW YORK, N.Y.) 2020; 26:240-250. [PMID: 31801798 PMCID: PMC7025502 DOI: 10.1261/rna.072066.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/01/2019] [Indexed: 05/27/2023]
Abstract
Transfer RNA (tRNA) is an adaptor molecule indispensable for assigning amino acids to codons on mRNA during protein synthesis. 2-thiouridine (s2U) derivatives in the anticodons (position 34) of tRNAs for glutamate, glutamine, and lysine are post-transcriptional modifications essential for precise and efficient codon recognition in all organisms. s2U34 is introduced either by (i) bacterial MnmA/eukaryote mitochondrial Mtu1 or (ii) eukaryote cytosolic Ncs6/archaeal NcsA, and the latter enzymes possess iron-sulfur (Fe-S) cluster. Here, we report the identification of novel-type MnmA homologs containing three conserved Cys residues, which could support Fe-S cluster binding and catalysis, in a broad range of bacteria, including thermophiles, Cyanobacteria, Mycobacteria, Actinomyces, Clostridium, and Helicobacter Using EPR spectroscopy, we revealed that Thermus thermophilus MnmA (TtMnmA) contains an oxygen-sensitive [4Fe-4S]-type cluster. Efficient in vitro formation of s2U34 in tRNALys and tRNAGln by holo-TtMnmA occurred only under anaerobic conditions. Mutational analysis of TtMnmA suggested that the Fe-S cluster is coordinated by the three conserved Cys residues (Cys105, Cys108, and Cys200), and is essential for its activity. Evolutionary scenarios for the sulfurtransferases, including the Fe-S cluster containing Ncs6/NcsA s2U thiouridylases and several distantly related sulfurtransferases, are proposed.
Collapse
Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masaki Horitani
- Faculty of Agriculture, Department of Applied Biochemistry and Food Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Misao Kuroki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| |
Collapse
|
12
|
2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae. PLoS One 2020; 15:e0229103. [PMID: 32053677 PMCID: PMC7018073 DOI: 10.1371/journal.pone.0229103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
Chemical modifications that regulate protein expression at the translational level are emerging as vital components of the cellular stress response. Transfer RNAs (tRNAs) are significant targets for methyl-based modifications, which are catalyzed by tRNA methyltransferases (Trms). Here, Saccharomyces cerevisiae served as a model eukaryote system to investigate the role of 2'-O-ribose tRNA methylation in the cell's response to oxidative stress. Using 2'-O-ribose deletion mutants for trms 3, 7, 13, and 44, in acute and chronic exposure settings, we demonstrate a broad cell sensitivity to oxidative stress-inducing toxicants (i.e., hydrogen peroxide, rotenone, and acetic acid). A global analysis of hydrogen peroxide-induced tRNA modifications shows a complex profile of decreased, or undetectable, 2'-O-ribose modification events in 2’-O-ribose trm mutant strains, providing a critical link between this type of modification event and Trm status post-exposure. Based on the pronounced oxidative stress sensitivity observed for trm7 mutants, we used a bioinformatic tool to identify transcripts as candidates for regulation by Trm7-catalyzed modifications (i.e., enriched in UUC codons decoded by tRNAPheGmAA). This screen identified transcripts linked to diverse biological processes that promote cellular recovery after oxidative stress exposure, including DNA repair, chromatin remodeling, and nutrient acquisition (i.e., CRT10, HIR3, HXT2, and GNP1); moreover, these mutants were also oxidative stress-sensitive. Together, these results solidify a role for TRM3, 7, 13, and 44, in the cellular response to oxidative stress, and implicate 2'-O-ribose tRNA modification as an epitranscriptomic strategy for oxidative stress recovery.
Collapse
|
13
|
Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019; 10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
Collapse
Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| |
Collapse
|
14
|
Shigi N. Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs. Front Microbiol 2018; 9:2679. [PMID: 30450093 PMCID: PMC6225789 DOI: 10.3389/fmicb.2018.02679] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Sulfur is an essential element in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, introduced post-transcriptionally, that function to ensure proper codon recognition or stabilization of tRNA structure, thereby enabling accurate and efficient translation. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems that are closely related to cellular sulfur metabolism, and “modification enzymes” that incorporate sulfur atoms into tRNA. Herein, recent biochemical and structural characterization of the biosynthesis of sulfur modifications in tRNA is reviewed, with special emphasis on the reaction mechanisms of modification enzymes. It was recently revealed that TtuA/Ncs6-type 2-thiouridylases from thermophilic bacteria/archaea/eukaryotes are oxygen-sensitive iron-sulfur proteins that utilize a quite different mechanism from other 2-thiouridylase subtypes lacking iron-sulfur clusters such as bacterial MnmA. The various reaction mechanisms of RNA sulfurtransferases are also discussed, including tRNA methylthiotransferase MiaB (a radical S-adenosylmethionine-type iron-sulfur enzyme) and other sulfurtransferases involved in both primary and secondary sulfur-containing metabolites.
