1
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Jin M, Zhang Z, Yu Z, Chen W, Wang X, Lei D, Zhang W. Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases. Nucleic Acids Res 2023; 51:8711-8729. [PMID: 37427786 PMCID: PMC10484737 DOI: 10.1093/nar/gkad587] [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: 02/14/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023] Open
Abstract
N 6-threonylcarbamoyladenosine (t6A) is a post-transcriptional modification found uniquely at position 37 of tRNAs that decipher ANN-codons in the three domains of life. tRNA t6A plays a pivotal role in promoting translational fidelity and maintaining protein homeostasis. The biosynthesis of tRNA t6A requires members from two evolutionarily conserved protein families TsaC/Sua5 and TsaD/Kae1/Qri7, and a varying number of auxiliary proteins. Furthermore, tRNA t6A is modified into a cyclic hydantoin form of t6A (ct6A) by TcdA in bacteria. In this work, we have identified a TsaD-TsaC-SUA5-TcdA modular protein (TsaN) from Pandoraviruses and determined a 3.2 Å resolution cryo-EM structure of P. salinus TsaN. The four domains of TsaN share strong structural similarities with TsaD/Kae1/Qri7 proteins, TsaC/Sua5 proteins, and Escherichia coli TcdA. TsaN catalyzes the formation of threonylcarbamoyladenylate (TC-AMP) using L-threonine, HCO3- and ATP, but does not participate further in tRNA t6A biosynthesis. We report for the first time that TsaN catalyzes a tRNA-independent threonylcarbamoyl modification of adenosine phosphates, leading to t6ADP and t6ATP. Moreover, TsaN is also active in catalyzing tRNA-independent conversion of t6A nucleoside to ct6A. Our results imply that TsaN from Pandoraviruses might be a prototype of the tRNA t6A- and ct6A-modifying enzymes in some cellular organisms.
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Affiliation(s)
- Mengqi Jin
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Zelin Zhang
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Zhijiang Yu
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Wei Chen
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Dongsheng Lei
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Wenhua Zhang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
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2
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Peña-Soler E, Aranda J, López-Estepa M, Gómez S, Garces F, Coll M, Fernández FJ, Tuñon I, Vega MC. Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE. PLoS One 2017; 12:e0186286. [PMID: 29045454 PMCID: PMC5646864 DOI: 10.1371/journal.pone.0186286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/28/2017] [Indexed: 11/18/2022] Open
Abstract
Sulfur trafficking in living organisms relies on transpersulfuration reactions consisting in the enzyme-catalyzed transfer of S atoms via activated persulfidic S across protein-protein interfaces. The recent elucidation of the mechanistic basis for transpersulfuration in the CsdA-CsdE model system has paved the way for a better understanding of its role under oxidative stress. Herein we present the crystal structure of the oxidized, inactivated CsdE dimer at 2.4 Å resolution. The structure sheds light into the activation of the Cys61 nucleophile on its way from a solvent-secluded position in free CsdE to a fully extended conformation in the persulfurated CsdA-CsdE complex. Molecular dynamics simulations of available CsdE structures allow to delineate the sequence of conformational changes underwent by CsdE and to pinpoint the key role played by the deprotonation of the Cys61 thiol. The low-energy subunit orientation in the disulfide-bridged CsdE dimer demonstrates the likely physiologic relevance of this oxidative dead-end form of CsdE, suggesting that CsdE could act as a redox sensor in vivo.
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Affiliation(s)
- Esther Peña-Soler
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Juan Aranda
- Departamento de Química Física, Universitat de València, Burjassot, Spain
| | - Miguel López-Estepa
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sara Gómez
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Francisco J. Fernández
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Abvance Biotech srl, Madrid, Spain
| | - Iñaki Tuñon
- Departamento de Química Física, Universitat de València, Burjassot, Spain
- * E-mail: , (MCV); (IT)
| | - M. Cristina Vega
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- * E-mail: , (MCV); (IT)
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3
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Matuszewski M, Wojciechowski J, Miyauchi K, Gdaniec Z, Wolf WM, Suzuki T, Sochacka E. A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs. Nucleic Acids Res 2017; 45:2137-2149. [PMID: 27913732 PMCID: PMC5389693 DOI: 10.1093/nar/gkw1189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/25/2016] [Indexed: 02/06/2023] Open
Abstract
N6-Threonylcarbamoyladenosine (t6A) and its derivatives are universally conserved modified nucleosides found at position 37, 3΄ adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t6A is further modified to the cyclic t6A (ct6A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNALys. Previous work indicated that the chemical structure of ct6A is a cyclic active ester with an oxazolone ring. In this study, we solved the crystal structure of chemically synthesized ct6A nucleoside. Unexpectedly, we found that the ct6A adopted a hydantoin isoform rather than an oxazolone isoform, and further showed that the hydantoin isoform of ct6A was actually present in Escherichia coli tRNAs. In addition, we observed that hydantoin ct6A is susceptible to epimerization under mild alkaline conditions, warning us to avoid conventional deacylation of tRNAs. A hallmark structural feature of this isoform is the twisted arrangement of the hydantoin and adenine rings. Functional roles of ct6A37 in tRNAs should be reconsidered.