Collapse
Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| |
Collapse
|
15
|
Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
Collapse
Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| |
Collapse
|
16
|
Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
|
17
|
Hepowit NL, de Vera IMS, Cao S, Fu X, Wu Y, Uthandi S, Chavarria NE, Englert M, Su D, Sӧll D, Kojetin DJ, Maupin-Furlow JA. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J 2017; 283:3567-3586. [PMID: 27459543 DOI: 10.1111/febs.13819] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/17/2016] [Accepted: 07/22/2016] [Indexed: 01/01/2023]
Abstract
Here we provide the first detailed biochemical study of a noncanonical E1-like enzyme with broad specificity for cognate ubiquitin-like (Ubl) proteins that mediates Ubl protein modification and sulfur mobilization to form molybdopterin and thiolated tRNA. Isothermal titration calorimetry and in vivo analyses proved useful in discovering that environmental conditions, ATP binding, and Ubl type controlled the mechanism of association of the Ubl protein with its cognate E1-like enzyme (SAMP and UbaA of the archaeon Haloferax volcanii, respectively). Further analysis revealed that ATP hydrolysis triggered the formation of thioester and peptide bonds within the Ubl:E1-like complex. Importantly, the thioester was an apparent precursor to Ubl protein modification but not sulfur mobilization. Comparative modeling to MoeB/ThiF guided the discovery of key residues within the adenylation domain of UbaA that were needed to bind ATP as well as residues that were specifically needed to catalyze the downstream reactions of sulfur mobilization and/or Ubl protein modification. UbaA was also found to be Ubl-automodified at lysine residues required for early (ATP binding) and late (sulfur mobilization) stages of enzyme activity revealing multiple layers of autoregulation. Cysteine residues, distinct from the canonical E1 'active site' cysteine, were found important in UbaA function supporting a model that this noncanonical E1 is structurally flexible in its active site to allow Ubl~adenylate, Ubl~E1-like thioester and cysteine persulfide(s) intermediates to form.
Collapse
Affiliation(s)
- Nathaniel L Hepowit
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Ian Mitchelle S de Vera
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Shiyun Cao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Xian Fu
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Yifei Wu
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sivakumar Uthandi
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Sӧll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA. .,Genetics Institute, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
18
|
Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA. Proc Natl Acad Sci U S A 2017; 114:4954-4959. [PMID: 28439027 DOI: 10.1073/pnas.1615585114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two-thiouridine (s2U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s2U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer. Here we demonstrate by spectroscopic, biochemical, and crystal structure analyses that TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity, which explains the previously observed inactivation of this enzyme in vitro. The [4Fe-4S] cluster was coordinated by three highly conserved cysteine residues, and one of the Fe atoms was exposed to the active site. Furthermore, the crystal structure of the TtuA-TtuB complex was determined at a resolution of 2.5 Å, which clearly shows the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding. Based on these observations, we propose a molecular mechanism of S transfer by TtuA using the ubiquitin-like S donor and the [4Fe-4S] cluster.
Collapse
|
19
|
Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
Collapse
Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
| | | | | |
Collapse
|
20
|
Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways. Biomolecules 2017; 7:biom7010027. [PMID: 28287455 PMCID: PMC5372739 DOI: 10.3390/biom7010027] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 01/12/2023] Open
Abstract
Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s2U) derivatives, 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s2U and s4U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s2C and ms2A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s4U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s2U and s4U formation await further investigations.
Collapse
|
21
|
Leimkühler S, Bühning M, Beilschmidt L. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes. Biomolecules 2017; 7:biom7010005. [PMID: 28098827 PMCID: PMC5372717 DOI: 10.3390/biom7010005] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.
Collapse
Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Martin Bühning
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Lena Beilschmidt
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| |
Collapse
|
22
|
Shigi N, Asai SI, Watanabe K. Identification of a rhodanese-like protein involved in thiouridine biosynthesis in Thermus thermophilus tRNA. FEBS Lett 2016; 590:4628-4637. [PMID: 27878988 DOI: 10.1002/1873-3468.12499] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/05/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022]
Abstract
Incorporation of a sulfur atom into 2-thioribothymidine (s2 T or 5-methyl-2-thiouridine) at position 54 in thermophile tRNA is accomplished by an elaborate system composed of many proteins which confers thermostability to the translation system. We identified ttuD (tRNA-two-thiouridine D) as a gene for the synthesis of s2 T54 in Thermus thermophilus. The rhodanese-like protein TtuD enhances the activity of cysteine desulfurases and receives the persulfide generated by cysteine desulfurases in vitro. TtuD also enhances the formation of thiocarboxylated TtuB, the sulfur donor for the tRNA sulfurtransferase TtuA. Since cysteine desulfurases are the first enzymes in the synthesis of s2 T and other sulfur-containing compounds, TtuD has a role to direct sulfur flow to s2 T synthesis.
Collapse
Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Shin-Ichi Asai
- Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Kimitsuna Watanabe
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| |
Collapse
|
23
|
A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc Natl Acad Sci U S A 2016; 113:12703-12708. [PMID: 27791189 DOI: 10.1073/pnas.1615732113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.
Collapse
|
24
|
Chen M, Narai S, Omura N, Shigi N, Chimnaronk S, Tanaka Y, Yao M. Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:777-781. [PMID: 27710943 DOI: 10.1107/s2053230x16014242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022]
Abstract
The ubiquitin-like protein TtuB is a sulfur carrier for the biosynthesis of 2-thioribothymidine (s2T) at position 54 in some thermophilic bacterial tRNAs. TtuB captures a S atom at its C-terminus as a thiocarboxylate and transfers it to tRNA by the transferase activity of TtuA. TtuB also functions to suppress s2T formation by forming a covalent bond with TtuA. To explore how TtuB interacts with TtuA and switches between these two different functions, high-resolution structure analysis of the TtuA-TtuB complex is required. In this study, the TtuA-TtuB complex from Thermus thermophilus was expressed, purified and crystallized. To mimic the thiocarboxylated TtuB, the C-terminal Gly residue was replaced with Cys (G65C) to obtain crystals of the TtuA-TtuB complex. A Zn-MAD data set was collected to a resolution of 2.5 Å. MAD analysis successfully determined eight Zn sites, and a partial structure model composed of four TtuA-TtuB complexes in the asymmetric unit was constructed.
Collapse
Affiliation(s)
- Minghao Chen
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Shun Narai
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Naoki Omura
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Sarin Chimnaronk
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
25
|
Shigi N. Sulfur Modifications in tRNA: Function and Implications for Human Disease. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
26
|
Tao W, Yurkovich ME, Wen S, Lebe KE, Samborskyy M, Liu Y, Yang A, Liu Y, Ju Y, Deng Z, Tosin M, Sun Y, Leadlay PF. A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis. Chem Sci 2016; 7:376-385. [PMID: 28791099 PMCID: PMC5518548 DOI: 10.1039/c5sc03059e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/06/2015] [Indexed: 12/31/2022] Open
Abstract
Thiolactomycin (TLM) is a thiotetronate antibiotic that selectively targets bacterial fatty acid biosynthesis through inhibition of the β-ketoacyl-acyl carrier protein synthases (KASI/II) that catalyse chain elongation on the type II (dissociated) fatty acid synthase. It has proved effective in in vivo infection models of Mycobacterium tuberculosis and continues to attract interest as a template for drug discovery. We have used a comparative genomics approach to uncover the (hitherto elusive) biosynthetic pathway to TLM and related thiotetronates. Analysis of the whole-genome sequence of Streptomyces olivaceus Tü 3010 producing the more ramified thiotetronate Tü 3010 provided initial evidence that such thiotetronates are assembled by a novel iterative polyketide synthase-nonribosomal peptide synthetase, and revealed the identity of other pathway enzymes, encoded by adjacent genes. Subsequent genome sequencing of three other thiotetronate-producing actinomycetes, including the Lentzea sp. ATCC 31319 that produces TLM, confirmed that near-identical clusters were also present in these genomes. In-frame gene deletion within the cluster for Tü 3010 from Streptomyces thiolactonus NRRL 15439, or within the TLM cluster, led to loss of production of the respective thiotetronate, confirming their identity. Each cluster houses at least one gene encoding a KASI/II enzyme, suggesting plausible mechanisms for self-resistance. A separate genetic locus encodes a cysteine desulfurase and a (thiouridylase-like) sulfur transferase to supply the sulfur atom for thiotetronate ring formation. Transfer of the main Tü 3010 gene cluster (stu gene cluster) into Streptomyces avermitilis led to heterologous production of this thiotetronate, showing that an equivalent sulfur donor can be supplied by this host strain. Mutational analysis of the Tü 3010 and TLM clusters has revealed the unexpected role of a cytochrome P450 enzyme in thiotetronate ring formation. These insights have allowed us to propose a mechanism for sulfur insertion, and have opened the way to engineering of the biosynthesis of TLM and other thiotetronates to produce novel analogues.
Collapse
Affiliation(s)
- W Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M E Yurkovich
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - S Wen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - K E Lebe
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - M Samborskyy
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - A Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Ju
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Z Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M Tosin
- Department of Chemistry , University of Warwick , Library Road , Coventry CV4 7AL , UK
| | - Y Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - P F Leadlay
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| |
Collapse
|
27
|
Chavarria NE, Hwang S, Cao S, Fu X, Holman M, Elbanna D, Rodriguez S, Arrington D, Englert M, Uthandi S, Söll D, Maupin-Furlow JA. Archaeal Tuc1/Ncs6 homolog required for wobble uridine tRNA thiolation is associated with ubiquitin-proteasome, translation, and RNA processing system homologs. PLoS One 2014; 9:e99104. [PMID: 24906001 PMCID: PMC4048286 DOI: 10.1371/journal.pone.0099104] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/11/2014] [Indexed: 11/29/2022] Open
Abstract
While cytoplasmic tRNA 2-thiolation protein 1 (Tuc1/Ncs6) and ubiquitin-related modifier-1 (Urm1) are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at wobble uridines of tRNAs in eukaryotes, the biocatalytic roles and properties of Ncs6/Tuc1 and its homologs are poorly understood. Here we present the first report of an Ncs6 homolog of archaea (NcsA of Haloferax volcanii) that is essential for maintaining cellular pools of thiolated tRNALysUUU and for growth at high temperature. When purified from Hfx. volcanii, NcsA was found to be modified at Lys204 by isopeptide linkage to polymeric chains of the ubiquitin-fold protein SAMP2. The ubiquitin-activating E1 enzyme homolog of archaea (UbaA) was required for this covalent modification. Non-covalent protein partners that specifically associated with NcsA were also identified including UbaA, SAMP2, proteasome activating nucleotidase (PAN)-A/1, translation elongation factor aEF-1α and a β-CASP ribonuclease homolog of the archaeal cleavage and polyadenylation specificity factor 1 family (aCPSF1). Together, our study reveals that NcsA is essential for growth at high temperature, required for formation of thiolated tRNALysUUU and intimately linked to homologs of ubiquitin-proteasome, translation and RNA processing systems.
Collapse
Affiliation(s)
- Nikita E. Chavarria
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Shiyun Cao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Xian Fu
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mary Holman
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Dina Elbanna
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Suzanne Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Deanna Arrington
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Sivakumar Uthandi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| |
Collapse
|
28
|
Abstract
Prokaryotes form ubiquitin (Ub)-like isopeptide bonds on the lysine residues of proteins by at least two distinct pathways that are reversible and regulated. In mycobacteria, the C-terminal Gln of Pup (prokaryotic ubiquitin-like protein) is deamidated and isopeptide linked to proteins by a mechanism distinct from ubiquitylation in enzymology yet analogous to ubiquitylation in targeting proteins for destruction by proteasomes. Ub-fold proteins of archaea (SAMPs, small archaeal modifier proteins) and Thermus (TtuB, tRNA-two-thiouridine B) that differ from Ub in amino acid sequence, yet share a common β-grasp fold, also form isopeptide bonds by a mechanism that appears streamlined compared with ubiquitylation. SAMPs and TtuB are found to be members of a small group of Ub-fold proteins that function not only in protein modification but also in sulfur-transfer pathways associated with tRNA thiolation and molybdopterin biosynthesis. These multifunctional Ub-fold proteins are thought to be some of the most ancient of Ub-like protein modifiers.