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Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Jakub Wojciechowski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech M Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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4
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Fernández FJ, Gómez S, Navas-Yuste S, López-Estepa M, Vega MC. Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N 6-threonylcarbamoyladenosine TcdA Function. J Vis Exp 2017. [PMID: 28671653 DOI: 10.3791/55638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We demonstrate methods for the expression and purification of tRNA(UUU) in Escherichia coli and the analysis by gel retardation assays of the binding of tRNA(UUU) to TcdA, an N6-threonylcarbamoyladenosine (t6A) dehydratase, which cyclizes the threonylcarbamoyl side chain attached to A37 in the anticodon stem loop (ASL) of tRNAs to cyclic t6A (ct6A). Transcription of the synthetic gene encoding tRNA(UUU) is induced in E. coli with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and the cells containing tRNA are harvested 24 h post-induction. The RNA fraction is purified using the acid phenol extraction method. Pure tRNA is obtained by a gel filtration chromatography that efficiently separates the small-sized tRNA molecules from larger intact or fragmented nucleic acids. To analyze TcdA binding to tRNA(UUU), TcdA is mixed with tRNA(UUU) and separated on a native agarose gel at 4 °C. The free tRNA(UUU) migrates faster, while the TcdA-tRNA(UUU) complexes undergo a mobility retardation that can be observed upon staining of the gel. We demonstrate that TcdA is a tRNA(UUU)-binding enzyme. This gel retardation assay can be used to study TcdA mutants and the effects of additives and other proteins on binding.
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Affiliation(s)
- Francisco J Fernández
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC); Department of Immunology, Complutense University School of Medicine; Abvance Biotech srl
| | - Sara Gómez
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - Sergio Navas-Yuste
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - Miguel López-Estepa
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - M Cristina Vega
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC);
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5
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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.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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6
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Fernández FJ, Ardá A, López-Estepa M, Aranda J, Peña-Soler E, Garces F, Round A, Campos-Olivas R, Bruix M, Coll M, Tuñón I, Jiménez-Barbero J, Vega MC. Mechanism of Sulfur Transfer Across Protein–Protein Interfaces: The Cysteine Desulfurase Model System. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Francisco J. Fernández
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Ana Ardá
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
| | - Miguel López-Estepa
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Juan Aranda
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esther Peña-Soler
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La
Jolla, 92037 California, United States
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for
Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | | | - Marta Bruix
- Instituto de Química Física Rocasolano (IQFR-CSIC), 28006 Madrid, Spain
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), 08028 Barcelona, Spain
| | - Iñaki Tuñón
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Jesús Jiménez-Barbero
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - M. Cristina Vega
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
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7
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Kenne AN, Kim S, Park S. The crystal structure of Escherichia coli CsdE. Int J Biol Macromol 2016; 87:317-21. [PMID: 26944665 DOI: 10.1016/j.ijbiomac.2016.02.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 11/19/2022]
Abstract
Sulfur incorporations both in the biosynthesis of sulfur-containing cofactors and in the sulfur-modifications of certain tRNAs are all mediated by the sulfur initially delivered from the cysteine desulfurases. Sulfur generated as persulfide from cysteine is transferred to the sulfur acceptor protein to further allow delivery to the required steps within an enzymatic process. CsdA which is one of the three cysteine desulfurases identified in Escherichia coli transfers sulfur to the non Fe-S sulfur-acceptor CsdE, however, the consequence of CsdE accepted sulfur is mostly unknown. In this study, we report the 2.4Å structure of free CsdE determined using X-ray crystallography, and compare the structure with the CsdE structure determined using NMR and also CsdE within the crystal CsdA-CsdE complex. Further analysis suggests that the positive electrostatic potential surfaces of CsdE may mediate interaction with a yet unidentified protein or possibly tRNA to deliver sulfur.
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Affiliation(s)
- Adela N Kenne
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Sunmin Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea.
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8
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López-Estepa M, Ardá A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernández FJ, Jiménez-Barbero J, Vega MC. Correction: The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily. PLoS One 2015. [PMID: 26208179 PMCID: PMC4514599 DOI: 10.1371/journal.pone.0134070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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