Collapse
Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611;
| |
Collapse
|
29
|
Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
Collapse
Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
| |
Collapse
|
30
|
Sasaki E, Zhang X, Sun HG, Lu MYJ, Liu TL, Ou A, Li JY, Chen YH, Ealick SE, Liu HW. Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis. Nature 2014; 510:427-31. [PMID: 24814342 PMCID: PMC4082789 DOI: 10.1038/nature13256] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/18/2014] [Indexed: 02/04/2023]
Abstract
Sulphur is an essential element for life and exists ubiquitously in living systems1,2. Yet, how the sulphur atom is incorporated in many sulphur-containing secondary metabolites remains poorly understood. For C-S bond formation in primary metabolites, the major ionic sulphur sources are the protein-persulphide and protein-thiocarboxylate3,4. In each case, the persulphide and thiocarboxylate group on these sulphur-carrier (donor) proteins are post-translationally generated through the action of a specific activating enzyme. In all bacterial cases reported thus far, the genes encoding the enzyme that catalyzes the actual C-S bond formation reaction and its cognate sulphur-carrier protein co-exist in the same gene cluster5. To study 2-thiosugar production in BE-7585A, an antibiotic from Amycolatopsis orientalis, we identified a putative 2-thioglucose synthase, BexX, whose protein sequence and mode of action appear similar to those of ThiG, the enzyme catalyzing thiazole formation in thiamin biosynthesis6,7. However, no sulphur-carrier protein gene could be located in the BE-7585A cluster. Subsequent genome sequencing revealed the presence of a few sulphur-carrier proteins likely involved in the biosynthesis of primary metabolites, but surprisingly only a single activating enzyme gene in the entire genome of A. orientalis. Further experiments showed that this activating enzyme is capable of adenylating each of these sulphur-carrier proteins, and likely also catalyzing the subsequent thiolation taking advantage of its rhodanese activity. A proper combination of these sulphur delivery systems is effective for BexX-catalyzed 2-thioglucose production. The ability of BexX to selectively distinguish sulphur-carrier proteins is given a structural basis using X-ray crystallography. These studies represent the first complete characterization of a thiosugar formation in nature and also demonstrate the receptor promiscuity of the sulphur-delivery system in A. orientalis. Our results also provide evidence that exploitation of sulphur-delivery machineries of primary metabolism for the biosynthesis of sulphur-containing natural products is likely a general strategy found in nature.
Collapse
Affiliation(s)
- Eita Sasaki
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Xuan Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - He G Sun
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, USA
| | - Mei-yeh Jade Lu
- 1] Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan [2] Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-lin Liu
- 1] Genomics Research Center, Academia Sinica, Taipei 115, Taiwan [2] Institute of Bioinformatics and Biosignal Transduction, National Cheng-Kung University, Tainan 701, Taiwan
| | - Albert Ou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jeng-yi Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-hsiang Chen
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Hung-wen Liu
- 1] Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA [2] Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
31
|
Xie Y, Li Q, Song Y, Ma J, Ju J. Involvement of SgvP in Carbon-Sulfur Bond Formation during Griseoviridin Biosynthesis. Chembiochem 2014; 15:1183-9. [DOI: 10.1002/cbic.201400062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Indexed: 01/26/2023]
|
32
|
Shigi N. Biosynthesis and functions of sulfur modifications in tRNA. Front Genet 2014; 5:67. [PMID: 24765101 PMCID: PMC3980101 DOI: 10.3389/fgene.2014.00067] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/17/2014] [Indexed: 12/19/2022] Open
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Earlier studies established the functions of these modifications for accurate and efficient translation, including proper recognition of the codons in mRNA or stabilization of tRNA structure. In many cases, the biosynthesis of these sulfur modifications starts with cysteine desulfurases, which catalyze the generation of persulfide (an activated form of sulfur) from cysteine. Many sulfur-carrier proteins are responsible for delivering this activated sulfur to each biosynthesis pathway. Finally, specific “modification enzymes” activate target tRNAs and then incorporate sulfur atoms. Intriguingly, the biosynthesis of 2-thiouridine in all domains of life is functionally and evolutionarily related to the ubiquitin-like post-translational modification system of cellular proteins in eukaryotes. This review summarizes the recent characterization of the biosynthesis of sulfur modifications in tRNA and the novel roles of this modification in cellular functions in various model organisms, with a special emphasis on 2-thiouridine derivatives. Each biosynthesis pathway of sulfur-containing molecules is mutually modulated via sulfur trafficking, and 2-thiouridine and codon usage bias have been proposed to control the translation of specific genes.
Collapse
Affiliation(s)
- Naoki Shigi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology Tokyo, Japan
| |
Collapse
|
33
|
Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. ACTA ACUST UNITED AC 2013; 21:174-85. [PMID: 24315934 DOI: 10.1016/j.chembiol.2013.10.015] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 12/15/2022]
Abstract
Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level.
Collapse
|
34
|
Miranda HV, Antelmann H, Hepowit N, Chavarria NE, Krause DJ, Pritz JR, Bäsell K, Becher D, Humbard MA, Brocchieri L, Maupin-Furlow JA. Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a UbaA-dependent mechanism. Mol Cell Proteomics 2013; 13:220-39. [PMID: 24097257 DOI: 10.1074/mcp.m113.029652] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SAMP1 and SAMP2 are ubiquitin-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon Haloferax volcanii. Here we report a novel small archaeal modifier protein (named SAMP3) with a β-grasp fold and C-terminal diglycine motif characteristic of ubiquitin that is functional in protein conjugation in Hfx. volcanii. SAMP3 conjugates were dependent on the ubiquitin-activating E1 enzyme homolog of archaea (UbaA) for synthesis and were cleaved by the JAMM/MPN+ domain metalloprotease HvJAMM1. Twenty-three proteins (28 lysine residues) were found to be isopeptide-linked to the C-terminal carboxylate of SAMP3, and 331 proteins were reproducibly found associated with SAMP3 in a UbaA-dependent manner based on tandem mass spectrometry (MS/MS) analysis. The molybdopterin (MPT) synthase large subunit homolog MoaE, found samp3ylated at conserved active site lysine residues in MS/MS analysis, was also shown to be covalently bound to SAMP3 by immunoprecipitation and tandem affinity purifications. HvJAMM1 was demonstrated to catalyze the cleavage of SAMP3 from MoaE, suggesting a mechanism of controlling MPT synthase activity. The levels of samp3ylated proteins and samp3 transcripts were found to be increased by the addition of dimethyl sulfoxide to aerobically growing cells. Thus, we propose a model in which samp3ylation is covalent and reversible and controls the activity of enzymes such as MPT synthase. Sampylation of MPT synthase may govern the levels of molybdenum cofactor available and thus facilitate the scavenging of oxygen prior to the transition to respiration with molybdenum-cofactor-containing terminal reductases that use alternative electron acceptors such as dimethyl sulfoxide. Overall, our study of SAMP3 provides new insight into the diversity of functional ubiquitin-like protein modifiers and the network of ubiquitin-like protein targets in Archaea.
Collapse
Affiliation(s)
- Hugo V Miranda
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine SI, Shigi N, Yokoyama S. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Proteins 2013; 81:1232-44. [DOI: 10.1002/prot.24273] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
| | - Mitsuo Kuratani
- RIKEN Systems and Structural Biology Center; 1-7-22 Suehiro-cho; Tsurumi; Yokohama 230-0045; Japan
| | | | | | - Kazushige Katsura
- RIKEN Systems and Structural Biology Center; 1-7-22 Suehiro-cho; Tsurumi; Yokohama 230-0045; Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center; 1-7-22 Suehiro-cho; Tsurumi; Yokohama 230-0045; Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center; 1-7-22 Suehiro-cho; Tsurumi; Yokohama 230-0045; Japan
| | | | - Naoki Shigi
- Biomedicinal Information Research Center (BIRC); National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi, Koto-ku; Tokyo 135-0064; Japan
| | | |
Collapse
|
36
|
Abstract
Archaea contain, both a functional proteasome and an ubiquitin-like protein conjugation system (termed sampylation) that is related to the ubiquitin proteasome system (UPS) of eukaryotes. Archaeal proteasomes have served as excellent models for understanding how proteins are degraded by the central energy-dependent proteolytic machine of eukaryotes, the 26S proteasome. While sampylation has only recently been discovered, it is thought to be linked to proteasome-mediated degradation in archaea. Unlike eukaryotes, sampylation only requires an E1 enzyme homolog of the E1-E2-E3 ubiquitylation cascade to mediate protein conjugation. Furthermore, recent evidence suggests that archaeal and eurkaryotic E1 enzyme homologs can serve dual roles in mediating protein conjugation and activating sulfur for incorporation into biomolecules. The focus of this book chapter is the energy-dependent proteasome and sampylation systems of Archaea.
Collapse
Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA,
| |
Collapse
|
37
|
Jackman JE, Alfonzo JD. Transfer RNA modifications: nature's combinatorial chemistry playground. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:35-48. [PMID: 23139145 DOI: 10.1002/wrna.1144] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Following synthesis, tRNAs are peppered by numerous chemical modifications which may differentially affect a tRNA's structure and function. Although modifications affecting the business ends of a tRNA are predictably important for cell viability, a majority of modifications play more subtle structural roles that can affect tRNA stability and folding. The current trend is that modifications act in concert and it is in the context of the specific sequence of a given tRNA that they impart their differing effects. Recent developments in the modification field have highlighted the diversity of modifications in tRNA. From these, the combinatorial nature of modifications in explaining previously described phenotypes derived from their absence has emerged as a growing theme.
Collapse
Affiliation(s)
- Jane E Jackman
- The Ohio State Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | | |
Collapse
|
38
|
Ubiquitin-like proteins and their roles in archaea. Trends Microbiol 2012; 21:31-8. [PMID: 23140889 DOI: 10.1016/j.tim.2012.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 01/01/2023]
Abstract
This review highlights the finding that ubiquitin-like (Ubl) proteins of archaea (termed SAMPs) function not only as sulfur carriers but also as protein modifiers. UbaA (an E1 ubiquitin-activating enzyme homolog of archaea) is required for the SAMPs to be covalently attached to proteins. The SAMPs and UbaA are also needed to form sulfur-containing biomolecules (e.g., thiolated tRNA and molybdenum cofactor). These findings provide a new perspective on how Ubl proteins can serve as both sulfur carriers and protein modifiers in the absence of canonical E2 ubiquitin conjugating or E3 ubiquitin ligase enzyme homologs.
Collapse
|
39
|
Yamagami R, Yamashita K, Nishimasu H, Tomikawa C, Ochi A, Iwashita C, Hirata A, Ishitani R, Nureki O, Hori H. The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO). J Biol Chem 2012; 287:42480-94. [PMID: 23095745 DOI: 10.1074/jbc.m112.390112] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conserved U54 in tRNA is often modified to 5-methyluridine (m(5)U) and forms a reverse Hoogsteen base pair with A58 that stabilizes the L-shaped tRNA structure. In Gram-positive and some Gram-negative eubacteria, m(5)U54 is produced by folate/FAD-dependent tRNA (m(5)U54) methyltransferase (TrmFO). TrmFO utilizes N(5),N(10)-methylenetetrahydrofolate (CH(2)THF) as a methyl donor. We previously reported an in vitro TrmFO assay system, in which unstable [(14)C]CH(2)THF was supplied from [(14)C]serine and tetrahydrofolate by serine hydroxymethyltransferase. In the current study, we have improved the TrmFO assay system by optimization of enzyme and substrate concentrations and introduction of a filter assay system. Using this assay, we have focused on the tRNA recognition mechanism of TrmFO. 42 tRNA mutant variants were prepared, and experiments with truncated tRNA and microhelix RNAs revealed that the minimum requirement of TrmFO exists in the T-arm structure. The positive determinants for TrmFO were found to be the U54U55C56 sequence and G53-C61 base pair. The gel mobility shift assay and fluorescence quenching showed that the affinity of TrmFO for tRNA in the initial binding process is weak. The inhibition experiments showed that the methylated tRNA is released before the structural change process. Furthermore, we found that A38 prevents incorrect methylation of U32 in the anticodon loop. Moreover, the m(1)A58 modification clearly accelerates the TrmFO reaction, suggesting a synergistic effect of the m(5)U54, m(1)A58, and s(2)U54 modifications on m(5)s(2)U54 formation in Thermus thermophilus cells. The docking model of TrmFO and the T-arm showed that the G53-C61 base pair is not able to directly contact the enzyme.
Collapse
Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Liu J, Chen L, Wang J, Qiao J, Zhang W. Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:68. [PMID: 22958739 PMCID: PMC3479031 DOI: 10.1186/1754-6834-5-68] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 08/30/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Recent studies have demonstrated that photosynthetic cyanobacteria could be an excellent cell factory to produce renewable biofuels and chemicals due to their capability to utilize solar energy and CO2 as the sole energy and carbon sources. Biosynthesis of carbon-neutral biofuel alkanes with good chemical and physical properties has been proposed. However, to make the process economically feasible, one major hurdle to improve the low cell tolerance to alkanes needed to be overcome. RESULTS Towards the goal to develop robust and high-alkane-tolerant hosts, in this study, the responses of model cyanobacterial Synechocystis PCC 6803 to hexane, a representative of alkane, were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. In total, 1,492 unique proteins were identified, representing about 42% of all predicted protein in the Synechocystis genome. Among all proteins identified, a total of 164 and 77 proteins were found up- and down-regulated, respectively. Functional annotation and KEGG pathway enrichment analyses showed that common stress responses were induced by hexane in Synechocystis. Notably, a large number of transporters and membrane-bound proteins, proteins against oxidative stress and proteins related to sulfur relay system and photosynthesis were induced, suggesting that they are possibly the major protection mechanisms against hexane toxicity. CONCLUSION The study provided the first comprehensive view of the complicated molecular mechanism employed by cyanobacterial model species, Synechocystis to defend against hexane stress. The study also provided a list of potential targets to engineer Synechocystis against hexane stress.
Collapse
Affiliation(s)
- Jie Liu
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
| | - Lei Chen
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
| | - Jiangxin Wang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
| | - Jianjun Qiao
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
| | - Weiwen Zhang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
| |
Collapse
|
41
|
Singh S, Yadav LDS. Unprecedented dithiolation of enals via their NHC-catalysed umpolung reaction with organic disulfides. Org Biomol Chem 2012; 10:3932-6. [PMID: 22476170 DOI: 10.1039/c2ob25238d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel one-pot N-heterocyclic carbene (NHC)-catalysed dithiolation of α,β-unsaturated aldehydes (enals) with organic disulfides is reported. The protocol involves homoenolate reactivity of enals, where the homoenolate attacks on the disulfide as a d(3) nucleophile followed by thioesterification to afford β-aryl/alkylsulfanyl thioesters with complete atom economy.
Collapse
Affiliation(s)
- Santosh Singh
- Department of Chemistry, University of Allahabad, Allahabad, India
| | | |
Collapse
|
42
|
Shigi N. Posttranslational modification of cellular proteins by a ubiquitin-like protein in bacteria. J Biol Chem 2012; 287:17568-17577. [PMID: 22467871 DOI: 10.1074/jbc.m112.359844] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Posttranslational modification of proteins with ubiquitin and ubiquitin-like proteins plays important regulatory roles in eukaryotes. Although a homologous conjugation system has recently been reported in Archaea, there is no similar report in Bacteria. This report describes the identification of a ubiquitin-like conjugation system in the bacterium Thermus thermophilus. A series of in vivo analyses revealed that TtuB, a bacterial ubiquitin-like protein that functions as a sulfur carrier in tRNA thiouridine synthesis, was covalently attached to target proteins, most likely via its C-terminal glycine. The involvement of the ubiquitin-activating enzyme-like protein TtuC in conjugate formation and the attachments of TtuB to TtuC and TtuA, which are proteins required for tRNA thiouridine synthesis, were demonstrated. Mass spectrometry analysis revealed that lysine residues (Lys-137/Lys-226/Lys-229) of TtuA were covalently modified by the C-terminal carboxylate of TtuB. Intriguingly, a deletion mutant of a JAMM (JAB1/MPN/Mov34 metalloenzyme) ubiquitin isopeptidase homolog showed aberrant TtuB conjugates of TtuC and TtuA and an ∼50% decrease in thiouridine amounts in tRNA. These results would support the hypothesis that thiouridine synthesis is regulated by TtuB-conjugation.
Collapse
Affiliation(s)
- Naoki Shigi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
| |
Collapse
|
43
|
Tran TH, Krishnamoorthy K, Begley TP, Ealick SE. A novel mechanism of sulfur transfer catalyzed by O-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of Wolinella succinogenes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:831-8. [PMID: 21931214 PMCID: PMC3176619 DOI: 10.1107/s0907444911028010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/12/2011] [Indexed: 11/10/2022]
Abstract
O-Acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5'-phosphate (PLP) dependent sulfide-utilizing enzyme in the L-cysteine and L-methionine biosynthetic pathways of various enteric bacteria and fungi. OAHS catalyzes the conversion of O-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. However, the source of the sulfur has not been identified and no structures of OAHS have been reported in the literature. Here, the crystal structure of Wolinella succinogenes OAHS (MetY) determined at 2.2 Å resolution is reported. MetY crystallized in space group C2 with two monomers in the asymmetric unit. Size-exclusion chromatography, dynamic light scattering and crystal packing indicate that the biological unit is a tetramer in solution. This is further supported by the crystal structure, in which a tetramer is formed using a combination of noncrystallographic and crystallographic twofold axes. A search for structurally homologous proteins revealed that MetY has the same fold as cystathionine γ-lyase and methionine γ-lyase. The active sites of these enzymes, which are also PLP-dependent, share a high degree of structural similarity, suggesting that MetY belongs to the γ-elimination subclass of the Cys/Met metabolism PLP-dependent family of enzymes. The structure of MetY, together with biochemical data, provides insight into the mechanism of sulfur transfer to a small molecule via a protein thiocarboxylate intermediate.
Collapse
Affiliation(s)
- Timothy H. Tran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
| | | | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
| |
Collapse
|
44
|
Molecular strategy for survival at a critical high temperature in Eschierichia coli. PLoS One 2011; 6:e20063. [PMID: 21695201 PMCID: PMC3112155 DOI: 10.1371/journal.pone.0020063] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/12/2011] [Indexed: 01/19/2023] Open
Abstract
The molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except for dnaJ and dnaK, indicating that a specific set of non-heat shock genes is required for the organism to survive under such a severe condition. More than half of the mutants of the thermotolerant genes were found to be sensitive to H2O2 at 30°C, suggesting that the mechanism of thermotolerance partially overlaps with that of oxidative stress resistance. Their encoded enzymes or proteins are related to outer membrane organization, DNA double-strand break repair, tRNA modification, protein quality control, translation control or cell division. DNA chip analyses of essential genes suggest that many of the genes encoding ribosomal proteins are down-regulated at CHT. Bioinformatics analysis and comparison with the genomic information of other microbes suggest that E. coli possesses several systems for survival at CHT. This analysis allows us to speculate that a lipopolysaccharide biosynthesis system for outer membrane organization and a sulfur-relay system for tRNA modification have been acquired by horizontal gene transfer.
Collapse
|
45
|
Ishida K, Kunibayashi T, Tomikawa C, Ochi A, Kanai T, Hirata A, Iwashita C, Hori H. Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res 2011; 39:2304-18. [PMID: 21097467 PMCID: PMC3064792 DOI: 10.1093/nar/gkq1180] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/02/2010] [Accepted: 11/02/2010] [Indexed: 11/13/2022] Open
Abstract
Pseudouridine at position 55 (Ψ55) in eubacterial tRNA is produced by TruB. To clarify the role of the Ψ55 modification, we constructed a truB gene disruptant (ΔtruB) strain of Thermus thermophilus which is an extreme-thermophilic eubacterium. Unexpectedly, the ΔtruB strain exhibited severe growth retardation at 50 °C. We assumed that these phenomena might be caused by lack of RNA chaperone activity of TruB, which was previously hypothetically proposed by others. To confirm this idea, we replaced the truB gene in the genome with mutant genes, which express TruB proteins with very weak or no enzymatic activity. However the growth retardation at 50 °C was not rescued by these mutant proteins. Nucleoside analysis revealed that Gm18, m(5)s(2)U54 and m(1)A58 in tRNA from the ΔtruB strain were abnormally increased. An in vitro assay using purified tRNA modification enzymes demonstrated that the Ψ55 modification has a negative effect on Gm18 formation by TrmH. These experimental results show that the Ψ55 modification is required for low-temperature adaptation to control other modified. (35)S-Met incorporation analysis showed that the protein synthesis activity of the ΔtruB strain was inferior to that of the wild-type strain and that the cold-shock proteins were absence in the ΔtruB cells at 50°C.
Collapse
Affiliation(s)
- Kazuo Ishida
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Takashi Kunibayashi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Tamotsu Kanai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Chikako Iwashita
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| |
Collapse
|
46
|
Krishnamoorthy K, Begley TP. Protein thiocarboxylate-dependent methionine biosynthesis in Wolinella succinogenes. J Am Chem Soc 2011; 133:379-86. [PMID: 21162571 PMCID: PMC3089676 DOI: 10.1021/ja107424t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiocarboxylated proteins are important intermediates in a variety of biochemical sulfide transfer reactions. Here we identify a protein thiocarboxylate-dependent methionine biosynthetic pathway in Wolinella succinogenes. In this pathway, the carboxy terminal alanine of a novel sulfur transfer protein, HcyS-Ala, is removed in a reaction catalyzed by a metalloprotease, HcyD. HcyF, an ATP-utilizing enzyme, catalyzes the adenylation of HcyS. HcyS acyl-adenylate then undergoes nucleophilic substitution by bisulfide produced by Sir to give the HcyS thiocarboxylate. This adds to O-acetylhomoserine to give HcyS-homocysteine in a PLP-dependent reaction catalyzed by MetY. HcyD-mediated hydrolysis liberates homocysteine. A final methylation completes the biosynthesis. The biosynthetic gene cluster also encodes the enzymes involved in the conversion of sulfate to sulfide suggesting that sulfate is the sulfur source for protein thiocarboxylate formation in this system.
Collapse
Affiliation(s)
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station 77840
| |
Collapse
|
47
|
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20936112 PMCID: PMC2948915 DOI: 10.1155/2010/710303] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 07/20/2010] [Indexed: 11/30/2022]
Abstract
The recent discovery of protein modification by SAMPs, ubiquitin-like (Ubl) proteins from the archaeon Haloferax volcanii, prompted a comprehensive comparative-genomic analysis of archaeal Ubl protein genes and the genes for enzymes thought to be functionally associated with Ubl proteins. This analysis showed that most archaea encode members of two major groups of Ubl proteins with the β-grasp fold, the ThiS and MoaD families, and indicated that the ThiS family genes are rarely linked to genes for thiamine or Mo/W cofactor metabolism enzymes but instead are most often associated with genes for enzymes of tRNA modification. Therefore it is hypothesized that the ancestral function of the archaeal Ubl proteins is sulfur insertion into modified nucleotides in tRNAs, an activity analogous to that of the URM1 protein in eukaryotes. Together with additional, previously described genomic associations, these findings indicate that systems for protein quality control operating at different levels, including tRNA modification that controls translation fidelity, protein ubiquitination that regulates protein degradation, and, possibly, mRNA degradation by the exosome, are functionally and evolutionarily linked.
Collapse
|
48
|
Awai T, Kimura S, Tomikawa C, Ochi A, Ihsanawati, Bessho Y, Yokoyama S, Ohno S, Nishikawa K, Yokogawa T, Suzuki T, Hori H. Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. J Biol Chem 2009; 284:20467-78. [PMID: 19491098 PMCID: PMC2742811 DOI: 10.1074/jbc.m109.020024] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/13/2009] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes N2,N2-dimethylguanine formation at position 26 (m(2)(2)G26) in tRNA. In the reaction, N2-guanine at position 26 (m(2)G26) is generated as an intermediate. The trm1 genes are found only in archaea and eukaryotes, although it has been reported that Aquifex aeolicus, a hyper-thermophilic eubacterium, has a putative trm1 gene. To confirm whether A. aeolicus Trm1 has tRNA methyltransferase activity, we purified recombinant Trm1 protein. In vitro methyl transfer assay revealed that the protein has a strong tRNA methyltransferase activity. We confirmed that this gene product is expressed in living A. aeolicus cells and that the enzymatic activity exists in cell extract. By preparing 22 tRNA transcripts and testing their methyl group acceptance activities, it was demonstrated that this Trm1 protein has a novel tRNA specificity. Mass spectrometry analysis revealed that it catalyzes methyl transfers not only to G26 but also to G27 in substrate tRNA. Furthermore, it was confirmed that native tRNA(Cys) has an m(2)(2)G26m(2)G27 or m(2)(2)G26m(2)(2)G27 sequence, demonstrating that these modifications occur in living cells. Kinetic studies reveal that the m2G26 formation is faster than the m(2)G27 formation and that disruption of the G27-C43 base pair accelerates velocity of the G27 modification. Moreover, we prepared an additional 22 mutant tRNA transcripts and clarified that the recognition sites exist in the T-arm structure. This long distance recognition results in multisite recognition by the enzyme.
Collapse
Affiliation(s)
- Takako Awai
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Satoshi Kimura
- the Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656
| | - Chie Tomikawa
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Anna Ochi
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Ihsanawati
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
| | - Yoshitaka Bessho
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the RIKEN SPring-8 Center, Harima Institute, Kouto 1-1-1, Sayo, Hyogo 679-5148
| | - Shigeyuki Yokoyama
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the RIKEN SPring-8 Center, Harima Institute, Kouto 1-1-1, Sayo, Hyogo 679-5148
- the Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033
| | - Satoshi Ohno
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Kazuya Nishikawa
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Takashi Yokogawa
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Tsutomu Suzuki
- the Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656
| | - Hiroyuki Hori
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
49
|
Noma A, Sakaguchi Y, Suzuki T. Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions. Nucleic Acids Res 2009; 37:1335-52. [PMID: 19151091 PMCID: PMC2651780 DOI: 10.1093/nar/gkn1023] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group confers conformational rigidity of mcm5s2U by largely fixing the C3′-endo ribose puckering, ensuring stable and accurate codon–anticodon pairing. We have identified five genes in Saccharomyces cerevisiae, YIL008w (URM1), YHR111w (UBA4), YOR251c (TUM1), YNL119w (NCS2) and YGL211w (NCS6), that are required for 2-thiolation of mcm5s2U. An in vitro sulfur transfer experiment revealed that Tum1p stimulated the cysteine desulfurase of Nfs1p, and accepted persulfide sulfurs from Nfs1p. URM1 is a ubiquitin-related modifier, and UBA4 is an E1-like enzyme involved in protein urmylation. The carboxy-terminus of Urm1p was activated as an acyl-adenylate (-COAMP), then thiocarboxylated (-COSH) by Uba4p. The activated thiocarboxylate can be utilized in the subsequent reactions for 2-thiouridine formation, mediated by Ncs2p/Ncs6p. We could successfully reconstitute the 2-thiouridine formation in vitro using recombinant proteins. This study revealed that 2-thiouridine formation shares a pathway and chemical reactions with protein urmylation. The sulfur-flow of eukaryotic 2-thiouridine formation is distinct mechanism from the bacterial sulfur-relay system which is based on the persulfide chemistry.
Collapse
Affiliation(s)
- Akiko Noma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bldg. 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | | |
Collapse
|